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diff --git a/tools/moltemplate/LICENSE.TXT b/tools/moltemplate/LICENSE.TXT
deleted file mode 100644
index 73eec3238..000000000
--- a/tools/moltemplate/LICENSE.TXT
+++ /dev/null
@@ -1,28 +0,0 @@
-
-Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/
-Copyright (c) 2014, Regents of the University of California
-All rights reserved.
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- * Neither the name of the University of California, Santa Barbara nor the
- names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
-THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/tools/moltemplate/README.TXT b/tools/moltemplate/README.TXT
deleted file mode 100644
index 773464d01..000000000
--- a/tools/moltemplate/README.TXT
+++ /dev/null
@@ -1,61 +0,0 @@
- -- Description: --
-
-Moltemplate is a cross-platform text-based molecule builder for LAMMPS.
-
- -- Typical usage: --
-
-moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd] system.lt
-
- -- Web page: --
-
-Documentation, examples, and supporting code can be downloaded at:
-
- http://www.moltemplate.org
-The most up-to-date version of moltemplate can be downloaded here.
-(After download, you can unpack the archive using:
- tar xzf moltemplate_2012-3-31.tar.gz
-The date will vary from version to version.)
-
-----------------------------------------------------
----------- INSTALLATION INSTRUCTIONS: ------------
-----------------------------------------------------
-
-This directory should contain two folders:
- src/ <-- location of all python and bash scripts
- common/ <-- location of shared force fields and molecules
-
-The ``moltemplate.sh'' script and the python scripts that it invokes are
-located in the ``src/'' subdirectory. You should update your PATH environment
-variable to include this directory.
-
-If you do not know what a PATH environment variable is, read:
- http://www.linfo.org/path_env_var.html
-(I receive this question often.)
-
-It is also a good idea to set your MOLTEMPLATE_PATH environment variable to
-point to the ``common/'' subdirectory.
-(Force fields and commonly used molecules will eventually be located here.)
-
- -- Installation example ---
-
-Suppose the directory with this README.TXT file is located at ~/moltemplate.
-
-If you use the bash shell, typically you would edit your
-~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines:
- export PATH="$PATH:$HOME/moltemplate/src"
- export MOLTEMPLATE_PATH="$HOME/moltemplate/common"
-If you use the tcsh shell, typically you would edit your
-~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines:
- setenv PATH "$PATH:$HOME/moltemplate/src"
- setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common"
-
- -- Requirements: --
-
-Moltemplate requires the Bourne-shell, and a recent version of python
-(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a
-suitable shell environment has been installed).
-
- -- License: --
-
-Moltemplate is available under the terms of the open-source 3-clause BSD
-license. (See LICENSE.TXT.)
diff --git a/tools/moltemplate/examples/README.TXT b/tools/moltemplate/examples/README.TXT
deleted file mode 100644
index e3602541c..000000000
--- a/tools/moltemplate/examples/README.TXT
+++ /dev/null
@@ -1,24 +0,0 @@
-These are examples for the "moltemplate" molecule builder for LAMMPS.
-http://www.moltemplate.org
-
-Each directory contains one or more examples.
-
-Each example directory contains:
-
- images/ This folder has pictures of the molecules in the system
- moltemplate_files/ This folder contains LT files and other auxiliary files
- README_setup.sh Instructions for how to use moltemplate (executable)
- README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD
-
- ...and one or more LAMMPS input scripts with names like
-
- run.in.min
- run.in.npt
- run.in.nvt
-
-You can run these scripts using
- lmp_linux -i run.in.npt
-(The name of your lammps binary, "lmp_linux" in this example, may vary.
- Sometimes, these scripts must be run in a certain order. For example
- it may be necessary to run run.in.min to minimize the system before you can use run.in.npt, and later run.in.nvt. The README_run.sh file in each subdirectory
- specifies indicates the order. These files have not been optimized.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README.TXT
deleted file mode 100644
index 33eeddda6..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README.TXT
+++ /dev/null
@@ -1,28 +0,0 @@
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "MANYBODY" package.
-# As of 2012-9, it is included by default, but this may change in the future.
-# If lammps complains of a missing pair style enter "make yes-MANYBODY"
-# into the shell before compiling lammps. For details see:
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-This is a relatively complex example containing two different types of
-molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles.
-
-The cyclododecane molecule uses the
-TraPPE force field for hydrocarbon chains.
-The parameters for the TraPPE force field are
-in a file named "trappe1998.lt" which should be
-located in the MOLTEMPLATE_PATH.
-(See moltemplate installation instructions.)
-
-The water solvent is implemented using the 3-body single-particle
-coarse-grained "mW" water model:
-Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step 2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh
deleted file mode 100755
index 68acee49b..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data, system.in.sw
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation are ignored when beginning the simulation at constant volume.
-# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
-
-
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh
deleted file mode 100755
index cb4d90898..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
-
- # Here we just want to make sure that the "mW" atom type is assigned to
- # number "1". It should be by default, so usually you can leave out
- # -a "@atom:/WatMW/mW 1".
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=0ps_LR.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane.jpg b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images/watMW.jpg b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images/watMW.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/README.sh
deleted file mode 100755
index 97b9f577d..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/README.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-# Use this command to generate the LAMMPS input files:
-
-moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
-
-# The -a argument insures that the "mW" atom type is assigned to "1".
-# (This is necessary for the pair_coeff command to work.
-# See system.lt for details.)
-
-# Note: To get rid of the annoying "atom_style unspecified warnings,
-# use the "-atomstyle" command line argument, as in:
-# moltemplate.sh -atomstyle full -a "@atom:/WatMW/mW 1" system.lt
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/cyclododecane.lt
deleted file mode 100644
index ceaa1c69d..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/cyclododecane.lt
+++ /dev/null
@@ -1,55 +0,0 @@
-import "trappe1998.lt"
-
-# The "trappe1998.lt" file is usually located in $MOLTEMPLATE_PATH (and is
-# distributed with moltemplate. See the "Installation" section in the manual.)
-# It contains definitions of the atoms "CH2", "CH3", and "CH4", as well
-# as "saturated" bonds, and the parameters for (bonded/nonbonded)
-# interactions between these atoms (all enclosed within the "TraPPE" namespace).
-
-
-Cyclododecane {
-
- write('Data Atoms') {
- $atom:C1 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.94118 0.0
- $atom:C2 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 1.47059
- $atom:C3 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 2.54714
- $atom:C4 $mol:. @atom:TraPPE/CH2 0.0 0.00000 0.0 2.94118
- $atom:C5 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 2.54714
- $atom:C6 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 1.47059
- $atom:C7 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.94118 0.0
- $atom:C8 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 -1.47059
- $atom:C9 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 -2.54714
- $atom:C10 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -0.0 -2.94118
- $atom:C11 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 -2.54714
- $atom:C12 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 -1.47059
- }
-
- # The "." in "$mol:." refers to the current object's molecule ID,
- # and "@atom:TraPPE/CH2" refers to the "CH2" atom-type defined in TraPPE
-
- write('Data Bonds') {
- $bond:bond1 @bond:TraPPE/saturated $atom:C1 $atom:C2
- $bond:bond2 @bond:TraPPE/saturated $atom:C2 $atom:C3
- $bond:bond3 @bond:TraPPE/saturated $atom:C3 $atom:C4
- $bond:bond4 @bond:TraPPE/saturated $atom:C4 $atom:C5
- $bond:bond5 @bond:TraPPE/saturated $atom:C5 $atom:C6
- $bond:bond6 @bond:TraPPE/saturated $atom:C6 $atom:C7
- $bond:bond7 @bond:TraPPE/saturated $atom:C7 $atom:C8
- $bond:bond8 @bond:TraPPE/saturated $atom:C8 $atom:C9
- $bond:bond9 @bond:TraPPE/saturated $atom:C9 $atom:C10
- $bond:bond10 @bond:TraPPE/saturated $atom:C10 $atom:C11
- $bond:bond11 @bond:TraPPE/saturated $atom:C11 $atom:C12
- $bond:bond12 @bond:TraPPE/saturated $atom:C12 $atom:C1
- }
-
-} # Cyclododecane
-
-
-# coordinates in the "Data Atoms" section generated by this python code:
-# from math import *
-# bond_length=1.54
-# N=12
-# R=(N*bond_length)/(2*pi)
-# for i in range(0,N):
-# print('$atom:C'+str(i+1)+' $mol:... @atom:TraPPE/CH2 0.0 0.00000 '+
-# str(round(R*cos(i*2*pi/N),5))+' '+str(round(R*sin(i*2*pi/N),5)))
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt
deleted file mode 100644
index 4a7063491..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt
+++ /dev/null
@@ -1,62 +0,0 @@
-# This is a relatively complex example containing two different types of
-# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles.
-
-import "watmw.lt"
-import "cyclododecane.lt"
-
-write_once("Data Boundary") {
- 0.000000 48.000 xlo xhi
- 0.000000 48.000 ylo yhi
- 0.000000 48.000 zlo zhi
-}
-
-wat = new WatMW [12].move(0, 0, 4.0)
- [12].move(0, 4.0, 0)
- [12].move(4.0, 0, 0)
-
-cyclododecane = new Cyclododecane [4].move(0, 0, 12.0)
- [4].move(0, 12.0, 0)
- [4].move(12.0, 0, 0)
-
-# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.)
-cyclododecane[*][*][*].move(6.0,6.0,6.0)
-
-write_once("In Init") {
- # -- Tell LAMMPS we want to use two different pair styles
- # -- (This overrides earlier settings.)
- pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
-}
-
-
-write_once("In Settings") {
- # -- Now indicate which atom type(s) are simulated using the "sw" pair style
- # -- In this case only one of the atom types is used (the mW water "atom").
-
- pair_coeff * * sw system.in.sw mW NULL NULL NULL
-
- # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
- # -- the atoms are identified by order in the list, not by name. (The "mW"
- # -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
- # -- This command says that the first atom type corresponds to the "mW"
- # -- atom in system.in.sw, and to ignore the remaining three atom types
- # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
- # -- We don't want to use the "sw" force field for interactions involving
- # -- these atom types, so we put "NULL" there.)
- # -- Note: For this to work, you should probably run moltemplate this way:
- # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
- # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom)
-}
-
-
-
-# -- Somewhere we must eventually define interactions
-# -- between atoms from different molecule types
-
-write_once("In Settings") {
- pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558
- pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458
- pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448
-}
-
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/trappe1998.lt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/trappe1998.lt
deleted file mode 100644
index 9bcc80cb1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/trappe1998.lt
+++ /dev/null
@@ -1,50 +0,0 @@
-# This file stores complete LAMMPS data for the TraPPE model of saturated
-# hydrocarbon chains. In this "united-atom" model, each methyl group is
-# represented by a single atom. Forces between "atoms" are taken from the
-# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577)
-
-TraPPE {
-
- write_once("In Init") {
- # -- Default styles for "TraPPE" --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid opls
- improper_style none
- pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:CH2 14.1707
- @atom:CH3 15.2507
- @atom:CH4 16.3307
- }
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated
- }
-
- write_once("Data Dihedrals By Type") {
- @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated
- }
-
- write_once("In Settings") {
- pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95
- pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75
- pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73
- bond_coeff @bond:saturated harmonic 120.0 1.54
- angle_coeff @angle:backbone harmonic 62.0022 114
- dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0
- }
-
- write_once("In Settings") {
- group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4
- }
-
-} # class TraPPE
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments/system.lt
deleted file mode 100644
index 34bdfead7..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments/system.lt
+++ /dev/null
@@ -1,80 +0,0 @@
-# This is a relatively complex example containing two different types of
-# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles.
-
-import "watmw.lt"
-import "cyclododecane.lt"
-
-write_once("Data Boundary") {
- 0.000000 48.000 xlo xhi
- 0.000000 48.000 ylo yhi
- 0.000000 48.000 zlo zhi
-}
-
-wat = new WatMW [12].move(0, 0, 4.0)
- [12].move(0, 4.0, 0)
- [12].move(4.0, 0, 0)
-
-cyclododecane = new Cyclododecane [4].move(0, 0, 12.0)
- [4].move(0, 12.0, 0)
- [4].move(12.0, 0, 0)
-
-# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.)
-cyclododecane[*][*][*].move(6.0,6.0,6.0)
-
-write_once("In Init") {
- # -- Tell LAMMPS we want to use two different pair styles
- # -- (This overrides earlier settings.)
- pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
-}
-
-
-
-write_once("In Settings") {
- # -- Now indicate which atom type(s) are simulated using the "sw" pair style
- # -- In this case only one of the atom types is used (the mW water "atom").
-
- pair_coeff * * sw system.in.sw mW NULL NULL NULL
-
- # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
- # -- the atoms are identified by order in the list, not by name. (The "mW"
- # -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
- # -- This command says that the first atom type corresponds to the "mW"
- # -- atom in system.in.sw, and to ignore the remaining three atom types
- # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
- # -- We don't want to use the "sw" force field for interactions involving
- # -- these atom types, so we put "NULL" there.)
- #
- # For this to work, the first atom type (assigned to "1")
- # must refer to the "mW" atom type (defined in watmw.lt).
- # (This is why we included "watmw.lt" first, to insure that the
- # atom counters in WatMW are assinged first, starting with 1.)
- # Alternately we can further insure that this happens, it's
- # a good idea to run moltemplate.sh using the "-a" argument:
- # moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
- # This assigns the atom type named @atom:/WatMW/mW to 1
-}
-
-
-
-
-# -- Somewhere we must eventually define interactions
-# -- between atoms from different molecule types
-# -- Now define interactions between DIFFERENT molecules
-# Note: In the SPC/E model, the epsilon,sigma parameters for water is 0.1553
-# 3.166. As a crude guess, I chose the LJ parameters for the interaction
-# between water & the CH2,CH3,CH4 atoms using Lorentz-Berthelot mixing rules
-
-write_once("In Settings") {
- pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558
- pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458
- pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448
-}
-
-
-
-
-
-
-
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/watmw.lt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/watmw.lt
deleted file mode 100644
index c7aaecebb..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/watmw.lt
+++ /dev/null
@@ -1,54 +0,0 @@
-# This file stores LAMMPS data for the "mW" water model.
-# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016)
-#
-# In this model, each water molecule is represented by a single "mW" particle.
-# These particles interact with their neighbors via 3-body Stillinger-Weber
-# forces whose parameters are tuned to mimic directional hydrogen-bonding
-# in liquid water (as well as hexagonal ice, type II ice, and
-# low-density super-cooled liquid/amorphous water phases).
-
-WatMW {
- write("Data Atoms") {
- $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:mW 18.02
- }
-
- write_once("system.in.sw") {
- mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0
- }
-
- write_once("In Init") {
- # -- Default styles for "WatMW" --
- units real
- pair_style sw
- }
-
- write_once("In Settings") {
- # --Now indicate which atom type(s) are simulated using the "sw" pair style
- # -- In this case only one of the atom types is used (the mW water "atom").
-
- pair_coeff * * sw system.in.sw mW NULL NULL NULL
-
- # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
- # -- the atoms are identified by order in the list, not by name. (The "mW"
- # -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
- # -- This command says that the first atom type corresponds to the "mW"
- # -- atom in system.in.sw, and to ignore the remaining three atom types
- # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
- # -- We don't want to use the "sw" force field for interactions involving
- # -- these atom types, so we put "NULL" there.)
- # -- Note: For this to work, you should probably run moltemplate this way:
- # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
- # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom)
- }
-
- # -- optional --
-
- write_once("In Settings") {
- group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group)
- }
-
-} # WatMW
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/run.in.npt
deleted file mode 100644
index 544daee70..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/run.in.npt
+++ /dev/null
@@ -1,61 +0,0 @@
-# run.in.npt
-#
-# -- Usage --
-#
-# lmp_linux -i run.in.npt
-# (assuming lmp_linux is the name of your lammps binary)
-#
-# -- Prerequisite Input Files: --
-# systen.data, system.in.init, system.in.settings, system.in.sw
-#
-# You can generate these files with this command:
-# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
-# ---------------------------------
-
-# ----- Init Section -----
-
-
-include system.in.init
-
-
-# ----- Atom Definition Section -----
-
-
-read_data system.data
-
-
-# ----- Settings Section -----
-
-
-include system.in.settings
-
-
-# ----- Run Section -----
-
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-
-minimize 1.0e-5 1.0e-7 100000 400000
-
-
-# -- simulation protocol --
-
-
-timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water
-dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 500 # time interval for printing out "thermo" data
-
-run 200000
-
-write_data system_after_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt
deleted file mode 100644
index 4a74ecd31..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt
+++ /dev/null
@@ -1,81 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# run.in.nvt
-#
-# -- Usage --
-#
-# lmp_g++ -i run.in.nvt
-# (assuming lmp_g++ is the name of your lammps binary)
-#
-# -- Prerequisite Input Files: --
-# systen.data, system.in.init, system.in.settings, system.in.sw
-# system_after_npt.data
-#
-# You can generate these files using this procedure
-#
-# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
-#
-# lmp_linux -i run.in.npt
-
-# ---------------------------------
-
-
-# -- init section --
-
-
-include system.in.init
-
-
-
-# -- atom definition section --
-
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-
-# -- settings section --
-
-
-include system.in.settings
-
-
-# -- run section --
-
-
-timestep 2.0
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-
-# The following commands are useful if you want to calculate the distribution
-# of alkane-chain radius-of-gyration at a given temperature & pressure.
-#compute cRg TraPPE gyration
-#variable vRg equal c_cRg
-#compute cPE all pe
-#variable vPE equal c_cPE
-#fix FprintPE all print 1000 "${vPE}" file U.dat
-#fix FprintRg all print 1000 "${vRg}" file Rg.dat
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 1000 # time interval for printing out "thermo" data
-#thermo_modify flush yes
-
-restart 100000 restart_nvt
-
-run 1000000
-
-write_data system_after_nvt.data
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README.TXT
deleted file mode 100644
index f9a4fe3f6..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README.TXT
+++ /dev/null
@@ -1,15 +0,0 @@
-
-This example of the formation of a coarse-grained DPPC lipid-bilayer uses the
-Martini force-field v2.0 (2013-10), was provided by Saeed Momeni Bashusqeh.
-In this example, the initial coordinates are generated by PACKMOL.
-If you prefer, there is also an example of a Martini DPPC bilayer
-which has been preassembled using moltemplate commands.
-(That example does not require PACKMOL.)
-
-step 1)
-To build the files which LAMMPS needs, follow the instructions in:
-README_setup.sh
-
-step 2)
-To run LAMMPS with these files, follow these instructions:
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh
deleted file mode 100755
index 9d2b0fbc5..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-# --- Running LAMMPS ---
-# -------- PREREQUISITES: --------
-# The 2 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.min # minimization
-lmp_mpi -i run.in.npt # simulation at constant pressure
-lmp_mpi -i run.in.nvt # simulation at constant volume
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_setup.sh
deleted file mode 100755
index 1e6630a94..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-
-# Create the coordinates of the atoms using PACKMOL
-cd packmol_files
-
- packmol < mix_lipids+water.inp
- mv -f system.xyz ../moltemplate_files/
-
-cd ..
-
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -xyz system.xyz system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_visualize.txt
deleted file mode 100644
index 587b80044..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 -0.5}
- pbc box -shiftcenterrel {0.0 0.0 -0.5} -style tubes -width 0.75
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/images/water_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/images/water_martini_LR.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt
deleted file mode 100644
index 3fe1b5530..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt
+++ /dev/null
@@ -1,78 +0,0 @@
-DPPC {
-
- write_once("In Init") {
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid cosine/squared
- dihedral_style none
- improper_style none
- pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12
- special_bonds lj/coul 0 1 1
- dielectric 15
- neigh_modify every 10
- }
-
- write("Data Atoms") {
- $atom:1 $mol:. @atom:Q0 1.0 9.09 9.83 0.75
- $atom:2 $mol:. @atom:Qa -1.0 5.68 7.31 0.00
- $atom:3 $mol:. @atom:Na 0.0 5.50 5.61 3.28
- $atom:4 $mol:. @atom:Na 0.0 6.65 2.22 3.04
- $atom:5 $mol:. @atom:C1 0.0 5.15 7.65 7.06
- $atom:6 $mol:. @atom:C1 0.0 7.91 7.17 10.54
- $atom:7 $mol:. @atom:C1 0.0 9.24 8.25 14.96
- $atom:8 $mol:. @atom:C1 0.0 12.19 11.75 16.38
- $atom:9 $mol:. @atom:C1 0.0 5.52 1.61 7.40
- $atom:10 $mol:. @atom:C1 0.0 6.53 2.26 12.25
- $atom:11 $mol:. @atom:C1 0.0 3.51 1.81 16.01
- $atom:12 $mol:. @atom:C1 0.0 0.00 0.00 18.19
- }
- write("Data Bonds") {
- $bond:b1 @bond:Bo $atom:1 $atom:2
- $bond:b2 @bond:Bo $atom:2 $atom:3
- $bond:b3 @bond:Short $atom:3 $atom:4
- $bond:b4 @bond:Bo $atom:3 $atom:5
- $bond:b5 @bond:Bo $atom:5 $atom:6
- $bond:b6 @bond:Bo $atom:6 $atom:7
- $bond:b7 @bond:Bo $atom:7 $atom:8
- $bond:b8 @bond:Bo $atom:4 $atom:9
- $bond:b9 @bond:Bo $atom:9 $atom:10
- $bond:b10 @bond:Bo $atom:10 $atom:11
- $bond:b11 @bond:Bo $atom:11 $atom:12
- }
- write("Data Angles") {
- $angle:a1 @angle:An1 $atom:1 $atom:2 $atom:3
- $angle:a2 @angle:An2 $atom:2 $atom:3 $atom:5
- $angle:a3 @angle:An2 $atom:2 $atom:3 $atom:4
- $angle:a4 @angle:An2 $atom:4 $atom:3 $atom:5
- $angle:a5 @angle:An1 $atom:3 $atom:4 $atom:9
- $angle:a6 @angle:An1 $atom:3 $atom:5 $atom:6
- $angle:a7 @angle:An1 $atom:5 $atom:6 $atom:7
- $angle:a8 @angle:An1 $atom:6 $atom:7 $atom:8
- $angle:a9 @angle:An1 $atom:4 $atom:9 $atom:10
- $angle:a10 @angle:An1 $atom:9 $atom:10 $atom:11
- $angle:a11 @angle:An1 $atom:10 $atom:11 $atom:12
- }
- write_once("Data Masses") {
- @atom:Q0 72.0
- @atom:Qa 72.0
- @atom:Na 72.0
- @atom:C1 72.0
- }
- write_once("In Settings") {
- pair_coeff @atom:Q0 @atom:Q0 lj/gromacs/coul/gromacs 0.8365200764818 4.7
- pair_coeff @atom:Q0 @atom:Qa lj/gromacs/coul/gromacs 1.0755258126195 4.7
- pair_coeff @atom:Q0 @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
- pair_coeff @atom:Q0 @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2
- pair_coeff @atom:Qa @atom:Qa lj/gromacs/coul/gromacs 1.1950286806883 4.7
- pair_coeff @atom:Qa @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
- pair_coeff @atom:Qa @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2
- pair_coeff @atom:Na @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
- pair_coeff @atom:Na @atom:C1 lj/gromacs/coul/gromacs 0.6453154875717 4.7
- pair_coeff @atom:C1 @atom:C1 lj/gromacs/coul/gromacs 0.8365200764818 4.7
- bond_coeff @bond:Bo harmonic 1.4937858508604 4.7
- bond_coeff @bond:Short harmonic 1.4937858508604 3.7
- angle_coeff @angle:An1 cosine/squared 2.9875717017208 180
- angle_coeff @angle:An2 cosine/squared 2.9875717017208 120
- }
-} #DPPC
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/system.lt
deleted file mode 100644
index 3339e2738..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/system.lt
+++ /dev/null
@@ -1,24 +0,0 @@
-import "water.lt"
-import "lipid.lt"
-
-# The lipids and water must be listed instantiated in the same order
-# they appear in the packmol_files/mix_lipids+water.inp file:
-
-lipids = new DPPC[300]
-
-waters = new MW[6000]
-
-
-write_once("Data Boundary") {
- 0 100.0 xlo xhi
- 0 100.0 ylo yhi
- 0 100.0 zlo zhi
-}
-
-
-write_once("In Settings") {
-pair_coeff @atom:MW/P4 @atom:DPPC/Q0 lj/gromacs/coul/gromacs 1.3384321223709 4.7
-pair_coeff @atom:MW/P4 @atom:DPPC/Qa lj/gromacs/coul/gromacs 1.3384321223709 4.7
-pair_coeff @atom:MW/P4 @atom:DPPC/Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
-pair_coeff @atom:MW/P4 @atom:DPPC/C1 lj/gromacs/coul/gromacs 0.4780114722753 4.7
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/water.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/water.lt
deleted file mode 100644
index c8d850f9c..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/water.lt
+++ /dev/null
@@ -1,17 +0,0 @@
-MW {
- write_once("In Init") {
- units real
- atom_style full
- pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12
- }
-
- write("Data Atoms") {
- $atom:1 $mol:. @atom:P4 0 0 0 0
- }
- write_once("Data Masses") {
- @atom:P4 72.0
- }
- write_once("In Settings") {
- pair_coeff @atom:P4 @atom:P4 lj/gromacs/coul/gromacs 1.1950286806883 4.7
- }
-} #MW
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/README.TXT
deleted file mode 100644
index c61369a22..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/README.TXT
+++ /dev/null
@@ -1,8 +0,0 @@
-You can use packmol to create a file containing the atomic coordinates
-for a system of coarse-grained lipids mixed with water using this command:
-
-If it takes too long for packmol to run, try lowering the tolerance.
-(tolerance 2.0 should work)
-
-packmol < mix_lipids+water.inp
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/lipid.xyz b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/lipid.xyz
deleted file mode 100644
index a576a09f6..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/lipid.xyz
+++ /dev/null
@@ -1,14 +0,0 @@
-12
- DPPC
-Q0 9.09 9.83 0.75
-Qa 5.68 7.31 0.00
-Na 5.50 5.61 3.28
-Na 6.65 2.22 3.04
-C1 5.15 7.65 7.06
-C1 7.91 7.17 10.54
-C1 9.24 8.25 14.96
-C1 12.19 11.75 16.38
-C1 5.52 1.61 7.40
-C1 6.53 2.26 12.25
-C1 3.51 1.81 16.01
-C1 0.00 0.00 18.19
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/mix_lipids+water.inp b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/mix_lipids+water.inp
deleted file mode 100644
index 1bc8a2a9d..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/mix_lipids+water.inp
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# A mixture of coarse-grained (martini) DPPC (lipid) and water.
-#
-
-# All the atoms from diferent molecules will be separated at least 3.0
-# Anstroms at the solution.
-
-tolerance 3.0 # minimal distance between atoms in different molecules
- # (you should also consider changing the "discale"
- # parameter. I think discale=1.0 by default.)
-seed 123 # seed for random number generator
-
-# The file type of input and output files is XYZ
-
-filetype xyz
-
-# The name of the output file
-
-output system.xyz
-
-# DPPC (lipid) molecules and water molecules will be put in a box
-# defined by the minimum coordinates x, y and z = 0 0 0. and maximum
-# coordinates 100 100 100. (Box size: 100x100x100)
-
-structure lipid.xyz
- number 300
- inside box 0.0 0.0 0.0 100.0 100.0 100.0
-end structure
-
-structure water.xyz
- number 6000
- inside box 0.0 0.0 0.0 100.0 100.0 100.0
-end structure
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/water.xyz b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/water.xyz
deleted file mode 100644
index 84fe1f74c..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files/water.xyz
+++ /dev/null
@@ -1,3 +0,0 @@
-1
- water
-W 0 0 0
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.min
deleted file mode 100644
index fc9aa8fbd..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.min
+++ /dev/null
@@ -1,31 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-thermo 5
-dump 1 all custom 100 traj_equib0_min.lammpstrj id mol type x y z ix iy iz
-minimize 1.0e-4 1.0e-6 100000 400000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.npt
deleted file mode 100644
index bbb0da392..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.npt
+++ /dev/null
@@ -1,117 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-# 2) You must minimize the coordinates using by running lammps witn
-# run.in.min
-#
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-#read_data "system.data"
-read_data "system_after_min.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-print "---------------------------------------------------------------------------"
-print "I often use Langevin dynamics initially at high temperatures and small"
-print "timesteps to relax the system. It seems more stable than Nose-Hoover."
-print "(This is probably not necessary.)"
-print "---------------------------------------------------------------------------"
-print " Note: Turning off 1-3 interactions during equilibration. (Turn them on later)"
-print "---------------------------------------------------------------------------"
-special_bonds lj/coul 0 0 1
-
-fix fxlan all langevin 450.0 450.0 100 123456 # temp: 450 K
-fix fxnph all nph iso 170.0 170.0 10000.0 # pressure: 170 barr
-thermo 100
-dump dmAll all custom 2000 traj_equib1_npt.lammpstrj id mol type x y z ix iy iz
-
-timestep 1.0 # (safer to use a small timestep initially)
-run 1000
-timestep 2.0
-run 1000
-timestep 5.0
-run 1000
-timestep 10.0
-run 2000
-timestep 20.0
-run 5000
-timestep 30.0 # (40.0 should be possible for lipid systems)
-
-run 50000
-
-unfix fxlan
-unfix fxnph
-undump dmAll
-
-print "---------------------------------------------------------------------------"
-print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---"
-print "---------------------------------------------------------------------------"
-
-velocity all zero linear # <- eliminate drift due to non-zero total momentum
- #fix 1 all momentum 1000 linear 1 1 1 # also works
-thermo 100
-#thermo_modify flush yes
-
-# temperature: 300 K, pressure: 1 barr
-fix fxnpt all npt temp 300.0 300.0 3000.0 iso 1.0 1.0 30000.0 drag 1.0
-dump dmAll all custom 5000 traj_equib2_npt.lammpstrj id mol type x y z ix iy iz
-
-run 50000
-unfix fxnpt
-undump dmAll
-
-
-# Pressure was equilibrated at 300K, but I initially run the simulation at
-# higher temperatures temporarily to speed up the proces of bilayer formation.
-# (Note: The boiling point of Martini-water is
-# I have to keep the volume constant (NVT) to prevent the water from boiling.
-dump dmAll all custom 10000 traj_equib3_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 450.0 450.0 1000.0 tchain 1
-
-run 1000000
-unfix fxnvt
-undump dmAll
-
-
-print "---------------------------------------------------------------------------"
-print " Note: Turning ON 1-3 interactions again."
-print "---------------------------------------------------------------------------"
-special_bonds lj/coul 0 1 1
-
-dump dmAll all custom 100 traj_equib4_min.lammpstrj id mol type x y z ix iy iz
-minimize 1.0e-4 1.0e-6 100000 400000
-undump dmAll
-
-
-# Hopefully a bilayer has formed at this point.
-# (If not, run the equilibration simulation for longer.)
-# Now I lower the temperature back to 300K.
-# I should probably re-equilibrate the solvent pressure and surface tension
-# (Simulation under NPT conditions using "anisotropic" boundaries.)
-# (so that the surface tension in the plane is allowed to relax independently
-# of the water volume, perpendicular to the plane.) I do that now:
-# temperature: 300 K, pressure: 1 barr
-fix fxnpt all npt temp 300.0 300.0 30000.0 couple xy aniso 1.0 1.0 1000.0 drag 1.0
-dump dmAll all custom 10000 traj_equib5_npt.lammpstrj id mol type x y z ix iy iz
-
-timestep 30.0
-run 100000
-unfix fxnpt
-undump dmAll
-
-
-write_data system_after_npt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.nvt
deleted file mode 100644
index 1f38df275..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/run.in.nvt
+++ /dev/null
@@ -1,50 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-# 2) You must minimize the coordinates using by running lammps witn
-# run.in.min
-# 3) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier simulation
-
-#read_data "system.data"
-#read_data "system_after_min.data"
-read_data "system_after_npt.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-velocity all zero linear # <- eliminate drift due to non-zero total momentum
- #fix 1 all momentum 1000 linear 1 1 1 # also works
-timestep 30.0 # (40.0 should be possible for lipid systems)
-thermo 100
-#thermo_modify flush yes
-
-
-
-# Continue the simulation at constant volume (NVT) at 300K.
-dump dmAll all custom 10000 traj_nvt_300K.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 3000.0 tchain 1
-
-run 10000000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README.TXT
deleted file mode 100644
index c290e3db3..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README.TXT
+++ /dev/null
@@ -1,13 +0,0 @@
-
-This example of the formation of a coarse-grained DPPC lipid-bilayer uses the
-Martini force-field v2.0 (2013-10), was provided by Saeed Momeni Bashusqeh.
-It's probably a good idea to run the simulation for a few ns to allow the
-lipids to reorient themselves.
-
-step 1)
-To build the files which LAMMPS needs, follow the instructions in:
-README_setup.sh
-
-step 2)
-To run LAMMPS with these files, follow these instructions:
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh
deleted file mode 100755
index 8cc857a5b..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-# --- Running LAMMPS ---
-# -------- PREREQUISITES: --------
-# The 2 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.min # minimization
-lmp_mpi -i run.in.npt # simulation at constant pressure
-lmp_mpi -i run.in.nvt # simulation at constant volume
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_setup.sh
deleted file mode 100755
index acc5fbbaa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_visualize.txt
deleted file mode 100644
index 587b80044..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 -0.5}
- pbc box -shiftcenterrel {0.0 0.0 -0.5} -style tubes -width 0.75
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/DPPC_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/DPPC_martini_LR.jpg
deleted file mode 100644
index cc85e79ff..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/t=0_bilayer_preformed_GL_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/t=0_bilayer_preformed_GL_LR.jpg
deleted file mode 100644
index 8f092c926..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/t=4ns_bilayer_preformed_GL_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/t=4ns_bilayer_preformed_GL_LR.jpg
deleted file mode 100644
index 9d5b6b594..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/water_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images/water_martini_LR.jpg
deleted file mode 100644
index a43675a5a..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt
deleted file mode 100644
index df92940b1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt
+++ /dev/null
@@ -1,78 +0,0 @@
-DPPC {
-
- write_once("In Init") {
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid cosine/squared
- dihedral_style none
- improper_style none
- pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12
- special_bonds lj/coul 0 1 1
- dielectric 15
- neigh_modify every 10
- }
-
- write("Data Atoms") {
- $atom:1 $mol:. @atom:Q0 1.0 2.67583 4.37417 19.25
- $atom:2 $mol:. @atom:Qa -1.0 -0.73417 1.85417 20.00
- $atom:3 $mol:. @atom:Na 0.0 -0.91417 0.15417 16.72
- $atom:4 $mol:. @atom:Na 0.0 0.23583 -3.23583 16.96
- $atom:5 $mol:. @atom:C1 0.0 -1.26417 2.19417 12.94
- $atom:6 $mol:. @atom:C1 0.0 1.49583 1.71417 9.46
- $atom:7 $mol:. @atom:C1 0.0 2.82583 2.79417 5.04
- $atom:8 $mol:. @atom:C1 0.0 5.77583 6.29417 3.62
- $atom:9 $mol:. @atom:C1 0.0 -0.89417 -3.84583 12.6
- $atom:10 $mol:. @atom:C1 0.0 0.11583 -3.19583 7.75
- $atom:11 $mol:. @atom:C1 0.0 -2.90417 -3.64583 3.99
- $atom:12 $mol:. @atom:C1 0.0 -6.41417 -5.45583 1.81
- }
- write("Data Bonds") {
- $bond:b1 @bond:Bo $atom:1 $atom:2
- $bond:b2 @bond:Bo $atom:2 $atom:3
- $bond:b3 @bond:Short $atom:3 $atom:4
- $bond:b4 @bond:Bo $atom:3 $atom:5
- $bond:b5 @bond:Bo $atom:5 $atom:6
- $bond:b6 @bond:Bo $atom:6 $atom:7
- $bond:b7 @bond:Bo $atom:7 $atom:8
- $bond:b8 @bond:Bo $atom:4 $atom:9
- $bond:b9 @bond:Bo $atom:9 $atom:10
- $bond:b10 @bond:Bo $atom:10 $atom:11
- $bond:b11 @bond:Bo $atom:11 $atom:12
- }
- write("Data Angles") {
- $angle:a1 @angle:An1 $atom:1 $atom:2 $atom:3
- $angle:a2 @angle:An2 $atom:2 $atom:3 $atom:5
- $angle:a3 @angle:An2 $atom:2 $atom:3 $atom:4
- $angle:a4 @angle:An2 $atom:4 $atom:3 $atom:5
- $angle:a5 @angle:An1 $atom:3 $atom:4 $atom:9
- $angle:a6 @angle:An1 $atom:3 $atom:5 $atom:6
- $angle:a7 @angle:An1 $atom:5 $atom:6 $atom:7
- $angle:a8 @angle:An1 $atom:6 $atom:7 $atom:8
- $angle:a9 @angle:An1 $atom:4 $atom:9 $atom:10
- $angle:a10 @angle:An1 $atom:9 $atom:10 $atom:11
- $angle:a11 @angle:An1 $atom:10 $atom:11 $atom:12
- }
- write_once("Data Masses") {
- @atom:Q0 72.0
- @atom:Qa 72.0
- @atom:Na 72.0
- @atom:C1 72.0
- }
- write_once("In Settings") {
- pair_coeff @atom:Q0 @atom:Q0 lj/gromacs/coul/gromacs 0.8365200764818 4.7
- pair_coeff @atom:Q0 @atom:Qa lj/gromacs/coul/gromacs 1.0755258126195 4.7
- pair_coeff @atom:Q0 @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
- pair_coeff @atom:Q0 @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2
- pair_coeff @atom:Qa @atom:Qa lj/gromacs/coul/gromacs 1.1950286806883 4.7
- pair_coeff @atom:Qa @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
- pair_coeff @atom:Qa @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2
- pair_coeff @atom:Na @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
- pair_coeff @atom:Na @atom:C1 lj/gromacs/coul/gromacs 0.6453154875717 4.7
- pair_coeff @atom:C1 @atom:C1 lj/gromacs/coul/gromacs 0.8365200764818 4.7
- bond_coeff @bond:Bo harmonic 1.4937858508604 4.7
- bond_coeff @bond:Short harmonic 1.4937858508604 3.7
- angle_coeff @angle:An1 cosine/squared 2.9875717017208 180
- angle_coeff @angle:An2 cosine/squared 2.9875717017208 120
- }
-} #DPPC
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/system.lt
deleted file mode 100644
index 696adaf86..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/system.lt
+++ /dev/null
@@ -1,27 +0,0 @@
-import "water.lt"
-import "lipid.lt"
-
-write_once("Data Boundary") {
- 0.0 100.0 xlo xhi
- 0.0 100.0 ylo yhi
- -50.0 50.0 zlo zhi
-}
-
-lipids = new DPPC [13].move(7.6923, 0, 0)
- [13].move(0, 7.6923, 0)
- [2].rot(180, 1, 0, 0)
-
-waters = new MW [25].move(4.0, 0, 0)
- [25].move(0, 4.0, 0)
- [13].move(0, 0, 4.23)
-
-# Move the waters upwards so that they don't overlap with the lipids.
-
-waters[*][*][*].move(0, 0, 22.4)
-
-write_once("In Settings") {
-pair_coeff @atom:MW/P4 @atom:DPPC/Q0 lj/gromacs/coul/gromacs 1.3384321223709 4.7
-pair_coeff @atom:MW/P4 @atom:DPPC/Qa lj/gromacs/coul/gromacs 1.3384321223709 4.7
-pair_coeff @atom:MW/P4 @atom:DPPC/Na lj/gromacs/coul/gromacs 0.9560229445507 4.7
-pair_coeff @atom:MW/P4 @atom:DPPC/C1 lj/gromacs/coul/gromacs 0.4780114722753 4.7
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/water.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/water.lt
deleted file mode 100644
index ab7f06890..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/water.lt
+++ /dev/null
@@ -1,17 +0,0 @@
-MW {
- write_once("In Init") {
- units real
- atom_style full
- pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12
- }
-
- write("Data Atoms") {
- $atom:1 $mol:. @atom:P4 0 0 0 0
- }
- write_once("Data Masses") {
- @atom:P4 72.0
- }
- write_once("In Settings") {
- pair_coeff @atom:P4 @atom:P4 lj/gromacs/coul/gromacs 1.1950286806883 4.7
- }
-} #MW
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.min
deleted file mode 100644
index 5cdf2f419..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.min
+++ /dev/null
@@ -1,31 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-thermo 5
-dump 1 all custom 100 traj_min.lammpstrj id mol type x y z ix iy iz
-minimize 1.0e-4 1.0e-6 100000 400000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.npt
deleted file mode 100644
index 1a995edcc..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.npt
+++ /dev/null
@@ -1,66 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-# 2) You must minimize the coordinates using by running lammps witn
-# run.in.min
-#
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-#read_data "system.data"
-read_data "system_after_min.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-print "---------------------------------------------------------------------------"
-print "I often use Langevin dynamics initially at high temperatures and small"
-print "timesteps to relax the system. It seems more stable than Nose-Hoover."
-print "(This is probably not necessary.)"
-print "---------------------------------------------------------------------------"
-
-fix fxlan all langevin 450.0 450.0 100 12345 # temp: 450 K
-fix fxnph all nph aniso 100.0 100.0 1000.0 couple xy drag 1.0 #pressure:100barr
-thermo 100
-dump dmNPTall all custom 5000 traj_npt_step1.lammpstrj id mol type x y z ix iy iz
-
-timestep 1.0 # (safer to use a small timestep initially)
-run 1000
-timestep 3.0
-run 1000
-timestep 10.0
-run 1000
-timestep 30.0 # (40.0 should be possible for lipid systems)
-run 100000
-
-unfix fxlan
-unfix fxnph
-undump dmNPTall
-
-print "---------------------------------------------------------------------------"
-print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---"
-print "---------------------------------------------------------------------------"
-
-velocity all zero linear # <- eliminate drift due to non-zero total momentum
- #fix 1 all momentum 1000 linear 1 1 1 # also works
-
-# temperature: 300 K, pressure: 1 barr
-fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0 couple xy
-thermo 100
-#thermo_modify flush yes
-dump dmNPTall all custom 10000 traj_npt_step2.lammpstrj id mol type x y z ix iy iz
-
-run 100000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.nvt
deleted file mode 100644
index 14b0cb5fa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/run.in.nvt
+++ /dev/null
@@ -1,47 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-# 2) You must minimize the coordinates using by running lammps witn
-# run.in.min
-# 3) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier simulation
-
-#read_data "system.data"
-#read_data "system_after_min.data"
-read_data "system_after_npt.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-velocity all zero linear # <- eliminate drift due to non-zero total momentum
- #fix 1 all momentum 1000 linear 1 1 1 # also works
-
-timestep 30.0 # (40.0 should be possible for lipid systems)
-dump 1 all custom 20000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 100
-#thermo_modify flush yes
-
-run 10000000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README.TXT
deleted file mode 100644
index c3173a1e1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README.TXT
+++ /dev/null
@@ -1,17 +0,0 @@
-
-This directory contains an example of a couarse-grained (vaguely protein-like)
-heteropolymer consisting of 14 residues, each of which has 2 atoms
-(one backbone atom, one residue atom.)
-
-There are two types of residues, H and P.
-The R-atom for the H residue are attracted to eachother.
-All other atoms are repulsive.
-
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh
deleted file mode 100755
index 8bf8e2764..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" file is a LAMMPS input script containing
-# references to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.nvt
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_setup.sh
deleted file mode 100755
index acc5fbbaa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_visualize.txt
deleted file mode 100644
index 5d97ea56a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_visualize.txt
+++ /dev/null
@@ -1,86 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/polymer.png b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/polymer.png
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/t=40ns_occ.png b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/t=40ns_occ.png
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/t=4ns_occ.png b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/t=4ns_occ.png
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/README.sh
deleted file mode 100755
index a5157b710..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/README.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-moltemplate.sh system.lt
-
-# This will generate various files with names ending in *.in* and *.data.
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt
deleted file mode 100644
index c2c01a8ee..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt
+++ /dev/null
@@ -1,139 +0,0 @@
-# The "2beadFF" is a force-field environment object containing
-# force-field data, atomic masses, and bond rules.
-# Later, when we define molecules (such as "H" and "P"), we can inherit
-# atom types and bond-rules from this force-field. This will automatically
-# assign bonds and angular interactions according to atom (and bond) type.
-# (You can also assign charge by atom type. However in this example I assigned
-# charge to each atom manually (not by type). The OPLSAA examples in the
-# "all_atoms" directory demonstrate how to assign charge by atom type.)
-
-
-
-2beadFF {
-
- # There are 3 atom types:
-
- write_once("Data Masses") {
- @atom:CA 13.0
- @atom:HR 50.0
- @atom:PR 50.0
- }
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 )
- #
- # Hydrophobic side-chain (R) atoms are attractive (large epsilon parameter).
- # Polar side-chains and backbone atoms are not attractive (small epsilon).
- #
- # i j pairstylename eps sig
- #
- write_once("In Settings") {
- pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0
- pair_coeff @atom:HR @atom:HR lj/cut 2.50 3.6
- pair_coeff @atom:PR @atom:PR lj/cut 0.10 3.6
- }
-
- # (By default, interactions between different AtomTypes use "arithmetic"rules:
- # eps_ij=sqrt(eps_ii*eps_ij) and sig_ij=0.5*(sig_ii+sig_jj)
- # Look for the line containing "pair_modify mix arithmetic" below...)
-
- # Optional: Assign bond types @bond:Backbone or @bond:Sidechain
- # according to atom type. (This can be overridden.)
-
- write_once("Data Bonds By Type") {
- @bond:Backbone @atom:CA @atom:CA
- @bond:Sidechain @atom:CA @atom:HR
- @bond:Sidechain @atom:CA @atom:PR
- }
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond_coeff bondType bondstylename k r0
- #
-
- write_once("In Settings") {
- bond_coeff @bond:Sidechain harmonic 30.0 3.4
- bond_coeff @bond:Backbone harmonic 30.0 3.7
- }
-
-
- # Rules for determining 3 and 4-body bonded interactions by type
-
- # angle-type atomType1 atomType2 atomType3
-
- write_once("Data Angles By Type") {
- @angle:Backbone @atom:CA @atom:CA @atom:CA
- @angle:Sidechain @atom:CA @atom:CA @atom:*R # Note: "*R" <--> "HR" or "PR"
- }
-
- # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4
-
- write_once("Data Dihedrals By Type") {
- @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA
- @dihedral:RCCR @atom:*R @atom:CA @atom:CA @atom:*R #"*R" <--> "HR" or "PR"
- }
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # The corresponding command is:
- #
- # angle_coeff angleType anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:Backbone harmonic 30.00 114
- angle_coeff @angle:Sidechain harmonic 30.00 123
- }
-
-
- # 4-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Udihedral(phi) = K * (1 + cos(n*phi - d))
- #
- # The d parameter is in degrees, K is in kcal/mol/rad^2.
- #
- # The corresponding command is
- # dihedral_coeff dihedralType dihedralstylename K n d w (ignore "w")
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0
- dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0
- } # write_once("In Settings")
-
-
- # LAMMPS supports a large number of force-field styles. We must select
- # which ones we need. This information belongs in the "In Init" section.
- # (Hybrid styles used for portability. These choices can be overridden later.)
-
- write_once("In Init") {
- # -- Default styles for "2bead" --
- # (Hybrid force fields were not necessary but are used for portability.)
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid charmm
- pair_style hybrid lj/cut 11.0
-
- # If charges are needed, (assuming biopolymers), try one of:
- #dielectric 80.0
- #pair_style hybrid lj/cut/coul/debye 0.1 11.0
- # or (for short distances, below a couple nm)
- #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0
-
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 0.0
- }
-
-
-} # 2beadFF
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/monomers.lt
deleted file mode 100644
index 98aece5b8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/monomers.lt
+++ /dev/null
@@ -1,86 +0,0 @@
-# In this example, we define two types of molecules: "H" and "P",
-# both containing two atoms, whose ids (names) are "ca" and "r",
-# and whose atom-types vary.
-#
-# "H" molecules: "P" molecules:
-#
-# @HR @PR
-# | |
-# @CA @CA
-#
-# Eventually, we will connect multiple "H" and "P" molecules
-# together to form a polymer, as shown below:
-#
-# @HR @HR
-# | |
-# _@CA_ _@CA_
-# ... -.@CA-' `-@CA-' ` ...
-# | |
-# @PR @PR
-#
-# The "H" and "P" molecules both share the same type of
-# backbone atom ("CA"), but have their own custom "r"
-# sidechain atoms with different properties:
-# The "HR" atoms belonging to "H" molecules are attracted to each other.
-# The "PR" atoms in "P" molecules are not.
-
-
-
-
-
-import "forcefield.lt" # defines "2beadFF"
-
-
-
-
-
-# Define the "H" monomer type ("H" <--> "hydrophobic")
-
-H inherits 2beadFF {
- # atom-id(name) mol-id atom-type charge x y z
- write("Data Atoms") {
- $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000
- $atom:r $mol:... @atom:HR 0.0 0.000 4.4000 0.0000000
- }
-
- write("Data Bond List") {
- $bond:cr $atom:ca $atom:r
- }
-
- # This will look up the bond-parameters according to atom type.
- # Use "Data Bonds" instead if you prefer to assign the bond type manually:
- # write("Data Bonds") {
- # $bond:cr @bond:Sidechain $atom:ca $atom:r
- # }
-
-}
-
-
-
-# Define the "P" monomer type ("P" <--> "polar")
-
-P inherits 2beadFF {
-
- # atom-id(name) mol-id atom-type charge x y z
- write("Data Atoms") {
- $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000
- $atom:r $mol:... @atom:PR 0.0 0.000 4.4000 0.0000000
- }
-
- write("Data Bond List") {
- $bond:CR $atom:ca $atom:r
- }
-
- # This will look up the bond-parameters according to atom type.
- # Use "Data Bonds" instead if you prefer to assign the bond type manually:
- # write("Data Bonds") {
- # $bond:cr @bond:Sidechain $atom:ca $atom:r
- # }
-
-}
-
-
-
-# Note: The "..." in "$mol:..." tells moltemplate that this molecule may
-# be a part of a larger molecule, and (if so) to use the larger
-# molecule's id number as it's own.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/polymer.lt
deleted file mode 100644
index 5be93322d..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/polymer.lt
+++ /dev/null
@@ -1,64 +0,0 @@
-
-import "monomers.lt" # This defines the monomer types named "H" and "P"
-
-
-
-Polymer {
-
- create_var {$mol} # optional:force all monomers to share the same molecule-ID
- # (The "Data Atoms" in H and P must use "$mol:..." notation.)
-
- # This causes mon1,mon2,mon3,...,mon14 to share the same molecule counter
- # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks
- # for a counter of that type in a parent molecule or earlier ancestor.
-
-
- # A polymer of alternating "H" and "P" monomers:
-
- mon1 = new P
- mon2 = new P.rot(180.0, 1,0,0).move(3.2,0,0)
- mon3 = new H.rot( 0.0, 1,0,0).move(6.4,0,0)
- mon4 = new H.rot(180.0, 1,0,0).move(9.6,0,0)
- mon5 = new H.rot( 0.0, 1,0,0).move(12.8,0,0)
- mon6 = new H.rot(180.0, 1,0,0).move(16.0,0,0)
- mon7 = new P.rot( 0.0, 1,0,0).move(19.2,0,0)
- mon8 = new P.rot(180.0, 1,0,0).move(22.4,0,0)
- mon9 = new P.rot( 0.0, 1,0,0).move(25.6,0,0)
- mon10 = new H.rot(180.0, 1,0,0).move(28.8,0,0)
- mon11 = new H.rot( 0.0, 1,0,0).move(32.0,0,0)
- mon12 = new H.rot(180.0, 1,0,0).move(35.2,0,0)
- mon13 = new P.rot( 0.0, 1,0,0).move(38.4,0,0)
- mon14 = new P.rot(180.0, 1,0,0).move(41.6,0,0)
-
-
- # Now, link the monomers together this way:
- write("Data Bond List") {
- $bond:backbone1 $atom:mon1/ca $atom:mon2/ca
- $bond:backbone2 $atom:mon2/ca $atom:mon3/ca
- $bond:backbone3 $atom:mon3/ca $atom:mon4/ca
- $bond:backbone4 $atom:mon4/ca $atom:mon5/ca
- $bond:backbone5 $atom:mon5/ca $atom:mon6/ca
- $bond:backbone6 $atom:mon6/ca $atom:mon7/ca
- $bond:backbone7 $atom:mon7/ca $atom:mon8/ca
- $bond:backbone8 $atom:mon8/ca $atom:mon9/ca
- $bond:backbone9 $atom:mon9/ca $atom:mon10/ca
- $bond:backbone10 $atom:mon10/ca $atom:mon11/ca
- $bond:backbone11 $atom:mon11/ca $atom:mon12/ca
- $bond:backbone12 $atom:mon12/ca $atom:mon13/ca
- $bond:backbone13 $atom:mon13/ca $atom:mon14/ca
- }
-
-
- # Use "Data Bonds" instead if you prefer to assign the bond types manually:
- # write("Data Bonds") {
- # $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca
- # $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca
- # : : : :
- # }
-
-} # Polymer
-
-
-
-# Angle, dihedral and improper interactions between monomers will be generated
-# automatically according to the instructions in the "force_field.lt" file.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/system.lt
deleted file mode 100644
index e3d8317aa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files/system.lt
+++ /dev/null
@@ -1,36 +0,0 @@
-import "polymer.lt"
-
-
-# Specify the periodic boundary conditions:
-write_once("Data Boundary") {
- 0 180.0 xlo xhi
- 0 180.0 ylo yhi
- 0 180.0 zlo zhi
-}
-
-
-# Create 27 polymers (=3x3x3) in a rectangular grid
-
-polymers = new Polymer [3].move(60.0, 0, 0)
- [3].move(0, 60.0, 0)
- [3].move(0, 0, 60.0)
-
-
-
-
-
-
-
-
-# ----- everything below is optional: -----
-# Shift some of the polymers in the Z direction by a distance of 20.0
-
-polymers[1][*][*].move(0,0,20)
-
-# We applied this move command to all the
-# polymers in the middle slab (with constant X).
-# More examples of applying the "move" command:
-
-polymers[*][1][*].move(20,0,0)
-polymers[*][*][1].move(0,20,0)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/run.in.nvt
deleted file mode 100644
index 35488d659..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/run.in.nvt
+++ /dev/null
@@ -1,32 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 2.0
-dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-fix fxlan all langevin 300.0 300.0 5000.0 48279
-fix fxnve all nve
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 2500 # time interval for printing out "thermo" data
-
-run 20000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README.TXT
deleted file mode 100644
index 15638c153..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README.TXT
+++ /dev/null
@@ -1,19 +0,0 @@
-This is an example of how to build a polymer out of randomly-chosen monomers.
-In this case, monomers will be chosen at random from two types
-(denoted "2bead" and "3bead", although you can have as many types as you like).
-You can also constrain the end-caps to be a particular type (eg "3bead").
-
-The properties of the bonds connecting monomers (ie length, rigidity) will
-be automatically determined, depending on the type of monomers at that location
-in the polymer. The same is true for the 3-body angle, and 4-body dihedral
-interactions.
-
-
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh
deleted file mode 100755
index 9343d763f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" file is a LAMMPS input script containing
-# references to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.nvt
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_setup.sh
deleted file mode 100755
index acc5fbbaa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images/2bead.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=0.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=0.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=700ps.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=700ps.jpg
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/forcefield.lt
deleted file mode 100644
index 6bdb4697b..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/forcefield.lt
+++ /dev/null
@@ -1,107 +0,0 @@
-# The "ForceField" object contains a list of atom types, masses, force-field
-# parameters, and rules for generating 3-body & 4-body bonded interactions.
-# Molecules which use "inherit ForceField" share these rules, and consequently
-# can usually be written in a much more concise way.
-
-
-ForceField {
-
- # LAMMPS supports a large number of force-field styles. We must select
- # which ones we need. This information belongs in the "In Init" section (and
- # (you can specify it anywhere in your LT files, multiple times if you like).
- # If different molecules use different force-field styles, you can use hybrid
- # styles. (In this example the molecules share the same pair_style.)
-
- write_once("In Init") {
- units real
- atom_style full
- bond_style harmonic
- angle_style harmonic
- dihedral_style opls
- pair_style lj/cut 9.0
- # If you have charged molecules immersed in a salty implicit
- # solvent, you might try something like this this instead:
- # pair_style lj/cut/coul/debye 0.1 9.0
- pair_modify mix arithmetic
- dielectric 80.0
- special_bonds lj 0.0 0.0 0.0
- }
-
- # atom-type mass
-
- write_once("Data Masses") {
- @atom:CA2 12.0
- @atom:R2 17.0
- @atom:CA3 12.0
- @atom:R3 17.0
- }
-
-
- # Connect different monomers together with bonds whose type
- # (length, rigidity, etc) depend on the type of atom at either end.
-
- write_once("Data Bonds By Type") {
- @bond:sidechain @atom:CA* @atom:R*
- @bond:two_two @atom:CA2 @atom:CA2
- @bond:two_three @atom:CA2 @atom:CA3
- @bond:three_three @atom:CA3 @atom:CA3
- }
- # Note: The next line is redundant and unnecessary:
- # @bond:two_three @atom:CA3 @atom:CA2
-
-
-
- # You can also generate angles and dihedrals and impropers in a similar way:
-
- # Rules for determining 3 and 4-body bonded interactions by type
-
- # angle-type atomType1 atomType2 atomType3 bondType1 bondType2
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:CA* @atom:CA* @atom:CA* @bond:* @bond:*
- @angle:sidechain @atom:CA* @atom:CA* @atom:R* @bond:* @bond:*
- @angle:RCR @atom:R* @atom:CA* @atom:R* @bond:* @bond:*
- }
- # Note: The next line is redundant and unnecessary:
- # @angle:sidechain @atom:R* @atom:CA* @atom:CA* @bond:* @bond:*
-
-
- # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3
-
- write_once("Data Dihedrals By Type") {
- @dihedral:backbone @atom:CA* @atom:CA* @atom:CA* @atom:CA* * * *
- @dihedral:two_two @atom:R2 @atom:CA* @atom:CA* @atom:R2 * * *
- @dihedral:two_three @atom:R2 @atom:CA* @atom:CA* @atom:R3 * * *
- @dihedral:three_three @atom:R3 @atom:CA* @atom:CA* @atom:R3 * * *
- }
- # Note: The next line is redundant and unnecessary:
- # @dihedral:two_three @atom:R3 @atom:CA* @atom:CA* @atom:R2 * * *
-
- # Force field parameters:
- write_once("In Settings") {
- # atom-type atom-type epsilon sigma
- pair_coeff @atom:CA2 @atom:CA2 0.05 3.0
- pair_coeff @atom:R2 @atom:R2 0.60 4.0
- pair_coeff @atom:CA3 @atom:CA3 0.10 2.0
- pair_coeff @atom:R3 @atom:R3 0.50 3.0
-
- # bond-type k r0
- bond_coeff @bond:sidechain 20.0 3.4
- bond_coeff @bond:two_two 20.0 3.7
- bond_coeff @bond:two_three 20.0 3.5
- bond_coeff @bond:three_three 20.0 3.3
-
- # angle-type k theta0
- angle_coeff @angle:backbone 40.00 120
- angle_coeff @angle:sidechain 40.00 120
- angle_coeff @angle:RCR 40.00 120
-
- # dihedral-type K1 K2 K3 K4
- dihedral_coeff @dihedral:backbone 0.3 0.0 0.0 0.0
- dihedral_coeff @dihedral:two_two 0.08 0.0 0.0 0.0
- dihedral_coeff @dihedral:two_three 0.08 0.0 -0.05 0.0
- dihedral_coeff @dihedral:three_three 0.08 0.0 0.0 0.05
- }
-
-} # ForceField
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/monomers.lt
deleted file mode 100644
index a6b685cc9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/monomers.lt
+++ /dev/null
@@ -1,62 +0,0 @@
-import "forcefield.lt" #<-- "forcefield.lt" contains atom type definitions,
- # force-field parameters, and rules for generating
- # 3-body and 4-body angle, dihedral, and improper
- # interactions for molecules (polymers) made using
- # "2bead" and "3bead" objects as building blocks.
-
-
-
- # ----------------------------------------------------------------------
- # -- General comment: --
- # -- The write() and write_once() commands create and append text to --
- # -- files (replacing variables beginning with @ or $ with counters.) --
- # -- File names beginning with "In " or "Data " are special. --
- # -- They will be pasted into the LAMMPS input script and --
- # -- data files which are generated by moltemplate. The syntax --
- # -- of these files is exactly the same as the syntax from the --
- # -- corresponding sections of a LAMMPS input script or data file. --
- # ----------------------------------------------------------------------
-
-
-
-
-
-
-3bead inherits ForceField {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:CA $mol:... @atom:CA3 0.0 0.000 1.000 0.000
- $atom:R1 $mol:... @atom:R3 0.0 0.000 2.700 2.950
- $atom:R2 $mol:... @atom:R3 0.0 0.000 2.700 -2.950
- }
-
- # bond-id atom-id1 atom-id2
- write("Data Bond List") {
- $bond:CR1 $atom:CA $atom:R1
- $bond:CR2 $atom:CA $atom:R2
- }
-
-} # 3bead
-
-
-
-
-2bead inherits ForceField {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:CA $mol:... @atom:CA2 0.0 0.000 1.000 0.0000
- $atom:R $mol:... @atom:R2 0.0 0.000 4.400 0.0000
- }
-
- # bond-id atom-id1 atom-id2
- write("Data Bond List") {
- $bond:CR $atom:CA $atom:R
- }
-
-} # 2bead
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/polymer.lt
deleted file mode 100644
index 4502934eb..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/polymer.lt
+++ /dev/null
@@ -1,163 +0,0 @@
-import "forcefield.lt" # <-- Defines force-field parameters, and rules.
-import "monomers.lt" # <-- Defines the "2bead", "3bead" objects we will use
- # as building-blocks to build the polymer.
-
-
-
-
-RandomHeteropolymer inherits ForceField {
-
-
-
- create_var {$mol} # optional:force all monomers to share the same molecule-ID
- # If you want to share molecule-IDs, do this first
- # (This matches with "$mol:..." in "monomers.lt")
-
-
-
- monomers[0] = new 3bead # Let the first monomer be of type "3bead"
-
- # Now, fill the middle of the chain with random monomers (2bead, 3bead):
-
- monomers[1-48] = new random([2bead,3bead],
- [30, # <-- 30 "2bead" molecules and
- 18], # <-- 18 "3bead" molecules
- 12345) # <-- optional random seed
-
- # and place them on the X-axis (separated by 2.95 Angstroms)
- [48].rot(180,1,0,0).move(2.95, 0, 0)
-
- # Note: The two numbers (30 and 18) must sum up to the number of
- # monomers we created ("[48]").
-
- monomers[49] = new 3bead # Let the last monomer be of type "3bead"
-
-
- # Afterwards, there should be 20 "3bead" monomers and 30 "2bead" monomers
-
-
-
-
- # Now, physically move the monomers to make sure the monomers on the end of
- # the chain (monomers[0] & monomers[49]) don't overlap with monomers[1-48]
-
- monomers[0].rot(180,1,0,0) #leave monomer[0] where it is, but rotate it
- monomers[1-48].move(2.95,0,0) #move the remaining monomers to make room for it
- monomers[49].move(144.55,0,0) #move the last monomer (note:144.55=2.95*50))
-
-
-
-
- # Now, link the monomers together using "Data Bond List"
- # (Using "Data Bond List" instead of "Data Bonds", allows you to omit the
- # bond type. This tells moltemplate to look up the appropriate
- # bond type according to the type of atom at either end of the bond, which
- # depends on what type of monomer is on either side: "2bead" or "3bead".
- # This all happens automatically. The user can control how this is done
- # by editing the file "forcefield.lt".)
-
-
- write("Data Bond List") {
- $bond:bb1 $atom:monomers[0]/CA $atom:monomers[1]/CA
- $bond:bb2 $atom:monomers[1]/CA $atom:monomers[2]/CA
- $bond:bb3 $atom:monomers[2]/CA $atom:monomers[3]/CA
- $bond:bb4 $atom:monomers[3]/CA $atom:monomers[4]/CA
- $bond:bb5 $atom:monomers[4]/CA $atom:monomers[5]/CA
- $bond:bb6 $atom:monomers[5]/CA $atom:monomers[6]/CA
- $bond:bb7 $atom:monomers[6]/CA $atom:monomers[7]/CA
- $bond:bb8 $atom:monomers[7]/CA $atom:monomers[8]/CA
- $bond:bb9 $atom:monomers[8]/CA $atom:monomers[9]/CA
- $bond:bb10 $atom:monomers[9]/CA $atom:monomers[10]/CA
- $bond:bb11 $atom:monomers[10]/CA $atom:monomers[11]/CA
- $bond:bb12 $atom:monomers[11]/CA $atom:monomers[12]/CA
- $bond:bb13 $atom:monomers[12]/CA $atom:monomers[13]/CA
- $bond:bb14 $atom:monomers[13]/CA $atom:monomers[14]/CA
- $bond:bb15 $atom:monomers[14]/CA $atom:monomers[15]/CA
- $bond:bb16 $atom:monomers[15]/CA $atom:monomers[16]/CA
- $bond:bb17 $atom:monomers[16]/CA $atom:monomers[17]/CA
- $bond:bb18 $atom:monomers[17]/CA $atom:monomers[18]/CA
- $bond:bb19 $atom:monomers[18]/CA $atom:monomers[19]/CA
- $bond:bb20 $atom:monomers[19]/CA $atom:monomers[20]/CA
- $bond:bb21 $atom:monomers[20]/CA $atom:monomers[21]/CA
- $bond:bb22 $atom:monomers[21]/CA $atom:monomers[22]/CA
- $bond:bb23 $atom:monomers[22]/CA $atom:monomers[23]/CA
- $bond:bb24 $atom:monomers[23]/CA $atom:monomers[24]/CA
- $bond:bb25 $atom:monomers[24]/CA $atom:monomers[25]/CA
- $bond:bb26 $atom:monomers[25]/CA $atom:monomers[26]/CA
- $bond:bb27 $atom:monomers[26]/CA $atom:monomers[27]/CA
- $bond:bb28 $atom:monomers[27]/CA $atom:monomers[28]/CA
- $bond:bb29 $atom:monomers[28]/CA $atom:monomers[29]/CA
- $bond:bb30 $atom:monomers[29]/CA $atom:monomers[30]/CA
- $bond:bb31 $atom:monomers[30]/CA $atom:monomers[31]/CA
- $bond:bb32 $atom:monomers[31]/CA $atom:monomers[32]/CA
- $bond:bb33 $atom:monomers[32]/CA $atom:monomers[33]/CA
- $bond:bb34 $atom:monomers[33]/CA $atom:monomers[34]/CA
- $bond:bb35 $atom:monomers[34]/CA $atom:monomers[35]/CA
- $bond:bb36 $atom:monomers[35]/CA $atom:monomers[36]/CA
- $bond:bb37 $atom:monomers[36]/CA $atom:monomers[37]/CA
- $bond:bb38 $atom:monomers[37]/CA $atom:monomers[38]/CA
- $bond:bb39 $atom:monomers[38]/CA $atom:monomers[39]/CA
- $bond:bb40 $atom:monomers[39]/CA $atom:monomers[40]/CA
- $bond:bb41 $atom:monomers[40]/CA $atom:monomers[41]/CA
- $bond:bb42 $atom:monomers[41]/CA $atom:monomers[42]/CA
- $bond:bb43 $atom:monomers[42]/CA $atom:monomers[43]/CA
- $bond:bb44 $atom:monomers[43]/CA $atom:monomers[44]/CA
- $bond:bb45 $atom:monomers[44]/CA $atom:monomers[45]/CA
- $bond:bb46 $atom:monomers[45]/CA $atom:monomers[46]/CA
- $bond:bb47 $atom:monomers[46]/CA $atom:monomers[47]/CA
- $bond:bb48 $atom:monomers[47]/CA $atom:monomers[48]/CA
- $bond:bb49 $atom:monomers[48]/CA $atom:monomers[49]/CA
- }
-
-} # RandomHeteropolymer
-
-
-
-
-# COMMENTS:
-#
-#
-# 1)
-# Angle, dihedral and improper interactions will be generated
-# automatically according to the instructions in "monomers.lt"
-#
-#
-#
-#
-# 2)
-# These lines in the "Data Bond List" section can be quickly generated in python
-# N = 50
-# for i in range(0,N-1):
-# print(' $bond:bb'+str(i+1)+' $atom:monomers['
-# +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA')
-#
-#
-#
-# 3)
-# The "[1-50]" in "monomers[1-50] = new random([2bead,3bead], ..."
-# causes moltemplate to create a list of molecules with names beginning with
-# "monomers[1]", for example:
-# "monomers[1], "monomers[2]", "monomers[3], ..., "monomers[50]"
-# (This causes the indexing to begin at [1] instead of [0].)
-#
-#
-#
-# 4)
-# ALTERNATE METHOD: You can also generate a random array this way:
-#
-# monomers[1-48] = new random([2bead,3bead],
-# [0.625, 0.375], # <-- probabilities
-# 12345) # <-- optional random seed
-# [48].rot(180,1,0,0).move(2.95, 0, 0)
-#
-# The command above also works, but it chooses each molecule (monomer) randomly
-# (independently of the others). Consequently, this does not gaurantee that
-# exactly 62.5% and 37.5% of the monomers will be of type 2bead and 3bead.
-#
-#
-#
-# 5) RandomHeteropolymer uses "2bead" and "3bead" objects as building-blocks,
-# and these objects inherit the properties from the "ForceField" object
-# (atom types, bond types, etc, defined in "forcefield.lt" in this example).
-# So I declared that "RandomHeteropolymer inherits ForceField {" so that
-# you can easily access those atom types, bond types, etc as well.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/system.lt
deleted file mode 100644
index 565edc3f0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files/system.lt
+++ /dev/null
@@ -1,11 +0,0 @@
-
-write_once("Data Boundary") {
- 0.0 150.0 xlo xhi
- 0.0 150.0 ylo yhi
- 0.0 150.0 zlo zhi
-}
-
-
-import "polymer.lt"
-
-polymer = new RandomHeteropolymer
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/run.in.nvt
deleted file mode 100644
index 645dac344..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/run.in.nvt
+++ /dev/null
@@ -1,29 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-timestep 2.0
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 1000 # time interval for printing out "thermo" data
-
-fix fxlan all langevin 300.0 300.0 120 48279
-fix fxnve all nve
-
-# Temperature = 500 degrees
-
-run 500000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README.TXT
deleted file mode 100644
index b9bac96d5..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README.TXT
+++ /dev/null
@@ -1,23 +0,0 @@
-
-This example contains a (crude and somewhat simple) example of
-the translocation of a (rather short) polymer through a hole in a wall,
-surrounded by an explicit LJ solvent.
-
-(I used a short polymer because a longer polymer would require a larger box.
- But this example looked more impressive visually when I used a smaller box.)
-----
-Note: You must compile LAMMPS with the optional "RIGID" package installed. To
- do this, go to the "src" directory of your lammps installation and type:
- make yes-RIGID
- make clean-all
- make NAME_OF_TARGET #<--("make ubuntu", "make g++", "make linux".)
-----
-
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh
deleted file mode 100755
index 0828a7f09..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" file is a LAMMPS input script containing
-# references to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.nvt # Run a simulation at constant volume
-
-#or
-
-lmp_mpi -i run.in.npt # Run a simulation at constant pressure
- # (Note: Constant pressure conditions have not been
- # well tested. The "run.in.npt" script may fail.)
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-#or
-#mpirun -np 4 lmp_mpi -i run.in.npt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_setup.sh
deleted file mode 100755
index acc5fbbaa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/polymer_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/polymer_LR.jpg
deleted file mode 100644
index 5529fc74b..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/solvent_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/solvent_LR.jpg
deleted file mode 100644
index 304693e2a..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/walls+solvent+polymer_t=0.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/walls+solvent+polymer_t=0.jpg
deleted file mode 100644
index c1dcc4c18..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/walls_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images/walls_LR.jpg
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/monomer.lt
deleted file mode 100644
index a8a35339f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/monomer.lt
+++ /dev/null
@@ -1,111 +0,0 @@
- # ----------------------------------------------------------------------
- # -- General comment: --
- # -- The write() and write_once() commands create and append text to --
- # -- files (replacing variables beginning with @ or $ with counters.) --
- # -- File names beginning with "In " or "Data " are special. --
- # -- They will be pasted into the LAMMPS input script and --
- # -- data files which are generated by moltemplate. The syntax --
- # -- of these files is exactly the same as the syntax from the --
- # -- corresponding sections of a LAMMPS input script or data file. --
- # ----------------------------------------------------------------------
-
-
-Monomer {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:CA $mol:... @atom:CA 0.0 0.000 0.4000 0.00000
- $atom:R1 $mol:... @atom:R 0.0 0.000 1.000 1.000
- $atom:R2 $mol:... @atom:R 0.0 0.000 1.000 -1.000
- }
-
- # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
- # be a part of a larger molecule, and (if so) to use the larger
- # parent object's molecule id number as it's own
-
-
- # atom-type mass
-
- write_once("Data Masses") {
- @atom:CA 13.0
- @atom:R 50.0
- }
-
- # atom-type atom-type epsilon sigma
-
- write_once("In Settings") {
- pair_coeff @atom:CA @atom:CA 0.05 2.0
- pair_coeff @atom:R @atom:R 0.50 2.0
- }
-
- # bond-id bond-type atom-id1 atom-id2
-
- write("Data Bonds") {
- $bond:CR1 @bond:sidechain $atom:CA $atom:R1
- $bond:CR2 @bond:sidechain $atom:CA $atom:R2
- }
-
- write_once("In Settings") {
- # bond-type k r0
- bond_coeff @bond:sidechain 30.0 1.2
- bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone"
- }
-
- # For a compound molecule consisting of smaller building blocks (such as a
- # polymer built from monomers), it is tedious to explicitly list all of the
- # angles, dihedrals in the entire molecule. Instead, you can define rules
- # for automatically generating all the angular interactions between bonded
- # atoms according to their connectivity and the atom/bond type.
- # Later, when you connect multiple monomers together to form a polymer,
- # appropriate bond-angle forces will be applied to these atoms automatically
- # (as well as dihedral and improper forces, if defined).
-
- # Rules for determining 3 and 4-body bonded interactions by type
-
- # angle-type atomType1 atomType2 atomType3 bondType1 bondType2
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:*
- @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:*
- @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:*
- }
-
- # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer.
- # The other angular interactions are between atoms in neighboring monomers.)
-
-
- # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3
-
- write_once("Data Dihedrals By Type") {
- @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:*
- }
-
- # Parameters for these new angular interactions must be defined. (I recommend
- # putting all force-field parameters (coeffs) in the "In Settings" section.)
-
- write_once("In Settings") {
- # angle-type k theta0
- angle_coeff @angle:backbone 50.00 160
- angle_coeff @angle:sidechain 50.00 120
- angle_coeff @angle:RCR 50.00 120
- # dihedral-type K1 K2 K3 K4
- dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0
- }
-
-} # Monomer
-
-
-
-
-
-
-# -------------------------------------------------------------------------
-# Heteropolymers:
-#
-# There is a similar example for heteropolymers which is distributed online
-# bundled with the moltemplate software. It is named "2bead_heteropolymer",
-# and it demonstrates how to share backbone (CA) atoms, bonds and angles
-# (so that you don't have to define them seperately for each type of monomer).
-# -------------------------------------------------------------------------
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/polymer.lt
deleted file mode 100644
index 31a36d07c..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/polymer.lt
+++ /dev/null
@@ -1,32 +0,0 @@
-import "monomer.lt"
-
-Polymer {
-
- create_var {$mol} # optional:force all monomers to share the same molecule-ID
- # (The "Data Atoms" in Monomer must use "$mol:..." notation.)
-
- # Make a chain of monomers
- monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0)
-
-
- # Now, link the monomers together this way:
- write("Data Bonds") {
- $bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA
- $bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA
- $bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA
- $bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA
- $bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA
- $bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA
- $bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA
- $bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA
- $bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA
- $bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA
- $bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA
- }
-
-} # Polymer
-
-
-
-# Angle, dihedral and improper interactions will be generated
-# automatically according to the instructions in "monomer.lt"
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/solvent.lt
deleted file mode 100644
index 1073a58a1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/solvent.lt
+++ /dev/null
@@ -1,23 +0,0 @@
-###################### SOLVENT #########################
-
-import "solvent_single.lt"
-
-# Fill the simulation box with a solvent.
-# In this example, the solvent is made of many
-# copies of "MoleculeA" (which has only one atom).
-
-solvent = new MoleculeA [12].move(3.0,0,0)
- [12].move(0,3.0,0)
- [12].move(0,0,3.0)
-
-# To start with a reasonable conformation, it's a good idea to delete the
-# solvent where the walls or the polymer is going to be. Here we do it manually:
-
-delete solvent[*][*][2] # <-- 1st wall will go here
-delete solvent[*][*][8] # <-- 2nd wall will go here
-delete solvent[6-7][0-8][5-6] # <-- polymer will go here
-
-# Alternate notation:
-# [a:b] notation also works, however the "b" is a strict upper bound...
-# ...hence the last line is equivalent to "delete solvent[6:8][0:9][5:7]"
-# [a*b] notation also works, and is equivalent to [a-b]
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/solvent_single.lt
deleted file mode 100644
index 8057e3c6f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/solvent_single.lt
+++ /dev/null
@@ -1,22 +0,0 @@
-# The two files "solvent_single.lt" and "wall_single.lt"
-# define two very simple molecules containing one atom each.
-# Both atoms have a similar size (the have the same sigma parameter).
-
-
-MoleculeA {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:a $mol:. @atom:a 0.0 0.0 0.0 0.0
- }
- write_once("Data Masses") {
- @atom:a 10.0
- }
- write_once("In Settings") {
- # i j epsilon sigma cutoff
- pair_coeff @atom:a @atom:a 0.60 3.0 7.5 #<--attractive
- group groupA type @atom:a #(Atoms of this type belong to the "A" group)
- }
-
-}
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/system.lt
deleted file mode 100644
index 0ed272710..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/system.lt
+++ /dev/null
@@ -1,57 +0,0 @@
-
-# LAMMPS supports a large number of force-field styles. We must select
-# which ones we need. This information belongs in the "In Init" section (and
-# (you can specify it anywhere in your LT files, multiple times if you like).
-# If different molecules use different force-field styles, you can use hybrid
-# styles. (In this example the molecules share the same pair_style.)
-
-write_once("In Init") {
- units real
- atom_style full
- bond_style harmonic
- angle_style harmonic
- dihedral_style opls
- pair_style lj/cut 9.0
- # If you have charged molecules immersed in a salty implicit
- # solvent, you might try something like this this instead:
- # pair_style lj/cut/coul/debye 0.1 9.0
- pair_modify mix arithmetic
- dielectric 80.0
- special_bonds lj 0.0 0.0 0.0
-}
-
-
-write_once("Data Boundary") {
- 0.0 36.0 xlo xhi
- 0.0 36.0 ylo yhi
- -18.0 18.0 zlo zhi
-}
-
-
-import "solvent.lt"
-
-import "walls.lt"
-
-import "polymer.lt"
-
-polymer = new Polymer
-polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis
-polymer.move(19.5,22.5,16.5) # move it near the openning of the hole
-
-
-
-####################### Notes: #########################
-#
-# In this example we deleted solvent and wall molecule objects.
-# You can also delete a monomer inside the polymer. To do that use:
-# delete polymer/monomers[6]
-# You can also delete individual atoms, bonds, angles, dihedrals, & impropers
-# from existing molecules. For example to delete an atom in the middle
-# of the polymer try this. (Bonds and other interactions will also be removed.)
-# delete polymer/monomers[6]/CA
-# To delete a bond, try this
-# delete polymer/bb6
-# Note: This will not delete the angular interactions if they were explicitly
-# defined (ie, using "Data Angles" instead of "Data Angles By Type").
-# Delete explicit angle, dihedral, and improper interactions manually.
-# Note: In both cases the two molecule fragments will keep the same mol counter.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/wall_single.lt
deleted file mode 100644
index 79275a06b..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/wall_single.lt
+++ /dev/null
@@ -1,21 +0,0 @@
-# The two files "solvent_single.lt" and "wall_single.lt"
-# define two very simple molecules containing one atom each.
-# Both atoms have a similar size (the have the same sigma parameter).
-
-MoleculeB {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:b $mol:. @atom:b 0.0 0.0 0.0 0.0
- }
- write_once("Data Masses") {
- @atom:b 10.0
- }
- write_once("In Settings") {
- # i j epsilon sigma cutoff
- pair_coeff @atom:b @atom:b 0.05 3.0 7.5 #<--repulsive (approximately)
- group groupB type @atom:b #(Atoms of this type belong to the "B" group)
- }
-
-}
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/walls.lt
deleted file mode 100644
index dcccac941..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/walls.lt
+++ /dev/null
@@ -1,23 +0,0 @@
-####################### WALLS ##########################
-
-import "wall_single.lt"
-
-# Create a wall at position z=6.0 (6.0 = 2*3.0)
-
-wall1 = new MoleculeB [12].move(3.0, 0, 0)
- [12].move(0, 3.0, 0)
-
-wall1[*][*].move(0,0,6.0)
-
-# Create a second wall at position z=24.0 (24.0 = 8*3.0)
-
-wall2 = new MoleculeB [12].move(3.0, 0, 0)
- [12].move(0, 3.0, 0)
-
-wall2[*][*].move(0,0,24.0)
-
-# Now delete some of the molecules in "wall2" to create a hole.
-
-delete wall2[6-7][6-9]
-delete wall2[5-8][7-8]
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.npt
deleted file mode 100644
index 0b58a8e1b..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.npt
+++ /dev/null
@@ -1,120 +0,0 @@
-# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED.
-# (This simulation may fail.
-# However the "run.in.nvt" example in this directory should work.)
-#
-# Requirements:
-# To run this system at constant pressure, it might help to compile LAMMPS with
-# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.)
-# The use of fix rigid is controversial. This method is demonstrated below.
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# Only the groupB atoms are immobile.
-group mobile subtract all groupB
-
-# Unfortunately you can not use the LAMMPS "minimize" command on this system
-# because there is no way to immobilize the wall atoms during minimization.
-# Instead, we can use langevin dynamics with a fast
-# damping parameter and a small timestep.
-
-print "--------- beginning minimization (using fix langevin) ---------"
-
-timestep 0.1
-fix fxlan mobile langevin 1.0 1.0 100.0 48279
-fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation)
-thermo 100
-run 2500
-
-unfix fxlan
-unfix fxnve
-
-# -- simulation protocol --
-
-print "--------- beginning simulation (using fix nvt) ---------"
-
-dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 200 # time interval for printing out "thermo" data
-
-
-# ------------------------- NPT ---------------------------
-
-
-# ------ QUESTIONABLE (see below): ------
-
-fix Ffreezestuff groupB rigid single force * off off off torque * off off off
-
-# Comment:
-# The use of "fix rigid" to immobilize an object is somewhat controversial.
-# Feel free to omit it.
-# (Neither Trung or Steve Plimpton use fix rigid for immobilizing
-# molecules, but I noticed that at NPT, it does a better job of maintaining
-# the correct volume. However "fix rigid" has changed since then (2011),
-# so this may no longer be true. Please use this example with caution.)
-
-
-
-# Thermostat+Barostat
-# Set temp=300K, pressure=200bar, and equilibrate volume only in the z direction
-
-fix fxMoveStuff mobile npt temp 300 300 100 z 200 200 1000.0 dilate mobile drag 2.0
-
-# ----------------------------------------
-
-# The next two lines recalculate the temperature using
-# only the mobile degrees of freedom (ie. water atom velocities):
-
-compute tempMobile mobile temp
-compute pressMobile all pressure tempMobile
-
-thermo_style custom step c_tempMobile c_pressMobile temp press vol
-
-fix_modify fxMoveStuff temp tempMobile
-
-reset_timestep 0
-
-timestep 0.5
-
-run 100000
-
-timestep 1.0
-
-run 100000
-
-
-write_data system_after_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also.)
-
-
-
-
-
-
-
-# ----- Comment: Avoid using fix rigid/npt on large single rigid objects -----
-#
-# Use of the following is not recommended:
-#
-# fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 200 200 1000.0 force * off off off torque * off off off dilate mobile
-# (temp=300K, pressure=200bar, and equilibrate volume only in the z direction)
-#
-# In my experience, the system becomes unstable when applying "fix rigid/npt"
-# to the immobile atoms, while also applying "fix npt" on the solvent atoms.
-# (It is probably a bad idea to use two barostats simultaneously.)
-# ----------------------------------------------------------------------------
diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.nvt
deleted file mode 100644
index c483d0b9a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.nvt
+++ /dev/null
@@ -1,53 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details)
-
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# Use "neigh_modify" to turn off calculation of interactions between immobilized
-# atoms. (Note: The "groupB" group was defined in the file "system.insettings")
-neigh_modify exclude group groupB groupB
-
-# -- Run Section --
-
-
-timestep 1.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-thermo_style custom step temp pe etotal vol epair ebond eangle edihed
-thermo 500 # time interval for printing out "thermo" data
-
-
-# Optional: Improve efficiency by omitting the calcuation of interactions
-# between immobile atoms. (Note: This is not optional under NPT conditions.)
-neigh_modify exclude group groupB groupB
-
-# Only the groupB atoms are immobile.
-group mobile subtract all groupB
-
-# The next two lines recalculate the temperature
-# using only the mobile degrees of freedom:
-
-compute tempMobile mobile temp
-
-# Integrate the equations of motion:
-fix fMoveStuff mobile nvt temp 300.0 300.0 100.0
-fix_modify fMoveStuff temp tempMobile
-
-
-run 100000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_FIRST.txt b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_FIRST.txt
deleted file mode 100644
index 03fb40b16..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_FIRST.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-This is an implementation of the "two-stage" model used by Maxim Imakaev
-in the Naumova et Al 2013 Science paper on metaphase chromatin.
-(Download the supplemental materials section and scroll down to the section:
- "Two-stage process: linear compaction - axial compression")
-
----- SMALL MODIFICATION ----
-
-Unlike that study, I did not use "softened" Lennard-Jones potentials
-(which allow the chains to pass through each other).
-
---- Why use moltemplate? ---
-
-Honestly, you don't need to use moltemplate to build this polymer.
-It is almost counter-productive to use moltemplate to build this kind of
-polymer because it is so simple. (The polymer has only 1 bead per atom.
-It just makes it more complicated to introduce all these extra
-files including monomer.lt, condensin.lt and system.lt, especially considering
-that system.lt is a complex file which is generated by a separate script.)
-
-However building the sytem using moltemplate may pay off if you
-replace each point-like monomer with a multi-atom molecule later on.
-(Right now, using moltemplate to build this system is sort of overkill.
- I'll post an example of building more complex models of chromatin eventually.)
-
-Anyway, the two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section.
-
----- 10-nm fiber model: ----
-
-For the 10nm model,
- n=128000,
- L=200,
- U(alpha)=5*(1 - cos(alpha))
- bond_length=1.0 (=10nm)
- sigma=1.0 (particle radius = 10nm)
-
----- 30-nm fiber model: ----
-
-"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level."
-
-I interpret this to mean that, for the 30nm model,
- n=128000/4.25~=30117 (however I rounded up to 32768=2^15)
- L=200/4.25~=47 (however I rounded up to 51)
- U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647)
-
-To increase the volume by a factor o 4.25, I increase both the diameter of each
-bead (the "sigma" parameter), and the bond-lengths connecting them from
-1.0 (corresponding to 10nm) to 4.25^(1/3)~=1.6198 (corresponding to 16.198nm).
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt
deleted file mode 100644
index 38ad9c1c0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt
+++ /dev/null
@@ -1,29 +0,0 @@
----------------
-The average diameter of a mammalian cell nucleus is is 6 micrometers (μm),
-which occupies about 10% of the total cell volume.
-
-(See "Molecular Biology of the Cell, Chapter 4, pages 191–234 (4th ed.)", by
- Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 2002)
-
-... of that, 25% of it is occupied by the nucleolus
-http://en.wikipedia.org/wiki/Nucleolus
-("citation needed")
----------------
-
-From the supplemental material for the original HiC paper
-(Lieberman-Aiden et al., Science 2009)
-
-Appendix 1.
- Estimate of the Volume Fraction of Chromatin in Human Cells
-In the simulations we sought to obtain an ensemble of structures that, in their statistical properties, resemble some of the features of chromatin arrangement in the cell. Below we demonstrate that chromatin occupies a significant fraction of cell volume, a property that we reproduced in simulations. Taking the nuclear diameter of a tissue culture cell to be 5-10um, and assuming close to a spherical shape we obtain the volume in the range 50-500 um^3, with a (geometric) mean of ~160 um^3. If we assume that the chromatin is built of DNA wrapped around nucleosomes, then we have 6x10^9bp/200bp=3x10^7 nucleosomes. Each may be approximated as a cylinder ~10nm in diameter and ~5nm in height, suggesting a volume of about 500nm3 each. The linker DNA after each nucleosome is about 50bps long, suggesting a volume of about 50*0.34nm*3.14*1nm^2=50nm^3. Thus the total volume of chromatin = 550x3x10^7 =16 um^3, or ~10% (3-23%) of the nuclear volume. This strikingly large volume fraction is itself a significant underestimate, since we ignored, among other things, all other DNA-bound proteins. Note that any further packing or localization of chromatin inside the nucleus will increase local density.
----- This next section mostly only justifies why they ----
----- they did not stop the simulation when the globules ----
----- were fully crumpled (ie with uniform density) ----
- In our simulations, the radius of the final crumpled globule was R≈12.5 and the volume V≈8000 cubic units. The total volume of the 4000 monomers, 1 unit in diameters each, is V≈2000. This implies a volume fraction of about 25%, which is consistent with the volume fraction estimated above.
- ---- ----
-
-Appendix 2.
- Monomer length in base pairs
-Each monomer of the chain corresponds to a fragment of chromatin that equals the Kuhn length of the chromatin fiber, i.e. approximately twice the persistence length of the fiber. Although the persistence length of the chromatin fiber is unknown it can be estimated using the following arguments. DNA is packed into nucleosomes, where 150 bps are wrapped around the histone core and do not contribute to flexibility of the fiber. The linker DNA of about 50 bps that connects consecutive nucleosomes is bendable, and is the source of flexibility in the fiber. Since the persistence length of double-stranded DNA is 150 bps, an equally flexible region of the nucleosomal DNA should contain 3 linkers, i.e. 3 consecutive nucleosomes packing about 600 bps of DNA. The excluded volume of the nucleosomes, nucleosome interactions, and other DNA-bound proteins can make the fiber less flexible or prohibit certain conformation and may tend to increase the persistence length of the fiber. Using this estimated lower bound estimate for the persistence length, we obtain the Kuhn length of the equivalent freely-jointed chain to be 6 nucleosomes, or ~ 1200bp. A simulated chain of 4000 monomers corresponds to 4.8Mb of packed DNA. The size of each monomer was chosen such that its volume is equal to (or slightly above) that of 6 nucleosomes (V=6 x 600 nm^3); thus the radius of the spherical monomer is R=10nm. The diameter of each globule shown in Figure 4 is about 200 nm.
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh
deleted file mode 100755
index 19674c88b..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-# Run lammps using the following 3 commands:
-# (assuming "lmp_mpi" is the name of your LAMMPS binary)
-
-lmp_mpi -i run.in.min
-lmp_mpi -i run.in.stage1
-lmp_mpi -i run.in.stage2
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_setup.sh
deleted file mode 100755
index 14700a29c..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_setup.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # First, rescale and interpolate the positions
- # where the monomers will be located. (This step is
- # not needed if the coords_orig.raw file already has correct coordinates.)
-
- ./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw
-
- # Then, build the "system.lt" file
-
- ./generate_system_lt.py 32768 51 < coords.raw > system.lt
-
- # 32768 is the number of monomers in the polymer
- # (which may be different from the number of coordinates
- # in the "coords_orig.raw" file) This number will vary
- # depending on how long you want the polymer to be.
- # The second argument "51" is the average interval between
- # condensin anchors (IE the "loop size" in monomers.)
-
-
- # Run moltemplate
-
- moltemplate.sh system.lt -a "@bond:stage1 1" \
- -a "@bond:stage2 2" \
- -a "@atom:Monomer/A 1"
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
- #
- # We used the "-a" command to set the variable @bond:condensin to "2"
- # because we will refer to it later in the "run.in" LAMMPS input script.
- # (Of coarse, LAMMPS knows nothing about moltemplate variables,
- # so in that file we refer to it as dihedral type "1")
-
- mv -f system.in* system.data ../
-
- # We also need the table of bond forces used during "stage 2".
- # (Like the system.data and the various input scripts, this file is needed by
- # LAMMPS, so we need to copy it to the directory where we will run the sim.)
- cp -f table_bonds_stage2.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
- # Optional:
- # Remove the "system.lt" file created by "generate_system_lt.py"
- #rm -f system.lt
-
-cd ../
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_visualize.txt
deleted file mode 100644
index a5b46dc8a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_visualize.txt
+++ /dev/null
@@ -1,131 +0,0 @@
-NOTE: VMD DOES NOT ALLOW YOU TO VISUALIZE SYSTEMS WITH MANY BONDS ATTACHED
- TO EACH ATOM. (IF IT DID, THE RESULTS WOULD BE UGLY ANWAY.)
-
-HOWEVER THIS MODEL ATTACHES APPROXIMATELY 60 BONDS TO EACH CONDENSIN ATOM.
-IN ORDER TO PULL THE CONDENSIN MONOMERS TOGETHER. YOU MUST DELETE THOSE
-BONDS (of type "1" or "2") FROM THE "system.data" FILE BEFORE YOU CARRY
-OUT THE COMMANDS BELOW. (...And backup your "system.data" file. You'll need
-all the bonds when you run the simulations.)
-
--------------- COLORS ---------------
-In order to show how the polymer is distributed along the length of the
-cylinder, I recommend to select the
-Graphics->Graphical Representations
-menu option, and select "Index" from the "Coloring Method" pull-down menu.
-
-After doing this, you can switch from a red-white-blue scheme, to a
-rainbow ("jet") scheme, by selecting the Extensions->Tk Console menu option
-and loading the "vmd_colorscale_jet.tcl" file located in the "images" directory.
--------------------------------------------
-
-First, if you have not done so, download and install VMD:
-
-http://www.ks.uiuc.edu/Research/vmd/
-http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
-
-
- ------- To view a lammps trajectory in VMD --------
-
-The system coordinates are initialy stored in a LAMMPS' ".data" file.
-(If that file was built with moltemplate, it will be named "system.data".)
-
-The first step is to view that file.
-Then you should create a ".psf" file
-(The .psf file is necessary after you run the simulation
- for viewing trajectories.)
-
-1) Build a PSF file for use in viewing with VMD
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-You will see a snapshot of the system on the screen.
-(presumably the initial conformation at t=0)
-
-2)
-
-Later once you have run a simulation,
-to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file
- (It usually has names like "traj.lammpstrj". It depends on how you saved it.)
- If necessary, for "file type" select: "LAMMPS Trajectory".
- (However VMD should recognize the file type by the file extension.)
- Load it.
-
-
-
-
-
-##################### PERIODIC BOUNDARY CONDITIONS #####################
- If you are only simulating a single molecule and you are not
- using periodic boundary conditions, then ignore everything below.
-########################################################################
-
- ---- A note on trajectory format: -----
-If the trajectory is the standard LAMMPS format, (aka a "DUMP" file with
-a ".lammpstrj" extension), then it's a good idea when you run the simulation
-to tell LAMMPS you want to store the information needed for showing periodic
-boundary conditions. (Even if you are not using periodic boundaries.
-It never hurts to include a tiny bit of extra information.) To do that,
-I've been using this command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 traj.lammpstrj id mol type x y z ix iy iz
-
-(Also: it's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. I think this is needed
-to wrap atom coordinates visually without breaking molecules in half. Again
-you don't need to worry about this if you are not using periodic boundaries.)
-
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {-0.5 -0.5 -0.5}
- pbc box -shiftcenterrel {-0.5 -0.5 -0.5}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/stage2_interior.jpg b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/stage2_interior.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/stage2_interior_rotated.jpg b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/stage2_interior_rotated.jpg
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/t=0_before_minimizaion.jpg b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/t=0_before_minimizaion.jpg
deleted file mode 100644
index 06600ecc9..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/vmd_colorscale_jet.tcl b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/vmd_colorscale_jet.tcl
deleted file mode 100644
index 7434eca99..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images/vmd_colorscale_jet.tcl
+++ /dev/null
@@ -1,87 +0,0 @@
-
-proc lerpcolor { col1 col2 alpha } {
- set dc [vecsub $col2 $col1]
- set nc [vecadd $col1 [vecscale $dc $alpha]]
- return $nc
-}
-
-proc coltogs { col } {
- foreach {r g b} $col {}
- set gray [expr ($r + $g + $b) / 3.0]
- return [list $gray $gray $gray]
-}
-
-proc jet_tricolor_scale {} {
- display update off
- set mincolorid [expr [colorinfo num] - 1]
- set maxcolorid [expr [colorinfo max] - 1]
- set colrange [expr $maxcolorid - $mincolorid]
- set colhalf [expr $colrange / 2]
- for {set i $mincolorid} {$i < $maxcolorid} {incr i} {
- set colpcnt [expr ($i - $mincolorid) / double($colrange)]
-
- # The following color definitions for "jet" sort-of came from:
- #http://stackoverflow.com/questions/7706339/grayscale-to-red-green-blue-matlab-jet-color-scale
- # but it was missing "green", so I inserted a green somewhere in the middle.
-
- # darkblue/violet 0.0
- set color0 { 0.08 0.0 0.77 }
-
- # blue 0.19
- set color1 { 0.0 0.0 1.0 }
-
- # cyan 0.34
- set color2 { 0.0 1.0 1.0 }
-
- # turquoise 0.4001
- set color3 { 0.0 1.0 0.78 }
-
- # green 0.445
- set color4 { 0.0 1.0 0.0 }
-
- # chartreuse 0.535
- set color5 { 0.875 1.0 0.0 }
-
- # yellow 0.69
- set color6 { 1.0 1.0 0.0 }
-
- # orange 0.73
- set color7 { 1.0 0.25 0.0 }
-
- # red 0.755
- set color8 { 1.0 0.0 0.0 }
-
- # darkred 1.0
- set color9 { 0.93 0.0 0.0 }
-
- if { $colpcnt < 0.19 } {
- set nc [lerpcolor $color0 $color1 [expr $colpcnt/(0.19-0.0)]]
- } elseif { $colpcnt < 0.34 } {
- set nc [lerpcolor $color1 $color2 [expr ($colpcnt-0.19)/(0.34-0.19)]]
- } elseif { $colpcnt < 0.4001 } {
- set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.34)/(0.4001-0.34)]]
- } elseif { $colpcnt < 0.445 } {
- set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.4001)/(0.445-0.4001)]]
- } elseif { $colpcnt < 0.535 } {
- set nc [lerpcolor $color3 $color4 [expr ($colpcnt-0.445)/(0.535-0.445)]]
- } elseif { $colpcnt < 0.69 } {
- set nc [lerpcolor $color4 $color5 [expr ($colpcnt-0.535)/(0.69-0.535)]]
- } elseif { $colpcnt < 0.73} {
- set nc [lerpcolor $color5 $color6 [expr ($colpcnt-0.69)/(0.73-0.69)]]
- } elseif { $colpcnt < 0.755} {
- set nc [lerpcolor $color6 $color7 [expr ($colpcnt-0.73)/(0.755-0.73)]]
- } else {
- set nc [lerpcolor $color7 $color8 [expr ($colpcnt-0.755)/(1.0-0.755)]]
- }
-
- # set nc [coltogs $nc]
- foreach {r g b} $nc {}
- puts "index: $i $r $g $b -- $colpcnt"
- display update ui
- color change rgb $i $r $g $b
- }
- display update on
-}
-
-jet_tricolor_scale
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/README_how_to_generate_system_lt.sh b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/README_how_to_generate_system_lt.sh
deleted file mode 100755
index c23b222fa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/README_how_to_generate_system_lt.sh
+++ /dev/null
@@ -1,19 +0,0 @@
- # First, rescale and interpolate the positions
- # where the monomers will be located. (This step is not needed
- # if the coords_orig.raw file already has correct coordinates.)
- # The first argument, 32768 is the number of atoms in the desired file.
- # The second argument, 1.6198059 = 4.25^(1/3), tells interpolate_coords.py
- # to multiply all the coordinates (scale them up) by 1.6198059.
-
- ./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw
-
- # Then, build the "system.lt" file
-
- ./generate_system_lt.py 32768 51 < coords.raw > system.lt
-
- # 32768 is the number of monomers in the polymer
- # (which may be different from the number of coordinates
- # in the "coords_orig.raw" file) This number will vary
- # depending on how long you want the polymer to be.
- # The second argument "51" is the average interval between
- # condensin anchors (IE the "loop size" in monomers.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/README_length_flexibility_details.txt b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/README_length_flexibility_details.txt
deleted file mode 100644
index 1d30ceb17..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/README_length_flexibility_details.txt
+++ /dev/null
@@ -1,57 +0,0 @@
----- Andrew's comments ----
-
-The two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section.
-
-For the 10nm model,
- n=128000,
- L=200,
- U(alpha)=5*(1 - cos(alpha))
- bond_length=1.0 (=10nm)
- sigma=1.0 (particle radius = 10nm)
-
-30nm-fiber model details:
-"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level."
-
-I interpret this to mean that, for the 30nm model,
- n=128000/4.25~=30117
- L=200/4.25~=47
- U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647)
-To increase the volume by a factor o 4.25, originally I thought I should increase the "sigma" parameter from 1.0 to 4.25^(1/3)~=1.6198. But I suspect that the bond-lengths between monomers should be fixed at 1.0. If that is the case, then, perhaps I should increase "sigma" from 1.0 to 4.25^(1/2)~=2.061552, and keep the bond-length fixed at 1.0 (which in the units used by thsi paper, corresponds to 10nm). (That would increase the volume of a cylinder of radius "sigma" and length="bond-length" by a factor of 4.25)
- bond_length=1.0 (10nm again)
- sigma=2.061552 (Yes, this is less than 3.0<-->30nm. See below.)
-
-
-
-
---- Excerpts from the Supplemental section of Naumova et al Science 2013 ---
-
-From p. 18 of the supplemental materials section of Naumova et al Science 2013.
-
- (This section was probably written by Maxim Imakaev.)
-
- In vivo, the structure of the chromatin fiber can be complicated and many details remain unknown, particularly in metaphase. Given this uncertainty, we simulated chromatin as a homogeneous “beads-on-a-string” polymer fiber. We consider a 10nm fiber, as the pervasiveness of the 30nm fiber in vivo has become increasingly contested. In our simulations, 77Mb is represented by a densely-packed 10nm fiber of 128,000 monomers. Each monomer represents a 10nm-sized DNA-histone complex containing 3 nucleosomes (around 600bp). The fiber has a persistence length of 4 monomers (~2.4Kb), which is based on earlier estimates of 5-10 nucleosomes for interphase (14). Those estimates arise from the assumption that 5-10 linker DNA fragments, each of 20-40bp, can collectively provide flexibility equal to that of the 150bp persistence length of DNA. Binding of proteins to the linker DNA (e.g. histone H1) and interactions between neighboring nucleosomes can further constrain dynamics, requiring more linkers to provide the persistence length. Due to the tight packing of nucleosomes in metaphase, we use the upper limit of this range, i.e. 12 nucleosomes.
- For the consecutive loops on a scaffold model (the final folded state model with the best agreement with Hi-C data), we also performed simulations with a more flexible 10nm fiber, or with a 30nm fiber, and found similar results. The more flexible 10nm fiber was modeled by decreasing persistence length to 1.8 monomers. The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level. We note that a classic model of a 30nm fiber is much less dense than a compact metaphase chromosome. A textbook model of a 30nm fiber assumes packing of about 6 nucleosomes per 10nm of fiber length. This model predicts that only 28% of the volume of the fiber (a 30nm-diameter cylinder) is occupied by nucleosomes, assuming a nucleosome shell volume of 328 nm^3. This is much less than the estimated 30-50% density of nucleosomes in a metaphase chromosome, assuming a diameter of 600nm, a packing density of 50-70 Mb/um, and the same nucleosome volume. (See also (15), which gives an estimate of 0.14-0.18 pg/μm for DNA only, and would give about twice the density if DNA is counted with nucleosomes). As follows, these fibers would have to interdigitate, and fill in gaps within each other. We account for this overlap by assuming the effective diameter of the fiber to be less than 30nm. The effective diameter was chosen to make the volume of the fiber equal the total volume of all the nucleosomes.
-
- We accounted for topoisomerase II activity by allowing chromatin fibers to pass through each other, while still having excluded volume interactions. This was achieved by using a soft-core Lennard-Jones potential with 1kT energy cost for monomer overlap (see below). This allows for changes in the topological state of a chromosome that are known to occur during compaction in vivo.
-
-Our simulations of a two-step folding process show that Hi-C data for mitotic chromosomes is consistent with a linearly compressed array of consecutive chromatin loops. Whereas mechanisms for formation of consecutive chromatin loops have been proposed, the process of axial compression is less understood. Chromatid compression cannot be accomplished by increased chromatin-chromatin affinity alone, as this would lead to condensation into a globular geometry (14, 16, 17). However, mechanisms which locally compress the fiber of loop bases naturally allow for anisotropic compression into a shorter and thicker fiber, with the same width regardless of chromosome length (18). Differences in the duration or efficiency of the first and second stages of chromosomal condensation provide a natural mechanism for condensation-related proteins to separately affect mitotic chromosome length and width (19). We also note that the axis of loop-bases in our two-stage model does not necessarily form a continuous and rigid scaffold (Figure S26). As follows, we remain agnostic about the molecular details of the chromosomal scaffold, which might for example be formed by a network consisting of protein-protein and/or protein-DNA interactions (20).
-
- 1. Polymer simulations
-
- To perform Langevin dynamics polymer simulations we used OpenMM, a high-performance GPU-assisted molecular dynamics API (21, 22). To represent chromatin fibers as polymers, we used a sequence of spherical monomers of 1 unit of length in diameter. Here and below all distances are measured in monomer sizes, set to be 10nm unless specified otherwise. Neighboring monomers are connected by harmonic bonds, with a potential U = 100*(r - 1)^2 (here and below in units of kT). Polymer stiffness is modeled with a three point interaction term, with the potential U = 5*(1 - cos(alpha)), where alpha is the angle between neighboring bonds. All monomers interact via either a shifted Lennard-Jones (LJ) repulsive potential, or an attractive Lennard-Jones potential. At high densities in a confined volume, the details of the inter-monomer interactions become negligible due to screening (23), and we therefore used the computationally efficient shifted LJ potential. The shifted LJ potential allows for a short-range repulsion by truncating the LJ potential at its minimum and shifting the minimum to zero: U = 4 * (1/r^12 - 1/r^6) + 1, for r<2^(1/6); U=0 for r > 2^(1/6). The shifted LJ potential is one of the most computationally efficient repulsive potentials due to a very short cutoff radius.
-
- To allow chain passing, which represents activity of topoisomerase II, we softened the shifted LJ potential by truncating the interaction energy at Ecutoff = 1 kT. At energies more than 0.5 Ecutoff, the LJ potential was softened via: Usoftened = 0.5 * Ecutoff * (1 + tanh(2*U/Ecutoff - 1)). To avoid numerical 19instabilities in the calculation of U at r ~ 0, the interaction radius r was truncated at r=0.3 via: rtruncated = (r^10 + (0.3)^10)^0.1, which introduced negligible shift in a final softened potential. For an attractive LJ potential, we used: U = 4 * e * (1/r^12 - 1/r^6), with e = 0.46 kT, slightly below the theta-temperature. The attractive potential was similarly softened at 2 kT and cut off at r=2.5. Unless noted, we used a softened shifted LJ repulsive potential.
-
- Polymer models were visualized using Pymol and Rasmol. For images with loop bases highlighted, a base of each loop and 3 monomers surrounding it in each direction were labeled in red.
-
- SECTIONS 2-5 SKIPPED
-
-6. Two-stage process: linear compaction - axial compression
-
-To simulate the two-stage process of metaphase chromosome folding, we used the 30nm fiber representation described above for its computational efficiency. Simulations were initialized from 30000 monomer fractal globule conformations; fractal globule is a model for interphase chromatin organization. First, random consecutive loops with L=100 monomers (see above) were introduced, and anchors of neighboring loops were brought together using harmonic springs with a potential U = k * (r – r0)2; r0=0.5. To avoid abrupt motion of the loop anchors, the force was gradually turned on over the first
-300000 timesteps, with k linearly increasing in time from 0 to 10 kT. We used softened shifted repulsive LJ potential for inter-monomer interaction.
-
-Upon completion of linear compaction, axial compression was initiated. This involves following changes: the repulsive LJ force is replaced with an attractive LJ force for all monomers, and the chromosomal core of loop anchors is homogeneously compressed. To achieve the latter, all anchor pairs separated by less than 30 anchors were attracted via a potential U = step(d-3) * abs(d-3) * 10 kT, which implements a constant attractive force between two anchors if they are separated by a distance larger than 3. The interactions between neighboring loop anchors were kept throughout this process.
-
-To obtain the contact map from this simulation, 50 independent runs of 1.5e7 timesteps were performed, and 250 conformations were collected from the second half of each run. The contact map was calculated from all conformations of all runs at a 30-monomer resolution, and was further averaged over three 10000-monomer blocks along the diagonal of the heatmap. The latter was done to show contact map at a relevant length scale (0 to 25 Mb), and to achieve a better averaging of the contact map.
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/calc_table.sh b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/calc_table.sh
deleted file mode 100755
index aed66719f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/calc_table.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-for ((i=0; i<60; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` 0 0; done
-
-echo 61 3.0 0 -5
-
-for ((i=61; i<=4000; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` `echo "($i-60)*0.5"|bc` -10; done
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/condensin.lt b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/condensin.lt
deleted file mode 100644
index f8dfea089..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/condensin.lt
+++ /dev/null
@@ -1,47 +0,0 @@
-# This file contains the definition of a molecule named "CondensinMonomer".
-# (This particular molecule contain only one atom, but that is up to you.)
-# Later, multiple CondensinMonomers can be connected together to build a molecule.
-
-
-
-CondensinMonomer {
-
- # atom-id mol-id(ignore) atom-type q x y z
-
- write("Data Atoms") {
- $atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000
- }
-
- # (The x y z positions will be changed later with move commands
- # You can spedify charge and other properties by changing the atom_style.)
-
-
-
- # atom-type mass
-
- write_once("Data Masses") {
- @atom:A 1.0
- }
-
- # pairwise interactions (between non-bonded atoms):
- #
- # U(r) = 4*eps*((r/sig)^12 - (r/sig)^6)
- #
- # Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0
- #
- # atom-type atom-type pair_style epsilon sigma
-
- write_once("In Settings") {
- # I usually use sigma = 2^(-(1/6)), with a cutoff of 1
- #pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0
- # In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0
- # with a cutoff of 2^(1/6). Here we are trying to reproduce his results.
- # 10nm fiber
- #pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373
- # 30nm fiber (4.25^(1/2)=2.0615528128088303)
- #pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349
- # 30nm fiber (4.25^(1/3)=1.6198059006387417)
- pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708
- }
-
-} # CondensinMonomer
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/coords_orig.raw b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/coords_orig.raw
deleted file mode 100644
index 9137c7061..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/coords_orig.raw
+++ /dev/null
@@ -1,32768 +0,0 @@
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--14.9343 4.63209 -20.1751
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--20.2387 -4.52844 -11.5665
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--20.1441 -4.34337 -13.4481
--20.4303 -4.25003 -14.3514
--21.0711 -3.57061 -14.0453
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--22.8333 -3.96238 -13.6698
--23.0963 -4.29805 -12.7972
--23.897 -4.26723 -12.2585
--23.7472 -3.32062 -12.0912
--24.039 -2.43183 -11.8307
--24.1953 -1.43199 -11.9438
--23.5045 -1.71444 -12.517
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py
deleted file mode 100755
index 796347bb0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py
+++ /dev/null
@@ -1,301 +0,0 @@
-#!/usr/bin/env python
-
-err_msg = """
-Usage:
-
- generate_system_lt.py n < monomer_coords.raw > system.lt
-
-Example:
-
- generate_system_lt.py 30118 47 < coords.raw > system.lt
-
-Explanation:
- ARGUMENTS:
- n = total length of the polymer (in monomers)
- L = the (average) length of each condensin interval (Poisson-
- distributed) This is also 1/probability that each monomer
- is a "condensin monomer".
-
- (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner,
- and 47 = 200/4.25. Note that 128000 and 200 are for the 10nm model.
- See the supplemental section of Naumova et al Science 2013, p 18.)
-
-"""
-
-
-import sys
-import random
-from math import *
-
-# Parse the argument list:
-if len(sys.argv) <= 2:
- sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n")
- exit(1)
-N=int(sys.argv[1])
-L=float(sys.argv[2])
-if len(sys.argv) > 3:
- delta_x = float(sys.argv[3])
-else:
- delta_x = 2.0
-if len(sys.argv) > 4:
- x_offset = float(sys.argv[4])
-else:
- x_offset = -((N-1.0)/2) * delta_x
-
-
-coords = [[0.0, 0.0, 0.0] for i in range(0,N)]
-lines = sys.stdin.readlines()
-if len(lines) != N:
- sys.stderr.write("Error: Number of lines in input file ("+str(len(lines))+")\n"
- " does not match first argument ("+str(N)+")\n")
- exit(1)
-for i in range(0, N):
- coords[i] = map(float, lines[i].split())
-
-# Now calculate the box_boundaries:
-box_bounds_min = [0.0, 0.0, 0.0]
-box_bounds_max = [0.0, 0.0, 0.0]
-for i in range(0, N):
- for d in range(0, 3):
- if i == 0:
- box_bounds_min[d] = coords[i][d]
- box_bounds_max[d] = coords[i][d]
- else:
- if coords[i][d] > box_bounds_max[d]:
- box_bounds_max[d] = coords[i][d]
- if coords[i][d] < box_bounds_min[d]:
- box_bounds_min[d] = coords[i][d]
-
-# Now scale the box boundaries outward by 50%
-box_scale = 1.5
-for d in range(0,3):
- box_bounds_cen = 0.5*(box_bounds_max[d] + box_bounds_min[d])
- box_bounds_width = box_bounds_max[d] - box_bounds_min[d]
- box_bounds_min[d] = box_bounds_cen - 0.5*box_scale*box_bounds_width
- box_bounds_max[d] = box_bounds_cen + 0.5*box_scale*box_bounds_width
-
-# Now calculate the direction each molecule should be pointing at:
-direction_vects = [[0.0, 0.0, 0.0] for i in range(0,N)]
-for d in range(0, 3):
- direction_vects[0][d] = coords[1][d] - coords[0][d]
- direction_vects[N-1][d] = coords[N-1][d] - coords[N-2][d]
-for i in range(1, N-1):
- for d in range(0, 3):
- direction_vects[i][d] = coords[i+1][d] - coords[i-1][d]
-
-# Optional: normalize the direction vectors
-for i in range(1, N-1):
- direction_len = 0.0
- for d in range(0, 3):
- direction_len += (direction_vects[i][d])**2
- direction_len = sqrt(direction_len)
- for d in range(0, 3):
- direction_vects[i][d] /= direction_len
-
-# Now, begin writing the text for the system.lt file:
-
-sys.stdout.write(
-"""
-import "monomer.lt" # <-- defines "Monomer"
-import "condensin.lt" # <-- defines "CondensinMonomer"
-
-
-"""
-)
-
-
-
-# Figure out which monomers are "Monomers" and which monomers are
-# "CondensinMonomers"
-
-ic = 0 # count the number of condensins added so far
-condensin_is_here = [False for i in range(0, N)]
-for i in range(0, N):
- #add_condensin_here = random.random() < (1.0 / L)
- add_condensin_here = random.random() < (1.0 / (L-2.0))
-
- # We do not allow condensin at successive sites separated by less than 2
- # subunits (the "L-2.0" above is to compensate for this)
- if (((i > 0) and condensin_is_here[i-1]) or
- ((i > 1) and condensin_is_here[i-2])):
- add_condensin_here = False
-
- if add_condensin_here:
- condensin_is_here[i] = True
- ic += 1
-Nc = ic
-
-
-ic = 0
-for i in range(0, N):
- if condensin_is_here[i]:
- sys.stdout.write("condensins["+str(ic)+"] = new CondensinMonomer.scale(0.5,0.8,0.8).rotvv(1,0,0,")
- ic+=1
- else:
- sys.stdout.write("monomers["+str(i)+"] = new Monomer.scale(0.5,0.8,0.8).rotvv(1,0,0,")
- sys.stdout.write(str(direction_vects[i][0])+","
- +str(direction_vects[i][1])+","
- +str(direction_vects[i][2])+
- ").move("
- +str(coords[i][0])+","
- +str(coords[i][1])+","
- +str(coords[i][2])+")\n")
-
- #if condensin_is_here[i]:
- # if i < N-1:
- # sys.stdout.write("\n"
- # "#(override the dihedral angle for this monomer)\n"
- # "write(\"Data Dihedrals\") {\n"
- # " $dihedral:twistor"+str(i+1)+" @dihedral:CondensinMonomer/TWISTOR $atom:monomers["+str(i)+"]/t $atom:monomers["+str(i)+"]/c $atom:monomers["+str(i+1)+"]/c $atom:monomers["+str(i+1)+"]/t\n"
- # "}\n"
- # "\n")
-
-
-
-sys.stdout.write(
-"""
-
-# ---------------- simulation box -----------------
-
-# Now define a box big enough to hold a polymer with this (initial) shape
-
-"""
-)
-
-
-sys.stdout.write("write_once(\"Data Boundary\") {\n"
- +str(box_bounds_min[0])+" "+str(box_bounds_max[0])+" xlo xhi\n"
- +str(box_bounds_min[1])+" "+str(box_bounds_max[1])+" ylo yhi\n"
- +str(box_bounds_min[2])+" "+str(box_bounds_max[2])+" zlo zhi\n"
- "}\n\n\n")
-
-
-sys.stdout.write(
-"""
-# What kind of boundary conditions are we using?
-
-write_once("In Init") {
- boundary s s s # <-- boundary conditions in x y z directions
- #boundary p p p # <-- boundary conditions in x y z directions
-}
-# "p" stands for "periodic"
-# "s" stands for "shrink-wrapped" (non-periodic)
-
-
-# ---- Bonds ----
-
-
-write_once("In Settings") {
- # 10nm model:
- #bond_coeff @bond:backbone harmonic 100.0 1.0
- # 30nm fiber (4.25^(1/3)=1.6198059006387417)
- bond_coeff @bond:backbone harmonic 100.0 1.6198059006387417
-}
-
-
-"""
-)
-
-
-sys.stdout.write("write(\"Data Bonds\") {\n")
-
-# Old bond-loop was simple:
-#for i in range(0, N-1):
-# sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a $atom:monomers["+str(i+1)+"]/a\n")
-
-ic = 0
-for i in range(0, N-1):
- #sys.stderr.write("i="+str(i)+", ic="+str(ic)+", Nc="+str(Nc)+"\n")
-
- # Figure out if the first atom in the bond pair
- # belongs to a regular Monomer or a CondensinMonomer
- if condensin_is_here[i]:
- sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:condensins["+str(ic)+"]/a")
- ic+=1
- else:
- sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a")
-
- # Do the same thing for the second atom in the bond pair
- if condensin_is_here[i+1]:
- assert(ic<Nc)
- sys.stdout.write(" $atom:condensins["+str(ic)+"]/a\n")
- else:
- sys.stdout.write(" $atom:monomers["+str(i+1)+"]/a\n")
-
-sys.stdout.write("}\n\n\n")
-
-
-sys.stdout.write("""
-
-write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:backbone @bond:backbone
-}
-
-write_once("In Settings") {
- # Most parameters here were taken from the supplemental material of
- # Naumova et al. Science 2013 (simulations by Maxim Imakaev, see Supp Mat)
- #angle_coeff @angle:backbone cosine 5.0 #<-10nm fiber
- angle_coeff @angle:backbone cosine 1.1764705882352942 #<-30nm fiber
-}
-
-""")
-
-
-sys.stdout.write(
-"""
-
-# ---- Condensins randomly located on the polymer ----
-
-# Stage 1:
-# Add bonds between consecutive condensin anchors.
-# Imakaev calls this "stage 1: linear compaction":
-
-"""
-)
-
-sys.stdout.write("write(\"Data Bonds\") {\n")
-ic = 0
-for i in range(0, N):
- if condensin_is_here[i]:
- if (0 < ic):
- sys.stdout.write(" $bond:bstage1_"+str(ic-1)+" @bond:stage1 $atom:condensins["+str(ic-1)+"]/a $atom:condensins["+str(ic)+"]/a\n")
- ic += 1
-
-sys.stdout.write("}\n\n")
-
-
-
-sys.stdout.write("""
-
-# Stage 2:
-# Add additional bonds between all pairs of condensin anchors
-# in a window of |ic-jc| <= 30 anchors (along the chain).
-# In the paper, they call this stage 2 axial compression.
-
-write("Data Bonds") {
-""")
-
-jcwindowsize = 30
-for ic in range(0, Nc):
- #jcmin = max(ic-jcwindowsize, 0)
- #jcmax = min(ic+jcwindowsize, Nc-1)
- jcmax = min(ic+jcwindowsize, Nc-1)
- for jc in range(ic+2, jcmax+1):
- sys.stdout.write(" $bond:bstage2_"+str(ic)+"_"+str(jc)+" @bond:stage2 $atom:condensins["+str(ic)+"]/a $atom:condensins["+str(jc)+"]/a\n")
-
-sys.stdout.write("}\n")
-
-
-sys.stdout.write("""
-
-write_once("In Settings") {
- # stage 1 bonds are initially off
- bond_coeff @bond:stage1 harmonic 0.0 0.5 # <--(we can override this later)"
- # stage 2 bonds are initially off
- bond_coeff @bond:stage2 harmonic 0.0 0.0 # <--(we can override this later)"
-}
-
-""")
-
-sys.stdout.write("\n\n# "+str(Nc)+" condensin molecules added\n\n")
-sys.stderr.write("\n\n# "+str(Nc)+" condensin molecules added\n\n")
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py
deleted file mode 100755
index 06f995931..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env python
-
-
-err_msg = """
-Usage:
-
- interpolate_coords.py Ndesired [scale] < coords_orig.raw > coords.raw
-
-Example:
-
- interpolate_coords.py 30118 3.0 < coords_orig.raw > coords.raw
-
- # (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner.
- # See the supplemental section of Naumova et al Science 2013, p 18.)
-
-"""
-
-
-import sys
-from math import *
-
-# Parse the argument list:
-if len(sys.argv) <= 1:
- sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n")
- exit(1)
-
-n_new = int(sys.argv[1])
-
-if len(sys.argv) > 2:
- scale = float(sys.argv[2])
-else:
- scale = 1.0
-
-coords_orig = []
-
-lines = sys.stdin.readlines()
-
-for line in lines:
- tokens = line.split()
- if (len(tokens) > 0):
- coords_orig.append(map(float, tokens))
- g_dim = len(tokens)
-
-n_orig = len(coords_orig)
-
-if n_orig < 2:
- sys.stderr.write("Error:\n\nInput file contains less than two lines of coordinates\n")
- exit(1)
-
-if n_new < 2:
- sys.stderr.write("Error:\n\nOutput file will contain less than two lines of coordinates\n")
- exit(1)
-
-coords_new = [[0.0 for d in range(0, g_dim)] for i in range(0, n_new)]
-
-for i_new in range(0, n_new):
- I_orig = (i_new) * (float(n_orig-1) / float(n_new-1))
- i_orig = int(floor(I_orig))
- i_remainder = I_orig - i_orig
-
- if (i_new < n_new-1):
- for d in range(0, g_dim):
- coords_new[i_new][d] = scale*(coords_orig[i_orig][d]
- +
- i_remainder*(coords_orig[i_orig+1][d]-
- coords_orig[i_orig][d]))
- else:
- for d in range(0, g_dim):
- coords_new[i_new][d] = scale*coords_orig[n_orig-1][d]
-
- # print the coordates
- for d in range(0, g_dim-1):
- sys.stdout.write(str(coords_new[i_new][d]) + ' ')
- sys.stdout.write(str(coords_new[i_new][g_dim-1]) + "\n")
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/monomer.lt
deleted file mode 100644
index 9ef2b0398..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/monomer.lt
+++ /dev/null
@@ -1,84 +0,0 @@
-# This file contains the definition of a molecule named "Monomer".
-# (This particular molecule contain only one atom, but that is up to you.)
-# Later, multiple monomers can be connected together to build a molecule.
-
-
-
-Monomer {
-
- # atom-id mol-id(ignore) atom-type q x y z
-
- write("Data Atoms") {
- $atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000
- }
-
- # (The x y z positions will be changed later with move commands
- # You can spedify charge and other properties by changing the atom_style.)
-
-
-
- # atom-type mass
-
- write_once("Data Masses") {
- @atom:A 1.0
- }
-
- # pairwise interactions (between non-bonded atoms):
- #
- # U(r) = 4*eps*((r/sig)^12 - (r/sig)^6)
- #
- # Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0
- #
- # atom-type atom-type pair_style epsilon sigma rcutoff
-
- write_once("In Settings") {
- # I usually use sigma = 2^(-(1/6)), with a cutoff of 1
- #pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0
- # In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0
- # with a cutoff of 2^(1/6). Here we are trying to reproduce his results.
- # 10nm fiber
- #pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373
- # 30nm fiber (4.25^(1/2)=2.0615528128088303)
- #pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349
- # 30nm fiber (4.25^(1/3)=1.6198059006387417)
- pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708
- }
-
-} # Monomer
-
-
-
-
-# --------------------------------------------------------------------
-#
-# At some point we need to specify which force-field styles we want.
-# LAMMPS also allows you to customize the kinds of properties you want
-# each atom to have (the "atom_style"), such as charge, molecule-id, dipole etc.
-# I typically specify this here. Doing it this way means that all systems built
-# from "Monomers" (ie which import "monomer.lt") share these atom-styles
-# and force-field styles by default. You can override these settings later.
-
-
-write_once("In Init") {
- # Default styles for molecules built out of "Monomers"
- units lj
- atom_style full
-
- bond_style hybrid harmonic table linear 4001
- angle_style hybrid cosine
- dihedral_style none
-
- # If you need angles, dihedrals and impropers, uncomment or replace:
- # angle_style hybrid harmonic
- # dihedral_style hybrid fourier
-
- pair_style hybrid lj/cut 2.5
-
- # If you are using gpu acceleration uncomment these lines:
- # package gpu force/neigh 0 0 1.0
- # pair_style hybrid lj/cut/gpu 4.0
-
- pair_modify mix arithmetic
- special_bonds lj/coul 1 1 1
-}
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/table_bonds_stage2.dat b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/table_bonds_stage2.dat
deleted file mode 100644
index 1bfb911c0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files/table_bonds_stage2.dat
+++ /dev/null
@@ -1,4011 +0,0 @@
-# This table contains the bond potential between condensin-anchors
-# used by Imakaev in the Science 2013 (metaphase chromatin HiC) paper,
-# two-stage model, during stage 2.
-#
-# i r_i U(r_i) -dU/dr|r_i
-# where U(r) = step(d-3) * abs(d-3) * 10
-
-STAGE2
-N 4001 FP 0 0 EQ 0
-
-1 0 0 0
-2 .05 0 0
-3 .10 0 0
-4 .15 0 0
-5 .20 0 0
-6 .25 0 0
-7 .30 0 0
-8 .35 0 0
-9 .40 0 0
-10 .45 0 0
-11 .50 0 0
-12 .55 0 0
-13 .60 0 0
-14 .65 0 0
-15 .70 0 0
-16 .75 0 0
-17 .80 0 0
-18 .85 0 0
-19 .90 0 0
-20 .95 0 0
-21 1.00 0 0
-22 1.05 0 0
-23 1.10 0 0
-24 1.15 0 0
-25 1.20 0 0
-26 1.25 0 0
-27 1.30 0 0
-28 1.35 0 0
-29 1.40 0 0
-30 1.45 0 0
-31 1.50 0 0
-32 1.55 0 0
-33 1.60 0 0
-34 1.65 0 0
-35 1.70 0 0
-36 1.75 0 0
-37 1.80 0 0
-38 1.85 0 0
-39 1.90 0 0
-40 1.95 0 0
-41 2.00 0 0
-42 2.05 0 0
-43 2.10 0 0
-44 2.15 0 0
-45 2.20 0 0
-46 2.25 0 0
-47 2.30 0 0
-48 2.35 0 0
-49 2.40 0 0
-50 2.45 0 0
-51 2.50 0 0
-52 2.55 0 0
-53 2.60 0 0
-54 2.65 0 0
-55 2.70 0 0
-56 2.75 0 0
-57 2.80 0 0
-58 2.85 0 0
-59 2.90 0 0
-60 2.95 0 0
-61 3.0 0 -5
-62 3.05 .5 -10
-63 3.10 1.0 -10
-64 3.15 1.5 -10
-65 3.20 2.0 -10
-66 3.25 2.5 -10
-67 3.30 3.0 -10
-68 3.35 3.5 -10
-69 3.40 4.0 -10
-70 3.45 4.5 -10
-71 3.50 5.0 -10
-72 3.55 5.5 -10
-73 3.60 6.0 -10
-74 3.65 6.5 -10
-75 3.70 7.0 -10
-76 3.75 7.5 -10
-77 3.80 8.0 -10
-78 3.85 8.5 -10
-79 3.90 9.0 -10
-80 3.95 9.5 -10
-81 4.00 10.0 -10
-82 4.05 10.5 -10
-83 4.10 11.0 -10
-84 4.15 11.5 -10
-85 4.20 12.0 -10
-86 4.25 12.5 -10
-87 4.30 13.0 -10
-88 4.35 13.5 -10
-89 4.40 14.0 -10
-90 4.45 14.5 -10
-91 4.50 15.0 -10
-92 4.55 15.5 -10
-93 4.60 16.0 -10
-94 4.65 16.5 -10
-95 4.70 17.0 -10
-96 4.75 17.5 -10
-97 4.80 18.0 -10
-98 4.85 18.5 -10
-99 4.90 19.0 -10
-100 4.95 19.5 -10
-101 5.00 20.0 -10
-102 5.05 20.5 -10
-103 5.10 21.0 -10
-104 5.15 21.5 -10
-105 5.20 22.0 -10
-106 5.25 22.5 -10
-107 5.30 23.0 -10
-108 5.35 23.5 -10
-109 5.40 24.0 -10
-110 5.45 24.5 -10
-111 5.50 25.0 -10
-112 5.55 25.5 -10
-113 5.60 26.0 -10
-114 5.65 26.5 -10
-115 5.70 27.0 -10
-116 5.75 27.5 -10
-117 5.80 28.0 -10
-118 5.85 28.5 -10
-119 5.90 29.0 -10
-120 5.95 29.5 -10
-121 6.00 30.0 -10
-122 6.05 30.5 -10
-123 6.10 31.0 -10
-124 6.15 31.5 -10
-125 6.20 32.0 -10
-126 6.25 32.5 -10
-127 6.30 33.0 -10
-128 6.35 33.5 -10
-129 6.40 34.0 -10
-130 6.45 34.5 -10
-131 6.50 35.0 -10
-132 6.55 35.5 -10
-133 6.60 36.0 -10
-134 6.65 36.5 -10
-135 6.70 37.0 -10
-136 6.75 37.5 -10
-137 6.80 38.0 -10
-138 6.85 38.5 -10
-139 6.90 39.0 -10
-140 6.95 39.5 -10
-141 7.00 40.0 -10
-142 7.05 40.5 -10
-143 7.10 41.0 -10
-144 7.15 41.5 -10
-145 7.20 42.0 -10
-146 7.25 42.5 -10
-147 7.30 43.0 -10
-148 7.35 43.5 -10
-149 7.40 44.0 -10
-150 7.45 44.5 -10
-151 7.50 45.0 -10
-152 7.55 45.5 -10
-153 7.60 46.0 -10
-154 7.65 46.5 -10
-155 7.70 47.0 -10
-156 7.75 47.5 -10
-157 7.80 48.0 -10
-158 7.85 48.5 -10
-159 7.90 49.0 -10
-160 7.95 49.5 -10
-161 8.00 50.0 -10
-162 8.05 50.5 -10
-163 8.10 51.0 -10
-164 8.15 51.5 -10
-165 8.20 52.0 -10
-166 8.25 52.5 -10
-167 8.30 53.0 -10
-168 8.35 53.5 -10
-169 8.40 54.0 -10
-170 8.45 54.5 -10
-171 8.50 55.0 -10
-172 8.55 55.5 -10
-173 8.60 56.0 -10
-174 8.65 56.5 -10
-175 8.70 57.0 -10
-176 8.75 57.5 -10
-177 8.80 58.0 -10
-178 8.85 58.5 -10
-179 8.90 59.0 -10
-180 8.95 59.5 -10
-181 9.00 60.0 -10
-182 9.05 60.5 -10
-183 9.10 61.0 -10
-184 9.15 61.5 -10
-185 9.20 62.0 -10
-186 9.25 62.5 -10
-187 9.30 63.0 -10
-188 9.35 63.5 -10
-189 9.40 64.0 -10
-190 9.45 64.5 -10
-191 9.50 65.0 -10
-192 9.55 65.5 -10
-193 9.60 66.0 -10
-194 9.65 66.5 -10
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-3838 191.85 1888.5 -10
-3839 191.90 1889.0 -10
-3840 191.95 1889.5 -10
-3841 192.00 1890.0 -10
-3842 192.05 1890.5 -10
-3843 192.10 1891.0 -10
-3844 192.15 1891.5 -10
-3845 192.20 1892.0 -10
-3846 192.25 1892.5 -10
-3847 192.30 1893.0 -10
-3848 192.35 1893.5 -10
-3849 192.40 1894.0 -10
-3850 192.45 1894.5 -10
-3851 192.50 1895.0 -10
-3852 192.55 1895.5 -10
-3853 192.60 1896.0 -10
-3854 192.65 1896.5 -10
-3855 192.70 1897.0 -10
-3856 192.75 1897.5 -10
-3857 192.80 1898.0 -10
-3858 192.85 1898.5 -10
-3859 192.90 1899.0 -10
-3860 192.95 1899.5 -10
-3861 193.00 1900.0 -10
-3862 193.05 1900.5 -10
-3863 193.10 1901.0 -10
-3864 193.15 1901.5 -10
-3865 193.20 1902.0 -10
-3866 193.25 1902.5 -10
-3867 193.30 1903.0 -10
-3868 193.35 1903.5 -10
-3869 193.40 1904.0 -10
-3870 193.45 1904.5 -10
-3871 193.50 1905.0 -10
-3872 193.55 1905.5 -10
-3873 193.60 1906.0 -10
-3874 193.65 1906.5 -10
-3875 193.70 1907.0 -10
-3876 193.75 1907.5 -10
-3877 193.80 1908.0 -10
-3878 193.85 1908.5 -10
-3879 193.90 1909.0 -10
-3880 193.95 1909.5 -10
-3881 194.00 1910.0 -10
-3882 194.05 1910.5 -10
-3883 194.10 1911.0 -10
-3884 194.15 1911.5 -10
-3885 194.20 1912.0 -10
-3886 194.25 1912.5 -10
-3887 194.30 1913.0 -10
-3888 194.35 1913.5 -10
-3889 194.40 1914.0 -10
-3890 194.45 1914.5 -10
-3891 194.50 1915.0 -10
-3892 194.55 1915.5 -10
-3893 194.60 1916.0 -10
-3894 194.65 1916.5 -10
-3895 194.70 1917.0 -10
-3896 194.75 1917.5 -10
-3897 194.80 1918.0 -10
-3898 194.85 1918.5 -10
-3899 194.90 1919.0 -10
-3900 194.95 1919.5 -10
-3901 195.00 1920.0 -10
-3902 195.05 1920.5 -10
-3903 195.10 1921.0 -10
-3904 195.15 1921.5 -10
-3905 195.20 1922.0 -10
-3906 195.25 1922.5 -10
-3907 195.30 1923.0 -10
-3908 195.35 1923.5 -10
-3909 195.40 1924.0 -10
-3910 195.45 1924.5 -10
-3911 195.50 1925.0 -10
-3912 195.55 1925.5 -10
-3913 195.60 1926.0 -10
-3914 195.65 1926.5 -10
-3915 195.70 1927.0 -10
-3916 195.75 1927.5 -10
-3917 195.80 1928.0 -10
-3918 195.85 1928.5 -10
-3919 195.90 1929.0 -10
-3920 195.95 1929.5 -10
-3921 196.00 1930.0 -10
-3922 196.05 1930.5 -10
-3923 196.10 1931.0 -10
-3924 196.15 1931.5 -10
-3925 196.20 1932.0 -10
-3926 196.25 1932.5 -10
-3927 196.30 1933.0 -10
-3928 196.35 1933.5 -10
-3929 196.40 1934.0 -10
-3930 196.45 1934.5 -10
-3931 196.50 1935.0 -10
-3932 196.55 1935.5 -10
-3933 196.60 1936.0 -10
-3934 196.65 1936.5 -10
-3935 196.70 1937.0 -10
-3936 196.75 1937.5 -10
-3937 196.80 1938.0 -10
-3938 196.85 1938.5 -10
-3939 196.90 1939.0 -10
-3940 196.95 1939.5 -10
-3941 197.00 1940.0 -10
-3942 197.05 1940.5 -10
-3943 197.10 1941.0 -10
-3944 197.15 1941.5 -10
-3945 197.20 1942.0 -10
-3946 197.25 1942.5 -10
-3947 197.30 1943.0 -10
-3948 197.35 1943.5 -10
-3949 197.40 1944.0 -10
-3950 197.45 1944.5 -10
-3951 197.50 1945.0 -10
-3952 197.55 1945.5 -10
-3953 197.60 1946.0 -10
-3954 197.65 1946.5 -10
-3955 197.70 1947.0 -10
-3956 197.75 1947.5 -10
-3957 197.80 1948.0 -10
-3958 197.85 1948.5 -10
-3959 197.90 1949.0 -10
-3960 197.95 1949.5 -10
-3961 198.00 1950.0 -10
-3962 198.05 1950.5 -10
-3963 198.10 1951.0 -10
-3964 198.15 1951.5 -10
-3965 198.20 1952.0 -10
-3966 198.25 1952.5 -10
-3967 198.30 1953.0 -10
-3968 198.35 1953.5 -10
-3969 198.40 1954.0 -10
-3970 198.45 1954.5 -10
-3971 198.50 1955.0 -10
-3972 198.55 1955.5 -10
-3973 198.60 1956.0 -10
-3974 198.65 1956.5 -10
-3975 198.70 1957.0 -10
-3976 198.75 1957.5 -10
-3977 198.80 1958.0 -10
-3978 198.85 1958.5 -10
-3979 198.90 1959.0 -10
-3980 198.95 1959.5 -10
-3981 199.00 1960.0 -10
-3982 199.05 1960.5 -10
-3983 199.10 1961.0 -10
-3984 199.15 1961.5 -10
-3985 199.20 1962.0 -10
-3986 199.25 1962.5 -10
-3987 199.30 1963.0 -10
-3988 199.35 1963.5 -10
-3989 199.40 1964.0 -10
-3990 199.45 1964.5 -10
-3991 199.50 1965.0 -10
-3992 199.55 1965.5 -10
-3993 199.60 1966.0 -10
-3994 199.65 1966.5 -10
-3995 199.70 1967.0 -10
-3996 199.75 1967.5 -10
-3997 199.80 1968.0 -10
-3998 199.85 1968.5 -10
-3999 199.90 1969.0 -10
-4000 199.95 1969.5 -10
-4001 200.00 1970.0 -10
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.min
deleted file mode 100644
index c8c28cd7a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.min
+++ /dev/null
@@ -1,41 +0,0 @@
-#########################################################
-# Example how to run this file:
-#
-# 1) Choose a ransom seed (in this case 141203)
-# (or use `bash -c 'echo $RANDOM'`)
-#
-# 2) Then, from the shell, invoke LAMMPS to collapse the polymer:
-#
-# lmp_ubuntu_parallel -i run.in -var seed 141203
-#
-#########################################################
-# eg:
-# time mpirun -np 2 lmp_ubuntu_parallel -i run.in.min
-#########################################################
-
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-dump 1 all custom 10000 traj_min.lammpstrj id mol type x y z ix iy iz
-thermo_style custom step pe etotal vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 100 #(time interval for printing out "thermo" data)
-
-# Now minimize the system:
-
-min_style quickmin
-min_modify dmax 0.05
-minimize 1.0e-7 1.0e-8 30000 100000000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.stage1 b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.stage1
deleted file mode 100644
index bf129df04..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.stage1
+++ /dev/null
@@ -1,110 +0,0 @@
-# PREREQUISITES: You must run LAMMPS using "run.in.min" beforehand.
-# (This will create the "system_after_min0.data" file needed below.)
-#########################################################
-# Run using:
-#
-# lmp_ubuntu_parallel -i run.in.stage1
-#
-#########################################################
-# GPUs:
-# To enable gpu acceleration, make sure settings.in.init includes this line:
-# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.)
-# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings"
-# files with "lj/cut/gpu"
-
-
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-#read_data system.data
-read_data system_after_min.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-# DON'T MINIMIZE FIRST UNLESS YOU CHOOSE THE CORRECT INITIAL KbondC FORMULA
-#thermo_style custom step pe etotal vol epair ebond eangle edihed
-#thermo_modify norm no #(report total energy not energy / num_atoms)
-#thermo 20 #(time interval for printing out "thermo" data)
-#min_style sd
-#min_modify dmax 0.05
-#minimize 1.0e-7 1.0e-8 20000 1000000
-#write_data system_after_min_t=0.data
-
-
-mass * 1.0
-timestep 0.005 # "dt"
-dump 1 all custom 25000 traj_stage1.lammpstrj id mol type x y z ix iy iz
-reset_timestep 0
-
-
-# --- run the simulation ---
-
-
-# set the velocity to zero
-velocity all create 0.0 123456
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve"
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-# Tstart Tstop tdamp randomseed
-
-fix fxlan all langevin 1.0 1.0 10.0 123456
-
-# pstart pstop pdamp(time-units, 2000 iters usually)
-#fix fxnph all nph x -0.000 -0.000 1.0
-fix fxnve all nve
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-fix fxcenter all recenter 0.0 0.0 0.0
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 1000 #(time interval for printing out "thermo" data)
-
-#balance dynamic x 20 1.0 -out tmp.balance
-#balance x uniform
-
-
-variable nloop1 loop 300
-
- label loop1
-
- print "############### LOOP ${nloop1} ###############"
-
- # Now, change the bond-strength between condensin monomers.
- # From the Naumova et al Science 2013 paper (supp materials)
- # "Two-stage model: linear compaction + axial compression"
- # "First, random consecutive loops with L=100 monomers (see above) were
- # introduced, and anchors of neighboring loops were brought together
- # using harmonic springs with a potential U = k * (r – r0)2; r0=0.5.
- # To avoid abrupt motion of the loop anchors, the force was gradually
- # turned on over the first 300000 timesteps, with k linearly increasing
- # in time from 0 to 10 kT."
- # Do this by changing the parameters in the force-field for these
- # bonds.
- #
- # Formula used for "bond_style harmonic":
- # Ubond(r) = k*(r-r0)^2
- # bondType style
- #bond_coeff 1 harmonic 0.1 0.5
-
- variable time equal step
- variable KbondC equal $((v_time+1)*(10.0/300000.0))
- print "timestep = ${time}, KbondC = ${KbondC}" file KbondC_vs_time.dat
-
- #bond_coeff 1 harmonic ${KbondC} 0.5
- bond_coeff 1 harmonic ${KbondC} 0.5
- run 1000
-
- next nloop1
- jump SELF loop1
-
-write_data system_after_stage1.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.stage2 b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.stage2
deleted file mode 100644
index e429fc882..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/run.in.stage2
+++ /dev/null
@@ -1,90 +0,0 @@
-# PREREQUISITES: You must run LAMMPS using "run.in.stage1" beforehand.
-# (This will create the "system_after_stage1.data" file.)
-#########################################################
-# Run using:
-#
-# lmp_ubuntu_parallel -i run.in.stage2
-#
-#########################################################
-# eg:
-# time mpirun -np 2 lmp_ubuntu_parallel -i run.in -var seed 1
-#########################################################
-# GPUs:
-# To enable gpu acceleration, make sure settings.in.init includes this line:
-# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.)
-# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings"
-# files with "lj/cut/gpu"
-
-
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-#read_data system.data
-read_data system_after_stage1.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-mass * 1.0
-timestep 0.005 # "dt"
-dump 1 all custom 50000 traj_stage2.lammpstrj id mol type x y z ix iy iz
-reset_timestep 300000
-
-
-# --- run the simulation ---
-
-# set the velocity to zero
-velocity all create 0.0 123456
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve"
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-# Tstart Tstop tdamp randomseed
-
-fix fxlan all langevin 1.0 1.0 10.0 123456
-
-# pstart pstop pdamp(time-units, 2000 iters usually)
-fix fxnve all nve
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-fix fxcenter all recenter 0.0 0.0 0.0
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 1000 #(time interval for printing out "thermo" data)
-
-#balance dynamic x 20 1.0 -out tmp.balance
-#balance x uniform
-
-# atomTypes pairStyle epsilon sigma rcutoff
-# 10nm-fiber
-#pair_coeff 1 1 lj/cut 1.0 1.0 2.5
-#pair_coeff 2 2 lj/cut 1.0 1.0 2.5
-# 30nm fiber (4.25^(1/3)=1.6198059006387417)
-pair_coeff 1 1 lj/cut 1.0 1.6198059006387417 4.049514751596854
-pair_coeff 2 2 lj/cut 1.0 1.6198059006387417 4.049514751596854
-
-
-# During stage 2, add attractive forces between all pairs of non-consecutive
-# condensin anchors. These forces are stored in the table file below:
-# bondType bondStyle filename label
-bond_coeff 2 table table_bonds_stage2.dat STAGE2
-
-# During stage 2, I assume the stage-1 bonds remain in place
-# (They have length 0.5.
-# After 300000 timesteps during stage 1, the "k" value should be 10.0.)
-
-# bondType bondStyle k r0
-bond_coeff 1 harmonic 10.0 0.5
-
-timestep 0.005
-run 1700000
-
-write_data system_after_stage2.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README.TXT
deleted file mode 100644
index 09abbc4b2..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README.TXT
+++ /dev/null
@@ -1,70 +0,0 @@
- This example shows how to put a protein (inclusion) in a
- lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
- The DPPC lipid model is described here:
- G. Brannigan, P.F. Philips, and F.L.H. Brown,
- Physical Review E, Vol 72, 011915 (2005)
- (The DLPC model is a truncated version of DPPC. Modifications discussed below.)
- The protein model is described here:
- G. Bellesia, AI Jewett, and J-E Shea,
- Protein Science, Vol19 141-154 (2010)
-
---- PREREQUISITES: ---
-
-1) This example requires the "dihedral_style fourier", which is currently
-in the USER-MISC package. Build LAMMPS with this package enabled using
- make yes-user-misc
-before compiling LAMMPS.
-(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.)
-
-2) This example may require additional features to be added to LAMMPS.
-If LAMMPS complains about an "Invalid pair_style", then
- a) download the "additional_lammps_code" from
- http://moltemplate.org (upper-left corner menu)
- b) unpack it
- c) copy the .cpp and .h files to the src folding of your lammps installation.
- d) (re)compile LAMMPS.
-
-
------ Details --------
-
-This example contains a coarse-grained model of a 4-helix bundle protein
-inserted into a lipid bilayer (made from a mixture of DPPC and DLPC).
-
- -- Protein Model: --
-
-The coarse-grained protein is described in:
- G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
-Here we use the "AUF2" model described in that paper.
-(The hydrophobic beads face outwards.)
-
- -- Memebrane Model: --
-
-The DPPC lipid bilayer described in:
- G. Brannigan, P.F. Philips, and F.L.H. Brown,
- Physical Review E, Vol 72, 011915 (2005)
-and:
- M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
- J. Chem. Phys. 135, 244701 (2011)
-
-As in Watson(JCP 2011), rigid bond-length constraints
-have been replaced by harmonic bonds.
-
-A truncated version of this lipid (named "DLPC") has also been added.
-The bending stiffness of each lipid has been increased to compensate
-for the additional disorder resulting from mixing two different types
-of lipids together. (Otherwise pores appear.)
-Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models
-have not been carefully parameterized to reproduce the correct behavior in
-a lipid bilayer mixture.
-
-
--------------
-
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT
deleted file mode 100644
index 8864c3e04..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT
+++ /dev/null
@@ -1,10 +0,0 @@
-WARNING:
-
- This is not a realistic simulation of proteins in a lipid membrane. This
-example was only intented to be a technical demonstration to show how to
-combine totally different kinds of coarse-grained molecules (with different
-kinds of force-fields) together in the same simulation in LAMMPS. Tuning the
-force-field parameters to get realistic results was not the goal. I did
-not take the extra time to do this. If you have suggestions for changes,
-please email me (jewett.aij at gmail dot com).
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_run.sh
deleted file mode 100755
index d7ea30569..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_run.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" file is a LAMMPS input script containing
-# references to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data, and table_int.dat
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension)
-
-#or
-
-lmp_mpi -i run.in.nvt # Run a simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation are ignored when beginning the simulation at constant volume.
-# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#or
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_setup.sh
deleted file mode 100755
index abf2fce64..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # The "table_int.dat" file contains tabular data for the lipid INT-INT atom
- # 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
- # so I might look for a way to get rid of it later.)
- cp -f table_int.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt
deleted file mode 100644
index 2e510ebd9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt
+++ /dev/null
@@ -1,233 +0,0 @@
-# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in
-# G. Bellesia, AI Jewett, and J-E Shea,
-# Protein Science, Vol19 141-154 (2010)
-#
-# Strategy:
-#
-#1) First I'll define some building blocks (A16, B16, T3)
-# which are helices, sheets and turns of a predetermined length)
-#
-#2) Then I'll copy and paste them together to build
-# a 4-helix bundle (or a 4-strand beta-barrel).
-# This approach is optional. If your protein has helices which are not
-# identical, you should probably just include all 4 helices in a single
-# "Data Atoms" section and don't try to subdivide the protein into pieces.)
-
-
-
-1beadProtSci2010 { # <-- enclose definitions in a namespace for portability
-
- # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
-
- A16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0
- $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6
- $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2
- $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8
- $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4
- $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0
- $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6
- $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2
- $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8
- $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4
- $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0
- $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6
- $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2
- $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8
- $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4
- $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # A16
-
-
- T3 { # T3 is a "turn" region consisting of 3 beads
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0
- $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44
- $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- }
-
- } # T3
-
-
- # ----- Now build a larger molecule using A16 and T3 -------
-
- # Create a 4-Helix bundle.
- # In this version, the hydrophobic beads are poing outward.
- # I oriented them this way because I want to place this protein in a membrane.
- # (There is another file in this directory containing alternate version
- # of this same molecule with the hydrophobic beads pointing inward.)
-
- 4HelixInsideOut {
- helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4)
- helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8)
- helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2)
- helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6)
-
- turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9)
- turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0)
- turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixInsideOut
-
-
- # -------- Minor coordinates adjustment: -----------
-
- # Those coordinates in the commands above are a little too large.
- # To make it easier to type them in, I was using sigma=6.0 Angstroms.
- # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6 = 0.8)
-
- 4HelixInsideOut.scale(0.8)
-
- # Note: "scale()" only effects the initial coordinates of
- # the molecule, not the force field parameters.
- # (If you plan to minimize the molecule, you don't need to
- # be so careful about the initial coordinates. In that case,
- # you don't have worry about "scale()". Feel free to remove.)
-
-
-
- # -------------- Force-Field Parameters ------------
-
- # Units and force-field styles for this protein model
- # (These can be overridden later.)
-
- write_once("In Init") {
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid fourier
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
- # --- Distance Units ---
- # In this version of the model, sigma (the bond-length
- # and particle diameter) is rounded to 4.8 Angstroms.
- #
- # --- Energy & Temperature Units ---
- # In this protein model, "epsilon" represents the free energy
- # bonus for bringing two hydrophobic amino acids together.
- # Here I choose to set epsilon to 1.806551818181818 kCal/mole.
- # This value was chosen so that a temperature of 300 Kelvin lies at
- # 0.33 epsilon, which is the unfolding temperature of the marginally stable
- # "ASF1" protein model from the Bellesia et al 2010 paper.
- # This choice insures that both the "ASF1" model from that paper,
- # as well as the much more stable "AUF2" protein we use here (which
- # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin,
- # in the bulk at least. (However it's not clear that these energy
- # parameters will work well for a protein in membrane. Perhaps I'll
- # run some tests and fine tune these parameters for this scenario.)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 4.8 1 -1
- pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0
- pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0
- }
-
- # The exact value of the bond_coeff does not matter too much as long as
- # it is "stiff enough". Here I use a softer bond spring than the one
- # used in the paper so that I can increase the time step.
- # I also use a relatively soft spring to constrain the bond angles.
-
- # bond_coeff bondType bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 4.8
- }
-
-
- # angleType atomtypes1 2 3 bondtypes1 2
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # angle_coeff angleType anglestylename k theta0
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 100.0 105.0
- }
-
-
- # dihedralType atomtypes1 2 3 4 bondtypes1 2 3
-
- write_once("Data Dihedrals By Type") {
- # For a chain of sH and sL atoms, use the @dihedral:delta65_0
- # parameters. (This corresponds to the "AUF2" model from the
- # Bellesia et. al 2010 paper.)
-
- @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * *
-
- # If "tN" (turn) atoms are present, use the @dihedral:turn parameters
-
- @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * *
- }
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0
- dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0
- dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0
- # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
- }
-
-
- # --- Mass Units ---
- # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down):
- write_once("Data Masses") {
- @atom:1beadProtSci2010/sH 100.0
- @atom:1beadProtSci2010/sL 100.0
- @atom:1beadProtSci2010/tN 100.0
- }
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
deleted file mode 100644
index 38b1b48f8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
+++ /dev/null
@@ -1,225 +0,0 @@
-### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ##
-### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE##
-#
-# This file defines a family of coarse-grained protein models used in:
-# G. Bellesia, AI Jewett, and J-E Shea,
-# Protein Science, Vol19 141-154 (2010)
-#
-# Strategy:
-#
-#1) First I'll define some building blocks (A16, B16, T3)
-# which are helices, sheets and turns of a predetermined length)
-
-import "1beadProtSci2010.lt"
-
-# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below
-#
-#2) Then I'll copy and paste them together to build
-# a 4-helix bundle or a 4-strand beta-barrel.
-
-
-1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier
- # This way we don't have to start from scratch. We can
- # use all the atom types and angle settings defined earlier
-
- # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
-
- B16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0
- $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8
- $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6
- $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4
- $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2
- $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0
- $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8
- $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6
- $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4
- $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2
- $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0
- $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8
- $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6
- $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4
- $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2
- $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # B16
-
- # ----- Now build larger molecules using B16 and T3 -------
-
-
- 4SheetBarrel {
- sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0)
- sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0)
- sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0)
- sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0)
-
- turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6)
- turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4)
- turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- # Below I define several alternate conformations of the"4HelixBundleInsideOut"
- # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however.
-
- 4HelixBundle {
- helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4)
- helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8)
- helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2)
- helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
-
- turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2)
- turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9)
- turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4)
-
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixBundle
-
-
-
-
- # --- alternate conformations (same molecule) ----
-
- # In the following version, the helices are oriented in a similar way,
- # but they are separated a little further away from eachother.
-
- 4HelixBundleLoose {
-
- helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
- helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
- helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
- helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
-
- turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4)
- turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8)
- turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- # In following version, the helices are oriented in a similar way,
- # but they are separated a little further away from eachother.
-
- 4HelixInsideOutLoose {
- helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
- helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
- helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
- helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
-
- turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8)
- turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2)
- turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixInsideOutLoose
-
-
-
-
- # In the following version, the 4 helices are arranged next to each other,
- # side-by-side, in a planar conformation (instead of a compact bundle).
-
- 4HelixPlanar {
- helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0)
- helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0)
- helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0)
- helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0)
-
- turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8)
- turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8)
- turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixPlanar
-
-
- # -------- Minor coordinates adjustment: -----------
- # Those coordinates in the commands above are a little too large.
- # To make it easier to type them in, I was using sigma=6.0 Angstroms.
- # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6.0 = 0.8)
-
- 4SheetBarrel.scale(0.8)
- 4HelixBundle.scale(0.8)
- 4HelixBundleLoose.scale(0.8)
- 4HelixInsideOutLoose.scale(0.8)
- 4HelixPlanar.scale(0.8)
-
- # Note: "scale()" only effects the initial coordinates of
- # the molecule, not the force field parameters.
- # (If you plan to minimize the molecule, you don't need to
- # be so careful about the initial coordinates. In that case,
- # you don't have worry about "scale()". Feel free to remove.)
-
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt
deleted file mode 100644
index 24be50ace..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt
+++ /dev/null
@@ -1,196 +0,0 @@
-# Note:
-#
-# This example may require additional features to be added to LAMMPS. If
-# LAMMPS complains about an "Invalid pair_style", then download copy the
-# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
-# "src" directory and recompile LAMMPS.
-#
-# -------- Description --------
-#
-# This example contains an implementation of the DPPC lipid bilayer described in
-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
-# Physical Review E, Vol 72, 011915 (2005)
-# and:
-# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
-# J. Chem. Phys. 135, 244701 (2011)
-#
-# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
-# by harmonic bonds.
-#
-# A truncated version of this lipid (named "DLPC") has also been added.
-# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
-# parameterized to reproduce the correct behavior in a lipid bilayer mixture.
-#
-# Units:
-#
-# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
-# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
-# The "sigma" parameter corresponds to 7.5 angstroms.
-
-
-CGLipidBr2005 {
-
-
- write_once("In Init") {
- # -- Default styles for "CGLipidBr2005" --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
-
- #angle_style hybrid cosine/delta # <- used in the original article
- angle_style hybrid harmonic # <- prevents unphysical acute angle turns
- # Explanation:
- # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0))
- # angle_style harmonic: U(theta) = k*(theta-theta0)^2
-
- dihedral_style none
- improper_style none
-
- pair_style hybrid table linear 1130 &
- lj/charmm/coul/charmm/inter es4k4l 14.5 15
-
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
- }
-
-
- DPPC {
- write("Data Atoms") {
- $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
- $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
- $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
- $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
- $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
- }
- write("Data Bonds") {
- $bond:b1 @bond:../backbone $atom:h $atom:i
- $bond:b2 @bond:../backbone $atom:i $atom:t1
- $bond:b3 @bond:../backbone $atom:t1 $atom:t2
- $bond:b4 @bond:../backbone $atom:t2 $atom:t3
- }
- write("Data Angles") {
- $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
- $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
- $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
- }
-
- # Define properties of the local (lipid-specific) atom:head type atom:
- write_once("Data Masses") {
- @atom:head 200.0
- }
- write_once("In Settings") {
- pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- }
-
- } #DPPC
-
-
- DLPC {
- write("Data Atoms") {
- $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
- $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
- $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
- $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
- }
- write("Data Bonds") {
- $bond:b1 @bond:../backbone $atom:h $atom:i
- $bond:b2 @bond:../backbone $atom:i $atom:t1
- $bond:b3 @bond:../backbone $atom:t1 $atom:t2
- }
- write("Data Angles") {
- $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
- $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
- }
- # Define properties of the local (lipid-specific) atom:head type atom:
- write_once("Data Masses") {
- @atom:head 200.0
- }
- write_once("In Settings") {
- pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- }
- } #DLPC
-
-
- # Particles and properties shared by all lipid types:
-
- write_once("Data Masses") {
- @atom:int 200.0
- @atom:tail 200.0
- }
-
- write_once("In Settings") {
- # -- Default settings/parameters for "CGLipidBr2005" --
- # (Hybrid bond & angle styles were used for portability.)
-
- # As in Watson(JCP 2011), rigid bond-length constraints
- # have been replaced by harmonic bonds.
- # The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
- bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
- }
-
- write_once("In Settings") {
- # cosine/delta: U(theta) = k*(1-cos(theta-theta0))
- #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
- # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2
- angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps
- }
- # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper
- # to attempt to compensate for the fact that here we are using a lipid
- # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal
- # of disorder into the bilayer which would not be present in a DPPC bilayer.
- # This causes pores to form. Increasing the angle stiffness prevents this.)
-
- write_once("In Settings") {
-
- # The interaction of "atom:int" with other "atom:int" atoms is given by
- # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
- # r=3*sigma. This was implemented using pair_style table.
- # Unfortunately, mixing lj/charmm and "table" pair styles in the same
- # simulation is very inneficient.
-
- pair_coeff @atom:int @atom:int table table_int.dat INT
-
- # The interaction of tail beads with eachother is given by the formula below
- # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
- # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
- pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
- pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
-
- # The interaction between head beads from different types of lipids
- # is (currently) repulsive:
- pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
-
- } # write_once("In Settings")
-
-
- # Note: I divided epsilon by 4 to get "0.1643" because we are using the
- # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
- # (The "es4k4l" coeffstyle is the default.) Using this convention makes it
- # easier to mix this coarse-grained lipid model with other molecular models.
-
-
-
-} # CGLipidBr2005
-
-
-
-
-
-
-
-
-# Note: This example has not been optimized for speed.
-#
-# Unfortunately, using both lj/charmm and "table" pair styles in the same
-# simulation seems to be very inneficient. (The simulation is twice as slow
-# as using only the "lj/charmm" pair styles for every pairwise interaction,
-# ...and about 25% slower than using "table" for every pairwise interaction.
-# However the lennard-jones pair styles support mixing, so we use them to
-# make it easier to run these molecules with other molecules which don't use
-# pair_table. I felt that portability was worth the extra 25% slow down.)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
deleted file mode 100755
index 0d09e4d02..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between "INT" atoms
-# in the lipid membrane model described in
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
-
-def U(r, eps, sigma):
- return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
-def F(r, eps, sigma):
- return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-
-epsilon = 2.75/4.184 # kCal/mole
-sigma = 7.5
-Rmin = 0.02
-Rmax = 22.6
-rcut = 22.5
-N = 1130
-
-for i in range(0,N):
- r = Rmin + i*(Rmax-Rmin)/(N-1)
- U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
- F_r = F(r, epsilon, sigma)
- if r > rcut:
- U_r = 0.0
- F_r = 0.0
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
deleted file mode 100755
index 32147e444..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between "INT" atoms
-# in the lipid membrane model described in
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-# I realized later this is not what we want because although energy is conserved
-# all enrgies are shifted with respect to energies used in the Brannigan paper
-# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
-# (So don't use this.)
-
-# Calculate and print a
-
-def S(r, rc1, rc2, derivative=False):
- """
- Calculate the switching function S(r) which decays continuously
- between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
- S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
- I'm using the same smoothing/switching cutoff function used by the CHARMM
- force-fields. (I'm even using the same code to implement it, taken
- from lammps charmm/coul/charmm pair style, rewritten in python.)
-
- """
- assert(rc2>rc1)
- rsq = r*r
- rc1sq = rc1*rc1
- rc2sq = rc2*rc2
- denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
- (rc2sq-rc1sq)*
- (rc2sq-rc1sq)))
- if rsq > rc2sq:
- return 0.0
- elif rsq < rc1sq:
- if derivative:
- return 0.0
- else:
- return 1.0
- else:
- rc2sq_minus_rsq = (rc2sq - rsq)
- rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
- if derivative:
- return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
- else:
- return (rc2sq_minus_rsq_sq *
- (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
-
-
-def U(r, eps, sigma):
- return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
-
-def F(r, eps, sigma):
- return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-
-epsilon = 2.75/4.184 # kCal/mole
-sigma = 7.5
-Rmin = 0.02
-Rmax = 22.6
-Rc1 = 22.0
-Rc2 = 22.5
-N = 1130
-
-for i in range(0,N):
- r = Rmin + i*(Rmax-Rmin)/(N-1)
- U_r = U(r, epsilon, sigma)
- F_r = F(r, epsilon, sigma)
- # Multiply U(r) & F(r) by the smoothing/switch function
- U_r = U_r * S(r, Rc1, Rc2)
- F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt
deleted file mode 100644
index 3e521b0f9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt
+++ /dev/null
@@ -1,178 +0,0 @@
-# Description:
-
-# This example shows how to put a protein (inclusion) in a
-# lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
-# The DPPC lipid model is described here:
-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
-# Physical Review E, Vol 72, 011915 (2005)
-# The protein model is described here:
-# G. Bellesia, AI Jewett, and J-E Shea,
-# Protein Science, Vol19 141-154 (2010)
-# The new DLPC model is a truncated version of DPPC,
-# (Its behaviour has not been rigorously tested.)
-# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
-# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
-
-# Note:
-# This example may require additional features to be added to LAMMPS.
-# If LAMMPS complains about an "Invalid pair_style", then copy the code
-# in the "additional_lammps_code" directory into your LAMMPS "src" directory
-# and recompile LAMMPS.
-
-
-
-import "CGLipidBr2005.lt"
-
-using namespace CGLipidBr2005
-
-# The "= new random" syntax chooses one of several molecules at random
-
-lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed
- [13].move(7.5, 0, 0)
- [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice
- [2].rot(180, 1, 0, 0) # <-- 2 monolayers
-
-# Move all the lipds up to the center of the box
-
-lipids[*][*][*].move(0,0,75.0)
-
-
-
-
-# Although this patch of lipids is not square or rectangular, (it looks
-# like a parallelogram), this is no longer the case after rectangular
-# periodic boundary conditions are applied. (Check by visualising in VMD.)
-
-
-write_once("Data Boundary") {
- 0 97.5 xlo xhi
- 0 97.42785792 ylo yhi
- 0 150.0 zlo zhi
-}
-
-
-# A note on geometry:
-# We want to create a bilayer arranged in a hexagonal lattice consisting of
-# 15 rows (each row is aligned with the x-axis)
-# 13 columns (aligned at a 60 degree angle from the x axis)
-# The lattice spacing is 7.5 Angstroms.
-# When wrapped onto a rectangular box, the dimensions of the system are:
-# 13 * 7.5 Angstroms in the X direction
-# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction
-
-
-
-
-
-
-
-# ------------------- protein inclusion ---------------------
-
-import "1beadProtSci2010.lt"
-
-using namespace 1beadProtSci2010
-
-protein = new 4HelixInsideOut
-
-protein.move(45.0, 25.98076211, 75.0)
-
-
-# Delete a hole in the membrane to create space for the protein.
-# (In the future moltemplate will be able to avoid occlusion automatically.)
-
-
-delete lipids[4][2][*]
-delete lipids[6][2][*]
-delete lipids[3-6][3][*]
-delete lipids[3-5][4][*]
-delete lipids[2-5][5][*]
-delete lipids[2][6][*]
-delete lipids[4][6][*]
-
-
-# -------- interactions between protein and lipids ----------
-
-# Note: All atom types must include the full path (the name of
-# the namespace which defined them as well as the atom type name).
-# (This is because we are no longer inside that namespace.)
-
-
-write_once("In Settings") {
-
- # Interactions between the protein and lipid atoms are usually
- # determined by mixing rules. However this is not possible some
- # for atoms (such as the "int" atoms in the lipid model which
- # interact using -1/r^2 attraction). Lorentz-Berthelot mixing
- # rules do not make sense for these atoms so we must explicitly
- # define their interaction with all other atoms.
-
- # i j pairstylename eps sig K L
-
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
-
- # We want the interactions between hydrophobic residues and atoms in
- # the interior of the lipid to be energetically similar to the attractive
- # interactions between hydrophobic residues. (See 1beadProtSci2010.)
-
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1
-
- # All other interactions between proteins and lipids are steric.
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
-
-
- # We also add an artificial attractive interaction between the
- # turn residues of the protein and the lipid head groups in
- # order to keep the protein upright. This might not be necessary
-
- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
-
- # Add a weak attractive interaction between hydrophilic "sL" beads
- # (Whose strength mimics the strength of interaction between tail beads
- # in the lipid. This was absent from the original protein model.
- # However without some kind of weak attraction between residues,
- # the negative pressure in the interior of the bilayer membrane
- # allways pulls the protein apart. Recall that in the membrane,
- # the hydrophobic beads in the protein will face outwards towards the lipid
- # tails leaving the hydrophilic amino acids of the protein in the interior.
- # In reality, these polar groups form hydrogen bonds with each other.)
-
- pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 6.0 0.4 -1
-
- # However these hydrophilic amino acids are not attrected to
- # the bilayer interior.
-
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
-
-}
-
-
-
-
-# Finally, we must combine the two force-field styles which were used for
-# the coarse-grained lipid and protein. To do that, we write one last time
-# to the "In Init" section. When reading the "Init" section LAMMPS will
-# read these commands last and this will override any earlier settings.
-
-write_once("In Init") {
- # -- These styles override earlier settings --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
- angle_style hybrid cosine/delta harmonic
- dihedral_style hybrid fourier
- improper_style none
- pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
-}
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/table_int.dat
deleted file mode 100644
index b0d651d67..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/table_int.dat
+++ /dev/null
@@ -1,1139 +0,0 @@
-# Table for the INT-INT interaction from
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# This table contains
-# i r_i U(r_i) -dU/dr|r_i
-# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-
-INT
-N 1130
-
-1 0.02 2.0331818401e+30 1.21990910406e+33
-2 0.04 4.9638228518e+26 1.48914685554e+29
-3 0.06 3.82579033251e+24 7.65158066501e+26
-4 0.08 1.21187081343e+23 1.81780622014e+25
-5 0.1 8.32791281704e+21 9.99349538045e+23
-6 0.12 9.34030842897e+20 9.34030842897e+22
-7 0.14 1.46892540453e+20 1.25907891817e+22
-8 0.16 2.95866897809e+19 2.21900173357e+21
-9 0.18 7.19889946863e+18 4.79926631242e+20
-10 0.2 2.0331818401e+18 1.21990910406e+20
-11 0.22 6.47834392264e+17 3.53364213962e+19
-12 0.24 2.28034873754e+17 1.14017436877e+19
-13 0.26 8.72681951932e+16 4.02776285507e+18
-14 0.28 3.58624366341e+16 1.53696157003e+18
-15 0.3 1.56704372019e+16 6.26817488078e+17
-16 0.32 7.2233129348e+15 2.70874235055e+17
-17 0.34 3.48970861422e+15 1.23166186384e+17
-18 0.36 1.75754381558e+15 5.85847938527e+16
-19 0.38 9.18613895646e+14 2.90088598625e+16
-20 0.4 4.96382285179e+14 1.48914685554e+16
-21 0.42 2.76404230108e+14 7.89726371739e+15
-22 0.44 1.58162693423e+14 4.31352800247e+15
-23 0.46 9.27773983256e+13 2.42027995633e+15
-24 0.48 5.56725765996e+13 1.391814415e+15
-25 0.5 3.41111308981e+13 8.18667141564e+14
-26 0.52 2.13057117167e+13 4.91670270393e+14
-27 0.54 1.35459994024e+13 3.0102220895e+14
-28 0.56 8.75547769351e+12 1.87617379153e+14
-29 0.58 5.74645813711e+12 1.18892237325e+14
-30 0.6 3.8257903322e+12 7.65158066491e+13
-31 0.62 2.58128463312e+12 4.99603477424e+13
-32 0.64 1.7635041342e+12 3.30657025205e+13
-33 0.66 1.21901470178e+12 2.21639036726e+13
-34 0.68 8.51979641904e+11 1.50349348607e+13
-35 0.7 6.0167184547e+11 1.0314374497e+13
-36 0.72 4.29087845387e+11 7.15146409276e+12
-37 0.74 3.08855637556e+11 5.00846980094e+12
-38 0.76 2.24270970425e+11 3.54112058818e+12
-39 0.78 1.64210505205e+11 2.52631546702e+12
-40 0.8 1.2118708117e+11 1.81780621971e+12
-41 0.82 90109367359.1 1.31867367068e+12
-42 0.84 67481501334.4 9.64021449503e+11
-43 0.86 50880896383.4 7.09965997788e+11
-44 0.88 38613938681.2 5.26553710913e+11
-45 0.9 29486692086.8 3.93155896009e+11
-46 0.92 22650731882.4 2.95444330322e+11
-47 0.94 17498544395.3 2.23385674464e+11
-48 0.96 13591937526.4 1.69899220331e+11
-49 0.98 10612635712.6 1.29950642555e+11
-50 1.0 8327912706.34 99934953582.6
-51 1.02 6566502316.69 77252969474.2
-52 1.04 5201589672.36 60018343356.8
-53 1.06 4138717434.11 46853405843.3
-54 1.08 3307128665.58 36745874940.0
-55 1.1 2653529579.27 28947596241.1
-56 1.12 2137567708.15 22902511945.9
-57 1.14 1728534024.3 18195095739.0
-58 1.16 1402943799.0 14513212422.1
-59 1.18 1142752163.37 11621209113.9
-60 1.2 934030766.093 9340308300.6
-61 1.22 765981286.774 7534242773.65
-62 1.24 630196371.787 6098675145.29
-63 1.26 520103253.414 4953364870.6
-64 1.28 430542934.103 4036340534.04
-65 1.3 357450462.101 3299543229.91
-66 1.32 297610947.802 2705554551.18
-67 1.34 248472587.186 2225128105.44
-68 1.36 208002782.573 1835319108.76
-69 1.38 174576985.011 1518061159.35
-70 1.4 146892484.084 1259078837.33
-71 1.42 123901294.937 1047053582.16
-72 1.44 104757721.536 872981382.419
-73 1.46 88777241.639 729676313.267
-74 1.48 75404158.02 611385405.387
-75 1.5 64186061.7033 513488820.507
-76 1.52 54753607.1486 432265633.695
-77 1.54 46804443.7318 364710253.134
-78 1.56 40090410.0598 308388060.159
-79 1.58 34407297.9713 261321529.95
-80 1.6 29586646.6744 221900119.2
-81 1.62 25489145.661 188808745.634
-82 1.64 21999316.2868 160970856.824
-83 1.66 19021212.5921 137502982.517
-84 1.68 16474936.8715 117678352.86
-85 1.7 14293808.3245 100897694.735
-86 1.72 12422056.6082 86665727.6626
-87 1.74 10812938.3788 74572197.8496
-88 1.76 9427195.57103 64276535.39
-89 1.78 8231790.46096 55495411.7777
-90 1.8 7198865.45512 47992625.088
-91 1.82 6304885.77339 41570857.9644
-92 1.84 5529931.32911 36064946.1544
-93 1.86 4857110.59557 31336368.341
-94 1.88 4272074.43377 27268725.7382
-95 1.9 3762612.01167 23764025.6584
-96 1.92 3318314.28383 20739619.609
-97 1.94 2930293.18879 18125675.4316
-98 1.96 2590946.89128 15863086.114
-99 1.98 2293763.15199 13901736.4186
-100 2.0 2033154.33079 12199063.3122
-101 2.02 1804318.68586 10718858.1296
-102 2.04 1603123.57305 9430268.02169
-103 2.06 1426006.91783 8306962.01537
-104 2.08 1269893.96121 7326433.30293
-105 2.1 1132126.79514 6469414.48445
-106 2.12 1010404.62602 5719386.63441
-107 2.14 902733.052344 5062166.44376
-108 2.16 807380.928986 4485558.44681
-109 2.18 722843.627253 3979061.59742
-110 2.2 647811.695319 3533621.30686
-111 2.22 581144.085827 3141419.57242
-112 2.24 521845.251959 2795697.07302
-113 2.26 469045.525153 2490602.13576
-114 2.28 421984.280794 2221062.32522
-115 2.3 379995.475978 1982675.10836
-116 2.32 342495.208369 1771614.62868
-117 2.34 308970.999537 1584552.10475
-118 2.36 278972.551763 1418587.76828
-119 2.38 252103.765513 1271192.59046
-120 2.4 228015.837009 1140158.32224
-121 2.42 206401.282366 1023554.60663
-122 2.44 186988.75765 919692.114521
-123 2.46 169538.563484 827090.818108
-124 2.48 153838.739168 744452.651831
-125 2.5 139701.665073 670637.92543
-126 2.52 126961.103835 604644.949624
-127 2.54 115469.620781 545592.416037
-128 2.56 105096.332511 492704.141327
-129 2.58 95724.9397832 445295.843157
-130 2.6 87252.0069441 402763.664479
-131 2.62 79585.4554502 364574.203947
-132 2.64 72643.2434671 330255.845328
-133 2.66 66352.2073932 299391.208536
-134 2.68 60647.0444312 271610.570248
-135 2.7 55469.4181565 246586.123584
-136 2.72 50767.1714483 224026.964698
-137 2.74 46493.633237 203674.709811
-138 2.76 42607.0073083 185299.659567
-139 2.78 39069.8329526 168697.439095
-140 2.8 35848.5085794 153686.051901
-141 2.82 32912.8705664 140103.294183
-142 2.84 30235.8206098 127804.483324
-143 2.86 27792.9956998 116660.460548
-144 2.88 25562.4755962 106555.833042
-145 2.9 23524.5233195 97387.4254387
-146 2.92 21661.3547409 89062.9145204
-147 2.94 19956.9338374 81499.6244039
-148 2.96 18396.7906059 74623.4624292
-149 2.98 16967.8589974 68367.9785194
-150 3.0 15658.3325568 62673.5329856
-151 3.02 14457.5357325 57486.5596649
-152 3.04 13355.809067 52758.912937
-153 3.06 12344.4066925 48447.2886046
-154 3.08 11415.4047444 44512.7098736
-155 3.1 10561.6194689 40920.0707567
-156 3.12 9776.5339459 37637.7301715
-157 3.14 9054.23247117 34637.1508274
-158 3.16 8389.34175838 31892.5777179
-159 3.18 7776.97821258 29380.7516608
-160 3.2 7212.7006167 27080.6538766
-161 3.22 6692.4676457 24973.2780793
-162 3.24 6212.59969004 23041.4269669
-163 3.26 5769.74452856 21269.5303734
-164 3.28 5360.84644195 19643.4826615
-165 3.3 4983.1184041 18150.4972204
-166 3.32 4634.01702836 16778.97618
-167 3.34 4311.21998136 15518.393672
-168 3.36 4012.60560869 14359.191159
-169 3.38 3736.23454428 13292.6835236
-170 3.4 3480.33310029 12310.9747549
-171 3.42 3243.27825585 11406.8822043
-172 3.44 3023.58408279 10573.8684961
-173 3.46 2819.88946345 9805.98028003
-174 3.48 2630.94697101 9097.79310596
-175 3.5 2455.61279669 8444.36177626
-176 3.52 2292.83761972 7841.17560602
-177 3.54 2141.65832756 7284.11808108
-178 3.56 2001.19050257 6769.43046025
-179 3.58 1870.62160083 6293.67891689
-180 3.6 1749.20475558 5853.72485855
-181 3.62 1636.25314534 5446.69810179
-182 3.64 1531.13487237 5069.97261409
-183 3.66 1433.26830277 4721.1445646
-184 3.68 1342.11782445 4398.01245332
-185 3.7 1257.18998347 4098.55911171
-186 3.72 1178.02996319 3820.93539003
-187 3.74 1104.21837425 3563.44536511
-188 3.76 1035.36832639 3324.53291993
-189 3.78 971.122756088 3102.76956138
-190 3.8 911.151986554 2896.84335615
-191 3.82 855.151498616 2705.54887715
-192 3.84 802.83989347 2527.77806329
-193 3.86 753.957029799 2362.51190574
-194 3.88 708.262319576 2208.81288195
-195 3.9 665.533168297 2065.81806693
-196 3.92 625.563546756 1932.73285812
-197 3.94 588.162682667 1808.82525631
-198 3.96 553.153861545 1693.42065104
-199 3.98 520.373327227 1585.89706361
-200 4.0 489.669273313 1485.68080556
-201 4.02 460.900917596 1392.24251449
-202 4.04 433.937652306 1305.09353282
-203 4.06 408.6582636 1223.78259822
-204 4.08 384.950214367 1147.89281764
-205 4.1 362.708984933 1077.03889938
-206 4.12 341.837466738 1010.86461999
-207 4.14 322.245404503 949.040505266
-208 4.16 303.848882793 891.261706073
-209 4.18 286.569853265 837.246052066
-210 4.2 270.33569919 786.732267446
-211 4.22 255.078834164 739.47833469
-212 4.24 240.736332164 695.259993326
-213 4.26 227.249586386 653.869362042
-214 4.28 214.563994495 615.113673492
-215 4.3 202.628668126 578.814112106
-216 4.32 191.396164684 544.804746089
-217 4.34 180.822239621 512.931545605
-218 4.36 170.865617553 483.051479815
-219 4.38 161.487780703 455.031686127
-220 4.4 152.652773286 428.748705595
-221 4.42 144.327020575 404.087778912
-222 4.44 136.479161479 380.942197972
-223 4.46 129.07989358 359.212708377
-224 4.48 122.101829632 338.806958688
-225 4.5 115.519364658 319.638992577
-226 4.52 109.308552789 301.628780369
-227 4.54 103.446993117 284.701786758
-228 4.56 97.9137238447 268.788571763
-229 4.58 92.6891241175 253.824422244
-230 4.6 87.7548229339 239.749011508
-231 4.62 83.0936146036 226.506084761
-232 4.64 78.6893802546 214.043168343
-233 4.66 74.5270149351 202.31130085
-234 4.68 70.5923598871 191.264784422
-235 4.7 66.8721396072 180.860954593
-236 4.72 63.353903336 171.05996726
-237 4.74 60.0259706488 161.824601429
-238 4.76 56.8773808439 153.120076496
-239 4.78 53.8978458491 144.913882966
-240 4.8 51.0777063884 137.175625538
-241 4.82 48.4078911713 129.876877635
-242 4.84 45.8798788842 122.991046476
-243 4.86 43.485662782 116.493247913
-244 4.88 41.2177176913 110.360190267
-245 4.9 39.0689692529 104.570066494
-246 4.92 37.0327652428 99.1024540566
-247 4.94 35.102848823 93.9382219092
-248 4.96 33.2733335874 89.05944408
-249 4.98 31.5386802724 84.4493193479
-250 5.0 29.8936750183 80.0920965658
-251 5.02 28.3334090704 75.9730052143
-252 5.04 26.8532598202 72.0781907976
-253 5.06 25.4488730938 68.3946547294
-254 5.08 24.116146599 64.9101983786
-255 5.1 22.8512144543 61.6133709734
-256 5.12 21.650432722 58.4934210835
-257 5.14 20.5103658787 55.5402514226
-258 5.16 19.4277741591 52.7443767307
-259 5.18 18.3996017121 50.0968845179
-260 5.2 17.4229655155 47.5893984632
-261 5.22 16.4951449988 45.2140442802
-262 5.24 15.6135723236 42.9634178757
-263 5.26 14.775823281 40.8305556374
-264 5.28 13.979608762 38.808906703
-265 5.3 13.2227667648 36.8923070701
-266 5.32 12.5032549016 35.0749554196
-267 5.34 11.8191433738 33.3513905323
-268 5.36 11.1686083831 31.7164701895
-269 5.38 10.5499259512 30.1653514539
-270 5.4 9.96146612005 28.693472236
-271 5.42 9.40168750976 27.2965340593
-272 5.44 8.86913220892 25.9704859397
-273 5.46 8.36242097742 24.7115093061
-274 5.48 7.88024874079 23.5160038893
-275 5.5 7.4213803577 22.3805745153
-276 5.52 6.98464664308 21.3020187412
-277 5.54 6.56894063048 20.2773152771
-278 5.56 6.1732140587 19.3036131423
-279 5.58 5.79647406826 18.3782215059
-280 5.6 5.43778009463 17.4986001669
-281 5.62 5.09624094585 16.6623506308
-282 5.64 4.77101205293 15.867207745
-283 5.66 4.46129288233 15.1110318537
-284 5.68 4.16632450031 14.3918014404
-285 5.7 3.88538727999 13.7076062261
-286 5.72 3.61779874199 13.0566406912
-287 5.74 3.36291152072 12.4371979973
-288 5.76 3.12011144838 11.8476642796
-289 5.78 2.8888157497 11.2865132882
-290 5.8 2.66847134042 10.7523013555
-291 5.82 2.45855322349 10.2436626676
-292 5.84 2.25856297681 9.7593048226
-293 5.86 2.06802732724 9.2980046552
-294 5.88 1.88649680546 8.85860431242
-295 5.9 1.71354447704 8.44000756375
-296 5.92 1.548764745 8.04117633127
-297 5.94 1.39177221978 7.66112742597
-298 5.96 1.24220065245 7.29892947717
-299 5.98 1.09970192753 6.9537000433
-300 6.0 0.963945111861 6.62460289254
-301 6.02 0.83461555631 6.31084544295
-302 6.04 0.711414047074 6.01167635216
-303 6.06 0.594056003831 5.72638324756
-304 6.08 0.482270721937 5.45429058822
-305 6.1 0.375800656137 5.19475765055
-306 6.12 0.274400743381 4.94717663025
-307 6.14 0.177837762511 4.71097085338
-308 6.16 0.0858897286772 4.48559308998
-309 6.18 -0.00165467948361 4.27052396409
-310 6.2 -0.0849966617872 4.06527045435
-311 6.22 -0.164327809314 3.8693644797
-312 6.24 -0.239830589745 3.68236156522
-313 6.26 -0.311678806773 3.50383958321
-314 6.28 -0.380038035049 3.33339756513
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-1115 22.3 -0.00394740685922 -0.0200029372512
-1116 22.32 -0.00354788564052 -0.0199492167196
-1117 22.34 -0.0031494369093 -0.0198956883597
-1118 22.36 -0.00275205683071 -0.0198423513132
-1119 22.38 -0.00235574158704 -0.0197892047262
-1120 22.4 -0.00196048737759 -0.0197362477497
-1121 22.42 -0.00156629041861 -0.0196834795391
-1122 22.44 -0.00117314694319 -0.0196308992543
-1123 22.46 -0.000781053201174 -0.0195785060596
-1124 22.48 -0.000390005459079 -0.019526299124
-1125 22.5 0.0 -0.0194742776206
-1126 22.52 0.0 0.0
-1127 22.54 0.0 0.0
-1128 22.56 0.0 0.0
-1129 22.58 0.0 0.0
-1130 22.6 0.0 0.0
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.min
deleted file mode 100644
index 2fc8fbba7..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.min
+++ /dev/null
@@ -1,35 +0,0 @@
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# So, after typing "make yes-user-misc" in to the shell, ...
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-#
-# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
-# then you made a mistake in the instructions above.
-
-
-
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.npt
deleted file mode 100644
index cbf76ac2d..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.npt
+++ /dev/null
@@ -1,66 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
-#
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# So, after typing "make yes-user-misc" in to the shell, ...
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-#
-# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
-# then you made a mistake in the instructions above.
-#
-
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-#read_data system.data
-read_data system_after_min.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-#minimize 1.0e-5 1.0e-7 500 2000
-
-timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
-dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
-
-
-thermo_style custom step temp pe etotal vol epair ebond eangle
-thermo 1000 # time interval for printing out "thermo" data
-
-
-fix fxlan all langevin 300.0 300.0 120 48279
-fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
-
-
-# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
-# (for the "epsilon" used by the coarse-grained lipid), and
-# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
-# Note: The langevin damping parameter "120" corresponds to
-# the 0.12ps damping time used in Watson et. al JCP 2011.
-# Note: We maintain the system system at constant (zero) tention
-# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
-
-
-# optional (not sure if this helps):
-# balance x uniform y uniform
-
-
-run 100000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.nvt
deleted file mode 100644
index 05f533339..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.nvt
+++ /dev/null
@@ -1,71 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-#
-# -------- LAMMPS REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# So, after typing "make yes-user-misc" in to the shell, ...
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-#
-# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
-# then you made a mistake in the instructions above.
-#
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
-dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-
-thermo_style custom step temp pe etotal vol epair ebond eangle
-thermo 1000 # time interval for printing out "thermo" data
-
-
-fix fxlan all langevin 300.0 300.0 120 48279
-fix fxnve all nve
-
-# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
-# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
-# Note: The langevin damping parameter "120" corresponds to
-# the 0.12ps damping time used in Watson et. al JCP 2011.
-
-#restart 500000
-
-run 50000000
-
-
-write_data system_after_nvt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also.)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README.TXT
deleted file mode 100644
index 1bf9d00b9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README.TXT
+++ /dev/null
@@ -1,33 +0,0 @@
-Note:
- This example may require additional features to be added to LAMMPS.
-If LAMMPS complains about an "Invalid pair_style", then copy the code
-in the "additional_lammps_code" directory into your LAMMPS "src" directory
-and recompile LAMMPS.
-
------ Description --------
-
-This example contains an implementation of the DPPC lipid bilayer described in:
- G. Brannigan, P.F. Philips, and F.L.H. Brown,
- Physical Review E, Vol 72, 011915 (2005)
-and:
- M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
- J. Chem. Phys. 135, 244701 (2011)
-
-As in Watson(JCP 2011), rigid bond-length constraints
-have been replaced by harmonic bonds.
-
-A truncated version of this lipid (named "DLPC") has also been added.
-Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
-parameterized to reproduce the correct behavior in a lipid bilayer.
-
-
--------------
-
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh
deleted file mode 100755
index d7ea30569..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" file is a LAMMPS input script containing
-# references to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data, and table_int.dat
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension)
-
-#or
-
-lmp_mpi -i run.in.nvt # Run a simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation are ignored when beginning the simulation at constant volume.
-# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#or
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_setup.sh
deleted file mode 100755
index abf2fce64..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # The "table_int.dat" file contains tabular data for the lipid INT-INT atom
- # 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
- # so I might look for a way to get rid of it later.)
- cp -f table_int.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/images/DLPC.jpg
deleted file mode 100644
index 637f2f1c7..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt
deleted file mode 100644
index aabf2bcc8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt
+++ /dev/null
@@ -1,208 +0,0 @@
-# Note:
-#
-# This example may require additional features to be added to LAMMPS. If
-# LAMMPS complains about an "Invalid pair_style", then download copy the
-# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
-# "src" directory and recompile LAMMPS.
-#
-# -------- Description --------
-#
-# This example contains an implementation of the DPPC lipid bilayer described in
-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
-# Physical Review E, Vol 72, 011915 (2005)
-# and:
-# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
-# J. Chem. Phys. 135, 244701 (2011)
-#
-# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
-# by harmonic bonds.
-#
-# --- DLPC lipids ---
-# A truncated version of the DPPC lipid (named "DLPC") has also been added.
-# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
-# parameterized to reproduce the correct behavior in a lipid bilayer/mixture.
-# (You may need to stiffen the bond-angle forces to make it behave correctly,
-# but I did not do this here.)
-#
-# Units:
-#
-# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
-# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
-# The "sigma" parameter corresponds to 7.5 angstroms.
-#
-#
-# The new DLPC model is a truncated version of DPPC,
-# (Its behaviour has not been rigorously tested.)
-
-
-
-CGLipidBr2005 {
-
-
- write_once("In Init") {
- # -- Default styles for "CGLipidBr2005" --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
-
- angle_style hybrid cosine/delta # <- used in the original article
- #angle_style hybrid harmonic # <- prevents unphysical acute angle turns
- # Explanation:
- # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0))
- # angle_style harmonic: U(theta) = k*(theta-theta0)^2
-
- dihedral_style none
- improper_style none
-
- pair_style hybrid table linear 1130 &
- lj/charmm/coul/charmm/inter es4k4l 14.5 15
-
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
- }
-
-
- DPPC {
- write("Data Atoms") {
- $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
- $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
- $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
- $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
- $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
- }
- write("Data Bonds") {
- $bond:b1 @bond:../backbone $atom:h $atom:i
- $bond:b2 @bond:../backbone $atom:i $atom:t1
- $bond:b3 @bond:../backbone $atom:t1 $atom:t2
- $bond:b4 @bond:../backbone $atom:t2 $atom:t3
- }
- write("Data Angles") {
- $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
- $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
- $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
- }
-
- # Define properties of the local (lipid-specific) atom:head type atom:
- write_once("Data Masses") {
- @atom:head 200.0
- }
- write_once("In Settings") {
- pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- }
-
- } #DPPC
-
-
- DLPC {
- write("Data Atoms") {
- $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
- $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
- $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
- $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
- }
- write("Data Bonds") {
- $bond:b1 @bond:../backbone $atom:h $atom:i
- $bond:b2 @bond:../backbone $atom:i $atom:t1
- $bond:b3 @bond:../backbone $atom:t1 $atom:t2
- }
- write("Data Angles") {
- $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
- $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
- }
- # Define properties of the local (lipid-specific) atom:head type atom:
- write_once("Data Masses") {
- @atom:head 200.0
- }
- write_once("In Settings") {
- pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- }
- } #DLPC
-
-
- # Particles and properties shared by all lipid types:
-
- write_once("Data Masses") {
- @atom:int 200.0
- @atom:tail 200.0
- }
-
- write_once("In Settings") {
- # -- Default settings/parameters for "CGLipidBr2005" --
- # (Hybrid bond & angle styles were used for portability.)
-
- # As in Watson(JCP 2011), rigid bond-length constraints
- # have been replaced by harmonic bonds.
- # The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
- bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
- }
-
- write_once("In Settings") {
-
- # cosine/delta: U(theta) = k*(1-cos(theta-theta0))
- angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
-
- ## Alternately, to stiffen the bond-angles, try this:
- ##angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps
- ## harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2
- ##angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps
- }
- # Note: You may want to use a stiffer bond-angle than the original
- # Brannigan&Brown 2005 paper if you want to mix two different lipids together.
- # (The mixture of lipids introduces a great deal of disorder into the bilayer
- # which would not be present in a DPPC bilayer. This caused pores to form
- # in my simulations. But increasing the angle stiffness prevents this.)
-
- write_once("In Settings") {
-
- # The interaction of "atom:int" with other "atom:int" atoms is given by
- # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
- # r=3*sigma. This was implemented using pair_style table.
- # Unfortunately, mixing lj/charmm and "table" pair styles in the same
- # simulation is very inneficient.
-
- pair_coeff @atom:int @atom:int table table_int.dat INT
-
- # The interaction of tail beads with eachother is given by the formula below
- # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
- # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
- pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
- pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
-
- # The interaction between head beads from different types of lipids
- # is (currently) repulsive:
- pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
-
- } # write_once("In Settings")
-
-
- # Note: I divided epsilon by 4 to get "0.1643" because we are using the
- # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
- # (The "es4k4l" coeffstyle is the default.) Using this convention makes it
- # easier to mix this coarse-grained lipid model with other molecular models.
-
-
-
-} # CGLipidBr2005
-
-
-
-
-
-
-
-
-# Note: This example has not been optimized for speed.
-#
-# Unfortunately, using both lj/charmm and "table" pair styles in the same
-# simulation seems to be very inneficient. (The simulation is twice as slow
-# as using only the "lj/charmm" pair styles for every pairwise interaction,
-# ...and about 25% slower than using "table" for every pairwise interaction.
-# However the lennard-jones pair styles support mixing, so we use them to
-# make it easier to run these molecules with other molecules which don't use
-# pair_table. I felt that portability was worth the extra 25% slow down.)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
deleted file mode 100755
index 0d09e4d02..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between "INT" atoms
-# in the lipid membrane model described in
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
-
-def U(r, eps, sigma):
- return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
-def F(r, eps, sigma):
- return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-
-epsilon = 2.75/4.184 # kCal/mole
-sigma = 7.5
-Rmin = 0.02
-Rmax = 22.6
-rcut = 22.5
-N = 1130
-
-for i in range(0,N):
- r = Rmin + i*(Rmax-Rmin)/(N-1)
- U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
- F_r = F(r, epsilon, sigma)
- if r > rcut:
- U_r = 0.0
- F_r = 0.0
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
deleted file mode 100755
index 32147e444..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between "INT" atoms
-# in the lipid membrane model described in
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-# I realized later this is not what we want because although energy is conserved
-# all enrgies are shifted with respect to energies used in the Brannigan paper
-# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
-# (So don't use this.)
-
-# Calculate and print a
-
-def S(r, rc1, rc2, derivative=False):
- """
- Calculate the switching function S(r) which decays continuously
- between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
- S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
- I'm using the same smoothing/switching cutoff function used by the CHARMM
- force-fields. (I'm even using the same code to implement it, taken
- from lammps charmm/coul/charmm pair style, rewritten in python.)
-
- """
- assert(rc2>rc1)
- rsq = r*r
- rc1sq = rc1*rc1
- rc2sq = rc2*rc2
- denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
- (rc2sq-rc1sq)*
- (rc2sq-rc1sq)))
- if rsq > rc2sq:
- return 0.0
- elif rsq < rc1sq:
- if derivative:
- return 0.0
- else:
- return 1.0
- else:
- rc2sq_minus_rsq = (rc2sq - rsq)
- rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
- if derivative:
- return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
- else:
- return (rc2sq_minus_rsq_sq *
- (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
-
-
-def U(r, eps, sigma):
- return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
-
-def F(r, eps, sigma):
- return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-
-epsilon = 2.75/4.184 # kCal/mole
-sigma = 7.5
-Rmin = 0.02
-Rmax = 22.6
-Rc1 = 22.0
-Rc2 = 22.5
-N = 1130
-
-for i in range(0,N):
- r = Rmin + i*(Rmax-Rmin)/(N-1)
- U_r = U(r, epsilon, sigma)
- F_r = F(r, epsilon, sigma)
- # Multiply U(r) & F(r) by the smoothing/switch function
- U_r = U_r * S(r, Rc1, Rc2)
- F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt
deleted file mode 100644
index c556233c0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt
+++ /dev/null
@@ -1,94 +0,0 @@
-# Description:
-
-# This constructs a bilayer constructed from coarse-grained DPPC lipids
-# (implicit solvent). The DPPC lipid model is described here:
-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
-# Physical Review E, Vol 72, 011915 (2005)
-#
-# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture
-# in the "membrane+protein" and "vesicle" examples.
-
-
-
-
-
-
-import "CGLipidBr2005Orig.lt"
-
-using namespace CGLipidBr2005
-
-lipids = new DPPC [32].move(7.5, 0, 0)
- [37].move(3.75, 6.49519, 0)
- [2].rot(180, 1, 0, 0)
-
-
-# Move the lipds up to the center of the box
-lipids[*][*][*].move(0,0,75.0)
-
-
-# Although this patch of lipids is not square or rectangular, (it looks
-# like a parallelogram), this is no longer the case after rectangular
-# periodic boundary conditions are applied. We apply them below:
-# width: 240 = 32*7.5
-# height: 240.322 = 37*6.49519
-
-write_once("Data Boundary") {
- 0 240 xlo xhi
- 0 240.322 ylo yhi
- 0 150.0 zlo zhi
-}
-
-
-
-
-
-
-
-
-# -------------- File ends here. Only comments below.-------------------
-
-# ------------------------------------
-# ------------- COMMENTS: ------------
-# ------------------------------------
-#
-# A note on geometry:
-# We want to create a bilayer arranged in a hexagonal lattice consisting of
-# 32 rows (each row is aligned with the x-axis)
-# 37 columns (aligned at a 60 degree angle from the x axis)
-# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5)
-# When wrapped onto a rectangular box, the dimensions of the system are:
-# 32 * 7.5 Angstroms in the X direction
-# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction
-# ------------------------------------
-#
-# Below I show simple ways to create a lipid bilayer:
-#
-# 1) If you just want to make lipid bilayer out of DPPC,
-# without specifying the location of each lipid, you could use this syntax:
-# lipids = new DPPC [32][37][2] # 3-D array
-# Later you can load in the coordinates of the lipds from a PDB file.
-# Alternately you could also use a 1-dimensional array:
-# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2
-# It does not matter as long as the number of lipids is correct.
-# Multidimensional arrays are only useful if you plan to apply independent
-# coordinate transformations to each row and column and monolayer. See below:
-#
-# 2) Instead of loading a PDB file later, we can directly specify the location
-# of each DPPC lipid in the LT file itself. For lipid bilayers, this is
-# easy, because the bilayer structure resembles 2 planar lattices.
-# We can use "move" commands to place each lipid, and the "rot" command
-# to turn the lipids in one of the monolayers upside down.
-#
-# lipids = new DPPC [32].move(7.5, 0, 0)
-# [37].move(3.75, 6.49519, 0)
-# [2].rot(180, 1, 0, 0)
-#
-# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must
-# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345)
-# Here "0.5,0.5" are the probabilities for each molecule type, and "12345"
-# is an optional random seed.
-# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345)
-# [32].move(7.5, 0, 0)
-# [37].move(3.75, 6.49519, 0)
-# [2].rot(180, 1, 0, 0)
-#
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
deleted file mode 100644
index b0d651d67..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
+++ /dev/null
@@ -1,1139 +0,0 @@
-# Table for the INT-INT interaction from
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# This table contains
-# i r_i U(r_i) -dU/dr|r_i
-# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-
-INT
-N 1130
-
-1 0.02 2.0331818401e+30 1.21990910406e+33
-2 0.04 4.9638228518e+26 1.48914685554e+29
-3 0.06 3.82579033251e+24 7.65158066501e+26
-4 0.08 1.21187081343e+23 1.81780622014e+25
-5 0.1 8.32791281704e+21 9.99349538045e+23
-6 0.12 9.34030842897e+20 9.34030842897e+22
-7 0.14 1.46892540453e+20 1.25907891817e+22
-8 0.16 2.95866897809e+19 2.21900173357e+21
-9 0.18 7.19889946863e+18 4.79926631242e+20
-10 0.2 2.0331818401e+18 1.21990910406e+20
-11 0.22 6.47834392264e+17 3.53364213962e+19
-12 0.24 2.28034873754e+17 1.14017436877e+19
-13 0.26 8.72681951932e+16 4.02776285507e+18
-14 0.28 3.58624366341e+16 1.53696157003e+18
-15 0.3 1.56704372019e+16 6.26817488078e+17
-16 0.32 7.2233129348e+15 2.70874235055e+17
-17 0.34 3.48970861422e+15 1.23166186384e+17
-18 0.36 1.75754381558e+15 5.85847938527e+16
-19 0.38 9.18613895646e+14 2.90088598625e+16
-20 0.4 4.96382285179e+14 1.48914685554e+16
-21 0.42 2.76404230108e+14 7.89726371739e+15
-22 0.44 1.58162693423e+14 4.31352800247e+15
-23 0.46 9.27773983256e+13 2.42027995633e+15
-24 0.48 5.56725765996e+13 1.391814415e+15
-25 0.5 3.41111308981e+13 8.18667141564e+14
-26 0.52 2.13057117167e+13 4.91670270393e+14
-27 0.54 1.35459994024e+13 3.0102220895e+14
-28 0.56 8.75547769351e+12 1.87617379153e+14
-29 0.58 5.74645813711e+12 1.18892237325e+14
-30 0.6 3.8257903322e+12 7.65158066491e+13
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-1112 22.24 -0.00515244404737 -0.0201652605278
-1113 22.26 -0.00474968218459 -0.0201109582853
-1114 22.28 -0.00434800441746 -0.0200568508172
-1115 22.3 -0.00394740685922 -0.0200029372512
-1116 22.32 -0.00354788564052 -0.0199492167196
-1117 22.34 -0.0031494369093 -0.0198956883597
-1118 22.36 -0.00275205683071 -0.0198423513132
-1119 22.38 -0.00235574158704 -0.0197892047262
-1120 22.4 -0.00196048737759 -0.0197362477497
-1121 22.42 -0.00156629041861 -0.0196834795391
-1122 22.44 -0.00117314694319 -0.0196308992543
-1123 22.46 -0.000781053201174 -0.0195785060596
-1124 22.48 -0.000390005459079 -0.019526299124
-1125 22.5 0.0 -0.0194742776206
-1126 22.52 0.0 0.0
-1127 22.54 0.0 0.0
-1128 22.56 0.0 0.0
-1129 22.58 0.0 0.0
-1130 22.6 0.0 0.0
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.min
deleted file mode 100644
index 6cbb92ad8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.min
+++ /dev/null
@@ -1,28 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# Optional: Make sure the pairwise energies look reasonable:
-#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0
-#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0
-#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0
-#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0
-#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0
-#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0
-
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.npt
deleted file mode 100644
index ab37d34b3..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.npt
+++ /dev/null
@@ -1,57 +0,0 @@
-# -------- REQUIREMENTS: ---------
-# 1) This example may require additional features and bug fixes for LAMMPS.
-# Be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 2) Unpack it
-# 3) copy the .cpp and .h files to the src folding of your lammps installation.
-# 4) Compile LAMMPS.
-#
-# (If LAMMPS complains about an "Invalid pair_style"
-# then you made a mistake in the instructions above.)
-#
-
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
-dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz
-
-
-thermo_style custom step temp pe etotal vol epair ebond eangle
-thermo 1000 # time interval for printing out "thermo" data
-
-
-fix fxlan all langevin 300.0 300.0 120 48279
-fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
-
-
-# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
-# for the "epsilon" used by the coarse-grained lipid.
-# Note: The langevin damping parameter "120" corresponds to
-# the 0.12ps damping time used in Watson et. al JCP 2011.
-# Note: We maintain the system system at constant (zero) tention
-# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
-
-
-# optional (not sure if this helps):
-# balance x uniform y uniform
-
-
-#restart 1000000
-
-run 2000000
-
-write_data system_after_npt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.nvt
deleted file mode 100644
index 63d4cde4a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/run.in.nvt
+++ /dev/null
@@ -1,45 +0,0 @@
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-
-# Normally, I would minimize the system and equilibrate the system at constant
-# pressure and temperature beforehand. If you run lammps with "run.in.npt",
-# it will generate a data file "system_after_npt.data" with reasonable
-# coordinates at that temperature and pressure. Then we could load it now:
-#
-#read_data system_after_npt.data
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
-dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-
-thermo_style custom step temp pe etotal vol epair ebond eangle
-thermo 1000 # time interval for printing out "thermo" data
-
-
-fix fxlan all langevin 300.0 300.0 120 48279
-fix fxnve all nve
-
-# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
-# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
-# Note: The langevin damping parameter "120" corresponds to
-# the 0.12ps damping time used in Watson et. al JCP 2011.
-
-#restart 1000000
-
-run 1000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/README.TXT
deleted file mode 100644
index 31abcd66e..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/README.TXT
+++ /dev/null
@@ -1,33 +0,0 @@
-# This directory contains examples of how to run a short simulation of a
-# coarse-grained protein-like polymer, folding in the presence and absence of
-# a chaperone (modeled as an attractive or repulsie spherical shell).
-#
-# The protein models and the chaperone models are described and used here:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-# ...and also here:
-# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006)
-#
-# (In the "frustrated+minichaperone" directory, the protein is
-# placed outside the chaperone sphere, as opposed to inside.)
-#
-# -------- REQUIREMENTS: ---------
-# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) They also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-#
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files in each directory.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT
deleted file mode 100644
index a52f73ff7..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT
+++ /dev/null
@@ -1,32 +0,0 @@
-# This directory demonstrates how to run a long simulation of
-# the "frustrated" coarse-grained protein confined in a frustrated
-# coarse-grained chaperonin (R=6, h=0.475) as described in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-#
-# Note: If you want to use a "hydrophilic" chaperone (with h=0.0
-# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475"
-# (at the end of "system.lt") with "CHAP_INTERIOR_H0"
-#
-# Because this process takes a long time (even with the help of the chaperone)
-# I save the data relatively infrequently.
-#
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh
deleted file mode 100755
index d5ae1fe5a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# You would probably run lammps this way:
-#
-# lmp_ubuntu -i run.in.nvt
-
-# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
-# to the input scripts & data files you created earlier when you ran moltemplate
-# system.in.init, system.in.settings, system.data
-
-
-
-
-# -----------------------------------
-
-
-
-LAMMPS_COMMAND="lmp_mpi"
-
-# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary.
-
-# Run lammps using the following 3 commands:
-
-"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-"$LAMMPS_COMMAND" -i run.in.nvt # production run
-
-# Alternately, if you have MPI installed, try something like this:
-
-#NUMPROCS=4
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh
deleted file mode 100755
index df49f4384..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -overlay-dihedrals system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
- cp -r table*.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
deleted file mode 100644
index 9e34246f8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
+++ /dev/null
@@ -1,86 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 28 !NATOM
- 1 1 2 2 0.000000 1.0000 0
- 2 1 1 1 0.000000 1.0000 0
- 3 1 2 2 0.000000 1.0000 0
- 4 1 1 1 0.000000 1.0000 0
- 5 1 2 2 0.000000 1.0000 0
- 6 1 1 1 0.000000 1.0000 0
- 7 1 3 3 0.000000 1.0000 0
- 8 1 3 3 0.000000 1.0000 0
- 9 1 1 1 0.000000 1.0000 0
- 10 1 2 2 0.000000 1.0000 0
- 11 1 1 1 0.000000 1.0000 0
- 12 1 2 2 0.000000 1.0000 0
- 13 1 1 1 0.000000 1.0000 0
- 14 1 2 2 0.000000 1.0000 0
- 15 1 3 3 0.000000 1.0000 0
- 16 1 3 3 0.000000 1.0000 0
- 17 1 3 3 0.000000 1.0000 0
- 18 1 1 1 0.000000 1.0000 0
- 19 1 1 1 0.000000 1.0000 0
- 20 1 2 2 0.000000 1.0000 0
- 21 1 2 2 0.000000 1.0000 0
- 22 1 1 1 0.000000 1.0000 0
- 23 1 1 1 0.000000 1.0000 0
- 24 1 2 2 0.000000 1.0000 0
- 25 1 2 2 0.000000 1.0000 0
- 26 1 1 1 0.000000 1.0000 0
- 27 1 2 2 0.000000 1.0000 0
- 28 2 4 4 0.000000 100.0000 0
-
- 26 !NBOND: bonds
- 1 2 2 3 3 4 4 5
- 5 6 6 7 7 8 8 9
- 9 10 10 11 11 12 12 13
- 13 14 14 15 15 16 16 17
- 17 18 18 19 19 20 20 21
- 21 22 22 23 23 24 24 25
- 25 26 26 27
-
- 25 !NTHETA: angles
- 13 14 15 7 8 9 6 7 8
- 16 17 18 15 16 17 2 3 4
- 4 5 6 9 10 11 11 12 13
- 14 15 16 1 2 3 3 4 5
- 10 11 12 12 13 14 25 26 27
- 5 6 7 8 9 10 17 18 19
- 18 19 20 22 23 24 21 22 23
- 19 20 21 20 21 22 23 24 25
- 24 25 26
-
- 19 !NPHI: dihedrals
- 1 2 3 4 2 3 4 5
- 3 4 5 6 4 5 6 7
- 8 9 10 11 9 10 11 12
- 10 11 12 13 11 12 13 14
- 12 13 14 15 15 16 17 18
- 16 17 18 19 17 18 19 20
- 18 19 20 21 19 20 21 22
- 20 21 22 23 21 22 23 24
- 22 23 24 25 23 24 25 26
- 24 25 26 27
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg
deleted file mode 100644
index 31853cd5a..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg
deleted file mode 100644
index fdc5c890b..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt
deleted file mode 100644
index e43026ba9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt
+++ /dev/null
@@ -1,216 +0,0 @@
-# This file defines the "frustrated" coarse-grained protein model used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-
-
-1beadFrustrated {
-
- # There are 3 atom types (referred to above as B, L, and N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:B 1.0
- @atom:L 1.0
- @atom:N 1.0
- }
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679
- $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341
- $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966
- $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709
- $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737
- $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098
- $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919
- $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901
- $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617
- $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043
- $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721
- $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951
- $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019
- $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217
- $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429
- $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711
- $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358
- $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719
- $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014
- $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053
- $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748
- $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224
- $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255
- $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346
- $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166
- $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097
- $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463
- }
-
- # bond-ID bond-Type atom-ID atom-ID
-
- write('Data Bonds') {
- $bond:b1 @bond:backbone $atom:a1 $atom:a2
- $bond:b2 @bond:backbone $atom:a2 $atom:a3
- $bond:b3 @bond:backbone $atom:a3 $atom:a4
- $bond:b4 @bond:backbone $atom:a4 $atom:a5
- $bond:b5 @bond:backbone $atom:a5 $atom:a6
- $bond:b6 @bond:backbone $atom:a6 $atom:a7
- $bond:b7 @bond:backbone $atom:a7 $atom:a8
- $bond:b8 @bond:backbone $atom:a8 $atom:a9
- $bond:b9 @bond:backbone $atom:a9 $atom:a10
- $bond:b10 @bond:backbone $atom:a10 $atom:a11
- $bond:b11 @bond:backbone $atom:a11 $atom:a12
- $bond:b12 @bond:backbone $atom:a12 $atom:a13
- $bond:b13 @bond:backbone $atom:a13 $atom:a14
- $bond:b14 @bond:backbone $atom:a14 $atom:a15
- $bond:b15 @bond:backbone $atom:a15 $atom:a16
- $bond:b16 @bond:backbone $atom:a16 $atom:a17
- $bond:b17 @bond:backbone $atom:a17 $atom:a18
- $bond:b18 @bond:backbone $atom:a18 $atom:a19
- $bond:b19 @bond:backbone $atom:a19 $atom:a20
- $bond:b20 @bond:backbone $atom:a20 $atom:a21
- $bond:b21 @bond:backbone $atom:a21 $atom:a22
- $bond:b22 @bond:backbone $atom:a22 $atom:a23
- $bond:b23 @bond:backbone $atom:a23 $atom:a24
- $bond:b24 @bond:backbone $atom:a24 $atom:a25
- $bond:b25 @bond:backbone $atom:a25 $atom:a26
- $bond:b26 @bond:backbone $atom:a26 $atom:a27
- }
-
- # (3-body) Angles are specified below
-
- # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
- # (These interactions are not determined by atom type.)
-
- # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
-
- write('Data Dihedrals') {
-
- $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7
-
- # Dihedral angle forces in the turn regions were switched off
- # (in this model) so just I comment them out (and \ the variable names).
- # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8
- # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9
- # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10
-
- $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15
-
- # Dihedral angle forces in the turn regions were switched off
- # (in this model) so just I comment them out (and \ the variable names).
- # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16
- # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17
-
- $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27
- }
-
- # All consecutively bonded triplets of atoms same 3-body bond-angle
- # interaction parameters. Of coarse, we could specify them all explicitly
- # (as we did for the dihedrals above), but I wanted to show how to specify
- # angles by atom type instead. (You can do this for dihedrals & impropers
- # also.)
-
- # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
-
- write_once('Data Angles By Type') {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # (The "*" is a wildcard character. I use "*" to denote any atom-type or
- # bond-type which is defined within the current namespace: 1beadFrustrated)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
- pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
- pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
- }
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond-Type bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 100.0 1.0
- }
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # angle-Type anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 13.3333333333 105.0
- }
-
-
- # We use tabular dihedral potentials to implement the dihedral forces.
- # (Actually there is a way to use Fourier series, using multiple charmm
- # style dihedral interactions, but it's slower and messier.)
-
- write_once("In Settings") {
- # style file keyword
- dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
- dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
- # No need to specify dihedral interactions in the turn regions. (none exist)
- }
-
- write_once("In Settings") {
- # Optional: define the atoms in the "proteins" group
- group proteins type @atom:B
- group proteins type @atom:L
- group proteins type @atom:N
- }
-
- # LAMMPS has many available force field styles (and atom styles).
- # Here, we pick the ones which work well for this molecular model:
-
- write_once("In Init") {
- # --- Default options for the "1BeadFrustrated" protein model ---
- # --- (These can be overridden later.) ---
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid table spline 360
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-} # 1beadFrustrated
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt
deleted file mode 100644
index 54e2de437..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt
+++ /dev/null
@@ -1,85 +0,0 @@
-import "1beadFrustrated.lt"
-
-
-# Alternate starting conformation (same molecule):
-
-
-1beadMisfolded inherits 1beadFrustrated {
-
- # This molecule "inherits" all of its features from "1beadFrustrated".
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876
- $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251
- $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085
- $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451
- $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135
- $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977
- $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409
- $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275
- $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938
- $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398
- $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186
- $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916
- $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704
- $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331
- $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056
- $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167
- $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633
- $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523
- $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791
- $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346
- $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555
- $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946
- $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493
- $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934
- $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086
- $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181
- $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868
- }
-
-} # 1beadMisfolded
-
-
-1beadUnfolded inherits 1beadFrustrated {
-
- # This molecule "inherits" all of its features from "1beadFrustrated"
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
- $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
- $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
- $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
- $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
- $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
- $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
- $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
- $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
- $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
- $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
- $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
- $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
- $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
- $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
- $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
- $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
- $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
- $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
- $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
- $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
- $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
- $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
- $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
- $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
- $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
- $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
- }
-
-} # 1beadUnfolded
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt
deleted file mode 100644
index 8266d2a89..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt
+++ /dev/null
@@ -1,41 +0,0 @@
-# Here we define a trivial molecule containing only one particle.
-
-Chaperonin {
-
- # atomID molID atomType charge x y z
-
- write("Data Atoms") {
- $atom:C $mol @atom:C 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:C 100.0
- }
-
- write_once("In Settings") {
- # If for some reason there are multiple chaperones present,
- # I assume that they interact repulsively (hence, L=0)
- # i j epsilon sigma K L
-
- pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0
-
- # Optional: define the atoms in the "chaperonins" group:
- # (Defining a group for the chaperone makes it easy to immobilize it later.)
-
- group chaperonins type @atom:C
- }
-
-
- # Specify which pair_styles, and atom styles work well with
- # this model. (Again this can be overridden later.)
-
- write_once("In Init") {
- units lj
- atom_style full
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0
- }
-
-} # Chaperonin
-
-# We have not specified how this particle interacts with other particles
-# besides itself. Later on you must do this.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
deleted file mode 100755
index 9b86809cc..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between atoms in the
-# protein and a chaperone provided in the supplemental materials section of:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# This is stored in a tabulated force field with a singularity at a distance R.
-#
-# To calculate the table for interaction between
-# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
-# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181
-# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
-# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True
-
-from math import *
-import sys
-
-def U(r, eps, sigma, R, h):
- #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
- # Formula is undefined at r=0, but you can take the limit:
- if r <= 0:
- return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
- - h*pow((sigma/R), 6.0))
- xp = sigma/(r+R)
- xm = sigma/(r-R)
- term10 = pow(xm, 10.0) - pow(xp, 10.0)
- term4 = pow(xm, 4.0) - pow(xp, 4.0)
- return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
-
-def F(r, eps, sigma, R, h):
- # Formula is undefined at r=0, but you can take the limit:
- if r <= 0:
- return 0.0
- product_term_a = U(r, eps, sigma, R, h) / r
- ixp = (r+R)/sigma
- ixm = (r-R)/sigma
- dix_dr = 1.0/sigma
- term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
- term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0))
- product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
- return product_term_a + product_term_b
-
-
-class InputError(Exception):
- """ A generic exception object containing a string for error reporting.
-
- """
- def __init__(self, err_msg):
- self.err_msg = err_msg
- def __str__(self):
- return self.err_msg
- def __repr__(self):
- return str(self)
-
-if len(sys.argv) < 8:
- sys.stderr.write("Error: expected 7 arguments:\n"
- "\n"
- "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
- sys.exit(-1)
-
-epsilon = float(sys.argv[1])
-sigma = float(sys.argv[2])
-R = float(sys.argv[3])
-h = float(sys.argv[4])
-rmin = float(sys.argv[5])
-rmax = float(sys.argv[6])
-N = int(sys.argv[7])
-
-subtract_Urcut = False
-if len(sys.argv) == 9:
- subtract_Urcut = True
-rcut = rmax
-
-for i in range(0,N):
- r = rmin + i*(rmax-rmin)/(N-1)
- U_r = U(r, epsilon, sigma, R, h)
- F_r = F(r, epsilon, sigma, R, h)
- if subtract_Urcut:
- U_r -= U(rcut, epsilon, sigma, R, h)
- if (r >= rcut) or (i==N-1):
- U_r = 0.0
- F_r = 0.0
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py
deleted file mode 100755
index 34c66418a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of dihedral angle interactions used in the alpha-helix
-# and beta-sheet regions of the frustrated protein model described in
-# provided in figure 8 of the supplemental materials section of:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# Note that the "A" and "B" parameters were incorrectly reported to be
-# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
-# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
-# and 180 degrees, respectively. Both expA and expB were 6.0.
-#
-# To generate the table used for the alpha-helix (1 degree resolution) use this:
-# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
-# To generate the table used for the beta-sheets (1 degree resolution) use this:
-# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
-#
-# (If you're curious as to why I set the location of the minima at phi_alpha
-# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
-# I think the correct value turns out to be something closer to 50 degrees.)
-
-
-from math import *
-import sys
-
-
-# The previous version included the repulsive core term
-def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
- conv_units = pi/180.0
- if use_radians:
- conv_units = 1.0
- termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
- termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
- return -A*termA - B*termB
-
-# The previous version included the repulsive core term
-def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
- conv_units = pi/180.0
- if use_radians:
- conv_units = 1.0
- termA = (0.5*sin(0.5*(phi-phiA)*conv_units) *
- expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
- termB = (0.5*sin(0.5*(phi-phiB)*conv_units) *
- expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
- return -conv_units*(A*termA + B*termB)
-
-if len(sys.argv) != 10:
- sys.stderr.write("Error: expected 9 arguments:\n"
- "\n"
- "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
- sys.exit(-1)
-
-A = float(sys.argv[1])
-phiA = float(sys.argv[2])
-expA = float(sys.argv[3])
-B = float(sys.argv[4])
-phiB = float(sys.argv[5])
-expB = float(sys.argv[6])
-phi_min = float(sys.argv[7])
-phi_max = float(sys.argv[8])
-N = int(sys.argv[9])
-
-for i in range(0,N):
- phi = phi_min + i*(phi_max - phi_min)/(N-1)
- U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
- F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
- print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt
deleted file mode 100644
index d70ea9b1f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt
+++ /dev/null
@@ -1,45 +0,0 @@
-write_once("Data Boundary") {
- 0.0 20.0 xlo xhi
- 0.0 20.0 ylo yhi
- 0.0 20.0 zlo zhi
-}
-
-
-import "1beadFrustrated_variants.lt"
-import "chaperonin.lt"
-
-
-protein = new 1beadMisfolded # (frustrated protein, misfolded conformation)
-chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile)
-
-
-
-# ---- Now define interactions between the atoms in the protein ----
-# ---- (named "B", "L", "N") and the atom which represents the ----
-# ---- chaperone ("C"). These interactions are tabulated. ----
-
-write_once("In Settings") {
- pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475
- pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0
- pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0
-}
-
-# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475)
-# then replace "table_chaperonin_h=0_475.dat CH_H0.475"
-# with "table_chaperonin_h=0.dat CH_H0"
-
-# LAMMPS has many available force field styles (and atom styles). Here we
-# select the ones which work well for the full combine system. (This should
-# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt")
-
-
-write_once("In Init") {
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid table spline 360
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
deleted file mode 100644
index 675d228a9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
+++ /dev/null
@@ -1,1188 +0,0 @@
-# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475).
-# LAMMPS would crash unless I set the minimum radius to a positive value (not 0)
-
-CH_H0.475
-N 1181 R 0.00000000001 5.9
-
-1 0.00000000001 -0.018422088583 0.0
-2 0.005 -0.0184221525389 2.55824082873e-05
-3 0.01 -0.0184223444081 5.11654127471e-05
-4 0.015 -0.018422664195 7.67496107175e-05
-5 0.02 -0.0184231119071 0.000102335598797
-6 0.025 -0.018423687555 0.000127923973785
-7 0.03 -0.0184243911519 0.000153515332637
-8 0.035 -0.0184252227143 0.000179110272379
-9 0.04 -0.0184261822615 0.000204709390236
-10 0.045 -0.0184272698161 0.000230313283607
-11 0.05 -0.0184284854033 0.000255922550119
-12 0.055 -0.0184298290516 0.000281537787625
-13 0.06 -0.0184313007922 0.000307159594253
-14 0.065 -0.0184329006595 0.000332788568419
-15 0.07 -0.0184346286908 0.000358425308862
-16 0.075 -0.0184364849265 0.000384070414671
-17 0.08 -0.0184384694099 0.000409724485298
-18 0.085 -0.0184405821873 0.000435388120601
-19 0.09 -0.018442823308 0.000461061920867
-20 0.095 -0.0184451928244 0.000486746486835
-21 0.1 -0.0184476907918 0.000512442419724
-22 0.105 -0.0184503172686 0.00053815032126
-23 0.11 -0.018453072316 0.000563870793707
-24 0.115 -0.0184559559985 0.00058960443989
-25 0.12 -0.0184589683834 0.000615351863219
-26 0.125 -0.0184621095411 0.000641113667723
-27 0.13 -0.018465379545 0.000666890458074
-28 0.135 -0.0184687784716 0.000692682839612
-29 0.14 -0.0184723064004 0.000718491418378
-30 0.145 -0.0184759634138 0.000744316801133
-31 0.15 -0.0184797495974 0.000770159595394
-32 0.155 -0.0184836650398 0.000796020409456
-33 0.16 -0.0184877098326 0.000821899852421
-34 0.165 -0.0184918840704 0.000847798534223
-35 0.17 -0.018496187851 0.000873717065662
-36 0.175 -0.0185006212752 0.000899656058423
-37 0.18 -0.0185051844467 0.000925616125112
-38 0.185 -0.0185098774726 0.000951597879278
-39 0.19 -0.0185147004627 0.000977601935442
-40 0.195 -0.0185196535301 0.00100362890913
-41 0.2 -0.018524736791 0.00102967941688
-42 0.205 -0.0185299503645 0.00105575407632
-43 0.21 -0.018535294373 0.00108185350613
-44 0.215 -0.0185407689419 0.00110797832612
-45 0.22 -0.0185463741997 0.00113412915723
-46 0.225 -0.0185521102779 0.00116030662158
-47 0.23 -0.0185579773113 0.00118651134249
-48 0.235 -0.0185639754378 0.00121274394448
-49 0.24 -0.0185701047983 0.00123900505337
-50 0.245 -0.0185763655369 0.00126529529622
-51 0.25 -0.0185827578008 0.00129161530144
-52 0.255 -0.0185892817405 0.00131796569874
-53 0.26 -0.0185959375095 0.00134434711924
-54 0.265 -0.0186027252645 0.00137076019543
-55 0.27 -0.0186096451653 0.00139720556125
-56 0.275 -0.018616697375 0.00142368385209
-57 0.28 -0.0186238820597 0.00145019570482
-58 0.285 -0.018631199389 0.00147674175783
-59 0.29 -0.0186386495354 0.00150332265107
-60 0.295 -0.0186462326747 0.00152993902605
-61 0.3 -0.0186539489859 0.00155659152589
-62 0.305 -0.0186617986512 0.00158328079535
-63 0.31 -0.0186697818562 0.00161000748085
-64 0.315 -0.0186778987894 0.00163677223051
-65 0.32 -0.018686149643 0.00166357569418
-66 0.325 -0.018694534612 0.00169041852345
-67 0.33 -0.0187030538949 0.00171730137172
-68 0.335 -0.0187117076935 0.0017442248942
-69 0.34 -0.0187204962128 0.00177118974793
-70 0.345 -0.018729419661 0.00179819659187
-71 0.35 -0.0187384782498 0.00182524608685
-72 0.355 -0.018747672194 0.00185233889566
-73 0.36 -0.018757001712 0.00187947568307
-74 0.365 -0.0187664670253 0.00190665711585
-75 0.37 -0.0187760683587 0.0019338838628
-76 0.375 -0.0187858059405 0.00196115659479
-77 0.38 -0.0187956800024 0.00198847598479
-78 0.385 -0.0188056907793 0.00201584270792
-79 0.39 -0.0188158385095 0.00204325744145
-80 0.395 -0.0188261234348 0.00207072086484
-81 0.4 -0.0188365458004 0.00209823365979
-82 0.405 -0.0188471058549 0.00212579651027
-83 0.41 -0.0188578038501 0.00215341010252
-84 0.415 -0.0188686400416 0.00218107512514
-85 0.42 -0.0188796146882 0.00220879226907
-86 0.425 -0.0188907280523 0.00223656222766
-87 0.43 -0.0189019803997 0.00226438569667
-88 0.435 -0.0189133719996 0.00229226337435
-89 0.44 -0.0189249031249 0.00232019596142
-90 0.445 -0.0189365740519 0.00234818416114
-91 0.45 -0.0189483850604 0.00237622867935
-92 0.455 -0.0189603364338 0.00240433022447
-93 0.46 -0.0189724284589 0.00243248950756
-94 0.465 -0.0189846614263 0.00246070724235
-95 0.47 -0.0189970356299 0.00248898414528
-96 0.475 -0.0190095513675 0.00251732093553
-97 0.48 -0.0190222089403 0.00254571833504
-98 0.485 -0.0190350086531 0.00257417706858
-99 0.49 -0.0190479508144 0.00260269786377
-100 0.495 -0.0190610357364 0.00263128145108
-101 0.5 -0.0190742637348 0.00265992856393
-102 0.505 -0.0190876351291 0.0026886399387
-103 0.51 -0.0191011502425 0.00271741631474
-104 0.515 -0.0191148094019 0.00274625843445
-105 0.52 -0.0191286129377 0.00277516704329
-106 0.525 -0.0191425611844 0.00280414288981
-107 0.53 -0.0191566544799 0.00283318672573
-108 0.535 -0.0191708931662 0.00286229930593
-109 0.54 -0.0191852775888 0.00289148138852
-110 0.545 -0.0191998080972 0.00292073373487
-111 0.55 -0.0192144850445 0.00295005710962
-112 0.555 -0.0192293087879 0.00297945228079
-113 0.56 -0.0192442796883 0.00300892001972
-114 0.565 -0.0192593981104 0.00303846110121
-115 0.57 -0.0192746644228 0.00306807630348
-116 0.575 -0.0192900789982 0.00309776640827
-117 0.58 -0.0193056422131 0.00312753220084
-118 0.585 -0.0193213544477 0.00315737447002
-119 0.59 -0.0193372160865 0.00318729400826
-120 0.595 -0.0193532275179 0.00321729161167
-121 0.6 -0.0193693891341 0.00324736808004
-122 0.605 -0.0193857013315 0.00327752421692
-123 0.61 -0.0194021645104 0.00330776082963
-124 0.615 -0.0194187790753 0.00333807872931
-125 0.62 -0.0194355454345 0.00336847873097
-126 0.625 -0.0194524640008 0.00339896165353
-127 0.63 -0.0194695351906 0.00342952831985
-128 0.635 -0.0194867594249 0.00346017955681
-129 0.64 -0.0195041371285 0.00349091619529
-130 0.645 -0.0195216687306 0.00352173907028
-131 0.65 -0.0195393546644 0.00355264902089
-132 0.655 -0.0195571953673 0.0035836468904
-133 0.66 -0.0195751912812 0.0036147335263
-134 0.665 -0.019593342852 0.00364590978035
-135 0.67 -0.0196116505298 0.00367717650862
-136 0.675 -0.0196301147693 0.00370853457151
-137 0.68 -0.0196487360292 0.00373998483385
-138 0.685 -0.0196675147727 0.0037715281649
-139 0.69 -0.0196864514674 0.00380316543841
-140 0.695 -0.0197055465851 0.00383489753267
-141 0.7 -0.0197248006022 0.00386672533057
-142 0.705 -0.0197442139994 0.00389864971962
-143 0.71 -0.0197637872619 0.00393067159203
-144 0.715 -0.0197835208793 0.00396279184472
-145 0.72 -0.0198034153458 0.00399501137941
-146 0.725 -0.0198234711601 0.00402733110266
-147 0.73 -0.0198436888254 0.00405975192588
-148 0.735 -0.0198640688494 0.00409227476545
-149 0.74 -0.0198846117446 0.00412490054269
-150 0.745 -0.0199053180279 0.004157630184
-151 0.75 -0.0199261882211 0.00419046462082
-152 0.755 -0.0199472228503 0.00422340478976
-153 0.76 -0.0199684224468 0.00425645163261
-154 0.765 -0.019989787546 0.00428960609639
-155 0.77 -0.0200113186887 0.00432286913342
-156 0.775 -0.0200330164199 0.00435624170138
-157 0.78 -0.0200548812898 0.00438972476334
-158 0.785 -0.0200769138533 0.00442331928783
-159 0.79 -0.0200991146701 0.00445702624889
-160 0.795 -0.0201214843048 0.00449084662613
-161 0.8 -0.020144023327 0.00452478140479
-162 0.805 -0.0201667323112 0.00455883157576
-163 0.81 -0.0201896118368 0.0045929981357
-164 0.815 -0.0202126624882 0.00462728208704
-165 0.82 -0.020235884855 0.00466168443808
-166 0.825 -0.0202592795316 0.00469620620299
-167 0.83 -0.0202828471177 0.00473084840195
-168 0.835 -0.0203065882181 0.00476561206114
-169 0.84 -0.0203305034425 0.00480049821283
-170 0.845 -0.0203545934061 0.00483550789544
-171 0.85 -0.0203788587291 0.00487064215359
-172 0.855 -0.020403300037 0.00490590203817
-173 0.86 -0.0204279179606 0.00494128860638
-174 0.865 -0.020452713136 0.00497680292184
-175 0.87 -0.0204776862045 0.00501244605461
-176 0.875 -0.020502837813 0.00504821908124
-177 0.88 -0.0205281686136 0.00508412308491
-178 0.885 -0.020553679264 0.00512015915539
-179 0.89 -0.0205793704271 0.0051563283892
-180 0.895 -0.0206052427716 0.0051926318896
-181 0.9 -0.0206312969716 0.00522907076671
-182 0.905 -0.0206575337068 0.00526564613755
-183 0.91 -0.0206839536624 0.00530235912611
-184 0.915 -0.0207105575293 0.00533921086343
-185 0.92 -0.0207373460042 0.00537620248763
-186 0.925 -0.0207643197892 0.00541333514403
-187 0.93 -0.0207914795926 0.0054506099852
-188 0.935 -0.020818826128 0.00548802817101
-189 0.94 -0.0208463601151 0.00552559086871
-190 0.945 -0.0208740822795 0.00556329925304
-191 0.95 -0.0209019933525 0.00560115450624
-192 0.955 -0.0209300940713 0.00563915781816
-193 0.96 -0.0209583851794 0.00567731038631
-194 0.965 -0.020986867426 0.00571561341599
-195 0.97 -0.0210155415663 0.00575406812027
-196 0.975 -0.021044408362 0.00579267572016
-197 0.98 -0.0210734685804 0.00583143744461
-198 0.985 -0.0211027229954 0.00587035453065
-199 0.99 -0.0211321723867 0.00590942822342
-200 0.995 -0.0211618175407 0.00594865977625
-201 1.0 -0.0211916592497 0.00598805045079
-202 1.005 -0.0212216983125 0.00602760151701
-203 1.01 -0.0212519355343 0.00606731425336
-204 1.015 -0.0212823717267 0.00610718994679
-205 1.02 -0.0213130077075 0.00614722989286
-206 1.025 -0.0213438443015 0.00618743539581
-207 1.03 -0.0213748823396 0.00622780776866
-208 1.035 -0.0214061226595 0.00626834833326
-209 1.04 -0.0214375661055 0.00630905842043
-210 1.045 -0.0214692135285 0.00634993936999
-211 1.05 -0.0215010657862 0.00639099253086
-212 1.055 -0.0215331237431 0.00643221926118
-213 1.06 -0.0215653882704 0.00647362092835
-214 1.065 -0.0215978602462 0.00651519890914
-215 1.07 -0.0216305405556 0.0065569545898
-216 1.075 -0.0216634300906 0.00659888936611
-217 1.08 -0.0216965297501 0.00664100464349
-218 1.085 -0.0217298404402 0.00668330183711
-219 1.09 -0.0217633630741 0.00672578237194
-220 1.095 -0.0217970985719 0.00676844768288
-221 1.1 -0.0218310478613 0.00681129921484
-222 1.105 -0.0218652118769 0.00685433842285
-223 1.11 -0.0218995915607 0.00689756677211
-224 1.115 -0.0219341878623 0.00694098573816
-225 1.12 -0.0219690017383 0.0069845968069
-226 1.125 -0.022004034153 0.00702840147476
-227 1.13 -0.0220392860782 0.00707240124874
-228 1.135 -0.0220747584932 0.00711659764655
-229 1.14 -0.0221104523849 0.00716099219671
-230 1.145 -0.022146368748 0.00720558643861
-231 1.15 -0.0221825085847 0.00725038192267
-232 1.155 -0.0222188729052 0.00729538021041
-233 1.16 -0.0222554627274 0.00734058287457
-234 1.165 -0.0222922790772 0.0073859914992
-235 1.17 -0.0223293229884 0.0074316076798
-236 1.175 -0.0223665955026 0.0074774330234
-237 1.18 -0.0224040976699 0.00752346914866
-238 1.185 -0.0224418305481 0.00756971768601
-239 1.19 -0.0224797952035 0.00761618027777
-240 1.195 -0.0225179927104 0.00766285857821
-241 1.2 -0.0225564241516 0.00770975425373
-242 1.205 -0.0225950906181 0.00775686898291
-243 1.21 -0.0226339932093 0.00780420445668
-244 1.215 -0.0226731330334 0.00785176237842
-245 1.22 -0.0227125112067 0.00789954446406
-246 1.225 -0.0227521288545 0.00794755244222
-247 1.23 -0.0227919871105 0.00799578805433
-248 1.235 -0.0228320871174 0.00804425305474
-249 1.24 -0.0228724300263 0.00809294921086
-250 1.245 -0.0229130169977 0.00814187830327
-251 1.25 -0.0229538492006 0.00819104212586
-252 1.255 -0.0229949278132 0.00824044248594
-253 1.26 -0.0230362540227 0.00829008120437
-254 1.265 -0.0230778290255 0.00833996011571
-255 1.27 -0.0231196540273 0.00839008106834
-256 1.275 -0.0231617302427 0.00844044592457
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-1114 5.565 11079.6234321 -253952.586497
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-1177 5.88 4141901662.1 -3.44454801129e+11
-1178 5.885 6333810219.82 -5.49690750348e+11
-1179 5.89 9870702215.02 -8.95661856872e+11
-1180 5.895 15704120493.1 -1.49296797827e+12
-1181 5.9 25558689542.6 -2.55153879404e+12
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
deleted file mode 100644
index 2ad6d7b69..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
+++ /dev/null
@@ -1,1187 +0,0 @@
-# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0)
-
-CH_H0
-N 1181 R 0.00000000001 5.9
-
-1 0.00000000001 8.31299178857e-07 0.0
-2 0.005 8.31311879342e-07 -5.08022586688e-09
-3 0.01 8.31349981758e-07 -1.01608369733e-08
-4 0.015 8.31413488996e-07 -1.52422186449e-08
-5 0.02 8.31502405871e-07 -2.03247562721e-08
-6 0.025 8.31616739127e-07 -2.54088353865e-08
-7 0.03 8.31756497437e-07 -3.04948417048e-08
-8 0.035 8.319216914e-07 -3.55831611709e-08
-9 0.04 8.32112333547e-07 -4.06741800058e-08
-10 0.045 8.32328438343e-07 -4.57682847516e-08
-11 0.05 8.32570022183e-07 -5.08658623183e-08
-12 0.055 8.328371034e-07 -5.59673000292e-08
-13 0.06 8.33129702263e-07 -6.10729856679e-08
-14 0.065 8.33447840983e-07 -6.61833075238e-08
-15 0.07 8.33791543713e-07 -7.12986544391e-08
-16 0.075 8.34160836552e-07 -7.64194158551e-08
-17 0.08 8.34555747546e-07 -8.15459818584e-08
-18 0.085 8.34976306696e-07 -8.66787432278e-08
-19 0.09 8.35422545957e-07 -9.18180914814e-08
-20 0.095 8.35894499243e-07 -9.69644189231e-08
-21 0.1 8.36392202433e-07 -1.0211811869e-07
-22 0.105 8.36915693374e-07 -1.07279584798e-07
-23 0.11 8.37465011883e-07 -1.12449212192e-07
-24 0.115 8.38040199757e-07 -1.17627396792e-07
-25 0.12 8.38641300774e-07 -1.22814535539e-07
-26 0.125 8.392683607e-07 -1.28011026445e-07
-27 0.13 8.39921427291e-07 -1.33217268641e-07
-28 0.135 8.40600550305e-07 -1.38433662423e-07
-29 0.14 8.41305781504e-07 -1.43660609303e-07
-30 0.145 8.42037174658e-07 -1.48898512057e-07
-31 0.15 8.42794785557e-07 -1.54147774771e-07
-32 0.155 8.43578672015e-07 -1.59408802894e-07
-33 0.16 8.44388893873e-07 -1.64682003285e-07
-34 0.165 8.45225513015e-07 -1.69967784262e-07
-35 0.17 8.46088593367e-07 -1.75266555654e-07
-36 0.175 8.46978200908e-07 -1.80578728847e-07
-37 0.18 8.4789440368e-07 -1.85904716839e-07
-38 0.185 8.48837271792e-07 -1.91244934288e-07
-39 0.19 8.49806877432e-07 -1.96599797561e-07
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-44 0.215 8.55058641658e-07 -2.23608500394e-07
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-48 0.235 8.59749467885e-07 -2.4552224295e-07
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-50 0.245 8.62259968921e-07 -2.56590866647e-07
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-53 0.26 8.66234245555e-07 -2.73343376025e-07
-54 0.265 8.67615018129e-07 -2.78969213098e-07
-55 0.27 8.69023973658e-07 -2.84616633187e-07
-56 0.275 8.70461221189e-07 -2.90286089823e-07
-57 0.28 8.71926872044e-07 -2.95978039217e-07
-58 0.285 8.73421039834e-07 -3.0169294032e-07
-59 0.29 8.74943840469e-07 -3.07431254881e-07
-60 0.295 8.76495392179e-07 -3.13193447505e-07
-61 0.3 8.7807581552e-07 -3.18979985713e-07
-62 0.305 8.79685233396e-07 -3.24791340003e-07
-63 0.31 8.8132377107e-07 -3.30627983906e-07
-64 0.315 8.82991556179e-07 -3.36490394052e-07
-65 0.32 8.84688718753e-07 -3.42379050225e-07
-66 0.325 8.86415391229e-07 -3.48294435432e-07
-67 0.33 8.88171708466e-07 -3.54237035959e-07
-68 0.335 8.89957807764e-07 -3.60207341438e-07
-69 0.34 8.91773828877e-07 -3.66205844906e-07
-70 0.345 8.93619914037e-07 -3.72233042875e-07
-71 0.35 8.95496207963e-07 -3.78289435392e-07
-72 0.355 8.97402857887e-07 -3.84375526106e-07
-73 0.36 8.99340013567e-07 -3.90491822333e-07
-74 0.365 9.01307827305e-07 -3.96638835124e-07
-75 0.37 9.0330645397e-07 -4.02817079329e-07
-76 0.375 9.05336051015e-07 -4.09027073668e-07
-77 0.38 9.07396778494e-07 -4.152693408e-07
-78 0.385 9.09488799088e-07 -4.21544407387e-07
-79 0.39 9.11612278118e-07 -4.2785280417e-07
-80 0.395 9.13767383571e-07 -4.34195066035e-07
-81 0.4 9.15954286119e-07 -4.40571732086e-07
-82 0.405 9.18173159138e-07 -4.46983345718e-07
-83 0.41 9.20424178735e-07 -4.53430454687e-07
-84 0.415 9.22707523764e-07 -4.59913611186e-07
-85 0.42 9.25023375853e-07 -4.66433371919e-07
-86 0.425 9.27371919425e-07 -4.72990298174e-07
-87 0.43 9.29753341721e-07 -4.795849559e-07
-88 0.435 9.32167832821e-07 -4.86217915785e-07
-89 0.44 9.34615585674e-07 -4.9288975333e-07
-90 0.445 9.37096796117e-07 -4.99601048932e-07
-91 0.45 9.39611662902e-07 -5.0635238796e-07
-92 0.455 9.4216038772e-07 -5.13144360835e-07
-93 0.46 9.44743175226e-07 -5.19977563112e-07
-94 0.465 9.47360233068e-07 -5.26852595561e-07
-95 0.47 9.50011771908e-07 -5.33770064252e-07
-96 0.475 9.52698005456e-07 -5.40730580635e-07
-97 0.48 9.55419150489e-07 -5.47734761627e-07
-98 0.485 9.58175426884e-07 -5.54783229699e-07
-99 0.49 9.60967057644e-07 -5.61876612959e-07
-100 0.495 9.63794268928e-07 -5.69015545241e-07
-101 0.5 9.66657290077e-07 -5.76200666196e-07
-102 0.505 9.69556353647e-07 -5.83432621378e-07
-103 0.51 9.72491695434e-07 -5.90712062337e-07
-104 0.515 9.75463554509e-07 -5.9803964671e-07
-105 0.52 9.78472173246e-07 -6.05416038315e-07
-106 0.525 9.81517797354e-07 -6.12841907243e-07
-107 0.53 9.84600675908e-07 -6.20317929954e-07
-108 0.535 9.87721061381e-07 -6.27844789373e-07
-109 0.54 9.90879209678e-07 -6.3542317499e-07
-110 0.545 9.94075380168e-07 -6.43053782955e-07
-111 0.55 9.97309835716e-07 -6.50737316177e-07
-112 0.555 1.00058284272e-06 -6.58474484431e-07
-113 0.56 1.00389467115e-06 -6.66266004455e-07
-114 0.565 1.00724559456e-06 -6.74112600053e-07
-115 0.57 1.01063589016e-06 -6.82015002204e-07
-116 0.575 1.01406583882e-06 -6.89973949166e-07
-117 0.58 1.01753572513e-06 -6.97990186581e-07
-118 0.585 1.02104583743e-06 -7.06064467589e-07
-119 0.59 1.02459646782e-06 -7.14197552934e-07
-120 0.595 1.02818791224e-06 -7.22390211075e-07
-121 0.6 1.03182047051e-06 -7.30643218304e-07
-122 0.605 1.03549444631e-06 -7.38957358854e-07
-123 0.61 1.0392101473e-06 -7.47333425021e-07
-124 0.615 1.04296788511e-06 -7.55772217275e-07
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-1181 5.9 25558719893.6 -2.55154000294e+12
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat
deleted file mode 100644
index d660fee30..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat
+++ /dev/null
@@ -1,735 +0,0 @@
-# Table of the potential and its negative derivative for frustrated alpha helix
-# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
-# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
-
-FRUSTRATED_ALPHA
-N 360 DEGREES
-
-1 0.0 -2.74081145103 0.0783990792662
-2 1.0 -2.81950869101 0.0789852583442
-3 2.0 -2.89876136749 0.0795096391909
-4 3.0 -2.97850675562 0.0799703813963
-5 4.0 -3.05868032959 0.0803657243943
-6 5.0 -3.13921584545 0.0806939935737
-7 6.0 -3.22004543014 0.0809536062381
-8 7.0 -3.30109967628 0.0811430773977
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-10 9.0 -3.46359746038 0.0813061772009
-11 10.0 -3.54489544401 0.0812773738039
-12 11.0 -3.62612720812 0.0811735749433
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-15 14.0 -3.86866640485 0.0804036822781
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-271 270.0 -0.702988047855 -0.0361186847156
-272 271.0 -0.667547592939 -0.0347626934072
-273 272.0 -0.633461588675 -0.0334099162773
-274 273.0 -0.600726436882 -0.0320611067354
-275 274.0 -0.569337829756 -0.0307169306269
-276 275.0 -0.539290837348 -0.0293779664649
-277 276.0 -0.510579994645 -0.0280447059807
-278 277.0 -0.483199387947 -0.0267175549897
-279 278.0 -0.457142740217 -0.0253968345674
-280 279.0 -0.432403495111 -0.0240827825309
-281 280.0 -0.408974899365 -0.0227755552188
-282 281.0 -0.386850083265 -0.0214752295619
-283 282.0 -0.366022138902 -0.020181805438
-284 283.0 -0.346484195932 -0.0188952082997
-285 284.0 -0.328229494574 -0.0176152920667
-286 285.0 -0.311251455597 -0.0163418422722
-287 286.0 -0.295543747024 -0.0150745794496
-288 287.0 -0.28110034735 -0.0138131627512
-289 288.0 -0.267915605017 -0.0125571937823
-290 289.0 -0.255984293962 -0.011306220639
-291 290.0 -0.245301665026 -0.0100597421363
-292 291.0 -0.235863493049 -0.00881721220956
-293 292.0 -0.22766611948 -0.00757804447631
-294 293.0 -0.220706490355 -0.00634161694135
-295 294.0 -0.214982189503 -0.00510727682957
-296 295.0 -0.210491466861 -0.00387434552992
-297 296.0 -0.207233261801 -0.00264212363344
-298 297.0 -0.205207221373 -0.00140989604849
-299 298.0 -0.204413713408 -0.00017693717569
-300 299.0 -0.204853834414 0.0010574838751
-301 300.0 -0.206529412255 0.00229409804323
-302 301.0 -0.209443003569 0.00353363106913
-303 302.0 -0.213597885954 0.00477679825726
-304 303.0 -0.218998044922 0.00602429926791
-305 304.0 -0.22564815567 0.00727681295572
-306 305.0 -0.23355355972 0.00853499227222
-307 306.0 -0.2427202365 0.00979945924997
-308 307.0 -0.253154769958 0.0110708000854
-309 308.0 -0.264864310313 0.0123495603372
-310 309.0 -0.277856531075 0.0136362402565
-311 310.0 -0.292139581459 0.0149312902659
-312 311.0 -0.307722034364 0.0162351066015
-313 312.0 -0.324612830087 0.0175480271349
-314 313.0 -0.342821215943 0.0188703273888
-315 314.0 -0.362356682012 0.0202022167596
-316 315.0 -0.383228893218 0.0215438349636
-317 316.0 -0.405447617967 0.0228952487148
-318 317.0 -0.429022653586 0.0242564486517
-319 318.0 -0.45396374882 0.0256273465206
-320 319.0 -0.480280523637 0.0270077726275
-321 320.0 -0.507982386639 0.0283974735696
-322 321.0 -0.537078450328 0.029796110253
-323 322.0 -0.567577444555 0.0312032562068
-324 323.0 -0.59948762842 0.0326183962009
-325 324.0 -0.632816700956 0.0340409251716
-326 325.0 -0.667571710883 0.0354701474639
-327 326.0 -0.703758965776 0.0369052763923
-328 327.0 -0.741383940946 0.038345434125
-329 328.0 -0.780451188376 0.0397896518935
-330 329.0 -0.820964246018 0.0412368705304
-331 330.0 -0.862925547807 0.042685941334
-332 331.0 -0.906336334692 0.0441356272615
-333 332.0 -0.951196567028 0.045584604448
-334 333.0 -0.997504838648 0.0470314640498
-335 334.0 -1.04525829294 0.048474714408
-336 335.0 -1.09445254125 0.0499127835288
-337 336.0 -1.1450815839 0.0513440218749
-338 337.0 -1.1971377342 0.0527667054614
-339 338.0 -1.25061154564 0.0541790392498
-340 339.0 -1.30549174267 0.0555791608316
-341 340.0 -1.36176515529 0.0569651443923
-342 341.0 -1.41941665773 0.0583350049463
-343 342.0 -1.47842911151 0.0596867028317
-344 343.0 -1.53878331313 0.061018148454
-345 344.0 -1.60045794659 0.0623272072653
-346 345.0 -1.66342954101 0.0636117049668
-347 346.0 -1.72767243359 0.0648694329207
-348 347.0 -1.79315873807 0.0660981537565
-349 348.0 -1.85985831882 0.0672956071568
-350 349.0 -1.92773877092 0.0684595158069
-351 350.0 -1.99676540616 0.0695875914917
-352 351.0 -2.06690124527 0.0706775413231
-353 352.0 -2.13810701636 0.0717270740805
-354 353.0 -2.21034115987 0.0727339066469
-355 354.0 -2.28355983986 0.0736957705223
-356 355.0 -2.35771696194 0.0746104183955
-357 356.0 -2.43276419776 0.0754756307561
-358 357.0 -2.50865101613 0.0762892225281
-359 358.0 -2.58532472075 0.0770490497051
-360 359.0 -2.66273049463 0.0777530159679
-
-# Table of the potential and its negative derivative for frustrated beta sheet
-# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
-# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
-
-FRUSTRATED_BETA
-N 360 DEGREES
-
-1 0.0 -2.55809068762 0.0731724739818
-2 1.0 -2.63154144494 0.0737195744566
-3 2.0 -2.70551060968 0.0742089966437
-4 3.0 -2.77993963883 0.074639023134
-5 4.0 -2.85476830901 0.0750080115297
-6 5.0 -2.92993479441 0.0753144003899
-7 6.0 -3.00537575069 0.0755567150326
-8 7.0 -3.08102640456 0.0757335731758
-9 8.0 -3.15682064892 0.0758436903983
-10 9.0 -3.23269114341 0.075885885404
-11 10.0 -3.30856942003 0.0758590850738
-12 11.0 -3.38438599377 0.0757623292865
-13 12.0 -3.46007047791 0.0755947754951
-14 13.0 -3.53555170381 0.0753557030426
-15 14.0 -3.61075784476 0.0750445172025
-16 15.0 -3.68561654392 0.0746607529305
-17 16.0 -3.76005504566 0.0742040783151
-18 17.0 -3.83400033034 0.0736742977129
-19 18.0 -3.907379252 0.0730713545594
-20 19.0 -3.98011867868 0.0723953338429
-21 20.0 -4.0521456351 0.0716464642332
-22 21.0 -4.12338744726 0.0708251198546
-23 22.0 -4.19377188857 0.0699318216967
-24 23.0 -4.26322732737 0.0689672386556
-25 24.0 -4.33168287509 0.0679321881993
-26 25.0 -4.39906853508 0.0668276366524
-27 26.0 -4.46531535141 0.0656546990963
-28 27.0 -4.53035555742 0.0644146388823
-29 28.0 -4.59412272358 0.0631088667546
-30 29.0 -4.65655190431 0.061738939584
-31 30.0 -4.71757978327 0.0603065587109
-32 31.0 -4.77714481686 0.0588135679005
-33 32.0 -4.83518737548 0.057261950911
-34 33.0 -4.89164988211 0.0556538286799
-35 34.0 -4.94647694795 0.0539914561312
-36 35.0 -4.99961550465 0.0522772186102
-37 36.0 -5.05101493277 0.0505136279528
-38 37.0 -5.10062718621 0.048703318195
-39 38.0 -5.14840691207 0.0468490409338
-40 39.0 -5.19431156578 0.0449536603471
-41 40.0 -5.23830152101 0.0430201478838
-42 41.0 -5.28034017422 0.0410515766363
-43 42.0 -5.3203940433 0.0390511154063
-44 43.0 -5.35843286021 0.0370220224793
-45 44.0 -5.39442965726 0.0349676391193
-46 45.0 -5.4283608467 0.0328913828015
-47 46.0 -5.46020629342 0.0307967401964
-48 47.0 -5.48994938059 0.028687259923
-49 48.0 -5.51757706789 0.0265665450883
-50 49.0 -5.54307994213 0.0244382456298
-51 50.0 -5.56645226024 0.0223060504811
-52 51.0 -5.58769198425 0.0201736795783
-53 52.0 -5.60680080825 0.0180448757265
-54 53.0 -5.62378417713 0.0159233963481
-55 54.0 -5.63865129702 0.0138130051308
-56 55.0 -5.6514151374 0.0117174635982
-57 56.0 -5.66209242462 0.00964052262251
-58 57.0 -5.67070362704 0.00758591390103
-59 58.0 -5.67727293157 0.00555734141841
-60 59.0 -5.6818282117 0.00355847291538
-61 60.0 -5.68440098698 0.00159293138608
-62 61.0 -5.68502637408 -0.000335713374531
-63 62.0 -5.68374302934 -0.00222395315148
-64 63.0 -5.68059308309 -0.0040683495974
-65 64.0 -5.67562206565 -0.00586554240548
-66 65.0 -5.66887882528 -0.00761225734683
-67 66.0 -5.66041543813 -0.00930531415106
-68 67.0 -5.65028711044 -0.0109416342099
-69 68.0 -5.63855207307 -0.0125182480831
-70 69.0 -5.6252714687 -0.0140323027883
-71 70.0 -5.61050923182 -0.0154810688529
-72 71.0 -5.59433196178 -0.0168619471125
-73 72.0 -5.57680878923 -0.0181724752358
-74 73.0 -5.5580112361 -0.019410333958
-75 74.0 -5.53801306959 -0.0205733530082
-76 75.0 -5.51689015031 -0.0216595167121
-77 76.0 -5.49472027505 -0.0226669692568
-78 77.0 -5.47158301441 -0.0235940196022
-79 78.0 -5.44755954575 -0.0244391460249
-80 79.0 -5.42273248172 -0.0252010002837
-81 80.0 -5.3971856949 -0.0258784113929
-82 81.0 -5.37100413881 -0.0264703889936
-83 82.0 -5.34427366574 -0.0269761263135
-84 83.0 -5.31708084192 -0.0273950027051
-85 84.0 -5.28951276022 -0.0277265857564
-86 85.0 -5.26165685114 -0.0279706329651
-87 86.0 -5.23360069216 -0.0281270929735
-88 87.0 -5.20543181621 -0.0281961063563
-89 88.0 -5.17723751951 -0.0281780059613
-90 89.0 -5.14910466934 -0.0280733167983
-91 90.0 -5.12111951208 -0.0278827554757
-92 91.0 -5.09336748214 -0.0276072291861
-93 92.0 -5.06593301201 -0.0272478342399
-94 93.0 -5.0388993441 -0.026805854151
-95 94.0 -5.01234834466 -0.0262827572773
-96 95.0 -4.98636032033 -0.0256801940208
-97 96.0 -4.96101383762 -0.0249999935924
-98 97.0 -4.93638554598 -0.0242441603499
-99 98.0 -4.91255000457 -0.0234148697145
-100 99.0 -4.88957951348 -0.0225144636776
-101 100.0 -4.86754394953 -0.0215454459053
-102 101.0 -4.84651060724 -0.0205104764546
-103 102.0 -4.8265440452 -0.01941236611
-104 103.0 -4.80770593836 -0.0182540703564
-105 104.0 -4.79005493648 -0.0170386830008
-106 105.0 -4.77364652914 -0.0157694294583
-107 106.0 -4.7585329176 -0.0144496597171
-108 107.0 -4.74476289391 -0.0130828410011
-109 108.0 -4.73238172744 -0.0116725501446
-110 109.0 -4.72143105919 -0.0102224657007
-111 110.0 -4.71194880414 -0.00873635979846
-112 111.0 -4.70396906182 -0.0072180897712
-113 112.0 -4.69752203541 -0.00567158957449
-114 113.0 -4.69263395945 -0.00410086101469
-115 114.0 -4.68932703648 -0.00250996480925
-116 115.0 -4.68761938265 -0.000903011500147
-117 116.0 -4.68752498248 0.00071584775762
-118 117.0 -4.68905365291 0.00234243051027
-119 118.0 -4.69221101668 0.00397253239976
-120 119.0 -4.69699848518 0.00560193661579
-121 120.0 -4.70341325069 0.00722642338265
-122 121.0 -4.71144828821 0.00884177945771
-123 122.0 -4.72109236669 0.0104438076188
-124 123.0 -4.73233006984 0.0120283361174
-125 124.0 -4.74514182625 0.0135912280748
-126 125.0 -4.75950394898 0.0151283907985
-127 126.0 -4.77538868431 0.0166357849963
-128 127.0 -4.79276426974 0.0181094338658
-129 128.0 -4.81159500092 0.0195454320375
-130 129.0 -4.83184130754 0.0209399543498
-131 130.0 -4.8534598378 0.0222892644342
-132 131.0 -4.87640355143 0.0235897230915
-133 132.0 -4.90062182095 0.0248377964369
-134 133.0 -4.92606054096 0.0260300637961
-135 134.0 -4.95266224518 0.0271632253326
-136 135.0 -4.98036623096 0.028234109388
-137 136.0 -5.00910869107 0.0292396795182
-138 137.0 -5.03882285221 0.0301770412082
-139 138.0 -5.06943912022 0.0310434482505
-140 139.0 -5.10088523142 0.0318363087705
-141 140.0 -5.13308640979 0.0325531908865
-142 141.0 -5.16596552963 0.0331918279898
-143 142.0 -5.19944328334 0.0337501236332
-144 143.0 -5.23343835383 0.0342261560164
-145 144.0 -5.26786759123 0.0346181820585
-146 145.0 -5.30264619353 0.0349246410472
-147 146.0 -5.33768789051 0.0351441578585
-148 147.0 -5.37290513082 0.0352755457383
-149 148.0 -5.40820927152 0.0353178086401
-150 149.0 -5.4435107698 0.0352701431151
-151 150.0 -5.4787193763 0.0351319397498
-152 151.0 -5.51374432971 0.0349027841491
-153 152.0 -5.54849455206 0.0345824574643
-154 153.0 -5.58287884436 0.0341709364636
-155 154.0 -5.61680608206 0.0336683931487
-156 155.0 -5.65018540988 0.0330751939177
-157 156.0 -5.68292643563 0.0323918982779
-158 157.0 -5.71493942249 0.0316192571138
-159 158.0 -5.74613547931 0.0307582105139
-160 159.0 -5.77642674856 0.029809885165
-161 160.0 -5.80572659147 0.0287755913197
-162 161.0 -5.83394976986 0.0276568193473
-163 162.0 -5.86101262442 0.0264552358763
-164 163.0 -5.8868332488 0.025172679541
-165 164.0 -5.91133165941 0.0238111563427
-166 165.0 -5.93442996024 0.0223728346376
-167 166.0 -5.95605250261 0.0208600397671
-168 167.0 -5.97612603931 0.0192752483425
-169 168.0 -5.99457987285 0.0176210822011
-170 169.0 -6.01134599757 0.015900302049
-171 170.0 -6.02635923519 0.014115800807
-172 171.0 -6.03955736358 0.0122705966784
-173 172.0 -6.05088123845 0.0103678259555
-174 173.0 -6.0602749078 0.00841073558436
-175 174.0 -6.06768571866 0.00640267550713
-176 175.0 -6.0730644163 0.00434709080102
-177 176.0 -6.07636523524 0.00224751363529
-178 177.0 -6.07754598232 0.000107555066143
-179 178.0 -6.07656811141 -0.00206910330914
-180 179.0 -6.07339678973 -0.00427871781763
-181 180.0 -6.06800095563 -0.00651749127408
-182 181.0 -6.06035336781 -0.00878158162059
-183 182.0 -6.05043064586 -0.0110671106207
-184 183.0 -6.03821330204 -0.0133701725859
-185 184.0 -6.02368576439 -0.0156868431131
-186 185.0 -6.00683639108 -0.0180131878107
-187 186.0 -5.98765747603 -0.0203452709919
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-189 188.0 -5.94229984843 -0.025010955339
-190 189.0 -5.91612533236 -0.0273367560054
-191 190.0 -5.88762961878 -0.0296527109716
-192 191.0 -5.85682446433 -0.0319550058299
-193 192.0 -5.82372541626 -0.0342398751598
-194 193.0 -5.78835175943 -0.0365036104045
-195 194.0 -5.75072645562 -0.0387425675516
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-213 212.0 -4.7343208347 -0.0712155960973
-214 213.0 -4.66249453466 -0.0724246501921
-215 214.0 -4.58949643037 -0.0735590213066
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-221 220.0 -4.13116891218 -0.0787505371538
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-227 226.0 -3.65013016636 -0.0811283640964
-228 227.0 -3.56893240921 -0.0812545264246
-229 228.0 -3.48764620813 -0.0813054090744
-230 229.0 -3.4063463509 -0.0812820162266
-231 230.0 -3.32510656064 -0.0811854723104
-232 231.0 -3.24399937793 -0.081017017134
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-236 235.0 -2.92229997393 -0.079652625851
-237 236.0 -2.84289494829 -0.0791468798106
-238 237.0 -2.76402699866 -0.0785787832348
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-260 259.0 -1.26669806833 -0.0545945238457
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-263 262.0 -1.1092784581 -0.0503369020679
-264 263.0 -1.05965912771 -0.0489006781451
-265 264.0 -1.01147898802 -0.0474587930279
-266 265.0 -0.964742896092 -0.0460128419505
-267 266.0 -0.919454153297 -0.0445643406057
-268 267.0 -0.875614586172 -0.0431147225719
-269 268.0 -0.833224629688 -0.0416653370554
-270 269.0 -0.792283412613 -0.0402174469521
-271 270.0 -0.752788844664 -0.038772227232
-272 271.0 -0.714737705101 -0.0373307636499
-273 272.0 -0.67812573245 -0.0358940517831
-274 273.0 -0.642947715028 -0.0344629963972
-275 274.0 -0.609197581934 -0.0330384111393
-276 275.0 -0.576868494182 -0.0316210185584
-277 276.0 -0.545952935658 -0.0302114504483
-278 277.0 -0.51644280357 -0.0288102485125
-279 278.0 -0.488329498068 -0.0274178653447
-280 279.0 -0.461604010741 -0.0260346657211
-281 280.0 -0.436257011655 -0.0246609281969
-282 281.0 -0.412278934657 -0.023296847002
-283 282.0 -0.389660060626 -0.0219425342253
-284 283.0 -0.368390598407 -0.0205980222818
-285 284.0 -0.348460763137 -0.01926326665
-286 285.0 -0.329860851704 -0.0179381488715
-287 286.0 -0.312581315078 -0.0166224797996
-288 287.0 -0.296612827279 -0.015316003087
-289 288.0 -0.281946350734 -0.0140183988977
-290 289.0 -0.268573197826 -0.0127292878319
-291 290.0 -0.256485088408 -0.0114482350481
-292 291.0 -0.245674203109 -0.0101747545698
-293 292.0 -0.236133232246 -0.00890831375923
-294 293.0 -0.227855420178 -0.00764833794542
-295 294.0 -0.220834604976 -0.00639421518813
-296 295.0 -0.215065253253 -0.00514530116277
-297 296.0 -0.210542490065 -0.00390092414876
-298 297.0 -0.207262123775 -0.00266039010467
-299 298.0 -0.205220665805 -0.00142298781263
-300 299.0 -0.204415345223 -0.000187994074493
-301 300.0 -0.204844118104 0.00104532105779
-302 301.0 -0.206505671662 0.00227768903543
-303 302.0 -0.209399423126 0.0035098375675
-304 303.0 -0.213525513386 0.00474248539479
-305 304.0 -0.218884795423 0.00597633710062
-306 305.0 -0.225478817581 0.00721207797616
-307 306.0 -0.233309801737 0.00845036895769
-308 307.0 -0.242380616448 0.00969184165314
-309 308.0 -0.252694745185 0.0109370934746
-310 309.0 -0.264256249747 0.0121866828936
-311 310.0 -0.277069729013 0.0134411248358
-312 311.0 -0.291140273151 0.0147008862297
-313 312.0 -0.306473413467 0.0159663817261
-314 313.0 -0.323075068066 0.0172379696031
-315 314.0 -0.340951483513 0.018515947869
-316 315.0 -0.360109172702 0.0198005505798
-317 316.0 -0.380554849155 0.0210919443819
-318 317.0 -0.402295357987 0.0223902252933
-319 318.0 -0.425337603767 0.0236954157356
-320 319.0 -0.449688475549 0.0250074618263
-321 320.0 -0.475354769327 0.0263262309427
-322 321.0 -0.50234310819 0.0276515095659
-323 322.0 -0.530659860472 0.0289830014145
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-326 325.0 -0.623638695141 0.0330105212056
-327 326.0 -0.657324736579 0.0343621993296
-328 327.0 -0.692364243488 0.0357173235955
-329 328.0 -0.728760261774 0.0370750789637
-330 329.0 -0.766514978659 0.0384345631765
-331 330.0 -0.805629635748 0.0397947873984
-332 331.0 -0.846104442913 0.04115467718
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-335 334.0 -0.975674613021 0.0452203404434
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-337 336.0 -1.06880527714 0.0479056997168
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-341 340.0 -1.27100201415 0.0531611720525
-342 341.0 -1.32480451282 0.0544411134304
-343 342.0 -1.37987850417 0.055703842622
-344 343.0 -1.43620582346 0.0569474464963
-345 344.0 -1.49376636966 0.0581699665097
-346 345.0 -1.55253806258 0.05936940366
-347 346.0 -1.61249680493 0.0605437236497
-348 347.0 -1.67361644969 0.0616908622471
-349 348.0 -1.73586877296 0.0628087308273
-350 349.0 -1.79922345238 0.0638952220804
-351 350.0 -1.86364805137 0.0649482158688
-352 351.0 -1.92910800931 0.0659655852184
-353 352.0 -1.9955666377 0.066945202426
-354 353.0 -2.06298512258 0.0678849452658
-355 354.0 -2.13132253309 0.0687827032771
-356 355.0 -2.20053583647 0.0696363841147
-357 356.0 -2.27057991931 0.0704439199439
-358 357.0 -2.3414076153 0.0712032738621
-359 358.0 -2.41296973939 0.0719124463259
-360 359.0 -2.48521512832 0.072569481568
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min
deleted file mode 100644
index 88ff31635..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min
+++ /dev/null
@@ -1,25 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# Optional: Make sure the pairwise energies look reasonable:
-pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0
-pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0
-pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0
-
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt
deleted file mode 100644
index 01b156a2a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt
+++ /dev/null
@@ -1,48 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-# I you want to be careful, you can minimize the system first.
-# (Try using "run.in.min" and uncomment the line below.)
-# read_data system_after_min.data
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.025
-dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-# Keep the chaperonin fixed. Only let the protein move.
-
-fix fxlan proteins langevin 0.25 0.25 1.0 48279
-fix fxnve proteins nve
-
-# Notes:
-# The temperature is in reduced units and is set to 0.25
-# which is the folding temperature for the frustrated protein
-# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
-# as it was in the paper. (Hopefully folding times should be similar.)
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 50000 #(time interval for printing out "thermo" data)
-
-#restart 100000000 restart_nvt
-
-run 1000000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT
deleted file mode 100644
index ecb9adad2..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT
+++ /dev/null
@@ -1,38 +0,0 @@
-# This directory demonstrates how to run a long simulation of
-# the "frustrated" coarse-grained protein in the presence of one
-# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in:
-#
-# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006)
-# and earlier in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-#
-# Because this process takes a long time (even with the help of the chaperone)
-# I save the data relatively infrequently.
-#
-# Note: In the 2006 paper, only one protein and one chaperone was simulated.
-# In this example, 8 proteins and 8 chaperones were simulated.
-#
-# Note: In this case, the chaperones appear to catalyze aggregation.
-# This is due to an artifact in the protein model. That model
-# was not designed to study aggregation. However the simulation
-# is suitable for making pretty pictures (to show off moltemplate).
-#
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
deleted file mode 100755
index d5ae1fe5a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# You would probably run lammps this way:
-#
-# lmp_ubuntu -i run.in.nvt
-
-# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
-# to the input scripts & data files you created earlier when you ran moltemplate
-# system.in.init, system.in.settings, system.data
-
-
-
-
-# -----------------------------------
-
-
-
-LAMMPS_COMMAND="lmp_mpi"
-
-# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary.
-
-# Run lammps using the following 3 commands:
-
-"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-"$LAMMPS_COMMAND" -i run.in.nvt # production run
-
-# Alternately, if you have MPI installed, try something like this:
-
-#NUMPROCS=4
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh
deleted file mode 100755
index df49f4384..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -overlay-dihedrals system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
- cp -r table*.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf
deleted file mode 100644
index b0013ccc6..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf
+++ /dev/null
@@ -1,476 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 224 !NATOM
- 1 1 2 2 0.000000 1.0000 0
- 2 1 1 1 0.000000 1.0000 0
- 3 1 2 2 0.000000 1.0000 0
- 4 1 1 1 0.000000 1.0000 0
- 5 1 2 2 0.000000 1.0000 0
- 6 1 1 1 0.000000 1.0000 0
- 7 1 3 3 0.000000 1.0000 0
- 8 1 3 3 0.000000 1.0000 0
- 9 1 1 1 0.000000 1.0000 0
- 10 1 2 2 0.000000 1.0000 0
- 11 1 1 1 0.000000 1.0000 0
- 12 1 2 2 0.000000 1.0000 0
- 13 1 1 1 0.000000 1.0000 0
- 14 1 2 2 0.000000 1.0000 0
- 15 1 3 3 0.000000 1.0000 0
- 16 1 3 3 0.000000 1.0000 0
- 17 1 3 3 0.000000 1.0000 0
- 18 1 1 1 0.000000 1.0000 0
- 19 1 1 1 0.000000 1.0000 0
- 20 1 2 2 0.000000 1.0000 0
- 21 1 2 2 0.000000 1.0000 0
- 22 1 1 1 0.000000 1.0000 0
- 23 1 1 1 0.000000 1.0000 0
- 24 1 2 2 0.000000 1.0000 0
- 25 1 2 2 0.000000 1.0000 0
- 26 1 1 1 0.000000 1.0000 0
- 27 1 2 2 0.000000 1.0000 0
- 28 2 2 2 0.000000 1.0000 0
- 29 2 1 1 0.000000 1.0000 0
- 30 2 2 2 0.000000 1.0000 0
- 31 2 1 1 0.000000 1.0000 0
- 32 2 2 2 0.000000 1.0000 0
- 33 2 1 1 0.000000 1.0000 0
- 34 2 3 3 0.000000 1.0000 0
- 35 2 3 3 0.000000 1.0000 0
- 36 2 1 1 0.000000 1.0000 0
- 37 2 2 2 0.000000 1.0000 0
- 38 2 1 1 0.000000 1.0000 0
- 39 2 2 2 0.000000 1.0000 0
- 40 2 1 1 0.000000 1.0000 0
- 41 2 2 2 0.000000 1.0000 0
- 42 2 3 3 0.000000 1.0000 0
- 43 2 3 3 0.000000 1.0000 0
- 44 2 3 3 0.000000 1.0000 0
- 45 2 1 1 0.000000 1.0000 0
- 46 2 1 1 0.000000 1.0000 0
- 47 2 2 2 0.000000 1.0000 0
- 48 2 2 2 0.000000 1.0000 0
- 49 2 1 1 0.000000 1.0000 0
- 50 2 1 1 0.000000 1.0000 0
- 51 2 2 2 0.000000 1.0000 0
- 52 2 2 2 0.000000 1.0000 0
- 53 2 1 1 0.000000 1.0000 0
- 54 2 2 2 0.000000 1.0000 0
- 55 3 2 2 0.000000 1.0000 0
- 56 3 1 1 0.000000 1.0000 0
- 57 3 2 2 0.000000 1.0000 0
- 58 3 1 1 0.000000 1.0000 0
- 59 3 2 2 0.000000 1.0000 0
- 60 3 1 1 0.000000 1.0000 0
- 61 3 3 3 0.000000 1.0000 0
- 62 3 3 3 0.000000 1.0000 0
- 63 3 1 1 0.000000 1.0000 0
- 64 3 2 2 0.000000 1.0000 0
- 65 3 1 1 0.000000 1.0000 0
- 66 3 2 2 0.000000 1.0000 0
- 67 3 1 1 0.000000 1.0000 0
- 68 3 2 2 0.000000 1.0000 0
- 69 3 3 3 0.000000 1.0000 0
- 70 3 3 3 0.000000 1.0000 0
- 71 3 3 3 0.000000 1.0000 0
- 72 3 1 1 0.000000 1.0000 0
- 73 3 1 1 0.000000 1.0000 0
- 74 3 2 2 0.000000 1.0000 0
- 75 3 2 2 0.000000 1.0000 0
- 76 3 1 1 0.000000 1.0000 0
- 77 3 1 1 0.000000 1.0000 0
- 78 3 2 2 0.000000 1.0000 0
- 79 3 2 2 0.000000 1.0000 0
- 80 3 1 1 0.000000 1.0000 0
- 81 3 2 2 0.000000 1.0000 0
- 82 4 2 2 0.000000 1.0000 0
- 83 4 1 1 0.000000 1.0000 0
- 84 4 2 2 0.000000 1.0000 0
- 85 4 1 1 0.000000 1.0000 0
- 86 4 2 2 0.000000 1.0000 0
- 87 4 1 1 0.000000 1.0000 0
- 88 4 3 3 0.000000 1.0000 0
- 89 4 3 3 0.000000 1.0000 0
- 90 4 1 1 0.000000 1.0000 0
- 91 4 2 2 0.000000 1.0000 0
- 92 4 1 1 0.000000 1.0000 0
- 93 4 2 2 0.000000 1.0000 0
- 94 4 1 1 0.000000 1.0000 0
- 95 4 2 2 0.000000 1.0000 0
- 96 4 3 3 0.000000 1.0000 0
- 97 4 3 3 0.000000 1.0000 0
- 98 4 3 3 0.000000 1.0000 0
- 99 4 1 1 0.000000 1.0000 0
- 100 4 1 1 0.000000 1.0000 0
- 101 4 2 2 0.000000 1.0000 0
- 102 4 2 2 0.000000 1.0000 0
- 103 4 1 1 0.000000 1.0000 0
- 104 4 1 1 0.000000 1.0000 0
- 105 4 2 2 0.000000 1.0000 0
- 106 4 2 2 0.000000 1.0000 0
- 107 4 1 1 0.000000 1.0000 0
- 108 4 2 2 0.000000 1.0000 0
- 109 5 2 2 0.000000 1.0000 0
- 110 5 1 1 0.000000 1.0000 0
- 111 5 2 2 0.000000 1.0000 0
- 112 5 1 1 0.000000 1.0000 0
- 113 5 2 2 0.000000 1.0000 0
- 114 5 1 1 0.000000 1.0000 0
- 115 5 3 3 0.000000 1.0000 0
- 116 5 3 3 0.000000 1.0000 0
- 117 5 1 1 0.000000 1.0000 0
- 118 5 2 2 0.000000 1.0000 0
- 119 5 1 1 0.000000 1.0000 0
- 120 5 2 2 0.000000 1.0000 0
- 121 5 1 1 0.000000 1.0000 0
- 122 5 2 2 0.000000 1.0000 0
- 123 5 3 3 0.000000 1.0000 0
- 124 5 3 3 0.000000 1.0000 0
- 125 5 3 3 0.000000 1.0000 0
- 126 5 1 1 0.000000 1.0000 0
- 127 5 1 1 0.000000 1.0000 0
- 128 5 2 2 0.000000 1.0000 0
- 129 5 2 2 0.000000 1.0000 0
- 130 5 1 1 0.000000 1.0000 0
- 131 5 1 1 0.000000 1.0000 0
- 132 5 2 2 0.000000 1.0000 0
- 133 5 2 2 0.000000 1.0000 0
- 134 5 1 1 0.000000 1.0000 0
- 135 5 2 2 0.000000 1.0000 0
- 136 6 2 2 0.000000 1.0000 0
- 137 6 1 1 0.000000 1.0000 0
- 138 6 2 2 0.000000 1.0000 0
- 139 6 1 1 0.000000 1.0000 0
- 140 6 2 2 0.000000 1.0000 0
- 141 6 1 1 0.000000 1.0000 0
- 142 6 3 3 0.000000 1.0000 0
- 143 6 3 3 0.000000 1.0000 0
- 144 6 1 1 0.000000 1.0000 0
- 145 6 2 2 0.000000 1.0000 0
- 146 6 1 1 0.000000 1.0000 0
- 147 6 2 2 0.000000 1.0000 0
- 148 6 1 1 0.000000 1.0000 0
- 149 6 2 2 0.000000 1.0000 0
- 150 6 3 3 0.000000 1.0000 0
- 151 6 3 3 0.000000 1.0000 0
- 152 6 3 3 0.000000 1.0000 0
- 153 6 1 1 0.000000 1.0000 0
- 154 6 1 1 0.000000 1.0000 0
- 155 6 2 2 0.000000 1.0000 0
- 156 6 2 2 0.000000 1.0000 0
- 157 6 1 1 0.000000 1.0000 0
- 158 6 1 1 0.000000 1.0000 0
- 159 6 2 2 0.000000 1.0000 0
- 160 6 2 2 0.000000 1.0000 0
- 161 6 1 1 0.000000 1.0000 0
- 162 6 2 2 0.000000 1.0000 0
- 163 7 2 2 0.000000 1.0000 0
- 164 7 1 1 0.000000 1.0000 0
- 165 7 2 2 0.000000 1.0000 0
- 166 7 1 1 0.000000 1.0000 0
- 167 7 2 2 0.000000 1.0000 0
- 168 7 1 1 0.000000 1.0000 0
- 169 7 3 3 0.000000 1.0000 0
- 170 7 3 3 0.000000 1.0000 0
- 171 7 1 1 0.000000 1.0000 0
- 172 7 2 2 0.000000 1.0000 0
- 173 7 1 1 0.000000 1.0000 0
- 174 7 2 2 0.000000 1.0000 0
- 175 7 1 1 0.000000 1.0000 0
- 176 7 2 2 0.000000 1.0000 0
- 177 7 3 3 0.000000 1.0000 0
- 178 7 3 3 0.000000 1.0000 0
- 179 7 3 3 0.000000 1.0000 0
- 180 7 1 1 0.000000 1.0000 0
- 181 7 1 1 0.000000 1.0000 0
- 182 7 2 2 0.000000 1.0000 0
- 183 7 2 2 0.000000 1.0000 0
- 184 7 1 1 0.000000 1.0000 0
- 185 7 1 1 0.000000 1.0000 0
- 186 7 2 2 0.000000 1.0000 0
- 187 7 2 2 0.000000 1.0000 0
- 188 7 1 1 0.000000 1.0000 0
- 189 7 2 2 0.000000 1.0000 0
- 190 8 2 2 0.000000 1.0000 0
- 191 8 1 1 0.000000 1.0000 0
- 192 8 2 2 0.000000 1.0000 0
- 193 8 1 1 0.000000 1.0000 0
- 194 8 2 2 0.000000 1.0000 0
- 195 8 1 1 0.000000 1.0000 0
- 196 8 3 3 0.000000 1.0000 0
- 197 8 3 3 0.000000 1.0000 0
- 198 8 1 1 0.000000 1.0000 0
- 199 8 2 2 0.000000 1.0000 0
- 200 8 1 1 0.000000 1.0000 0
- 201 8 2 2 0.000000 1.0000 0
- 202 8 1 1 0.000000 1.0000 0
- 203 8 2 2 0.000000 1.0000 0
- 204 8 3 3 0.000000 1.0000 0
- 205 8 3 3 0.000000 1.0000 0
- 206 8 3 3 0.000000 1.0000 0
- 207 8 1 1 0.000000 1.0000 0
- 208 8 1 1 0.000000 1.0000 0
- 209 8 2 2 0.000000 1.0000 0
- 210 8 2 2 0.000000 1.0000 0
- 211 8 1 1 0.000000 1.0000 0
- 212 8 1 1 0.000000 1.0000 0
- 213 8 2 2 0.000000 1.0000 0
- 214 8 2 2 0.000000 1.0000 0
- 215 8 1 1 0.000000 1.0000 0
- 216 8 2 2 0.000000 1.0000 0
- 217 9 4 4 0.000000 100.0000 0
- 218 10 4 4 0.000000 100.0000 0
- 219 11 4 4 0.000000 100.0000 0
- 220 12 4 4 0.000000 100.0000 0
- 221 13 4 4 0.000000 100.0000 0
- 222 14 4 4 0.000000 100.0000 0
- 223 15 4 4 0.000000 100.0000 0
- 224 16 4 4 0.000000 100.0000 0
-
- 208 !NBOND: bonds
- 1 2 2 3 3 4 4 5
- 5 6 6 7 7 8 8 9
- 9 10 10 11 11 12 12 13
- 13 14 14 15 15 16 16 17
- 17 18 18 19 19 20 20 21
- 21 22 22 23 23 24 24 25
- 25 26 26 27 28 29 29 30
- 30 31 31 32 32 33 33 34
- 34 35 35 36 36 37 37 38
- 38 39 39 40 40 41 41 42
- 42 43 43 44 44 45 45 46
- 46 47 47 48 48 49 49 50
- 50 51 51 52 52 53 53 54
- 55 56 56 57 57 58 58 59
- 59 60 60 61 61 62 62 63
- 63 64 64 65 65 66 66 67
- 67 68 68 69 69 70 70 71
- 71 72 72 73 73 74 74 75
- 75 76 76 77 77 78 78 79
- 79 80 80 81 82 83 83 84
- 84 85 85 86 86 87 87 88
- 88 89 89 90 90 91 91 92
- 92 93 93 94 94 95 95 96
- 96 97 97 98 98 99 99 100
- 100 101 101 102 102 103 103 104
- 104 105 105 106 106 107 107 108
- 109 110 110 111 111 112 112 113
- 113 114 114 115 115 116 116 117
- 117 118 118 119 119 120 120 121
- 121 122 122 123 123 124 124 125
- 125 126 126 127 127 128 128 129
- 129 130 130 131 131 132 132 133
- 133 134 134 135 136 137 137 138
- 138 139 139 140 140 141 141 142
- 142 143 143 144 144 145 145 146
- 146 147 147 148 148 149 149 150
- 150 151 151 152 152 153 153 154
- 154 155 155 156 156 157 157 158
- 158 159 159 160 160 161 161 162
- 163 164 164 165 165 166 166 167
- 167 168 168 169 169 170 170 171
- 171 172 172 173 173 174 174 175
- 175 176 176 177 177 178 178 179
- 179 180 180 181 181 182 182 183
- 183 184 184 185 185 186 186 187
- 187 188 188 189 190 191 191 192
- 192 193 193 194 194 195 195 196
- 196 197 197 198 198 199 199 200
- 200 201 201 202 202 203 203 204
- 204 205 205 206 206 207 207 208
- 208 209 209 210 210 211 211 212
- 212 213 213 214 214 215 215 216
-
- 200 !NTHETA: angles
- 13 14 15 40 41 42 67 68 69
- 94 95 96 121 122 123 148 149 150
- 175 176 177 202 203 204 7 8 9
- 6 7 8 16 17 18 34 35 36
- 33 34 35 43 44 45 61 62 63
- 60 61 62 70 71 72 88 89 90
- 87 88 89 97 98 99 115 116 117
- 114 115 116 124 125 126 142 143 144
- 141 142 143 151 152 153 169 170 171
- 168 169 170 178 179 180 196 197 198
- 195 196 197 205 206 207 15 16 17
- 42 43 44 69 70 71 96 97 98
- 123 124 125 150 151 152 177 178 179
- 204 205 206 2 3 4 4 5 6
- 9 10 11 11 12 13 29 30 31
- 31 32 33 36 37 38 38 39 40
- 56 57 58 58 59 60 63 64 65
- 65 66 67 83 84 85 85 86 87
- 90 91 92 92 93 94 110 111 112
- 112 113 114 117 118 119 119 120 121
- 137 138 139 139 140 141 144 145 146
- 146 147 148 164 165 166 166 167 168
- 171 172 173 173 174 175 191 192 193
- 193 194 195 198 199 200 200 201 202
- 14 15 16 41 42 43 68 69 70
- 95 96 97 122 123 124 149 150 151
- 176 177 178 203 204 205 1 2 3
- 3 4 5 10 11 12 12 13 14
- 25 26 27 28 29 30 30 31 32
- 37 38 39 39 40 41 52 53 54
- 55 56 57 57 58 59 64 65 66
- 66 67 68 79 80 81 82 83 84
- 84 85 86 91 92 93 93 94 95
- 106 107 108 109 110 111 111 112 113
- 118 119 120 120 121 122 133 134 135
- 136 137 138 138 139 140 145 146 147
- 147 148 149 160 161 162 163 164 165
- 165 166 167 172 173 174 174 175 176
- 187 188 189 190 191 192 192 193 194
- 199 200 201 201 202 203 214 215 216
- 5 6 7 8 9 10 32 33 34
- 35 36 37 59 60 61 62 63 64
- 86 87 88 89 90 91 113 114 115
- 116 117 118 140 141 142 143 144 145
- 167 168 169 170 171 172 194 195 196
- 197 198 199 17 18 19 44 45 46
- 71 72 73 98 99 100 125 126 127
- 152 153 154 179 180 181 206 207 208
- 18 19 20 22 23 24 21 22 23
- 45 46 47 49 50 51 48 49 50
- 72 73 74 76 77 78 75 76 77
- 99 100 101 103 104 105 102 103 104
- 126 127 128 130 131 132 129 130 131
- 153 154 155 157 158 159 156 157 158
- 180 181 182 184 185 186 183 184 185
- 207 208 209 211 212 213 210 211 212
- 19 20 21 20 21 22 23 24 25
- 24 25 26 46 47 48 47 48 49
- 50 51 52 51 52 53 73 74 75
- 74 75 76 77 78 79 78 79 80
- 100 101 102 101 102 103 104 105 106
- 105 106 107 127 128 129 128 129 130
- 131 132 133 132 133 134 154 155 156
- 155 156 157 158 159 160 159 160 161
- 181 182 183 182 183 184 185 186 187
- 186 187 188 208 209 210 209 210 211
- 212 213 214 213 214 215
-
- 152 !NPHI: dihedrals
- 1 2 3 4 2 3 4 5
- 3 4 5 6 4 5 6 7
- 8 9 10 11 9 10 11 12
- 10 11 12 13 11 12 13 14
- 12 13 14 15 15 16 17 18
- 16 17 18 19 17 18 19 20
- 18 19 20 21 19 20 21 22
- 20 21 22 23 21 22 23 24
- 22 23 24 25 23 24 25 26
- 24 25 26 27 28 29 30 31
- 29 30 31 32 30 31 32 33
- 31 32 33 34 35 36 37 38
- 36 37 38 39 37 38 39 40
- 38 39 40 41 39 40 41 42
- 42 43 44 45 43 44 45 46
- 44 45 46 47 45 46 47 48
- 46 47 48 49 47 48 49 50
- 48 49 50 51 49 50 51 52
- 50 51 52 53 51 52 53 54
- 55 56 57 58 56 57 58 59
- 57 58 59 60 58 59 60 61
- 62 63 64 65 63 64 65 66
- 64 65 66 67 65 66 67 68
- 66 67 68 69 69 70 71 72
- 70 71 72 73 71 72 73 74
- 72 73 74 75 73 74 75 76
- 74 75 76 77 75 76 77 78
- 76 77 78 79 77 78 79 80
- 78 79 80 81 82 83 84 85
- 83 84 85 86 84 85 86 87
- 85 86 87 88 89 90 91 92
- 90 91 92 93 91 92 93 94
- 92 93 94 95 93 94 95 96
- 96 97 98 99 97 98 99 100
- 98 99 100 101 99 100 101 102
- 100 101 102 103 101 102 103 104
- 102 103 104 105 103 104 105 106
- 104 105 106 107 105 106 107 108
- 109 110 111 112 110 111 112 113
- 111 112 113 114 112 113 114 115
- 116 117 118 119 117 118 119 120
- 118 119 120 121 119 120 121 122
- 120 121 122 123 123 124 125 126
- 124 125 126 127 125 126 127 128
- 126 127 128 129 127 128 129 130
- 128 129 130 131 129 130 131 132
- 130 131 132 133 131 132 133 134
- 132 133 134 135 136 137 138 139
- 137 138 139 140 138 139 140 141
- 139 140 141 142 143 144 145 146
- 144 145 146 147 145 146 147 148
- 146 147 148 149 147 148 149 150
- 150 151 152 153 151 152 153 154
- 152 153 154 155 153 154 155 156
- 154 155 156 157 155 156 157 158
- 156 157 158 159 157 158 159 160
- 158 159 160 161 159 160 161 162
- 163 164 165 166 164 165 166 167
- 165 166 167 168 166 167 168 169
- 170 171 172 173 171 172 173 174
- 172 173 174 175 173 174 175 176
- 174 175 176 177 177 178 179 180
- 178 179 180 181 179 180 181 182
- 180 181 182 183 181 182 183 184
- 182 183 184 185 183 184 185 186
- 184 185 186 187 185 186 187 188
- 186 187 188 189 190 191 192 193
- 191 192 193 194 192 193 194 195
- 193 194 195 196 197 198 199 200
- 198 199 200 201 199 200 201 202
- 200 201 202 203 201 202 203 204
- 204 205 206 207 205 206 207 208
- 206 207 208 209 207 208 209 210
- 208 209 210 211 209 210 211 212
- 210 211 212 213 211 212 213 214
- 212 213 214 215 213 214 215 216
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
-
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg
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index c62a881b2..000000000
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg
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index 38ef54396..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt
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--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt
+++ /dev/null
@@ -1,216 +0,0 @@
-# This file defines the "frustrated" coarse-grained protein model used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-
-
-1beadFrustrated {
-
- # There are 3 atom types (referred to above as B, L, and N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:B 1.0
- @atom:L 1.0
- @atom:N 1.0
- }
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679
- $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341
- $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966
- $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709
- $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737
- $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098
- $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919
- $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901
- $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617
- $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043
- $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721
- $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951
- $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019
- $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217
- $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429
- $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711
- $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358
- $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719
- $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014
- $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053
- $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748
- $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224
- $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255
- $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346
- $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166
- $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097
- $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463
- }
-
- # bond-ID bond-Type atom-ID atom-ID
-
- write('Data Bonds') {
- $bond:b1 @bond:backbone $atom:a1 $atom:a2
- $bond:b2 @bond:backbone $atom:a2 $atom:a3
- $bond:b3 @bond:backbone $atom:a3 $atom:a4
- $bond:b4 @bond:backbone $atom:a4 $atom:a5
- $bond:b5 @bond:backbone $atom:a5 $atom:a6
- $bond:b6 @bond:backbone $atom:a6 $atom:a7
- $bond:b7 @bond:backbone $atom:a7 $atom:a8
- $bond:b8 @bond:backbone $atom:a8 $atom:a9
- $bond:b9 @bond:backbone $atom:a9 $atom:a10
- $bond:b10 @bond:backbone $atom:a10 $atom:a11
- $bond:b11 @bond:backbone $atom:a11 $atom:a12
- $bond:b12 @bond:backbone $atom:a12 $atom:a13
- $bond:b13 @bond:backbone $atom:a13 $atom:a14
- $bond:b14 @bond:backbone $atom:a14 $atom:a15
- $bond:b15 @bond:backbone $atom:a15 $atom:a16
- $bond:b16 @bond:backbone $atom:a16 $atom:a17
- $bond:b17 @bond:backbone $atom:a17 $atom:a18
- $bond:b18 @bond:backbone $atom:a18 $atom:a19
- $bond:b19 @bond:backbone $atom:a19 $atom:a20
- $bond:b20 @bond:backbone $atom:a20 $atom:a21
- $bond:b21 @bond:backbone $atom:a21 $atom:a22
- $bond:b22 @bond:backbone $atom:a22 $atom:a23
- $bond:b23 @bond:backbone $atom:a23 $atom:a24
- $bond:b24 @bond:backbone $atom:a24 $atom:a25
- $bond:b25 @bond:backbone $atom:a25 $atom:a26
- $bond:b26 @bond:backbone $atom:a26 $atom:a27
- }
-
- # (3-body) Angles are specified below
-
- # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
- # (These interactions are not determined by atom type.)
-
- # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
-
- write('Data Dihedrals') {
-
- $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7
-
- # Dihedral angle forces in the turn regions were switched off
- # (in this model) so just I comment them out (and \ the variable names).
- # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8
- # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9
- # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10
-
- $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15
-
- # Dihedral angle forces in the turn regions were switched off
- # (in this model) so just I comment them out (and \ the variable names).
- # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16
- # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17
-
- $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27
- }
-
- # All consecutively bonded triplets of atoms same 3-body bond-angle
- # interaction parameters. Of coarse, we could specify them all explicitly
- # (as we did for the dihedrals above), but I wanted to show how to specify
- # angles by atom type instead. (You can do this for dihedrals & impropers
- # also.)
-
- # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
-
- write_once('Data Angles By Type') {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # (The "*" is a wildcard character. I use "*" to denote any atom-type or
- # bond-type which is defined within the current namespace: 1beadFrustrated)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
- pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
- pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
- }
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond-Type bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 100.0 1.0
- }
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # angle-Type anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 13.3333333333 105.0
- }
-
-
- # We use tabular dihedral potentials to implement the dihedral forces.
- # (Actually there is a way to use Fourier series, using multiple charmm
- # style dihedral interactions, but it's slower and messier.)
-
- write_once("In Settings") {
- # style file keyword
- dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
- dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
- # No need to specify dihedral interactions in the turn regions. (none exist)
- }
-
- write_once("In Settings") {
- # Optional: define the atoms in the "proteins" group
- group proteins type @atom:B
- group proteins type @atom:L
- group proteins type @atom:N
- }
-
- # LAMMPS has many available force field styles (and atom styles).
- # Here, we pick the ones which work well for this molecular model:
-
- write_once("In Init") {
- # --- Default options for the "1BeadFrustrated" protein model ---
- # --- (These can be overridden later.) ---
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid table spline 360
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-} # 1beadFrustrated
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt
deleted file mode 100644
index 54e2de437..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt
+++ /dev/null
@@ -1,85 +0,0 @@
-import "1beadFrustrated.lt"
-
-
-# Alternate starting conformation (same molecule):
-
-
-1beadMisfolded inherits 1beadFrustrated {
-
- # This molecule "inherits" all of its features from "1beadFrustrated".
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876
- $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251
- $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085
- $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451
- $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135
- $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977
- $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409
- $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275
- $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938
- $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398
- $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186
- $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916
- $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704
- $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331
- $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056
- $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167
- $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633
- $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523
- $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791
- $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346
- $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555
- $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946
- $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493
- $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934
- $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086
- $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181
- $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868
- }
-
-} # 1beadMisfolded
-
-
-1beadUnfolded inherits 1beadFrustrated {
-
- # This molecule "inherits" all of its features from "1beadFrustrated"
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
- $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
- $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
- $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
- $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
- $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
- $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
- $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
- $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
- $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
- $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
- $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
- $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
- $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
- $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
- $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
- $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
- $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
- $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
- $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
- $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
- $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
- $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
- $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
- $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
- $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
- $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
- }
-
-} # 1beadUnfolded
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py
deleted file mode 100755
index 9b86809cc..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between atoms in the
-# protein and a chaperone provided in the supplemental materials section of:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# This is stored in a tabulated force field with a singularity at a distance R.
-#
-# To calculate the table for interaction between
-# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
-# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181
-# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
-# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True
-
-from math import *
-import sys
-
-def U(r, eps, sigma, R, h):
- #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
- # Formula is undefined at r=0, but you can take the limit:
- if r <= 0:
- return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
- - h*pow((sigma/R), 6.0))
- xp = sigma/(r+R)
- xm = sigma/(r-R)
- term10 = pow(xm, 10.0) - pow(xp, 10.0)
- term4 = pow(xm, 4.0) - pow(xp, 4.0)
- return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
-
-def F(r, eps, sigma, R, h):
- # Formula is undefined at r=0, but you can take the limit:
- if r <= 0:
- return 0.0
- product_term_a = U(r, eps, sigma, R, h) / r
- ixp = (r+R)/sigma
- ixm = (r-R)/sigma
- dix_dr = 1.0/sigma
- term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
- term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0))
- product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
- return product_term_a + product_term_b
-
-
-class InputError(Exception):
- """ A generic exception object containing a string for error reporting.
-
- """
- def __init__(self, err_msg):
- self.err_msg = err_msg
- def __str__(self):
- return self.err_msg
- def __repr__(self):
- return str(self)
-
-if len(sys.argv) < 8:
- sys.stderr.write("Error: expected 7 arguments:\n"
- "\n"
- "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
- sys.exit(-1)
-
-epsilon = float(sys.argv[1])
-sigma = float(sys.argv[2])
-R = float(sys.argv[3])
-h = float(sys.argv[4])
-rmin = float(sys.argv[5])
-rmax = float(sys.argv[6])
-N = int(sys.argv[7])
-
-subtract_Urcut = False
-if len(sys.argv) == 9:
- subtract_Urcut = True
-rcut = rmax
-
-for i in range(0,N):
- r = rmin + i*(rmax-rmin)/(N-1)
- U_r = U(r, epsilon, sigma, R, h)
- F_r = F(r, epsilon, sigma, R, h)
- if subtract_Urcut:
- U_r -= U(rcut, epsilon, sigma, R, h)
- if (r >= rcut) or (i==N-1):
- U_r = 0.0
- F_r = 0.0
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py
deleted file mode 100755
index 34c66418a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of dihedral angle interactions used in the alpha-helix
-# and beta-sheet regions of the frustrated protein model described in
-# provided in figure 8 of the supplemental materials section of:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# Note that the "A" and "B" parameters were incorrectly reported to be
-# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
-# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
-# and 180 degrees, respectively. Both expA and expB were 6.0.
-#
-# To generate the table used for the alpha-helix (1 degree resolution) use this:
-# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
-# To generate the table used for the beta-sheets (1 degree resolution) use this:
-# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
-#
-# (If you're curious as to why I set the location of the minima at phi_alpha
-# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
-# I think the correct value turns out to be something closer to 50 degrees.)
-
-
-from math import *
-import sys
-
-
-# The previous version included the repulsive core term
-def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
- conv_units = pi/180.0
- if use_radians:
- conv_units = 1.0
- termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
- termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
- return -A*termA - B*termB
-
-# The previous version included the repulsive core term
-def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
- conv_units = pi/180.0
- if use_radians:
- conv_units = 1.0
- termA = (0.5*sin(0.5*(phi-phiA)*conv_units) *
- expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
- termB = (0.5*sin(0.5*(phi-phiB)*conv_units) *
- expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
- return -conv_units*(A*termA + B*termB)
-
-if len(sys.argv) != 10:
- sys.stderr.write("Error: expected 9 arguments:\n"
- "\n"
- "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
- sys.exit(-1)
-
-A = float(sys.argv[1])
-phiA = float(sys.argv[2])
-expA = float(sys.argv[3])
-B = float(sys.argv[4])
-phiB = float(sys.argv[5])
-expB = float(sys.argv[6])
-phi_min = float(sys.argv[7])
-phi_max = float(sys.argv[8])
-N = int(sys.argv[9])
-
-for i in range(0,N):
- phi = phi_min + i*(phi_max - phi_min)/(N-1)
- U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
- F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
- print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt
deleted file mode 100644
index 1d37823b7..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt
+++ /dev/null
@@ -1,41 +0,0 @@
-# Here we define a trivial molecule containing only one particle.
-
-Minichaperone {
-
- # atomID molID atomType charge x y z
-
- write("Data Atoms") {
- $atom:C $mol @atom:C 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:C 100.0
- }
-
- write_once("In Settings") {
- # If for some reason there are multiple chaperones present,
- # I assume that they interact repulsively (hence, L=0)
-
- # i j pairStyle eps sig K L
-
- pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0
-
- # Optional: define the atoms in the "chaperonins" group:
- # (Defining a group for the chaperone makes it easy to immobilize it later.)
-
- group chaperones type @atom:C
- }
-
- # Specify which pair_styles, and atom styles work well with
- # this model. (Again this can be overridden later.)
-
- write_once("In Init") {
- units lj
- atom_style full
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0
- }
-
-} # Minichaperone
-
-# We have not specified how this particle interacts with other particles
-# besides itself. Later on you must do this.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt
deleted file mode 100644
index 8f8c37d08..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt
+++ /dev/null
@@ -1,72 +0,0 @@
-write_once("Data Boundary") {
- 0.0 80.0 xlo xhi
- 0.0 80.0 ylo yhi
- 0.0 80.0 zlo zhi
-}
-
-
-import "1beadFrustrated_variants.lt"
-import "minichaperone.lt"
-
-
-# Create 8 proteins and 8 chaperones (2x2x2 array):
-# NOTE: Below I create multiple proteins and multiple chaperones
-# to see what would happen. (I suspect nothing good. In the
-# 2006 paper, only 1 protein and 1 chaperone were present.)
-
-
-proteins = new 1beadUnfolded [2].move(40,0,0)
- [2].move(0,40,0)
- [2].move(0,0,40)
-
-chaperones = new Minichaperone [2].move(40,0,0)
- [2].move(0,40,0)
- [2].move(0,0,40)
-
-proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones
-
-
-
-# If you only want 1 protein and 1 chaperone
-# then replace the lines above with:
-#
-# protein = new 1beadMisfolded
-# chaperone = new Minichaperone
-
-
-
-
-
-# ---- Now define interactions between the atoms in the protein ----
-# ---- (named "B", "L", "N") and the atom which represents the ----
-# ---- chaperone ("c"). These interactions are tabulated. ----
-
-write_once("In Settings") {
- pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6
- pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0
- pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0
-}
-
-# Note: If you want purely repulsive spheres (crowding, h=0.0)
-# instead of an attractive "hydrophobic" chaperone (h=0.6)
-# then replace "table_minichaperone_h=0_6.dat CH_H0_6"
-# with "table_minichaperone_h=0.dat CH_H0"
-# (... or just use an ordinary Lennard-Jones interaction
-# with sigma = 6.0 and epsilon near 0.0)
-
-
-# LAMMPS has many available force field styles (and atom styles). Here we
-# select the ones which work well for the full combine system. (This should
-# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt")
-
-
-write_once("In Init") {
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid table spline 360
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat
deleted file mode 100644
index d660fee30..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat
+++ /dev/null
@@ -1,735 +0,0 @@
-# Table of the potential and its negative derivative for frustrated alpha helix
-# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
-# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
-
-FRUSTRATED_ALPHA
-N 360 DEGREES
-
-1 0.0 -2.74081145103 0.0783990792662
-2 1.0 -2.81950869101 0.0789852583442
-3 2.0 -2.89876136749 0.0795096391909
-4 3.0 -2.97850675562 0.0799703813963
-5 4.0 -3.05868032959 0.0803657243943
-6 5.0 -3.13921584545 0.0806939935737
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-
-# Table of the potential and its negative derivative for frustrated beta sheet
-# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
-# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
-
-FRUSTRATED_BETA
-N 360 DEGREES
-
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-359 358.0 -2.41296973939 0.0719124463259
-360 359.0 -2.48521512832 0.072569481568
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat
deleted file mode 100644
index d2b1ed3aa..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat
+++ /dev/null
@@ -1,988 +0,0 @@
-# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6)
-# Generated using:
-# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
-
-CH_H0.6
-N 981 R 3.1 8.0
-
-1 3.1 24321971157.7 2.4400451019e+12
-2 3.105 14907528428.0 1.42456746092e+12
-3 3.11 9347010266.92 8.52735030437e+11
-4 3.115 5983057175.03 5.22187648991e+11
-5 3.12 3902942155.05 3.26496996649e+11
-6 3.125 2590648415.38 2.0808159227e+11
-7 3.13 1747350825.1 1.34970444886e+11
-8 3.135 1196139798.89 88984974583.5
-9 3.14 830130182.341 59559787515.6
-10 3.145 583518174.975 40428507749.3
-11 3.15 415078797.287 27803974550.9
-12 3.155 298562827.719 19356989964.4
-13 3.16 217001769.743 13631486848.5
-14 3.165 159270305.159 9703243449.66
-15 3.17 117976881.962 6977184032.49
-16 3.175 88149161.6455 5064988683.98
-17 3.18 66402860.1298 3710042118.5
-18 3.185 50409022.6215 2740737360.59
-19 3.19 38548170.6708 2041021063.98
-20 3.195 29683036.1074 1531572773.33
-21 3.2 23007502.8905 1157631256.92
-22 3.205 17945109.6836 881028781.898
-23 3.21 14080149.2893 674921399.554
-24 3.215 11110438.2418 520266326.167
-25 3.22 8814639.75879 403443800.764
-26 3.225 7029455.47123 314636408.027
-27 3.23 5633571.16439 246714657.082
-28 3.235 4536265.59262 194464091.949
-29 3.24 3669265.83647 154044868.616
-30 3.245 2980881.1453 122610915.077
-31 3.25 2431748.15466 98039536.8272
-32 3.255 1991724.07297 78738058.3506
-33 3.26 1637603.46485 63504600.2322
-34 3.265 1351429.90872 51427172.534
-35 3.27 1119240.11293 41810074.9071
-36 3.275 930124.378436 34119886.2947
-37 3.28 775519.857832 27945597.578
-38 3.285 648676.115123 22969017.4933
-39 3.29 544248.919174 18942684.9889
-40 3.295 457989.984944 15673297.5619
-41 3.3 386508.875651 13009215.1485
-42 3.305 327089.446276 10830991.226
-43 3.31 277547.709074 9044163.93118
-44 3.315 236121.303553 7573742.76366
-45 3.32 201383.18845 6359973.47163
-46 3.325 172173.978278 5355070.91875
-47 3.33 147548.691578 4520688.28477
-48 3.335 126734.684289 3825948.80978
-49 3.34 109098.298235 3245909.11014
-50 3.345 94118.3261235 2760354.93052
-51 3.35 81364.827777 2352853.97713
-52 3.355 70482.1624146 2010008.31682
-53 3.36 61175.3541703 1720862.26897
-54 3.365 53199.1018261 1476431.88582
-55 3.37 46348.8930587 1269329.84244
-56 3.375 40453.7990113 1093465.44786
-57 3.38 35370.6146686 943803.998782
-58 3.385 30979.0803706 816173.162054
-59 3.39 27177.9744013 707106.743488
-60 3.395 23881.9094124 613718.268337
-61 3.4 21018.6991377 533598.403624
-62 3.405 18527.1884441 464731.50307
-63 3.41 16355.4608211 405427.532611
-64 3.415 14459.3541284 354266.400629
-65 3.42 12801.228731 310052.319542
-66 3.425 11348.9427887 271776.300627
-67 3.43 10074.9979765 238585.259865
-68 3.435 8955.82575185 209756.510836
-69 3.44 7971.18978782 184676.657916
-70 3.445 7103.68463562 162824.092297
-71 3.45 6338.31427303 143754.444665
-72 3.455 5662.13711315 127088.469763
-73 3.46 5063.9664184 112501.9356
-74 3.465 4534.11699728 99717.1686967
-75 3.47 4064.19064042 88495.970274
-76 3.475 3646.89404446 78633.6696895
-77 3.48 3275.88403311 69954.1231906
-78 3.485 2945.63575657 62305.4999784
-79 3.49 2651.33026883 55556.7252625
-80 3.495 2388.75847582 49594.4725913
-81 3.5 2154.23893796 44320.6162531
-82 3.505 1944.54741747 39650.0697323
-83 3.51 1756.8563988 35508.9486835
-84 3.515 1588.68309151 31833.0071751
-85 3.52 1437.84465949 28566.3044359
-86 3.525 1302.41961585 25660.0663588
-87 3.53 1180.71448694 23071.7118275
-88 3.535 1071.23498579 20764.0187577
-89 3.54 972.661050857 18704.4087568
-90 3.545 883.825202407 16864.3326446
-91 3.55 803.693750954 15218.7418698
-92 3.555 731.350460573 13745.6331832
-93 3.56 665.982328363 12425.6558809
-94 3.565 606.867190408 11241.7725673
-95 3.57 553.362906393 10178.9657593
-96 3.575 504.897910387 9223.98381086
-97 3.58 460.962945446 8365.12060921
-98 3.585 421.103825306 7592.02431669
-99 3.59 384.915088285 6895.53112553
-100 3.595 352.034427161 6267.5205811
-101 3.6 322.137794751 5700.78952663
-102 3.605 294.935098544 5188.94214534
-103 3.61 270.166409464 4726.29393494
-104 3.615 247.598619855 4307.78775517
-105 3.62 227.022494431 3928.92034957
-106 3.625 208.250065337 3585.67796495
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-110 3.645 148.060491326 2502.83977901
-111 3.65 136.084113848 2291.05779528
-112 3.655 125.118099223 2098.37134728
-113 3.66 115.071648949 1922.94202847
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-139 3.79 13.3534346012 230.696628411
-140 3.795 12.2435282565 213.494500686
-141 3.8 11.2162976896 197.607847495
-142 3.805 10.2654345142 182.930656184
-143 3.81 9.38513741093 169.365969178
-144 3.815 8.57006893443 156.825064535
-145 3.82 7.81531621929 145.226714879
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-152 3.855 3.88222444642 84.8980793495
-153 3.86 3.47362542484 78.6206280516
-154 3.865 3.09525764949 72.7995867184
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat
deleted file mode 100644
index 82eaa7e15..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat
+++ /dev/null
@@ -1,989 +0,0 @@
-# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0)
-# Generated using:
-# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True
-
-CH_H0
-N 981 R 3.1 8.0
-
-1 3.1 24322007640.7 2.44004657299e+12
-2 3.105 14907558394.3 1.42456861215e+12
-3 3.11 9347035105.18 8.52735941633e+11
-4 3.115 5983077933.86 5.22188377701e+11
-5 3.12 3902959636.31 3.26497584961e+11
-6 3.125 2590663239.27 2.08082071378e+11
-7 3.13 1747363476.38 1.34970838198e+11
-8 3.135 1196150660.14 88985299862.7
-9 3.14 830139558.184 59560058382.9
-10 3.145 583526310.01 40428734750.9
-11 3.15 415085889.414 27804165925.8
-12 3.155 298569038.21 19357152203.7
-13 3.16 217007230.904 13631625105.8
-14 3.165 159275126.218 9703361847.17
-15 3.17 117981153.625 6977285889.84
-16 3.175 88152959.6539 5065076691.93
-17 3.18 66406248.0614 3710118471.36
-18 3.185 50412054.1061 2740803858.1
-19 3.19 38550891.1571 2041079190.29
-20 3.195 29685484.2812 1531623758.63
-21 3.2 23009711.8183 1157676125.86
-22 3.205 17947107.7408 881068391.885
-23 3.21 14081960.9175 674956471.214
-24 3.215 11112084.5698 520297467.685
-25 3.22 8816139.11379 403471527.483
-26 3.225 7030823.80219 314661158.279
-27 3.23 5634822.39381 246736805.049
-28 3.235 4537411.91017 194483958.161
-29 3.24 3670317.94503 154062728.557
-30 3.245 2981848.4679 122627006.268
-31 3.25 2432639.00923 98054064.6797
-32 3.255 1992545.82032 78751201.0309
-33 3.26 1638362.63452 63516512.707
-34 3.265 1352132.30623 51437989.9558
-35 3.27 1119890.91156 41819915.4536
-36 3.275 930728.197936 34128853.5593
-37 3.28 776080.832192 27953782.5881
-38 3.285 649197.950984 22976500.4202
-39 3.29 544734.946388 18949536.6006
-40 3.295 458443.200409 15679580.461
-41 3.3 386931.981432 13014984.83
-42 3.305 327484.882814 10836296.983
-43 3.31 277917.684205 9049049.63384
-44 3.315 236467.817902 7578247.52911
-45 3.32 201708.057716 6364132.2427
-46 3.325 172478.852825 5358914.96458
-47 3.33 147835.073691 4524245.63494
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-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min
deleted file mode 100644
index 0cde82b1f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min
+++ /dev/null
@@ -1,24 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# Optional: Make sure the pairwise energies look reasonable:
-pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0
-pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0
-pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt
deleted file mode 100644
index d28f48dd8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt
+++ /dev/null
@@ -1,46 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-# I you want to be careful, you can minimize the system first.
-# (Try using "run.in.min" and uncomment the line below.)
-# read_data system_after_min.data
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.025
-dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-fix fxlan all langevin 0.25 0.25 1.0 48279
-fix fxnve all nve
-
-# Notes:
-# The temperature is in reduced units and is set to 0.25
-# which is the folding temperature for the frustrated protein
-# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
-# as it was in the paper. (Hopefully folding times should be similar.)
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 5000 #(time interval for printing out "thermo" data)
-
-#restart 100000000 restart_nvt
-
-run 1000000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README.TXT
deleted file mode 100644
index 77af3de15..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README.TXT
+++ /dev/null
@@ -1,29 +0,0 @@
-# This directory demonstrates how to run a short simulation of
-# the "frustrated" coarse-grained protein model used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-#
-# During this short simulation (run_short_sim.nvt.in) the protein evolves
-# from an unfolded initial conformation to a misfolded conformation.
-# (Visualize using VMD. Note: It can take hundreds of millions of
-# timesteps to escape from this conformation and reach the folded state.)
-#
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh
deleted file mode 100755
index 6c5417239..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-# You would probably run lammps this way:
-#
-# lmp_ubuntu -i run.in.nvt
-
-# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
-# to the input scripts & data files you created earlier when you ran moltemplate
-# system.in.init, system.in.settings, system.data
-
-
-# -----------------------------------
-
-LAMMPS_COMMAND="lmp_mpi"
-
-# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary.
-
-# Run lammps using the following 3 commands:
-
-"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh
deleted file mode 100755
index df49f4384..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -overlay-dihedrals system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
- cp -r table*.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
deleted file mode 100644
index c7f8572b2..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
+++ /dev/null
@@ -1,85 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 27 !NATOM
- 1 1 2 2 0.000000 1.0000 0
- 2 1 1 1 0.000000 1.0000 0
- 3 1 2 2 0.000000 1.0000 0
- 4 1 1 1 0.000000 1.0000 0
- 5 1 2 2 0.000000 1.0000 0
- 6 1 1 1 0.000000 1.0000 0
- 7 1 3 3 0.000000 1.0000 0
- 8 1 3 3 0.000000 1.0000 0
- 9 1 1 1 0.000000 1.0000 0
- 10 1 2 2 0.000000 1.0000 0
- 11 1 1 1 0.000000 1.0000 0
- 12 1 2 2 0.000000 1.0000 0
- 13 1 1 1 0.000000 1.0000 0
- 14 1 2 2 0.000000 1.0000 0
- 15 1 3 3 0.000000 1.0000 0
- 16 1 3 3 0.000000 1.0000 0
- 17 1 3 3 0.000000 1.0000 0
- 18 1 1 1 0.000000 1.0000 0
- 19 1 1 1 0.000000 1.0000 0
- 20 1 2 2 0.000000 1.0000 0
- 21 1 2 2 0.000000 1.0000 0
- 22 1 1 1 0.000000 1.0000 0
- 23 1 1 1 0.000000 1.0000 0
- 24 1 2 2 0.000000 1.0000 0
- 25 1 2 2 0.000000 1.0000 0
- 26 1 1 1 0.000000 1.0000 0
- 27 1 2 2 0.000000 1.0000 0
-
- 26 !NBOND: bonds
- 1 2 2 3 3 4 4 5
- 5 6 6 7 7 8 8 9
- 9 10 10 11 11 12 12 13
- 13 14 14 15 15 16 16 17
- 17 18 18 19 19 20 20 21
- 21 22 22 23 23 24 24 25
- 25 26 26 27
-
- 25 !NTHETA: angles
- 13 14 15 7 8 9 6 7 8
- 16 17 18 15 16 17 2 3 4
- 4 5 6 9 10 11 11 12 13
- 14 15 16 1 2 3 3 4 5
- 10 11 12 12 13 14 25 26 27
- 5 6 7 8 9 10 17 18 19
- 18 19 20 22 23 24 21 22 23
- 19 20 21 20 21 22 23 24 25
- 24 25 26
-
- 19 !NPHI: dihedrals
- 1 2 3 4 2 3 4 5
- 3 4 5 6 4 5 6 7
- 8 9 10 11 9 10 11 12
- 10 11 12 13 11 12 13 14
- 12 13 14 15 15 16 17 18
- 16 17 18 19 17 18 19 20
- 18 19 20 21 19 20 21 22
- 20 21 22 23 21 22 23 24
- 22 23 24 25 23 24 25 26
- 24 25 26 27
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg
deleted file mode 100644
index 0869126bd..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg
deleted file mode 100644
index 357bc780a..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt
deleted file mode 100644
index 074b55c73..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt
+++ /dev/null
@@ -1,216 +0,0 @@
-# This file defines the "frustrated" coarse-grained protein model used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-
-
-1beadFrustrated {
-
- # There are 3 atom types (referred to above as B, L, and N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:B 1.0
- @atom:L 1.0
- @atom:N 1.0
- }
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679
- $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341
- $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966
- $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709
- $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737
- $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098
- $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919
- $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901
- $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617
- $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043
- $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721
- $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951
- $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019
- $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217
- $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429
- $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711
- $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358
- $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719
- $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014
- $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053
- $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748
- $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224
- $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255
- $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346
- $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166
- $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097
- $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463
- }
-
- # bond-ID bond-Type atom-ID atom-ID
-
- write("Data Bonds") {
- $bond:b1 @bond:backbone $atom:a1 $atom:a2
- $bond:b2 @bond:backbone $atom:a2 $atom:a3
- $bond:b3 @bond:backbone $atom:a3 $atom:a4
- $bond:b4 @bond:backbone $atom:a4 $atom:a5
- $bond:b5 @bond:backbone $atom:a5 $atom:a6
- $bond:b6 @bond:backbone $atom:a6 $atom:a7
- $bond:b7 @bond:backbone $atom:a7 $atom:a8
- $bond:b8 @bond:backbone $atom:a8 $atom:a9
- $bond:b9 @bond:backbone $atom:a9 $atom:a10
- $bond:b10 @bond:backbone $atom:a10 $atom:a11
- $bond:b11 @bond:backbone $atom:a11 $atom:a12
- $bond:b12 @bond:backbone $atom:a12 $atom:a13
- $bond:b13 @bond:backbone $atom:a13 $atom:a14
- $bond:b14 @bond:backbone $atom:a14 $atom:a15
- $bond:b15 @bond:backbone $atom:a15 $atom:a16
- $bond:b16 @bond:backbone $atom:a16 $atom:a17
- $bond:b17 @bond:backbone $atom:a17 $atom:a18
- $bond:b18 @bond:backbone $atom:a18 $atom:a19
- $bond:b19 @bond:backbone $atom:a19 $atom:a20
- $bond:b20 @bond:backbone $atom:a20 $atom:a21
- $bond:b21 @bond:backbone $atom:a21 $atom:a22
- $bond:b22 @bond:backbone $atom:a22 $atom:a23
- $bond:b23 @bond:backbone $atom:a23 $atom:a24
- $bond:b24 @bond:backbone $atom:a24 $atom:a25
- $bond:b25 @bond:backbone $atom:a25 $atom:a26
- $bond:b26 @bond:backbone $atom:a26 $atom:a27
- }
-
- # (3-body) Angles are specified below
-
- # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
- # (These interactions are not determined by atom type.)
-
- # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
-
- write("Data Dihedrals") {
-
- $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7
-
- # Dihedral angle forces in the turn regions were switched off
- # (in this model) so just I comment them out (and \ the variable names).
- # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8
- # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9
- # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10
-
- $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15
-
- # Dihedral angle forces in the turn regions were switched off
- # (in this model) so just I comment them out (and \ the variable names).
- # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16
- # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17
-
- $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27
- }
-
- # All consecutively bonded triplets of atoms same 3-body bond-angle
- # interaction parameters. Of coarse, we could specify them all explicitly
- # (as we did for the dihedrals above), but I wanted to show how to specify
- # angles by atom type instead. (You can do this for dihedrals & impropers
- # also.)
-
- # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # (The "*" is a wildcard character. I use "*" to denote any atom-type or
- # bond-type which is defined within the current namespace: 1beadFrustrated)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
- pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
- pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
- }
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond-Type bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 100.0 1.0
- }
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # angle-Type anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 13.3333333333 105.0
- }
-
-
- # We use tabular dihedral potentials to implement the dihedral forces.
- # (Actually there is a way to use Fourier series, using multiple charmm
- # style dihedral interactions, but it's slower and messier.)
-
- write_once("In Settings") {
- # style file keyword
- dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
- dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
- # No need to specify dihedral interactions in the turn regions. (none exist)
- }
-
- write_once("In Settings") {
- # Optional: define the atoms in the "proteins" group
- group proteins type @atom:B
- group proteins type @atom:L
- group proteins type @atom:N
- }
-
- # LAMMPS has many available force field styles (and atom styles).
- # Here, we pick the ones which work well for this molecular model:
-
- write_once("In Init") {
- # --- Default options for the "1BeadFrustrated" protein model ---
- # --- (These can be overridden later.) ---
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid table spline 360
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-} # 1beadFrustrated
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt
deleted file mode 100644
index 54e2de437..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt
+++ /dev/null
@@ -1,85 +0,0 @@
-import "1beadFrustrated.lt"
-
-
-# Alternate starting conformation (same molecule):
-
-
-1beadMisfolded inherits 1beadFrustrated {
-
- # This molecule "inherits" all of its features from "1beadFrustrated".
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876
- $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251
- $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085
- $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451
- $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135
- $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977
- $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409
- $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275
- $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938
- $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398
- $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186
- $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916
- $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704
- $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331
- $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056
- $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167
- $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633
- $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523
- $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791
- $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346
- $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555
- $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946
- $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493
- $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934
- $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086
- $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181
- $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868
- }
-
-} # 1beadMisfolded
-
-
-1beadUnfolded inherits 1beadFrustrated {
-
- # This molecule "inherits" all of its features from "1beadFrustrated"
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
- $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
- $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
- $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
- $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
- $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
- $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
- $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
- $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
- $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
- $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
- $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
- $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
- $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
- $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
- $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
- $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
- $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
- $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
- $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
- $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
- $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
- $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
- $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
- $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
- $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
- $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
- }
-
-} # 1beadUnfolded
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py
deleted file mode 100755
index 34c66418a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of dihedral angle interactions used in the alpha-helix
-# and beta-sheet regions of the frustrated protein model described in
-# provided in figure 8 of the supplemental materials section of:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# Note that the "A" and "B" parameters were incorrectly reported to be
-# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
-# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
-# and 180 degrees, respectively. Both expA and expB were 6.0.
-#
-# To generate the table used for the alpha-helix (1 degree resolution) use this:
-# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
-# To generate the table used for the beta-sheets (1 degree resolution) use this:
-# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
-#
-# (If you're curious as to why I set the location of the minima at phi_alpha
-# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
-# I think the correct value turns out to be something closer to 50 degrees.)
-
-
-from math import *
-import sys
-
-
-# The previous version included the repulsive core term
-def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
- conv_units = pi/180.0
- if use_radians:
- conv_units = 1.0
- termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
- termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
- return -A*termA - B*termB
-
-# The previous version included the repulsive core term
-def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
- conv_units = pi/180.0
- if use_radians:
- conv_units = 1.0
- termA = (0.5*sin(0.5*(phi-phiA)*conv_units) *
- expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
- termB = (0.5*sin(0.5*(phi-phiB)*conv_units) *
- expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
- return -conv_units*(A*termA + B*termB)
-
-if len(sys.argv) != 10:
- sys.stderr.write("Error: expected 9 arguments:\n"
- "\n"
- "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
- sys.exit(-1)
-
-A = float(sys.argv[1])
-phiA = float(sys.argv[2])
-expA = float(sys.argv[3])
-B = float(sys.argv[4])
-phiB = float(sys.argv[5])
-expB = float(sys.argv[6])
-phi_min = float(sys.argv[7])
-phi_max = float(sys.argv[8])
-N = int(sys.argv[9])
-
-for i in range(0,N):
- phi = phi_min + i*(phi_max - phi_min)/(N-1)
- U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
- F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
- print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt
deleted file mode 100644
index a27595559..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt
+++ /dev/null
@@ -1,20 +0,0 @@
-import "1beadFrustrated_variants.lt"
-
-
-protein = new 1beadUnfolded
-
-
-
-# Note: The protein begins in an "Unfolded" conformation. If instead
-# you want it to begin in the folded or misfolded conformations use:
-# protein = new 1beadFrustrated # or
-# protein = new 1beadMisfolded
-
-
-
-# ("27.0" is the length of the protein when maximally extended)
-write_once("Data Boundary") {
- 0.0 27.0 xlo xhi
- 0.0 27.0 ylo yhi
- 0.0 27.0 zlo zhi
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat
deleted file mode 100644
index d660fee30..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat
+++ /dev/null
@@ -1,735 +0,0 @@
-# Table of the potential and its negative derivative for frustrated alpha helix
-# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
-# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
-
-FRUSTRATED_ALPHA
-N 360 DEGREES
-
-1 0.0 -2.74081145103 0.0783990792662
-2 1.0 -2.81950869101 0.0789852583442
-3 2.0 -2.89876136749 0.0795096391909
-4 3.0 -2.97850675562 0.0799703813963
-5 4.0 -3.05868032959 0.0803657243943
-6 5.0 -3.13921584545 0.0806939935737
-7 6.0 -3.22004543014 0.0809536062381
-8 7.0 -3.30109967628 0.0811430773977
-9 8.0 -3.38230774267 0.0812610253741
-10 9.0 -3.46359746038 0.0813061772009
-11 10.0 -3.54489544401 0.0812773738039
-12 11.0 -3.62612720812 0.0811735749433
-13 12.0 -3.70721728841 0.0809938639029
-14 13.0 -3.78808936748 0.080737451911
-15 14.0 -3.86866640485 0.0804036822781
-16 15.0 -3.94887077101 0.0799920342374
-17 16.0 -4.02862438516 0.0795021264757
-18 17.0 -4.10784885622 0.0789337203415
-19 18.0 -4.18646562704 0.0782867227197
-20 19.0 -4.26439612115 0.0775611885609
-21 20.0 -4.34156189202 0.0767573230567
-22 21.0 -4.41788477419 0.0758754834523
-23 22.0 -4.49328703609 0.0749161804868
-24 23.0 -4.56769153408 0.0738800794563
-25 24.0 -4.64102186743 0.0727680008923
-26 25.0 -4.71320253365 0.0715809208518
-27 26.0 -4.78415908407 0.0703199708131
-28 27.0 -4.85381827903 0.0689864371778
-29 28.0 -4.92210824234 0.067581760373
-30 29.0 -4.98895861476 0.0661075335571
-31 30.0 -5.05430070586 0.0645655009259
-32 31.0 -5.11806764409 0.0629575556235
-33 32.0 -5.18019452449 0.061285737258
-34 33.0 -5.24061855376 0.0595522290273
-35 34.0 -5.29927919225 0.0577593544584
-36 35.0 -5.3561182925 0.0559095737673
-37 36.0 -5.41108023395 0.0540054798439
-38 37.0 -5.46411205346 0.0520497938726
-39 38.0 -5.51516357127 0.0500453605949
-40 39.0 -5.56418751203 0.0479951432253
-41 40.0 -5.61113962059 0.0459022180302
-42 41.0 -5.65597877221 0.0437697685824
-43 42.0 -5.69866707689 0.0416010797029
-44 43.0 -5.7391699774 0.0393995311046
-45 44.0 -5.77745634094 0.0371685907508
-46 45.0 -5.81349854393 0.034911807945
-47 46.0 -5.84727254977 0.0326328061676
-48 47.0 -5.87875797937 0.030335275675
-49 48.0 -5.90793817411 0.0280229658805
-50 49.0 -5.93480025113 0.0256996775336
-51 50.0 -5.95933515063 0.0233692547166
-52 51.0 -5.98153767519 0.0210355766777
-53 52.0 -6.00140652074 0.0187025495211
-54 53.0 -6.01894429926 0.016374097773
-55 54.0 -6.03415755288 0.0140541558448
-56 55.0 -6.04705675953 0.0117466594146
-57 56.0 -6.05765632981 0.00945553674764
-58 57.0 -6.06597459526 0.00718469997761
-59 58.0 -6.07203378786 0.00493803637051
-60 59.0 -6.07586001075 0.00271939959245
-61 60.0 -6.07748320034 0.000532601003776
-62 61.0 -6.07693707962 -0.00161859899905
-63 62.0 -6.07425910291 -0.00373049957158
-64 63.0 -6.06949039207 -0.00579946791801
-65 64.0 -6.06267566421 -0.00782194767468
-66 65.0 -6.05386315117 -0.00979446715893
-67 66.0 -6.04310451074 -0.0117136474624
-68 67.0 -6.03045472992 -0.0135762103679
-69 68.0 -6.01597202036 -0.0153789860691
-70 69.0 -5.99971770618 -0.0171189206741
-71 70.0 -5.98175610439 -0.0187930834719
-72 71.0 -5.9621543982 -0.0203986739443
-73 72.0 -5.9409825034 -0.0219330285036
-74 73.0 -5.91831292823 -0.0233936269399
-75 74.0 -5.89422062685 -0.0247780985587
-76 75.0 -5.86878284696 -0.0260842279959
-77 76.0 -5.84207897162 -0.0273099606906
-78 77.0 -5.81419035593 -0.0284534080045
-79 78.0 -5.78520015867 -0.0295128519729
-80 79.0 -5.7551931694 -0.0304867496727
-81 80.0 -5.72425563141 -0.0313737371989
-82 81.0 -5.6924750609 -0.0321726332348
-83 82.0 -5.65994006273 -0.0328824422092
-84 83.0 -5.62674014332 -0.0335023570292
-85 84.0 -5.59296552097 -0.0340317613814
-86 85.0 -5.55870693409 -0.0344702315961
-87 86.0 -5.52405544786 -0.0348175380654
-88 87.0 -5.48910225957 -0.0350736462148
-89 88.0 -5.45393850338 -0.0352387170203
-90 89.0 -5.41865505462 -0.0353131070729
-91 90.0 -5.38334233438 -0.0352973681855
-92 91.0 -5.34809011465 -0.0351922465446
-93 92.0 -5.31298732458 -0.0349986814067
-94 93.0 -5.27812185824 -0.034717803342
-95 94.0 -5.24358038438 -0.0343509320285
-96 95.0 -5.2094481586 -0.0338995736008
-97 96.0 -5.17580883839 -0.0333654175598
-98 97.0 -5.14274430152 -0.0327503332496
-99 98.0 -5.11033446814 -0.0320563659092
-100 99.0 -5.07865712698 -0.0312857323082
-101 100.0 -5.04778776623 -0.0304408159764
-102 101.0 -5.01779940929 -0.0295241620384
-103 102.0 -4.98876245596 -0.0285384716647
-104 103.0 -4.96074452928 -0.0274865961525
-105 104.0 -4.93381032851 -0.0263715306507
-106 105.0 -4.90802148862 -0.0251964075427
-107 106.0 -4.88343644644 -0.0239644895038
-108 107.0 -4.86011031397 -0.0226791622487
-109 108.0 -4.83809475914 -0.0213439269874
-110 109.0 -4.81743789414 -0.0199623926068
-111 110.0 -4.79818417182 -0.0185382675969
-112 111.0 -4.78037429015 -0.0170753517415
-113 112.0 -4.76404510526 -0.0155775275918
-114 113.0 -4.74922955293 -0.0140487517461
-115 114.0 -4.73595657904 -0.0124930459538
-116 115.0 -4.7242510789 -0.0109144880672
-117 116.0 -4.71413384576 -0.00931720286182
-118 117.0 -4.70562152846 -0.00770535274772
-119 118.0 -4.69872659855 -0.00608312839491
-120 119.0 -4.69345732669 -0.00445473929448
-121 120.0 -4.6898177686 -0.00282440427898
-122 121.0 -4.68780776044 -0.00119634202478
-123 122.0 -4.68742292374 0.000425238440527
-124 123.0 -4.68865467977 0.0020361472029
-125 124.0 -4.69149027336 0.00363222287571
-126 125.0 -4.69591280613 0.00520934194008
-127 126.0 -4.70190127895 0.0067634279891
-128 127.0 -4.70943064365 0.00829046085365
-129 128.0 -4.71847186379 0.00978648558781
-130 129.0 -4.72899198423 0.0112476212922
-131 130.0 -4.74095420961 0.0126700697544
-132 131.0 -4.7543179912 0.0140501238848
-133 132.0 -4.76903912216 0.0153841759291
-134 133.0 -4.78506984093 0.0166687254364
-135 134.0 -4.80235894235 0.0179003869651
-136 135.0 -4.82085189642 0.0190758975074
-137 136.0 -4.84049097437 0.0201921236154
-138 137.0 -4.86121538156 0.0212460682116
-139 138.0 -4.88296139722 0.0222348770682
-140 139.0 -4.90566252032 0.0231558449399
-141 140.0 -4.9292496215 0.0240064213355
-142 141.0 -4.95365110055 0.0247842159162
-143 142.0 -4.97879304911 0.0254870035063
-144 143.0 -5.00459941816 0.0261127287073
-145 144.0 -5.03099218995 0.0266595101027
-146 145.0 -5.05789155387 0.0271256440463
-147 146.0 -5.08521608601 0.0275096080241
-148 147.0 -5.11288293171 0.0278100635833
-149 148.0 -5.14080799097 0.0280258588231
-150 149.0 -5.16890610603 0.0281560304409
-151 150.0 -5.19709125082 0.0281998053314
-152 151.0 -5.22527672173 0.0281566017347
-153 152.0 -5.25337532941 0.0280260299338
-154 153.0 -5.28129959092 0.0278078924984
-155 154.0 -5.30896192196 0.0275021840788
-156 155.0 -5.33627482866 0.0271090907491
-157 156.0 -5.36315109852 0.0266289889046
-158 157.0 -5.38950398994 0.026062443717
-159 158.0 -5.41524742011 0.0254102071518
-160 159.0 -5.44029615055 0.0246732155563
-161 160.0 -5.46456597019 0.0238525868232
-162 161.0 -5.48797387528 0.0229496171403
-163 162.0 -5.51043824587 0.0219657773349
-164 163.0 -5.53187901853 0.0209027088232
-165 164.0 -5.55221785468 0.0197622191769
-166 165.0 -5.57137830441 0.0185462773191
-167 166.0 -5.58928596528 0.0172570083629
-168 167.0 -5.60586863576 0.0158966881068
-169 168.0 -5.62105646307 0.0144677372016
-170 169.0 -5.63478208493 0.0129727150063
-171 170.0 -5.64698076513 0.0114143131467
-172 171.0 -5.65759052241 0.00979534879707
-173 172.0 -5.66655225257 0.00811875770075
-174 173.0 -5.67380984344 0.00638758694863
-175 174.0 -5.67931028251 0.00460498753534
-176 175.0 -5.68300375706 0.00277420671195
-177 176.0 -5.68484374646 0.000898580155594
-178 177.0 -5.68478710669 -0.00101847602368
-179 178.0 -5.68279414663 -0.00297347341791
-180 179.0 -5.67882869631 -0.00496285957718
-181 180.0 -5.67285816674 -0.00698302636509
-182 181.0 -5.6648536014 -0.00903031839234
-183 182.0 -5.65478971926 -0.0111010415069
-184 183.0 -5.64264494925 -0.0131914713189
-185 184.0 -5.62840145627 -0.0152978617389
-186 185.0 -5.6120451586 -0.017416453508
-187 186.0 -5.59356573683 -0.0195434826976
-188 187.0 -5.57295663425 -0.0216751891584
-189 188.0 -5.55021504898 -0.0238078248974
-190 189.0 -5.52534191754 -0.0259376623617
-191 190.0 -5.4983418904 -0.0280610026087
-192 191.0 -5.46922329932 -0.0301741833429
-193 192.0 -5.43799811672 -0.0322735868002
-194 193.0 -5.40468190731 -0.0343556474589
-195 194.0 -5.36929377207 -0.0364168595607
-196 195.0 -5.33185628476 -0.0384537844225
-197 196.0 -5.29239542138 -0.0404630575223
-198 197.0 -5.25094048245 -0.0424413953416
-199 198.0 -5.20752400881 -0.0443856019501
-200 199.0 -5.16218169074 -0.0462925753151
-201 200.0 -5.11495227114 -0.0481593133234
-202 201.0 -5.06587744261 -0.0499829195012
-203 202.0 -5.01500173918 -0.0517606084187
-204 203.0 -4.96237242264 -0.0534897107689
-205 204.0 -4.90803936404 -0.055167678109
-206 205.0 -4.85205492059 -0.0567920872546
-207 206.0 -4.79447380837 -0.0583606443179
-208 207.0 -4.73535297113 -0.0598711883816
-209 208.0 -4.6747514457 -0.0613216948024
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-215 214.0 -4.28358237872 -0.0686683902899
-216 215.0 -4.21441534165 -0.0696539079796
-217 216.0 -4.14429825061 -0.070568367083
-218 217.0 -4.07330253293 -0.0714110548116
-219 218.0 -4.00150025463 -0.0721814065199
-220 219.0 -3.92896397266 -0.072879004774
-221 220.0 -3.85576658834 -0.0735035780505
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-229 228.0 -3.25513667985 -0.0758851894693
-230 229.0 -3.17925670492 -0.0758632951011
-231 230.0 -3.10343284123 -0.0757731496217
-232 231.0 -3.02773277394 -0.0756159028468
-233 232.0 -2.95222298559 -0.0753928092342
-234 233.0 -2.87696865416 -0.0751052226812
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-253 252.0 -1.57015013921 -0.059719451663
-254 253.0 -1.51102474011 -0.0585272303374
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-262 261.0 -1.08303317143 -0.0483002568854
-263 262.0 -1.03540066834 -0.046963389572
-264 263.0 -0.989108853377 -0.0456191365664
-265 264.0 -0.944164356669 -0.0442689966762
-266 265.0 -0.900572346917 -0.0429143935113
-267 266.0 -0.858336607922 -0.0415566728462
-268 267.0 -0.817459617608 -0.0401971002897
-269 268.0 -0.777942629232 -0.0388368592669
-270 269.0 -0.739785754436 -0.0374770493178
-271 270.0 -0.702988047855 -0.0361186847156
-272 271.0 -0.667547592939 -0.0347626934072
-273 272.0 -0.633461588675 -0.0334099162773
-274 273.0 -0.600726436882 -0.0320611067354
-275 274.0 -0.569337829756 -0.0307169306269
-276 275.0 -0.539290837348 -0.0293779664649
-277 276.0 -0.510579994645 -0.0280447059807
-278 277.0 -0.483199387947 -0.0267175549897
-279 278.0 -0.457142740217 -0.0253968345674
-280 279.0 -0.432403495111 -0.0240827825309
-281 280.0 -0.408974899365 -0.0227755552188
-282 281.0 -0.386850083265 -0.0214752295619
-283 282.0 -0.366022138902 -0.020181805438
-284 283.0 -0.346484195932 -0.0188952082997
-285 284.0 -0.328229494574 -0.0176152920667
-286 285.0 -0.311251455597 -0.0163418422722
-287 286.0 -0.295543747024 -0.0150745794496
-288 287.0 -0.28110034735 -0.0138131627512
-289 288.0 -0.267915605017 -0.0125571937823
-290 289.0 -0.255984293962 -0.011306220639
-291 290.0 -0.245301665026 -0.0100597421363
-292 291.0 -0.235863493049 -0.00881721220956
-293 292.0 -0.22766611948 -0.00757804447631
-294 293.0 -0.220706490355 -0.00634161694135
-295 294.0 -0.214982189503 -0.00510727682957
-296 295.0 -0.210491466861 -0.00387434552992
-297 296.0 -0.207233261801 -0.00264212363344
-298 297.0 -0.205207221373 -0.00140989604849
-299 298.0 -0.204413713408 -0.00017693717569
-300 299.0 -0.204853834414 0.0010574838751
-301 300.0 -0.206529412255 0.00229409804323
-302 301.0 -0.209443003569 0.00353363106913
-303 302.0 -0.213597885954 0.00477679825726
-304 303.0 -0.218998044922 0.00602429926791
-305 304.0 -0.22564815567 0.00727681295572
-306 305.0 -0.23355355972 0.00853499227222
-307 306.0 -0.2427202365 0.00979945924997
-308 307.0 -0.253154769958 0.0110708000854
-309 308.0 -0.264864310313 0.0123495603372
-310 309.0 -0.277856531075 0.0136362402565
-311 310.0 -0.292139581459 0.0149312902659
-312 311.0 -0.307722034364 0.0162351066015
-313 312.0 -0.324612830087 0.0175480271349
-314 313.0 -0.342821215943 0.0188703273888
-315 314.0 -0.362356682012 0.0202022167596
-316 315.0 -0.383228893218 0.0215438349636
-317 316.0 -0.405447617967 0.0228952487148
-318 317.0 -0.429022653586 0.0242564486517
-319 318.0 -0.45396374882 0.0256273465206
-320 319.0 -0.480280523637 0.0270077726275
-321 320.0 -0.507982386639 0.0283974735696
-322 321.0 -0.537078450328 0.029796110253
-323 322.0 -0.567577444555 0.0312032562068
-324 323.0 -0.59948762842 0.0326183962009
-325 324.0 -0.632816700956 0.0340409251716
-326 325.0 -0.667571710883 0.0354701474639
-327 326.0 -0.703758965776 0.0369052763923
-328 327.0 -0.741383940946 0.038345434125
-329 328.0 -0.780451188376 0.0397896518935
-330 329.0 -0.820964246018 0.0412368705304
-331 330.0 -0.862925547807 0.042685941334
-332 331.0 -0.906336334692 0.0441356272615
-333 332.0 -0.951196567028 0.045584604448
-334 333.0 -0.997504838648 0.0470314640498
-335 334.0 -1.04525829294 0.048474714408
-336 335.0 -1.09445254125 0.0499127835288
-337 336.0 -1.1450815839 0.0513440218749
-338 337.0 -1.1971377342 0.0527667054614
-339 338.0 -1.25061154564 0.0541790392498
-340 339.0 -1.30549174267 0.0555791608316
-341 340.0 -1.36176515529 0.0569651443923
-342 341.0 -1.41941665773 0.0583350049463
-343 342.0 -1.47842911151 0.0596867028317
-344 343.0 -1.53878331313 0.061018148454
-345 344.0 -1.60045794659 0.0623272072653
-346 345.0 -1.66342954101 0.0636117049668
-347 346.0 -1.72767243359 0.0648694329207
-348 347.0 -1.79315873807 0.0660981537565
-349 348.0 -1.85985831882 0.0672956071568
-350 349.0 -1.92773877092 0.0684595158069
-351 350.0 -1.99676540616 0.0695875914917
-352 351.0 -2.06690124527 0.0706775413231
-353 352.0 -2.13810701636 0.0717270740805
-354 353.0 -2.21034115987 0.0727339066469
-355 354.0 -2.28355983986 0.0736957705223
-356 355.0 -2.35771696194 0.0746104183955
-357 356.0 -2.43276419776 0.0754756307561
-358 357.0 -2.50865101613 0.0762892225281
-359 358.0 -2.58532472075 0.0770490497051
-360 359.0 -2.66273049463 0.0777530159679
-
-# Table of the potential and its negative derivative for frustrated beta sheet
-# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
-# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
-
-FRUSTRATED_BETA
-N 360 DEGREES
-
-1 0.0 -2.55809068762 0.0731724739818
-2 1.0 -2.63154144494 0.0737195744566
-3 2.0 -2.70551060968 0.0742089966437
-4 3.0 -2.77993963883 0.074639023134
-5 4.0 -2.85476830901 0.0750080115297
-6 5.0 -2.92993479441 0.0753144003899
-7 6.0 -3.00537575069 0.0755567150326
-8 7.0 -3.08102640456 0.0757335731758
-9 8.0 -3.15682064892 0.0758436903983
-10 9.0 -3.23269114341 0.075885885404
-11 10.0 -3.30856942003 0.0758590850738
-12 11.0 -3.38438599377 0.0757623292865
-13 12.0 -3.46007047791 0.0755947754951
-14 13.0 -3.53555170381 0.0753557030426
-15 14.0 -3.61075784476 0.0750445172025
-16 15.0 -3.68561654392 0.0746607529305
-17 16.0 -3.76005504566 0.0742040783151
-18 17.0 -3.83400033034 0.0736742977129
-19 18.0 -3.907379252 0.0730713545594
-20 19.0 -3.98011867868 0.0723953338429
-21 20.0 -4.0521456351 0.0716464642332
-22 21.0 -4.12338744726 0.0708251198546
-23 22.0 -4.19377188857 0.0699318216967
-24 23.0 -4.26322732737 0.0689672386556
-25 24.0 -4.33168287509 0.0679321881993
-26 25.0 -4.39906853508 0.0668276366524
-27 26.0 -4.46531535141 0.0656546990963
-28 27.0 -4.53035555742 0.0644146388823
-29 28.0 -4.59412272358 0.0631088667546
-30 29.0 -4.65655190431 0.061738939584
-31 30.0 -4.71757978327 0.0603065587109
-32 31.0 -4.77714481686 0.0588135679005
-33 32.0 -4.83518737548 0.057261950911
-34 33.0 -4.89164988211 0.0556538286799
-35 34.0 -4.94647694795 0.0539914561312
-36 35.0 -4.99961550465 0.0522772186102
-37 36.0 -5.05101493277 0.0505136279528
-38 37.0 -5.10062718621 0.048703318195
-39 38.0 -5.14840691207 0.0468490409338
-40 39.0 -5.19431156578 0.0449536603471
-41 40.0 -5.23830152101 0.0430201478838
-42 41.0 -5.28034017422 0.0410515766363
-43 42.0 -5.3203940433 0.0390511154063
-44 43.0 -5.35843286021 0.0370220224793
-45 44.0 -5.39442965726 0.0349676391193
-46 45.0 -5.4283608467 0.0328913828015
-47 46.0 -5.46020629342 0.0307967401964
-48 47.0 -5.48994938059 0.028687259923
-49 48.0 -5.51757706789 0.0265665450883
-50 49.0 -5.54307994213 0.0244382456298
-51 50.0 -5.56645226024 0.0223060504811
-52 51.0 -5.58769198425 0.0201736795783
-53 52.0 -5.60680080825 0.0180448757265
-54 53.0 -5.62378417713 0.0159233963481
-55 54.0 -5.63865129702 0.0138130051308
-56 55.0 -5.6514151374 0.0117174635982
-57 56.0 -5.66209242462 0.00964052262251
-58 57.0 -5.67070362704 0.00758591390103
-59 58.0 -5.67727293157 0.00555734141841
-60 59.0 -5.6818282117 0.00355847291538
-61 60.0 -5.68440098698 0.00159293138608
-62 61.0 -5.68502637408 -0.000335713374531
-63 62.0 -5.68374302934 -0.00222395315148
-64 63.0 -5.68059308309 -0.0040683495974
-65 64.0 -5.67562206565 -0.00586554240548
-66 65.0 -5.66887882528 -0.00761225734683
-67 66.0 -5.66041543813 -0.00930531415106
-68 67.0 -5.65028711044 -0.0109416342099
-69 68.0 -5.63855207307 -0.0125182480831
-70 69.0 -5.6252714687 -0.0140323027883
-71 70.0 -5.61050923182 -0.0154810688529
-72 71.0 -5.59433196178 -0.0168619471125
-73 72.0 -5.57680878923 -0.0181724752358
-74 73.0 -5.5580112361 -0.019410333958
-75 74.0 -5.53801306959 -0.0205733530082
-76 75.0 -5.51689015031 -0.0216595167121
-77 76.0 -5.49472027505 -0.0226669692568
-78 77.0 -5.47158301441 -0.0235940196022
-79 78.0 -5.44755954575 -0.0244391460249
-80 79.0 -5.42273248172 -0.0252010002837
-81 80.0 -5.3971856949 -0.0258784113929
-82 81.0 -5.37100413881 -0.0264703889936
-83 82.0 -5.34427366574 -0.0269761263135
-84 83.0 -5.31708084192 -0.0273950027051
-85 84.0 -5.28951276022 -0.0277265857564
-86 85.0 -5.26165685114 -0.0279706329651
-87 86.0 -5.23360069216 -0.0281270929735
-88 87.0 -5.20543181621 -0.0281961063563
-89 88.0 -5.17723751951 -0.0281780059613
-90 89.0 -5.14910466934 -0.0280733167983
-91 90.0 -5.12111951208 -0.0278827554757
-92 91.0 -5.09336748214 -0.0276072291861
-93 92.0 -5.06593301201 -0.0272478342399
-94 93.0 -5.0388993441 -0.026805854151
-95 94.0 -5.01234834466 -0.0262827572773
-96 95.0 -4.98636032033 -0.0256801940208
-97 96.0 -4.96101383762 -0.0249999935924
-98 97.0 -4.93638554598 -0.0242441603499
-99 98.0 -4.91255000457 -0.0234148697145
-100 99.0 -4.88957951348 -0.0225144636776
-101 100.0 -4.86754394953 -0.0215454459053
-102 101.0 -4.84651060724 -0.0205104764546
-103 102.0 -4.8265440452 -0.01941236611
-104 103.0 -4.80770593836 -0.0182540703564
-105 104.0 -4.79005493648 -0.0170386830008
-106 105.0 -4.77364652914 -0.0157694294583
-107 106.0 -4.7585329176 -0.0144496597171
-108 107.0 -4.74476289391 -0.0130828410011
-109 108.0 -4.73238172744 -0.0116725501446
-110 109.0 -4.72143105919 -0.0102224657007
-111 110.0 -4.71194880414 -0.00873635979846
-112 111.0 -4.70396906182 -0.0072180897712
-113 112.0 -4.69752203541 -0.00567158957449
-114 113.0 -4.69263395945 -0.00410086101469
-115 114.0 -4.68932703648 -0.00250996480925
-116 115.0 -4.68761938265 -0.000903011500147
-117 116.0 -4.68752498248 0.00071584775762
-118 117.0 -4.68905365291 0.00234243051027
-119 118.0 -4.69221101668 0.00397253239976
-120 119.0 -4.69699848518 0.00560193661579
-121 120.0 -4.70341325069 0.00722642338265
-122 121.0 -4.71144828821 0.00884177945771
-123 122.0 -4.72109236669 0.0104438076188
-124 123.0 -4.73233006984 0.0120283361174
-125 124.0 -4.74514182625 0.0135912280748
-126 125.0 -4.75950394898 0.0151283907985
-127 126.0 -4.77538868431 0.0166357849963
-128 127.0 -4.79276426974 0.0181094338658
-129 128.0 -4.81159500092 0.0195454320375
-130 129.0 -4.83184130754 0.0209399543498
-131 130.0 -4.8534598378 0.0222892644342
-132 131.0 -4.87640355143 0.0235897230915
-133 132.0 -4.90062182095 0.0248377964369
-134 133.0 -4.92606054096 0.0260300637961
-135 134.0 -4.95266224518 0.0271632253326
-136 135.0 -4.98036623096 0.028234109388
-137 136.0 -5.00910869107 0.0292396795182
-138 137.0 -5.03882285221 0.0301770412082
-139 138.0 -5.06943912022 0.0310434482505
-140 139.0 -5.10088523142 0.0318363087705
-141 140.0 -5.13308640979 0.0325531908865
-142 141.0 -5.16596552963 0.0331918279898
-143 142.0 -5.19944328334 0.0337501236332
-144 143.0 -5.23343835383 0.0342261560164
-145 144.0 -5.26786759123 0.0346181820585
-146 145.0 -5.30264619353 0.0349246410472
-147 146.0 -5.33768789051 0.0351441578585
-148 147.0 -5.37290513082 0.0352755457383
-149 148.0 -5.40820927152 0.0353178086401
-150 149.0 -5.4435107698 0.0352701431151
-151 150.0 -5.4787193763 0.0351319397498
-152 151.0 -5.51374432971 0.0349027841491
-153 152.0 -5.54849455206 0.0345824574643
-154 153.0 -5.58287884436 0.0341709364636
-155 154.0 -5.61680608206 0.0336683931487
-156 155.0 -5.65018540988 0.0330751939177
-157 156.0 -5.68292643563 0.0323918982779
-158 157.0 -5.71493942249 0.0316192571138
-159 158.0 -5.74613547931 0.0307582105139
-160 159.0 -5.77642674856 0.029809885165
-161 160.0 -5.80572659147 0.0287755913197
-162 161.0 -5.83394976986 0.0276568193473
-163 162.0 -5.86101262442 0.0264552358763
-164 163.0 -5.8868332488 0.025172679541
-165 164.0 -5.91133165941 0.0238111563427
-166 165.0 -5.93442996024 0.0223728346376
-167 166.0 -5.95605250261 0.0208600397671
-168 167.0 -5.97612603931 0.0192752483425
-169 168.0 -5.99457987285 0.0176210822011
-170 169.0 -6.01134599757 0.015900302049
-171 170.0 -6.02635923519 0.014115800807
-172 171.0 -6.03955736358 0.0122705966784
-173 172.0 -6.05088123845 0.0103678259555
-174 173.0 -6.0602749078 0.00841073558436
-175 174.0 -6.06768571866 0.00640267550713
-176 175.0 -6.0730644163 0.00434709080102
-177 176.0 -6.07636523524 0.00224751363529
-178 177.0 -6.07754598232 0.000107555066143
-179 178.0 -6.07656811141 -0.00206910330914
-180 179.0 -6.07339678973 -0.00427871781763
-181 180.0 -6.06800095563 -0.00651749127408
-182 181.0 -6.06035336781 -0.00878158162059
-183 182.0 -6.05043064586 -0.0110671106207
-184 183.0 -6.03821330204 -0.0133701725859
-185 184.0 -6.02368576439 -0.0156868431131
-186 185.0 -6.00683639108 -0.0180131878107
-187 186.0 -5.98765747603 -0.0203452709919
-188 187.0 -5.96614524589 -0.0226791643135
-189 188.0 -5.94229984843 -0.025010955339
-190 189.0 -5.91612533236 -0.0273367560054
-191 190.0 -5.88762961878 -0.0296527109716
-192 191.0 -5.85682446433 -0.0319550058299
-193 192.0 -5.82372541626 -0.0342398751598
-194 193.0 -5.78835175943 -0.0365036104045
-195 194.0 -5.75072645562 -0.0387425675516
-196 195.0 -5.71087607524 -0.0409531746008
-197 196.0 -5.66883072166 -0.0431319387984
-198 197.0 -5.62462394846 -0.0452754536249
-199 198.0 -5.57829266983 -0.0473804055171
-200 199.0 -5.5298770643 -0.0494435803104
-201 200.0 -5.47942047235 -0.0514618693867
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/run.in.min
deleted file mode 100644
index 8eb3a03cb..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/run.in.min
+++ /dev/null
@@ -1,19 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt
deleted file mode 100644
index 185d03cf1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt
+++ /dev/null
@@ -1,50 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-# I you want to be careful, you can minimize the system first.
-# (Try using "run.in.min" and uncomment line below.)
-# read_data system_after_min.data
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.025
-dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-# Keep the chaperonin fixed. Only let the protein move.
-
-fix fxlan proteins langevin 0.25 0.25 1.0 48279
-fix fxnve proteins nve
-
-# Notes:
-# The temperature is in reduced units and is set to 0.25
-# which is the folding temperature for the frustrated protein
-# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
-# as it was in the paper. (Hopefully folding times should be similar.)
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 50 #(time interval for printing out "thermo" data)
-
-#restart 100000000 restart_nvt
-
-# Just run it long enough for it to collapse (not fold)
-# (If you need to run it longer, then dump trajectory data less frequently.)
-run 50000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT
deleted file mode 100644
index 5da41b9a8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT
+++ /dev/null
@@ -1,32 +0,0 @@
-# This directory demonstrates how to run a short simulation of
-# the "unfrustrated" coarse-grained protein model used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-#
-# In this example, the protein is placed inside a repulsive sphere
-# of radius 6.0 sigma which confines its motion.
-# (This sphere is sometimes called the "chaperonin", because
-# we were using it to model the crude behavior of a chaperonin cavity.)
-#
-# During this short simulation (run.in.nvt) the protein evolves
-# from an unfolded initial conformation to the folded state.
-#
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh
deleted file mode 100755
index 45bd2d451..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# You would probably run lammps this way:
-#
-# lmp_ubuntu -i run.in.nvt
-
-# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
-# to the input scripts & data files you created earlier when you ran moltemplate
-# system.in.init, system.in.settings, system.data
-
-
-
-
-# -----------------------------------
-
-
-
-LAMMPS_COMMAND="lmp_ubuntu"
-
-# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
-
-# Run lammps using the following 3 commands:
-
-"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-"$LAMMPS_COMMAND" -i run.in.nvt # production run
-
-# Alternately, if you have MPI installed, try something like this:
-
-#NUMPROCS=4
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh
deleted file mode 100755
index df49f4384..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -overlay-dihedrals system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
- cp -r table*.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
deleted file mode 100644
index 7763505c0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
+++ /dev/null
@@ -1,98 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 28 !NATOM
- 1 1 1 1 0.000000 100.0000 0
- 2 2 3 3 0.000000 1.0000 0
- 3 2 2 2 0.000000 1.0000 0
- 4 2 3 3 0.000000 1.0000 0
- 5 2 2 2 0.000000 1.0000 0
- 6 2 3 3 0.000000 1.0000 0
- 7 2 2 2 0.000000 1.0000 0
- 8 2 4 4 0.000000 1.0000 0
- 9 2 4 4 0.000000 1.0000 0
- 10 2 2 2 0.000000 1.0000 0
- 11 2 3 3 0.000000 1.0000 0
- 12 2 2 2 0.000000 1.0000 0
- 13 2 3 3 0.000000 1.0000 0
- 14 2 2 2 0.000000 1.0000 0
- 15 2 3 3 0.000000 1.0000 0
- 16 2 4 4 0.000000 1.0000 0
- 17 2 4 4 0.000000 1.0000 0
- 18 2 4 4 0.000000 1.0000 0
- 19 2 2 2 0.000000 1.0000 0
- 20 2 2 2 0.000000 1.0000 0
- 21 2 3 3 0.000000 1.0000 0
- 22 2 3 3 0.000000 1.0000 0
- 23 2 2 2 0.000000 1.0000 0
- 24 2 2 2 0.000000 1.0000 0
- 25 2 3 3 0.000000 1.0000 0
- 26 2 3 3 0.000000 1.0000 0
- 27 2 2 2 0.000000 1.0000 0
- 28 2 3 3 0.000000 1.0000 0
-
- 26 !NBOND: bonds
- 2 3 3 4 4 5 5 6
- 6 7 7 8 8 9 9 10
- 10 11 11 12 12 13 13 14
- 14 15 15 16 16 17 17 18
- 18 19 19 20 20 21 21 22
- 22 23 23 24 24 25 25 26
- 26 27 27 28
-
- 25 !NTHETA: angles
- 3 4 5 5 6 7 10 11 12
- 12 13 14 8 9 10 7 8 9
- 17 18 19 19 20 21 23 24 25
- 22 23 24 2 3 4 4 5 6
- 11 12 13 13 14 15 26 27 28
- 15 16 17 6 7 8 9 10 11
- 14 15 16 18 19 20 20 21 22
- 21 22 23 24 25 26 25 26 27
- 16 17 18
-
- 43 !NPHI: dihedrals
- 2 3 4 5 2 3 4 5
- 3 4 5 6 3 4 5 6
- 4 5 6 7 4 5 6 7
- 5 6 7 8 5 6 7 8
- 6 7 8 9 7 8 9 10
- 8 9 10 11 9 10 11 12
- 9 10 11 12 10 11 12 13
- 10 11 12 13 11 12 13 14
- 11 12 13 14 12 13 14 15
- 12 13 14 15 13 14 15 16
- 13 14 15 16 14 15 16 17
- 15 16 17 18 16 17 18 19
- 16 17 18 19 17 18 19 20
- 17 18 19 20 18 19 20 21
- 18 19 20 21 19 20 21 22
- 19 20 21 22 20 21 22 23
- 20 21 22 23 21 22 23 24
- 21 22 23 24 22 23 24 25
- 22 23 24 25 23 24 25 26
- 23 24 25 26 24 25 26 27
- 24 25 26 27 25 26 27 28
- 25 26 27 28
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg
deleted file mode 100644
index a0da344db..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg
deleted file mode 100644
index a1aa5bd85..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt
deleted file mode 100644
index 0dc1f5dd0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt
+++ /dev/null
@@ -1,255 +0,0 @@
-# This file defines a pair of coarse-grained protein models used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-
-
-1beadUnfrustrated {
-
- # Note: the "unfrustrated" model is kind of funny looking. (My apologies.)
-
- # There are 3 atom types (referred to above as B, L, and N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:B 1.0
- @atom:L 1.0
- @atom:N 1.0
- }
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118
- $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074
- $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456
- $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926
- $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356
- $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634
- $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503
- $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852
- $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528
- $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863
- $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636
- $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065
- $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921
- $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738
- $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232
- $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693
- $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841
- $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008
- $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678
- $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878
- $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001
- $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365
- $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748
- $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731
- $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442
- $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789
- $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241
- }
-
- # bond-ID bond-Type atom-ID atom-ID
-
- write("Data Bonds") {
- $bond:b1 @bond:backbone $atom:a1 $atom:a2
- $bond:b2 @bond:backbone $atom:a2 $atom:a3
- $bond:b3 @bond:backbone $atom:a3 $atom:a4
- $bond:b4 @bond:backbone $atom:a4 $atom:a5
- $bond:b5 @bond:backbone $atom:a5 $atom:a6
- $bond:b6 @bond:backbone $atom:a6 $atom:a7
- $bond:b7 @bond:backbone $atom:a7 $atom:a8
- $bond:b8 @bond:backbone $atom:a8 $atom:a9
- $bond:b9 @bond:backbone $atom:a9 $atom:a10
- $bond:b10 @bond:backbone $atom:a10 $atom:a11
- $bond:b11 @bond:backbone $atom:a11 $atom:a12
- $bond:b12 @bond:backbone $atom:a12 $atom:a13
- $bond:b13 @bond:backbone $atom:a13 $atom:a14
- $bond:b14 @bond:backbone $atom:a14 $atom:a15
- $bond:b15 @bond:backbone $atom:a15 $atom:a16
- $bond:b16 @bond:backbone $atom:a16 $atom:a17
- $bond:b17 @bond:backbone $atom:a17 $atom:a18
- $bond:b18 @bond:backbone $atom:a18 $atom:a19
- $bond:b19 @bond:backbone $atom:a19 $atom:a20
- $bond:b20 @bond:backbone $atom:a20 $atom:a21
- $bond:b21 @bond:backbone $atom:a21 $atom:a22
- $bond:b22 @bond:backbone $atom:a22 $atom:a23
- $bond:b23 @bond:backbone $atom:a23 $atom:a24
- $bond:b24 @bond:backbone $atom:a24 $atom:a25
- $bond:b25 @bond:backbone $atom:a25 $atom:a26
- $bond:b26 @bond:backbone $atom:a26 $atom:a27
- }
-
- # (3-body) Angles are specified below
-
- # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
- # (These interactions are not determined by atom type.)
- #
- # Note that some quartets of atoms are listed because their
- # potentials contain multiple terms in the Fourier expansion.
- # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!)
- #
- # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
-
- write("Data Dihedrals") {
- $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7
- $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7
- $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8
- $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9
- $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10
- $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15
- $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15
- $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16
- $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17
- $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27
- $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27
- }
-
- # All consecutively bonded triplets of atoms same 3-body bond-angle
- # interaction parameters. Of coarse, we could specify them all explicitly
- # (as we did for the dihedrals above), but I wanted to show how to specify
- # angles by atom type instead. (You can do this for dihedrals & impropers
- # also.)
-
- # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # (The "*" is a wildcard character. I use "*" to denote any atom-type or
- # bond-type which is defined within the current namespace: 1beadUnfrustrated)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
- pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
- pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
- }
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond-Type bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 100.0 1.0
- }
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # angle-Type anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 13.3333333333 105.0
- }
-
- # 4-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Udihedral(phi) = K * (1 + cos(n*phi - d))
- #
- # The d parameter is in degrees, K is in kcal/mol/rad^2.
- #
- # The corresponding command is:
- #
- # dihedral_coeff dihedralType dihedralstylename K n d w
- # ("w" is the weight for 1-4 pair interactions, which we set to 0)
-
- # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d
- # parameters. I'm hoping this will be fixed eventually.
-
- write_once("In Settings") {
- # Correct version:
- #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0
- # Replacing with
- dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0
- # Correct version:
- #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0
- # Replacing with
- dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0
- dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0
- dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0
- dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0
- # Correct version:
- # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0
- # Replacing with
- dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0
- dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0
- dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0
- dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0
- }
-
- write_once("In Settings") {
- # Optional: define the atoms in the "proteins" group
- group proteins type @atom:B
- group proteins type @atom:L
- group proteins type @atom:N
- }
-
- # LAMMPS has many available force field styles (and atom styles).
- # Here, we pick the ones which work well for this molecular model:
-
- write_once("In Init") {
- # --- Default options for the "1BeadUnfrustrated" protein model ---
- # --- (These can be overridden later.) ---
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid charmm
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-} # 1beadUnfrustrated
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt
deleted file mode 100644
index cbc8fe217..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt
+++ /dev/null
@@ -1,45 +0,0 @@
-import "1beadUnfrustrated.lt"
-
-
-# Alternate starting conformation (same molecule):
-
-
-1beadUnfolded inherits 1beadUnfrustrated {
-
- # This molecule "inherits" all of its features from "1beadUnfrustrated"
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
- $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
- $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
- $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
- $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
- $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
- $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
- $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
- $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
- $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
- $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
- $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
- $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
- $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
- $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
- $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
- $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
- $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
- $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
- $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
- $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
- $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
- $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
- $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
- $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
- $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
- $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
- }
-
-} # 1beadUnfolded
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt
deleted file mode 100644
index 8266d2a89..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt
+++ /dev/null
@@ -1,41 +0,0 @@
-# Here we define a trivial molecule containing only one particle.
-
-Chaperonin {
-
- # atomID molID atomType charge x y z
-
- write("Data Atoms") {
- $atom:C $mol @atom:C 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:C 100.0
- }
-
- write_once("In Settings") {
- # If for some reason there are multiple chaperones present,
- # I assume that they interact repulsively (hence, L=0)
- # i j epsilon sigma K L
-
- pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0
-
- # Optional: define the atoms in the "chaperonins" group:
- # (Defining a group for the chaperone makes it easy to immobilize it later.)
-
- group chaperonins type @atom:C
- }
-
-
- # Specify which pair_styles, and atom styles work well with
- # this model. (Again this can be overridden later.)
-
- write_once("In Init") {
- units lj
- atom_style full
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0
- }
-
-} # Chaperonin
-
-# We have not specified how this particle interacts with other particles
-# besides itself. Later on you must do this.
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
deleted file mode 100755
index 9b86809cc..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between atoms in the
-# protein and a chaperone provided in the supplemental materials section of:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# This is stored in a tabulated force field with a singularity at a distance R.
-#
-# To calculate the table for interaction between
-# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
-# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181
-# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
-# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
-# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True
-
-from math import *
-import sys
-
-def U(r, eps, sigma, R, h):
- #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
- # Formula is undefined at r=0, but you can take the limit:
- if r <= 0:
- return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
- - h*pow((sigma/R), 6.0))
- xp = sigma/(r+R)
- xm = sigma/(r-R)
- term10 = pow(xm, 10.0) - pow(xp, 10.0)
- term4 = pow(xm, 4.0) - pow(xp, 4.0)
- return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
-
-def F(r, eps, sigma, R, h):
- # Formula is undefined at r=0, but you can take the limit:
- if r <= 0:
- return 0.0
- product_term_a = U(r, eps, sigma, R, h) / r
- ixp = (r+R)/sigma
- ixm = (r-R)/sigma
- dix_dr = 1.0/sigma
- term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
- term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0))
- product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
- return product_term_a + product_term_b
-
-
-class InputError(Exception):
- """ A generic exception object containing a string for error reporting.
-
- """
- def __init__(self, err_msg):
- self.err_msg = err_msg
- def __str__(self):
- return self.err_msg
- def __repr__(self):
- return str(self)
-
-if len(sys.argv) < 8:
- sys.stderr.write("Error: expected 7 arguments:\n"
- "\n"
- "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
- sys.exit(-1)
-
-epsilon = float(sys.argv[1])
-sigma = float(sys.argv[2])
-R = float(sys.argv[3])
-h = float(sys.argv[4])
-rmin = float(sys.argv[5])
-rmax = float(sys.argv[6])
-N = int(sys.argv[7])
-
-subtract_Urcut = False
-if len(sys.argv) == 9:
- subtract_Urcut = True
-rcut = rmax
-
-for i in range(0,N):
- r = rmin + i*(rmax-rmin)/(N-1)
- U_r = U(r, epsilon, sigma, R, h)
- F_r = F(r, epsilon, sigma, R, h)
- if subtract_Urcut:
- U_r -= U(rcut, epsilon, sigma, R, h)
- if (r >= rcut) or (i==N-1):
- U_r = 0.0
- F_r = 0.0
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt
deleted file mode 100644
index d8781c26f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt
+++ /dev/null
@@ -1,45 +0,0 @@
-write_once("Data Boundary") {
- 0.0 20.0 xlo xhi
- 0.0 20.0 ylo yhi
- 0.0 20.0 zlo zhi
-}
-
-
-import "chaperonin.lt"
-import "1beadUnfrustrated_variants.lt"
-
-
-chaperinin = new Chaperonin # (hollow chaperonin, encloses protein)
-protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein)
-
-
-
-# Now define interactions between the "c" atom in the
-# chaperone and the "B", "L", "N" atoms in the protein:
-
-write_once("In Settings") {
- pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.dat CH_H0
- pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/L table table_chaperonin_h=0.dat CH_H0
- pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/N table table_chaperonin_h=0.dat CH_H0
- # Note: In this example, the chaperone is playing the role of a repulsive wall
- # (confinement). To use a sticky chaperonin, replace the first line with this:
- # pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475
-}
-
-
-
-# LAMMPS has many available force field styles (and atom styles).
-# Here, we pick the ones which work well for this molecular model:
-
-write_once("In Init") {
- # --- Default options for the "1BeadUnfrustrated" protein model ---
- # --- (These can be overridden later.) ---
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid charmm
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
deleted file mode 100644
index 675d228a9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
+++ /dev/null
@@ -1,1188 +0,0 @@
-# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475).
-# LAMMPS would crash unless I set the minimum radius to a positive value (not 0)
-
-CH_H0.475
-N 1181 R 0.00000000001 5.9
-
-1 0.00000000001 -0.018422088583 0.0
-2 0.005 -0.0184221525389 2.55824082873e-05
-3 0.01 -0.0184223444081 5.11654127471e-05
-4 0.015 -0.018422664195 7.67496107175e-05
-5 0.02 -0.0184231119071 0.000102335598797
-6 0.025 -0.018423687555 0.000127923973785
-7 0.03 -0.0184243911519 0.000153515332637
-8 0.035 -0.0184252227143 0.000179110272379
-9 0.04 -0.0184261822615 0.000204709390236
-10 0.045 -0.0184272698161 0.000230313283607
-11 0.05 -0.0184284854033 0.000255922550119
-12 0.055 -0.0184298290516 0.000281537787625
-13 0.06 -0.0184313007922 0.000307159594253
-14 0.065 -0.0184329006595 0.000332788568419
-15 0.07 -0.0184346286908 0.000358425308862
-16 0.075 -0.0184364849265 0.000384070414671
-17 0.08 -0.0184384694099 0.000409724485298
-18 0.085 -0.0184405821873 0.000435388120601
-19 0.09 -0.018442823308 0.000461061920867
-20 0.095 -0.0184451928244 0.000486746486835
-21 0.1 -0.0184476907918 0.000512442419724
-22 0.105 -0.0184503172686 0.00053815032126
-23 0.11 -0.018453072316 0.000563870793707
-24 0.115 -0.0184559559985 0.00058960443989
-25 0.12 -0.0184589683834 0.000615351863219
-26 0.125 -0.0184621095411 0.000641113667723
-27 0.13 -0.018465379545 0.000666890458074
-28 0.135 -0.0184687784716 0.000692682839612
-29 0.14 -0.0184723064004 0.000718491418378
-30 0.145 -0.0184759634138 0.000744316801133
-31 0.15 -0.0184797495974 0.000770159595394
-32 0.155 -0.0184836650398 0.000796020409456
-33 0.16 -0.0184877098326 0.000821899852421
-34 0.165 -0.0184918840704 0.000847798534223
-35 0.17 -0.018496187851 0.000873717065662
-36 0.175 -0.0185006212752 0.000899656058423
-37 0.18 -0.0185051844467 0.000925616125112
-38 0.185 -0.0185098774726 0.000951597879278
-39 0.19 -0.0185147004627 0.000977601935442
-40 0.195 -0.0185196535301 0.00100362890913
-41 0.2 -0.018524736791 0.00102967941688
-42 0.205 -0.0185299503645 0.00105575407632
-43 0.21 -0.018535294373 0.00108185350613
-44 0.215 -0.0185407689419 0.00110797832612
-45 0.22 -0.0185463741997 0.00113412915723
-46 0.225 -0.0185521102779 0.00116030662158
-47 0.23 -0.0185579773113 0.00118651134249
-48 0.235 -0.0185639754378 0.00121274394448
-49 0.24 -0.0185701047983 0.00123900505337
-50 0.245 -0.0185763655369 0.00126529529622
-51 0.25 -0.0185827578008 0.00129161530144
-52 0.255 -0.0185892817405 0.00131796569874
-53 0.26 -0.0185959375095 0.00134434711924
-54 0.265 -0.0186027252645 0.00137076019543
-55 0.27 -0.0186096451653 0.00139720556125
-56 0.275 -0.018616697375 0.00142368385209
-57 0.28 -0.0186238820597 0.00145019570482
-58 0.285 -0.018631199389 0.00147674175783
-59 0.29 -0.0186386495354 0.00150332265107
-60 0.295 -0.0186462326747 0.00152993902605
-61 0.3 -0.0186539489859 0.00155659152589
-62 0.305 -0.0186617986512 0.00158328079535
-63 0.31 -0.0186697818562 0.00161000748085
-64 0.315 -0.0186778987894 0.00163677223051
-65 0.32 -0.018686149643 0.00166357569418
-66 0.325 -0.018694534612 0.00169041852345
-67 0.33 -0.0187030538949 0.00171730137172
-68 0.335 -0.0187117076935 0.0017442248942
-69 0.34 -0.0187204962128 0.00177118974793
-70 0.345 -0.018729419661 0.00179819659187
-71 0.35 -0.0187384782498 0.00182524608685
-72 0.355 -0.018747672194 0.00185233889566
-73 0.36 -0.018757001712 0.00187947568307
-74 0.365 -0.0187664670253 0.00190665711585
-75 0.37 -0.0187760683587 0.0019338838628
-76 0.375 -0.0187858059405 0.00196115659479
-77 0.38 -0.0187956800024 0.00198847598479
-78 0.385 -0.0188056907793 0.00201584270792
-79 0.39 -0.0188158385095 0.00204325744145
-80 0.395 -0.0188261234348 0.00207072086484
-81 0.4 -0.0188365458004 0.00209823365979
-82 0.405 -0.0188471058549 0.00212579651027
-83 0.41 -0.0188578038501 0.00215341010252
-84 0.415 -0.0188686400416 0.00218107512514
-85 0.42 -0.0188796146882 0.00220879226907
-86 0.425 -0.0188907280523 0.00223656222766
-87 0.43 -0.0189019803997 0.00226438569667
-88 0.435 -0.0189133719996 0.00229226337435
-89 0.44 -0.0189249031249 0.00232019596142
-90 0.445 -0.0189365740519 0.00234818416114
-91 0.45 -0.0189483850604 0.00237622867935
-92 0.455 -0.0189603364338 0.00240433022447
-93 0.46 -0.0189724284589 0.00243248950756
-94 0.465 -0.0189846614263 0.00246070724235
-95 0.47 -0.0189970356299 0.00248898414528
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-97 0.48 -0.0190222089403 0.00254571833504
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-99 0.49 -0.0190479508144 0.00260269786377
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-101 0.5 -0.0190742637348 0.00265992856393
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-109 0.54 -0.0191852775888 0.00289148138852
-110 0.545 -0.0191998080972 0.00292073373487
-111 0.55 -0.0192144850445 0.00295005710962
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-113 0.56 -0.0192442796883 0.00300892001972
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-119 0.59 -0.0193372160865 0.00318729400826
-120 0.595 -0.0193532275179 0.00321729161167
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-123 0.61 -0.0194021645104 0.00330776082963
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-125 0.62 -0.0194355454345 0.00336847873097
-126 0.625 -0.0194524640008 0.00339896165353
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-130 0.645 -0.0195216687306 0.00352173907028
-131 0.65 -0.0195393546644 0.00355264902089
-132 0.655 -0.0195571953673 0.0035836468904
-133 0.66 -0.0195751912812 0.0036147335263
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-135 0.67 -0.0196116505298 0.00367717650862
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-141 0.7 -0.0197248006022 0.00386672533057
-142 0.705 -0.0197442139994 0.00389864971962
-143 0.71 -0.0197637872619 0.00393067159203
-144 0.715 -0.0197835208793 0.00396279184472
-145 0.72 -0.0198034153458 0.00399501137941
-146 0.725 -0.0198234711601 0.00402733110266
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-158 0.785 -0.0200769138533 0.00442331928783
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-163 0.81 -0.0201896118368 0.0045929981357
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-167 0.83 -0.0202828471177 0.00473084840195
-168 0.835 -0.0203065882181 0.00476561206114
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-170 0.845 -0.0203545934061 0.00483550789544
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-175 0.87 -0.0204776862045 0.00501244605461
-176 0.875 -0.020502837813 0.00504821908124
-177 0.88 -0.0205281686136 0.00508412308491
-178 0.885 -0.020553679264 0.00512015915539
-179 0.89 -0.0205793704271 0.0051563283892
-180 0.895 -0.0206052427716 0.0051926318896
-181 0.9 -0.0206312969716 0.00522907076671
-182 0.905 -0.0206575337068 0.00526564613755
-183 0.91 -0.0206839536624 0.00530235912611
-184 0.915 -0.0207105575293 0.00533921086343
-185 0.92 -0.0207373460042 0.00537620248763
-186 0.925 -0.0207643197892 0.00541333514403
-187 0.93 -0.0207914795926 0.0054506099852
-188 0.935 -0.020818826128 0.00548802817101
-189 0.94 -0.0208463601151 0.00552559086871
-190 0.945 -0.0208740822795 0.00556329925304
-191 0.95 -0.0209019933525 0.00560115450624
-192 0.955 -0.0209300940713 0.00563915781816
-193 0.96 -0.0209583851794 0.00567731038631
-194 0.965 -0.020986867426 0.00571561341599
-195 0.97 -0.0210155415663 0.00575406812027
-196 0.975 -0.021044408362 0.00579267572016
-197 0.98 -0.0210734685804 0.00583143744461
-198 0.985 -0.0211027229954 0.00587035453065
-199 0.99 -0.0211321723867 0.00590942822342
-200 0.995 -0.0211618175407 0.00594865977625
-201 1.0 -0.0211916592497 0.00598805045079
-202 1.005 -0.0212216983125 0.00602760151701
-203 1.01 -0.0212519355343 0.00606731425336
-204 1.015 -0.0212823717267 0.00610718994679
-205 1.02 -0.0213130077075 0.00614722989286
-206 1.025 -0.0213438443015 0.00618743539581
-207 1.03 -0.0213748823396 0.00622780776866
-208 1.035 -0.0214061226595 0.00626834833326
-209 1.04 -0.0214375661055 0.00630905842043
-210 1.045 -0.0214692135285 0.00634993936999
-211 1.05 -0.0215010657862 0.00639099253086
-212 1.055 -0.0215331237431 0.00643221926118
-213 1.06 -0.0215653882704 0.00647362092835
-214 1.065 -0.0215978602462 0.00651519890914
-215 1.07 -0.0216305405556 0.0065569545898
-216 1.075 -0.0216634300906 0.00659888936611
-217 1.08 -0.0216965297501 0.00664100464349
-218 1.085 -0.0217298404402 0.00668330183711
-219 1.09 -0.0217633630741 0.00672578237194
-220 1.095 -0.0217970985719 0.00676844768288
-221 1.1 -0.0218310478613 0.00681129921484
-222 1.105 -0.0218652118769 0.00685433842285
-223 1.11 -0.0218995915607 0.00689756677211
-224 1.115 -0.0219341878623 0.00694098573816
-225 1.12 -0.0219690017383 0.0069845968069
-226 1.125 -0.022004034153 0.00702840147476
-227 1.13 -0.0220392860782 0.00707240124874
-228 1.135 -0.0220747584932 0.00711659764655
-229 1.14 -0.0221104523849 0.00716099219671
-230 1.145 -0.022146368748 0.00720558643861
-231 1.15 -0.0221825085847 0.00725038192267
-232 1.155 -0.0222188729052 0.00729538021041
-233 1.16 -0.0222554627274 0.00734058287457
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-1181 5.9 25558689542.6 -2.55153879404e+12
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
deleted file mode 100644
index 2ad6d7b69..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
+++ /dev/null
@@ -1,1187 +0,0 @@
-# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0)
-
-CH_H0
-N 1181 R 0.00000000001 5.9
-
-1 0.00000000001 8.31299178857e-07 0.0
-2 0.005 8.31311879342e-07 -5.08022586688e-09
-3 0.01 8.31349981758e-07 -1.01608369733e-08
-4 0.015 8.31413488996e-07 -1.52422186449e-08
-5 0.02 8.31502405871e-07 -2.03247562721e-08
-6 0.025 8.31616739127e-07 -2.54088353865e-08
-7 0.03 8.31756497437e-07 -3.04948417048e-08
-8 0.035 8.319216914e-07 -3.55831611709e-08
-9 0.04 8.32112333547e-07 -4.06741800058e-08
-10 0.045 8.32328438343e-07 -4.57682847516e-08
-11 0.05 8.32570022183e-07 -5.08658623183e-08
-12 0.055 8.328371034e-07 -5.59673000292e-08
-13 0.06 8.33129702263e-07 -6.10729856679e-08
-14 0.065 8.33447840983e-07 -6.61833075238e-08
-15 0.07 8.33791543713e-07 -7.12986544391e-08
-16 0.075 8.34160836552e-07 -7.64194158551e-08
-17 0.08 8.34555747546e-07 -8.15459818584e-08
-18 0.085 8.34976306696e-07 -8.66787432278e-08
-19 0.09 8.35422545957e-07 -9.18180914814e-08
-20 0.095 8.35894499243e-07 -9.69644189231e-08
-21 0.1 8.36392202433e-07 -1.0211811869e-07
-22 0.105 8.36915693374e-07 -1.07279584798e-07
-23 0.11 8.37465011883e-07 -1.12449212192e-07
-24 0.115 8.38040199757e-07 -1.17627396792e-07
-25 0.12 8.38641300774e-07 -1.22814535539e-07
-26 0.125 8.392683607e-07 -1.28011026445e-07
-27 0.13 8.39921427291e-07 -1.33217268641e-07
-28 0.135 8.40600550305e-07 -1.38433662423e-07
-29 0.14 8.41305781504e-07 -1.43660609303e-07
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-31 0.15 8.42794785557e-07 -1.54147774771e-07
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-35 0.17 8.46088593367e-07 -1.75266555654e-07
-36 0.175 8.46978200908e-07 -1.80578728847e-07
-37 0.18 8.4789440368e-07 -1.85904716839e-07
-38 0.185 8.48837271792e-07 -1.91244934288e-07
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-53 0.26 8.66234245555e-07 -2.73343376025e-07
-54 0.265 8.67615018129e-07 -2.78969213098e-07
-55 0.27 8.69023973658e-07 -2.84616633187e-07
-56 0.275 8.70461221189e-07 -2.90286089823e-07
-57 0.28 8.71926872044e-07 -2.95978039217e-07
-58 0.285 8.73421039834e-07 -3.0169294032e-07
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-62 0.305 8.79685233396e-07 -3.24791340003e-07
-63 0.31 8.8132377107e-07 -3.30627983906e-07
-64 0.315 8.82991556179e-07 -3.36490394052e-07
-65 0.32 8.84688718753e-07 -3.42379050225e-07
-66 0.325 8.86415391229e-07 -3.48294435432e-07
-67 0.33 8.88171708466e-07 -3.54237035959e-07
-68 0.335 8.89957807764e-07 -3.60207341438e-07
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-70 0.345 8.93619914037e-07 -3.72233042875e-07
-71 0.35 8.95496207963e-07 -3.78289435392e-07
-72 0.355 8.97402857887e-07 -3.84375526106e-07
-73 0.36 8.99340013567e-07 -3.90491822333e-07
-74 0.365 9.01307827305e-07 -3.96638835124e-07
-75 0.37 9.0330645397e-07 -4.02817079329e-07
-76 0.375 9.05336051015e-07 -4.09027073668e-07
-77 0.38 9.07396778494e-07 -4.152693408e-07
-78 0.385 9.09488799088e-07 -4.21544407387e-07
-79 0.39 9.11612278118e-07 -4.2785280417e-07
-80 0.395 9.13767383571e-07 -4.34195066035e-07
-81 0.4 9.15954286119e-07 -4.40571732086e-07
-82 0.405 9.18173159138e-07 -4.46983345718e-07
-83 0.41 9.20424178735e-07 -4.53430454687e-07
-84 0.415 9.22707523764e-07 -4.59913611186e-07
-85 0.42 9.25023375853e-07 -4.66433371919e-07
-86 0.425 9.27371919425e-07 -4.72990298174e-07
-87 0.43 9.29753341721e-07 -4.795849559e-07
-88 0.435 9.32167832821e-07 -4.86217915785e-07
-89 0.44 9.34615585674e-07 -4.9288975333e-07
-90 0.445 9.37096796117e-07 -4.99601048932e-07
-91 0.45 9.39611662902e-07 -5.0635238796e-07
-92 0.455 9.4216038772e-07 -5.13144360835e-07
-93 0.46 9.44743175226e-07 -5.19977563112e-07
-94 0.465 9.47360233068e-07 -5.26852595561e-07
-95 0.47 9.50011771908e-07 -5.33770064252e-07
-96 0.475 9.52698005456e-07 -5.40730580635e-07
-97 0.48 9.55419150489e-07 -5.47734761627e-07
-98 0.485 9.58175426884e-07 -5.54783229699e-07
-99 0.49 9.60967057644e-07 -5.61876612959e-07
-100 0.495 9.63794268928e-07 -5.69015545241e-07
-101 0.5 9.66657290077e-07 -5.76200666196e-07
-102 0.505 9.69556353647e-07 -5.83432621378e-07
-103 0.51 9.72491695434e-07 -5.90712062337e-07
-104 0.515 9.75463554509e-07 -5.9803964671e-07
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-1078 5.385 361.788072356 -5815.54846929
-1079 5.39 392.196753863 -6356.69120514
-1080 5.395 425.447439765 -6953.32950597
-1081 5.4 461.832877143 -7611.69001217
-1082 5.405 501.678806405 -8338.75903774
-1083 5.41 545.348004761 -9142.38282363
-1084 5.415 593.244865738 -10031.3820373
-1085 5.42 645.820591276 -11015.68269
-1086 5.425 703.57908462 -12106.4659962
-1087 5.43 767.0836459 -13316.3401164
-1088 5.435 836.964588164 -14659.5372095
-1089 5.44 913.927910152 -16152.1397986
-1090 5.445 998.765183767 -17812.3411276
-1091 5.45 1092.36483954 -19660.7449851
-1092 5.455 1195.72506302 -21720.7114182
-1093 5.46 1309.96854996 -24018.7558713
-1094 5.465 1436.35940883 -26585.0106144
-1095 5.47 1576.32254765 -29453.7588927
-1096 5.475 1731.46593848 -32664.0541036
-1097 5.48 1903.60622026 -36260.4385302
-1098 5.485 2094.79817923 -40293.7788208
-1099 5.49 2307.36874045 -44822.2385774
-1100 5.495 2543.95621436 -49912.4122166
-1101 5.5 2807.55567471 -55640.6488261
-1102 5.505 3101.57150066 -62094.6002142
-1103 5.51 3429.87830306 -69375.0339383
-1104 5.515 3796.89167797 -77597.9600438
-1105 5.52 4207.65049744 -86897.1298384
-1106 5.525 4667.91276723 -97426.976642
-1107 5.53 5184.26746489 -109366.082529
-1108 5.535 5764.26523328 -122921.272189
-1109 5.54 6416.57136028 -138332.455868
-1110 5.545 7151.14514692 -155878.368733
-1111 5.55 7979.45057787 -175883.38511
-1112 5.555 8914.70419213 -198725.624049
-1113 5.56 9972.16724736 -224846.609452
-1114 5.565 11169.4907256 -254762.805471
-1115 5.57 12527.1235034 -289079.418826
-1116 5.575 14068.7961785 -328506.947433
-1117 5.58 15822.095705 -373881.063382
-1118 5.585 17819.1492531 -426186.553416
-1119 5.59 20097.4397323 -486586.208276
-1120 5.595 22700.7803778 -556455.762347
-1121 5.6 25680.48194 -637426.248155
-1122 5.605 29096.7536364 -731435.460488
-1123 5.61 33020.3884938 -840790.640792
-1124 5.615 37534.795529 -968245.017485
-1125 5.62 42738.4559856 -1117091.50268
-1126 5.625 48747.8993768 -1291277.69016
-1127 5.63 55701.3183864 -1495547.37524
-1128 5.635 63762.9710814 -1735615.19174
-1129 5.64 73128.5560849 -2018382.72409
-1130 5.645 84031.7935812 -2352206.71961
-1131 5.65 96752.5051511 -2747232.95284
-1132 5.655 111626.562261 -3215813.08417
-1133 5.66 129058.17172 -3773026.78288
-1134 5.665 149535.09312 -4437337.81351
-1135 5.67 173647.546875 -5231421.20537
-1136 5.675 202111.783487 -6183209.69609
-1137 5.68 235799.560429 -7327222.25628
-1138 5.685 275775.133279 -8706256.87756
-1139 5.69 323341.839971 -10373555.6006
-1140 5.695 380100.979 -12395584.2516
-1141 5.7 448026.504816 -14855615.686
-1142 5.705 529560.156125 -17858367.867
-1143 5.71 627733.090584 -21536032.8982
-1144 5.715 746322.053888 -26056148.6972
-1145 5.72 890050.744612 -31631923.3162
-1146 5.725 1064850.60201 -38535839.9678
-1147 5.73 1278200.09801 -47117672.8003
-1148 5.735 1539568.25801 -57828464.0874
-1149 5.74 1860997.27824 -71252602.8402
-1150 5.745 2257871.76507 -88150975.6842
-1151 5.75 2749939.74956 -109519339.591
-1152 5.755 3362675.33565 -136667749.506
-1153 5.76 4129107.68815 -171329294.699
-1154 5.765 5092290.5566 -215809903.716
-1155 5.77 6308657.30745 -273196093.331
-1156 5.775 7852608.40245 -347645058.856
-1157 5.78 9822826.27903 -444792652.679
-1158 5.785 12351029.1761 -572331463.941
-1159 5.79 15614195.007 -740836343.412
-1160 5.795 19851761.9704 -964952961.956
-1161 5.8 25390026.834 -1265123750.87
-1162 5.805 32677044.7126 -1670116762.16
-1163 5.81 42332992.355 -2220765999.89
-1164 5.815 55223522.7267 -2975558546.03
-1165 5.82 72567652.5207 -4019067582.33
-1166 5.825 96098076.1892 -5474821115.58
-1167 5.83 128301974.954 -7525167797.49
-1168 5.835 172786897.851 -10442321052.7
-1169 5.84 234843441.663 -14637502185.9
-1170 5.845 322321750.402 -20739806771.4
-1171 5.85 447015573.215 -29724625295.8
-1172 5.855 626879673.777 -43126013542.2
-1173 5.86 889637615.256 -63393728654.1
-1174 5.865 1278749299.07 -94504139730.6
-1175 5.87 1863457472.26 -1.43025428057e+11
-1176 5.875 2756024722.63 -2.20012867219e+11
-1177 5.88 4141916348.74 -3.44455288186e+11
-1178 5.885 6333827617.32 -5.49691352523e+11
-1179 5.89 9870722980.34 -8.95662608449e+11
-1180 5.895 15704145484.1 -1.49296892607e+12
-1181 5.9 25558719893.6 -2.55154000294e+12
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min
deleted file mode 100644
index 8eb3a03cb..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min
+++ /dev/null
@@ -1,19 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt
deleted file mode 100644
index 3e14f82b1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt
+++ /dev/null
@@ -1,48 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-# I you want to be careful, you can minimize the system first.
-# (Try using "run.in.min" and uncomment the line below.)
-# read_data system_after_min.data
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.025
-dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-# Keep the chaperonin fixed. Only let the protein move.
-
-fix fxlan proteins langevin 0.39 0.39 1.0 48279
-fix fxnve proteins nve
-
-# Notes:
-# The temperature is in reduced units and is set to 0.39
-# which is the folding temperature for the unfrustrated protein.
-# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
-# as it was in the paper. (Hopefully folding times should be similar.)
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 50 #(time interval for printing out "thermo" data)
-
-#restart 100000000 restart_nvt
-
-run 5000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT
deleted file mode 100644
index b2770e3e3..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT
+++ /dev/null
@@ -1,27 +0,0 @@
-# This directory demonstrates how to run a short simulation of
-# the "unfrustrated" coarse-grained protein model used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-#
-# During this short simulation (run.in.nvt) the protein evolves
-# from an unfolded initial conformation to the folded state.
-#
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh
deleted file mode 100755
index d5ae1fe5a..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# You would probably run lammps this way:
-#
-# lmp_ubuntu -i run.in.nvt
-
-# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
-# to the input scripts & data files you created earlier when you ran moltemplate
-# system.in.init, system.in.settings, system.data
-
-
-
-
-# -----------------------------------
-
-
-
-LAMMPS_COMMAND="lmp_mpi"
-
-# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary.
-
-# Run lammps using the following 3 commands:
-
-"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-"$LAMMPS_COMMAND" -i run.in.nvt # production run
-
-# Alternately, if you have MPI installed, try something like this:
-
-#NUMPROCS=4
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh
deleted file mode 100755
index fa10f5572..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -overlay-dihedrals system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
deleted file mode 100644
index 1470af4bc..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
+++ /dev/null
@@ -1,97 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 27 !NATOM
- 1 1 2 2 0.000000 1.0000 0
- 2 1 1 1 0.000000 1.0000 0
- 3 1 2 2 0.000000 1.0000 0
- 4 1 1 1 0.000000 1.0000 0
- 5 1 2 2 0.000000 1.0000 0
- 6 1 1 1 0.000000 1.0000 0
- 7 1 3 3 0.000000 1.0000 0
- 8 1 3 3 0.000000 1.0000 0
- 9 1 1 1 0.000000 1.0000 0
- 10 1 2 2 0.000000 1.0000 0
- 11 1 1 1 0.000000 1.0000 0
- 12 1 2 2 0.000000 1.0000 0
- 13 1 1 1 0.000000 1.0000 0
- 14 1 2 2 0.000000 1.0000 0
- 15 1 3 3 0.000000 1.0000 0
- 16 1 3 3 0.000000 1.0000 0
- 17 1 3 3 0.000000 1.0000 0
- 18 1 1 1 0.000000 1.0000 0
- 19 1 1 1 0.000000 1.0000 0
- 20 1 2 2 0.000000 1.0000 0
- 21 1 2 2 0.000000 1.0000 0
- 22 1 1 1 0.000000 1.0000 0
- 23 1 1 1 0.000000 1.0000 0
- 24 1 2 2 0.000000 1.0000 0
- 25 1 2 2 0.000000 1.0000 0
- 26 1 1 1 0.000000 1.0000 0
- 27 1 2 2 0.000000 1.0000 0
-
- 26 !NBOND: bonds
- 1 2 2 3 3 4 4 5
- 5 6 6 7 7 8 8 9
- 9 10 10 11 11 12 12 13
- 13 14 14 15 15 16 16 17
- 17 18 18 19 19 20 20 21
- 21 22 22 23 23 24 24 25
- 25 26 26 27
-
- 25 !NTHETA: angles
- 13 14 15 7 8 9 6 7 8
- 16 17 18 15 16 17 2 3 4
- 4 5 6 9 10 11 11 12 13
- 14 15 16 1 2 3 3 4 5
- 10 11 12 12 13 14 25 26 27
- 5 6 7 8 9 10 17 18 19
- 18 19 20 22 23 24 21 22 23
- 19 20 21 20 21 22 23 24 25
- 24 25 26
-
- 43 !NPHI: dihedrals
- 1 2 3 4 1 2 3 4
- 2 3 4 5 2 3 4 5
- 3 4 5 6 3 4 5 6
- 4 5 6 7 4 5 6 7
- 5 6 7 8 6 7 8 9
- 7 8 9 10 8 9 10 11
- 8 9 10 11 9 10 11 12
- 9 10 11 12 10 11 12 13
- 10 11 12 13 11 12 13 14
- 11 12 13 14 12 13 14 15
- 12 13 14 15 13 14 15 16
- 14 15 16 17 15 16 17 18
- 15 16 17 18 16 17 18 19
- 16 17 18 19 17 18 19 20
- 17 18 19 20 18 19 20 21
- 18 19 20 21 19 20 21 22
- 19 20 21 22 20 21 22 23
- 20 21 22 23 21 22 23 24
- 21 22 23 24 22 23 24 25
- 22 23 24 25 23 24 25 26
- 23 24 25 26 24 25 26 27
- 24 25 26 27
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg
deleted file mode 100644
index 152fa88ff..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg
deleted file mode 100644
index bb269f47f..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt
deleted file mode 100644
index 0dc1f5dd0..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt
+++ /dev/null
@@ -1,255 +0,0 @@
-# This file defines a pair of coarse-grained protein models used in:
-# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
-# (http://www.pnas.org/content/101/36/13192)
-
-
-1beadUnfrustrated {
-
- # Note: the "unfrustrated" model is kind of funny looking. (My apologies.)
-
- # There are 3 atom types (referred to above as B, L, and N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:B 1.0
- @atom:L 1.0
- @atom:N 1.0
- }
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118
- $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074
- $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456
- $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926
- $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356
- $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634
- $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503
- $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852
- $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528
- $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863
- $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636
- $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065
- $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921
- $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738
- $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232
- $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693
- $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841
- $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008
- $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678
- $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878
- $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001
- $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365
- $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748
- $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731
- $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442
- $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789
- $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241
- }
-
- # bond-ID bond-Type atom-ID atom-ID
-
- write("Data Bonds") {
- $bond:b1 @bond:backbone $atom:a1 $atom:a2
- $bond:b2 @bond:backbone $atom:a2 $atom:a3
- $bond:b3 @bond:backbone $atom:a3 $atom:a4
- $bond:b4 @bond:backbone $atom:a4 $atom:a5
- $bond:b5 @bond:backbone $atom:a5 $atom:a6
- $bond:b6 @bond:backbone $atom:a6 $atom:a7
- $bond:b7 @bond:backbone $atom:a7 $atom:a8
- $bond:b8 @bond:backbone $atom:a8 $atom:a9
- $bond:b9 @bond:backbone $atom:a9 $atom:a10
- $bond:b10 @bond:backbone $atom:a10 $atom:a11
- $bond:b11 @bond:backbone $atom:a11 $atom:a12
- $bond:b12 @bond:backbone $atom:a12 $atom:a13
- $bond:b13 @bond:backbone $atom:a13 $atom:a14
- $bond:b14 @bond:backbone $atom:a14 $atom:a15
- $bond:b15 @bond:backbone $atom:a15 $atom:a16
- $bond:b16 @bond:backbone $atom:a16 $atom:a17
- $bond:b17 @bond:backbone $atom:a17 $atom:a18
- $bond:b18 @bond:backbone $atom:a18 $atom:a19
- $bond:b19 @bond:backbone $atom:a19 $atom:a20
- $bond:b20 @bond:backbone $atom:a20 $atom:a21
- $bond:b21 @bond:backbone $atom:a21 $atom:a22
- $bond:b22 @bond:backbone $atom:a22 $atom:a23
- $bond:b23 @bond:backbone $atom:a23 $atom:a24
- $bond:b24 @bond:backbone $atom:a24 $atom:a25
- $bond:b25 @bond:backbone $atom:a25 $atom:a26
- $bond:b26 @bond:backbone $atom:a26 $atom:a27
- }
-
- # (3-body) Angles are specified below
-
- # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
- # (These interactions are not determined by atom type.)
- #
- # Note that some quartets of atoms are listed because their
- # potentials contain multiple terms in the Fourier expansion.
- # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!)
- #
- # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
-
- write("Data Dihedrals") {
- $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4
- $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5
- $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6
- $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7
- $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7
- $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8
- $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9
- $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10
- $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11
- $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12
- $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13
- $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14
- $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15
- $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15
- $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16
- $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17
- $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18
- $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19
- $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20
- $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21
- $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22
- $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23
- $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24
- $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25
- $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26
- $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27
- $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27
- }
-
- # All consecutively bonded triplets of atoms same 3-body bond-angle
- # interaction parameters. Of coarse, we could specify them all explicitly
- # (as we did for the dihedrals above), but I wanted to show how to specify
- # angles by atom type instead. (You can do this for dihedrals & impropers
- # also.)
-
- # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # (The "*" is a wildcard character. I use "*" to denote any atom-type or
- # bond-type which is defined within the current namespace: 1beadUnfrustrated)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
- pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
- pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
- }
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond-Type bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 100.0 1.0
- }
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # angle-Type anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 13.3333333333 105.0
- }
-
- # 4-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Udihedral(phi) = K * (1 + cos(n*phi - d))
- #
- # The d parameter is in degrees, K is in kcal/mol/rad^2.
- #
- # The corresponding command is:
- #
- # dihedral_coeff dihedralType dihedralstylename K n d w
- # ("w" is the weight for 1-4 pair interactions, which we set to 0)
-
- # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d
- # parameters. I'm hoping this will be fixed eventually.
-
- write_once("In Settings") {
- # Correct version:
- #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0
- # Replacing with
- dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0
- # Correct version:
- #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0
- # Replacing with
- dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0
- dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0
- dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0
- dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0
- # Correct version:
- # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0
- # Replacing with
- dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0
- dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0
- dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0
- dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0
- }
-
- write_once("In Settings") {
- # Optional: define the atoms in the "proteins" group
- group proteins type @atom:B
- group proteins type @atom:L
- group proteins type @atom:N
- }
-
- # LAMMPS has many available force field styles (and atom styles).
- # Here, we pick the ones which work well for this molecular model:
-
- write_once("In Init") {
- # --- Default options for the "1BeadUnfrustrated" protein model ---
- # --- (These can be overridden later.) ---
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid charmm
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-} # 1beadUnfrustrated
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt
deleted file mode 100644
index cbc8fe217..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt
+++ /dev/null
@@ -1,45 +0,0 @@
-import "1beadUnfrustrated.lt"
-
-
-# Alternate starting conformation (same molecule):
-
-
-1beadUnfolded inherits 1beadUnfrustrated {
-
- # This molecule "inherits" all of its features from "1beadUnfrustrated"
- # Here we override the atomic positions with new coordinates:
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
- $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
- $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
- $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
- $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
- $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
- $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
- $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
- $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
- $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
- $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
- $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
- $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
- $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
- $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
- $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
- $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
- $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
- $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
- $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
- $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
- $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
- $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
- $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
- $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
- $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
- $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
- }
-
-} # 1beadUnfolded
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt
deleted file mode 100644
index 5ebe6efb8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt
+++ /dev/null
@@ -1,11 +0,0 @@
-import "1beadUnfrustrated_variants.lt"
-
-
-protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein)
-
-
-write_once("Data Boundary") {
- 0.0 27.0 xlo xhi
- 0.0 27.0 ylo yhi
- 0.0 27.0 zlo zhi
-}
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min
deleted file mode 100644
index 8eb3a03cb..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min
+++ /dev/null
@@ -1,19 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt
deleted file mode 100644
index e49206ee3..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt
+++ /dev/null
@@ -1,46 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-# I you want to be careful, you can minimize the system first.
-# (Try using "run.in.min" and uncomment the line below.)
-# read_data system_after_min.data
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.025
-dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-fix fxlan all langevin 0.39 0.39 1.0 48279
-fix fxnve all nve
-
-# Notes:
-# The temperature is in reduced units and is set to 0.39
-# which is the folding temperature for the unfrustrated protein.
-# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
-# as it was in the paper. (Hopefully folding times should be similar.)
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 50 #(time interval for printing out "thermo" data)
-
-#restart 100000000 restart_nvt
-
-run 8000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README.TXT
deleted file mode 100644
index eda6a1ca2..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README.TXT
+++ /dev/null
@@ -1,44 +0,0 @@
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-
-This is an example of a very simple coarse-grained protein.
-
-This example contains a 1-bead (C-alpha model) representation of the
-"unfrustrated" 4-helix bundle model used in this paper:
-G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
-
-In this model, there are three atom-types (bead-types), H, L, and N
-representing one amino-acid each. The "H" beads represent the hydrophobic
-amino acids, and are attracted to eachother with a strength of "1.0"
-(in dimensionless units of "epsilon"). The "L" and "N" atoms are
-hydrophilic and purely repulsive, and only differ in their secondary-structure
-propensity (ie their dihedral parameters).
-
-The dihedral-interaction is bi-stable with two deep local minima (corresponding
-to helix-like and sheet-like secondary structure). You can adjust the bias
-in favor of one minima or another by modifying the angle-shift parameter in
-the appropriate "dihedral_coeff" command in the other .lt file.
-
-A definition for the 4-sheet beta-barell protein model is also included.
-If you want to simulate that molecule instead, then edit the "system.lt"
-file (in the "moltemplate_files" subdirectory), and replace this line:
-prot = new 4HelixBundle
- with
-prot = new 4SheetBundle
-
--------------
-Instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step2)
-README_run.sh
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh
deleted file mode 100755
index 4b0229453..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# You would probably run lammps this way:
-#
-# lmp_ubuntu -i run.in.nvt
-
-# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
-# to the input scripts & data files you created earlier when you ran moltemplate
-# system.in.init, system.in.settings, system.data
-
-
-
-
-# -----------------------------------
-
-
-
-LAMMPS_COMMAND="lmp_mpi"
-
-# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...) Change if necessary.
-
-# Run lammps using the following 3 commands:
-
-"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-"$LAMMPS_COMMAND" -i run.in.nvt # production run
-
-# Alternately, if you have MPI installed, try something like this:
-
-#NUMPROCS=4
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_setup.sh
deleted file mode 100755
index fa10f5572..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -overlay-dihedrals system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg
deleted file mode 100644
index b4d919f9e..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg
deleted file mode 100644
index cd65146ff..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf
deleted file mode 100644
index de47509ed..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf
+++ /dev/null
@@ -1,214 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 73 !NATOM
- 1 1 1 1 0.000000 1.0000 0
- 2 1 1 1 0.000000 1.0000 0
- 3 1 2 2 0.000000 1.0000 0
- 4 1 2 2 0.000000 1.0000 0
- 5 1 1 1 0.000000 1.0000 0
- 6 1 1 1 0.000000 1.0000 0
- 7 1 2 2 0.000000 1.0000 0
- 8 1 2 2 0.000000 1.0000 0
- 9 1 1 1 0.000000 1.0000 0
- 10 1 1 1 0.000000 1.0000 0
- 11 1 2 2 0.000000 1.0000 0
- 12 1 2 2 0.000000 1.0000 0
- 13 1 1 1 0.000000 1.0000 0
- 14 1 1 1 0.000000 1.0000 0
- 15 1 2 2 0.000000 1.0000 0
- 16 1 2 2 0.000000 1.0000 0
- 17 1 1 1 0.000000 1.0000 0
- 18 1 1 1 0.000000 1.0000 0
- 19 1 2 2 0.000000 1.0000 0
- 20 1 2 2 0.000000 1.0000 0
- 21 1 1 1 0.000000 1.0000 0
- 22 1 1 1 0.000000 1.0000 0
- 23 1 2 2 0.000000 1.0000 0
- 24 1 2 2 0.000000 1.0000 0
- 25 1 1 1 0.000000 1.0000 0
- 26 1 1 1 0.000000 1.0000 0
- 27 1 2 2 0.000000 1.0000 0
- 28 1 2 2 0.000000 1.0000 0
- 29 1 1 1 0.000000 1.0000 0
- 30 1 1 1 0.000000 1.0000 0
- 31 1 2 2 0.000000 1.0000 0
- 32 1 2 2 0.000000 1.0000 0
- 33 1 1 1 0.000000 1.0000 0
- 34 1 1 1 0.000000 1.0000 0
- 35 1 2 2 0.000000 1.0000 0
- 36 1 2 2 0.000000 1.0000 0
- 37 1 1 1 0.000000 1.0000 0
- 38 1 1 1 0.000000 1.0000 0
- 39 1 2 2 0.000000 1.0000 0
- 40 1 2 2 0.000000 1.0000 0
- 41 1 1 1 0.000000 1.0000 0
- 42 1 1 1 0.000000 1.0000 0
- 43 1 2 2 0.000000 1.0000 0
- 44 1 2 2 0.000000 1.0000 0
- 45 1 1 1 0.000000 1.0000 0
- 46 1 1 1 0.000000 1.0000 0
- 47 1 2 2 0.000000 1.0000 0
- 48 1 2 2 0.000000 1.0000 0
- 49 1 1 1 0.000000 1.0000 0
- 50 1 1 1 0.000000 1.0000 0
- 51 1 2 2 0.000000 1.0000 0
- 52 1 2 2 0.000000 1.0000 0
- 53 1 1 1 0.000000 1.0000 0
- 54 1 1 1 0.000000 1.0000 0
- 55 1 2 2 0.000000 1.0000 0
- 56 1 2 2 0.000000 1.0000 0
- 57 1 1 1 0.000000 1.0000 0
- 58 1 1 1 0.000000 1.0000 0
- 59 1 2 2 0.000000 1.0000 0
- 60 1 2 2 0.000000 1.0000 0
- 61 1 1 1 0.000000 1.0000 0
- 62 1 1 1 0.000000 1.0000 0
- 63 1 2 2 0.000000 1.0000 0
- 64 1 2 2 0.000000 1.0000 0
- 65 1 3 3 0.000000 1.0000 0
- 66 1 3 3 0.000000 1.0000 0
- 67 1 3 3 0.000000 1.0000 0
- 68 1 3 3 0.000000 1.0000 0
- 69 1 3 3 0.000000 1.0000 0
- 70 1 3 3 0.000000 1.0000 0
- 71 1 3 3 0.000000 1.0000 0
- 72 1 3 3 0.000000 1.0000 0
- 73 1 3 3 0.000000 1.0000 0
-
- 72 !NBOND: bonds
- 1 2 2 3 3 4 4 5
- 5 6 6 7 7 8 8 9
- 9 10 10 11 11 12 12 13
- 13 14 14 15 15 16 16 65
- 17 18 17 70 18 19 19 20
- 20 21 21 22 22 23 23 24
- 24 25 25 26 26 27 27 28
- 28 29 29 30 30 31 31 32
- 32 67 33 34 33 68 34 35
- 35 36 36 37 37 38 38 39
- 39 40 40 41 41 42 42 43
- 43 44 44 45 45 46 46 47
- 47 48 48 71 49 50 50 51
- 51 52 52 53 53 54 54 55
- 55 56 56 57 57 58 58 59
- 59 60 60 61 61 62 62 63
- 63 64 64 73 65 66 66 67
- 68 69 69 70 71 72 72 73
-
- 71 !NTHETA: angles
- 16 65 66 32 67 66 48 71 72
- 64 73 72 2 3 4 3 4 5
- 6 7 8 7 8 9 10 11 12
- 11 12 13 14 15 16 18 19 20
- 19 20 21 22 23 24 23 24 25
- 26 27 28 27 28 29 30 31 32
- 34 35 36 35 36 37 38 39 40
- 39 40 41 42 43 44 43 44 45
- 46 47 48 50 51 52 51 52 53
- 54 55 56 55 56 57 58 59 60
- 59 60 61 62 63 64 15 16 65
- 31 32 67 47 48 71 63 64 73
- 34 33 68 18 17 70 1 2 3
- 4 5 6 5 6 7 8 9 10
- 9 10 11 12 13 14 13 14 15
- 17 18 19 20 21 22 21 22 23
- 24 25 26 25 26 27 28 29 30
- 29 30 31 33 34 35 36 37 38
- 37 38 39 40 41 42 41 42 43
- 44 45 46 45 46 47 49 50 51
- 52 53 54 53 54 55 56 57 58
- 57 58 59 60 61 62 61 62 63
- 17 70 69 33 68 69 65 66 67
- 68 69 70 71 72 73
-
- 122 !NPHI: dihedrals
- 4 5 6 7 8 9 10 11
- 12 13 14 15 20 21 22 23
- 24 25 26 27 28 29 30 31
- 36 37 38 39 40 41 42 43
- 44 45 46 47 52 53 54 55
- 56 57 58 59 60 61 62 63
- 2 3 4 5 6 7 8 9
- 10 11 12 13 18 19 20 21
- 22 23 24 25 26 27 28 29
- 34 35 36 37 38 39 40 41
- 42 43 44 45 50 51 52 53
- 54 55 56 57 58 59 60 61
- 3 4 5 6 1 2 3 4
- 7 8 9 10 5 6 7 8
- 11 12 13 14 9 10 11 12
- 13 14 15 16 19 20 21 22
- 17 18 19 20 23 24 25 26
- 21 22 23 24 27 28 29 30
- 25 26 27 28 29 30 31 32
- 35 36 37 38 33 34 35 36
- 39 40 41 42 37 38 39 40
- 43 44 45 46 41 42 43 44
- 45 46 47 48 51 52 53 54
- 49 50 51 52 55 56 57 58
- 53 54 55 56 59 60 61 62
- 57 58 59 60 61 62 63 64
- 4 5 6 7 8 9 10 11
- 12 13 14 15 20 21 22 23
- 24 25 26 27 28 29 30 31
- 36 37 38 39 40 41 42 43
- 44 45 46 47 52 53 54 55
- 56 57 58 59 60 61 62 63
- 2 3 4 5 6 7 8 9
- 10 11 12 13 18 19 20 21
- 22 23 24 25 26 27 28 29
- 34 35 36 37 38 39 40 41
- 42 43 44 45 50 51 52 53
- 54 55 56 57 58 59 60 61
- 3 4 5 6 1 2 3 4
- 7 8 9 10 5 6 7 8
- 11 12 13 14 9 10 11 12
- 13 14 15 16 19 20 21 22
- 17 18 19 20 23 24 25 26
- 21 22 23 24 27 28 29 30
- 25 26 27 28 29 30 31 32
- 35 36 37 38 33 34 35 36
- 39 40 41 42 37 38 39 40
- 43 44 45 46 41 42 43 44
- 45 46 47 48 51 52 53 54
- 49 50 51 52 55 56 57 58
- 53 54 55 56 59 60 61 62
- 57 58 59 60 61 62 63 64
- 68 69 70 17 33 68 69 70
- 65 66 67 32 16 65 66 67
- 71 72 73 64 48 71 72 73
- 34 33 68 69 18 17 70 69
- 68 33 34 35 70 17 18 19
- 15 16 65 66 31 32 67 66
- 47 48 71 72 63 64 73 72
- 14 15 16 65 30 31 32 67
- 46 47 48 71 62 63 64 73
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt
deleted file mode 100644
index 9b4ff2535..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt
+++ /dev/null
@@ -1,274 +0,0 @@
-# This file defines a family of coarse-grained protein models used in:
-# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
-#
-# Strategy:
-#
-#1) First I'll define some building blocks (A16, B16, T3)
-# which are helices, sheets and turns of a predetermined length)
-#
-#2) Then I'll copy and paste them together to build
-# a 4-helix bundle or a 4-strand beta-barrel.
-# This approach is optional. If your protein has helices which are not
-# identical, you should probably just include all 4 helices in a single
-# "Data Atoms" section and don't try to subdivide the protein into pieces.)
-
-
-1beadProtSci2010 { # <-- enclose definitions in a namespace for portability
-
- write_once("In Init") {
- units lj
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid fourier
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-
- # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
-
- A16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0
- $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6
- $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2
- $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8
- $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4
- $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0
- $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6
- $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2
- $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8
- $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4
- $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0
- $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6
- $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2
- $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8
- $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4
- $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # A16
-
-
- # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
-
- B16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0
- $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8
- $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6
- $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4
- $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2
- $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0
- $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8
- $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6
- $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4
- $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2
- $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0
- $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8
- $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6
- $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4
- $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2
- $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # B16
-
- T3 { # T3 is a "turn" region consisting of 3 beads
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0
- $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24
- $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- }
-
- } # T3
-
- # ----- Now build larger molecules using A16, B16 and T3 -------
-
- 4SheetBarrel {
-
- sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, -6)
- sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, -6)
- sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, -6)
- sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, -6)
-
- turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,6.6)
- turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-6.9)
- turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,6.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- 4HelixBundle {
-
- helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, -4.5)
- helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, -4.5)
- helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, -4.5)
- helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, -4.5)
-
- turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,5.4)
- turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-4.8)
- turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,5.4)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0
- }
- # Interactions between different atoms use "repulsive wins" mixing rules
-
-
- # bond_coeff bondType bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 66.6 1.0
- }
-
-
- # angle_coeff angleType anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 66.6 105.0
- }
-
- # We use the same bond-angle forces whenever
- # there are 3 consecutively-bonded atoms:
- #
- # angleType atomtypes1 2 3 bondtypes1 2
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
-
-
- # From the Bellesia et al 2010 paper:
- # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta))
- # for turns: U_{dih}(\phi) = 0.2*cos(3\phi)
- #
- # General formula used for "dihedral_style fourier":
- # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ]
- #
- # Syntax:
- # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ...
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0
- dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5
- dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0
- dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0
- # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
- }
-
-
- # dihedralType atomtypes1 2 3 4 bondtypes1 2 3
-
- write_once("Data Dihedrals By Type") {
- @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * *
- @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * *
- @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * *
- @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * *
- @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * *
- }
- # Note: This next rule is not needed:
- # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * *
- # (By reflection symmetry, it's equivalent to the rule above.)
- #
- # Note: The example in ../../membrane+protein/moltemplate_files/
- # demonstrates how to define dihedral angles for this model
- # in an alternate way which might be easier to understand.
-
-
- # --- Mass Units ---
- # There are 3 atom types (referred to above as ../H, ../L, and ../N)
- # Define their masses (in reduced units):
-
- write_once("Data Masses") {
- @atom:H 1.0
- @atom:L 1.0
- @atom:N 1.0
- }
-
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh
deleted file mode 100755
index 852b9b76f..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-# run moltemplate this way
-
-moltemplate.sh system.lt
-
-# This will generate various files with names ending in *.in* and *.data
-# which are needed by LAMMPS.
-
-# ------ Other versions: --------
-#
-# If you are using the "other_versions/charmm/1beadProtSci2010.lt" file,
-# then you must run moltemplate this way:
-#
-# moltemplate.sh -overlay-dihdedrals system.lt
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT
deleted file mode 100644
index 82bc8c5c4..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT
+++ /dev/null
@@ -1,13 +0,0 @@
-This directory contains other versions of the same molecule
-(with the same force-field), implemented in different ways.
-
-charmm/1beadProtSci2010.lt <-- This applies multiple "charmm" dihedral angle
- forces to the same quartet of atoms to create
- a Fourier series. (No packages needed.)
-
- NOTE: You must run moltemplate this way:
-
- moltemplate.sh -overlay-dihdedrals system.lt
-
-class2/1beadProtSci2010.lt <-- This uses the "class2" dihedral angles forces
- (You must build LAMMPS with the CLASS2 package)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt
deleted file mode 100644
index d57186bee..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt
+++ /dev/null
@@ -1,411 +0,0 @@
-# This file defines a family of coarse-grained protein models used in:
-# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
-#
-#
-# For portability, all definitions in this file are enclosed within
-# the "1beadProtSci2010" namespace. To access them, put
-# "using namespace 1beadProtSci2010" in your LT file.
-
-# Strategy:
-#
-#1) First I'll define some building blocks
-# (short helices, sheets and turns of a predetermined length)
-#
-#2) Then I'll cut and paste them together to build
-# a 4-helix bundle or a 4-strand beta-barrel.
-#
-# Doing it this way is optional. It's simpler (but longer) to simply write
-# out the entire sequence of all 73 atoms in a single "Data Atoms" section.
-# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the
-# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions
-# manually (instead of inferring them from the atom type). If your protein
-# has helices which are not identical, this would probably be easier.
-# Use whichever style you prefer.
-#
-#
-# Note that atom types, bond types, angle types, and dihedral types
-# are shared between all molecules defined in the "1beadProtSci2010" family.
-# (That's why there is a "../" in their path-names. Otherwise atom, bond,
-# angle types, etc... are not shared between different molecules.)
-#
-# Confusing detail:
-# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer).
-# These are represented by the "$mol" variable written next to each atom.
-# Our protein has multiple subunits (in this case: helices, sheets, turns).
-# Because we want the subunits to share the same molecule-ID counter we use
-# "$mol:..." instead of "$mol" which tells moltemplate to search for the
-# parent molecule's ID. This is optional. If it bothers you, just use "$mol"
-
-
-
-1beadProtSci2010 {
-
- write_once("In Init") {
- # -- Default styles for "1beadProtSci2010" --
- units lj
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid charmm
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
-
- # If charges are needed, (assuming biopolymers), try one of:
- #dielectric 80.0
- #pair_style hybrid lj/cut/coul/debye 0.1 4.0
- # or (for short distances, below a couple nm)
- #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0
-
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-
- # ---- Building blocks: A16, B16, Turn3 ----
-
- # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
-
- A16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0
- $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6
- $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2
- $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8
- $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4
- $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0
- $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6
- $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2
- $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8
- $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4
- $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0
- $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6
- $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2
- $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8
- $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4
- $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # A16
-
-
- # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
-
- B16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0
- $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8
- $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6
- $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4
- $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2
- $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0
- $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8
- $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6
- $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4
- $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2
- $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0
- $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8
- $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6
- $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4
- $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2
- $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # B16
-
- T3 { # T3 is a "turn" region consisting of 3 beads
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0
- $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24
- $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- }
-
- } # T3
-
- # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc)
- # can be shared. The ".." in "@atom:../CA" tells moltemplate that
- # atom type CA is defined in the parent's environment. (We are
- # sharing the CA atom type between both the H and P residues.
- # The same is true of the ".." in "@bond:../sidechain".
- #
- #
- # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
- # be a part of a larger molecule, and (if so) to use the larger
- # molecule's id number as it's own.
-
-
-
- # ----- Now build larger molecules using A16, B16 and T3 -------
-
- 4HelixBundle {
-
- helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0)
- helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0)
- helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0)
- helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0)
- # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2)
-
- turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9)
- turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3)
- turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9)
-
- # Note: In the paper, this is described as the "UA2" conformation
- # (I played around with the angles until it looked "okay". This is not
- # the minimum energy conformation. Further minimization is necessary.)
-
- # Now bond the pieces together.
- # (Note: angle & dihedral interactions will be generated automatically.)
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # <-- create a variable for the parent's Molecule-ID
- }
-
- 4SheetBundle {
-
- sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0)
- sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0)
- sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0)
- sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0)
- # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2)
-
- turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6)
- turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9)
- turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- # There are 3 atom types (referred to above as ../H, ../L, and ../N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:H 1.0
- @atom:L 1.0
- @atom:N 1.0
-
- }
-
-
-
- # --------------------------------------------------------------------
- # -- In this example, all force field parameters are stored in the --
- # -- file named "In Settings". They can also go in sections like --
- # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... --
- # --------------------------------------------------------------------
-
-
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0
- }
- # (Interactions between different atom types use "arithmetic"
- # and "maxmax" ("repulsion-wins") mixing rules.)
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond_coeff bondType bondstylename k r0
- #
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 66.6 1.0
- }
-
-
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # The corresponding command is:
- #
- # angle_coeff angleType anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 66.6 105.0
- }
-
- # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded
- # together. We do this by to asking moltemplate to generate this
- # 3-body interaction whenever 3 consecutively bonded atoms satisfy
- # the following type requirement:
- #
- # angleType atomtypes1 2 3 bondtypes1 2
-
- write_once("Data Angles By Type") {
- @angle:backbone * * * * *
- }
-
-
-
-
-
- # 4-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Udihedral(phi) = K * (1 + cos(n*phi - d))
- #
- # The d parameter is in degrees, K is in kcal/mol/rad^2.
- #
- # The corresponding command is:
- #
- # dihedral_coeff dihedralType dihedralstylename K n d w
- # ("w" is the weight for 1-4 pair interactions, which we set to 0)
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:turn charmm 0.2 3 0 0
- dihedral_coeff @dihedral:term3 charmm 1.2 3 0 0
-
- dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65 0
- dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62 0
- dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60 0
- dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57 0
- dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55 0
- }
-
- #write_once("In Settings") {
- # dihedral_coeff @dihedral:turn charmm 0.2 3 0.0 0
- # dihedral_coeff @dihedral:term3 charmm 1.2 3 0.0 0
- # dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65.0 0
- # dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62.5 0
- # dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60.0 0
- # dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57.5 0
- # dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55.5 0
- #}
-
- # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy
- # the following type requirements:
-
- write_once("Data Dihedrals By Type") {
- # The dihedral interaction between backbone atoms in the helix or sheet-like
- # regions is proportional to the sum of two terms: cos(phi+delta)+cos(3*phi)
- # where delta is a constant used to control the bias between helices/sheets.
- # As of 2013-4-07, the "fourier", "table", "class2", and "charmm",
- " dihedral_styles can implement this potential.
- # However dihedral_style "charmm" can only handle one cosine term at a time.
- # So we use two commands to create two dihedral interactions for the same
- # set of of four atoms ("cos3" and "delta60_0"). (To allow the
- # superposition of multiple dihedral interactions on the same atoms,
- # be sure to run moltemplate with the "-overlay-dihdedrals" argument.)
- #
- # dihedralType atomtypes1 2 3 4 bondtypes1 2 3
-
- @dihedral:term3 @atom:H @atom:L @atom:H @atom:L * * *
- @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * *
-
- @dihedral:term3 @atom:H @atom:L @atom:L @atom:H * * *
- @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * *
-
- @dihedral:term3 @atom:L @atom:H @atom:H @atom:L * * *
- @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * *
-
- @dihedral:term3 @atom:H @atom:H @atom:L @atom:L * * *
- @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * *
-
- # Comment out the next 4 lines: (They are redundant with the lines above)
- #@dihedral:term3 @atom:L @atom:L @atom:H @atom:H * * *
- #@dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * *
- #@dihedral:term3 @atom:L @atom:H @atom:L @atom:H * * *
- #@dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * *
- # (Redundant: The LLHH pattern is identical to HHLL after order reversal)
- # (Redundant: The LHLH pattern is identical to HLHL after order reversal)
-
- # Right now the dihedral-angle settings are "unfrustrated", meaning that the
- # peptide backbone is equally happy to adopt helical or sheet-like secondary
- # structure (See Table IV of Bellesia et. al, Prot Sci, 19, 141 (2010)).
- # You can change that by changing "delta60_0" to one of the other choices.
-
- # Any dihedral interactions containing "N" atoms use the @dihedral:turn
- # interaction (which is much weaker).
- @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * *
- @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * *
- @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * *
- @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * *
- # Comment out the next 4 lines: (They are redundant with the lines above)
- # @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * *
- # @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * *
- # @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * *
- # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * *
- }
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt
deleted file mode 100644
index a0e305f84..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt
+++ /dev/null
@@ -1,385 +0,0 @@
-# This file defines a family of coarse-grained protein models used in:
-# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
-#
-#
-# For portability, all definitions in this file are enclosed within
-# the "1beadProtSci2010" namespace. To access them, put
-# "using namespace 1beadProtSci2010" in your LT file.
-
-# Strategy:
-#
-#1) First I'll define some building blocks
-# (short helices, sheets and turns of a predetermined length)
-#
-#2) Then I'll cut and paste them together to build
-# a 4-helix bundle or a 4-strand beta-barrel.
-#
-# Doing it this way is optional. It's simpler (but longer) to simply write
-# out the entire sequence of all 73 atoms in a single "Data Atoms" section.
-# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the
-# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions
-# manually (instead of inferring them from the atom type). If your protein
-# has helices which are not identical, this would probably be easier.
-# Use whichever style you prefer.
-#
-#
-# Note that atom types, bond types, angle types, and dihedral types
-# are shared between all molecules defined in the "1beadProtSci2010" family.
-# (That's why there is a "../" in their path-names. Otherwise atom, bond,
-# angle types, etc... are not shared between different molecules.)
-#
-# Confusing detail:
-# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer).
-# These are represented by the "$mol" variable written next to each atom.
-# Our protein has multiple subunits (in this case: helices, sheets, turns).
-# Because we want the subunits to share the same molecule-ID counter we use
-# "$mol:..." instead of "$mol" which tells moltemplate to search for the
-# parent molecule's ID. This is optional. If it bothers you, just use "$mol"
-
-
-
-1beadProtSci2010 {
-
- write_once("In Init") {
- # -- Default styles for "1beadProtSci2010" --
- units lj
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid class2
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 rsoftcore 1
-
- # If charges are needed, (assuming biopolymers), try one of:
- #dielectric 80.0
- #pair_style hybrid lj/cut/coul/debye 0.1 4.0
- # or (for short distances, below a couple nm)
- #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0
-
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
-
- # ---- Building blocks: A16, B16, Turn3 ----
-
- # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
-
- A16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0
- $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6
- $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2
- $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8
- $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4
- $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0
- $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6
- $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2
- $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8
- $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4
- $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0
- $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6
- $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2
- $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8
- $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4
- $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # A16
-
-
- # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
-
- B16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0
- $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8
- $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6
- $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4
- $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2
- $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0
- $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8
- $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6
- $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4
- $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2
- $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0
- $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8
- $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6
- $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4
- $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2
- $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # B16
-
- T3 { # T3 is a "turn" region consisting of 3 beads
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0
- $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24
- $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- }
-
- } # T3
-
- # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc)
- # can be shared. The ".." in "@atom:../CA" tells moltemplate that
- # atom type CA is defined in the parent's environment. (We are
- # sharing the CA atom type between both the H and P residues.
- # The same is true of the ".." in "@bond:../sidechain".
- #
- #
- # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
- # be a part of a larger molecule, and (if so) to use the larger
- # molecule's id number as it's own.
-
-
-
- # ----- Now build larger molecules using A16, B16 and T3 -------
-
- 4HelixBundle {
-
- helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0)
- helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0)
- helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0)
- helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0)
- # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2)
-
- turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9)
- turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3)
- turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9)
-
- # Note: In the paper, this is described as the "UA2" conformation
- # (I played around with the angles until it looked "okay". This is not
- # the minimum energy conformation. Further minimization is necessary.)
-
- # Now bond the pieces together.
- # (Note: angle & dihedral interactions will be generated automatically.)
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # <-- create a variable for the parent's Molecule-ID
- }
-
- 4SheetBundle {
-
- sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0)
- sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0)
- sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0)
- sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0)
- # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2)
-
- turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6)
- turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9)
- turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- # There are 3 atom types (referred to above as ../H, ../L, and ../N)
- # Define their masses:
-
- write_once("Data Masses") {
- @atom:H 1.0
- @atom:L 1.0
- @atom:N 1.0
-
- }
-
-
-
- # --------------------------------------------------------------------
- # -- In this example, all force field parameters are stored in the --
- # -- file named "In Settings". They can also go in sections like --
- # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... --
- # --------------------------------------------------------------------
-
-
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 0 0 0 0
- pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0
- pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0
- }
- # (Interactions between different atom types use "arithmetic"
- # and "maxmax" ("repulsion-wins") mixing rules.)
-
-
- # 2-body (bonded) interactions:
- #
- # Ubond(r) = (k/2)*(r-0)^2
- #
- # The corresponding command is:
- #
- # bond_coeff bondType bondstylename k r0
- #
-
- write_once("In Settings") {
- bond_coeff @bond:backbone harmonic 66.6 1.0
- }
-
-
-
- # 3-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Uangle(theta) = (k/2)*(theta-theta0)^2
- # (k in kcal/mol/rad^2, theta0 in degrees)
- #
- # The corresponding command is:
- #
- # angle_coeff angleType anglestylename k theta0
-
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 66.6 105.0
- }
-
- # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded
- # together. We do this by to asking moltemplate to generate this
- # 3-body interaction whenever 3 consecutively bonded atoms satisfy
- # the following type requirement:
- #
- # angleType atomtypes1 2 3 bondtypes1 2
-
- write_once("Data Angles By Type") {
- @angle:backbone * * * * *
- }
-
-
-
-
-
- # 4-body interactions in this example are listed by atomType and bondType
- # The atomIDs involved are determined automatically. The forumula used is:
- #
- # Udihedral(phi) = K * (1 + cos(n*phi - d))
- #
- # The d parameter is in degrees, K is in kcal/mol/rad^2.
- #
- # The corresponding command is:
- #
-
- # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60)
- # (scratchwork: 1.2*cos(x+60) = -1.2*cos(x+60-180) = -1.2*cos(x-120))
- # and 1.2*cos(3x) = -1.2*cos(3x-180)
- # and 0.2*cos(x) = -0.2*cos(x - 180)
- # This way, the energies match exactly with the implementation using charmm dihedrals.)
- #
- # dihedralType dihedralstylename K1 phi1 K2 phi2 K3 phi3
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:delta60_0 class2 1.2 120.0 0 0 1.2 180.0
- dihedral_coeff @dihedral:turn class2 0 0 0 0 0.2 180.0
-
- # All of the cross-terms (for the class2 force-field) are zero (see docs):
- dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0
- dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0
- dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0
- dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0
- dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0
- dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0
- dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0
- dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0
- dihedral_coeff @dihedral:turn class2 aat 0 0 0
- dihedral_coeff @dihedral:turn class2 bb13 0 0 0
- }
-
- # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy
- # the following type requirements:
-
- write_once("Data Dihedrals By Type") {
- # dihedralType atomtypes1 2 3 4 bondtypes1 2 3
-
- @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * *
- @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * *
- @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * *
- @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * *
-
- @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * *
- @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * *
- @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * *
- @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * *
-
- #### Comment out the next 6 lines: (They are redundant with the lines above)
- ## @dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * *
- ## @dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * *
- ## @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * *
- ## @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * *
- ## @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * *
- ## @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * *
- ###################################################################
- }
-
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
deleted file mode 100644
index 6300c4ce3..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
+++ /dev/null
@@ -1,12 +0,0 @@
-import "1beadProtSci2010.lt"
-
-using namespace 1beadProtSci2010
-
-prot = new 4HelixBundle
-
-write_once("Data Boundary") {
- 0 100 xlo xhi
- 0 100 ylo yhi
- 0 100 zlo zhi
-}
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/run.in.min
deleted file mode 100644
index 8eb3a03cb..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/run.in.min
+++ /dev/null
@@ -1,19 +0,0 @@
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run section --
-
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-
-minimize 1.0e-5 1.0e-7 500 2000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/run.in.nvt
deleted file mode 100644
index a0f02dc73..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/run.in.nvt
+++ /dev/null
@@ -1,44 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-
-# -- Atom Definition Section --
-
-# I you want to be careful, you can minimize the system first.
-# (Try using "run.in.min" and uncomment the line below)
-# read_data system_after_min.data
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.008
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-
-fix fxlan all langevin 0.4 0.4 1.0 48279
-fix fxnve all nve
-
-# Notes:
-# The temperature is in reduced units and is set to 0.4.
-# The inverse-damping-rate "damp" (which has units of time) is set to 1.0.
-# (See http://lammps.sandia.gov/doc/fix_langevin.html)
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo_modify norm no #(report total energy not energy / num_atoms)
-thermo 500 #(time interval for printing out "thermo" data)
-
-restart 10000000 restart_nvt
-
-run 1000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README.TXT
deleted file mode 100644
index 305d00d63..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README.TXT
+++ /dev/null
@@ -1,114 +0,0 @@
- This example shows how to build a multicomponent spherical vesicle.
- The lipid bilayer is composed of two different lipids (DPPC and DLPC).
- The vesicle also contains trans-membrane protein inclusions.
-
- The coordinates for the vesicle are constructed by PACKMOL (see below).
-
- The DPPC lipid model is described here:
- G. Brannigan, P.F. Philips, and F.L.H. Brown,
- Physical Review E, Vol 72, 011915 (2005)
- (The DLPC model is a truncated version of DPPC. Modifications discussed below.)
- The protein model is described here:
- G. Bellesia, AI Jewett, and J-E Shea,
- Protein Science, Vol19 141-154 (2010)
-
---- PREREQUISITES: ---
-
-1) This example requires PACKMOL. You can download PACKMOL here:
-
- http://www.ime.unicamp.br/~martinez/packmol/
-
- (Moltemplate does not come with an easy way to generate spherically-symmetric
- structures, so I used the PACKMOL program to move the molecules into position.)
-
-2) This example requires the "dihedral_style fourier", which is currently
-in the USER-MISC package. Build LAMMPS with this package enabled using
- make yes-user-misc
-before compiling LAMMPS.
-(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.)
-
-3) This example may require additional features to be added to LAMMPS.
-If LAMMPS complains about an "Invalid pair_style", then
- a) download the "additional_lammps_code" from
- http://moltemplate.org (upper-left corner menu)
- b) unpack it
- c) copy the .cpp and .h files to the src folding of your lammps installation.
- d) (re)compile LAMMPS.
-
------- Details -------
-
-This example contains a coarse-grained model of a 4-helix bundle protein
-inserted into a lipid bilayer (made from a mixture of DPPC and DLPC).
-
- -- Protein Model: --
-
-The coarse-grained protein is described in:
- G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
-Here we use the "AUF2" model described in that paper.
-(The hydrophobic beads face outwards.)
-
- -- Memebrane Model: --
-
-The DPPC lipid bilayer described in:
- G. Brannigan, P.F. Philips, and F.L.H. Brown,
- Physical Review E, Vol 72, 011915 (2005)
-and:
- M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
- J. Chem. Phys. 135, 244701 (2011)
-
-As in Watson(JCP 2011), rigid bond-length constraints
-have been replaced by harmonic bonds.
-
-A truncated version of this lipid (named "DLPC") has also been added.
-The bending stiffness of each lipid has been increased to compensate
-for the additional disorder resulting from mixing two different types
-of lipids together. (Otherwise pores appear.)
-Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models
-have not been carefully parameterized to reproduce the correct behavior in
-a lipid bilayer mixture.
-
- -- Interactions between the proteins and lipids --
-
-This is discussed in the "system.lt" file.
-
---- Building the files necessary to run a simulation in LAMMPS ---
-
-step 1) Run PACKMOL
-
- Type these commands into the shell.
- (Each command could take several hours.)
-
-cd packmol_files
- packmol < step1_proteins.inp # This step determines the protein's location
- packmol < step2_innerlayer.inp # this step builds the inner monolayer
- packmol < step3_outerlayer.inp # this step builds the outer monolayer
-cd ..
-
-step 2) Run MOLTEMPLATE
- Type these commands into the shell.
- (This could take up to 10 minutes.)
-
-cd moltemplate_files
- moltemplate.sh system.lt -xyz ../system.xyz
- mv -f system.in* system.data ../
- cp -f table_int.dat ../
-cd ..
-
---- Running LAMMPS ---
-
-step3) Run LAMMPS:
- Type these commands into the shell.
- (This could take days.)
-
-lmp_linux -i run.in.min # Minimize the system (important, and very slow)
-
-lmp_linux -i run.in.nvt # Run a simulation at constant volume
-
-If you have compiled the MPI version of lammps, you can run lammps in parallel:
-
-mpirun -np 4 lmp_linux -i run.in.min
- or
-mpirun -np 4 lmp_linux -i run.in.nvt
-
-(Assuming you have 4 cores, for example.)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT
deleted file mode 100644
index f11c438ad..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT
+++ /dev/null
@@ -1,20 +0,0 @@
-WARNING:
-
- This is not a realistic simulation of proteins in a lipid membrane. This
-example was only intented to be a technical demonstration to show how to
-combine totally different kinds of coarse-grained molecules (with different
-kinds of force-fields) together in the same simulation in LAMMPS. Tuning the
-force-field parameters to get realistic results was not the goal. I did
-not take the extra time to do this. If you have suggestions for changes,
-please email me (jewett.aij at gmail dot com).
-
- In addition, I have noticed that newer versions of PACKMOL do not
-always succeed at generating a spherical vesicle in a reasonable amount of time.
-(You may have to play with the .inp files in the packmol_files directory
- to get PACKMOL to produce any files at all.
-
-(NOTE: This example also demonstrantes how to use an external program
- ("packmol") to generate the coordinates for the atoms in the system.
- PLEASE USE "packmol", NOT "ppackmol". -the parallel version of "packmol".
- This is because "ppackmol" is more likely to get caught in infinite loops.)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh
deleted file mode 100755
index ab62f6fb5..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" file is a LAMMPS input script containing
-# references to the input scripts and data files
-# you hopefully have created earlier with MOLTEMPLATE and PACKMOL:
-# system.in.init, system.in.settings, system.in.coords, system.data,
-# and table_int.dat
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-lmp_mpi -i run.in.min # Minimize the system (important, and very slow)
-
-lmp_mpi -i run.in.nvt # Run a simulation at constant volume
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.min
-#or
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_setup.sh
deleted file mode 100755
index f695f6d0e..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_setup.sh
+++ /dev/null
@@ -1,65 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-# First, generate the coordinates (the "system.xyz" file).
-# (This can be a very slow process.)
-
-
-
-cd packmol_files
-
- # You must run each packmol commend one after the other.
- # NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding
- # "inp" file. This should not happen. You can also usually interrupt
- # packmol after 30 minutes, and the solution at that point (an .xyz file)
- # should be good enough for use.
- packmol < step1_proteins.inp # This step determines the protein's location
- # It takes ~20 minutes (on an intel i7)
- packmol < step2_innerlayer.inp # this step builds the inner monolayer
- # It takes ~90 minutes
- packmol < step3_outerlayer.inp # this step builds the outer monolayer
- # It takes ~4 hours
-
-
- # NOTE: PLEASE USE "packmol", NOT "ppackmol". ("ppackmol" is the parallel
- # version of packmol using OpemMP. This example has NOT been tested
- # with "ppackmol". Our impression was that the "ppackmol" version
- # is more likely to get stuck in an infinite loop. -Andrew 2015-8)
-
-
- # Step3 creates a file named "step3_outerlayer.xyz" containing the coordinates
- # in all the atoms of all the molecules. Later we will run moltemplate.sh
- # using the "-xyz ../system.xyz" command line argument. That will instruct
- # moltemplate to look for a file named "system.xyz" in the parent directory.
- # So I rename the "step3_outerlayer.xyz" file to "system.xyz", and move it
- # to this directory so that later moltemplate.sh can find it.
-
- mv -f step3_outerlayer.xyz ../system.xyz
-cd ..
-
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -xyz ../system.xyz system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # The "table_int.dat" file contains tabular data for the lipid INT-INT atom
- # 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
- # so I might look for a way to get rid of it later.)
- cp -f table_int.dat ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg
deleted file mode 100644
index c3ff59956..000000000
Binary files a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt
deleted file mode 100644
index 2e510ebd9..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt
+++ /dev/null
@@ -1,233 +0,0 @@
-# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in
-# G. Bellesia, AI Jewett, and J-E Shea,
-# Protein Science, Vol19 141-154 (2010)
-#
-# Strategy:
-#
-#1) First I'll define some building blocks (A16, B16, T3)
-# which are helices, sheets and turns of a predetermined length)
-#
-#2) Then I'll copy and paste them together to build
-# a 4-helix bundle (or a 4-strand beta-barrel).
-# This approach is optional. If your protein has helices which are not
-# identical, you should probably just include all 4 helices in a single
-# "Data Atoms" section and don't try to subdivide the protein into pieces.)
-
-
-
-1beadProtSci2010 { # <-- enclose definitions in a namespace for portability
-
- # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
-
- A16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0
- $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6
- $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2
- $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8
- $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4
- $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0
- $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6
- $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2
- $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8
- $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4
- $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0
- $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6
- $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2
- $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8
- $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4
- $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # A16
-
-
- T3 { # T3 is a "turn" region consisting of 3 beads
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0
- $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44
- $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- }
-
- } # T3
-
-
- # ----- Now build a larger molecule using A16 and T3 -------
-
- # Create a 4-Helix bundle.
- # In this version, the hydrophobic beads are poing outward.
- # I oriented them this way because I want to place this protein in a membrane.
- # (There is another file in this directory containing alternate version
- # of this same molecule with the hydrophobic beads pointing inward.)
-
- 4HelixInsideOut {
- helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4)
- helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8)
- helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2)
- helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6)
-
- turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9)
- turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0)
- turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixInsideOut
-
-
- # -------- Minor coordinates adjustment: -----------
-
- # Those coordinates in the commands above are a little too large.
- # To make it easier to type them in, I was using sigma=6.0 Angstroms.
- # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6 = 0.8)
-
- 4HelixInsideOut.scale(0.8)
-
- # Note: "scale()" only effects the initial coordinates of
- # the molecule, not the force field parameters.
- # (If you plan to minimize the molecule, you don't need to
- # be so careful about the initial coordinates. In that case,
- # you don't have worry about "scale()". Feel free to remove.)
-
-
-
- # -------------- Force-Field Parameters ------------
-
- # Units and force-field styles for this protein model
- # (These can be overridden later.)
-
- write_once("In Init") {
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid fourier
- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
- }
-
- # --- Distance Units ---
- # In this version of the model, sigma (the bond-length
- # and particle diameter) is rounded to 4.8 Angstroms.
- #
- # --- Energy & Temperature Units ---
- # In this protein model, "epsilon" represents the free energy
- # bonus for bringing two hydrophobic amino acids together.
- # Here I choose to set epsilon to 1.806551818181818 kCal/mole.
- # This value was chosen so that a temperature of 300 Kelvin lies at
- # 0.33 epsilon, which is the unfolding temperature of the marginally stable
- # "ASF1" protein model from the Bellesia et al 2010 paper.
- # This choice insures that both the "ASF1" model from that paper,
- # as well as the much more stable "AUF2" protein we use here (which
- # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin,
- # in the bulk at least. (However it's not clear that these energy
- # parameters will work well for a protein in membrane. Perhaps I'll
- # run some tests and fine tune these parameters for this scenario.)
-
-
- # 2-body (non-bonded) interactions:
- #
- # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
- #
- # i j pairstylename eps sig K L
- #
- write_once("In Settings") {
- pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 4.8 1 -1
- pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0
- pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0
- }
-
- # The exact value of the bond_coeff does not matter too much as long as
- # it is "stiff enough". Here I use a softer bond spring than the one
- # used in the paper so that I can increase the time step.
- # I also use a relatively soft spring to constrain the bond angles.
-
- # bond_coeff bondType bondstylename k r0
-
- write_once("In Settings") {
- bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 4.8
- }
-
-
- # angleType atomtypes1 2 3 bondtypes1 2
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
- }
-
- # angle_coeff angleType anglestylename k theta0
- write_once("In Settings") {
- angle_coeff @angle:backbone harmonic 100.0 105.0
- }
-
-
- # dihedralType atomtypes1 2 3 4 bondtypes1 2 3
-
- write_once("Data Dihedrals By Type") {
- # For a chain of sH and sL atoms, use the @dihedral:delta65_0
- # parameters. (This corresponds to the "AUF2" model from the
- # Bellesia et. al 2010 paper.)
-
- @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * *
-
- # If "tN" (turn) atoms are present, use the @dihedral:turn parameters
-
- @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * *
- }
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0
- dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0
- dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0
- # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
- }
-
-
- # --- Mass Units ---
- # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down):
- write_once("Data Masses") {
- @atom:1beadProtSci2010/sH 100.0
- @atom:1beadProtSci2010/sL 100.0
- @atom:1beadProtSci2010/tN 100.0
- }
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt
deleted file mode 100644
index 38b1b48f8..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt
+++ /dev/null
@@ -1,225 +0,0 @@
-### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ##
-### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE##
-#
-# This file defines a family of coarse-grained protein models used in:
-# G. Bellesia, AI Jewett, and J-E Shea,
-# Protein Science, Vol19 141-154 (2010)
-#
-# Strategy:
-#
-#1) First I'll define some building blocks (A16, B16, T3)
-# which are helices, sheets and turns of a predetermined length)
-
-import "1beadProtSci2010.lt"
-
-# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below
-#
-#2) Then I'll copy and paste them together to build
-# a 4-helix bundle or a 4-strand beta-barrel.
-
-
-1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier
- # This way we don't have to start from scratch. We can
- # use all the atom types and angle settings defined earlier
-
- # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
-
- B16 {
-
- # AtomID MoleculeID AtomType Charge X Y Z
-
- write('Data Atoms') {
- $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0
- $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8
- $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6
- $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4
- $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2
- $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0
- $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8
- $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6
- $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4
- $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2
- $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0
- $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8
- $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6
- $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4
- $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2
- $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0
- }
-
- write('Data Bonds') {
- $bond:b1 @bond:../backbone $atom:a1 $atom:a2
- $bond:b2 @bond:../backbone $atom:a2 $atom:a3
- $bond:b3 @bond:../backbone $atom:a3 $atom:a4
- $bond:b4 @bond:../backbone $atom:a4 $atom:a5
- $bond:b5 @bond:../backbone $atom:a5 $atom:a6
- $bond:b6 @bond:../backbone $atom:a6 $atom:a7
- $bond:b7 @bond:../backbone $atom:a7 $atom:a8
- $bond:b8 @bond:../backbone $atom:a8 $atom:a9
- $bond:b9 @bond:../backbone $atom:a9 $atom:a10
- $bond:b10 @bond:../backbone $atom:a10 $atom:a11
- $bond:b11 @bond:../backbone $atom:a11 $atom:a12
- $bond:b12 @bond:../backbone $atom:a12 $atom:a13
- $bond:b13 @bond:../backbone $atom:a13 $atom:a14
- $bond:b14 @bond:../backbone $atom:a14 $atom:a15
- $bond:b15 @bond:../backbone $atom:a15 $atom:a16
- }
-
- } # B16
-
- # ----- Now build larger molecules using B16 and T3 -------
-
-
- 4SheetBarrel {
- sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0)
- sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0)
- sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0)
- sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0)
-
- turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6)
- turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4)
- turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- # Below I define several alternate conformations of the"4HelixBundleInsideOut"
- # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however.
-
- 4HelixBundle {
- helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4)
- helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8)
- helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2)
- helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
-
- turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2)
- turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9)
- turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4)
-
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixBundle
-
-
-
-
- # --- alternate conformations (same molecule) ----
-
- # In the following version, the helices are oriented in a similar way,
- # but they are separated a little further away from eachother.
-
- 4HelixBundleLoose {
-
- helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
- helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
- helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
- helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
-
- turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4)
- turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8)
- turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
- }
-
-
- # In following version, the helices are oriented in a similar way,
- # but they are separated a little further away from eachother.
-
- 4HelixInsideOutLoose {
- helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
- helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
- helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
- helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
-
- turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8)
- turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2)
- turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixInsideOutLoose
-
-
-
-
- # In the following version, the 4 helices are arranged next to each other,
- # side-by-side, in a planar conformation (instead of a compact bundle).
-
- 4HelixPlanar {
- helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0)
- helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0)
- helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0)
- helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0)
-
- turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8)
- turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8)
- turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8)
-
- write('Data Bonds') {
- $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
- $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
- $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
- $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
- $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
- $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
- }
- create_var { $mol } # molecule ID number shared by all atoms in this protein
-
- } # 4HelixPlanar
-
-
- # -------- Minor coordinates adjustment: -----------
- # Those coordinates in the commands above are a little too large.
- # To make it easier to type them in, I was using sigma=6.0 Angstroms.
- # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6.0 = 0.8)
-
- 4SheetBarrel.scale(0.8)
- 4HelixBundle.scale(0.8)
- 4HelixBundleLoose.scale(0.8)
- 4HelixInsideOutLoose.scale(0.8)
- 4HelixPlanar.scale(0.8)
-
- # Note: "scale()" only effects the initial coordinates of
- # the molecule, not the force field parameters.
- # (If you plan to minimize the molecule, you don't need to
- # be so careful about the initial coordinates. In that case,
- # you don't have worry about "scale()". Feel free to remove.)
-
-
-} # 1beadProtSci2010 (namespace)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt
deleted file mode 100644
index 24be50ace..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt
+++ /dev/null
@@ -1,196 +0,0 @@
-# Note:
-#
-# This example may require additional features to be added to LAMMPS. If
-# LAMMPS complains about an "Invalid pair_style", then download copy the
-# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
-# "src" directory and recompile LAMMPS.
-#
-# -------- Description --------
-#
-# This example contains an implementation of the DPPC lipid bilayer described in
-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
-# Physical Review E, Vol 72, 011915 (2005)
-# and:
-# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
-# J. Chem. Phys. 135, 244701 (2011)
-#
-# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
-# by harmonic bonds.
-#
-# A truncated version of this lipid (named "DLPC") has also been added.
-# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
-# parameterized to reproduce the correct behavior in a lipid bilayer mixture.
-#
-# Units:
-#
-# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
-# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
-# The "sigma" parameter corresponds to 7.5 angstroms.
-
-
-CGLipidBr2005 {
-
-
- write_once("In Init") {
- # -- Default styles for "CGLipidBr2005" --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
-
- #angle_style hybrid cosine/delta # <- used in the original article
- angle_style hybrid harmonic # <- prevents unphysical acute angle turns
- # Explanation:
- # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0))
- # angle_style harmonic: U(theta) = k*(theta-theta0)^2
-
- dihedral_style none
- improper_style none
-
- pair_style hybrid table linear 1130 &
- lj/charmm/coul/charmm/inter es4k4l 14.5 15
-
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
- }
-
-
- DPPC {
- write("Data Atoms") {
- $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
- $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
- $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
- $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
- $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
- }
- write("Data Bonds") {
- $bond:b1 @bond:../backbone $atom:h $atom:i
- $bond:b2 @bond:../backbone $atom:i $atom:t1
- $bond:b3 @bond:../backbone $atom:t1 $atom:t2
- $bond:b4 @bond:../backbone $atom:t2 $atom:t3
- }
- write("Data Angles") {
- $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
- $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
- $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
- }
-
- # Define properties of the local (lipid-specific) atom:head type atom:
- write_once("Data Masses") {
- @atom:head 200.0
- }
- write_once("In Settings") {
- pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- }
-
- } #DPPC
-
-
- DLPC {
- write("Data Atoms") {
- $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
- $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
- $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
- $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
- }
- write("Data Bonds") {
- $bond:b1 @bond:../backbone $atom:h $atom:i
- $bond:b2 @bond:../backbone $atom:i $atom:t1
- $bond:b3 @bond:../backbone $atom:t1 $atom:t2
- }
- write("Data Angles") {
- $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
- $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
- }
- # Define properties of the local (lipid-specific) atom:head type atom:
- write_once("Data Masses") {
- @atom:head 200.0
- }
- write_once("In Settings") {
- pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- }
- } #DLPC
-
-
- # Particles and properties shared by all lipid types:
-
- write_once("Data Masses") {
- @atom:int 200.0
- @atom:tail 200.0
- }
-
- write_once("In Settings") {
- # -- Default settings/parameters for "CGLipidBr2005" --
- # (Hybrid bond & angle styles were used for portability.)
-
- # As in Watson(JCP 2011), rigid bond-length constraints
- # have been replaced by harmonic bonds.
- # The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
- bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
- }
-
- write_once("In Settings") {
- # cosine/delta: U(theta) = k*(1-cos(theta-theta0))
- #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
- # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2
- angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps
- }
- # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper
- # to attempt to compensate for the fact that here we are using a lipid
- # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal
- # of disorder into the bilayer which would not be present in a DPPC bilayer.
- # This causes pores to form. Increasing the angle stiffness prevents this.)
-
- write_once("In Settings") {
-
- # The interaction of "atom:int" with other "atom:int" atoms is given by
- # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
- # r=3*sigma. This was implemented using pair_style table.
- # Unfortunately, mixing lj/charmm and "table" pair styles in the same
- # simulation is very inneficient.
-
- pair_coeff @atom:int @atom:int table table_int.dat INT
-
- # The interaction of tail beads with eachother is given by the formula below
- # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
- # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
- pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
- pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
-
- # The interaction between head beads from different types of lipids
- # is (currently) repulsive:
- pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
-
- } # write_once("In Settings")
-
-
- # Note: I divided epsilon by 4 to get "0.1643" because we are using the
- # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
- # (The "es4k4l" coeffstyle is the default.) Using this convention makes it
- # easier to mix this coarse-grained lipid model with other molecular models.
-
-
-
-} # CGLipidBr2005
-
-
-
-
-
-
-
-
-# Note: This example has not been optimized for speed.
-#
-# Unfortunately, using both lj/charmm and "table" pair styles in the same
-# simulation seems to be very inneficient. (The simulation is twice as slow
-# as using only the "lj/charmm" pair styles for every pairwise interaction,
-# ...and about 25% slower than using "table" for every pairwise interaction.
-# However the lennard-jones pair styles support mixing, so we use them to
-# make it easier to run these molecules with other molecules which don't use
-# pair_table. I felt that portability was worth the extra 25% slow down.)
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh
deleted file mode 100755
index b0de63737..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-# This example shows how to build a multicomponent spherical vesicle.
-# The lipid bilayer is composed of two different lipids (DPPC and DLPC),
-# The vesicle contains 120 trans-membrane protein inclusions.
-#
-# ---------------- Prerequisites: ------------------
-# You must run packmol to generate the coordinates beforehand.
-# Afterwards, move and rename the final coordinate file to "../system.xyz"
-# To do this, check the README.sh file in the ../packmol_files directory.
-# (or follow these instructions below)
-#
-# cd ../packmol_files
-# packmol < step1_proteins.inp
-# packmol < step2_innerlayer.inp
-# packmol < step3_outerlayer.inp
-# cp step3_outerlayer.xyz ../system.xyz
-#
-# These steps could take a few hours.
-#
-# --- After you have done that, you can run moltemplate using this command: ---
-
-moltemplate.sh system.lt -xyz ../system.xyz
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
deleted file mode 100755
index 0d09e4d02..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between "INT" atoms
-# in the lipid membrane model described in
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
-
-def U(r, eps, sigma):
- return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
-def F(r, eps, sigma):
- return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-
-epsilon = 2.75/4.184 # kCal/mole
-sigma = 7.5
-Rmin = 0.02
-Rmax = 22.6
-rcut = 22.5
-N = 1130
-
-for i in range(0,N):
- r = Rmin + i*(Rmax-Rmin)/(N-1)
- U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
- F_r = F(r, epsilon, sigma)
- if r > rcut:
- U_r = 0.0
- F_r = 0.0
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
deleted file mode 100755
index 32147e444..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/usr/bin/env python
-
-# Calculate a table of pairwise energies and forces between "INT" atoms
-# in the lipid membrane model described in
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-# I realized later this is not what we want because although energy is conserved
-# all enrgies are shifted with respect to energies used in the Brannigan paper
-# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
-# (So don't use this.)
-
-# Calculate and print a
-
-def S(r, rc1, rc2, derivative=False):
- """
- Calculate the switching function S(r) which decays continuously
- between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
- S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
- I'm using the same smoothing/switching cutoff function used by the CHARMM
- force-fields. (I'm even using the same code to implement it, taken
- from lammps charmm/coul/charmm pair style, rewritten in python.)
-
- """
- assert(rc2>rc1)
- rsq = r*r
- rc1sq = rc1*rc1
- rc2sq = rc2*rc2
- denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
- (rc2sq-rc1sq)*
- (rc2sq-rc1sq)))
- if rsq > rc2sq:
- return 0.0
- elif rsq < rc1sq:
- if derivative:
- return 0.0
- else:
- return 1.0
- else:
- rc2sq_minus_rsq = (rc2sq - rsq)
- rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
- if derivative:
- return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
- else:
- return (rc2sq_minus_rsq_sq *
- (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
-
-
-def U(r, eps, sigma):
- return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
-
-def F(r, eps, sigma):
- return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-
-epsilon = 2.75/4.184 # kCal/mole
-sigma = 7.5
-Rmin = 0.02
-Rmax = 22.6
-Rc1 = 22.0
-Rc2 = 22.5
-N = 1130
-
-for i in range(0,N):
- r = Rmin + i*(Rmax-Rmin)/(N-1)
- U_r = U(r, epsilon, sigma)
- F_r = F(r, epsilon, sigma)
- # Multiply U(r) & F(r) by the smoothing/switch function
- U_r = U_r * S(r, Rc1, Rc2)
- F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
- print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
deleted file mode 100644
index f73c0d5f1..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
+++ /dev/null
@@ -1,166 +0,0 @@
-# Description:
-#
-# This example shows how to build a multicomponent spherical vesicle.
-# The lipid bilayer is composed of two different lipids (DPPC and DLPC),
-# The vesicle contains 120 trans-membrane protein inclusions.
-#
-# The DPPC lipid model is described here:
-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
-# Physical Review E, Vol 72, 011915 (2005)
-# The protein model is described here:
-# G. Bellesia, AI Jewett, and J-E Shea,
-# Protein Science, Vol19 141-154 (2010)
-# The new DLPC model is a truncated version of DPPC,
-# (Its behaviour has not been rigorously tested.)
-# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
-# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
-#
-# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below)
-#
-# NOTE:
-# This example may require additional features to be added to LAMMPS.
-# If LAMMPS complains about an "Invalid pair_style", then copy the code
-# in the "additional_lammps_code" directory into your LAMMPS "src" directory
-# and recompile LAMMPS.
-
-# First, load the definitions of the molecules we will need:
-
-import "CGLipidBr2005.lt"
-using namespace CGLipidBr2005
-
-import "1beadProtSci2010.lt"
-using namespace 1beadProtSci2010
-
-# PREREQUISITES:
-# Coordinates for the molecules in this example are loaded from an .XYZ file
-# created by PACKMOL. This must be done in advance. (See ../packmol_files/)
-#
-# The XYZ file was created by PACKMOL in 3 steps:
-# (Add the proteins, then pack lipids in the inner & outer layers around them.)
-#
-# step1) Creae 120 proteins. Distribute them on the surface of the sphere.
-#
-# step2) Keeping the coordinates from step1 fixed,
-# a) first we add 9500 DPPC lipids to the inner monolayer
-# b) then we add 9500 DLPC lipids to the inner monolayer
-#
-# step3) Keeping the coordinates from steps 1 and 2 fixed,
-# a) first we add 12500 DPPC lipids to the outer monolayer
-# b) then we add 12500 DLPC lipids to the outer monolayer
-#
-# The order that molecules are created in moltemplate should match the order
-# they appear in the final XYZ file created by PACKMOL. (See above.)
-# Consequently I instantiate the molecules in the same order here:
-
-
-# Step 1) ---- protein inclusions ----
-
-proteins = new 4HelixInsideOut [120]
-
-# Step 2a) ---- inner monolayer ----
-dppc_in = new DPPC [9500]
-# Step 2b)
-dlpc_in = new DLPC [9500]
-
-# Step 3a) ---- outer monolayer ----
-dppc_out = new DPPC [12500]
-# Step 3b)
-dlpc_out = new DLPC [12500]
-
-
-
-# ------------------ boundary conditions --------------------
-
-write_once("Data Boundary") {
- -500.0 500.0 xlo xhi
- -500.0 500.0 ylo yhi
- -500.0 500.0 zlo zhi
-}
-
-
-# -------- interactions between protein and lipids ----------
-
-# Note: All atom types must include the full path (the name of
-# the namespace which defined them as well as the atom type name).
-# (This is because we are no longer inside that namespace.)
-
-
-write_once("In Settings") {
-
- # Interactions between the protein and lipid atoms are usually
- # determined by mixing rules. However this is not possible some
- # for atoms (such as the "int" atoms in the lipid model which
- # interact using -1/r^2 attraction). Lorentz-Berthelot mixing
- # rules do not make sense for these atoms so we must explicitly
- # define their interaction with all other atoms.
-
- # i j pairstylename eps sig K L
-
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
-
- # We want the interactions between hydrophobic residues and atoms in
- # the interior of the lipid to be energetically similar to the attractive
- # interactions between hydrophobic residues. (See 1beadProtSci2010.)
-
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1
-
- # All other interactions between proteins and lipids are steric.
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
-
-
- # We also add an artificial attractive interaction between the
- # turn residues of the protein and the lipid head groups in
- # order to keep the protein upright. This might not be necessary
-
- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
-
- # Add a weak attractive interaction between hydrophilic "sL" beads
- # (Whose strength mimics the strength of interaction between tail beads
- # in the lipid. This was absent from the original protein model.
- # However without some kind of weak attraction between residues,
- # the negative pressure in the interior of the bilayer membrane
- # allways pulls the protein apart. Recall that in the membrane,
- # the hydrophobic beads in the protein will face outwards towards the lipid
- # tails leaving the hydrophilic amino acids of the protein in the interior.
- # In reality, these polar groups form hydrogen bonds with each other.)
-
- pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 6.0 0.4 -1
-
- # However these hydrophilic amino acids are not attracted to
- # the bilayer interior.
-
- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
-
-}
-
-
-
-
-# Finally, we must combine the two force-field styles which were used for
-# the coarse-grained lipid and protein. To do that, we write one last time
-# to the "In Init" section. When reading the "Init" section LAMMPS will
-# read these commands last and this will override any earlier settings.
-
-write_once("In Init") {
- # -- These styles override earlier settings --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
- angle_style hybrid cosine/delta harmonic
- dihedral_style hybrid fourier
- improper_style none
- pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
-}
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat
deleted file mode 100644
index b0d651d67..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat
+++ /dev/null
@@ -1,1139 +0,0 @@
-# Table for the INT-INT interaction from
-# Brannigan et al, Phys Rev E, 72, 011915 (2005)
-# This table contains
-# i r_i U(r_i) -dU/dr|r_i
-# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
-
-INT
-N 1130
-
-1 0.02 2.0331818401e+30 1.21990910406e+33
-2 0.04 4.9638228518e+26 1.48914685554e+29
-3 0.06 3.82579033251e+24 7.65158066501e+26
-4 0.08 1.21187081343e+23 1.81780622014e+25
-5 0.1 8.32791281704e+21 9.99349538045e+23
-6 0.12 9.34030842897e+20 9.34030842897e+22
-7 0.14 1.46892540453e+20 1.25907891817e+22
-8 0.16 2.95866897809e+19 2.21900173357e+21
-9 0.18 7.19889946863e+18 4.79926631242e+20
-10 0.2 2.0331818401e+18 1.21990910406e+20
-11 0.22 6.47834392264e+17 3.53364213962e+19
-12 0.24 2.28034873754e+17 1.14017436877e+19
-13 0.26 8.72681951932e+16 4.02776285507e+18
-14 0.28 3.58624366341e+16 1.53696157003e+18
-15 0.3 1.56704372019e+16 6.26817488078e+17
-16 0.32 7.2233129348e+15 2.70874235055e+17
-17 0.34 3.48970861422e+15 1.23166186384e+17
-18 0.36 1.75754381558e+15 5.85847938527e+16
-19 0.38 9.18613895646e+14 2.90088598625e+16
-20 0.4 4.96382285179e+14 1.48914685554e+16
-21 0.42 2.76404230108e+14 7.89726371739e+15
-22 0.44 1.58162693423e+14 4.31352800247e+15
-23 0.46 9.27773983256e+13 2.42027995633e+15
-24 0.48 5.56725765996e+13 1.391814415e+15
-25 0.5 3.41111308981e+13 8.18667141564e+14
-26 0.52 2.13057117167e+13 4.91670270393e+14
-27 0.54 1.35459994024e+13 3.0102220895e+14
-28 0.56 8.75547769351e+12 1.87617379153e+14
-29 0.58 5.74645813711e+12 1.18892237325e+14
-30 0.6 3.8257903322e+12 7.65158066491e+13
-31 0.62 2.58128463312e+12 4.99603477424e+13
-32 0.64 1.7635041342e+12 3.30657025205e+13
-33 0.66 1.21901470178e+12 2.21639036726e+13
-34 0.68 8.51979641904e+11 1.50349348607e+13
-35 0.7 6.0167184547e+11 1.0314374497e+13
-36 0.72 4.29087845387e+11 7.15146409276e+12
-37 0.74 3.08855637556e+11 5.00846980094e+12
-38 0.76 2.24270970425e+11 3.54112058818e+12
-39 0.78 1.64210505205e+11 2.52631546702e+12
-40 0.8 1.2118708117e+11 1.81780621971e+12
-41 0.82 90109367359.1 1.31867367068e+12
-42 0.84 67481501334.4 9.64021449503e+11
-43 0.86 50880896383.4 7.09965997788e+11
-44 0.88 38613938681.2 5.26553710913e+11
-45 0.9 29486692086.8 3.93155896009e+11
-46 0.92 22650731882.4 2.95444330322e+11
-47 0.94 17498544395.3 2.23385674464e+11
-48 0.96 13591937526.4 1.69899220331e+11
-49 0.98 10612635712.6 1.29950642555e+11
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diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
deleted file mode 100755
index 2fe282995..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# Here we generate the starting coordinates of the simulation
-# using PACKMOL.
-
-
-
-# You must run each packmol commend one after the other.
-# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding
-# "inp" file. This should not happen. You can also usually interrupt
-# packmol after 30 minutes, and the solution at that point (an .xyz file)
-# should be good enough for use.
-packmol < step1_proteins.inp # This step determines the protein's location
- # It takes ~20 minutes (on an intel i7)
-packmol < step2_innerlayer.inp # this step builds the inner monolayer
- # It takes ~90 minutes
-packmol < step3_outerlayer.inp # this step builds the outer monolayer
- # It takes ~4 hours
-
-
-# NOTE: PLEASE USE "packmol", NOT "ppackmol". ("ppackmol" is the
-# parallel-version of packmol using OpemMP. This example has NOT been
-# tested with "ppackmol". Our impression was that the "ppackmol"
-# version is more likely to get stuck in an infinite loop. -Andrew 2015-8)
-
-
-# Step3 creates a file named "step3_outerlayer.xyz" containing the coordinates
-# in all the atoms of all the molecules. Later we will run moltemplate.sh
-# using the "-xyz ../system.xyz" command line argument. That will instruct
-# moltemplate to look for a file named "system.xyz" in the parent directory.
-# So I rename the "step3_outerlayer.xyz" file to "system.xyz", and move it
-# to this directory so that later moltemplate.sh can find it.
-
-mv -f step3_outerlayer.xyz ../system.xyz
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp
deleted file mode 100644
index abb48db7d..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp
+++ /dev/null
@@ -1,49 +0,0 @@
-# Step 1: Create a sphere of proteins lying
-# (In step 2 we will pack lipids around these proteins
-#
-# ----- Run using: -----
-# packmol < step1_proteins.inp
-# (This takes about 30 minutes on an Intel i7 processor)
-
-
-# ----- Settings: -----
-
-# All the atoms from diferent proteins will be at least 50.0 Angstrons apart.
-tolerance 50.0
-# (Setting "discale" to 2.0 increases the typical separation
-# distance to approximately 2.0*50.0 = 100.0 Angstroms.)
-discale 2.0
-# The other parameters below are optional:
-nloop 10000
-maxit 20
-seed 12345
-sidemax 3000.0
-# What fraction of the molecules are moved during "large moves"? (default 0.05)
-movefrac 0.05
-
-
-# The output file name
-
-output step1_proteins.xyz
-
-
-# File types are in xyz format
-
-filetype xyz
-
-
-
-# First, specify the protein inclusions
-# We will pack the lipids around these later
-
-structure protein.xyz
- number 120
- atoms 68 69 70
- inside sphere 0. 0. 0. 273.75
- end atoms
- atoms 65 66 67 71 72 73
- outside sphere 0. 0. 0. 325.0
- end atoms
-end structure
-
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp
deleted file mode 100644
index 9f61960f2..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp
+++ /dev/null
@@ -1,70 +0,0 @@
-# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE
-
-# Step 2: Pack the lipids in the inner monolayer around the proteins from step1.
-#
-# ----- Run using: -----
-# packmol < step2_innerlayer.inp
-# (This takes about 90 minutes on an Intel i7 processor)
-
-
-# ----- Settings: -----
-
-# All the atoms from diferent molecules will be at least 5.5 Angstrons apart
-tolerance 5.5
-# (Setting "discale" to 1.4 increases the typical separation
-# distance to approximately 1.4*5.5 = 7.7 Angstroms.)
-discale 1.4
-# The other parameters below are optional:
-nloop 10000
-maxit 20
-seed 12345
-sidemax 3000.0
-# What fraction of the molecules are moved during "large moves"? (default 0.05)
-movefrac 0.05
-
-
-# The output file name
-
-output step2_innerlayer.xyz
-
-# File types are in xyz format
-
-filetype xyz
-
-
-# The proteins whose position we determined earlier in step 1
-# will be frozen in place during this step.
-
-structure step1_proteins.xyz
- number 1
- fixed 0. 0. 0. 0. 0. 0.
-end structure
-
-
-# 9500 DPPC lipids will be put in a shell with their hydrophilic heads
-# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards.
-
-
-structure DPPC.xyz
- number 9500
- atoms 1
- inside sphere 0. 0. 0. 270.0
- end atoms
- atoms 5
- outside sphere 0. 0. 0. 295.0
- end atoms
-end structure
-
-# 9500 DLPC lipids will be put in a shell with their hydrophilic heads
-# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards.
-
-structure DLPC.xyz
- number 9500
- atoms 1
- inside sphere 0. 0. 0. 273.0
- end atoms
- atoms 4
- outside sphere 0. 0. 0. 295.0
- end atoms
-end structure
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp
deleted file mode 100644
index bed1c0424..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp
+++ /dev/null
@@ -1,70 +0,0 @@
-# NOTE: YOU MUST COMPLETE STEPS 1 AND 2 BEFORE RUNNING PACKMOL ON THIS FILE
-
-# Step 3: Pack the lipids in the outer monolayer around the proteins from step1.
-#
-# ----- Run using: -----
-# packmol < step3_outerlayer.inp
-# (This takes about 4 hours on an Intel i7 processor)
-
-
-# ----- Settings: -----
-
-# All the atoms from diferent molecules will be at least 5.5 Angstrons apart
-tolerance 5.5
-# (Setting "discale" to 1.4 increases the typical separation
-# distance to approximately 1.4*5.5 = 7.7 Angstroms.)
-discale 1.4
-# The other parameters below are optional:
-nloop 10000
-maxit 20
-seed 12345
-sidemax 3000.0
-# What fraction of the molecules are moved during "large moves"? (default 0.05)
-movefrac 0.05
-
-
-# The output file name
-
-output step3_outerlayer.xyz
-
-# File types are in xyz format
-
-filetype xyz
-
-
-# The proteins and lipids whose position we determined earlier in steps 1-2
-# will be frozen in place during this step.
-
-structure step2_innerlayer.xyz
- number 1
- fixed 0. 0. 0. 0. 0. 0.
-end structure
-
-
-# 12500 DPPC lipids will be put in a shell with their hydrophilic heads
-# (atom 1) pointing outwards, and their tails (atom 5) pointing inwards.
-
-
-structure DPPC.xyz
- number 12500
- atoms 5
- inside sphere 0. 0. 0. 310.0
- end atoms
- atoms 1
- outside sphere 0. 0. 0. 336.0
- end atoms
-end structure
-
-# 12500 DLPC lipids will be put in a shell with their hydrophilic heads
-# (atom 1) pointing outwards, and their tails (atom 4) pointing inwards.
-
-structure DLPC.xyz
- number 12500
- atoms 4
- inside sphere 0. 0. 0. 313.0
- end atoms
- atoms 1
- outside sphere 0. 0. 0. 332.0
- end atoms
-end structure
-
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min
deleted file mode 100644
index 25ed25ad7..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min
+++ /dev/null
@@ -1,50 +0,0 @@
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# So, after typing "make yes-user-misc" in to the shell, ...
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-#
-# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
-# then you made a mistake in the instructions above.
-
-
-
-# -- Init section --
-
-include system.in.init
-
-# -- Atom definition section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run section --
-
-dump 1 all custom 250 traj_min.lammpstrj id mol type x y z ix iy iz
-
-# minimize
-
-#balance 1.3 rcb
-
-min_style quickmin
-min_modify dmax 0.1
-minimize 1.0e-5 1.0e-7 5000 20000
-
-# If minimization crashes, then instead try Langevin dynamics
-# with a small timestep and a fast damping parameter. For example:
-#
-# timestep 0.05
-# fix fxlan all langevin 300.0 300.0 100.0 48279
-# fix fxnve all nve
-#
-# run 10000
-
-write_data system_after_min.data
diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
deleted file mode 100644
index 253c04267..000000000
--- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
+++ /dev/null
@@ -1,63 +0,0 @@
-# -------- REQUIREMENTS: ---------
-# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# 2) It also may require additional features and bug fixes for LAMMPS.
-# So, after typing "make yes-user-misc" in to the shell, ...
-# be sure to download and copy the "additional_lammps_code" from
-# http://moltemplate.org (upper-left corner menu)
-# 3) Unpack it
-# 4) copy the .cpp and .h files to the src folding of your lammps installation.
-# 5) Compile LAMMPS.
-#
-# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
-# then you made a mistake in the instructions above.
-#
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Commenting out:
-#
-# read_data system.data
-#
-# Instead read the data file created by "run.in.min".
-
-read_data system_after_min.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# Just in case the previous minimization failed, try again.
-# (I don't know why this helps, but sometimes it does. Magic.)
-
-minimize 1.0e-5 1.0e-7 5000 20000
-
-# Run main simulation
-
-timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
-dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-
-thermo_style custom step temp pe etotal vol epair ebond eangle
-thermo 100 # time interval for printing out "thermo" data
-
-
-
-
-fix fxlan all langevin 300.0 300.0 120 48279
-fix fxnve all nve
-
-# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
-# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
-# Note: The langevin damping parameter "120" corresponds to
-# the 0.12ps damping time used in Watson et. al JCP 2011.
-
-run 1000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
deleted file mode 100644
index d69f1d6ff..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
+++ /dev/null
@@ -1,83 +0,0 @@
-###########################################################
-# Interaction of a carbon nanotube with a pair of "mystery
-# molecules" (extracted from the cnat-cnt.data/in files).
-###########################################################
-# Author: Aysun Itai and Andrew Jewett
-
-This example uses "ltemplify.py" to create molecule templates out
-of two different molecules in a pre-existing LAMMPS IN/DATA file.
-Then I show how to use "moltemplate.sh" to make copies of these
-molecules and to move and rotate them (creating new LAMMPS IN/DATA files).
-
- Disclaimer:
-The molecules in this example are not physically realistic.
-The purpose of this example is to demonstrate ltemplify usage.
-
- REQUIRED INPUT FILES
-
-cnad-cnt.data cnad-cnt.in system.lt
-
- cnad-cnt.data
- This is a LAMMPS data file containing the coordinates and the topology
- for a system combining the two molecules together. ltemplify will extract
- molecules from this file, one at a time.
-
- cnad-cnt.in
- This file contains force-field parameters and old run settings for the system.
- (We ignore the run settings in this file.) The force-field parameters in
- the "cnad-cnt.in" file are only necessary because we are going to build
- a completely new set of simulation input files. (We are not only going to
- rotate them and duplicate the molecules.) ltemplify.py will extract the
- force field parameters from this file. This approach allows us to combine
- these molecules with other types of molecules later on.)
-
- system.lt
- The "system.lt" contains the instructions what we will do with these molecules
- after ltemplify.py has converted them into .LT format. In this example
- it contains instructions for rotating and copying the two molecules,
- (It also defines the periodic boundary conditions.)
-
- OUTPUT FILES
-
-cnad.lt
-cnt.lt
-
-These files are referenced in system.lt.
-Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt")
-creates new LAMMPS data and input files:
-system.data, system.in, system.in.init, system.in.settings
-(These files are referenced in run.in.nvt.)
-
-You can run a simulation from the files created by moltemplate using
-
-lmp_linux -i run.in.nvt
-
-NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY
- ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED.
- (This was done to protect the original source of the files.)
- The goal of this example is only to demonstrate how to use
- "ltemplify.py" to convert lammps input and data files into
- LT format and back again.)
-
- -----------
-
-Instructions:
-Run the commands (follow the instructions) in these files:
-
-step 1)
-README_step1_run_ltemplify.sh
-
-and then
-
-step 2)
-README_step2_run_moltemplate.sh
-
-step 3) OPTIONAL
-
-To run a short LAMMPS simulation, you can use the "in.nvt" file, for example:
-
-$LAMMPS_BINARY -i run.in.nvt
-
-where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
-(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...).
- -----------
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh
deleted file mode 100755
index 4bb42d7ea..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/sh
-
-# Aysun Itai's LAMMPS files contain two molecules:
-
-# The CNAD molecule has molecule-id 1
-
-ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt
-
-# The CNT (carbon nanotube) corresponds to molecule-id 2
-ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt
-
-# This will extract both molecules and save them as separate .LT files.
-# (We can include these files later when preparing new simulations.)
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh
deleted file mode 100755
index 6903a855f..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-# --- Running Moltemplate ---
-# -- Prerequisites: --
-# The "system.lt" moltemplate file links to other ".lt" files
-# files you hopefully have created earlier when you ran "ltemplify.py:
-# cnad.lt and cnt.lt
-# If not, carry out the instructions in "README_run_ltemplify.sh".
-
-moltemplate.sh system.lt
-
-# (Note: If you have VMD installed, try this instead:)
-# moltemplate.sh system.lt -vmd
-
-
-# Moltemplate will generate various files with names ending in *.in* and *.data.
-# These files are the input files directly read by LAMMPS.
-
-# Optional:
-# The "./output_ttree/" directory is full of temporary files generated by
-# moltemplate. They can be useful for debugging, but are usually thrown away.
-
-rm -rf output_ttree/
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh
deleted file mode 100755
index ab9a7dc6e..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The "run.in.nvt" LAMMPS input script links to the input
-# scripts and data files you hopefully have created earlier
-# with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_run_moltemplate.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps this way:
-
-lmp_mpi -i run.in.nvt
-
-# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY
-# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY.
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt
deleted file mode 100644
index 3b9be3e9c..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt
+++ /dev/null
@@ -1,50 +0,0 @@
-
- ------- To view the trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-
-Later, to Load a trajectory in VMD:
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it
-
------ Wrap the coordinates to the unit cell
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Enter:
-
- DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT.
- LOOKUP "pbctools" FOR DETAILS.
-
- pbc wrap -compound res -all
- pbc box
-
-3) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data
deleted file mode 100644
index 1f18ff4ae..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data
+++ /dev/null
@@ -1,1157 +0,0 @@
-Created by Aysun Itai and modified by Andrew Jewett
-NOTE: This file has been extensively modified.
-Only the bond connectivity and atomic positions are accurate.
-
- 101 atoms
- 134 bonds
- 252 angles
- 457 dihedrals
- 0 impropers
-
- 16 atom types
- 24 bond types
- 50 angle types
- 78 dihedral types
- 0 improper types
-
- 0 50 xlo xhi
- 0 50 ylo yhi
- 0 50 zlo zhi
-
-Masses
-
- 1 10.0
- 2 10.0 # atom type names often appear
- 3 10.0 # in the comments follwing
- 4 10.0 # each line in the Masses section
- 5 10.0
- 6 10.0
- 7 10.0
- 8 10.0
- 9 10.0
- 10 10.0
- 11 10.0
- 12 10.0
- 13 10.0
- 14 10.0
- 15 10.0
- 16 10.0
-
-Atoms
-
-1 2 1 0.000000 12.345 10.000 4.328
-2 2 1 0.000000 12.031 11.173 5.037
-3 2 1 0.000000 12.031 11.173 6.455
-4 2 1 0.000000 11.173 12.031 7.164
-5 2 1 0.000000 11.173 12.031 4.328
-6 2 1 0.000000 10.000 12.345 5.037
-7 2 1 0.000000 10.000 12.345 6.455
-8 2 1 0.000000 8.827 12.031 7.164
-9 2 1 0.000000 8.827 12.031 4.328
-10 2 1 0.000000 7.969 11.173 5.037
-11 2 1 0.000000 7.969 11.173 6.455
-12 2 1 0.000000 7.655 10.000 7.164
-13 2 1 0.000000 7.655 10.000 4.328
-14 2 1 0.000000 7.969 8.827 5.037
-15 2 1 0.000000 7.969 8.827 6.455
-16 2 1 0.000000 8.827 7.969 7.164
-17 2 1 0.000000 8.827 7.969 4.328
-18 2 1 0.000000 10.000 7.655 5.037
-19 2 1 0.000000 10.000 7.655 6.455
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diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in
deleted file mode 100644
index 1f403e2bd..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in
+++ /dev/null
@@ -1,49 +0,0 @@
-#Created by Aysun Itai and modified by Andrew Jewett
-# NOTE: This file has been extensively modified.
-# Only the bond connectivity and atomic positions are accurate.
-
-units real
-
-neigh_modify delay 2 every 1
-
-atom_style full
-bond_style harmonic
-angle_style charmm
-dihedral_style charmm
-pair_style lj/charmm/coul/charmm 8.0 10.0
-pair_modify mix arithmetic
-
-read_data cnad-cnt.data
-
-pair_coeff 1 1 0.02 4.0
-pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically
-pair_coeff 3 3 0.02 2.0 # in this version of the file.
-pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed)
-pair_coeff 5 5 0.02 2.0
-pair_coeff 6 6 0.02 3.0
-pair_coeff 7 7 0.02 3.0
-pair_coeff 8 8 0.02 3.0
-pair_coeff 9 9 0.02 4.0
-pair_coeff 10 10 0.02 4.0
-pair_coeff 11 11 0.02 4.0
-pair_coeff 12 12 0.02 4.0
-pair_coeff 13 13 0.02 3.0
-pair_coeff 14 14 0.02 3.0
-pair_coeff 15 15 0.02 3.0
-pair_coeff 16 16 0.02 3.0
-
-group cnt type 1
-group cnad type 2:16
-
-displace_atoms cnad move 0 -7 0 units box
-special_bonds charmm
-
-velocity all create 0.0 54321 dist uniform
-
-thermo 1
-thermo_style multi
-timestep 0.005
-
-dump 1 all atom 10 cnad-cnt.dump
-
-run 20000
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg
deleted file mode 100644
index 3b79b405e..000000000
Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg
deleted file mode 100644
index 1f46c1b7b..000000000
Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg
deleted file mode 100644
index 628371b0d..000000000
Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg
deleted file mode 100644
index 3489773ad..000000000
Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf
deleted file mode 100644
index 7b2b06676..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf
+++ /dev/null
@@ -1,598 +0,0 @@
-PSF
-
- 1 !NTITLE
- REMARKS VMD generated structure x-plor psf file
-
- 130 !NATOM
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- 102 3 9 9 -0.180000 10.0000 0
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-
- 166 !NBOND: bonds
- 1 2 1 22 2 3 2 5
- 3 24 3 4 4 7 4 29
- 5 6 6 7 6 9 7 8
- 8 33 8 11 9 10 10 13
- 10 11 11 12 12 15 12 37
- 13 14 14 17 14 15 15 16
- 16 19 16 41 17 18 18 21
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-
- 312 !NTHETA: angles
- 2 1 22 1 2 3 1 2 5
- 3 2 5 2 3 24 2 3 4
- 4 3 24 3 4 7 3 4 29
- 7 4 29 2 5 6 5 6 7
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- 4 29 26 4 29 30 26 29 30
- 29 30 31 29 30 33 31 30 33
- 28 31 30 28 31 32 30 31 32
- 31 32 57 31 32 35 35 32 57
- 8 33 30 8 33 34 30 33 34
- 33 34 37 33 34 35 35 34 37
- 32 35 34 32 35 36 34 35 36
- 35 36 39 35 36 61 39 36 61
- 12 37 34 12 37 38 34 37 38
- 37 38 41 37 38 39 39 38 41
- 36 39 38 36 39 40 38 39 40
- 39 40 43 39 40 65 43 40 65
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- 41 42 45 41 42 43 43 42 45
- 40 43 42 40 43 44 42 43 44
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- 20 45 42 20 45 46 42 45 46
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-
- 554 !NPHI: dihedrals
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-
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-
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- 1 0 !NGRP
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diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf
deleted file mode 100644
index cb8d7eda9..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf
+++ /dev/null
@@ -1,489 +0,0 @@
-PSF
-
- 1 !NTITLE
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- 85 83 86 81 81 83 86 87
- 82 81 86 83 82 81 86 87
- 82 81 83 86 82 81 83 84
- 82 81 83 85 92 76 86 83
- 83 81 86 87 86 81 83 84
- 84 83 86 87 86 81 83 85
- 85 83 86 87 86 76 92 97
- 86 76 92 90 92 76 86 87
- 88 98 99 100 88 98 99 101
- 94 93 98 88 90 92 97 88
- 94 96 97 88 88 89 90 92
- 88 89 90 91 89 90 92 97
- 89 88 98 99 89 88 98 93
- 89 88 97 92 89 88 97 96
- 90 92 97 96 98 88 89 90
- 97 88 89 90 91 90 92 97
- 94 96 97 92 98 88 97 92
- 93 98 99 100 93 98 99 101
- 97 88 98 93 93 94 96 97
- 94 93 98 99 98 93 94 95
- 95 94 96 97 98 88 97 96
- 98 93 94 96
-
- 0 !NIMPHI: impropers
-
-
- 0 !NDON: donors
-
-
- 0 !NACC: acceptors
-
-
- 0 !NNB
-
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0
- 0 0 0 0 0
-
- 1 0 !NGRP
- 0 0 0
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt
deleted file mode 100644
index abaa3a225..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt
+++ /dev/null
@@ -1,46 +0,0 @@
-###########################################################
-# Interaction of a carbon nanotube with a pair of mystery
-# molecules (extracted from the cnat-cnt.data/in files).
-###########################################################
-#
-# define the system being simulated:
-
-# -- init section --
-include system.in.init
-
-# -- atom definition section --
-
-read_data system.data
-
-# -- settings section --
-
-include system.in.settings
-
-# -- run section --
-
-
-timestep 0.05
-dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking
-# dynamics in dilute systems with few atoms (such as this one).
-# Commenting this next line out:
-
-# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-
-# Alternately, I receive fewer questions if I use langevin/nve instead:
-fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5
-fix fxnve all nve
-
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 500 # time interval for printing out "thermo" data
-#thermo_modify flush yes
-
-#restart 1000000 restart_nvt
-
-run 500000
-
-write_data system_after_nvt.data
-
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt
deleted file mode 100644
index 70fdb7548..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt
+++ /dev/null
@@ -1,29 +0,0 @@
-#Define the CNT and CNAD molecules, by including the files which define them
-import cnt.lt
-import cnad.lt
-
-# The cnt's center was originally at position 10,10,10,
-# so I moved it back to the origin
-cnt = new CNT.move(-10,-10,-10)
-
-# Rotation around the center of mass does not work (yet),
-# so instead you have to move the molecule to the origin,
-# rotate it, and move it back to where you want it.
-# That's why the next line contains move().rot().move()
-# I'll add center-of-mass rotation as a later feature.
-
-cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0)
-cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0)
-
-
-# You can leave the periodic boundary conditions unspecified
-# and change them later, OR you can declare them
-# using the "write_once("Data Boundary") {}" command:
-
-write_once("Data Boundary")
-{
- 0 50.0 xlo xhi
- 0 50.0 ylo yhi
- 0 50.0 zlo zhi
-}
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT
deleted file mode 100644
index 0e58ef44c..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT
+++ /dev/null
@@ -1,10 +0,0 @@
-This is a simple system of 260 water molecules.
-
-In this example, the coordinates of the atoms are read from a PDB file
-instead of being specified manually (as well as the boundary information).
-
-The PDB file was generated by the useful "solvate" utility which comes with VMD.
-(To generate this file yourself, run VMD, click on the "Extensions" menu,
-and select Modeling-->Add Solvation Box.
-In this example, I made a box whose x,y,z dimensions were 16,24,24.)
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
deleted file mode 100755
index 2944f6840..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation are ignored when beginning the simulation at constant volume.
-# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
-
-
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh
deleted file mode 100755
index 5d2be2133..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-cd moltemplate_files/ # (The .lt input files are in this directory)
-
- moltemplate.sh -pdb solvate.pdb system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-#
-#This will prepare LAMMPS input files for a box of water
-#(In this example, we are using the "SPC/E" water model.)
-#The number of water molecules in the "wat = new SPCE [260]" command
-#must equal the number of water molecules in the PDB file.
-#
-#Coordinates and boundary-box information is read from the .pdb file.
-#
-#You can also specify this information directly in the ttree file.
-#See the comments section in "system.lt" for details.
-#
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt
deleted file mode 100644
index 8063d535f..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt
+++ /dev/null
@@ -1,64 +0,0 @@
- ------- Instructions to view a trajectory in VMD --------
-
- ------- Disclaimer -------
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
- (Note, at this point the image shown in the VMD graphics window may
- not appear correct or incomplete. The coordinates of the atoms may
- overlap if you asked moltemplate.sh to load your coordinates from
- a PDB or XYZ file.
- However, later after you have run a simulation, the trajectories
- should appear reasonably correct when you load them in VMD using
- the PSF file you just generated.)
-
-
-Later, to Load a trajectory in VMD:
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it
-
------ Wrap the coordinates to the unit cell
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Enter:
-
- DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT.
- LOOKUP "pbctools" FOR DETAILS.
-
- pbc wrap -compound res -all
- pbc box
-
- # If you have a solute of type 1, then use this:
- #pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-"1" corresponds to the "O" atom type
-"2" corresponds to the "H" atom type
-
-3) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types:
-
-sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf
-
-(If you do this, I guess that you might have to use
- "type=O" and "type=H" in step 2 above.)
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0
deleted file mode 100644
index e69de29bb..000000000
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh
deleted file mode 100755
index 4ebc7b17a..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-
-# Run moltemplate this way:
-
-moltemplate.sh -pdb solvate.pdb system.lt
-
-
-# The PDB file was generated by the "solvate" utility which comes with VMD.
-# (To generate this file yourself, run VMD, click on the "Extensions" menu,
-# and select Modeling-->Add Solvation Box.
-# In this example, I made a box whose x,y,z dimensions were 16,24,24.)
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
deleted file mode 100644
index 0ed5103cb..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
+++ /dev/null
@@ -1,782 +0,0 @@
-CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1
-ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O
-ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H
-ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H
-ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O
-ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H
-ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H
-ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O
-ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H
-ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H
-ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O
-ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H
-ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H
-ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O
-ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H
-ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H
-ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O
-ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H
-ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H
-ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O
-ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H
-ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H
-ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O
-ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H
-ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H
-ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O
-ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H
-ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H
-ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O
-ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H
-ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H
-ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O
-ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H
-ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H
-ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O
-ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H
-ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H
-ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O
-ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H
-ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H
-ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O
-ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H
-ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H
-ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O
-ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H
-ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H
-ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O
-ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H
-ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H
-ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O
-ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H
-ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H
-ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O
-ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H
-ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H
-ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O
-ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H
-ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H
-ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O
-ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H
-ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H
-ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O
-ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H
-ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H
-ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O
-ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H
-ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H
-ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O
-ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H
-ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H
-ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O
-ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H
-ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H
-ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O
-ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H
-ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H
-ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O
-ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H
-ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H
-ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O
-ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H
-ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H
-ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O
-ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H
-ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H
-ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O
-ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H
-ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H
-ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O
-ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H
-ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H
-ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O
-ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H
-ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H
-ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O
-ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H
-ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H
-ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O
-ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H
-ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H
-ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O
-ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H
-ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H
-ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O
-ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H
-ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H
-ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O
-ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H
-ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H
-ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O
-ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H
-ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H
-ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O
-ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H
-ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H
-ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O
-ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H
-ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H
-ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O
-ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H
-ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H
-ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O
-ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H
-ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H
-ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O
-ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H
-ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H
-ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O
-ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H
-ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H
-ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O
-ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H
-ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H
-ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O
-ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H
-ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H
-ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O
-ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H
-ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H
-ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O
-ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H
-ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H
-ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O
-ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H
-ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H
-ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O
-ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H
-ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H
-ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O
-ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H
-ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H
-ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O
-ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H
-ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H
-ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O
-ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H
-ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H
-ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O
-ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H
-ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H
-ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O
-ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H
-ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H
-ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O
-ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H
-ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H
-ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O
-ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H
-ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H
-ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O
-ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H
-ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H
-ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O
-ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H
-ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H
-ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O
-ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H
-ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H
-ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O
-ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H
-ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H
-ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O
-ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H
-ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H
-ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O
-ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H
-ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H
-ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O
-ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H
-ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H
-ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O
-ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H
-ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H
-ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O
-ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H
-ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H
-ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O
-ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H
-ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H
-ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O
-ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H
-ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H
-ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O
-ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H
-ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H
-ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O
-ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H
-ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H
-ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O
-ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H
-ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H
-ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O
-ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H
-ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H
-ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O
-ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H
-ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H
-ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O
-ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H
-ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H
-ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O
-ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H
-ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H
-ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O
-ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H
-ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H
-ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O
-ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H
-ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H
-ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O
-ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H
-ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H
-ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O
-ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H
-ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H
-ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O
-ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H
-ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H
-ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O
-ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H
-ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H
-ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O
-ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H
-ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H
-ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O
-ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H
-ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H
-ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O
-ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H
-ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H
-ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O
-ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H
-ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H
-ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O
-ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H
-ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H
-ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O
-ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H
-ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H
-ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O
-ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H
-ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H
-ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O
-ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H
-ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H
-ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O
-ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H
-ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H
-ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O
-ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H
-ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H
-ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O
-ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H
-ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H
-ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O
-ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H
-ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H
-ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O
-ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H
-ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H
-ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O
-ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H
-ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H
-ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O
-ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H
-ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H
-ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O
-ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H
-ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H
-ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O
-ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H
-ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H
-ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O
-ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H
-ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H
-ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O
-ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H
-ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H
-ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O
-ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H
-ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H
-ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O
-ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H
-ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H
-ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O
-ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H
-ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H
-ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O
-ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H
-ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H
-ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O
-ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H
-ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H
-ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O
-ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H
-ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H
-ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O
-ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H
-ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H
-ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O
-ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H
-ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H
-ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O
-ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H
-ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H
-ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O
-ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H
-ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H
-ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O
-ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H
-ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H
-ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O
-ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H
-ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H
-ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O
-ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H
-ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H
-ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O
-ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H
-ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H
-ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O
-ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H
-ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H
-ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O
-ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H
-ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H
-ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O
-ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H
-ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H
-ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O
-ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H
-ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H
-ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O
-ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H
-ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H
-ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O
-ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H
-ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H
-ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O
-ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H
-ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H
-ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O
-ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H
-ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H
-ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O
-ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H
-ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H
-ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O
-ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H
-ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H
-ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O
-ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H
-ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H
-ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O
-ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H
-ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H
-ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O
-ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H
-ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H
-ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O
-ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H
-ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H
-ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O
-ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H
-ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H
-ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O
-ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H
-ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H
-ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O
-ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H
-ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H
-ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O
-ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H
-ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H
-ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O
-ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H
-ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H
-ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O
-ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H
-ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H
-ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O
-ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H
-ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H
-ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O
-ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H
-ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H
-ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O
-ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H
-ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H
-ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O
-ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H
-ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H
-ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O
-ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H
-ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H
-ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O
-ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H
-ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H
-ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O
-ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H
-ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H
-ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O
-ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H
-ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H
-ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O
-ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H
-ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H
-ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O
-ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H
-ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H
-ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O
-ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H
-ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H
-ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O
-ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H
-ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H
-ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O
-ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H
-ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H
-ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O
-ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H
-ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H
-ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O
-ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H
-ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H
-ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O
-ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H
-ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H
-ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O
-ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H
-ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H
-ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O
-ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H
-ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H
-ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O
-ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H
-ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H
-ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O
-ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H
-ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H
-ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O
-ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H
-ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H
-ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O
-ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H
-ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H
-ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O
-ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H
-ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H
-ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O
-ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H
-ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H
-ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O
-ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H
-ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H
-ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O
-ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H
-ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H
-ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O
-ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H
-ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H
-ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O
-ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H
-ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H
-ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O
-ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H
-ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H
-ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O
-ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H
-ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H
-ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O
-ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H
-ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H
-ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O
-ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H
-ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H
-ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O
-ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H
-ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H
-ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O
-ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H
-ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H
-ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O
-ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H
-ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H
-ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O
-ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H
-ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H
-ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O
-ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H
-ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H
-ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O
-ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H
-ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H
-ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O
-ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H
-ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H
-ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O
-ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H
-ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H
-ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O
-ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H
-ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H
-ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O
-ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H
-ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H
-ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O
-ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H
-ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H
-ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O
-ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H
-ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H
-ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O
-ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H
-ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H
-ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O
-ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H
-ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H
-ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O
-ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H
-ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H
-ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O
-ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H
-ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H
-ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O
-ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H
-ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H
-ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O
-ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H
-ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H
-ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O
-ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H
-ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H
-ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O
-ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H
-ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H
-ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O
-ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H
-ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H
-ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O
-ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H
-ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H
-ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O
-ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H
-ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H
-ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O
-ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H
-ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H
-ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O
-ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H
-ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H
-ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O
-ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H
-ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H
-ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O
-ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H
-ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H
-ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O
-ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H
-ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H
-ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O
-ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H
-ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H
-ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O
-ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H
-ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H
-ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O
-ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H
-ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H
-ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O
-ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H
-ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H
-ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O
-ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H
-ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H
-ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O
-ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H
-ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H
-ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O
-ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H
-ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H
-ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O
-ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H
-ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H
-ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O
-ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H
-ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H
-ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O
-ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H
-ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H
-ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O
-ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H
-ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H
-ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O
-ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H
-ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H
-ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O
-ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H
-ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H
-ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O
-ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H
-ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H
-ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O
-ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H
-ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H
-ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O
-ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H
-ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H
-ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O
-ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H
-ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H
-ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O
-ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H
-ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H
-ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O
-ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H
-ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H
-ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O
-ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H
-ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H
-ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O
-ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H
-ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H
-ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O
-ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H
-ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H
-ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O
-ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H
-ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H
-ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O
-ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H
-ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H
-ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O
-ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H
-ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H
-ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O
-ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H
-ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H
-ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O
-ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H
-ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H
-ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O
-ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H
-ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H
-ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O
-ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H
-ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H
-ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O
-ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H
-ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H
-ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O
-ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H
-ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H
-ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O
-ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H
-ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H
-ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O
-ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H
-ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H
-ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O
-ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H
-ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H
-ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O
-ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H
-ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H
-ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O
-ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H
-ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H
-ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O
-ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H
-ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H
-ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O
-ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H
-ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H
-ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O
-ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H
-ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H
-ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O
-ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H
-ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H
-ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O
-ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H
-ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H
-ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O
-ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H
-ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H
-ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O
-ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H
-ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H
-ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O
-ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H
-ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H
-ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O
-ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H
-ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H
-ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O
-ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H
-ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H
-ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O
-ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H
-ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H
-ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O
-ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H
-ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H
-ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O
-ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H
-ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H
-ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O
-ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H
-ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H
-ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O
-ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H
-ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H
-ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O
-ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H
-ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H
-ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O
-ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H
-ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H
-ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O
-ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H
-ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H
-ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O
-ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H
-ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H
-ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O
-ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H
-ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H
-ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O
-ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H
-ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H
-ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O
-ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H
-ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H
-ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O
-ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H
-ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H
-ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O
-ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H
-ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H
-ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O
-ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H
-ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H
-ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O
-ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H
-ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H
-ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O
-ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H
-ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H
-ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O
-ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H
-ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H
-ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O
-ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H
-ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H
-ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O
-ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H
-ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H
-ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O
-ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H
-ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H
-END
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
deleted file mode 100644
index 019911c19..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
+++ /dev/null
@@ -1,52 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-SPCE {
-
- write_once("In Init") {
- # -- Default styles (for solo "SPCE" water) --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- pair_modify mix arithmetic
- }
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
- $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 1000.0 1.0
- angle_coeff @angle:HOH harmonic 1000.0 109.47
- pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166
- pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058
- group spce type @atom:O @atom:H
- fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeSPCE during minimization.)
- }
-
-} # end of definition of "SPCE" water molecule type
-
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
deleted file mode 100644
index 274d8aeb1..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
+++ /dev/null
@@ -1,16 +0,0 @@
-import "spce.lt"
-
-wat = new SPCE [260]
-
-
-
-
-
-
-
-# Open up the PDB file to count the number of water molecules inside. (Or just
-# divide the number of atoms by 3). Put that in between the brackets ("[260]")
-#
-# The command above does not set the positions of the atoms.
-# So they will have to be loaded later from a PDB or an XYZ file.
-# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt")
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
deleted file mode 100644
index 4d8af42b5..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
+++ /dev/null
@@ -1,48 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
-unfix fShakeSPCE
-minimize 1.0e-3 1.0e-5 100000 400000
-# Now read "system.in.settings" in order to redefine fShakeSPCE again:
-include system.in.settings
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-thermo 100
-
-run 10000
-
-# Now that the system's temperature has become more equilibrated,
-# we can increase the timestep:
-
-timestep 2.0
-run 50000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
deleted file mode 100644
index d039a5370..000000000
--- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
+++ /dev/null
@@ -1,61 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_npt.data
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-# Note: If you are reading the data file created by run.in.npt,
-# then you should not need to minimize the system beforehand.
-# fShakeSPCE was defined in system.in.settings.
-# (It is incompatible with "minimize".)
-
-unfix fShakeSPCE
-minimize 1.0e-5 1.0e-7 100000 400000
-
-# Now read "system.in.settings" in order to redefine fShakeSPCE again:
-
-include system.in.settings
-
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-
-run 10000
-
-# Now that the system's temperature has become more equilibrated,
-# we can increase the timestep:
-
-timestep 2.0
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/WARNING.TXT b/tools/moltemplate/examples/force_field_AMBER/WARNING.TXT
deleted file mode 100644
index 9d6d0e1b3..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/WARNING.TXT
+++ /dev/null
@@ -1,54 +0,0 @@
-# -------- WARNING: --------
-
-This directory contains some examples of all-atom simulations using the GAFF
-force field, prepared using moltemplate.
-
-This software is experimental, and the force-fields and equilbration protocols
-have not been tested carefully by me. There is no gaurantee that simulations
-prepared using moltemplate will reproduce the behavior of AmberTools/AMBER.
-
-# -------- REQUEST FOR HELP: --------
-
-If you notice a problem with these examples, please report it.
-Peer-review is the only way to improve this software (or any software).
-Other suggestions are also welcome!
-
-(Contact jewett.aij@gmail.com, 2013-12-01)
-
-
---- Charge ---
-
-Some force-fields (such as OPLSAA) can assign charge based on atom type.
-But AMBER simulations, charge is usually assigned using AmberTools which
-typically estimates partial charges using quantum chemistry.
-
-You must assign partial charges to each atom or LAMMPS will crash
-when it discovers your system has no charged particles.
-(To disable this, change the pair_style to lj/cut or something similar.)
-
-You have to assign charge manually, just as you would for an ordinary molecule.
-
-(For example, charges are explicitly assigned to each atom in these files:
- waterTIP3P+isobutane/moltemplate_files/isobutane.lt
- hexadecane/moltemplate_files/ch2group.lt
- hexadecane/moltemplate_files/ch3group.lt)
-
-(How you do this is up to you. In these examples, I obtained
-partial charges from the OPLSAA parameter file located here:
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm)
-
---- Improper angles ---
-
-I am also uncertain whether the improper angle interactions generated by
-moltemplate are equivalent to those generated by AmberTools. (I think they are,
-but I am worried that I might have listed the atom types in the wrong order.)
-
---- Bloated lammps input scripts ---
-
-LAMMPS input scripts prepared using moltemplate contain the entire contents
-of the GAFF force-field, even when simulating small systems with just a few
-atom types.
-
-This is harmless, but if you want to get rid of this extra information,
-follow the README instructions in the "optional_cleanup" directories.
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/README.TXT b/tools/moltemplate/examples/force_field_AMBER/benzene/README.TXT
deleted file mode 100644
index ba0f5e6f4..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/README.TXT
+++ /dev/null
@@ -1,10 +0,0 @@
-This example shows how to build a box of benzene molecules using the
-AMBER/GAFF force-field.
-
-step 1)
-To build the files which LAMMPS needs, follow the instructions in:
-README_setup.sh
-
-step 2)
-To run LAMMPS with these files, follow these instructions:
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/README_run.sh b/tools/moltemplate/examples/force_field_AMBER/benzene/README_run.sh
deleted file mode 100755
index 9f923a6c7..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/README_run.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-# --- Running LAMMPS ---
-# -------- REQUIREMENTS: ---------
-# 1) This example requires building LAMMPS with the "USER-MISC" package.
-# (because it makes use of "gaff.lt" which uses dihedral_style fourier)
-# To do this, type "make yes-user-misc" before compiling LAMMPS.
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# -------- PREREQUISITES: --------
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/README_setup.sh b/tools/moltemplate/examples/force_field_AMBER/benzene/README_setup.sh
deleted file mode 100755
index c2db73b45..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/README_setup.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- #rm -rf output_ttree/
-
-cd ../
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in GAFF which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/README_visualize.txt b/tools/moltemplate/examples/force_field_AMBER/benzene/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/benzene.lt
deleted file mode 100644
index 26ef1d535..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/benzene.lt
+++ /dev/null
@@ -1,51 +0,0 @@
-
-import "gaff.lt"
-
-# The "gaff.lt" file is usually located in "src/moltemplate_force_fields".
-# Excerpt:
-#
-# @atom:ca # Sp2 C in pure aromatic systems
-# @atom:ha # H bonded to aromatic carbon
-#
-# I looked up the charge of each atom using the OPLSAA parameters
-# from the "oplsaa.prm" file distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# ---------------------------------------------------------------
-# This is NOT how AmberTools assigns charge, and it will NOT
-# reproduce the behavior of AMBER force-fields.
-
-
-Benzene inherits GAFF {
-
- # atomID molID atomType charge X Y Z
- write('Data Atoms') {
- $atom:C1 $mol @atom:ca -0.115 5.274 1.999 -8.568
- $atom:C2 $mol @atom:ca -0.115 6.627 2.018 -8.209
- $atom:C3 $mol @atom:ca -0.115 7.366 0.829 -8.202
- $atom:C4 $mol @atom:ca -0.115 6.752 -0.379 -8.554
- $atom:C5 $mol @atom:ca -0.115 5.399 -0.398 -8.912
- $atom:C6 $mol @atom:ca -0.115 4.660 0.791 -8.919
- $atom:H11 $mol @atom:ha 0.115 4.704 2.916 -8.573
- $atom:H21 $mol @atom:ha 0.115 7.101 2.950 -7.938
- $atom:H31 $mol @atom:ha 0.115 8.410 0.844 -7.926
- $atom:H41 $mol @atom:ha 0.115 7.322 -1.296 -8.548
- $atom:H51 $mol @atom:ha 0.115 4.925 -1.330 -9.183
- $atom:H61 $mol @atom:ha 0.115 3.616 0.776 -9.196
- }
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C23 $atom:C2 $atom:C3
- $bond:C34 $atom:C3 $atom:C4
- $bond:C45 $atom:C4 $atom:C5
- $bond:C56 $atom:C5 $atom:C6
- $bond:C61 $atom:C6 $atom:C1
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C2H2 $atom:C2 $atom:H21
- $bond:C3H3 $atom:C3 $atom:H31
- $bond:C4H4 $atom:C4 $atom:H41
- $bond:C5H5 $atom:C5 $atom:H51
- $bond:C6H6 $atom:C6 $atom:H61
- }
-
-} # Benzene
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/system.lt
deleted file mode 100644
index 002c538da..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/system.lt
+++ /dev/null
@@ -1,14 +0,0 @@
-import "benzene.lt" # <- defines the "Benzene" molecule type.
-
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 64.00 xlo xhi
- 0.0 64.00 ylo yhi
- 0.0 64.00 zlo zhi
-}
-
-benzenes = new Benzene [8].move(8,0,0)
- [8].move(0,8,0)
- [8].move(0,0,8)
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh
deleted file mode 100755
index 325199177..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh
+++ /dev/null
@@ -1,63 +0,0 @@
- # MOST USERS CAN IGNORE THIS FILE
- #
- # Unfortunately, as of 2014-4-19, the system.data and system.in.settings file
- # which are created by moltemplate.sh contain a lot of irrelevant information,
- # such as definition of parameters for atom types not present in the current
- # system. This extra information takes up about 1 MB.
- #
- # This appears to be harmless.
- # (Loading this extra information does not seem to slow down LAMMPS.)
- #
- # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
- #
- # However if you want to eliminate this junk from these files
- # For now, we can strip this out using ltemplify.py to build a new .lt file.
- #
- # NOTE: If you decide to use this script, it was meant to be run it from
- # the parent directory (../) (If you run it from somewhere else, be sure to
- # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.)
- #
- # I suggest you do this in a temporary_directory
-
- PATH_TO_DATA_FILE="."
-
- pushd "$PATH_TO_DATA_FILE"
-
- mkdir new_lt_file
- cd new_lt_file/
-
- # now run ltemplify.py
-
- ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt
-
- # This creates a new .LT file named "system.lt" in the local directory.
-
- # The ltemplify.py script also does not copy the boundary dimensions.
- # We must do this manually.
- # If you did NOT throw away the "Data Boundary" file usually located in
- # "moltemplate_files/output_ttree/Data Boundary"
- # then you can copy that information from this file into system.lt
-
- PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree"
-
- echo "write_once(\"Data Boundary\") {" >> system.lt
- cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt
- echo "}" >> system.lt
- echo "" >> system.lt
-
- # Now, run moltemplate on this new .LT file.
- moltemplate.sh system.lt
- # This will create: "system.data" "system.in.init" "system.in.settings."
-
- # That's it. The new "system.data" and system.in.* files should
- # be ready to run in LAMMPS.
-
- # Now copy the system.data and system.in.* files to the place where
- # you plan to run LAMMPS
- mv -f system.data system.in.* ../
- cd ../
-
- # Now delete all of the temporary files we generated
- rm -rf new_lt_file/
- popd
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/run.in.npt b/tools/moltemplate/examples/force_field_AMBER/benzene/run.in.npt
deleted file mode 100644
index b2ee94440..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/run.in.npt
+++ /dev/null
@@ -1,72 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# -- simulation protocol --
-
-timestep 1.0
-
-thermo 100
-dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz
-
-print "---------------------------------------------------------------------------"
-print "First, use Langevin dynamics to randomize the initial shape of the molecules"
-print "---------------------------------------------------------------------------"
-
-
-fix 1 all momentum 100 linear 0 0 0
-fix fxlan all langevin 1000.0 1000.0 5000.0 123456 # temp: 1000 K
-fix fxnve all nve
-
-run 20000
-unfix fxlan
-unfix fxnve
-
-
-
-print "---------------------------------------------------------------------------"
-print "Optional: use short high pressure run to get rid of small bubbles."
-print " (In case there are any. I'm not certain there are."
-print " Later we will restore ordinary pressure.)"
-print "---------------------------------------------------------------------------"
-fix fxlan all langevin 298.0 298.0 5000 123456 # temp: 298 K
-fix fxnph all nph iso 500.0 500.0 1000.0 # pressure: 500 barr
-
-run 80000
-unfix fxlan
-unfix fxnph
-
-
-
-print "---------------------------------------------------------------------------"
-print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---"
-print "---------------------------------------------------------------------------"
-# temperature: 298 K, pressure: 1 barr
-fix fxnpt all npt temp 298.0 298.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-#thermo_modify flush yes
-
-run 5000000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/benzene/run.in.nvt b/tools/moltemplate/examples/force_field_AMBER/benzene/run.in.nvt
deleted file mode 100644
index 3901723dd..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/benzene/run.in.nvt
+++ /dev/null
@@ -1,51 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# OPLSAA atom charges are stored in a separate file.
-# Load that file now:
-
-include "system.in.charges"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 200000
-
-write_restart system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README.TXT b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README.TXT
deleted file mode 100644
index b02f184dd..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README.TXT
+++ /dev/null
@@ -1,13 +0,0 @@
-This example shows how to simulate a mixture of ethylene and benzene
-using the AMBER/GAFF force field.
-
-As of 2016-11-21, this code has not been tested for accuracy.
-(See the WARNING.TXT file.)
-
-step 1)
-To build the files which LAMMPS needs, follow the instructions in:
-README_setup.sh
-
-step 2)
-To run LAMMPS with these files, follow these instructions:
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_run.sh b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_run.sh
deleted file mode 100755
index 9f923a6c7..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_run.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-# --- Running LAMMPS ---
-# -------- REQUIREMENTS: ---------
-# 1) This example requires building LAMMPS with the "USER-MISC" package.
-# (because it makes use of "gaff.lt" which uses dihedral_style fourier)
-# To do this, type "make yes-user-misc" before compiling LAMMPS.
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# -------- PREREQUISITES: --------
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_setup.sh b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_setup.sh
deleted file mode 100755
index 0e2a17d9b..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_setup.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- #rm -rf output_ttree/
-
-cd ../
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in GAFF which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/benzene.jpg b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/benzene.jpg
deleted file mode 100644
index 356c78425..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/benzene.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg
deleted file mode 100644
index 00c82d3d9..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/ethylene.jpg b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/ethylene.jpg
deleted file mode 100644
index ab5bbbf49..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/images/ethylene.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt
deleted file mode 100644
index 47b1505c5..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt
+++ /dev/null
@@ -1,47 +0,0 @@
-
-import "gaff.lt"
-
-# The "gaff.lt" file is usually located in "src/moltemplate_force_fields".
-# It contains definitions of the atoms "ca", "ha", as well as the bonded
-# and non-bonded interactions between them (and many other atoms).
-#
-# Moltemplate is only a simple text manipulation tool. It cannot
-# calculate atomic charge using quantom chemistry methods.
-# Atom charges for this example were taken from the OPLSAA force field file:
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# However, normally simulations in AMBER are assigned charges using the
-# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools.
-
-Benzene inherits GAFF {
-
- write('Data Atoms') {
- $atom:C1 $mol @atom:ca 0.115 5.274 1.999 -8.568
- $atom:C2 $mol @atom:ca 0.115 6.627 2.018 -8.209
- $atom:C3 $mol @atom:ca 0.115 7.366 0.829 -8.202
- $atom:C4 $mol @atom:ca 0.115 6.752 -0.379 -8.554
- $atom:C5 $mol @atom:ca 0.115 5.399 -0.398 -8.912
- $atom:C6 $mol @atom:ca 0.115 4.660 0.791 -8.919
- $atom:H11 $mol @atom:ha -0.115 4.704 2.916 -8.573
- $atom:H21 $mol @atom:ha -0.115 7.101 2.950 -7.938
- $atom:H31 $mol @atom:ha -0.115 8.410 0.844 -7.926
- $atom:H41 $mol @atom:ha -0.115 7.322 -1.296 -8.548
- $atom:H51 $mol @atom:ha -0.115 4.925 -1.330 -9.183
- $atom:H61 $mol @atom:ha -0.115 3.616 0.776 -9.196
- }
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C23 $atom:C2 $atom:C3
- $bond:C34 $atom:C3 $atom:C4
- $bond:C45 $atom:C4 $atom:C5
- $bond:C56 $atom:C5 $atom:C6
- $bond:C61 $atom:C6 $atom:C1
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C2H2 $atom:C2 $atom:H21
- $bond:C3H3 $atom:C3 $atom:H31
- $bond:C4H4 $atom:C4 $atom:H41
- $bond:C5H5 $atom:C5 $atom:H51
- $bond:C6H6 $atom:C6 $atom:H61
- }
-
-} # Benzene
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm
deleted file mode 100644
index 8493a39f6..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm
+++ /dev/null
@@ -1,94 +0,0 @@
-# This is a modified version of the file "oplsaa.prm" distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# In this version, all of the lines beginning with "atom" have been deleted
-# except for the atom types we will be using in this simulation
-#
-# If you use this file, please also cite the software this file comes from:
-#
-# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024
-# "An efficient newton‐like method for molecular mechanics energy
-# minimization of large molecules."
-#
-# Ponder, J. W, (2004)
-# "TINKER: Software tools for molecular design"
-# http://dasher.wustl.edu/tinker/
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 88 3.5500 0.0760
-vdw 89 2.4200 0.0300
-vdw 90 3.5500 0.0700
-vdw 91 2.4200 0.0300
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt
deleted file mode 100644
index cad6ea4a8..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt
+++ /dev/null
@@ -1,38 +0,0 @@
-
-import "gaff.lt"
-
-# The "gaff.lt" file is usually located in "src/moltemplate_force_fields".
-# It contains definitions of the atoms "c2", "hc", as well as the bonded
-# and non-bonded interactions between them (and many other atoms).
-#
-# Moltemplate is only a simple text manipulation tool. It cannot
-# calculate atomic charge using quantom chemistry methods.
-# Atom charges for this example were taken from the OPLSAA force field file:
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# However, normally simulations in AMBER are assigned charges using the
-# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools.
-
-
-Ethylene inherits GAFF {
-
- # atom-id mol-id atom-type charge X Y Z
-
- write('Data Atoms') {
- $atom:C1 $mol @atom:c2 -0.23 -0.6695 0.000000 0.000000
- $atom:C2 $mol @atom:c2 -0.23 0.6695 0.000000 0.000000
- $atom:H11 $mol @atom:hc 0.115 -1.234217 -0.854458 0.000000
- $atom:H12 $mol @atom:hc 0.115 -1.234217 0.854458 0.000000
- $atom:H21 $mol @atom:hc 0.115 1.234217 -0.854458 0.000000
- $atom:H22 $mol @atom:hc 0.115 1.234217 0.854458 0.000000
- }
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C1H2 $atom:C1 $atom:H12
- $bond:C2H1 $atom:C2 $atom:H21
- $bond:C2H2 $atom:C2 $atom:H22
- }
-
-} # Ethylene
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt
deleted file mode 100644
index f9984a1bb..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt
+++ /dev/null
@@ -1,29 +0,0 @@
-import "ethylene.lt" # <- defines the "Ethylene" molecule type.
-import "benzene.lt" # <- defines the "Benzene" molecule type.
-
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 80.00 xlo xhi
- 0.0 80.00 ylo yhi
- 0.0 80.00 zlo zhi
-}
-
-# Create 1000 ethylenes and 500 benzenes
-
-ethylenes = new Ethylene[10].move(8.0, 0, 0)
- [10].move(0, 8.0, 0)
- [10].move(0, 0, 8.0)
-
-benzenes = new Benzene[10].move(8.0, 0, 0)
- [10].move(0, 8.0, 0)
- [5].move(0, 0, 16.0)
-
-# Now shift the positions of all of the benzene molecules,
-# to reduce the chance that they overlap with the ethylene molecules.
-
-benzenes[*][*][*].move(4.0, 4.0, 4.0)
-
-# Note: There is also an example in the OPLSAA directory which shows how to
-# generate the coordinates using PACKMOL. That allows us to omit all of
-# the coordinates and .move() commands. (This works with AMBER/GAFF too.)
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh
deleted file mode 100755
index 325199177..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh
+++ /dev/null
@@ -1,63 +0,0 @@
- # MOST USERS CAN IGNORE THIS FILE
- #
- # Unfortunately, as of 2014-4-19, the system.data and system.in.settings file
- # which are created by moltemplate.sh contain a lot of irrelevant information,
- # such as definition of parameters for atom types not present in the current
- # system. This extra information takes up about 1 MB.
- #
- # This appears to be harmless.
- # (Loading this extra information does not seem to slow down LAMMPS.)
- #
- # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
- #
- # However if you want to eliminate this junk from these files
- # For now, we can strip this out using ltemplify.py to build a new .lt file.
- #
- # NOTE: If you decide to use this script, it was meant to be run it from
- # the parent directory (../) (If you run it from somewhere else, be sure to
- # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.)
- #
- # I suggest you do this in a temporary_directory
-
- PATH_TO_DATA_FILE="."
-
- pushd "$PATH_TO_DATA_FILE"
-
- mkdir new_lt_file
- cd new_lt_file/
-
- # now run ltemplify.py
-
- ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt
-
- # This creates a new .LT file named "system.lt" in the local directory.
-
- # The ltemplify.py script also does not copy the boundary dimensions.
- # We must do this manually.
- # If you did NOT throw away the "Data Boundary" file usually located in
- # "moltemplate_files/output_ttree/Data Boundary"
- # then you can copy that information from this file into system.lt
-
- PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree"
-
- echo "write_once(\"Data Boundary\") {" >> system.lt
- cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt
- echo "}" >> system.lt
- echo "" >> system.lt
-
- # Now, run moltemplate on this new .LT file.
- moltemplate.sh system.lt
- # This will create: "system.data" "system.in.init" "system.in.settings."
-
- # That's it. The new "system.data" and system.in.* files should
- # be ready to run in LAMMPS.
-
- # Now copy the system.data and system.in.* files to the place where
- # you plan to run LAMMPS
- mv -f system.data system.in.* ../
- cd ../
-
- # Now delete all of the temporary files we generated
- rm -rf new_lt_file/
- popd
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/run.in.npt b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/run.in.npt
deleted file mode 100644
index 9e529624d..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/run.in.npt
+++ /dev/null
@@ -1,53 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# -- simulation protocol --
-
-timestep 1.0
-
-print "---------------------------------------------------------------------------"
-print "First, use Langevin dynamics to randomize the initial shape of the molecules"
-print "(This is not really necessary, but it seems to speed up equilibration.)"
-print "---------------------------------------------------------------------------"
-
-fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K
-fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr
-run 2000
-unfix fxlan
-unfix fxnph
-
-print "---------------------------------------------------------------------------"
-print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---"
-print "---------------------------------------------------------------------------"
-dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
-# temperature: 300 K, pressure: 50 barr
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0
-thermo 100
-#thermo_modify flush yes
-
-run 100000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/run.in.nvt
deleted file mode 100644
index 15283ff82..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/run.in.nvt
+++ /dev/null
@@ -1,46 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 200000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README.TXT b/tools/moltemplate/examples/force_field_AMBER/hexadecane/README.TXT
deleted file mode 100644
index a3f011167..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README.TXT
+++ /dev/null
@@ -1,44 +0,0 @@
-This example is a simple simulation of 288 hexadecane molecules in a box at
-room temperature and atmospheric pressure. Please read the WARNING.TXT file.
-
--------- REQUIREMENTS: ---------
-This example requires building LAMMPS with the "USER-MISC" package.
-(because it uses dihedral_style fourier)
-To do this, type "make yes-user-misc" before compiling LAMMPS.
-http://lammps.sandia.gov/doc/Section_start.html#start_3
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files:
-
-step 1) to setup the LAMMPS input files, run this file:
-README_setup.sh
-
- (Currently there is a bug which makes this step slow.
- I'll fix it later -Andrew 2013-10-15.)
-
-step 2) to run LAMMPS, follow the instructions in this file:
-README_run.sh
-
------------- NOTE: There are two versions of this example. ----------------
-
-Both examples use the same force-field parameters.
-
-1)
-In this version, the force-field parameters are loaded from the "gaff.lt" file
-(located in the "src/moltemplate_force_fields/" subdirectory).
-This frees the user from the drudgery of manually specifying all of these
-force-field details for every molecule. (However, the user must be careful
-to choose @atom-type names which match AMBER GAFF conventions,
-such as the "c3" and "h1" atoms, in this example.)
-
-2)
-Alternately, there is another "hexadecane" example in the "all_atom_examples"
-directory. In that example, force-field parameters are loaded from a file
-named "alkanes.lt" (instead of "gaff.lt"). The "alkanes.lt" file contains
-only the excerpts from "gaff.lt" which are relevant to the hydrocarbon
-molcules used in that example. ("gaff.lt" contains parameters for most
-small organic molecules, not just hydrocarbons.)
-In this way, by editing "alkanes.lt", the user can manually control all of the
-force-field details in the simulation. (Without feeling as though they are
-relying on some kind of mysterious "black box" to do it for them.)
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_run.sh b/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_run.sh
deleted file mode 100755
index 9f923a6c7..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_run.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-# --- Running LAMMPS ---
-# -------- REQUIREMENTS: ---------
-# 1) This example requires building LAMMPS with the "USER-MISC" package.
-# (because it makes use of "gaff.lt" which uses dihedral_style fourier)
-# To do this, type "make yes-user-misc" before compiling LAMMPS.
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# -------- PREREQUISITES: --------
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_setup.sh b/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_setup.sh
deleted file mode 100755
index c2db73b45..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_setup.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- #rm -rf output_ttree/
-
-cd ../
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in GAFF which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_visualize.txt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/WARNING.TXT b/tools/moltemplate/examples/force_field_AMBER/hexadecane/WARNING.TXT
deleted file mode 100644
index def26ba76..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/WARNING.TXT
+++ /dev/null
@@ -1,16 +0,0 @@
-# -------- WARNING: --------
-
-This software is experimental, and the force-fields and equilbration protocols
-have not been tested carefully by me. There is no gaurantee that the simulation
-will reproduce the behavior of real hexadecane molecules,
-(or even of hexadecane molecules simulated using AMBER, which should
- be using the same force-field).
-
-# -------- REQUEST FOR HELP: --------
-
-However, if you notice a problem with this example, please report it.
-I confess I do not have a lot of experience running all-atom simulations.
-Peer-review is the only way to improve this software (or any software).
-Other suggestions are also welcome!
-
-(Contact jewett.aij@gmail.com, 2013-10-16)
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
deleted file mode 100644
index b0d31f884..000000000
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diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
deleted file mode 100644
index f7c13d098..000000000
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diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg
deleted file mode 100644
index 3ad353dbb..000000000
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diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt
deleted file mode 100644
index 69978eeca..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt
+++ /dev/null
@@ -1,59 +0,0 @@
-
-import "gaff.lt" # <-- defines the "GAFF" force field
-
-
-# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is
-# distributed with moltemplate. See the "Installation" section in the manual.)
-# It contains definitions of the atoms "c3", "hc", as well as the force-field
-# parameters for bonded and non-bonded interactions between them
-# (and many other atoms).
-
-# Atom charges were taken from the OPLSAA force field file:
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-
-
-CH2 inherits GAFF {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:C $mol:... @atom:c3 -0.120 0.000 0.000 0.000
- $atom:H1 $mol:... @atom:hc 0.060 0.000 0.63104384422426 0.892430762954
- $atom:H2 $mol:... @atom:hc 0.060 0.000 0.63104384422426 -0.892430762954
- }
-
- # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
- # be a part of a larger molecule, and (if so) to use the larger
- # parent object's molecule id number as it's own.
- # The CH2 group is part of the Hexadecane molecule.
-
- # Now specify which pairs of atoms are bonded:
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- }
-
-} # CH2
-
-
-# Optional: Shift all the coordinates in the +Y direction by 0.4431163.
-# This way, the carbon atom is no longer located at 0,0,0, but the
-# axis of an alkane chain containing this monomer is at 0,0,0.
-# (This makes it more convenient to construct a polymer later.
-# If this is confusing, then simply add 0.4431163 to the Y
-# coordinates in the "Data Atoms" section above.)
-
-CH2.move(0,0.4431163,0)
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163316030377
-# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
-# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt
deleted file mode 100644
index ef431f8d7..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt
+++ /dev/null
@@ -1,65 +0,0 @@
-import "gaff.lt" # <-- defines the "GAFF" force field
-
-
-# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is
-# distributed with moltemplate. See the "Installation" section in the manual.)
-# It contains definitions of the atoms "c3", "hc", as well as the force-field
-# parameters for bonded and non-bonded interactions between them
-# (and many other atoms).
-#
-# Moltemplate is only a simple text manipulation tool. It cannot
-# calculate atomic charge using quantom chemistry methods.
-# Atom charges for this example were taken from the OPLSAA force field file:
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# However, normally simulations in AMBER are assigned charges using the
-# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools.
-
-
-CH3 inherits GAFF {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:C $mol:... @atom:c3 -0.180 0.000000 0.000000 0.000000
- $atom:H1 $mol:... @atom:hc 0.060 0.000000 0.6310438442242609 0.8924307629540046
- $atom:H2 $mol:... @atom:hc 0.060 0.000000 0.6310438442242609 -0.8924307629540046
- $atom:H3 $mol:... @atom:hc 0.060 -0.8924307629540046 -0.6310438442242609 0.000000
- }
-
- # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
- # be a part of a larger molecule, and (if so) to use the larger
- # parent object's molecule id number as it's own.
- # The CH3 group is part of the Hexadecane molecule.
-
- # Now specify which pairs of atoms are bonded:
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- $bond:CH3 $atom:C $atom:H3
- }
-
-} # CH3
-
-
-# Optional: Shift all the coordinates in the +Y direction by 0.4431163.
-# This way, the carbon atom is no longer located at 0,0,0, but the
-# axis of an alkane chain containing this monomer is at 0,0,0.
-# (This makes it more convenient to construct a polymer later.
-# If this is confusing, then simply add 0.4431163 to the Y
-# coordinates in the "Data Atoms" section above.)
-
-CH3.move(0,0.4431163,0)
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163316030377
-# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
-# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt
deleted file mode 100644
index d28502f48..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt
+++ /dev/null
@@ -1,89 +0,0 @@
-# This example looks complicated because I split the
-# hexadecane molecule into individual CH2 and CH3 monomers.
-#
-# I defined it this way so that you can easily modify
-# it to change the length of the alkane chain.
-
-
-import "gaff.lt" # load the "GAFF" force-field information
-import "ch2group.lt" # load the definition of the "CH2" object
-import "ch3group.lt" # load the definition of the "CH3" object
-
-
-
-Hexadecane inherits GAFF {
-
-
- create_var {$mol} # optional:force all monomers to share the same molecule-ID
-
-
- # Now create an array of 16 "CH2" objects distributed along the X axis
-
- monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0)
-
- # Each monomer is rotated 180 degrees with respect to the previous
- # monomer, and then moved 1.2533223 Angstroms down the X axis.
-
- # ---- Now, modify the ends: ---
- # Delete the CH2 groups at the beginning and end, and replace them with CH3.
- # (Note: Alternately, instead of deleting the CH2 groups at each end, you
- # could modify them by adding an extra hydrogen atom to those carbons.)
-
- delete monomers[0]
- delete monomers[15]
- monomers[0] = new CH3
- monomers[15] = new CH3
-
- # Move the CH3 groups to the correct location at either end of the chain:
-
- monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0)
-
- # Note: 18.7998345 = (16-1) * 1.2533223
-
-
- # Now add a list of bonds connecting the carbon atoms together:
-
- write('Data Bond List') {
- $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C
- $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C
- $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C
- $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C
- $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C
- $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C
- $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C
- $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C
- $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C
- $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C
- $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C
- $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C
- $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C
- $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C
- $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C
- }
-
-} # Hexadecane
-
-
-
-
-
-
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-#
-# 1.2533223 = DeltaXc = how far each CH2 group is shifted along
-# the X axis (in Angstoms).
-# 0.4431163 = DeltaYc/2 = lateral displacement of carbons away
-# from the central axis. (See below.)
-#
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163316030377
-# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
-# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/system.lt
deleted file mode 100644
index 4e0cfaec6..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/moltemplate_files/system.lt
+++ /dev/null
@@ -1,18 +0,0 @@
-import "hexadecane.lt" # <- defines the "Hexadecane" molecule type.
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 62.4 xlo xhi
- 0.0 62.4 ylo yhi
- 0.0 62.4 zlo zhi
-}
-
-molecules = new Hexadecane [12].move(0, 0, 5.2)
- [12].move(0, 5.2, 0)
- [2].move(31.2, 0, 0)
-
-
-# NOTE: The spacing between molecules is large. There should be extra room to
-# move during the initial stages of equilibration. However, you will have to
-# run the simulation at NPT conditions later to compress the system to a
-# more realistic density.
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh
deleted file mode 100755
index 325199177..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh
+++ /dev/null
@@ -1,63 +0,0 @@
- # MOST USERS CAN IGNORE THIS FILE
- #
- # Unfortunately, as of 2014-4-19, the system.data and system.in.settings file
- # which are created by moltemplate.sh contain a lot of irrelevant information,
- # such as definition of parameters for atom types not present in the current
- # system. This extra information takes up about 1 MB.
- #
- # This appears to be harmless.
- # (Loading this extra information does not seem to slow down LAMMPS.)
- #
- # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
- #
- # However if you want to eliminate this junk from these files
- # For now, we can strip this out using ltemplify.py to build a new .lt file.
- #
- # NOTE: If you decide to use this script, it was meant to be run it from
- # the parent directory (../) (If you run it from somewhere else, be sure to
- # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.)
- #
- # I suggest you do this in a temporary_directory
-
- PATH_TO_DATA_FILE="."
-
- pushd "$PATH_TO_DATA_FILE"
-
- mkdir new_lt_file
- cd new_lt_file/
-
- # now run ltemplify.py
-
- ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt
-
- # This creates a new .LT file named "system.lt" in the local directory.
-
- # The ltemplify.py script also does not copy the boundary dimensions.
- # We must do this manually.
- # If you did NOT throw away the "Data Boundary" file usually located in
- # "moltemplate_files/output_ttree/Data Boundary"
- # then you can copy that information from this file into system.lt
-
- PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree"
-
- echo "write_once(\"Data Boundary\") {" >> system.lt
- cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt
- echo "}" >> system.lt
- echo "" >> system.lt
-
- # Now, run moltemplate on this new .LT file.
- moltemplate.sh system.lt
- # This will create: "system.data" "system.in.init" "system.in.settings."
-
- # That's it. The new "system.data" and system.in.* files should
- # be ready to run in LAMMPS.
-
- # Now copy the system.data and system.in.* files to the place where
- # you plan to run LAMMPS
- mv -f system.data system.in.* ../
- cd ../
-
- # Now delete all of the temporary files we generated
- rm -rf new_lt_file/
- popd
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/run.in.npt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/run.in.npt
deleted file mode 100644
index a1b934522..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/run.in.npt
+++ /dev/null
@@ -1,86 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize,
-# reorient, compress). The system (as defined in the "system.data" file)
-# is already expanded. That means there are 3 steps left:
-
-dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz
-thermo 50
-
-# -- Equilibration: part 1: initial minimization --
-
-# Note: In general, it's always a good idea to minimize the system at first.
-
-minimize 1.0e-5 1.0e-7 100000 400000
-undump dumpeq1
-
-write_data system_after_eq1_min.data
-
-# -- Equilibration part 2: reorienting the molecules (NVT) --
-
-timestep 1.0
-dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz
-
-# Run the system at high temperature (at constant volume) to reorient the
-# the molecules (which would otherwise be pointing in the same direction).
-
-# To speed it up, I randomize the atomic positions for a few thousand steps
-# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover).
-# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.)
-
-
-fix fxlan all langevin 900.0 900.0 120 48279
-fix fxnve all nve
-
-run 4000
-
-unfix fxlan
-unfix fxnve
-# Now continue the simulation at high temperature using fix nvt (Nose-Hoover).
-fix fxnvt all nvt temp 900.0 900.0 100.0
-
-run 50000
-undump dumpeq2
-
-
-write_data system_after_eq2_reorient.data
-
-unfix fxnvt
-
-# -- equilibration part 3: Equilibrating the density (NPT) --
-
-# Originally, the simulation box (in "system.data" and "system.lt") was
-# unrealistically large. The spacing between the molecules was large also.
-# I did this to enable the molecules to move freely and reorient themselves.
-# After doing that, we should run the simulation under NPT conditions to
-# allow the simulation box to contract to it's natural size. We do that here:
-# We begin the simulation at 100 barr (a relatively low pressure), and
-# slowly decrease it to 1 barr, maintianing the temperature at 300K.
-
-dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 900.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0
-
-timestep 1.0
-run 100000
-
-write_data system_after_eq3_npt.data
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/hexadecane/run.in.nvt b/tools/moltemplate/examples/force_field_AMBER/hexadecane/run.in.nvt
deleted file mode 100644
index 0bb769989..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/hexadecane/run.in.nvt
+++ /dev/null
@@ -1,43 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_eq3_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1
-thermo 100
-#thermo_modify flush yes
-
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
deleted file mode 100644
index 6ec463efa..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
+++ /dev/null
@@ -1,41 +0,0 @@
-The simulation consists of a mixture of isobutane and water.
-Over time (less than 1 ns), the two molecules phase-separate.
-
-The GAFF parameters are applied only to the isobutane molecule.
-(The water molecule parameters are defined explicitly in
- src/moltemplate_force_fields/tip3p_2004.lt)
-
-WARNING: THIS IS A PRELIMINARY EXAMPLE WHICH USES AMBER'S GAFF FORCE FIELD.
- AS OF 2014-4-19, these features have not been tested.
- THE ABILITY TO DETECT AND ASSIGN GAFF FORCE FIELD PARAMETERS
- MOLECULES ACCORDING TO ATOM TYPE IS AN EXPERIMENTAL FEATURE
- AND CURRENTLY PROBABLY HAS BUGS (IN THE DIHEDRALS AND IMPROPERS).
- PLEASE REPORT BUGS AND/OR SEND CORRECTIONS. -A 2014-4-19
-
------------------ CHARGE ----------------------
-
-NOTE: The GAFF force-field DOES NOT ASSIGN ATOM CHARGE.
- In this example, atom charges were taken from the OPLSAA force field file:
- http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This is not the charge in AMBER simunlations is typically assigned.
- (As of 2014, it is assigned using the "HF/6-31G* RESP2" or "AM1-BCC3"
- methods using AmberTools (which are not available in moltemplate).
- http://ambermd.org/doc6/html/AMBER-sh-19.4.html
- http://ambermd.org/tutorials/basic/tutorial4b/)
-
-
--------- REQUIREMENTS: ---------
-
- This example requires building LAMMPS with the "USER-MISC" package.
- (because it makes use of "gaff.lt" which uses dihedral_style fourier)
- To do this, type "make yes-user-misc" before compiling LAMMPS.
- http://lammps.sandia.gov/doc/Section_start.html#start_3
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step 2)
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
deleted file mode 100755
index 9f923a6c7..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-# --- Running LAMMPS ---
-# -------- REQUIREMENTS: ---------
-# 1) This example requires building LAMMPS with the "USER-MISC" package.
-# (because it makes use of "gaff.lt" which uses dihedral_style fourier)
-# To do this, type "make yes-user-misc" before compiling LAMMPS.
-# http://lammps.sandia.gov/doc/Section_start.html#start_3
-# -------- PREREQUISITES: --------
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
deleted file mode 100755
index c2db73b45..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- #rm -rf output_ttree/
-
-cd ../
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in GAFF which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg
deleted file mode 100644
index 8c548fba8..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
deleted file mode 100644
index fab496aa2..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
deleted file mode 100644
index aaa4abaf5..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg
deleted file mode 100644
index 9d578b4ef..000000000
Binary files a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
deleted file mode 100644
index e244d4427..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
+++ /dev/null
@@ -1,56 +0,0 @@
-
-import "gaff.lt"
-
-# The "gaff.lt" file is usually located in "src/moltemplate_force_fields".
-# It contains definitions of the atoms "c3", "h1", as well as the bonded
-# and non-bonded interactions between them (and many other atoms).
-#
-# Moltemplate is only a simple text manipulation tool. It cannot
-# calculate atomic charge using quantom chemistry methods.
-# Atom charges for this example were taken from the OPLSAA force field file:
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# However, normally simulations in AMBER are assigned charges using the
-# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools.
-
-
-Isobutane inherits GAFF {
-
- # atomID molID atomTyle charge X Y Z
- write('Data Atoms') {
- $atom:C0 $mol:. @atom:c3 -0.0600 -0.001 -0.001 -0.439
- $atom:C1 $mol:. @atom:c3 -0.1800 -1.257 -0.726 0.078
- $atom:C2 $mol:. @atom:c3 -0.1800 1.258 -0.726 0.072
- $atom:C3 $mol:. @atom:c3 -0.1800 -0.001 1.453 0.069
- $atom:H0 $mol:. @atom:hc 0.0600 -0.003 -0.004 -1.439
- $atom:H11 $mol:. @atom:hc 0.0600 -2.075 -0.255 -0.254
- $atom:H12 $mol:. @atom:hc 0.0600 -1.256 -0.724 1.078
- $atom:H13 $mol:. @atom:hc 0.0600 -1.259 -1.669 -0.253
- $atom:H21 $mol:. @atom:hc 0.0600 2.074 -0.255 -0.264
- $atom:H22 $mol:. @atom:hc 0.0600 1.258 -1.669 -0.259
- $atom:H23 $mol:. @atom:hc 0.0600 1.261 -0.724 1.072
- $atom:H31 $mol:. @atom:hc 0.0600 -0.817 1.923 -0.263
- $atom:H32 $mol:. @atom:hc 0.0600 0.816 1.923 -0.268
- $atom:H33 $mol:. @atom:hc 0.0600 0.003 1.456 1.070
- }
-
- # The "." in "$mol:." refers to this molecule object's molecule ID
- # (It means we do not expect this molecule to be a group or a subunit
- # of a larger molecule. Otherwise we would use "$mol:..." instead.)
-
- write('Data Bond List') {
- $bond:C01 $atom:C0 $atom:C1
- $bond:C02 $atom:C0 $atom:C2
- $bond:C03 $atom:C0 $atom:C3
- $bond:C0H $atom:C0 $atom:H0
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C1H2 $atom:C1 $atom:H12
- $bond:C1H3 $atom:C1 $atom:H13
- $bond:C2H1 $atom:C2 $atom:H21
- $bond:C2H2 $atom:C2 $atom:H22
- $bond:C2H3 $atom:C2 $atom:H23
- $bond:C3H1 $atom:C3 $atom:H31
- $bond:C3H2 $atom:C3 $atom:H32
- $bond:C3H3 $atom:C3 $atom:H33
- }
-
-} # Isobutane
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt
deleted file mode 100644
index e10f0bcec..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt
+++ /dev/null
@@ -1,29 +0,0 @@
-import "tip3p_2004.lt"
- # <- This defines the TIP3P water molecule. This file is
- # located in the "src/moltemplate_force_fields" directory.
-
-import "isobutane.lt" # <- defines the "Isobutane" molecule type.
-
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 41.50 xlo xhi
- 0.0 41.50 ylo yhi
- 0.0 41.50 zlo zhi
-}
-
-
-# The next command generates a (rather dense) cubic lattice with
-# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
-
-wat = new TIP3P_2004 [12].move(0.00, 0.00, 3.45)
- [12].move(0.00, 3.45, 0.00)
- [12].move(3.45, 0.00, 0.00)
-
-isobutane = new Isobutane [4].move(0, 0, 10.35)
- [4].move(0, 10.35, 0)
- [4].move(10.35, 0, 0)
-
-# move the isobutane molecules slightly to reduce overlap with the water
-isobutane[*][*][*].move(1.725, 1.725, 1.725)
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh
deleted file mode 100755
index 325199177..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh
+++ /dev/null
@@ -1,63 +0,0 @@
- # MOST USERS CAN IGNORE THIS FILE
- #
- # Unfortunately, as of 2014-4-19, the system.data and system.in.settings file
- # which are created by moltemplate.sh contain a lot of irrelevant information,
- # such as definition of parameters for atom types not present in the current
- # system. This extra information takes up about 1 MB.
- #
- # This appears to be harmless.
- # (Loading this extra information does not seem to slow down LAMMPS.)
- #
- # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
- #
- # However if you want to eliminate this junk from these files
- # For now, we can strip this out using ltemplify.py to build a new .lt file.
- #
- # NOTE: If you decide to use this script, it was meant to be run it from
- # the parent directory (../) (If you run it from somewhere else, be sure to
- # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.)
- #
- # I suggest you do this in a temporary_directory
-
- PATH_TO_DATA_FILE="."
-
- pushd "$PATH_TO_DATA_FILE"
-
- mkdir new_lt_file
- cd new_lt_file/
-
- # now run ltemplify.py
-
- ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt
-
- # This creates a new .LT file named "system.lt" in the local directory.
-
- # The ltemplify.py script also does not copy the boundary dimensions.
- # We must do this manually.
- # If you did NOT throw away the "Data Boundary" file usually located in
- # "moltemplate_files/output_ttree/Data Boundary"
- # then you can copy that information from this file into system.lt
-
- PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree"
-
- echo "write_once(\"Data Boundary\") {" >> system.lt
- cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt
- echo "}" >> system.lt
- echo "" >> system.lt
-
- # Now, run moltemplate on this new .LT file.
- moltemplate.sh system.lt
- # This will create: "system.data" "system.in.init" "system.in.settings."
-
- # That's it. The new "system.data" and system.in.* files should
- # be ready to run in LAMMPS.
-
- # Now copy the system.data and system.in.* files to the place where
- # you plan to run LAMMPS
- mv -f system.data system.in.* ../
- cd ../
-
- # Now delete all of the temporary files we generated
- rm -rf new_lt_file/
- popd
-
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.npt b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.npt
deleted file mode 100644
index b4e407889..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.npt
+++ /dev/null
@@ -1,44 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-#
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# fShakeTIP3P was defined in system.in.settings. It is incompatible with "minimize".
-unfix fShakeTIP3P
-minimize 1.0e-4 1.0e-6 100000 400000
-# Now read "system.in.settings" in order to redefine fShakeTIP3P again:
-include system.in.settings
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-thermo 100
-#thermo_modify flush yes
-
-run 40000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt
deleted file mode 100644
index 602b8c329..000000000
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt
+++ /dev/null
@@ -1,52 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# COMMENTING OUT MINIMIZATION STEPS:
-# If you are reading the coordinates generated by the NPT run
-# then you should not need to minimize the system beforehand.
-# -- minimization protocol --
-## ("fix shake" is incompatible with "minimize".)
-#unfix fShakeTIP3P
-#minimize 1.0e-4 1.0e-6 100000 400000
-## Now read "system.in.settings" in order to redefine fShakeTIP3P again:
-#include system.in.settings
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/WARNING.TXT b/tools/moltemplate/examples/force_field_OPLSAA/WARNING.TXT
deleted file mode 100644
index 0d8c8e030..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/WARNING.TXT
+++ /dev/null
@@ -1,28 +0,0 @@
-# -------- WARNING: --------
-
-This directory contains some examples of all-atom simulations using the OPLSAA
-force field.
-
-This software is experimental, and the force-fields and equilbration protocols
-have not been tested carefully by me. There is no gaurantee that simulations
-prepared using moltemplate will reproduce the behavior of other MD codes.
-
-# -------- REQUEST FOR HELP: --------
-
-If you notice a problem with these examples, please report it.
-Peer-review is the only way to improve this software (or any software).
-Other suggestions are also welcome!
-
-(Contact jewett.aij@gmail.com, 2014-4-19)
-
---- Improper angles ---
-
-I am also uncertain whether the improper angle interactions generated by
-moltemplate are equivalent to those generated by BOSS or other molecule
-builders. (I think they are, but I am worried that we might have listed
-the atom types in the wrong order. Let us know if you see discrepancies
-between what moltemplate and other molecule builders generates.)
-
------------
-For more details how to use the OPLSAA force-field, read the "README.TXT"
-file located in "ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README.TXT
deleted file mode 100644
index abef639d4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README.TXT
+++ /dev/null
@@ -1,40 +0,0 @@
-This example is a simple simulation of a long alkane chain,
-in a vacuum at room temperature using the OPLSAA force field.
-
-NOTE: This particular example uses the OPLSAA force-field
- However, moltemplate is not limited to OPLSAA.
-
-1) Create the "system.data", "system.in.init", and "system.in.settings"
-files which LAMMPS will read by running:
-
-moltemplate.sh system.lt
-
-
-2) Run LAMMPS in this order:
-
-lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before...
-lmp_mpi -i run.in.nvt # running the simulation at constant temperature
-
-(The name of the LAMMPS executable, eg "lmp_mpi", may vary.)
-
----- Details ----
-
-The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains
-use the OPLSAA force-field. This means that when we define these molecules,
-we only specify the atom names, bond list, and coordinates.
-We do not have to list the atom charges, angles, dihedrals, or impropers.
-The rules for creating atomic charge and angle topology are contained in
-the "loplsaa.lt" file created by step 3) above. The "ch2group.lt",
-"ch3group.lt", and "alkane50.lt" files all refer to "loplsaa.lt",
-(as well as the "OPLSAA" force-field object which it defines). Excerpt:
-
-import "loplsaa.lt"
-CH2 inherits OPLSAA { ...
-CH3 inherits OPLSAA { ...
-Alkane50 inherits OPLSAA { ...
-
-Alternatively, you can manually define a list of angles, dihedrals, and
-improper interactions in these files, instead of asking the force-field
-to generate them for you. You can also specify some of the angles and
-dihedrals explicitly, and let the force-field handle the rest.
-(Many of the examples which come with moltemplate do this.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_run.sh
deleted file mode 100755
index b31401f13..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.min # minimization
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh
deleted file mode 100755
index 54a6484da..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg
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diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg
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diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt
deleted file mode 100644
index f4a21ebe4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt
+++ /dev/null
@@ -1,138 +0,0 @@
-# This is a simple example showing how to build a long polymer
-# (in this case, an alkane chain). I split the
-# hexadecane molecule into individual CH2 and CH3 monomers.
-# I defined it this way so that you can easily modify
-# it to change the length of the alkane chain.
-
-
-import "oplsaa.lt" # load the "OPLSAA" force-field information
-import "ch2group.lt" # load the definition of the "CH2" object
-import "ch3group.lt" # load the definition of the "CH3" object
-
-
-
-Alkane50 inherits OPLSAA {
-
-
- create_var {$mol} # optional:force all monomers to share the same molecule-ID
-
- # This is a long polymer consisting of 48 CH2 groups and 2 CH3 end-caps.
- # Rather than create them one-by-one, I decided to create them all
- # using a single "new" command. Later, I can modify this array.
-
- # Create an array of 50 "CH2" objects distributed along the X axis
-
- monomers = new CH2 [50].rot(180,1,0,0).move(1.2533223,0,0)
-
- # NOTE: the ".rot(180,1,0,0).move(1.2533223,0,0)" means that each
- # successive monomer is rotated 180 degrees (with respect to the previous
- # monomer), and then moved 1.2533223 Angstroms down the X axis.
- # Alternately, if you are reading the coordinates from a file, you don't have
- # to indicate the position & orientation of each monomer. In that case, use:
- # monomers = new CH2 [50]
-
-
- # ---- Now, modify the ends: ---
- # Delete the CH2 groups at the beginning and end, and replace them with CH3.
-
- delete monomers[0]
- delete monomers[49]
-
- monomers[0] = new CH3
- monomers[49] = new CH3
-
- # Move the CH3 groups to the correct location at either end of the chain:
-
- #monomers[0].move(0,0,0) # <--(this monomer is already in the correct place)
- monomers[49].rot(180.0,0,0,1).move(61.4127927,0,0) #61.4127927=49*1.2533223
-
-
- ## NOTE: Alternately, you can define the polymer without deleting the ends:
- # monomers[0] = new CH3
- # monomers[1-48] = new CH2[48].rot(180,1,0,0).move(1.2533223,0,0)
- ## Note: monomers[0] and monomers[1] overlap, so we move 1-48 to make room:
- # monomers[1-48].rot(180,1,0,0).move(1.2533223,0,0) # move many monomers
- ## Now add the final monomer at the end:
- # monomers[49] = new CH3.rot(180.0,0,0,1).move(61.4127927,0,0)
- #
- ## NOTE: Alternately, you can read the coordinates from a file.
- ## In that case, you can use simpler commands:
- # monomers[0] = new CH3
- # monomers[1-48] = new CH2[48]
- # monomers[49] = new CH3
-
-
-
- # Now add a list of bonds connecting the carbon atoms together:
- # (Angles, dihedrals, impropers will be automatically added later.)
-
- write('Data Bond List') {
- $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C
- $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C
- $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C
- $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C
- $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C
- $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C
- $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C
- $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C
- $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C
- $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C
- $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C
- $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C
- $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C
- $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C
- $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C
- $bond:b16 $atom:monomers[15]/C $atom:monomers[16]/C
- $bond:b17 $atom:monomers[16]/C $atom:monomers[17]/C
- $bond:b18 $atom:monomers[17]/C $atom:monomers[18]/C
- $bond:b19 $atom:monomers[18]/C $atom:monomers[19]/C
- $bond:b20 $atom:monomers[19]/C $atom:monomers[20]/C
- $bond:b21 $atom:monomers[20]/C $atom:monomers[21]/C
- $bond:b22 $atom:monomers[21]/C $atom:monomers[22]/C
- $bond:b23 $atom:monomers[22]/C $atom:monomers[23]/C
- $bond:b24 $atom:monomers[23]/C $atom:monomers[24]/C
- $bond:b25 $atom:monomers[24]/C $atom:monomers[25]/C
- $bond:b26 $atom:monomers[25]/C $atom:monomers[26]/C
- $bond:b27 $atom:monomers[26]/C $atom:monomers[27]/C
- $bond:b28 $atom:monomers[27]/C $atom:monomers[28]/C
- $bond:b29 $atom:monomers[28]/C $atom:monomers[29]/C
- $bond:b30 $atom:monomers[29]/C $atom:monomers[30]/C
- $bond:b31 $atom:monomers[30]/C $atom:monomers[31]/C
- $bond:b32 $atom:monomers[31]/C $atom:monomers[32]/C
- $bond:b33 $atom:monomers[32]/C $atom:monomers[33]/C
- $bond:b34 $atom:monomers[33]/C $atom:monomers[34]/C
- $bond:b35 $atom:monomers[34]/C $atom:monomers[35]/C
- $bond:b36 $atom:monomers[35]/C $atom:monomers[36]/C
- $bond:b37 $atom:monomers[36]/C $atom:monomers[37]/C
- $bond:b38 $atom:monomers[37]/C $atom:monomers[38]/C
- $bond:b39 $atom:monomers[38]/C $atom:monomers[39]/C
- $bond:b40 $atom:monomers[39]/C $atom:monomers[40]/C
- $bond:b41 $atom:monomers[40]/C $atom:monomers[41]/C
- $bond:b42 $atom:monomers[41]/C $atom:monomers[42]/C
- $bond:b43 $atom:monomers[42]/C $atom:monomers[43]/C
- $bond:b44 $atom:monomers[43]/C $atom:monomers[44]/C
- $bond:b45 $atom:monomers[44]/C $atom:monomers[45]/C
- $bond:b46 $atom:monomers[45]/C $atom:monomers[46]/C
- $bond:b47 $atom:monomers[46]/C $atom:monomers[47]/C
- $bond:b48 $atom:monomers[47]/C $atom:monomers[48]/C
- $bond:b49 $atom:monomers[48]/C $atom:monomers[49]/C
- }
-
-} # Alkane50
-
-
-
-
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163316030377
-# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
-# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt
deleted file mode 100644
index 510b7e111..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt
+++ /dev/null
@@ -1,82 +0,0 @@
-# This file contains a definition for the "CH2" molecular subunit.
-
-# First, load the OPLS force field parameters we will need.
-# These 2 files are located in the "src/moltemplate_force_fields/" subdirectory:
-
-import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field
-import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from
- # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459
- # To use the ordinary OPLSAA force field parameters,
- # (instead of the Sui et al. parameters), change the
- # atom types below from "@atom:81L","@atom:85LCH2" to
- # "@atom:81" and "@atom:85" (defined in "oplsaa.lt")
-
-
-
-# Then define "CH2":
-
-
-CH2 inherits OPLSAA {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:C $mol:... @atom:81L 0.0 0.000000 0.000000 0.000000
- $atom:H1 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 0.892431
- $atom:H2 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 -0.892431
- }
-
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- }
-
- # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt",
- # which is usually located in the "src/moltemplate_force_fields/" subdirectory
- # @atom:80L "Alkane CH3- (LOPLS CT_CH3)"
- # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)"
- # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)"
- # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)"
- # In this example, atomic charges are generated by atom type (according to the
- # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now.
- # The "..." in "$mol:..." tells moltemplate that this molecule may be part
- # of a larger molecule, and (if so) to use the larger parent object's
- # molecule id number as it's own.
-
-} # CH2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-# Optional: Shift all the coordinates in the +Y direction by 0.4431163.
-# This way, the carbon atom is no longer located at 0,0,0, but the
-# axis of an alkane chain containing this monomer is at 0,0,0.
-# (This makes it more convenient to construct a polymer later.
-# If this is confusing, then simply add 0.4431163 to the Y
-# coordinates in the "Data Atoms" section above.)
-
-CH2.move(0,0.4431163,0)
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163
-# DeltaZh = Lch*sin(theta/2) # = 0.892431
-# DeltaYh = Lch*cos(theta/2) # = 0.631044
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt
deleted file mode 100644
index b01c8c0cd..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt
+++ /dev/null
@@ -1,83 +0,0 @@
-# This file contains a definition for the "CH3" molecular subunit.
-
-# First, load the OPLS force field parameters we will need.
-# These 2 files are located in the "src/moltemplate_force_fields/" subdirectory:
-
-import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field
-import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from
- # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459
- # To use the ordinary OPLSAA force field parameters,
- # (instead of the Sui et al. parameters), change the
- # atom types below from "@atom:80L","@atom:85LCH3" to
- # "@atom:80" and "@atom:85" (defined in "oplsaa.lt")
-
-
-
-# Then define "CH3":
-
-
-CH3 inherits OPLSAA {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:C $mol:... @atom:80L 0.0 0.000000 0.000000 0.000000
- $atom:H1 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 0.892431
- $atom:H2 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 -0.892431
- $atom:H3 $mol:... @atom:85LCH3 0.0 -0.892431 -0.631044 0.000000
- }
-
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- $bond:CH3 $atom:C $atom:H3
- }
-
- # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt",
- # @atom:80L "Alkane CH3- (LOPLS CT_CH3)"
- # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)"
- # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)"
- # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)"
- # In this example, atomic charges are generated by atom type (according to the
- # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now.
- # The "..." in "$mol:..." tells moltemplate that this molecule may be part
- # of a larger molecule, and (if so) to use the larger parent object's
- # molecule id number as it's own.
-
-} # CH3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-# Optional: Shift all the coordinates in the +Y direction by 0.4431163.
-# This way, the carbon atom is no longer located at 0,0,0, but the
-# axis of an alkane chain containing this monomer is at 0,0,0.
-# (This makes it more convenient to construct a polymer later.
-# If this is confusing, then simply add 0.4431163 to the Y
-# coordinates in the "Data Atoms" section above.)
-
-CH3.move(0,0.4431163,0)
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163
-# DeltaZh = Lch*sin(theta/2) # = 0.892431
-# DeltaYh = Lch*cos(theta/2) # = 0.631044
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index dedba938b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,109 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the "Alkane50"
-molecule. (However, these instructions should work for other molecules too.)
-
---- Instructions ---
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file unmodified!)
-
-For example:
-If you were working with a simple alkane chain, you would delete every line
-beginning with the word "atom", except for these three lines:
-
-
-atom 80 13 CT "Alkane CH3-" 6 12.011 4
-atom 81 13 CT "Alkane -CH2-" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: The atom type numbers, like "89", "81", "85", "13", "46", etc... may vary
- depending on when you downloaded the "oplsaa.prm" file. Be sure to check
- the descriptions of each atom type after you download it: "Alkane CH3-")
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "methane.lt":
-
-import "oplsaa.lt"
-Methane inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Andrew Jewett and Jason Lambert
-May, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index 1260acdbd..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,151 +0,0 @@
-# This file is a heavily redacted version of the "oplsaa.prm" file distributed
-# with TINKER (Downloaded April, 2014). This version only contains information
-# relevant to alkane chains. The complete version of that file works with most
-# small organic molecules and you can use that file with moltemplate too.
-# Unfortunately, I do not own or have permission to distribute that file.
-# You can download the latest complete version of that file here:
-#
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-#
-# When building your own molecules, you should download this file, and delete
-# only the lines from the "atoms" section which you don't need. (But leave the
-# rest of that file alone. I deleted other sections of this file here in order
-# to reduce the file size, but this is not necessary.)
-#
-# Rename the resulting file "oplsaa_subset.prm"
-#
-# Then you can create an oplsaa.lt file (which moltemplate.sh needs) this way:
-# oplsaa_moltemplate.py oplsaa_subset.prm
-#
-# Then copy the newly created "oplsa.lt" file to the directory where you
-# plan to run moltemplate, and run moltemplate:
-# moltemplate system.lt
-
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-
-atom 80 13 CT "Alkane CH3-" 6 12.011 4
-atom 81 13 CT "Alkane -CH2-" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 80 3.5000 0.0660
-vdw 81 3.5000 0.0660
-vdw 85 2.5000 0.0300
-
-
-bond 13 13 268.00 1.5290
-bond 13 46 340.00 1.0900
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 13 13 13 58.35 112.70
-angle 46 13 46 33.00 107.80
-angle 13 13 46 37.50 110.70
-
-
- ############################
- ## ##
- ## Torsional Parameters ##
- ## ##
- ############################
-
-
- ###################################################################
- ## ##
- ## Alternative Torsional Parameter Values for Use with OPLS-AA ##
- ## ##
- ## For some torsions, OPLS-AA has multiple possible parameter ##
- ## values; the list below shows functional groups for which ##
- ## these alternate (commented) values should be preferred; the ##
- ## values are in the same order as in the full parameter list ##
- ## ##
- ## 13 13 13 13 hydrocarbon (default) ##
- ## 13 13 13 13 perfluoroalkane ##
- ## ##
- ###################################################################
-
-
-torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3
-#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4
-torsion 13 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 46 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-
-
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 80 -0.1800
-charge 81 -0.1200
-charge 85 0.0600
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt
deleted file mode 100644
index f62ecc09b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt
+++ /dev/null
@@ -1,31 +0,0 @@
-import "alkane50.lt" # Defines the "Alkane50" molecule
-
-
-polymer = new Alkane50
-
-
-
-# Specify the size of the world the polymer lives in:
-write_once("Data Boundary") {
- 0.0 72.0 xlo xhi
- 0.0 72.0 ylo yhi
- 0.0 72.0 zlo zhi
-}
-
-
-
-
-
-###############################################################################
-# Note: If you want to create multiple polymers, and/or mix them with other
-# molecules, just add more "new" commands, for example:
-# polymer1 = new Alkane50.move(0,0,10)
-# polymer2 = new Alkane50.move(0,0,20)
-# :
-# ...or use array notation, for example:
-# polymers = new Alkane50[20].move(0,0,10)
-#
-# Note: Multidimensional arrays can be used to fill a planar region or a volume
-# polymers = new Alkane50 [4].move(0, 0, 30.0)
-# [4].move(0, 30.0, 0)
-# [2].move(70.0, 0, 0)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.min b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.min
deleted file mode 100644
index 5d0bcffd8..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.min
+++ /dev/null
@@ -1,37 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-#
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-
-thermo 50
-dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
-minimize 1.0e-4 1.0e-6 100000 400000
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-write_data system_after_min.data
-
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
deleted file mode 100644
index d5b77423a..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
+++ /dev/null
@@ -1,38 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must minimize the system beforehand by using "run.in.min".
-# This will create the file "system_after_min.data" which this file reads.
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier simulation
-
-read_data "system_after_min.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 1000000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README.TXT
deleted file mode 100644
index f744e1718..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README.TXT
+++ /dev/null
@@ -1,12 +0,0 @@
-This is an example of how to use the OPLSAA force-field in LAMMPS
-
-As of 2016-11-21, this code has not been tested for accuracy.
-(See the WARNING.TXT file.)
-
-step 1)
-To build the files which LAMMPS needs, follow the instructions in:
-README_setup.sh
-
-step 2)
-To run LAMMPS with these files, follow these instructions:
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_run.sh
deleted file mode 100755
index 5f8286664..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh
deleted file mode 100755
index 54a6484da..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg
deleted file mode 100644
index 356c78425..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg
deleted file mode 100644
index 00c82d3d9..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg
deleted file mode 100644
index ab5bbbf49..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt
deleted file mode 100644
index 1293cb1e4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt
+++ /dev/null
@@ -1,45 +0,0 @@
-import "oplsaa.lt"
-
-# The "oplsaa.lt" file contains force-field definitions and masses for the
-# atoms in your system. See oplsaa_lt_generator/README.TXT for details.
-
-# Note:
-# Atom type @atom:90 corresponds to "Aromatic C"
-# Atom type @atom:91 corresponds to "Aromatic H-C"
-
-Benzene inherits OPLSAA {
-
- write('Data Atoms') {
- $atom:C1 $mol @atom:90 0.00 5.274 1.999 -8.568 # "Aromatic C"
- $atom:C2 $mol @atom:90 0.00 6.627 2.018 -8.209 # "Aromatic C"
- $atom:C3 $mol @atom:90 0.00 7.366 0.829 -8.202 # "Aromatic C"
- $atom:C4 $mol @atom:90 0.00 6.752 -0.379 -8.554 # "Aromatic C"
- $atom:C5 $mol @atom:90 0.00 5.399 -0.398 -8.912 # "Aromatic C"
- $atom:C6 $mol @atom:90 0.00 4.660 0.791 -8.919 # "Aromatic C"
- $atom:H11 $mol @atom:91 0.00 4.704 2.916 -8.573 # "Aromatic H-C"
- $atom:H21 $mol @atom:91 0.00 7.101 2.950 -7.938 # "Aromatic H-C"
- $atom:H31 $mol @atom:91 0.00 8.410 0.844 -7.926 # "Aromatic H-C"
- $atom:H41 $mol @atom:91 0.00 7.322 -1.296 -8.548 # "Aromatic H-C"
- $atom:H51 $mol @atom:91 0.00 4.925 -1.330 -9.183 # "Aromatic H-C"
- $atom:H61 $mol @atom:91 0.00 3.616 0.776 -9.196 # "Aromatic H-C"
- }
- # Note: You don't have to specify the charge in this example because
- # we are using the OPLSAA force-field assigns this by atom-type.
- # Just leave these numbers as 0.00 for now.
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C23 $atom:C2 $atom:C3
- $bond:C34 $atom:C3 $atom:C4
- $bond:C45 $atom:C4 $atom:C5
- $bond:C56 $atom:C5 $atom:C6
- $bond:C61 $atom:C6 $atom:C1
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C2H2 $atom:C2 $atom:H21
- $bond:C3H3 $atom:C3 $atom:H31
- $bond:C4H4 $atom:C4 $atom:H41
- $bond:C5H5 $atom:C5 $atom:H51
- $bond:C6H6 $atom:C6 $atom:H61
- }
-
-} # Benzene
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt
deleted file mode 100644
index 626c731b0..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt
+++ /dev/null
@@ -1,43 +0,0 @@
-import "oplsaa.lt"
-
-# The "oplsaa.lt" file contains force-field definitions and masses for the
-# atoms in your system. See oplsaa_lt_generator/README.TXT for details.
-
-# Note:
-# Atom type 88 corresponds to "Alkene H2-C="
-# Atom type 89 corresponds to "Alkene H-C="
-
-
-
-Ethylene inherits OPLSAA {
-
- # atom-id mol-id atom-type charge X Y Z
-
- write('Data Atoms') {
- $atom:C1 $mol @atom:88 0.00 -0.6695 0.000000 0.000000
- $atom:C2 $mol @atom:88 0.00 0.6695 0.000000 0.000000
- $atom:H11 $mol @atom:89 0.00 -1.234217 -0.854458 0.000000
- $atom:H12 $mol @atom:89 0.00 -1.234217 0.854458 0.000000
- $atom:H21 $mol @atom:89 0.00 1.234217 -0.854458 0.000000
- $atom:H22 $mol @atom:89 0.00 1.234217 0.854458 0.000000
- }
- # Note: You don't have to specify the charge in this example because
- # we are using the OPLSAA force-field assigns this by atom-type.
- # Just leave these numbers as 0.00 for now.
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C1H2 $atom:C1 $atom:H12
- $bond:C2H1 $atom:C2 $atom:H21
- $bond:C2H2 $atom:C2 $atom:H22
- }
-
-} # Ethylene
-
-
-
-# Note: You don't need to supply the partial partial charges of the atoms.
-# If you like, just fill the fourth column with zeros ("0.000").
-# Moltemplate and LAMMPS will automatically assign the charge later
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index 6da345602..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,110 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the
-"ethylene+benzene" example. (However, these instructions should work
-for other molecules too.)
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with ethylene and benzene you would delete every line
-beginning with the word "atom", except for these four lines:
-
-# for ethylene:
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-# for benzene:
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "88", "89", "47", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "ethyelene.lt":
-
-import "oplsaa.lt"
-Ethylene inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Jason Lambert and Andrew Jewett
-April, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
deleted file mode 100644
index 2fc1ea29e..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
+++ /dev/null
@@ -1,16 +0,0 @@
-MOST USERS SHOULD IGNORE THIS DIRECTORY.
-
-This directory contains versions of the oplsaa_subset.prm file
-which nearly all of the OPLSAA force-field information removed.
-However for the "ethylene+benzene" example, all of the essential
-parameters are contained in these files. You can use oplsaa_moltemplate.py
-with either of these files and the physics should be the same.
-
-However there is no reason to do this.
-When you download the "oplsaa.prm" file from:
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-(also http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm)
-...just remove the lines beginning with "atom" for atoms you don't need.
-You don't have to delete all the other irrelevant interactions.
-(In fact, it is hard to do that without making a mistake.
- I recommend that you leave the rest of the oplsaa.prm file alone.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
deleted file mode 100644
index b4078f121..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
+++ /dev/null
@@ -1,37 +0,0 @@
- #############################
- ## Atom Type Definitions ##
- #############################
-
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-vdw 88 3.5500 0.0760
-vdw 89 2.4200 0.0300
-vdw 90 3.5500 0.0700
-vdw 91 2.4200 0.0300
-
-bond 46 47 340.00 1.0800
-bond 47 47 549.00 1.3400
-bond 48 48 469.00 1.4000
-bond 48 49 367.00 1.0800
-
-angle 46 47 46 35.00 117.00
-angle 46 47 47 35.00 120.00
-angle 48 48 48 63.00 120.00
-angle 48 48 49 35.00 120.00
-
-torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-
-imptors 0 0 47 0 30.000 180.0 2
-imptors 0 0 48 0 5.000 180.0 2
-
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
deleted file mode 100644
index 6dbc6861a..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
+++ /dev/null
@@ -1,49 +0,0 @@
- #############################
- ## Atom Type Definitions ##
- #############################
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-vdw 88 3.5500 0.0760
-vdw 89 2.4200 0.0300
-vdw 90 3.5500 0.0700
-vdw 91 2.4200 0.0300
-
-bond 46 47 340.00 1.0800
-bond 47 47 549.00 1.3400
-bond 47 48 427.00 1.4330
-bond 48 48 469.00 1.4000
-bond 48 49 367.00 1.0800
-
-angle 46 47 46 35.00 117.00
-angle 46 47 47 35.00 120.00
-angle 46 47 48 35.00 123.30
-angle 47 47 48 85.00 117.00
-angle 48 48 48 63.00 120.00
-angle 47 48 48 70.00 124.00
-angle 48 48 49 35.00 120.00
-
-imptors 0 0 47 0 30.000 180.0 2
-imptors 0 0 48 0 5.000 180.0 2
-
-torsion 47 46 47 46 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3
-torsion 0 47 47 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 47 47 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 47 48 48 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3
-torsion 47 47 48 48 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3
-torsion 0 48 48 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 47 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index c802793ad..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,5129 +0,0 @@
-# This is a modified version of the file "oplsaa.prm" distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# In this version, all of the lines beginning with "atom" have been deleted
-# except for the atom types we will be using in this simulation
-# (I also deleted some other lines from that file data to reduce the file size,
-# but doing that is not necessary.)
-#
-# If you use this file, please also cite the software this file comes from:
-#
-# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024
-# "An efficient newton‐like method for molecular mechanics energy
-# minimization of large molecules."
-#
-# Ponder, J. W, (2004)
-# "TINKER: Software tools for molecular design"
-# http://dasher.wustl.edu/tinker/
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 1 2.9400 0.0610
-vdw 2 3.9050 0.1180
-vdw 3 3.7500 0.1050
-vdw 4 2.9600 0.2100
-vdw 5 3.0000 0.1700
-vdw 6 3.9100 0.1600
-vdw 7 0.0000 0.0000
-vdw 8 3.7300 0.2940
-vdw 9 3.7750 0.2070
-vdw 10 3.9050 0.1750
-vdw 11 3.9100 0.1600
-vdw 12 3.9600 0.1450
-vdw 13 3.9050 0.1180
-vdw 14 3.8500 0.1400
-vdw 15 3.8500 0.0800
-vdw 16 3.8000 0.1150
-vdw 17 3.7500 0.1100
-vdw 18 3.8000 0.0500
-vdw 19 3.7500 0.1050
-vdw 20 3.0700 0.1700
-vdw 21 0.0000 0.0000
-vdw 22 3.7750 0.2070
-vdw 23 3.9050 0.1180
-vdw 24 3.7000 0.2500
-vdw 25 3.5500 0.2500
-vdw 26 3.5500 0.2500
-vdw 27 3.5500 0.2500
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-vdw 641 3.5500 0.0760
-vdw 642 3.5000 0.0660
-vdw 643 2.5000 0.0300
-vdw 644 3.7500 0.0600
-vdw 645 3.4730 0.0540
-vdw 646 3.3000 0.0500
-vdw 647 3.3000 0.0500
-vdw 648 2.9500 0.0400
-vdw 649 3.5500 0.0760
-vdw 650 3.4000 0.3000
-vdw 651 2.4200 0.0300
-vdw 652 3.5000 0.0660
-vdw 653 3.5000 0.0660
-vdw 654 3.5000 0.0660
-vdw 655 3.5500 0.0700
-vdw 656 2.4200 0.0300
-vdw 657 3.5500 0.0700
-vdw 658 2.4200 0.0300
-vdw 659 3.5500 0.0700
-vdw 660 2.8500 0.0610
-vdw 661 3.5500 0.0700
-vdw 662 2.8500 0.0610
-vdw 663 3.4700 0.4700
-vdw 664 3.9050 0.1180
-vdw 665 3.5500 0.0700
-vdw 666 3.2500 0.0620
-vdw 667 2.9400 0.0610
-vdw 668 3.5500 0.0700
-vdw 669 2.8500 0.0610
-vdw 670 3.5500 0.0700
-vdw 671 3.4700 0.4700
-vdw 672 3.5500 0.0700
-vdw 673 3.7500 0.6000
-vdw 674 3.5000 0.0660
-vdw 675 3.5500 0.2500
-vdw 676 3.5500 0.0700
-vdw 677 3.5500 0.0700
-vdw 678 3.5500 0.0700
-vdw 679 3.5500 0.0700
-vdw 680 3.5500 0.0700
-vdw 681 2.4200 0.0300
-vdw 682 2.4200 0.0300
-vdw 683 3.5500 0.0500
-vdw 684 3.2500 0.1700
-vdw 685 0.0000 0.0000
-vdw 686 0.0000 0.0000
-vdw 687 2.4200 0.0300
-vdw 688 3.5000 0.0660
-vdw 689 3.5000 0.0660
-vdw 690 3.2500 0.1700
-vdw 691 3.2500 0.1700
-vdw 692 3.2500 0.1700
-vdw 693 3.5500 0.0500
-vdw 694 3.2000 0.1700
-vdw 695 3.3000 0.0660
-vdw 696 3.3000 0.0660
-vdw 697 3.3000 0.0660
-vdw 698 3.3000 0.0660
-vdw 699 3.3000 0.0660
-vdw 700 2.5000 0.0150
-vdw 701 3.2500 0.1200
-vdw 702 2.9600 0.1700
-vdw 703 3.5000 0.0660
-vdw 704 2.5000 0.0150
-vdw 705 3.5000 0.0660
-vdw 706 3.5000 0.0660
-vdw 707 3.5000 0.0660
-vdw 708 3.2500 0.1200
-vdw 709 3.5500 0.0700
-vdw 710 3.3000 0.0660
-vdw 711 3.2500 0.1700
-vdw 712 2.9600 0.2100
-vdw 713 3.7500 0.1050
-vdw 714 3.0000 0.1700
-vdw 715 3.5000 0.0660
-vdw 716 3.5000 0.0660
-vdw 717 3.5000 0.0660
-vdw 718 2.4200 0.0150
-vdw 719 2.4200 0.0150
-vdw 720 2.4200 0.0150
-vdw 721 2.9000 0.1400
-vdw 722 3.7400 0.2000
-vdw 723 3.5000 0.0660
-vdw 724 3.5000 0.0660
-vdw 725 2.5000 0.0300
-vdw 726 3.7400 0.2000
-vdw 727 3.1181 0.0610
-vdw 728 3.1500 0.1700
-vdw 729 2.8600 0.2100
-vdw 730 3.3000 0.1700
-vdw 731 3.3000 0.1700
-vdw 732 3.3000 0.1700
-vdw 733 3.5000 0.0660
-vdw 734 3.5000 0.0660
-vdw 735 3.5000 0.0660
-vdw 736 3.5000 0.0660
-vdw 737 3.5000 0.0660
-vdw 738 3.5000 0.0660
-vdw 739 0.0000 0.0000
-vdw 740 0.0000 0.0000
-vdw 741 2.5000 0.0150
-vdw 742 3.5000 0.0660
-vdw 743 3.5000 0.0660
-vdw 744 3.5000 0.0660
-vdw 745 3.5000 0.0660
-vdw 746 3.5500 0.0700
-vdw 747 3.5500 0.0700
-vdw 748 3.5500 0.0700
-vdw 749 3.5000 0.0660
-vdw 750 3.5000 0.0660
-vdw 751 3.5000 0.0660
-vdw 752 3.5000 0.0660
-vdw 753 3.5000 0.0660
-vdw 754 3.5000 0.0660
-vdw 755 3.3000 0.0860
-vdw 756 2.4200 0.0150
-vdw 757 3.3000 0.2100
-vdw 758 3.3000 0.1350
-vdw 759 3.3000 0.1000
-vdw 760 2.5000 0.0150
-vdw 761 3.5000 0.0660
-vdw 762 3.5000 0.0660
-vdw 763 3.5000 0.0660
-vdw 764 3.1200 0.1700
-vdw 765 0.0000 0.0000
-vdw 766 3.2500 0.1700
-vdw 767 3.2500 0.1700
-vdw 768 3.2500 0.1700
-vdw 769 3.3000 0.2100
-vdw 770 3.2500 0.1700
-vdw 771 0.0000 0.0000
-vdw 772 3.5000 0.0660
-vdw 773 3.5000 0.0660
-vdw 774 3.5000 0.0660
-vdw 775 3.5000 0.0660
-vdw 776 3.5500 0.0700
-vdw 777 3.5500 0.0760
-vdw 778 3.5500 0.0700
-vdw 779 3.5500 0.0700
-vdw 780 2.5000 0.0300
-vdw 781 3.5000 0.0660
-vdw 782 3.7500 0.1050
-vdw 783 3.2500 0.1700
-vdw 784 2.9600 0.2100
-vdw 785 0.0000 0.0000
-vdw 786 2.9400 0.0610
-vdw 787 3.5000 0.0660
-vdw 788 2.5000 0.0300
-vdw 789 3.5000 0.0660
-vdw 790 3.5000 0.0660
-vdw 791 3.5000 0.0660
-vdw 792 3.5000 0.0660
-vdw 793 3.5000 0.0660
-vdw 794 3.5000 0.0970
-vdw 795 2.9500 0.0530
-vdw 796 3.2500 0.0620
-vdw 797 2.5000 0.0300
-vdw 798 3.5000 0.0660
-vdw 799 3.5000 0.0660
-vdw 800 3.4000 0.3000
-vdw 801 3.5000 0.0660
-vdw 802 2.5000 0.0300
-vdw 803 3.5000 0.0660
-vdw 804 3.5000 0.0660
-vdw 805 3.4700 0.4700
-vdw 806 3.5000 0.0660
-vdw 807 2.5000 0.0300
-vdw 808 3.5000 0.0660
-vdw 809 3.5000 0.0660
-vdw 810 2.9400 0.0610
-vdw 811 3.4000 0.3000
-vdw 812 3.4700 0.4700
-vdw 813 3.5500 0.0700
-vdw 814 2.9000 0.1400
-vdw 815 3.5000 0.0660
-vdw 816 2.9000 0.0600
-vdw 817 3.2500 0.1700
-vdw 818 3.5500 0.0700
-vdw 819 3.5000 0.0660
-vdw 820 3.7500 0.1050
-vdw 821 3.7500 0.1050
-vdw 822 2.9600 0.2100
-vdw 823 3.2500 0.1700
-vdw 824 0.0000 0.0000
-vdw 825 3.1200 0.1700
-vdw 826 0.0000 0.0000
-vdw 827 3.5000 0.0660
-vdw 828 3.5000 0.0660
-vdw 829 3.5500 0.0700
-vdw 830 3.5500 0.0700
-vdw 831 3.5500 0.0700
-vdw 832 3.5500 0.0700
-vdw 833 3.5500 0.0700
-vdw 834 1.9600 0.0125
-vdw 835 3.5000 0.0660
-vdw 836 3.5000 0.0660
-vdw 837 3.5000 0.0660
-vdw 838 3.7500 0.6000
-vdw 839 2.5000 0.0300
-vdw 840 3.2500 0.1700
-vdw 841 3.5500 0.0700
-vdw 842 3.5500 0.0700
-vdw 843 3.2500 0.1700
-vdw 844 3.5500 0.0700
-vdw 845 3.7500 0.1050
-vdw 846 2.9600 0.2100
-vdw 847 3.2500 0.1700
-vdw 848 3.5000 0.0660
-vdw 849 3.5000 0.0660
-vdw 850 3.5000 0.0660
-vdw 851 3.5000 0.0660
-vdw 852 2.4200 0.0150
-vdw 853 3.7500 0.1050
-vdw 854 2.9600 0.2100
-vdw 855 2.4200 0.0150
-vdw 856 3.5000 0.0660
-vdw 857 3.5000 0.0660
-vdw 858 3.5000 0.0660
-vdw 859 3.5000 0.0660
-vdw 860 3.5000 0.0660
-vdw 861 3.5000 0.0660
-vdw 862 3.5000 0.0660
-vdw 863 3.5000 0.0660
-vdw 864 3.5000 0.0660
-vdw 865 3.5000 0.0660
-vdw 866 4.0000 0.1000
-vdw 867 4.0000 0.1000
-vdw 868 4.0000 0.1000
-vdw 869 4.0000 0.1000
-vdw 870 2.5000 0.0300
-vdw 871 3.5000 0.0660
-vdw 872 3.5000 0.0660
-vdw 873 3.5000 0.0660
-vdw 874 3.5000 0.0660
-vdw 875 3.0800 0.7200
-vdw 876 4.1800 0.11779
-vdw 877 4.5100 0.0900
-vdw 878 5.1500 0.0700
-vdw 879 2.7000 0.018279
-vdw 880 3.3500 0.002772
-vdw 881 4.0600 0.000328
-vdw 882 4.3200 0.000171
-vdw 883 4.8200 0.000081
-vdw 884 2.9100 0.875044
-vdw 885 3.4700 0.449657
-vdw 886 3.8200 0.118226
-vdw 887 4.1800 0.047096
-vdw 888 3.5000 0.0660
-vdw 889 3.5000 0.0660
-vdw 890 3.5000 0.0660
-vdw 891 3.5000 0.0660
-vdw 892 2.5000 0.0300
-vdw 893 3.2500 0.1700
-vdw 894 3.5500 0.0700
-vdw 895 3.2500 0.1700
-vdw 896 3.5500 0.0700
-vdw 897 3.5500 0.0760
-vdw 898 3.5500 0.0760
-vdw 899 2.4200 0.0300
-vdw 900 3.3000 0.0860
-vdw 901 3.3000 0.0860
-vdw 902 3.3000 0.0860
-vdw 903 3.3000 0.0860
-vdw 904 3.3000 0.0860
-vdw 905 2.9600 0.2100
-vdw 906 3.5000 0.0660
-
-
- ##################################
- ## ##
- ## Bond Stretching Parameters ##
- ## ##
- ##################################
-
-
-bond 1 2 367.00 1.3800
-bond 1 3 420.00 1.3570
-bond 1 13 367.00 1.3600
-bond 1 19 450.00 1.2790
-bond 1 25 300.00 0.3000
-bond 1 47 420.00 1.3400
-bond 1 48 420.00 1.3540
-bond 1 82 420.00 1.3540
-bond 1 83 420.00 1.3540
-bond 1 84 420.00 1.3540
-bond 1 87 420.00 1.3540
-bond 1 88 420.00 1.3540
-bond 1 108 461.00 1.5700
-bond 2 2 260.00 1.5260
-bond 2 3 317.00 1.5220
-bond 2 5 386.00 1.4250
-bond 2 6 260.00 1.5260
-bond 2 10 260.00 1.5260
-bond 2 11 317.00 1.5000
-bond 2 12 317.00 1.5100
-bond 2 13 260.00 1.5260
-bond 2 14 317.00 1.5000
-bond 2 15 222.00 1.8100
-bond 2 16 222.00 1.8100
-bond 2 20 320.00 1.4250
-bond 2 24 337.00 1.4490
-bond 2 44 382.00 1.4480
-bond 2 48 317.00 1.5100
-bond 2 51 260.00 1.5260
-bond 2 53 367.00 1.4710
-bond 2 55 337.00 1.4630
-bond 2 80 317.00 1.4950
-bond 3 3 350.00 1.5100
-bond 3 4 570.00 1.2290
-bond 3 5 450.00 1.3640
-bond 3 6 317.00 1.5220
-bond 3 10 317.00 1.5220
-bond 3 12 469.00 1.4000
-bond 3 13 317.00 1.5220
-bond 3 19 400.00 1.4440
-bond 3 20 214.00 1.3270
-bond 3 21 300.00 1.7900
-bond 3 24 490.00 1.3350
-bond 3 44 317.00 1.5220
-bond 3 46 340.00 1.0900
-bond 3 47 410.00 1.4440
-bond 3 48 400.00 1.4900
-bond 3 50 385.00 1.4600
-bond 3 52 656.00 1.2500
-bond 3 56 457.00 1.3580
-bond 3 57 418.00 1.3880
-bond 3 60 447.00 1.4190
-bond 3 65 300.00 1.9800
-bond 3 84 400.00 1.4900
-bond 3 86 385.00 1.4600
-bond 3 105 424.00 1.3830
-bond 3 107 490.00 1.3350
-bond 4 25 553.00 0.3000
-bond 4 64 525.00 1.4800
-bond 4 89 570.00 1.2290
-bond 4 110 700.00 1.1710
-bond 5 6 386.00 1.4250
-bond 5 7 553.00 0.9450
-bond 5 10 386.00 1.4250
-bond 5 13 320.00 1.4100
-bond 5 20 250.00 1.4700
-bond 5 24 400.00 1.3800
-bond 5 25 340.00 0.3000
-bond 5 44 320.00 1.4500
-bond 5 47 450.00 1.3700
-bond 5 48 450.00 1.3640
-bond 5 51 320.00 1.3800
-bond 5 64 230.00 1.6100
-bond 5 79 450.00 1.6700
-bond 5 106 94.00 1.8000
-bond 5 108 374.00 1.6400
-bond 6 6 260.00 1.5260
-bond 6 10 260.00 1.5260
-bond 6 11 317.00 1.5000
-bond 6 13 260.00 1.5260
-bond 6 14 317.00 1.5000
-bond 6 15 222.00 1.8100
-bond 6 16 222.00 1.8100
-bond 6 20 320.00 1.4250
-bond 6 24 337.00 1.4490
-bond 6 44 382.00 1.4480
-bond 6 47 317.00 1.5100
-bond 6 51 260.00 1.5260
-bond 6 53 367.00 1.4710
-bond 6 55 337.00 1.4630
-bond 6 79 222.00 1.8100
-bond 6 105 337.00 1.4750
-bond 7 20 553.00 0.9450
-bond 7 25 340.00 0.1000
-bond 9 9 530.00 1.3400
-bond 9 11 530.00 1.3400
-bond 9 14 530.00 1.3400
-bond 10 10 260.00 1.5260
-bond 10 11 317.00 1.5000
-bond 10 14 317.00 1.5000
-bond 10 20 320.00 1.4250
-bond 10 24 337.00 1.4490
-bond 10 44 382.00 1.4480
-bond 10 105 337.00 1.4750
-bond 11 11 530.00 1.3400
-bond 11 13 317.00 1.5000
-bond 11 14 530.00 1.3400
-bond 11 79 222.00 1.7600
-bond 12 12 469.00 1.4000
-bond 12 48 469.00 1.4000
-bond 12 60 469.00 1.4000
-bond 12 81 469.00 1.4000
-bond 13 13 268.00 1.5290
-bond 13 14 317.00 1.5000
-bond 13 15 222.00 1.8100
-bond 13 16 222.00 1.8100
-bond 13 18 390.00 1.4300
-bond 13 19 390.00 1.4700
-bond 13 20 320.00 1.4100
-bond 13 21 245.00 1.7810
-bond 13 22 340.00 1.7900
-bond 13 24 337.00 1.4490
-bond 13 25 340.00 0.3000
-bond 13 44 382.00 1.4480
-bond 13 46 340.00 1.0900
-bond 13 47 317.00 1.5100
-bond 13 48 317.00 1.5100
-bond 13 50 317.00 1.5100
-bond 13 51 268.00 1.5290
-bond 13 53 367.00 1.4710
-bond 13 55 337.00 1.4630
-bond 13 56 337.00 1.4490
-bond 13 57 337.00 1.4750
-bond 13 60 317.00 1.5100
-bond 13 64 212.00 1.8430
-bond 13 65 245.00 1.9450
-bond 13 66 200.00 2.1900
-bond 13 79 340.00 1.7700
-bond 13 80 317.00 1.4950
-bond 13 83 317.00 1.5040
-bond 13 84 317.00 1.5040
-bond 13 85 317.00 1.5040
-bond 13 87 317.00 1.4950
-bond 13 90 337.00 1.4490
-bond 13 91 280.00 1.5100
-bond 13 95 532.80 1.4600
-bond 13 101 382.00 1.4480
-bond 13 102 375.00 1.4900
-bond 13 104 212.00 1.8200
-bond 13 105 337.00 1.4750
-bond 13 107 337.00 1.4490
-bond 13 108 187.00 1.8600
-bond 13 109 317.00 1.5100
-bond 14 14 530.00 1.3400
-bond 15 17 274.00 1.3360
-bond 15 48 250.00 1.7400
-bond 16 16 166.00 2.0380
-bond 16 19 300.00 1.6850
-bond 16 24 250.00 1.7300
-bond 16 25 340.00 0.5000
-bond 16 47 250.00 1.7600
-bond 16 48 250.00 1.7600
-bond 16 61 250.00 1.7300
-bond 16 82 250.00 1.7600
-bond 16 84 250.00 1.7400
-bond 16 91 222.00 1.8100
-bond 16 108 144.00 2.1500
-bond 17 25 340.00 0.1000
-bond 18 18 550.00 1.1200
-bond 18 19 650.00 1.1570
-bond 18 48 400.00 1.4100
-bond 18 56 550.00 1.2400
-bond 19 19 1150.00 1.2100
-bond 19 21 330.00 1.6370
-bond 19 46 420.00 1.0800
-bond 19 47 400.00 1.4260
-bond 19 48 400.00 1.4510
-bond 19 50 400.00 1.4260
-bond 19 65 330.00 1.7840
-bond 19 88 400.00 1.4510
-bond 19 91 400.00 1.4510
-bond 20 20 250.00 1.4700
-bond 20 21 200.00 1.6900
-bond 20 24 320.00 1.4500
-bond 20 25 340.00 0.3000
-bond 20 44 320.00 1.4500
-bond 20 47 450.00 1.3700
-bond 20 48 450.00 1.3640
-bond 20 51 320.00 1.3800
-bond 20 60 340.00 1.3600
-bond 20 61 462.00 1.3990
-bond 20 64 230.00 1.6100
-bond 20 82 462.00 1.3570
-bond 20 84 340.00 1.3600
-bond 20 108 374.00 1.6400
-bond 21 25 300.00 0.3000
-bond 21 47 300.00 1.7250
-bond 21 48 300.00 1.7250
-bond 21 82 300.00 1.7250
-bond 21 83 300.00 1.7250
-bond 21 84 300.00 1.7250
-bond 21 87 300.00 1.7250
-bond 21 88 300.00 1.7250
-bond 21 108 223.00 2.0200
-bond 22 23 700.00 1.5300
-bond 22 25 340.00 0.5000
-bond 23 25 340.00 0.3000
-bond 23 79 700.00 1.4400
-bond 24 25 367.00 0.3000
-bond 24 45 434.00 1.0100
-bond 24 48 427.00 1.3810
-bond 24 59 427.00 1.3810
-bond 24 79 434.00 1.6700
-bond 24 84 427.00 1.3810
-bond 24 88 427.00 1.3810
-bond 24 91 337.00 1.4490
-bond 24 103 500.00 1.2700
-bond 24 106 40.00 2.0500
-bond 25 25 340.00 0.3000
-bond 25 44 340.00 0.3000
-bond 25 45 340.00 0.1000
-bond 25 46 340.00 0.3000
-bond 25 47 340.00 0.3000
-bond 25 48 367.00 0.3000
-bond 25 49 340.00 0.3000
-bond 25 53 340.00 0.3000
-bond 25 56 367.00 0.3000
-bond 25 61 367.00 0.3000
-bond 25 65 300.00 0.3000
-bond 25 103 340.00 0.1000
-bond 31 32 600.00 0.9572
-bond 31 33 900.00 0.1500
-bond 31 106 40.00 2.0500
-bond 34 35 529.60 0.9572
-bond 36 37 600.00 0.9572
-bond 36 38 900.00 0.1750
-bond 39 40 600.00 0.9572
-bond 39 41 900.00 0.7000
-bond 42 43 600.00 1.0000
-bond 44 44 350.00 1.4450
-bond 44 45 434.00 1.0100
-bond 44 48 481.00 1.3400
-bond 44 79 340.00 1.7700
-bond 44 91 382.00 1.4480
-bond 44 108 266.00 1.7400
-bond 45 53 434.00 1.0100
-bond 45 55 434.00 1.0100
-bond 45 56 434.00 1.0100
-bond 45 57 434.00 1.0100
-bond 45 101 434.00 1.0100
-bond 45 105 434.00 1.0100
-bond 45 108 166.00 1.4800
-bond 46 47 340.00 1.0800
-bond 46 50 340.00 1.0800
-bond 46 51 340.00 1.0900
-bond 46 80 340.00 1.0800
-bond 46 91 340.00 1.0880
-bond 46 95 532.80 1.0840
-bond 46 108 166.00 1.4800
-bond 46 109 340.00 1.0800
-bond 47 47 549.00 1.3400
-bond 47 48 427.00 1.4330
-bond 47 50 549.00 1.3400
-bond 47 57 448.00 1.3650
-bond 47 58 367.00 1.0800
-bond 47 65 300.00 1.9000
-bond 47 66 250.00 2.0800
-bond 47 86 385.00 1.4600
-bond 47 91 317.00 1.5100
-bond 47 105 448.00 1.3650
-bond 47 110 700.00 1.3050
-bond 48 48 469.00 1.4000
-bond 48 49 367.00 1.0800
-bond 48 50 427.00 1.4330
-bond 48 53 400.00 1.4500
-bond 48 55 481.00 1.3400
-bond 48 56 483.00 1.3390
-bond 48 57 427.00 1.3810
-bond 48 60 469.00 1.4040
-bond 48 61 414.00 1.3910
-bond 48 64 220.00 1.7800
-bond 48 65 300.00 1.8700
-bond 48 66 250.00 2.0800
-bond 48 79 340.00 1.7700
-bond 48 81 469.00 1.4000
-bond 48 84 546.00 1.3670
-bond 48 86 469.00 1.4000
-bond 48 88 469.00 1.4210
-bond 48 91 317.00 1.4900
-bond 48 101 382.00 1.3850
-bond 48 102 400.00 1.4600
-bond 48 109 427.00 1.4330
-bond 49 59 367.00 1.0800
-bond 49 62 340.00 1.0800
-bond 49 82 367.00 1.0800
-bond 49 83 367.00 1.0800
-bond 49 84 367.00 1.0800
-bond 49 85 367.00 1.0800
-bond 49 87 367.00 1.0800
-bond 49 88 367.00 1.0800
-bond 50 50 385.00 1.4600
-bond 50 56 457.00 1.2900
-bond 50 84 549.00 1.3650
-bond 50 109 385.00 1.4600
-bond 51 105 337.00 1.4750
-bond 52 64 525.00 1.4800
-bond 53 54 434.00 1.0100
-bond 54 55 434.00 1.0100
-bond 55 59 481.00 1.3400
-bond 55 82 481.00 1.3400
-bond 56 56 500.00 1.3200
-bond 56 59 502.00 1.3240
-bond 56 60 461.00 1.3540
-bond 56 82 461.00 1.3540
-bond 56 86 483.00 1.3390
-bond 56 103 550.00 1.2100
-bond 56 109 457.00 1.2900
-bond 57 60 436.00 1.3740
-bond 57 61 400.00 1.3490
-bond 57 62 440.00 1.3710
-bond 57 81 428.00 1.3800
-bond 57 82 477.00 1.3430
-bond 57 84 427.00 1.3810
-bond 57 85 427.00 1.3810
-bond 57 86 385.00 1.4400
-bond 58 83 367.00 1.0800
-bond 58 84 367.00 1.0800
-bond 59 63 367.00 1.0800
-bond 60 60 520.00 1.3700
-bond 60 61 414.00 1.3910
-bond 60 80 388.00 1.4590
-bond 60 81 447.00 1.4190
-bond 60 87 469.00 1.4240
-bond 60 105 436.00 1.3740
-bond 61 61 400.00 1.2800
-bond 61 62 529.00 1.3040
-bond 61 82 488.00 1.3350
-bond 61 83 410.00 1.3940
-bond 61 84 410.00 1.3940
-bond 61 88 410.00 1.3200
-bond 62 63 367.00 1.0800
-bond 62 105 440.00 1.3710
-bond 63 82 367.00 1.0800
-bond 64 108 108.00 2.2500
-bond 65 82 300.00 1.8700
-bond 65 83 300.00 1.8700
-bond 65 84 300.00 1.8700
-bond 65 87 300.00 1.8700
-bond 65 88 300.00 1.8700
-bond 65 108 151.00 2.1900
-bond 66 82 250.00 2.0800
-bond 66 83 250.00 2.0800
-bond 66 84 250.00 2.0800
-bond 66 87 250.00 2.0800
-bond 66 88 250.00 2.0800
-bond 66 108 108.00 2.4400
-bond 77 78 500.00 1.8000
-bond 80 84 546.00 1.3520
-bond 82 86 385.00 1.4600
-bond 82 87 520.00 1.3700
-bond 83 84 520.00 1.3700
-bond 83 86 385.00 1.4600
-bond 84 84 512.00 1.3750
-bond 84 86 385.00 1.4600
-bond 84 87 546.00 1.3670
-bond 84 88 520.00 1.3700
-bond 85 85 520.00 1.3700
-bond 86 86 385.00 1.4600
-bond 86 87 385.00 1.4600
-bond 86 88 385.00 1.4600
-bond 87 87 469.00 1.4240
-bond 87 88 469.00 1.4240
-bond 89 90 490.00 1.3350
-bond 89 91 317.00 1.5220
-bond 90 91 337.00 1.4490
-bond 91 91 260.00 1.5200
-bond 102 103 550.00 1.2250
-bond 108 108 94.00 2.3200
-bond 109 109 549.00 1.3450
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 25 1 25 33.00 109.47
-angle 1 2 2 50.00 109.50
-angle 2 2 2 63.00 112.40
-angle 2 2 3 63.00 112.40
-angle 2 2 5 80.00 109.50
-angle 2 2 6 63.00 112.40
-angle 6 2 6 63.00 112.40
-angle 5 2 6 80.00 109.50
-angle 2 2 10 63.00 112.40
-angle 3 2 10 63.00 112.40
-angle 6 2 10 63.00 112.40
-angle 10 2 10 63.00 112.40
-angle 5 2 10 80.00 109.50
-angle 10 2 12 63.00 114.00
-angle 6 2 13 63.00 112.40
-angle 10 2 15 50.00 108.60
-angle 2 2 16 50.00 114.70
-angle 10 2 16 50.00 114.70
-angle 2 2 20 80.00 109.50
-angle 6 2 20 80.00 109.50
-angle 10 2 20 80.00 109.50
-angle 3 2 24 80.00 110.30
-angle 2 2 24 80.00 111.20
-angle 2 2 44 56.20 109.47
-angle 6 2 44 56.20 109.47
-angle 10 2 44 56.20 109.47
-angle 13 2 44 56.20 109.47
-angle 3 2 44 80.00 111.20
-angle 2 2 48 63.00 112.40
-angle 10 2 48 63.00 114.00
-angle 2 2 51 63.00 112.40
-angle 6 2 51 63.00 112.40
-angle 2 2 53 80.00 111.20
-angle 2 2 55 80.00 111.20
-angle 10 2 80 63.00 115.60
-angle 2 3 4 80.00 120.40
-angle 1 3 4 80.00 121.00
-angle 3 3 4 80.00 121.40
-angle 4 3 4 80.00 126.00
-angle 4 3 5 80.00 121.00
-angle 4 3 6 80.00 120.40
-angle 5 3 10 70.00 115.00
-angle 4 3 10 80.00 120.40
-angle 5 3 12 70.00 120.00
-angle 12 3 12 85.00 120.00
-angle 5 3 13 70.00 108.00
-angle 13 3 13 70.00 116.00
-angle 1 3 13 80.00 111.00
-angle 3 3 13 80.00 117.20
-angle 4 3 13 80.00 120.40
-angle 10 3 20 81.00 111.40
-angle 13 3 20 81.00 111.40
-angle 4 3 20 83.00 123.40
-angle 13 3 21 75.00 109.00
-angle 4 3 21 75.00 119.00
-angle 24 3 24 70.00 114.20
-angle 2 3 24 70.00 116.60
-angle 3 3 24 70.00 116.60
-angle 6 3 24 70.00 116.60
-angle 10 3 24 70.00 116.60
-angle 13 3 24 70.00 116.60
-angle 4 3 24 80.00 122.90
-angle 20 3 24 81.00 111.40
-angle 13 3 44 70.00 116.00
-angle 4 3 44 80.00 120.40
-angle 13 3 46 35.00 115.00
-angle 46 3 46 35.00 115.00
-angle 4 3 46 35.00 123.00
-angle 24 3 46 40.00 114.00
-angle 5 3 46 40.00 115.00
-angle 20 3 46 40.00 115.00
-angle 24 3 47 70.00 115.50
-angle 4 3 47 80.00 125.30
-angle 46 3 48 35.00 115.00
-angle 24 3 48 70.00 115.50
-angle 13 3 48 70.00 116.00
-angle 5 3 48 70.00 120.00
-angle 4 3 48 80.00 120.40
-angle 20 3 48 81.00 111.40
-angle 48 3 48 85.00 120.00
-angle 13 3 50 70.00 116.00
-angle 46 3 50 80.00 116.00
-angle 4 3 50 80.00 124.00
-angle 10 3 52 65.00 117.00
-angle 2 3 52 70.00 117.00
-angle 6 3 52 70.00 117.00
-angle 13 3 52 70.00 117.00
-angle 48 3 52 70.00 117.00
-angle 4 3 52 80.00 126.00
-angle 52 3 52 80.00 126.00
-angle 46 3 56 35.00 116.00
-angle 46 3 56 35.00 122.00
-angle 4 3 56 80.00 122.50
-angle 47 3 57 70.00 114.10
-angle 56 3 57 70.00 118.60
-angle 57 3 57 70.00 118.60
-angle 4 3 57 80.00 120.60
-angle 24 3 60 70.00 111.30
-angle 57 3 60 70.00 111.30
-angle 4 3 60 80.00 128.80
-angle 13 3 65 75.00 109.00
-angle 4 3 65 75.00 119.00
-angle 44 3 84 70.00 116.00
-angle 4 3 84 80.00 120.40
-angle 4 3 87 80.00 128.20
-angle 57 3 105 70.00 115.40
-angle 56 3 105 70.00 118.60
-angle 4 3 105 80.00 120.90
-angle 13 3 107 70.00 116.60
-angle 4 3 107 80.00 122.90
-angle 25 4 25 10.00 117.00
-angle 3 4 25 35.00 113.00
-angle 3 5 7 35.00 113.00
-angle 2 5 7 55.00 108.50
-angle 6 5 7 55.00 108.50
-angle 7 5 10 55.00 108.50
-angle 7 5 13 55.00 108.50
-angle 7 5 24 49.00 105.40
-angle 25 5 25 5.00 109.47
-angle 7 5 25 10.00 109.47
-angle 13 5 25 10.00 109.47
-angle 7 5 47 35.00 109.00
-angle 25 5 48 10.00 109.47
-angle 7 5 48 35.00 113.00
-angle 7 5 51 55.00 108.50
-angle 7 5 64 55.00 108.50
-angle 13 5 64 100.00 120.50
-angle 7 5 79 74.00 110.00
-angle 7 5 106 100.00 126.00
-angle 5 7 25 10.00 109.47
-angle 25 7 25 33.00 109.47
-angle 2 10 2 63.00 112.40
-angle 2 10 3 63.00 111.10
-angle 2 10 5 80.00 109.50
-angle 3 10 6 63.00 111.10
-angle 6 10 6 63.00 111.50
-angle 2 10 6 63.00 112.40
-angle 5 10 6 80.00 109.50
-angle 3 10 10 63.00 111.10
-angle 2 10 10 63.00 111.50
-angle 6 10 10 63.00 111.50
-angle 10 10 10 63.00 111.50
-angle 5 10 10 80.00 109.50
-angle 2 10 20 80.00 109.50
-angle 6 10 20 80.00 109.50
-angle 10 10 20 80.00 109.50
-angle 3 10 24 63.00 110.10
-angle 6 10 24 80.00 109.50
-angle 2 10 24 80.00 109.70
-angle 10 10 24 80.00 109.70
-angle 2 10 44 56.20 109.47
-angle 6 10 44 56.20 109.47
-angle 10 10 44 56.20 109.47
-angle 13 10 44 56.20 109.47
-angle 3 10 44 80.00 109.70
-angle 2 10 48 63.00 112.40
-angle 20 10 48 80.00 109.50
-angle 2 10 105 80.00 109.50
-angle 10 10 105 80.00 109.50
-angle 20 10 105 80.00 109.50
-angle 2 11 2 70.00 124.00
-angle 2 11 6 70.00 124.00
-angle 6 11 6 70.00 124.00
-angle 2 11 9 70.00 118.00
-angle 6 11 9 70.00 118.00
-angle 9 11 10 70.00 118.00
-angle 2 11 10 70.00 124.00
-angle 6 11 10 70.00 124.00
-angle 10 11 10 70.00 124.00
-angle 2 11 11 70.00 118.00
-angle 6 11 11 70.00 118.00
-angle 9 11 11 70.00 118.00
-angle 10 11 11 70.00 118.00
-angle 11 11 11 70.00 118.00
-angle 9 11 13 70.00 118.00
-angle 11 11 13 70.00 118.00
-angle 2 11 13 70.00 124.00
-angle 6 11 13 70.00 124.00
-angle 10 11 13 70.00 124.00
-angle 13 11 13 70.00 124.00
-angle 9 11 14 70.00 118.00
-angle 11 11 14 70.00 118.00
-angle 9 11 79 70.00 118.00
-angle 2 12 12 70.00 120.00
-angle 3 12 12 85.00 120.00
-angle 12 12 12 85.00 120.00
-angle 12 12 48 85.00 120.00
-angle 12 12 60 85.00 120.00
-angle 12 12 81 85.00 120.00
-angle 1 13 1 77.00 109.10
-angle 2 13 2 40.00 109.50
-angle 1 13 3 50.00 109.50
-angle 2 13 3 63.00 111.10
-angle 3 13 3 63.00 111.10
-angle 2 13 6 40.00 109.50
-angle 6 13 6 40.00 109.50
-angle 3 13 6 63.00 109.50
-angle 1 13 13 50.00 109.50
-angle 5 13 13 50.00 109.50
-angle 13 13 13 58.35 112.70
-angle 3 13 13 63.00 111.10
-angle 13 13 15 50.00 108.60
-angle 13 13 16 50.00 114.70
-angle 13 13 19 58.35 112.70
-angle 3 13 20 50.00 109.50
-angle 13 13 20 50.00 109.50
-angle 3 13 21 69.00 109.80
-angle 13 13 21 69.00 109.80
-angle 21 13 21 78.00 111.70
-angle 13 13 22 50.00 108.60
-angle 20 13 24 50.00 109.50
-angle 3 13 24 63.00 110.10
-angle 2 13 24 80.00 109.70
-angle 13 13 24 80.00 109.70
-angle 16 13 44 50.00 114.70
-angle 2 13 44 56.20 109.47
-angle 6 13 44 56.20 109.47
-angle 10 13 44 56.20 109.47
-angle 13 13 44 56.20 109.47
-angle 3 13 44 80.00 111.20
-angle 46 13 46 33.00 107.80
-angle 18 13 46 35.00 108.50
-angle 19 13 46 35.00 108.50
-angle 2 13 46 35.00 109.50
-angle 3 13 46 35.00 109.50
-angle 5 13 46 35.00 109.50
-angle 15 13 46 35.00 109.50
-angle 16 13 46 35.00 109.50
-angle 20 13 46 35.00 109.50
-angle 22 13 46 35.00 109.50
-angle 24 13 46 35.00 109.50
-angle 44 13 46 35.00 109.50
-angle 13 13 46 37.50 110.70
-angle 1 13 46 40.00 107.00
-angle 21 13 46 51.00 107.60
-angle 46 13 47 35.00 109.50
-angle 1 13 47 50.00 109.50
-angle 13 13 47 63.00 111.10
-angle 47 13 47 63.00 112.40
-angle 46 13 48 35.00 109.50
-angle 47 13 48 40.00 109.50
-angle 48 13 48 40.00 109.50
-angle 1 13 48 50.00 109.50
-angle 5 13 48 50.00 109.50
-angle 20 13 48 50.00 109.50
-angle 16 13 48 50.00 114.70
-angle 3 13 48 63.00 112.00
-angle 2 13 48 63.00 114.00
-angle 13 13 48 63.00 114.00
-angle 44 13 48 80.00 111.20
-angle 46 13 50 35.00 109.50
-angle 46 13 51 37.50 110.70
-angle 5 13 51 50.00 109.50
-angle 13 13 51 58.35 112.70
-angle 46 13 53 35.00 109.50
-angle 3 13 53 80.00 111.20
-angle 13 13 53 80.00 111.20
-angle 46 13 55 35.00 109.50
-angle 13 13 55 80.00 111.20
-angle 46 13 56 35.00 109.50
-angle 3 13 56 63.00 110.10
-angle 13 13 56 65.00 109.00
-angle 46 13 57 35.00 109.50
-angle 48 13 57 80.00 111.20
-angle 46 13 60 35.00 109.50
-angle 13 13 60 63.00 114.00
-angle 46 13 64 41.00 109.50
-angle 13 13 64 43.00 109.50
-angle 48 13 64 43.00 109.50
-angle 46 13 65 51.00 107.60
-angle 3 13 65 69.00 109.80
-angle 13 13 65 69.00 110.00
-angle 48 13 65 69.00 110.00
-angle 65 13 65 78.00 111.70
-angle 46 13 66 75.00 111.00
-angle 13 13 66 75.00 112.00
-angle 46 13 79 35.00 109.50
-angle 13 13 79 50.00 108.60
-angle 1 13 79 50.00 109.50
-angle 46 13 80 35.00 109.50
-angle 13 13 80 63.00 115.60
-angle 46 13 83 35.00 109.50
-angle 13 13 83 63.00 114.00
-angle 46 13 84 35.00 109.50
-angle 16 13 84 50.00 114.70
-angle 13 13 84 63.00 114.00
-angle 46 13 85 35.00 109.50
-angle 13 13 85 63.00 114.00
-angle 46 13 87 35.00 109.50
-angle 13 13 87 63.00 115.60
-angle 46 13 90 35.00 109.50
-angle 13 13 90 80.00 110.00
-angle 3 13 90 80.00 113.00
-angle 46 13 91 37.50 110.70
-angle 46 13 95 35.00 105.00
-angle 13 13 95 63.00 105.00
-angle 46 13 101 35.00 109.50
-angle 13 13 101 80.00 111.20
-angle 46 13 102 35.00 105.00
-angle 13 13 102 63.00 111.10
-angle 46 13 104 41.00 109.50
-angle 13 13 104 43.00 109.50
-angle 46 13 105 35.00 109.50
-angle 13 13 105 50.00 109.50
-angle 20 13 105 50.00 109.50
-angle 46 13 107 35.00 109.50
-angle 13 13 107 80.00 109.70
-angle 46 13 108 35.00 109.50
-angle 13 13 108 60.00 112.00
-angle 2 14 2 70.00 124.00
-angle 2 14 6 70.00 124.00
-angle 6 14 6 70.00 124.00
-angle 2 14 9 70.00 118.00
-angle 6 14 9 70.00 118.00
-angle 9 14 10 70.00 118.00
-angle 2 14 10 70.00 124.00
-angle 6 14 10 70.00 124.00
-angle 10 14 10 70.00 124.00
-angle 2 14 11 70.00 118.00
-angle 6 14 11 70.00 118.00
-angle 9 14 11 70.00 118.00
-angle 10 14 11 70.00 118.00
-angle 11 14 11 70.00 118.00
-angle 9 14 13 70.00 118.00
-angle 11 14 13 70.00 118.00
-angle 2 14 13 70.00 124.00
-angle 6 14 13 70.00 124.00
-angle 10 14 13 70.00 124.00
-angle 13 14 13 70.00 124.00
-angle 2 14 14 70.00 118.00
-angle 6 14 14 70.00 118.00
-angle 9 14 14 70.00 118.00
-angle 10 14 14 70.00 118.00
-angle 11 14 14 70.00 118.00
-angle 13 14 14 70.00 118.00
-angle 14 14 14 70.00 118.00
-angle 17 15 17 35.00 92.07
-angle 2 15 17 44.00 96.00
-angle 6 15 17 44.00 96.00
-angle 13 15 17 44.00 96.00
-angle 25 15 25 5.00 109.47
-angle 13 15 25 10.00 109.47
-angle 33 15 33 10.00 160.00
-angle 2 15 33 150.00 96.70
-angle 6 15 33 150.00 96.70
-angle 13 15 33 150.00 96.70
-angle 17 15 33 150.00 96.70
-angle 17 15 48 50.00 96.00
-angle 2 16 6 62.00 98.90
-angle 13 16 13 62.00 98.90
-angle 2 16 16 68.00 103.70
-angle 6 16 16 68.00 103.70
-angle 13 16 16 68.00 103.70
-angle 13 16 19 65.00 100.00
-angle 25 16 25 5.00 109.47
-angle 13 16 25 10.00 109.47
-angle 33 16 33 10.00 160.00
-angle 2 16 33 150.00 96.70
-angle 6 16 33 150.00 96.70
-angle 13 16 33 150.00 96.70
-angle 16 16 33 150.00 96.70
-angle 13 16 48 62.00 104.20
-angle 47 16 48 62.00 104.20
-angle 24 16 60 74.00 92.40
-angle 25 16 61 10.00 130.00
-angle 25 16 82 10.00 130.00
-angle 60 16 82 74.00 97.00
-angle 25 16 84 10.00 130.00
-angle 82 16 84 74.00 90.00
-angle 60 16 84 74.00 97.00
-angle 84 16 84 74.00 97.00
-angle 13 16 91 62.00 94.00
-angle 15 17 25 10.00 109.47
-angle 25 17 25 33.00 109.47
-angle 13 18 19 150.00 180.00
-angle 19 18 48 170.00 180.00
-angle 18 18 56 100.00 180.00
-angle 13 19 18 150.00 180.00
-angle 16 19 19 140.00 180.00
-angle 13 19 19 150.00 180.00
-angle 18 19 25 10.00 90.00
-angle 19 19 46 112.00 180.00
-angle 18 19 47 150.00 180.00
-angle 19 19 47 160.00 180.00
-angle 18 19 48 150.00 180.00
-angle 19 19 48 160.00 180.00
-angle 19 19 50 160.00 180.00
-angle 18 19 55 150.00 180.00
-angle 18 19 88 150.00 180.00
-angle 2 20 2 100.00 111.80
-angle 2 20 3 83.00 116.90
-angle 3 20 6 83.00 116.90
-angle 2 20 6 100.00 111.80
-angle 2 20 7 55.00 108.50
-angle 7 20 10 55.00 108.50
-angle 3 20 10 83.00 116.90
-angle 10 20 10 100.00 111.80
-angle 13 20 13 60.00 109.50
-angle 3 20 13 83.00 116.90
-angle 25 20 25 5.00 109.47
-angle 13 20 25 10.00 109.47
-angle 13 20 47 75.00 111.00
-angle 25 20 48 10.00 109.47
-angle 13 20 48 75.00 111.00
-angle 47 20 48 75.00 111.00
-angle 48 20 48 75.00 111.00
-angle 3 20 48 83.00 116.90
-angle 2 20 48 100.00 111.80
-angle 13 20 51 60.00 109.50
-angle 2 20 51 100.00 113.00
-angle 6 20 51 100.00 113.00
-angle 10 20 51 100.00 113.00
-angle 24 20 60 70.00 104.50
-angle 25 20 61 10.00 125.00
-angle 2 20 64 100.00 120.50
-angle 6 20 64 100.00 120.50
-angle 10 20 64 100.00 120.50
-angle 13 20 64 100.00 120.50
-angle 48 20 64 100.00 120.50
-angle 64 20 64 100.00 120.50
-angle 25 20 82 10.00 125.00
-angle 60 20 82 70.00 106.50
-angle 82 20 82 70.00 107.00
-angle 25 20 84 10.00 125.00
-angle 82 20 84 70.00 104.00
-angle 60 20 84 70.00 106.50
-angle 84 20 84 70.00 106.50
-angle 61 20 84 70.00 108.90
-angle 108 20 108 20.00 145.00
-angle 13 20 108 40.00 130.00
-angle 25 21 25 33.00 109.47
-angle 13 22 13 62.00 96.00
-angle 13 22 23 74.00 107.00
-angle 23 22 25 10.00 90.00
-angle 2 24 3 50.00 121.90
-angle 3 24 3 70.00 126.40
-angle 3 24 5 46.00 115.70
-angle 2 24 6 50.00 121.90
-angle 3 24 6 50.00 121.90
-angle 2 24 10 50.00 118.00
-angle 3 24 10 50.00 121.90
-angle 13 24 13 50.00 118.00
-angle 3 24 13 50.00 121.90
-angle 3 24 16 70.00 112.00
-angle 3 24 20 70.00 108.60
-angle 3 24 25 10.00 109.50
-angle 25 24 45 10.00 100.00
-angle 5 24 45 35.00 110.20
-angle 3 24 45 35.00 119.80
-angle 45 24 45 35.00 120.00
-angle 2 24 45 38.00 118.40
-angle 6 24 45 38.00 118.40
-angle 10 24 45 38.00 118.40
-angle 13 24 45 38.00 118.40
-angle 45 24 48 35.00 119.80
-angle 13 24 48 50.00 118.00
-angle 3 24 48 50.00 121.90
-angle 48 24 48 70.00 118.00
-angle 54 24 54 35.00 120.00
-angle 45 24 59 35.00 118.00
-angle 3 24 59 70.00 125.20
-angle 13 24 79 50.00 120.00
-angle 45 24 79 100.00 111.00
-angle 45 24 84 35.00 119.80
-angle 48 24 84 70.00 118.00
-angle 16 24 86 70.00 117.00
-angle 45 24 87 35.00 119.80
-angle 48 24 87 70.00 118.00
-angle 45 24 88 35.00 119.80
-angle 48 24 88 70.00 118.00
-angle 45 24 91 40.00 113.00
-angle 3 24 91 55.00 128.00
-angle 48 24 103 70.00 121.00
-angle 3 24 106 20.00 126.00
-angle 25 25 25 33.00 109.47
-angle 32 31 32 75.00 104.52
-angle 32 31 33 50.00 52.26
-angle 35 34 35 34.05 104.52
-angle 37 36 37 75.00 109.50
-angle 37 36 38 50.00 54.75
-angle 40 39 40 75.00 104.52
-angle 41 39 41 50.00 109.47
-angle 40 39 41 50.00 110.6948
-angle 43 42 43 75.00 109.47
-angle 2 44 2 51.80 107.20
-angle 2 44 6 51.80 107.20
-angle 6 44 6 51.80 107.20
-angle 2 44 10 51.80 107.20
-angle 6 44 10 51.80 107.20
-angle 10 44 10 51.80 107.20
-angle 2 44 13 51.80 107.20
-angle 6 44 13 51.80 107.20
-angle 10 44 13 51.80 107.20
-angle 13 44 13 51.80 107.20
-angle 3 44 13 63.00 111.10
-angle 25 44 45 10.00 100.00
-angle 13 44 45 35.00 109.50
-angle 2 44 45 43.20 108.10
-angle 6 44 45 43.20 108.10
-angle 10 44 45 43.20 108.10
-angle 45 44 45 43.60 106.40
-angle 25 44 48 10.00 109.50
-angle 45 44 48 35.00 116.00
-angle 13 44 48 50.00 116.00
-angle 48 44 48 50.00 116.00
-angle 3 44 48 63.00 112.00
-angle 45 44 79 35.00 115.00
-angle 13 44 79 50.00 108.60
-angle 48 44 79 50.00 108.60
-angle 48 44 91 50.00 109.50
-angle 25 45 25 33.00 109.47
-angle 25 45 44 10.00 109.50
-angle 25 46 25 33.00 109.47
-angle 13 46 25 37.50 109.47
-angle 1 47 1 80.00 108.00
-angle 1 47 3 80.00 121.50
-angle 3 47 6 85.00 119.70
-angle 3 47 13 70.00 119.70
-angle 13 47 13 70.00 130.00
-angle 25 47 46 10.00 90.00
-angle 20 47 46 35.00 114.50
-angle 13 47 46 35.00 117.00
-angle 46 47 46 35.00 117.00
-angle 3 47 46 35.00 119.70
-angle 19 47 46 35.00 120.00
-angle 1 47 46 50.00 112.00
-angle 21 47 46 60.00 114.00
-angle 25 47 47 2.00 90.00
-angle 46 47 47 35.00 120.00
-angle 5 47 47 70.00 123.00
-angle 20 47 47 70.00 123.00
-angle 13 47 47 70.00 124.00
-angle 19 47 47 70.00 124.00
-angle 21 47 47 75.00 121.50
-angle 1 47 47 80.00 121.50
-angle 16 47 47 85.00 119.40
-angle 3 47 47 85.00 120.70
-angle 46 47 48 35.00 123.30
-angle 47 47 48 85.00 117.00
-angle 13 47 48 85.00 119.70
-angle 25 47 50 2.00 90.00
-angle 46 47 50 35.00 120.00
-angle 5 47 50 70.00 123.00
-angle 20 47 50 70.00 123.00
-angle 13 47 50 70.00 124.00
-angle 46 47 57 35.00 119.10
-angle 13 47 57 70.00 120.00
-angle 20 47 57 70.00 120.00
-angle 47 47 57 70.00 121.20
-angle 16 47 57 85.00 119.40
-angle 57 47 58 35.00 119.10
-angle 47 47 58 35.00 119.70
-angle 46 47 65 60.00 114.00
-angle 47 47 65 75.00 120.00
-angle 46 47 91 35.00 135.00
-angle 3 47 91 70.00 119.70
-angle 47 47 91 70.00 124.00
-angle 46 47 105 35.00 119.10
-angle 58 47 105 35.00 119.10
-angle 13 47 105 70.00 120.00
-angle 20 47 105 70.00 120.00
-angle 47 47 105 70.00 121.20
-angle 16 47 105 85.00 119.40
-angle 46 47 110 40.00 121.00
-angle 13 47 110 80.00 122.00
-angle 48 47 110 80.00 122.00
-angle 1 47 110 80.00 125.00
-angle 2 48 12 70.00 120.00
-angle 12 48 12 85.00 120.00
-angle 3 48 13 70.00 119.70
-angle 25 48 48 10.00 90.00
-angle 48 48 48 63.00 120.00
-angle 2 48 48 70.00 120.00
-angle 5 48 48 70.00 120.00
-angle 10 48 48 70.00 120.00
-angle 13 48 48 70.00 120.00
-angle 15 48 48 70.00 120.00
-angle 19 48 48 70.00 120.00
-angle 20 48 48 70.00 120.00
-angle 24 48 48 70.00 120.00
-angle 44 48 48 70.00 120.00
-angle 47 48 48 70.00 124.00
-angle 21 48 48 75.00 120.00
-angle 1 48 48 80.00 120.00
-angle 18 48 48 80.00 120.00
-angle 16 48 48 85.00 119.40
-angle 3 48 48 85.00 120.00
-angle 25 48 49 2.00 90.00
-angle 24 48 49 35.00 119.10
-angle 3 48 49 35.00 120.00
-angle 48 48 49 35.00 120.00
-angle 48 48 50 70.00 124.00
-angle 48 48 53 70.00 120.00
-angle 55 48 55 70.00 120.00
-angle 47 48 55 70.00 120.10
-angle 48 48 55 70.00 120.10
-angle 49 48 56 35.00 116.00
-angle 13 48 56 70.00 116.00
-angle 44 48 56 70.00 116.00
-angle 55 48 56 70.00 119.30
-angle 5 48 56 70.00 120.00
-angle 47 48 56 70.00 121.50
-angle 50 48 56 70.00 121.50
-angle 48 48 56 70.00 124.00
-angle 21 48 56 75.00 120.00
-angle 49 48 57 35.00 120.00
-angle 48 48 57 70.00 108.70
-angle 55 48 57 70.00 116.00
-angle 13 48 57 70.00 120.00
-angle 47 48 57 70.00 121.50
-angle 56 48 57 70.00 123.30
-angle 49 48 60 35.00 120.00
-angle 48 48 60 63.00 120.00
-angle 57 48 60 70.00 108.70
-angle 56 48 60 70.00 117.30
-angle 55 48 60 70.00 123.50
-angle 2 48 60 70.00 128.60
-angle 13 48 60 70.00 128.60
-angle 49 48 61 35.00 119.10
-angle 48 48 61 70.00 108.70
-angle 57 48 61 70.00 123.30
-angle 48 48 64 85.00 119.40
-angle 48 48 65 75.00 120.00
-angle 48 48 66 75.00 120.00
-angle 48 48 79 85.00 119.40
-angle 49 48 81 35.00 120.00
-angle 48 48 81 85.00 120.00
-angle 49 48 84 35.00 126.90
-angle 60 48 84 63.00 106.40
-angle 48 48 84 70.00 107.40
-angle 49 48 86 35.00 120.00
-angle 48 48 86 63.00 120.00
-angle 56 48 86 70.00 124.00
-angle 49 48 88 35.00 128.20
-angle 101 48 101 70.00 111.80
-angle 56 48 101 70.00 124.10
-angle 48 48 102 85.00 120.00
-angle 48 48 109 70.00 124.00
-angle 25 50 46 10.00 90.00
-angle 19 50 46 35.00 120.00
-angle 25 50 47 2.00 90.00
-angle 46 50 47 35.00 120.00
-angle 3 50 47 70.00 118.70
-angle 13 50 47 70.00 124.00
-angle 46 50 48 35.00 123.30
-angle 47 50 48 85.00 117.00
-angle 25 50 50 2.00 90.00
-angle 46 50 50 35.00 120.00
-angle 13 50 50 70.00 124.00
-angle 47 50 50 70.00 124.00
-angle 50 50 84 35.00 106.00
-angle 46 50 84 35.00 122.00
-angle 46 50 109 35.00 120.00
-angle 13 50 109 70.00 124.00
-angle 47 50 109 70.00 124.00
-angle 6 51 6 40.00 109.50
-angle 5 51 13 50.00 109.50
-angle 13 51 20 50.00 109.50
-angle 2 51 20 80.00 109.50
-angle 6 51 20 80.00 109.50
-angle 5 51 20 92.60 111.55
-angle 20 51 20 92.60 111.55
-angle 46 51 46 33.00 109.50
-angle 5 51 46 35.00 109.50
-angle 20 51 46 35.00 109.50
-angle 13 51 46 37.50 110.70
-angle 46 51 105 35.00 109.50
-angle 13 51 105 50.00 109.50
-angle 20 51 105 50.00 109.50
-angle 13 53 13 50.00 113.00
-angle 13 53 25 10.00 100.00
-angle 45 53 45 43.60 109.50
-angle 25 53 48 10.00 100.00
-angle 13 53 48 55.00 114.00
-angle 2 53 54 35.00 109.50
-angle 6 53 54 35.00 109.50
-angle 13 53 54 35.00 109.50
-angle 48 53 54 35.00 109.50
-angle 54 53 54 35.00 109.50
-angle 25 53 82 10.00 100.00
-angle 13 55 13 50.00 118.00
-angle 45 55 45 35.00 113.00
-angle 13 55 45 35.00 118.40
-angle 45 55 48 35.00 120.00
-angle 2 55 48 50.00 123.20
-angle 6 55 48 50.00 123.20
-angle 13 55 48 50.00 123.20
-angle 2 55 54 35.00 118.40
-angle 13 55 54 35.00 118.40
-angle 48 55 54 35.00 120.00
-angle 54 55 54 35.00 120.00
-angle 45 55 59 35.00 120.00
-angle 3 56 13 70.00 120.50
-angle 13 56 18 70.00 120.00
-angle 25 56 48 5.00 120.00
-angle 45 56 48 35.00 113.00
-angle 13 56 48 50.00 118.00
-angle 48 56 48 70.00 117.00
-angle 3 56 48 70.00 120.50
-angle 13 56 56 70.00 117.00
-angle 48 56 56 70.00 117.00
-angle 25 56 59 5.00 119.80
-angle 48 56 59 70.00 118.60
-angle 59 56 59 70.00 118.60
-angle 59 56 60 70.00 111.00
-angle 48 56 60 70.00 112.20
-angle 59 56 82 70.00 111.00
-angle 48 56 86 70.00 117.00
-angle 13 56 103 70.00 114.00
-angle 3 57 3 70.00 126.40
-angle 3 57 45 35.00 116.80
-angle 45 57 47 35.00 119.20
-angle 3 57 47 70.00 121.60
-angle 45 57 48 35.00 118.00
-angle 3 57 48 70.00 125.20
-angle 48 57 48 70.00 125.20
-angle 45 57 60 30.00 125.80
-angle 13 57 60 70.00 125.80
-angle 60 57 61 56.00 113.10
-angle 45 57 61 56.00 118.40
-angle 13 57 61 70.00 118.40
-angle 48 57 61 70.00 118.40
-angle 45 57 62 30.00 128.80
-angle 60 57 62 70.00 105.40
-angle 48 57 62 70.00 109.80
-angle 13 57 62 70.00 128.80
-angle 45 57 81 35.00 123.10
-angle 45 57 82 35.00 120.00
-angle 61 57 82 56.00 113.10
-angle 60 57 82 70.00 109.80
-angle 45 57 84 35.00 120.00
-angle 61 57 84 56.00 113.10
-angle 60 57 84 70.00 109.80
-angle 82 57 84 70.00 109.80
-angle 84 57 84 70.00 109.80
-angle 81 57 84 70.00 111.60
-angle 45 57 85 35.00 120.00
-angle 82 57 85 70.00 109.80
-angle 24 59 55 70.00 116.00
-angle 49 59 56 35.00 115.45
-angle 13 59 56 70.00 115.50
-angle 55 59 56 70.00 119.30
-angle 24 59 56 70.00 123.30
-angle 56 59 56 70.00 129.10
-angle 56 59 63 35.00 115.45
-angle 13 60 48 70.00 120.00
-angle 48 60 48 85.00 134.90
-angle 56 60 57 70.00 126.20
-angle 57 60 60 70.00 106.20
-angle 20 60 60 70.00 110.60
-angle 16 60 60 70.00 111.00
-angle 13 60 60 70.00 120.00
-angle 24 60 60 70.00 127.70
-angle 56 60 60 70.00 127.70
-angle 48 60 60 85.00 117.30
-angle 3 60 60 85.00 119.20
-angle 60 60 61 70.00 111.00
-angle 24 60 61 70.00 126.20
-angle 3 60 61 70.00 130.00
-angle 48 60 61 70.00 132.40
-angle 12 60 80 85.00 134.90
-angle 48 60 80 85.00 134.90
-angle 80 60 81 85.00 108.80
-angle 12 60 81 85.00 116.20
-angle 48 60 81 85.00 116.20
-angle 3 60 84 70.00 130.00
-angle 60 60 87 70.00 107.30
-angle 57 60 87 70.00 107.70
-angle 81 60 87 85.00 108.80
-angle 12 60 87 85.00 134.90
-angle 48 60 87 85.00 134.90
-angle 60 60 105 70.00 106.20
-angle 56 60 105 70.00 126.20
-angle 48 61 48 70.00 125.20
-angle 25 61 57 10.00 125.00
-angle 25 61 61 10.00 125.00
-angle 60 61 62 70.00 103.80
-angle 25 61 82 10.00 125.00
-angle 61 61 82 70.00 109.00
-angle 60 61 82 70.00 110.00
-angle 82 61 83 70.00 110.00
-angle 57 61 84 70.00 104.10
-angle 82 61 84 70.00 110.00
-angle 57 61 88 70.00 104.10
-angle 20 61 88 70.00 105.30
-angle 49 62 57 35.00 120.00
-angle 49 62 61 35.00 120.00
-angle 57 62 61 70.00 113.90
-angle 57 62 63 35.00 123.05
-angle 61 62 63 35.00 123.05
-angle 49 62 105 35.00 120.00
-angle 63 62 105 35.00 123.05
-angle 61 62 105 70.00 113.90
-angle 5 64 5 45.00 102.60
-angle 4 64 5 100.00 108.23
-angle 4 64 13 45.00 109.50
-angle 5 64 20 45.00 102.60
-angle 20 64 20 45.00 102.60
-angle 13 64 20 45.00 109.50
-angle 4 64 20 100.00 108.23
-angle 4 64 48 45.00 109.50
-angle 5 64 48 45.00 109.50
-angle 20 64 48 45.00 109.50
-angle 5 64 52 45.00 108.23
-angle 13 64 52 45.00 109.50
-angle 20 64 52 100.00 108.23
-angle 52 64 52 140.00 119.90
-angle 25 65 25 33.00 109.47
-angle 25 66 25 33.00 109.47
-angle 78 77 78 150.00 180.00
-angle 6 79 11 62.00 98.90
-angle 13 79 13 62.00 102.00
-angle 5 79 13 75.00 96.40
-angle 5 79 23 74.00 108.70
-angle 13 79 23 74.00 108.90
-angle 23 79 23 104.00 119.00
-angle 13 79 24 100.00 103.00
-angle 23 79 24 120.00 107.00
-angle 13 79 44 62.00 102.00
-angle 23 79 44 74.00 108.90
-angle 13 79 48 62.00 102.00
-angle 23 79 48 74.00 107.20
-angle 5 79 48 75.00 96.40
-angle 24 79 48 100.00 103.00
-angle 13 79 82 62.00 102.00
-angle 46 80 60 35.00 126.80
-angle 2 80 60 70.00 128.60
-angle 13 80 60 70.00 128.60
-angle 46 80 84 35.00 126.80
-angle 2 80 84 70.00 125.00
-angle 13 80 84 70.00 125.00
-angle 60 80 84 85.00 106.40
-angle 12 81 57 70.00 132.80
-angle 48 81 57 70.00 132.80
-angle 57 81 60 70.00 104.40
-angle 12 81 60 85.00 122.70
-angle 48 81 60 85.00 122.70
-angle 13 82 16 70.00 125.00
-angle 16 82 24 70.00 125.00
-angle 16 82 44 70.00 120.20
-angle 20 82 49 35.00 117.00
-angle 16 82 49 35.00 125.00
-angle 49 82 57 35.00 120.00
-angle 57 82 57 70.00 120.00
-angle 13 82 57 70.00 125.00
-angle 48 82 57 70.00 125.00
-angle 56 82 57 70.00 126.20
-angle 49 82 61 35.00 120.00
-angle 16 82 61 70.00 113.60
-angle 16 82 61 70.00 115.00
-angle 20 82 61 70.00 115.00
-angle 57 82 61 70.00 120.00
-angle 13 82 61 70.00 125.00
-angle 44 82 61 70.00 126.10
-angle 24 82 61 70.00 126.20
-angle 57 82 79 70.00 120.00
-angle 61 82 79 70.00 120.00
-angle 20 82 86 70.00 122.00
-angle 61 82 86 70.00 130.00
-angle 57 82 87 70.00 106.20
-angle 56 82 87 70.00 127.70
-angle 49 83 61 35.00 120.00
-angle 48 83 61 70.00 111.00
-angle 13 83 61 70.00 124.50
-angle 49 83 84 35.00 128.20
-angle 61 83 84 70.00 111.00
-angle 13 83 84 70.00 130.70
-angle 13 84 16 70.00 125.00
-angle 13 84 20 70.00 121.60
-angle 16 84 24 70.00 125.00
-angle 20 84 49 35.00 113.40
-angle 16 84 49 35.00 125.00
-angle 48 84 49 35.00 130.70
-angle 49 84 50 35.00 130.70
-angle 20 84 50 70.00 110.00
-angle 49 84 57 35.00 121.60
-angle 13 84 57 70.00 121.60
-angle 48 84 57 70.00 121.60
-angle 3 84 57 85.00 120.00
-angle 57 84 58 35.00 120.00
-angle 13 84 61 70.00 118.90
-angle 49 84 80 35.00 120.00
-angle 57 84 80 70.00 108.70
-angle 49 84 83 35.00 130.70
-angle 57 84 83 70.00 106.30
-angle 20 84 83 70.00 108.00
-angle 16 84 83 70.00 111.00
-angle 13 84 83 70.00 130.70
-angle 13 84 84 70.00 120.00
-angle 57 84 84 70.00 120.00
-angle 61 84 84 70.00 120.00
-angle 20 84 86 70.00 121.60
-angle 57 84 86 70.00 121.60
-angle 49 84 87 35.00 132.10
-angle 57 84 87 70.00 107.70
-angle 20 84 87 70.00 110.60
-angle 16 84 87 70.00 111.00
-angle 61 84 87 70.00 111.90
-angle 13 84 87 70.00 132.10
-angle 48 84 87 70.00 132.10
-angle 86 84 87 70.00 132.10
-angle 3 84 87 85.00 120.00
-angle 49 85 57 35.00 120.00
-angle 13 85 57 70.00 121.60
-angle 49 85 85 35.00 130.70
-angle 57 85 85 70.00 106.30
-angle 13 85 85 70.00 130.70
-angle 48 86 48 63.00 120.00
-angle 48 86 56 70.00 124.00
-angle 48 86 82 63.00 120.00
-angle 48 86 83 63.00 120.00
-angle 48 86 84 63.00 120.00
-angle 48 86 86 63.00 120.00
-angle 56 86 86 70.00 124.00
-angle 48 86 87 63.00 120.00
-angle 48 86 88 63.00 120.00
-angle 49 87 60 35.00 120.00
-angle 46 87 60 35.00 126.80
-angle 13 87 60 70.00 128.60
-angle 49 87 84 35.00 125.70
-angle 46 87 84 35.00 126.80
-angle 84 87 84 70.00 103.80
-angle 82 87 84 70.00 110.40
-angle 2 87 84 70.00 125.00
-angle 13 87 84 70.00 125.00
-angle 3 87 84 70.00 130.00
-angle 60 87 84 85.00 106.40
-angle 84 87 86 70.00 125.70
-angle 49 87 87 35.00 127.50
-angle 60 87 87 70.00 107.30
-angle 84 87 87 70.00 107.30
-angle 86 87 87 70.00 127.50
-angle 84 87 88 70.00 103.80
-angle 48 88 49 35.00 128.60
-angle 49 88 61 35.00 118.90
-angle 13 88 61 70.00 118.90
-angle 19 88 61 70.00 118.90
-angle 61 88 87 70.00 111.90
-angle 4 89 90 80.00 134.00
-angle 90 89 91 70.00 91.00
-angle 4 89 91 80.00 134.00
-angle 13 90 89 55.00 127.00
-angle 89 90 91 50.00 94.00
-angle 13 90 91 50.00 126.00
-angle 24 91 46 35.00 108.00
-angle 13 91 46 35.00 114.30
-angle 44 91 46 35.00 114.30
-angle 46 91 46 35.00 114.30
-angle 16 91 46 37.50 108.00
-angle 46 91 47 35.00 109.50
-angle 46 91 89 37.50 110.00
-angle 24 91 89 70.00 117.00
-angle 46 91 90 35.00 111.00
-angle 16 91 90 55.00 109.00
-angle 91 91 91 30.00 79.20
-angle 13 91 91 37.50 117.20
-angle 44 91 91 37.50 117.20
-angle 46 91 91 37.50 117.20
-angle 24 91 91 37.50 126.00
-angle 16 91 91 55.00 128.00
-angle 89 91 91 63.00 85.00
-angle 47 91 91 63.00 114.00
-angle 90 91 91 80.00 89.00
-angle 13 95 13 172.80 120.00
-angle 13 95 46 144.00 120.00
-angle 13 101 45 35.00 109.50
-angle 45 101 45 43.60 106.40
-angle 45 101 48 50.00 112.50
-angle 13 101 48 50.00 120.50
-angle 13 102 103 80.00 117.50
-angle 48 102 103 80.00 117.50
-angle 103 102 103 80.00 125.00
-angle 25 103 25 10.00 109.50
-angle 25 103 102 10.00 109.50
-angle 13 104 13 45.00 109.50
-angle 3 105 10 70.00 117.60
-angle 3 105 13 70.00 117.60
-angle 3 105 45 35.00 119.20
-angle 45 105 47 35.00 119.20
-angle 13 105 47 70.00 121.20
-angle 3 105 47 70.00 121.60
-angle 3 105 51 70.00 117.60
-angle 47 105 51 70.00 121.20
-angle 45 105 60 30.00 125.80
-angle 6 105 60 70.00 125.80
-angle 10 105 60 70.00 125.80
-angle 13 105 60 70.00 125.80
-angle 51 105 60 70.00 125.80
-angle 45 105 62 30.00 128.80
-angle 60 105 62 70.00 105.40
-angle 6 105 62 70.00 128.80
-angle 10 105 62 70.00 128.80
-angle 13 105 62 70.00 128.80
-angle 51 105 62 70.00 128.80
-angle 4 106 24 20.00 109.50
-angle 24 106 24 20.00 109.50
-angle 13 107 13 50.00 118.00
-angle 3 107 13 50.00 121.90
-angle 1 108 13 35.00 110.50
-angle 13 108 13 60.00 110.00
-angle 13 108 20 60.00 100.00
-angle 20 108 20 60.00 110.00
-angle 13 108 21 35.00 110.50
-angle 45 108 45 35.00 109.50
-angle 13 108 45 35.00 110.50
-angle 46 108 46 35.00 109.50
-angle 13 108 46 35.00 110.50
-angle 13 108 65 35.00 110.50
-angle 13 108 66 35.00 110.50
-angle 13 108 108 50.00 112.00
-angle 46 109 48 35.00 123.30
-angle 46 109 50 35.00 120.00
-angle 13 109 50 70.00 124.00
-angle 46 109 109 35.00 120.00
-angle 13 109 109 70.00 124.00
-angle 50 109 109 70.00 124.00
-angle 48 109 109 85.00 117.00
-angle 4 110 47 160.00 180.00
-angle 47 110 47 160.00 180.00
-
-
- ################################
- ## ##
- ## Urey-Bradley Parameters ##
- ## ##
- ################################
-
-
-ureybrad 35 34 35 38.25 1.5537
-
-
- #####################################
- ## ##
- ## Improper Torsional Parameters ##
- ## ##
- #####################################
-
-
-imptors 0 0 3 4 21.000 180.0 2
-imptors 0 0 3 52 21.000 180.0 2
-imptors 0 0 24 0 5.000 180.0 2
-imptors 0 0 47 0 30.000 180.0 2
-imptors 0 0 48 0 5.000 180.0 2
-
-
- ############################
- ## ##
- ## Torsional Parameters ##
- ## ##
- ############################
-
-
- ###################################################################
- ## ##
- ## Alternative Torsional Parameter Values for Use with OPLS-AA ##
- ## ##
- ## For some torsions, OPLS-AA has multiple possible parameter ##
- ## values; the list below shows functional groups for which ##
- ## these alternate (commented) values should be preferred; the ##
- ## values are in the same order as in the full parameter list ##
- ## ##
- ## 4 3 3 36 generic (default) ##
- ## 4 3 3 36 dicarbonyls ##
- ## 36 3 3 36 hydrocarbon (default) ##
- ## 36 3 3 36 dicarbonyls ##
- ## 13 3 5 7 carboxylic acid (default) ##
- ## 13 3 5 7 1,2-diacid monoanion ##
- ## 4 3 13 13 peptide (default) ##
- ## 4 3 13 13 propanamide ##
- ## 4 3 13 13 carboxylic acid ##
- ## 4 3 13 13 dicarboxylic acid ##
- ## 4 3 13 13 aldyhyde, ketone, acyl halide ##
- ## 4 3 13 13 1,2-diacid monoanion ##
- ## 5 3 13 13 carboxylic acid (default) ##
- ## 5 3 13 13 dicarboxylic acid ##
- ## 35 3 13 13 peptide psi' (default) ##
- ## 35 3 13 13 propanamide ##
- ## 35 3 13 13 beta-3-peptide, last psi ##
- ## 4 3 29 13 esters (default) ##
- ## 4 3 29 13 benzoic esters ##
- ## 7 5 13 13 alcohols (default) ##
- ## 7 5 13 13 trifluoroethanol ##
- ## 7 5 13 13 hexopyranoses ##
- ## 7 5 13 36 alcohols (default) ##
- ## 7 5 13 36 axial cyclohexanol ##
- ## 7 5 13 36 trifluoroethanol ##
- ## 0 13 13 13 alcohols, ethers (default) ##
- ## 0 13 13 13 hexopyranoses ##
- ## 3 13 13 3 dicarboxylic acid (default) ##
- ## 3 13 13 3 1,2-diacid monoanion ##
- ## 3 13 13 13 butanamide (default) ##
- ## 3 13 13 13 carboxylate ion ##
- ## 3 13 13 13 aldyhyde, ketone, acyl halide ##
- ## 3 13 13 36 all carbonyls (default) ##
- ## 3 13 13 36 dicarboxylic acid ##
- ## 3 13 13 36 aldehyde, ketone, acyl halide ##
- ## 5 13 13 5 diols only (default) ##
- ## 5 13 13 5 triols only ##
- ## 5 13 13 5 hexopyranoses ##
- ## 13 13 13 13 hydrocarbon (default) ##
- ## 13 13 13 13 perfluoroalkane ##
- ## 13 13 13 35 peptide chi-1 (default) ##
- ## 13 13 13 35 N-propylformamide ##
- ## 36 13 13 69 generic (default) ##
- ## 36 13 13 69 sulfone ##
- ## 13 13 33 13 amine (default) ##
- ## 13 13 33 13 exocyclic amine ##
- ## 13 13 33 13 exocyclic 1,4-diamine ##
- ## 13 13 33 34 amine (default) ##
- ## 13 13 33 34 azetidine, 4-ring ##
- ## 13 13 33 34 pyrrolidine, 5-ring ##
- ## 13 13 33 34 cyclic amine ##
- ## 13 13 33 34 cyclic 1,4-diamine ##
- ## 13 13 35 3 peptide phi' (default) ##
- ## 13 13 35 3 N-ethylformamide ##
- ## 13 13 35 3 beta-3-peptide, first theta tors ##
- ## 13 13 35 13 proline, CD-N-CA-CB (default) ##
- ## 13 13 35 13 proline, CG-CD-N-CA ##
- ## 36 13 35 3 peptide phi'' (default) ##
- ## 36 13 35 3 N-methylformamide ##
- ## 13 13 47 0 imidazole, indole, purine (default) ##
- ## 13 13 47 0 nucleoside chi ##
- ## 13 13 47 52 nucleoside (default) ##
- ## 13 13 47 52 imidazole, indole, purine ##
- ## 29 13 47 0 imidazole, indole, purine (default) ##
- ## 29 13 47 0 nucleoside chi ##
- ## 29 13 95 52 nucleoside (default) ##
- ## 29 13 95 52 imidazole, indole, purine ##
- ## 13 13 97 13 generic (default) ##
- ## 13 13 97 13 generic ##
- ## 17 15 38 0 aromatic thiol (default) ##
- ## 17 15 38 0 aromatic thiol, N-C-S-H ##
- ## 13 29 54 42 phosphonates (default) ##
- ## 13 29 54 42 dimethyl phosphate ##
- ## 34 35 72 16 diaryl amine (default) ##
- ## 34 35 72 16 aniline-like ##
- ## 34 35 72 29 diaryl amine (default) ##
- ## 34 35 72 29 aniline-like ##
- ## 13 40 40 37 diene (default) ##
- ## 13 40 40 37 2-methyl-1,3-butadiene ##
- ## 0 46 72 0 generic (default) ##
- ## 0 46 72 0 generic ##
- ## 0 47 72 0 generic (default) ##
- ## 0 47 72 0 generic ##
- ## 0 47 74 0 generic (default) ##
- ## 0 47 74 0 generic ##
- ## 0 47 74 0 generic ##
- ## 0 51 72 0 generic (default) ##
- ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ##
- ## 0 72 77 0 generic (default) ##
- ## 0 72 77 0 biphenyl-like, N-C-C-C ##
- ## ##
- ###################################################################
-
-
-torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3
-torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3
-torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3
-torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3
-torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3
-torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3
-torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3
-torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3
-torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3
-torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3
-torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3
-torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3
-torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3
-torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3
-torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3
-torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3
-#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3
-torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3
-torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3
-#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3
-#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3
-#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3
-#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3
-torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3
-torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3
-#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3
-torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3
-torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3
-torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3
-torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3
-torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3
-#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3
-#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3
-torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3
-torsion 24 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 48 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3
-torsion 52 3 13 13 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 52 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 52 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 65 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 65 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 107 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 20 13 0.000 0.0 1 5.124 180.0 2 0.000 0.0 3
-#torsion 4 3 29 13 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 4 3 20 48 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 13 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3
-torsion 13 3 20 48 1.500 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 24 3 20 13 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 46 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3
-torsion 48 3 20 13 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 3 3 24 13 0.400 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 3 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 3 24 5 0.000 0.0 1 6.603 180.0 2 0.000 0.0 3
-torsion 4 3 24 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 3 24 47 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 3 24 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 3 24 91 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 5 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 5 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 13 3 24 5 4.542 0.0 1 6.603 180.0 2 1.045 0.0 3
-torsion 13 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 13 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 13 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 20 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 20 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 24 3 24 3 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 24 3 24 13 4.600 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 46 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 46 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 47 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 48 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 48 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 48 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 48 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 84 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 84 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 84 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 87 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 87 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 87 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 87 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 0 3 47 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3
-torsion 4 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 47 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3
-torsion 5 3 47 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 24 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 107 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 107 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 5 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 13 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 20 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 24 3 48 48 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3
-torsion 46 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 0 3 50 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3
-torsion 4 3 50 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3
-torsion 5 3 50 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 13 3 50 47 0.800 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 13 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 3 56 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 3 56 45 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 0 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3
-torsion 4 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3
-torsion 4 3 82 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 82 57 2.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 4 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 82 3 82 57 -2.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 82 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 4 3 84 20 -0.750 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 4 3 84 87 0.750 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 84 3 84 20 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 84 3 84 87 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 48 3 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 3 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 4 3 87 84 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 4 3 87 87 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 24 3 87 84 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3
-torsion 24 3 87 87 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3
-torsion 4 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 13 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 3 109 109 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3
-torsion 5 3 109 109 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 0 4 106 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 10 2 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3
-torsion 7 5 10 6 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3
-torsion 7 5 13 2 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3
-torsion 7 5 13 6 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3
-torsion 7 5 13 13 -0.356 0.0 1 -0.174 180.0 2 0.492 0.0 3
-#torsion 7 5 13 13 4.478 0.0 1 -2.175 180.0 2 0.000 0.0 3
-#torsion 7 5 13 13 2.674 0.0 1 -2.883 180.0 2 1.026 0.0 3
-torsion 7 5 13 46 0.000 0.0 1 0.000 180.0 2 0.352 0.0 3
-#torsion 7 5 13 36 -2.589 0.0 1 -1.123 180.0 2 0.270 0.0 3
-#torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.476 0.0 3
-torsion 7 5 13 47 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 13 48 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 13 50 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 44 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 7 5 44 45 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 7 5 24 3 5.519 0.0 1 -6.700 180.0 2 0.581 0.0 3
-torsion 7 5 24 45 2.722 0.0 1 -5.154 180.0 2 0.000 0.0 3
-torsion 7 5 47 47 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3
-torsion 7 5 48 48 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3
-torsion 7 5 51 20 -1.257 0.0 1 -1.806 180.0 2 0.003 0.0 3
-torsion 7 5 56 3 3.000 0.0 1 3.000 180.0 2 0.000 0.0 3
-torsion 7 5 64 4 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 64 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 79 13 -0.750 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 79 23 0.750 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 79 48 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 13 13 3 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3
-torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3
-#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 13 13 24 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3
-torsion 1 13 13 1 -2.500 0.0 1 0.000 180.0 2 0.250 0.0 3
-torsion 1 13 13 5 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3
-torsion 1 13 13 13 0.300 0.0 1 -0.400 180.0 2 0.400 0.0 3
-torsion 1 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 3 13 13 3 -0.550 0.0 1 0.000 180.0 2 1.000 0.0 3
-#torsion 3 13 13 3 0.800 0.0 1 0.000 180.0 2 0.900 0.0 3
-torsion 3 13 13 5 -6.180 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 13 13 13 -2.060 0.0 1 -0.313 180.0 2 0.315 0.0 3
-#torsion 3 13 13 13 -3.185 0.0 1 -0.825 180.0 2 0.493 0.0 3
-#torsion 3 13 13 13 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 15 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3
-torsion 3 13 13 16 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3
-torsion 3 13 13 24 -9.000 0.0 1 2.000 180.0 2 0.800 0.0 3
-torsion 3 13 13 46 0.000 0.0 1 0.000 180.0 2 -0.100 0.0 3
-#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 0.074 0.0 3
-#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.076 0.0 3
-torsion 3 13 13 48 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 80 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 5 13 13 5 9.508 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 5 13 13 5 12.234 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 5 13 13 5 9.066 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 5 13 13 13 -1.552 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 5 13 13 20 4.319 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 5 13 13 44 8.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 5 13 13 24 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3
-torsion 5 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3
-torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4
-torsion 13 13 13 15 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3
-torsion 13 13 13 16 2.619 0.0 1 -0.620 180.0 2 0.258 0.0 3
-torsion 13 13 13 19 0.000 0.0 1 -0.650 180.0 2 0.000 0.0 3
-torsion 13 13 13 21 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 13 13 13 44 2.392 0.0 1 -0.674 180.0 2 0.550 0.0 3
-torsion 13 13 13 24 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-#torsion 13 13 13 35 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3
-torsion 13 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 13 13 13 51 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-torsion 13 13 13 53 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3
-torsion 13 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 13 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 13 13 13 79 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3
-torsion 13 13 13 107 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3
-torsion 13 13 13 108 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 15 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3
-torsion 16 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3
-torsion 19 13 13 46 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3
-torsion 20 13 13 20 -0.550 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 20 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3
-torsion 21 13 13 21 -0.250 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 21 13 13 44 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 21 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 44 13 13 44 11.035 0.0 1 -0.968 180.0 2 0.270 0.0 3
-torsion 44 13 13 46 -1.013 0.0 1 -0.709 180.0 2 0.473 0.0 3
-torsion 44 13 13 48 -0.800 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 13 13 46 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3
-torsion 24 13 13 48 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 24 13 13 80 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 46 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 46 13 13 47 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3
-torsion 46 13 13 48 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 51 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 46 13 13 53 0.000 0.0 1 0.000 180.0 2 0.384 0.0 3
-torsion 46 13 13 55 0.000 0.0 1 0.000 180.0 2 -0.582 0.0 3
-torsion 46 13 13 59 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 62 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 46 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 46 13 13 79 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3
-#torsion 36 13 13 69 0.000 0.0 1 0.000 180.0 2 0.350 0.0 3
-torsion 46 13 13 80 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 82 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 83 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 84 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 87 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 88 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 46 13 13 102 0.000 0.0 1 0.000 180.0 2 -0.225 0.0 3
-torsion 46 13 13 104 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 46 13 13 107 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3
-torsion 46 13 13 108 0.000 0.0 1 0.000 180.0 2 0.450 0.0 3
-torsion 46 13 13 109 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3
-torsion 48 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 108 13 13 108 5.200 0.0 1 -0.500 180.0 2 0.000 0.0 3
-torsion 13 13 15 17 -0.759 0.0 1 -0.282 180.0 2 0.680 0.0 3
-torsion 46 13 15 17 0.000 0.0 1 0.000 180.0 2 0.480 0.0 3
-torsion 13 13 16 13 0.925 0.0 1 -0.576 180.0 2 0.677 0.0 3
-torsion 13 13 16 16 1.941 0.0 1 -0.836 180.0 2 0.935 0.0 3
-torsion 46 13 16 13 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3
-torsion 46 13 16 16 0.000 0.0 1 0.000 180.0 2 0.558 0.0 3
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-torsion 0 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
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-torsion 0 90 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 90 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 91 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 91 91 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 91 91 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 91 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 91 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 91 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 91 91 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 109 109 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 50 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 50 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 109 109 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3
-
-
- ################################################################
- ## ##
- ## Additional Torsional Parameter Values Used with OPLS-AA ##
- ## ##
- ## The torsions listed below were added to official OPLS-AA ##
- ## to complete the set needed for proteins; the values were ##
- ## obtained by analogy from the closest OPLS-AA torsions; ##
- ## most of the added values are for HIP or N-terminal AAs; ##
- ## ##
- ################################################################
-
-
-torsion 24 3 13 53 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3
-torsion 52 3 13 24 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 3 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 13 13 83 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 84 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 85 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 5 13 13 53 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3
-torsion 15 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3
-torsion 16 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3
-torsion 13 13 13 55 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3
-torsion 24 13 13 83 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 53 13 13 83 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 13 13 84 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 53 13 13 84 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 13 13 85 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 46 13 13 85 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 53 13 13 85 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 13 53 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3
-torsion 3 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3
-torsion 13 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3
-torsion 46 13 55 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 13 85 57 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3
-torsion 46 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 55 48 55 54 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3
-torsion 0 48 81 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 57 85 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 0 85 85 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-
-
- ################################################################
- ## ##
- ## Additional Torsional Parameter Values Used with OPLS-AA ##
- ## ##
- ## The torsions listed below were added to official OPLS-AA ##
- ## to complete the values needed for selected organics ##
- ## ##
- ################################################################
-
-
-torsion 13 13 13 20 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 1 -0.2200
-charge 2 0.2200
-charge 3 0.5500
-charge 4 -0.5000
-charge 5 -0.5800
-charge 6 0.0800
-charge 7 0.4500
-charge 8 0.0000
-charge 9 0.0000
-charge 10 0.0000
-charge 11 0.0000
-charge 12 0.0000
-charge 13 0.0000
-charge 14 0.0000
-charge 15 0.0000
-charge 16 0.0000
-charge 17 0.0000
-charge 18 0.0000
-charge 19 0.0000
-charge 20 -0.7000
-charge 21 0.4350
-charge 22 0.2650
-charge 23 0.2650
-charge 24 -0.4700
-charge 25 -0.4500
-charge 26 -0.4700
-charge 27 -0.3000
-charge 28 0.2350
-charge 29 0.2700
-charge 30 0.1800
-charge 31 0.1800
-charge 32 0.2350
-charge 33 0.2350
-charge 34 0.3000
-charge 35 0.3000
-charge 36 -0.4300
-charge 37 0.2800
-charge 38 0.1500
-charge 39 0.2650
-charge 40 0.2650
-charge 41 -0.5000
-charge 42 0.2500
-charge 43 0.2500
-charge 44 0.5000
-charge 45 -0.2500
-charge 46 0.4200
-charge 47 -0.1400
-charge 48 0.2480
-charge 49 -0.0620
-charge 50 0.1390
-charge 51 -0.4590
-charge 52 0.1600
-charge 53 -0.5000
-charge 54 -0.5700
-charge 55 0.5000
-charge 56 0.2850
-charge 57 0.0000
-charge 58 0.0000
-charge 59 0.0000
-charge 60 0.0000
-charge 61 0.0000
-charge 62 0.0000
-charge 63 -0.8340
-charge 64 0.4170
-charge 65 0.0000
-charge 66 0.5200
-charge 67 -1.0400
-charge 68 -0.8220
-charge 69 0.4110
-charge 70 0.0000
-charge 71 0.5110
-charge 72 -1.0220
-charge 73 0.0000
-charge 74 0.2410
-charge 75 -0.2410
-charge 76 -0.8200
-charge 77 0.4100
-charge 78 -1.0200
-charge 79 0.3400
-charge 80 -0.1800
-charge 81 -0.1200
-charge 82 -0.0600
-charge 83 -0.2400
-charge 84 0.0000
-charge 85 0.0600
-charge 86 0.0000
-charge 87 -0.1150
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
-charge 92 0.0000
-charge 93 -0.0650
-charge 94 -0.0050
-charge 95 -0.1150
-charge 96 -0.6830
-charge 97 0.4180
-charge 98 0.0400
-charge 99 0.1450
-charge 100 0.2050
-charge 101 0.2650
-charge 102 0.1263
-charge 103 0.5323
-charge 104 -0.6351
-charge 105 0.4286
-charge 106 -0.2057
-charge 107 0.0825
-charge 108 0.1500
-charge 109 -0.5850
-charge 110 0.4350
-charge 111 -0.7000
-charge 112 0.4350
-charge 113 -0.7300
-charge 114 0.4650
-charge 115 0.1450
-charge 116 0.2050
-charge 117 0.2650
-charge 118 0.0600
-charge 119 -0.1700
-charge 120 0.0000
-charge 121 -0.2850
-charge 122 -0.4000
-charge 123 0.1100
-charge 124 0.1400
-charge 125 0.1700
-charge 126 0.2000
-charge 127 0.0300
-charge 128 -0.4000
-charge 129 -0.7000
-charge 130 0.4350
-charge 131 0.2000
-charge 132 0.1000
-charge 133 0.2650
-charge 134 0.1000
-charge 135 0.3000
-charge 136 0.1000
-charge 137 0.3650
-charge 138 0.1000
-charge 139 0.4000
-charge 140 0.4650
-charge 141 0.0850
-charge 142 -0.3350
-charge 143 -0.4700
-charge 144 -0.4350
-charge 145 -0.2175
-charge 146 0.1550
-charge 147 0.2350
-charge 148 0.0600
-charge 149 0.1200
-charge 150 0.1800
-charge 151 0.0375
-charge 152 0.0975
-charge 153 0.1575
-charge 154 0.2175
-charge 155 0.0375
-charge 156 0.0975
-charge 157 0.1575
-charge 158 0.2175
-charge 159 0.0000
-charge 160 0.2000
-charge 161 0.2600
-charge 162 0.3200
-charge 163 -0.0550
-charge 164 -0.3200
-charge 165 0.0800
-charge 166 0.1400
-charge 167 0.2000
-charge 168 -0.1200
-charge 169 0.0050
-charge 170 0.1025
-charge 171 0.1400
-charge 172 0.2000
-charge 173 0.7000
-charge 174 0.5650
-charge 175 0.5850
-charge 176 0.6150
-charge 177 0.5000
-charge 178 -0.5000
-charge 179 -0.7600
-charge 180 -0.5000
-charge 181 -0.1400
-charge 182 0.3800
-charge 183 0.3000
-charge 184 0.0200
-charge 185 -0.1100
-charge 186 0.0800
-charge 187 -0.0500
-charge 188 0.0100
-charge 189 0.1420
-charge 190 -0.3900
-charge 191 -0.5420
-charge 192 0.3330
-charge 193 -0.4900
-charge 194 0.4200
-charge 195 -0.4200
-charge 196 0.3700
-charge 197 0.0600
-charge 198 -0.1200
-charge 199 -0.0600
-charge 200 0.0000
-charge 201 0.0600
-charge 202 0.0350
-charge 203 0.3950
-charge 204 -0.4300
-charge 205 0.1800
-charge 206 -0.1800
-charge 207 -0.3850
-charge 208 0.0850
-charge 209 0.5200
-charge 210 -0.4400
-charge 211 -0.5300
-charge 212 0.4500
-charge 213 0.7000
-charge 214 -0.8000
-charge 215 -0.2800
-charge 216 -0.2200
-charge 217 -0.1600
-charge 218 -0.1000
-charge 219 0.4500
-charge 220 -0.4500
-charge 221 0.0000
-charge 222 0.4700
-charge 223 -0.4700
-charge 224 0.0600
-charge 225 0.0400
-charge 226 -0.0200
-charge 227 0.1000
-charge 228 -0.0900
-charge 229 -0.4000
-charge 230 -0.3000
-charge 231 0.0000
-charge 232 0.3500
-charge 233 0.3300
-charge 234 0.1300
-charge 235 0.1900
-charge 236 0.2500
-charge 237 0.3100
-charge 238 0.2300
-charge 239 0.1700
-charge 240 0.1100
-charge 241 0.0900
-charge 242 0.1500
-charge 243 -0.8000
-charge 244 0.4600
-charge 245 0.6400
-charge 246 -0.7000
-charge 247 0.4400
-charge 248 0.2000
-charge 249 -0.1100
-charge 250 0.1900
-charge 251 -0.0500
-charge 252 -0.2000
-charge 253 0.3100
-charge 254 -0.4600
-charge 255 0.3600
-charge 256 -0.8500
-charge 257 0.3700
-charge 258 -0.1500
-charge 259 0.1000
-charge 260 -0.0400
-charge 261 0.1000
-charge 262 -0.6000
-charge 263 0.5000
-charge 264 -0.5100
-charge 265 0.4500
-charge 266 -0.0700
-charge 267 0.0800
-charge 268 0.4100
-charge 269 -0.4000
-charge 270 0.3600
-charge 271 -0.4200
-charge 272 0.1000
-charge 273 0.1000
-charge 274 -0.1400
-charge 275 0.0800
-charge 276 -0.5600
-charge 277 0.5500
-charge 278 -0.5400
-charge 279 0.4600
-charge 280 -0.0600
-charge 281 0.1000
-charge 282 0.3800
-charge 283 -0.4800
-charge 284 -0.7900
-charge 285 0.3850
-charge 286 0.3550
-charge 287 0.1000
-charge 288 0.1000
-charge 289 -0.5300
-charge 290 0.2200
-charge 291 -0.5500
-charge 292 0.3800
-charge 293 0.1500
-charge 294 0.4400
-charge 295 -0.4900
-charge 296 0.2000
-charge 297 -0.5000
-charge 298 0.2000
-charge 299 -0.8100
-charge 300 0.3850
-charge 301 0.3550
-charge 302 0.2000
-charge 303 0.3500
-charge 304 -0.5600
-charge 305 0.4600
-charge 306 -0.5100
-charge 307 0.3400
-charge 308 0.1200
-charge 309 0.5200
-charge 310 0.3800
-charge 311 -0.8000
-charge 312 0.4000
-charge 313 -0.5100
-charge 314 -0.0100
-charge 315 0.1200
-charge 316 -0.0100
-charge 317 0.1400
-charge 318 -0.0100
-charge 319 0.1300
-charge 320 -0.6400
-charge 321 0.6500
-charge 322 -0.7400
-charge 323 0.6600
-charge 324 -0.0600
-charge 325 0.1000
-charge 326 0.4900
-charge 327 -0.3000
-charge 328 0.4800
-charge 329 -0.8100
-charge 330 0.4600
-charge 331 0.4300
-charge 332 0.1400
-charge 333 0.1400
-charge 334 0.0100
-charge 335 0.1600
-charge 336 0.7800
-charge 337 -0.6600
-charge 338 -0.4300
-charge 339 0.2000
-charge 340 0.1800
-charge 341 -0.0600
-charge 342 0.1200
-charge 343 -1.0000
-charge 344 -1.0000
-charge 345 -1.0000
-charge 346 -1.0000
-charge 347 1.0000
-charge 348 1.0000
-charge 349 1.0000
-charge 350 1.0000
-charge 351 1.0000
-charge 352 1.0000
-charge 353 2.0000
-charge 354 2.0000
-charge 355 2.0000
-charge 356 2.0000
-charge 357 -0.4000
-charge 358 0.1000
-charge 359 -0.9000
-charge 360 -0.2000
-charge 361 0.0600
-charge 362 -0.9800
-charge 363 -1.0700
-charge 364 0.1900
-charge 365 0.5100
-charge 366 -0.8200
-charge 367 -0.3000
-charge 368 0.0700
-charge 369 -1.3100
-charge 370 0.4000
-charge 371 -0.4000
-charge 372 0.0800
-charge 373 0.0000
-charge 374 0.0700
-charge 375 -0.9800
-charge 376 -1.3000
-charge 377 0.3000
-charge 378 2.5000
-charge 379 -0.2500
-charge 380 -0.8650
-charge 381 1.6200
-charge 382 -0.9200
-charge 383 -0.6000
-charge 384 0.3000
-charge 385 -0.0300
-charge 386 1.9200
-charge 387 -1.1200
-charge 388 -0.7000
-charge 389 0.4400
-charge 390 -0.1000
-charge 391 1.6200
-charge 392 -0.9700
-charge 393 -0.6300
-charge 394 0.2800
-charge 395 -0.0200
-charge 396 -0.5100
-charge 397 0.0800
-charge 398 -0.1400
-charge 399 0.3200
-charge 400 0.0200
-charge 401 -0.0400
-charge 402 -0.4700
-charge 403 0.1200
-charge 404 0.1400
-charge 405 0.2400
-charge 406 0.5100
-charge 407 -0.4300
-charge 408 -0.3300
-charge 409 0.1600
-charge 410 0.0300
-charge 411 0.6350
-charge 412 0.6250
-charge 413 0.1350
-charge 414 -0.2150
-charge 415 1.4800
-charge 416 -0.6800
-charge 417 -0.5400
-charge 418 0.1800
-charge 419 -1.0000
-charge 420 0.4400
-charge 421 -0.8000
-charge 422 0.4100
-charge 423 0.1800
-charge 424 0.0300
-charge 425 0.3900
-charge 426 -0.0600
-charge 427 -0.1800
-charge 428 0.0600
-charge 429 0.0000
-charge 430 0.0300
-charge 431 0.1900
-charge 432 0.2200
-charge 433 0.2500
-charge 434 1.3740
-charge 435 -0.6870
-charge 436 0.2450
-charge 437 0.1300
-charge 438 -0.4200
-charge 439 -0.0350
-charge 440 0.0250
-charge 441 0.0750
-charge 442 -0.0550
-charge 443 0.1300
-charge 444 -0.5700
-charge 445 0.4200
-charge 446 -0.0050
-charge 447 0.2950
-charge 448 -0.0150
-charge 449 0.0150
-charge 450 0.3850
-charge 451 0.2150
-charge 452 -0.4900
-charge 453 -0.5400
-charge 454 0.4600
-charge 455 -0.1150
-charge 456 0.0550
-charge 457 0.1150
-charge 458 -0.0300
-charge 459 0.0850
-charge 460 0.0000
-charge 461 -0.6780
-charge 462 0.4730
-charge 463 -0.4470
-charge 464 0.2270
-charge 465 0.0120
-charge 466 0.1550
-charge 467 0.0650
-charge 468 -0.4680
-charge 469 0.1920
-charge 470 0.0420
-charge 471 -0.8390
-charge 472 0.8740
-charge 473 0.6530
-charge 474 -0.6890
-charge 475 -0.0320
-charge 476 0.0110
-charge 477 0.1970
-charge 478 -0.3310
-charge 479 0.3780
-charge 480 -0.1600
-charge 481 -0.0090
-charge 482 0.1220
-charge 483 -0.2390
-charge 484 -0.1630
-charge 485 -0.1490
-charge 486 0.3170
-charge 487 0.1550
-charge 488 0.1180
-charge 489 -0.0590
-charge 490 -0.4910
-charge 491 0.2460
-charge 492 -0.3200
-charge 493 -0.0340
-charge 494 0.3010
-charge 495 0.0720
-charge 496 0.1500
-charge 497 0.1350
-charge 498 -0.2570
-charge 499 0.2750
-charge 500 -0.5630
-charge 501 0.1850
-charge 502 -0.2860
-charge 503 0.3060
-charge 504 0.0780
-charge 505 0.0750
-charge 506 0.1870
-charge 507 -0.1900
-charge 508 -0.0190
-charge 509 -0.1540
-charge 510 0.1420
-charge 511 0.1260
-charge 512 -0.2570
-charge 513 0.5110
-charge 514 -0.5900
-charge 515 0.1690
-charge 516 -0.1480
-charge 517 0.0430
-charge 518 0.0910
-charge 519 0.1810
-charge 520 -0.1220
-charge 521 -0.4130
-charge 522 0.4050
-charge 523 -0.4550
-charge 524 0.2500
-charge 525 0.0530
-charge 526 0.1840
-charge 527 0.0980
-charge 528 -0.5000
-charge 529 0.0010
-charge 530 -0.3900
-charge 531 -0.2700
-charge 532 -0.1270
-charge 533 -0.1080
-charge 534 -0.2580
-charge 535 0.2200
-charge 536 0.2250
-charge 537 0.3760
-charge 538 0.1470
-charge 539 0.1720
-charge 540 0.1550
-charge 541 0.1070
-charge 542 0.1100
-charge 543 0.1400
-charge 544 -0.6940
-charge 545 0.4250
-charge 546 -0.3590
-charge 547 -0.0080
-charge 548 -0.1970
-charge 549 -0.1120
-charge 550 -0.0700
-charge 551 -0.3070
-charge 552 0.5630
-charge 553 -0.0510
-charge 554 0.0280
-charge 555 0.1460
-charge 556 0.1190
-charge 557 0.1330
-charge 558 0.1130
-charge 559 0.1140
-charge 560 0.1570
-charge 561 -0.7600
-charge 562 0.6790
-charge 563 -0.7880
-charge 564 0.7360
-charge 565 0.0380
-charge 566 0.3430
-charge 567 -0.6420
-charge 568 0.4520
-charge 569 -0.6820
-charge 570 0.0240
-charge 571 0.1010
-charge 572 0.0860
-charge 573 0.4130
-charge 574 -0.0300
-charge 575 0.2420
-charge 576 -0.5150
-charge 577 0.2280
-charge 578 -0.2990
-charge 579 0.1010
-charge 580 0.0680
-charge 581 0.2050
-charge 582 -0.9510
-charge 583 0.9650
-charge 584 -0.0140
-charge 585 0.1300
-charge 586 0.0520
-charge 587 -0.5990
-charge 588 0.3920
-charge 589 -0.3480
-charge 590 0.0200
-charge 591 -0.0420
-charge 592 0.3470
-charge 593 -0.1960
-charge 594 0.0320
-charge 595 0.1460
-charge 596 0.1080
-charge 597 0.1400
-charge 598 0.1220
-charge 599 0.1660
-charge 600 -0.5800
-charge 601 0.1730
-charge 602 -0.3950
-charge 603 -0.1990
-charge 604 0.1180
-charge 605 0.0930
-charge 606 0.2080
-charge 607 0.0980
-charge 608 -0.1390
-charge 609 -0.0790
-charge 610 0.0990
-charge 611 -0.1680
-charge 612 -0.1080
-charge 613 -0.1890
-charge 614 -0.1290
-charge 615 -0.1690
-charge 616 -0.1090
-charge 617 -0.1380
-charge 618 -0.0780
-charge 619 -0.0250
-charge 620 0.0350
-charge 621 -0.0380
-charge 622 0.0220
-charge 623 -0.3340
-charge 624 0.2550
-charge 625 0.5230
-charge 626 0.5000
-charge 627 -0.1400
-charge 628 0.2275
-charge 629 0.1400
-charge 630 -0.0080
-charge 631 0.5880
-charge 632 -0.1030
-charge 633 -0.3320
-charge 634 0.0400
-charge 635 0.3420
-charge 636 -0.0500
-charge 637 -0.2050
-charge 638 3.0000
-charge 639 4.0000
-charge 640 3.0000
-charge 641 0.6190
-charge 642 -0.3950
-charge 643 0.1740
-charge 644 3.0000
-charge 645 3.0000
-charge 646 3.0000
-charge 647 3.0000
-charge 648 3.0000
-charge 649 -0.3440
-charge 650 -0.6280
-charge 651 0.2000
-charge 652 -0.1200
-charge 653 -0.0600
-charge 654 0.0000
-charge 655 -0.2300
-charge 656 0.0300
-charge 657 -0.0990
-charge 658 0.0990
-charge 659 0.2200
-charge 660 -0.2200
-charge 661 0.1300
-charge 662 -0.1300
-charge 663 -0.2200
-charge 664 0.2200
-charge 665 0.1500
-charge 666 0.4500
-charge 667 -0.2000
-charge 668 0.2000
-charge 669 -0.2000
-charge 670 0.2000
-charge 671 -0.2000
-charge 672 0.1000
-charge 673 -0.1000
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-
-
- ########################################
- ## ##
- ## Biopolymer Atom Type Conversions ##
- ## ##
- ########################################
-
-
-biotype 1 N "Glycine" 180
-biotype 2 CA "Glycine" 165
-biotype 3 C "Glycine" 177
-biotype 4 HN "Glycine" 183
-biotype 5 O "Glycine" 178
-biotype 6 HA "Glycine" 85
-biotype 7 N "Alanine" 180
-biotype 8 CA "Alanine" 166
-biotype 9 C "Alanine" 177
-biotype 10 HN "Alanine" 183
-biotype 11 O "Alanine" 178
-biotype 12 HA "Alanine" 85
-biotype 13 CB "Alanine" 80
-biotype 14 HB "Alanine" 85
-biotype 15 N "Valine" 180
-biotype 16 CA "Valine" 166
-biotype 17 C "Valine" 177
-biotype 18 HN "Valine" 183
-biotype 19 O "Valine" 178
-biotype 20 HA "Valine" 85
-biotype 21 CB "Valine" 82
-biotype 22 HB "Valine" 85
-biotype 23 CG1 "Valine" 80
-biotype 24 HG1 "Valine" 85
-biotype 25 CG2 "Valine" 80
-biotype 26 HG2 "Valine" 85
-biotype 27 N "Leucine" 180
-biotype 28 CA "Leucine" 166
-biotype 29 C "Leucine" 177
-biotype 30 HN "Leucine" 183
-biotype 31 O "Leucine" 178
-biotype 32 HA "Leucine" 85
-biotype 33 CB "Leucine" 81
-biotype 34 HB "Leucine" 85
-biotype 35 CG "Leucine" 82
-biotype 36 HG "Leucine" 85
-biotype 37 CD1 "Leucine" 80
-biotype 38 HD1 "Leucine" 85
-biotype 39 CD2 "Leucine" 80
-biotype 40 HD2 "Leucine" 85
-biotype 41 N "Isoleucine" 180
-biotype 42 CA "Isoleucine" 166
-biotype 43 C "Isoleucine" 177
-biotype 44 HN "Isoleucine" 183
-biotype 45 O "Isoleucine" 178
-biotype 46 HA "Isoleucine" 85
-biotype 47 CB "Isoleucine" 82
-biotype 48 HB "Isoleucine" 85
-biotype 49 CG1 "Isoleucine" 80
-biotype 50 HG1 "Isoleucine" 85
-biotype 51 CG2 "Isoleucine" 81
-biotype 52 HG2 "Isoleucine" 85
-biotype 53 CD "Isoleucine" 80
-biotype 54 HD "Isoleucine" 85
-biotype 55 N "Serine" 180
-biotype 56 CA "Serine" 166
-biotype 57 C "Serine" 177
-biotype 58 HN "Serine" 183
-biotype 59 O "Serine" 178
-biotype 60 HA "Serine" 85
-biotype 61 CB "Serine" 99
-biotype 62 HB "Serine" 85
-biotype 63 OG "Serine" 96
-biotype 64 HG "Serine" 97
-biotype 65 N "Threonine" 180
-biotype 66 CA "Threonine" 166
-biotype 67 C "Threonine" 177
-biotype 68 HN "Threonine" 183
-biotype 69 O "Threonine" 178
-biotype 70 HA "Threonine" 85
-biotype 71 CB "Threonine" 100
-biotype 72 HB "Threonine" 85
-biotype 73 OG1 "Threonine" 96
-biotype 74 HG1 "Threonine" 97
-biotype 75 CG2 "Threonine" 80
-biotype 76 HG2 "Threonine" 85
-biotype 77 N "Cysteine (SH)" 180
-biotype 78 CA "Cysteine (SH)" 166
-biotype 79 C "Cysteine (SH)" 177
-biotype 80 HN "Cysteine (SH)" 183
-biotype 81 O "Cysteine (SH)" 178
-biotype 82 HA "Cysteine (SH)" 85
-biotype 83 CB "Cysteine (SH)" 148
-biotype 84 HB "Cysteine (SH)" 85
-biotype 85 SG "Cysteine (SH)" 142
-biotype 86 HG "Cysteine (SH)" 146
-biotype 87 N "Cystine (SS)" 180
-biotype 88 CA "Cystine (SS)" 166
-biotype 89 C "Cystine (SS)" 177
-biotype 90 HN "Cystine (SS)" 183
-biotype 91 O "Cystine (SS)" 178
-biotype 92 HA "Cystine (SS)" 85
-biotype 93 CB "Cystine (SS)" 156
-biotype 94 HB "Cystine (SS)" 85
-biotype 95 SG "Cystine (SS)" 145
-biotype 96 N "Cysteine (S-)" -1
-biotype 97 CA "Cysteine (S-)" -1
-biotype 98 C "Cysteine (S-)" -1
-biotype 99 HN "Cysteine (S-)" -1
-biotype 100 O "Cysteine (S-)" -1
-biotype 101 HA "Cysteine (S-)" -1
-biotype 102 CB "Cysteine (S-)" -1
-biotype 103 HB "Cysteine (S-)" -1
-biotype 104 SG "Cysteine (S-)" -1
-biotype 105 N "Proline" 181
-biotype 106 CA "Proline" 188
-biotype 107 C "Proline" 177
-biotype 108 O "Proline" 178
-biotype 109 HA "Proline" 85
-biotype 110 CB "Proline" 81
-biotype 111 HB "Proline" 85
-biotype 112 CG "Proline" 81
-biotype 113 HG "Proline" 85
-biotype 114 CD "Proline" 187
-biotype 115 HD "Proline" 85
-biotype 116 N "Phenylalanine" 180
-biotype 117 CA "Phenylalanine" 166
-biotype 118 C "Phenylalanine" 177
-biotype 119 HN "Phenylalanine" 183
-biotype 120 O "Phenylalanine" 178
-biotype 121 HA "Phenylalanine" 85
-biotype 122 CB "Phenylalanine" 94
-biotype 123 HB "Phenylalanine" 85
-biotype 124 CG "Phenylalanine" 90
-biotype 125 CD "Phenylalanine" 90
-biotype 126 HD "Phenylalanine" 91
-biotype 127 CE "Phenylalanine" 90
-biotype 128 HE "Phenylalanine" 91
-biotype 129 CZ "Phenylalanine" 90
-biotype 130 HZ "Phenylalanine" 91
-biotype 131 N "Tyrosine" 180
-biotype 132 CA "Tyrosine" 166
-biotype 133 C "Tyrosine" 177
-biotype 134 HN "Tyrosine" 183
-biotype 135 O "Tyrosine" 178
-biotype 136 HA "Tyrosine" 85
-biotype 137 CB "Tyrosine" 94
-biotype 138 HB "Tyrosine" 85
-biotype 139 CG "Tyrosine" 90
-biotype 140 CD "Tyrosine" 90
-biotype 141 HD "Tyrosine" 91
-biotype 142 CE "Tyrosine" 90
-biotype 143 HE "Tyrosine" 91
-biotype 144 CZ "Tyrosine" 108
-biotype 145 OH "Tyrosine" 109
-biotype 146 HH "Tyrosine" 110
-biotype 147 N "Tyrosine (O-)" -1
-biotype 148 CA "Tyrosine (O-)" -1
-biotype 149 C "Tyrosine (O-)" -1
-biotype 150 HN "Tyrosine (O-)" -1
-biotype 151 O "Tyrosine (O-)" -1
-biotype 152 HA "Tyrosine (O-)" -1
-biotype 153 CB "Tyrosine (O-)" -1
-biotype 154 HB "Tyrosine (O-)" -1
-biotype 155 CG "Tyrosine (O-)" -1
-biotype 156 CD "Tyrosine (O-)" -1
-biotype 157 HD "Tyrosine (O-)" -1
-biotype 158 CE "Tyrosine (O-)" -1
-biotype 159 HE "Tyrosine (O-)" -1
-biotype 160 CZ "Tyrosine (O-)" -1
-biotype 161 OH "Tyrosine (O-)" -1
-biotype 162 N "Tryptophan" 180
-biotype 163 CA "Tryptophan" 166
-biotype 164 C "Tryptophan" 177
-biotype 165 HN "Tryptophan" 183
-biotype 166 O "Tryptophan" 178
-biotype 167 HA "Tryptophan" 85
-biotype 168 CB "Tryptophan" 81
-biotype 169 HB "Tryptophan" 85
-biotype 170 CG "Tryptophan" 441
-biotype 171 CD1 "Tryptophan" 455
-biotype 172 HD1 "Tryptophan" 91
-biotype 173 CD2 "Tryptophan" 442
-biotype 174 NE1 "Tryptophan" 444
-biotype 175 HE1 "Tryptophan" 445
-biotype 176 CE2 "Tryptophan" 443
-biotype 177 CE3 "Tryptophan" 90
-biotype 178 HE3 "Tryptophan" 91
-biotype 179 CZ2 "Tryptophan" 90
-biotype 180 HZ2 "Tryptophan" 91
-biotype 181 CZ3 "Tryptophan" 90
-biotype 182 HZ3 "Tryptophan" 91
-biotype 183 CH2 "Tryptophan" 90
-biotype 184 HH2 "Tryptophan" 91
-biotype 185 N "Histidine (+)" 180
-biotype 186 CA "Histidine (+)" 166
-biotype 187 C "Histidine (+)" 177
-biotype 188 HN "Histidine (+)" 183
-biotype 189 O "Histidine (+)" 178
-biotype 190 HA "Histidine (+)" 85
-biotype 191 CB "Histidine (+)" 446
-biotype 192 HB "Histidine (+)" 85
-biotype 193 CG "Histidine (+)" 451
-biotype 194 ND1 "Histidine (+)" 453
-biotype 195 HD1 "Histidine (+)" 454
-biotype 196 CD2 "Histidine (+)" 451
-biotype 197 HD2 "Histidine (+)" 91
-biotype 198 CE1 "Histidine (+)" 450
-biotype 199 HE1 "Histidine (+)" 91
-biotype 200 NE2 "Histidine (+)" 453
-biotype 201 HE2 "Histidine (+)" 454
-biotype 202 N "Histidine (HD)" 180
-biotype 203 CA "Histidine (HD)" 166
-biotype 204 C "Histidine (HD)" 177
-biotype 205 HN "Histidine (HD)" 183
-biotype 206 O "Histidine (HD)" 178
-biotype 207 HA "Histidine (HD)" 85
-biotype 208 CB "Histidine (HD)" 446
-biotype 209 HB "Histidine (HD)" 85
-biotype 210 CG "Histidine (HD)" 449
-biotype 211 ND1 "Histidine (HD)" 444
-biotype 212 HD1 "Histidine (HD)" 445
-biotype 213 CD2 "Histidine (HD)" 448
-biotype 214 HD2 "Histidine (HD)" 91
-biotype 215 CE1 "Histidine (HD)" 447
-biotype 216 HE1 "Histidine (HD)" 91
-biotype 217 NE2 "Histidine (HD)" 452
-biotype 218 N "Histidine (HE)" 180
-biotype 219 CA "Histidine (HE)" 166
-biotype 220 C "Histidine (HE)" 177
-biotype 221 HN "Histidine (HE)" 183
-biotype 222 O "Histidine (HE)" 178
-biotype 223 HA "Histidine (HE)" 85
-biotype 224 CB "Histidine (HE)" 446
-biotype 225 HB "Histidine (HE)" 85
-biotype 226 CG "Histidine (HE)" 448
-biotype 227 ND1 "Histidine (HE)" 452
-biotype 228 CD2 "Histidine (HE)" 449
-biotype 229 HD2 "Histidine (HE)" 91
-biotype 230 CE1 "Histidine (HE)" 447
-biotype 231 HE1 "Histidine (HE)" 91
-biotype 232 NE2 "Histidine (HE)" 444
-biotype 233 HE2 "Histidine (HE)" 445
-biotype 234 N "Aspartic Acid" 180
-biotype 235 CA "Aspartic Acid" 166
-biotype 236 C "Aspartic Acid" 177
-biotype 237 HN "Aspartic Acid" 183
-biotype 238 O "Aspartic Acid" 178
-biotype 239 HA "Aspartic Acid" 85
-biotype 240 CB "Aspartic Acid" 216
-biotype 241 HB "Aspartic Acid" 85
-biotype 242 CG "Aspartic Acid" 213
-biotype 243 OD "Aspartic Acid" 214
-biotype 244 N "Aspartic Acid (COOH)" -1
-biotype 245 CA "Aspartic Acid (COOH)" -1
-biotype 246 C "Aspartic Acid (COOH)" -1
-biotype 247 HN "Aspartic Acid (COOH)" -1
-biotype 248 O "Aspartic Acid (COOH)" -1
-biotype 249 HA "Aspartic Acid (COOH)" -1
-biotype 250 CB "Aspartic Acid (COOH)" -1
-biotype 251 HB "Aspartic Acid (COOH)" -1
-biotype 252 CG "Aspartic Acid (COOH)" -1
-biotype 253 OD1 "Aspartic Acid (COOH)" -1
-biotype 254 OD2 "Aspartic Acid (COOH)" -1
-biotype 255 HD2 "Aspartic Acid (COOH)" -1
-biotype 256 N "Asparagine" 180
-biotype 257 CA "Asparagine" 166
-biotype 258 C "Asparagine" 177
-biotype 259 HN "Asparagine" 183
-biotype 260 O "Asparagine" 178
-biotype 261 HA "Asparagine" 85
-biotype 262 CB "Asparagine" 81
-biotype 263 HB "Asparagine" 85
-biotype 264 CG "Asparagine" 177
-biotype 265 OD1 "Asparagine" 178
-biotype 266 ND2 "Asparagine" 179
-biotype 267 HD2 "Asparagine" 182
-biotype 268 N "Glutamic Acid" 180
-biotype 269 CA "Glutamic Acid" 166
-biotype 270 C "Glutamic Acid" 177
-biotype 271 HN "Glutamic Acid" 183
-biotype 272 O "Glutamic Acid" 178
-biotype 273 HA "Glutamic Acid" 85
-biotype 274 CB "Glutamic Acid" 81
-biotype 275 HB "Glutamic Acid" 85
-biotype 276 CG "Glutamic Acid" 216
-biotype 277 HG "Glutamic Acid" 85
-biotype 278 CD "Glutamic Acid" 213
-biotype 279 OE "Glutamic Acid" 214
-biotype 280 N "Glutamic Acid (COOH)" -1
-biotype 281 CA "Glutamic Acid (COOH)" -1
-biotype 282 C "Glutamic Acid (COOH)" -1
-biotype 283 HN "Glutamic Acid (COOH)" -1
-biotype 284 O "Glutamic Acid (COOH)" -1
-biotype 285 HA "Glutamic Acid (COOH)" -1
-biotype 286 CB "Glutamic Acid (COOH)" -1
-biotype 287 HB "Glutamic Acid (COOH)" -1
-biotype 288 CG "Glutamic Acid (COOH)" -1
-biotype 289 HG "Glutamic Acid (COOH)" -1
-biotype 290 CD "Glutamic Acid (COOH)" -1
-biotype 291 OE1 "Glutamic Acid (COOH)" -1
-biotype 292 OE2 "Glutamic Acid (COOH)" -1
-biotype 293 HE2 "Glutamic Acid (COOH)" -1
-biotype 294 N "Glutamine" 180
-biotype 295 CA "Glutamine" 166
-biotype 296 C "Glutamine" 177
-biotype 297 HN "Glutamine" 183
-biotype 298 O "Glutamine" 178
-biotype 299 HA "Glutamine" 85
-biotype 300 CB "Glutamine" 81
-biotype 301 HB "Glutamine" 85
-biotype 302 CG "Glutamine" 81
-biotype 303 HG "Glutamine" 85
-biotype 304 CD "Glutamine" 177
-biotype 305 OE1 "Glutamine" 178
-biotype 306 NE2 "Glutamine" 179
-biotype 307 HE2 "Glutamine" 182
-biotype 308 N "Methionine" 180
-biotype 309 CA "Methionine" 166
-biotype 310 C "Methionine" 177
-biotype 311 HN "Methionine" 183
-biotype 312 O "Methionine" 178
-biotype 313 HA "Methionine" 85
-biotype 314 CB "Methionine" 81
-biotype 315 HB "Methionine" 85
-biotype 316 CG "Methionine" 152
-biotype 317 HG "Methionine" 85
-biotype 318 SD "Methionine" 144
-biotype 319 CE "Methionine" 151
-biotype 320 HE "Methionine" 85
-biotype 321 N "Lysine" 180
-biotype 322 CA "Lysine" 166
-biotype 323 C "Lysine" 177
-biotype 324 HN "Lysine" 183
-biotype 325 O "Lysine" 178
-biotype 326 HA "Lysine" 85
-biotype 327 CB "Lysine" 81
-biotype 328 HB "Lysine" 85
-biotype 329 CG "Lysine" 81
-biotype 330 HG "Lysine" 85
-biotype 331 CD "Lysine" 81
-biotype 332 HD "Lysine" 85
-biotype 333 CE "Lysine" 235
-biotype 334 HE "Lysine" 85
-biotype 335 NZ "Lysine" 230
-biotype 336 HZ "Lysine" 233
-biotype 337 N "Lysine (NH2)" -1
-biotype 338 CA "Lysine (NH2)" -1
-biotype 339 C "Lysine (NH2)" -1
-biotype 340 HN "Lysine (NH2)" -1
-biotype 341 O "Lysine (NH2)" -1
-biotype 342 HA "Lysine (NH2)" -1
-biotype 343 CB "Lysine (NH2)" -1
-biotype 344 HB "Lysine (NH2)" -1
-biotype 345 CG "Lysine (NH2)" -1
-biotype 346 HG "Lysine (NH2)" -1
-biotype 347 CD "Lysine (NH2)" -1
-biotype 348 HD "Lysine (NH2)" -1
-biotype 349 CE "Lysine (NH2)" -1
-biotype 350 HE "Lysine (NH2)" -1
-biotype 351 NZ "Lysine (NH2)" -1
-biotype 352 HZ "Lysine (NH2)" -1
-biotype 353 N "Arginine" 180
-biotype 354 CA "Arginine" 166
-biotype 355 C "Arginine" 177
-biotype 356 HN "Arginine" 183
-biotype 357 O "Arginine" 178
-biotype 358 HA "Arginine" 85
-biotype 359 CB "Arginine" 81
-biotype 360 HB "Arginine" 85
-biotype 361 CG "Arginine" 251
-biotype 362 HG "Arginine" 85
-biotype 363 CD "Arginine" 250
-biotype 364 HD "Arginine" 85
-biotype 365 NE "Arginine" 246
-biotype 366 HE "Arginine" 247
-biotype 367 CZ "Arginine" 245
-biotype 368 NH "Arginine" 243
-biotype 369 HH "Arginine" 244
-biotype 370 N "Ornithine" 180
-biotype 371 CA "Ornithine" 166
-biotype 372 C "Ornithine" 177
-biotype 373 HN "Ornithine" 183
-biotype 374 O "Ornithine" 178
-biotype 375 HA "Ornithine" 85
-biotype 376 CB "Ornithine" 81
-biotype 377 HB "Ornithine" 85
-biotype 378 CG "Ornithine" 81
-biotype 379 HG "Ornithine" 85
-biotype 380 CD "Ornithine" 235
-biotype 381 HD "Ornithine" 85
-biotype 382 NE "Ornithine" 230
-biotype 383 HE "Ornithine" 233
-biotype 384 N "MethylAlanine (AIB)" 180
-biotype 385 CA "MethylAlanine (AIB)" 167
-biotype 386 C "MethylAlanine (AIB)" 177
-biotype 387 HN "MethylAlanine (AIB)" 183
-biotype 388 O "MethylAlanine (AIB)" 178
-biotype 389 CB "MethylAlanine (AIB)" 80
-biotype 390 HB "MethylAlanine (AIB)" 85
-biotype 391 N "Pyroglutamic Acid" 180
-biotype 392 CA "Pyroglutamic Acid" 166
-biotype 393 C "Pyroglutamic Acid" 177
-biotype 394 HN "Pyroglutamic Acid" 183
-biotype 395 O "Pyroglutamic Acid" 178
-biotype 396 HA "Pyroglutamic Acid" 85
-biotype 397 CB "Pyroglutamic Acid" 81
-biotype 398 HB "Pyroglutamic Acid" 85
-biotype 399 CG "Pyroglutamic Acid" 216
-biotype 400 HG "Pyroglutamic Acid" 85
-biotype 401 CD "Pyroglutamic Acid" 177
-biotype 402 OE "Pyroglutamic Acid" 178
-biotype 403 N "N-Terminal GLY" 230
-biotype 404 CA "N-Terminal GLY" 235
-biotype 405 C "N-Terminal GLY" 177
-biotype 406 HN "N-Terminal GLY" 233
-biotype 407 O "N-Terminal GLY" 178
-biotype 408 HA "N-Terminal GLY" 85
-biotype 409 N "N-Terminal ALA" 230
-biotype 410 CA "N-Terminal ALA" 236
-biotype 411 C "N-Terminal ALA" 177
-biotype 412 HN "N-Terminal ALA" 233
-biotype 413 O "N-Terminal ALA" 178
-biotype 414 HA "N-Terminal ALA" 85
-biotype 415 N "N-Terminal VAL" 230
-biotype 416 CA "N-Terminal VAL" 236
-biotype 417 C "N-Terminal VAL" 177
-biotype 418 HN "N-Terminal VAL" 233
-biotype 419 O "N-Terminal VAL" 178
-biotype 420 HA "N-Terminal VAL" 85
-biotype 421 N "N-Terminal LEU" 230
-biotype 422 CA "N-Terminal LEU" 236
-biotype 423 C "N-Terminal LEU" 177
-biotype 424 HN "N-Terminal LEU" 233
-biotype 425 O "N-Terminal LEU" 178
-biotype 426 HA "N-Terminal LEU" 85
-biotype 427 N "N-Terminal ILE" 230
-biotype 428 CA "N-Terminal ILE" 236
-biotype 429 C "N-Terminal ILE" 177
-biotype 430 HN "N-Terminal ILE" 233
-biotype 431 O "N-Terminal ILE" 178
-biotype 432 HA "N-Terminal ILE" 85
-biotype 433 N "N-Terminal SER" 230
-biotype 434 CA "N-Terminal SER" 236
-biotype 435 C "N-Terminal SER" 177
-biotype 436 HN "N-Terminal SER" 233
-biotype 437 O "N-Terminal SER" 178
-biotype 438 HA "N-Terminal SER" 85
-biotype 439 N "N-Terminal THR" 230
-biotype 440 CA "N-Terminal THR" 236
-biotype 441 C "N-Terminal THR" 177
-biotype 442 HN "N-Terminal THR" 233
-biotype 443 O "N-Terminal THR" 178
-biotype 444 HA "N-Terminal THR" 85
-biotype 445 N "N-Terminal CYS (SH)" 230
-biotype 446 CA "N-Terminal CYS (SH)" 236
-biotype 447 C "N-Terminal CYS (SH)" 177
-biotype 448 HN "N-Terminal CYS (SH)" 233
-biotype 449 O "N-Terminal CYS (SH)" 178
-biotype 450 HA "N-Terminal CYS (SH)" 85
-biotype 451 N "N-Terminal CYX (SS)" 230
-biotype 452 CA "N-Terminal CYX (SS)" 236
-biotype 453 C "N-Terminal CYX (SS)" 177
-biotype 454 HN "N-Terminal CYX (SS)" 233
-biotype 455 O "N-Terminal CYX (SS)" 178
-biotype 456 HA "N-Terminal CYX (SS)" 85
-biotype 457 N "N-Terminal CYD (S-)" -1
-biotype 458 CA "N-Terminal CYD (S-)" -1
-biotype 459 C "N-Terminal CYD (S-)" -1
-biotype 460 HN "N-Terminal CYD (S-)" -1
-biotype 461 O "N-Terminal CYD (S-)" -1
-biotype 462 HA "N-Terminal CYD (S-)" -1
-biotype 463 N "N-Terminal PRO" 252
-biotype 464 CA "N-Terminal PRO" 238
-biotype 465 C "N-Terminal PRO" 177
-biotype 466 HN "N-Terminal PRO" 253
-biotype 467 O "N-Terminal PRO" 178
-biotype 468 HA "N-Terminal PRO" 85
-biotype 469 CD "N-Terminal PRO" 239
-biotype 470 HD "N-Terminal PRO" 85
-biotype 471 N "N-Terminal PHE" 230
-biotype 472 CA "N-Terminal PHE" 236
-biotype 473 C "N-Terminal PHE" 177
-biotype 474 HN "N-Terminal PHE" 233
-biotype 475 O "N-Terminal PHE" 178
-biotype 476 HA "N-Terminal PHE" 85
-biotype 477 N "N-Terminal TYR" 230
-biotype 478 CA "N-Terminal TYR" 236
-biotype 479 C "N-Terminal TYR" 177
-biotype 480 HN "N-Terminal TYR" 233
-biotype 481 O "N-Terminal TYR" 178
-biotype 482 HA "N-Terminal TYR" 85
-biotype 483 N "N-Terminal TYD (O-)" -1
-biotype 484 CA "N-Terminal TYD (O-)" -1
-biotype 485 C "N-Terminal TYD (O-)" -1
-biotype 486 HN "N-Terminal TYD (O-)" -1
-biotype 487 O "N-Terminal TYD (O-)" -1
-biotype 488 HA "N-Terminal TYD (O-)" -1
-biotype 489 N "N-Terminal TRP" 230
-biotype 490 CA "N-Terminal TRP" 236
-biotype 491 C "N-Terminal TRP" 177
-biotype 492 HN "N-Terminal TRP" 233
-biotype 493 O "N-Terminal TRP" 178
-biotype 494 HA "N-Terminal TRP" 85
-biotype 495 N "N-Terminal HIS (+)" 230
-biotype 496 CA "N-Terminal HIS (+)" 236
-biotype 497 C "N-Terminal HIS (+)" 177
-biotype 498 HN "N-Terminal HIS (+)" 233
-biotype 499 O "N-Terminal HIS (+)" 178
-biotype 500 HA "N-Terminal HIS (+)" 85
-biotype 501 N "N-Terminal HIS (HD)" 230
-biotype 502 CA "N-Terminal HIS (HD)" 236
-biotype 503 C "N-Terminal HIS (HD)" 177
-biotype 504 HN "N-Terminal HIS (HD)" 233
-biotype 505 O "N-Terminal HIS (HD)" 178
-biotype 506 HA "N-Terminal HIS (HD)" 85
-biotype 507 N "N-Terminal HIS (HE)" 230
-biotype 508 CA "N-Terminal HIS (HE)" 236
-biotype 509 C "N-Terminal HIS (HE)" 177
-biotype 510 HN "N-Terminal HIS (HE)" 233
-biotype 511 O "N-Terminal HIS (HE)" 178
-biotype 512 HA "N-Terminal HIS (HE)" 85
-biotype 513 N "N-Terminal ASP" 230
-biotype 514 CA "N-Terminal ASP" 236
-biotype 515 C "N-Terminal ASP" 177
-biotype 516 HN "N-Terminal ASP" 233
-biotype 517 O "N-Terminal ASP" 178
-biotype 518 HA "N-Terminal ASP" 85
-biotype 519 N "N-Terminal ASH (COOH)" -1
-biotype 520 CA "N-Terminal ASH (COOH)" -1
-biotype 521 C "N-Terminal ASH (COOH)" -1
-biotype 522 HN "N-Terminal ASH (COOH)" -1
-biotype 523 O "N-Terminal ASH (COOH)" -1
-biotype 524 HA "N-Terminal ASH (COOH)" -1
-biotype 525 N "N-Terminal ASN" 230
-biotype 526 CA "N-Terminal ASN" 236
-biotype 527 C "N-Terminal ASN" 177
-biotype 528 HN "N-Terminal ASN" 233
-biotype 529 O "N-Terminal ASN" 178
-biotype 530 HA "N-Terminal ASN" 85
-biotype 531 N "N-Terminal GLU" 230
-biotype 532 CA "N-Terminal GLU" 236
-biotype 533 C "N-Terminal GLU" 177
-biotype 534 HN "N-Terminal GLU" 233
-biotype 535 O "N-Terminal GLU" 178
-biotype 536 HA "N-Terminal GLU" 85
-biotype 537 N "N-Terminal GLH (COOH)" -1
-biotype 538 CA "N-Terminal GLH (COOH)" -1
-biotype 539 C "N-Terminal GLH (COOH)" -1
-biotype 540 HN "N-Terminal GLH (COOH)" -1
-biotype 541 O "N-Terminal GLH (COOH)" -1
-biotype 542 HA "N-Terminal GLH (COOH)" -1
-biotype 543 N "N-Terminal GLN" 230
-biotype 544 CA "N-Terminal GLN" 236
-biotype 545 C "N-Terminal GLN" 177
-biotype 546 HN "N-Terminal GLN" 233
-biotype 547 O "N-Terminal GLN" 178
-biotype 548 HA "N-Terminal GLN" 85
-biotype 549 N "N-Terminal MET" 230
-biotype 550 CA "N-Terminal MET" 236
-biotype 551 C "N-Terminal MET" 177
-biotype 552 HN "N-Terminal MET" 233
-biotype 553 O "N-Terminal MET" 178
-biotype 554 HA "N-Terminal MET" 85
-biotype 555 N "N-Terminal LYS" 230
-biotype 556 CA "N-Terminal LYS" 236
-biotype 557 C "N-Terminal LYS" 177
-biotype 558 HN "N-Terminal LYS" 233
-biotype 559 O "N-Terminal LYS" 178
-biotype 560 HA "N-Terminal LYS" 85
-biotype 561 N "N-Terminal LYD (NH2)" -1
-biotype 562 CA "N-Terminal LYD (NH2)" -1
-biotype 563 C "N-Terminal LYD (NH2)" -1
-biotype 564 HN "N-Terminal LYD (NH2)" -1
-biotype 565 O "N-Terminal LYD (NH2)" -1
-biotype 566 HA "N-Terminal LYD (NH2)" -1
-biotype 567 N "N-Terminal ARG" 230
-biotype 568 CA "N-Terminal ARG" 236
-biotype 569 C "N-Terminal ARG" 177
-biotype 570 HN "N-Terminal ARG" 233
-biotype 571 O "N-Terminal ARG" 178
-biotype 572 HA "N-Terminal ARG" 85
-biotype 573 N "N-Terminal ORN" 230
-biotype 574 CA "N-Terminal ORN" 236
-biotype 575 C "N-Terminal ORN" 177
-biotype 576 HN "N-Terminal ORN" 233
-biotype 577 O "N-Terminal ORN" 178
-biotype 578 HA "N-Terminal ORN" 85
-biotype 579 N "N-Terminal AIB" 230
-biotype 580 CA "N-Terminal AIB" 237
-biotype 581 C "N-Terminal AIB" 177
-biotype 582 HN "N-Terminal AIB" 233
-biotype 583 O "N-Terminal AIB" 178
-biotype 584 N "C-Terminal GLY" 180
-biotype 585 CA "C-Terminal GLY" 226
-biotype 586 C "C-Terminal GLY" 213
-biotype 587 HN "C-Terminal GLY" 183
-biotype 588 OXT "C-Terminal GLY" 214
-biotype 589 HA "C-Terminal GLY" 85
-biotype 590 N "C-Terminal ALA" 180
-biotype 591 CA "C-Terminal ALA" 225
-biotype 592 C "C-Terminal ALA" 213
-biotype 593 HN "C-Terminal ALA" 183
-biotype 594 OXT "C-Terminal ALA" 214
-biotype 595 HA "C-Terminal ALA" 85
-biotype 596 N "C-Terminal VAL" 180
-biotype 597 CA "C-Terminal VAL" 225
-biotype 598 C "C-Terminal VAL" 213
-biotype 599 HN "C-Terminal VAL" 183
-biotype 600 OXT "C-Terminal VAL" 214
-biotype 601 HA "C-Terminal VAL" 85
-biotype 602 N "C-Terminal LEU" 180
-biotype 603 CA "C-Terminal LEU" 225
-biotype 604 C "C-Terminal LEU" 213
-biotype 605 HN "C-Terminal LEU" 183
-biotype 606 OXT "C-Terminal LEU" 214
-biotype 607 HA "C-Terminal LEU" 85
-biotype 608 N "C-Terminal ILE" 180
-biotype 609 CA "C-Terminal ILE" 225
-biotype 610 C "C-Terminal ILE" 213
-biotype 611 HN "C-Terminal ILE" 183
-biotype 612 OXT "C-Terminal ILE" 214
-biotype 613 HA "C-Terminal ILE" 85
-biotype 614 N "C-Terminal SER" 180
-biotype 615 CA "C-Terminal SER" 225
-biotype 616 C "C-Terminal SER" 213
-biotype 617 HN "C-Terminal SER" 183
-biotype 618 OXT "C-Terminal SER" 214
-biotype 619 HA "C-Terminal SER" 85
-biotype 620 N "C-Terminal THR" 180
-biotype 621 CA "C-Terminal THR" 225
-biotype 622 C "C-Terminal THR" 213
-biotype 623 HN "C-Terminal THR" 183
-biotype 624 OXT "C-Terminal THR" 214
-biotype 625 HA "C-Terminal THR" 85
-biotype 626 N "C-Terminal CYS (SH)" 180
-biotype 627 CA "C-Terminal CYS (SH)" 225
-biotype 628 C "C-Terminal CYS (SH)" 213
-biotype 629 HN "C-Terminal CYS (SH)" 183
-biotype 630 OXT "C-Terminal CYS (SH)" 214
-biotype 631 HA "C-Terminal CYS (SH)" 85
-biotype 632 N "C-Terminal CYX (SS)" 180
-biotype 633 CA "C-Terminal CYX (SS)" 225
-biotype 634 C "C-Terminal CYX (SS)" 213
-biotype 635 HN "C-Terminal CYX (SS)" 183
-biotype 636 OXT "C-Terminal CYX (SS)" 214
-biotype 637 HA "C-Terminal CYX (SS)" 85
-biotype 638 N "C-Terminal CYD (S-)" -1
-biotype 639 CA "C-Terminal CYD (S-)" -1
-biotype 640 C "C-Terminal CYD (S-)" -1
-biotype 641 HN "C-Terminal CYD (S-)" -1
-biotype 642 OXT "C-Terminal CYD (S-)" -1
-biotype 643 HA "C-Terminal CYD (S-)" -1
-biotype 644 N "C-Terminal PRO" 181
-biotype 645 CA "C-Terminal PRO" 228
-biotype 646 C "C-Terminal PRO" 213
-biotype 647 OXT "C-Terminal PRO" 214
-biotype 648 HA "C-Terminal PRO" 85
-biotype 649 N "C-Terminal PHE" 180
-biotype 650 CA "C-Terminal PHE" 225
-biotype 651 C "C-Terminal PHE" 213
-biotype 652 HN "C-Terminal PHE" 183
-biotype 653 OXT "C-Terminal PHE" 214
-biotype 654 HA "C-Terminal PHE" 85
-biotype 655 N "C-Terminal TYR" 180
-biotype 656 CA "C-Terminal TYR" 225
-biotype 657 C "C-Terminal TYR" 213
-biotype 658 HN "C-Terminal TYR" 183
-biotype 659 OXT "C-Terminal TYR" 214
-biotype 660 HA "C-Terminal TYR" 85
-biotype 661 N "C-Terminal TYD (O-)" -1
-biotype 662 CA "C-Terminal TYD (O-)" -1
-biotype 663 C "C-Terminal TYD (O-)" -1
-biotype 664 HN "C-Terminal TYD (O-)" -1
-biotype 665 OXT "C-Terminal TYD (O-)" -1
-biotype 666 HA "C-Terminal TYD (O-)" -1
-biotype 667 N "C-Terminal TRP" 180
-biotype 668 CA "C-Terminal TRP" 225
-biotype 669 C "C-Terminal TRP" 213
-biotype 670 HN "C-Terminal TRP" 183
-biotype 671 OXT "C-Terminal TRP" 214
-biotype 672 HA "C-Terminal TRP" 85
-biotype 673 N "C-Terminal HIS (+)" 180
-biotype 674 CA "C-Terminal HIS (+)" 225
-biotype 675 C "C-Terminal HIS (+)" 213
-biotype 676 HN "C-Terminal HIS (+)" 183
-biotype 677 OXT "C-Terminal HIS (+)" 214
-biotype 678 HA "C-Terminal HIS (+)" 85
-biotype 679 N "C-Terminal HIS (HD)" 180
-biotype 680 CA "C-Terminal HIS (HD)" 225
-biotype 681 C "C-Terminal HIS (HD)" 213
-biotype 682 HN "C-Terminal HIS (HD)" 183
-biotype 683 OXT "C-Terminal HIS (HD)" 214
-biotype 684 HA "C-Terminal HIS (HD)" 85
-biotype 685 N "C-Terminal HIS (HE)" 180
-biotype 686 CA "C-Terminal HIS (HE)" 225
-biotype 687 C "C-Terminal HIS (HE)" 213
-biotype 688 HN "C-Terminal HIS (HE)" 183
-biotype 689 OXT "C-Terminal HIS (HE)" 214
-biotype 690 HA "C-Terminal HIS (HE)" 85
-biotype 691 N "C-Terminal ASP" 180
-biotype 692 CA "C-Terminal ASP" 225
-biotype 693 C "C-Terminal ASP" 213
-biotype 694 HN "C-Terminal ASP" 183
-biotype 695 OXT "C-Terminal ASP" 214
-biotype 696 HA "C-Terminal ASP" 85
-biotype 697 N "C-Terminal ASH (COOH)" -1
-biotype 698 CA "C-Terminal ASH (COOH)" -1
-biotype 699 C "C-Terminal ASH (COOH)" -1
-biotype 700 HN "C-Terminal ASH (COOH)" -1
-biotype 701 OXT "C-Terminal ASH (COOH)" -1
-biotype 702 HA "C-Terminal ASH (COOH)" -1
-biotype 703 N "C-Terminal ASN" 180
-biotype 704 CA "C-Terminal ASN" 225
-biotype 705 C "C-Terminal ASN" 213
-biotype 706 HN "C-Terminal ASN" 183
-biotype 707 OXT "C-Terminal ASN" 214
-biotype 708 HA "C-Terminal ASN" 85
-biotype 709 N "C-Terminal GLU" 180
-biotype 710 CA "C-Terminal GLU" 225
-biotype 711 C "C-Terminal GLU" 213
-biotype 712 HN "C-Terminal GLU" 183
-biotype 713 OXT "C-Terminal GLU" 214
-biotype 714 HA "C-Terminal GLU" 85
-biotype 715 N "C-Terminal GLH (COOH)" -1
-biotype 716 CA "C-Terminal GLH (COOH)" -1
-biotype 717 C "C-Terminal GLH (COOH)" -1
-biotype 718 HN "C-Terminal GLH (COOH)" -1
-biotype 719 OXT "C-Terminal GLH (COOH)" -1
-biotype 720 HA "C-Terminal GLH (COOH)" -1
-biotype 721 N "C-Terminal GLN" 180
-biotype 722 CA "C-Terminal GLN" 225
-biotype 723 C "C-Terminal GLN" 213
-biotype 724 HN "C-Terminal GLN" 183
-biotype 725 OXT "C-Terminal GLN" 214
-biotype 726 HA "C-Terminal GLN" 85
-biotype 727 N "C-Terminal MET" 180
-biotype 728 CA "C-Terminal MET" 225
-biotype 729 C "C-Terminal MET" 213
-biotype 730 HN "C-Terminal MET" 183
-biotype 731 OXT "C-Terminal MET" 214
-biotype 732 HA "C-Terminal MET" 85
-biotype 733 N "C-Terminal LYS" 180
-biotype 734 CA "C-Terminal LYS" 225
-biotype 735 C "C-Terminal LYS" 213
-biotype 736 HN "C-Terminal LYS" 183
-biotype 737 OXT "C-Terminal LYS" 214
-biotype 738 HA "C-Terminal LYS" 85
-biotype 739 N "C-Terminal LYD (NH2)" -1
-biotype 740 CA "C-Terminal LYD (NH2)" -1
-biotype 741 C "C-Terminal LYD (NH2)" -1
-biotype 742 HN "C-Terminal LYD (NH2)" -1
-biotype 743 OXT "C-Terminal LYD (NH2)" -1
-biotype 744 HA "C-Terminal LYD (NH2)" -1
-biotype 745 N "C-Terminal ARG" 180
-biotype 746 CA "C-Terminal ARG" 225
-biotype 747 C "C-Terminal ARG" 213
-biotype 748 HN "C-Terminal ARG" 183
-biotype 749 OXT "C-Terminal ARG" 214
-biotype 750 HA "C-Terminal ARG" 85
-biotype 751 N "C-Terminal ORN" 180
-biotype 752 CA "C-Terminal ORN" 225
-biotype 753 C "C-Terminal ORN" 213
-biotype 754 HN "C-Terminal ORN" 183
-biotype 755 OXT "C-Terminal ORN" 214
-biotype 756 HA "C-Terminal ORN" 85
-biotype 757 N "C-Terminal AIB" 180
-biotype 758 CA "C-Terminal AIB" 227
-biotype 759 C "C-Terminal AIB" 213
-biotype 760 HN "C-Terminal AIB" 183
-biotype 761 OXT "C-Terminal AIB" 214
-biotype 762 N "Deprotonated N-Terminus" -1
-biotype 763 H "Deprotonated N-Terminus" -1
-biotype 764 C "Formyl N-Terminus" 177
-biotype 765 H "Formyl N-Terminus" 221
-biotype 766 O "Formyl N-Terminus" 178
-biotype 767 CH3 "Acetyl N-Terminus" 80
-biotype 768 H "Acetyl N-Terminus" 85
-biotype 769 C "Acetyl N-Terminus" 177
-biotype 770 O "Acetyl N-Terminus" 178
-biotype 771 C "Protonated C-Terminus" -1
-biotype 772 O "Protonated C-Terminus" -1
-biotype 773 OH "Protonated C-Terminus" -1
-biotype 774 HO "Protonated C-Terminus" -1
-biotype 775 N "Amide C-Terminus" 179
-biotype 776 HN "Amide C-Terminus" 182
-biotype 777 N "N-MeAmide C-Terminus" 180
-biotype 778 HN "N-MeAmide C-Terminus" 183
-biotype 779 CH3 "N-MeAmide C-Terminus" 184
-biotype 780 H "N-MeAmide C-Terminus" 85
-biotype 2001 O "Water" 63
-biotype 2002 H "Water" 64
-biotype 2003 NA "Sodium Ion" -1
-biotype 2004 K "Potassium Ion" -1
-biotype 2005 MG "Magnesium Ion" -1
-biotype 2006 CA "Calcium Ion" -1
-biotype 2007 CL "Chloride Ion" -1
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt
deleted file mode 100644
index 49458a5b4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt
+++ /dev/null
@@ -1,28 +0,0 @@
-import "ethylene.lt" # <- defines the "Ethylene" molecule type.
-import "benzene.lt" # <- defines the "Benzene" molecule type.
-
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 80.00 xlo xhi
- 0.0 80.00 ylo yhi
- 0.0 80.00 zlo zhi
-}
-
-# Create 1000 ethylenes and 500 benzenes
-
-ethylenes = new Ethylene[10].move(8.0, 0, 0)
- [10].move(0, 8.0, 0)
- [10].move(0, 0, 8.0)
-
-benzenes = new Benzene[10].move(8.0, 0, 0)
- [10].move(0, 8.0, 0)
- [5].move(0, 0, 16.0)
-
-# Now shift the positions of all of the benzene molecules,
-# to reduce the chance that they overlap with the ethylene molecules.
-
-benzenes[*][*][*].move(4.0, 4.0, 4.0)
-
-# Note: There is also an example which shows how to generate the coordinates
-# using PACKMOL. (That allows us to omit the coordinates and .move() commands.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/run.in.npt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/run.in.npt
deleted file mode 100644
index 527599ba8..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/run.in.npt
+++ /dev/null
@@ -1,58 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# OPLSAA atom charges are stored in a separate file.
-# Load that file now:
-
-include "system.in.charges"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# -- simulation protocol --
-
-timestep 1.0
-
-print "---------------------------------------------------------------------------"
-print "First, use Langevin dynamics to randomize the initial shape of the molecules"
-print "(This is not really necessary, but it seems to speed up equilibration.)"
-print "---------------------------------------------------------------------------"
-
-fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K
-fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr
-run 2000
-unfix fxlan
-unfix fxnph
-
-print "---------------------------------------------------------------------------"
-print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---"
-print "---------------------------------------------------------------------------"
-dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
-# temperature: 300 K, pressure: 50 barr
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0
-thermo 100
-#thermo_modify flush yes
-
-run 100000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/run.in.nvt
deleted file mode 100644
index 2f3b81c18..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/run.in.nvt
+++ /dev/null
@@ -1,51 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# OPLSAA atom charges are stored in a separate file.
-# Load that file now:
-
-include "system.in.charges"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 200000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.TXT
deleted file mode 100644
index af95dca52..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.TXT
+++ /dev/null
@@ -1,23 +0,0 @@
-
-This is an example of how to use the OPLSAA force-field in LAMMPS
-
-This example also shows how to use moltemplate in combination with PACKMOL.
-(PACKMOL is a useful program for generating atomic coordinates. In this example,
- moltemplate.sh is only used to create the topology, force-field and charges,
- and PACKMOL generates the coordinates, which moltemplate reads (in "step 1").
- Moltemplate can also be used for generating atomic coordinates, especially
- for mixing many small molecules together, as we do in this example. However
- I wanted to demonstrate how to combine PACKMOL with moltemplate.sh.
- In some other scenarios, such as protein solvation, PACKMOL does a much
- better job than moltemplate.)
-
-As of 2016-11-21, this code has not been tested for accuracy.
-(See the WARNING.TXT file.)
-
-step 1)
-To build the files which LAMMPS needs, follow the instructions in:
-README_setup.sh
-
-step 2)
-To run LAMMPS with these files, follow these instructions:
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh
deleted file mode 100755
index 5f8286664..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh
deleted file mode 100755
index 60daffc2b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-
-# Create the coordinates of the atoms using PACKMOL
-cd packmol_files
-
- packmol < mix_ethylene+benzene.inp
- mv -f system.xyz ../moltemplate_files/
-
-cd ..
-
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -xyz system.xyz system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg
deleted file mode 100644
index 356c78425..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg
deleted file mode 100644
index 00c82d3d9..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg
deleted file mode 100644
index ab5bbbf49..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt
deleted file mode 100644
index f240a091f..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt
+++ /dev/null
@@ -1,51 +0,0 @@
-import "oplsaa.lt"
-
-# The "oplsaa.lt" file contains force-field definitions and masses for the
-# atoms in your system. See oplsaa_lt_generator/README.TXT for details.
-
-# Note:
-# Atom type @atom:90 corresponds to "Aromatic C"
-# Atom type @atom:91 corresponds to "Aromatic H-C"
-
-Benzene inherits OPLSAA {
-
- # We just need a list of atom types and bonds.
- #
- # You don't have to specify the charge in this example because we are
- # using the OPLSAA force-field assigns this by atom-type.
- #
- # You also don't have to specify the coordinates, because
- # you are using PACKMOL to generate them for you.
- # Just leave these numbers as 0.00 for now..
-
- write('Data Atoms') {
- $atom:C1 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C"
- $atom:C2 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C"
- $atom:C3 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C"
- $atom:C4 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C"
- $atom:C5 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C"
- $atom:C6 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C"
- $atom:H11 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C"
- $atom:H21 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C"
- $atom:H31 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C"
- $atom:H41 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C"
- $atom:H51 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C"
- $atom:H61 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C"
- }
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C23 $atom:C2 $atom:C3
- $bond:C34 $atom:C3 $atom:C4
- $bond:C45 $atom:C4 $atom:C5
- $bond:C56 $atom:C5 $atom:C6
- $bond:C61 $atom:C6 $atom:C1
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C2H2 $atom:C2 $atom:H21
- $bond:C3H3 $atom:C3 $atom:H31
- $bond:C4H4 $atom:C4 $atom:H41
- $bond:C5H5 $atom:C5 $atom:H51
- $bond:C6H6 $atom:C6 $atom:H61
- }
-
-} # Benzene
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt
deleted file mode 100644
index 45adb1fae..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt
+++ /dev/null
@@ -1,40 +0,0 @@
-import "oplsaa.lt"
-
-# The "oplsaa.lt" file contains force-field definitions and masses for the
-# atoms in your system. See oplsaa_lt_generator/README.TXT for details.
-
-# Note:
-# Atom type 88 corresponds to "Alkene H2-C="
-# Atom type 89 corresponds to "Alkene H-C="
-
-
-
-Ethylene inherits OPLSAA {
-
- # atom-id mol-id atom-type charge X Y Z
-
- write('Data Atoms') {
- $atom:C1 $mol @atom:88 0.000 -0.6695 0.000000 0.000000
- $atom:C2 $mol @atom:88 0.000 0.6695 0.000000 0.000000
- $atom:H11 $mol @atom:89 0.000 -1.234217 -0.854458 0.000000
- $atom:H12 $mol @atom:89 0.000 -1.234217 0.854458 0.000000
- $atom:H21 $mol @atom:89 0.000 1.234217 -0.854458 0.000000
- $atom:H22 $mol @atom:89 0.000 1.234217 0.854458 0.000000
- }
-
- write('Data Bond List') {
- $bond:C12 $atom:C1 $atom:C2
- $bond:C1H1 $atom:C1 $atom:H11
- $bond:C1H2 $atom:C1 $atom:H12
- $bond:C2H1 $atom:C2 $atom:H21
- $bond:C2H2 $atom:C2 $atom:H22
- }
-
-} # Ethylene
-
-
-
-# Note: You don't need to supply the partial partial charges of the atoms.
-# If you like, just fill the fourth column with zeros ("0.000").
-# Moltemplate and LAMMPS will automatically assign the charge later
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index 6da345602..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,110 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the
-"ethylene+benzene" example. (However, these instructions should work
-for other molecules too.)
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with ethylene and benzene you would delete every line
-beginning with the word "atom", except for these four lines:
-
-# for ethylene:
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-# for benzene:
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "88", "89", "47", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "ethyelene.lt":
-
-import "oplsaa.lt"
-Ethylene inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Jason Lambert and Andrew Jewett
-April, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
deleted file mode 100644
index 2fc1ea29e..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
+++ /dev/null
@@ -1,16 +0,0 @@
-MOST USERS SHOULD IGNORE THIS DIRECTORY.
-
-This directory contains versions of the oplsaa_subset.prm file
-which nearly all of the OPLSAA force-field information removed.
-However for the "ethylene+benzene" example, all of the essential
-parameters are contained in these files. You can use oplsaa_moltemplate.py
-with either of these files and the physics should be the same.
-
-However there is no reason to do this.
-When you download the "oplsaa.prm" file from:
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-(also http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm)
-...just remove the lines beginning with "atom" for atoms you don't need.
-You don't have to delete all the other irrelevant interactions.
-(In fact, it is hard to do that without making a mistake.
- I recommend that you leave the rest of the oplsaa.prm file alone.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
deleted file mode 100644
index b4078f121..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
+++ /dev/null
@@ -1,37 +0,0 @@
- #############################
- ## Atom Type Definitions ##
- #############################
-
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-vdw 88 3.5500 0.0760
-vdw 89 2.4200 0.0300
-vdw 90 3.5500 0.0700
-vdw 91 2.4200 0.0300
-
-bond 46 47 340.00 1.0800
-bond 47 47 549.00 1.3400
-bond 48 48 469.00 1.4000
-bond 48 49 367.00 1.0800
-
-angle 46 47 46 35.00 117.00
-angle 46 47 47 35.00 120.00
-angle 48 48 48 63.00 120.00
-angle 48 48 49 35.00 120.00
-
-torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-
-imptors 0 0 47 0 30.000 180.0 2
-imptors 0 0 48 0 5.000 180.0 2
-
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
deleted file mode 100644
index 6dbc6861a..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
+++ /dev/null
@@ -1,49 +0,0 @@
- #############################
- ## Atom Type Definitions ##
- #############################
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-vdw 88 3.5500 0.0760
-vdw 89 2.4200 0.0300
-vdw 90 3.5500 0.0700
-vdw 91 2.4200 0.0300
-
-bond 46 47 340.00 1.0800
-bond 47 47 549.00 1.3400
-bond 47 48 427.00 1.4330
-bond 48 48 469.00 1.4000
-bond 48 49 367.00 1.0800
-
-angle 46 47 46 35.00 117.00
-angle 46 47 47 35.00 120.00
-angle 46 47 48 35.00 123.30
-angle 47 47 48 85.00 117.00
-angle 48 48 48 63.00 120.00
-angle 47 48 48 70.00 124.00
-angle 48 48 49 35.00 120.00
-
-imptors 0 0 47 0 30.000 180.0 2
-imptors 0 0 48 0 5.000 180.0 2
-
-torsion 47 46 47 46 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3
-torsion 0 47 47 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 47 47 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 47 48 48 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3
-torsion 47 47 48 48 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3
-torsion 0 48 48 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 47 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index c802793ad..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,5129 +0,0 @@
-# This is a modified version of the file "oplsaa.prm" distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# In this version, all of the lines beginning with "atom" have been deleted
-# except for the atom types we will be using in this simulation
-# (I also deleted some other lines from that file data to reduce the file size,
-# but doing that is not necessary.)
-#
-# If you use this file, please also cite the software this file comes from:
-#
-# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024
-# "An efficient newton‐like method for molecular mechanics energy
-# minimization of large molecules."
-#
-# Ponder, J. W, (2004)
-# "TINKER: Software tools for molecular design"
-# http://dasher.wustl.edu/tinker/
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 1 2.9400 0.0610
-vdw 2 3.9050 0.1180
-vdw 3 3.7500 0.1050
-vdw 4 2.9600 0.2100
-vdw 5 3.0000 0.1700
-vdw 6 3.9100 0.1600
-vdw 7 0.0000 0.0000
-vdw 8 3.7300 0.2940
-vdw 9 3.7750 0.2070
-vdw 10 3.9050 0.1750
-vdw 11 3.9100 0.1600
-vdw 12 3.9600 0.1450
-vdw 13 3.9050 0.1180
-vdw 14 3.8500 0.1400
-vdw 15 3.8500 0.0800
-vdw 16 3.8000 0.1150
-vdw 17 3.7500 0.1100
-vdw 18 3.8000 0.0500
-vdw 19 3.7500 0.1050
-vdw 20 3.0700 0.1700
-vdw 21 0.0000 0.0000
-vdw 22 3.7750 0.2070
-vdw 23 3.9050 0.1180
-vdw 24 3.7000 0.2500
-vdw 25 3.5500 0.2500
-vdw 26 3.5500 0.2500
-vdw 27 3.5500 0.2500
-vdw 28 0.0000 0.0000
-vdw 29 0.0000 0.0000
-vdw 30 3.7750 0.2070
-vdw 31 3.9050 0.1180
-vdw 32 3.8000 0.1700
-vdw 33 3.8000 0.1180
-vdw 34 3.8000 0.1700
-vdw 35 3.8000 0.1180
-vdw 36 3.2000 0.1700
-vdw 37 3.6500 0.1500
-vdw 38 3.7750 0.2070
-vdw 39 3.8500 0.0800
-vdw 40 3.8000 0.0500
-vdw 41 3.0000 0.1700
-vdw 42 3.8000 0.1700
-vdw 43 3.8000 0.1180
-vdw 44 3.8000 0.1180
-vdw 45 3.4000 0.3000
-vdw 46 3.8000 0.0800
-vdw 47 3.4700 0.3000
-vdw 48 3.8000 0.0500
-vdw 49 3.4700 0.2660
-vdw 50 3.5600 0.3950
-vdw 51 2.9300 0.2800
-vdw 52 3.8100 0.1600
-vdw 53 2.9600 0.2100
-vdw 54 3.2500 0.1700
-vdw 55 3.8000 0.1150
-vdw 56 3.8000 0.1700
-vdw 57 0.0000 0.0000
-vdw 58 2.5560 0.0200
-vdw 59 2.7800 0.0690
-vdw 60 3.4010 0.2339
-vdw 61 3.6240 0.3170
-vdw 62 3.9350 0.4330
-vdw 63 3.15061 0.1521
-vdw 64 0.0000 0.0000
-vdw 65 3.15365 0.1550
-vdw 66 0.0000 0.0000
-vdw 67 0.0000 0.0000
-vdw 68 3.1760 0.1500
-vdw 69 0.0000 0.0000
-vdw 70 3.2700 0.1000
-vdw 71 0.0000 0.0000
-vdw 72 0.0000 0.0000
-vdw 73 3.1200 0.1600
-vdw 74 0.0000 0.0000
-vdw 75 0.0000 0.0000
-vdw 76 3.16557 0.1554
-vdw 77 0.0000 0.0000
-vdw 78 3.4200 0.1700
-vdw 79 0.0000 0.0000
-vdw 80 3.5000 0.0660
-vdw 81 3.5000 0.0660
-vdw 82 3.5000 0.0660
-vdw 83 3.5000 0.0660
-vdw 84 3.5000 0.0660
-vdw 85 2.5000 0.0300
-vdw 86 3.5500 0.0760
-vdw 87 3.5500 0.0760
-vdw 88 3.5500 0.0760
-vdw 89 2.4200 0.0300
-vdw 90 3.5500 0.0700
-vdw 91 2.4200 0.0300
-vdw 92 3.5500 0.0700
-vdw 93 3.5000 0.0660
-vdw 94 3.5000 0.0660
-vdw 95 3.5500 0.0760
-vdw 96 3.1200 0.1700
-vdw 97 0.0000 0.0000
-vdw 98 2.5000 0.0300
-vdw 99 3.5000 0.0660
-vdw 100 3.5000 0.0660
-vdw 101 3.5000 0.0660
-vdw 102 3.5000 0.0660
-vdw 103 3.2500 0.0620
-vdw 104 3.0700 0.1700
-vdw 105 0.0000 0.0000
-vdw 106 2.9400 0.0610
-vdw 107 2.5000 0.0300
-vdw 108 3.5500 0.0700
-vdw 109 3.0700 0.1700
-vdw 110 0.0000 0.0000
-vdw 111 3.0700 0.1700
-vdw 112 0.0000 0.0000
-vdw 113 3.0700 0.1700
-vdw 114 0.0000 0.0000
-vdw 115 3.5000 0.0660
-vdw 116 3.5000 0.0660
-vdw 117 3.5000 0.0660
-vdw 118 2.5000 0.0300
-vdw 119 2.9000 0.1400
-vdw 120 3.5500 0.0760
-vdw 121 2.9000 0.1400
-vdw 122 2.9000 0.1400
-vdw 123 3.5000 0.0660
-vdw 124 3.5000 0.0660
-vdw 125 3.5000 0.0660
-vdw 126 3.5000 0.0660
-vdw 127 2.5000 0.0300
-vdw 128 2.9000 0.1400
-vdw 129 3.0700 0.1700
-vdw 130 0.0000 0.0000
-vdw 131 3.5000 0.0660
-vdw 132 2.5000 0.0300
-vdw 133 3.5000 0.0660
-vdw 134 2.5000 0.0300
-vdw 135 3.5000 0.0660
-vdw 136 2.5000 0.0300
-vdw 137 3.5000 0.0660
-vdw 138 2.5000 0.0300
-vdw 139 3.5000 0.0660
-vdw 140 3.5000 0.0660
-vdw 141 3.5500 0.0700
-vdw 142 3.5500 0.2500
-vdw 143 3.7000 0.2500
-vdw 144 3.5500 0.2500
-vdw 145 3.5500 0.2500
-vdw 146 0.0000 0.0000
-vdw 147 0.0000 0.0000
-vdw 148 3.5000 0.0660
-vdw 149 3.5000 0.0660
-vdw 150 3.5000 0.0660
-vdw 151 3.5000 0.0660
-vdw 152 3.5000 0.0660
-vdw 153 3.5000 0.0660
-vdw 154 3.5000 0.0660
-vdw 155 3.5000 0.0660
-vdw 156 3.5000 0.0660
-vdw 157 3.5000 0.0660
-vdw 158 3.5000 0.0660
-vdw 159 3.5000 0.0660
-vdw 160 3.5000 0.0660
-vdw 161 3.5000 0.0660
-vdw 162 3.5000 0.0660
-vdw 163 3.5500 0.0700
-vdw 164 3.5500 0.2500
-vdw 165 3.5000 0.0660
-vdw 166 3.5000 0.0660
-vdw 167 3.5000 0.0660
-vdw 168 3.4000 0.3000
-vdw 169 3.5500 0.0760
-vdw 170 3.5500 0.0700
-vdw 171 3.5000 0.0660
-vdw 172 3.5000 0.0660
-vdw 173 3.7500 0.1050
-vdw 174 3.7500 0.1050
-vdw 175 3.7500 0.1050
-vdw 176 3.7500 0.1050
-vdw 177 3.7500 0.1050
-vdw 178 2.9600 0.2100
-vdw 179 3.2500 0.1700
-vdw 180 3.2500 0.1700
-vdw 181 3.2500 0.1700
-vdw 182 0.0000 0.0000
-vdw 183 0.0000 0.0000
-vdw 184 3.5000 0.0660
-vdw 185 3.5000 0.0660
-vdw 186 3.5000 0.0660
-vdw 187 3.5000 0.0660
-vdw 188 3.5000 0.0660
-vdw 189 3.7500 0.1050
-vdw 190 2.9600 0.2100
-vdw 191 3.2500 0.1700
-vdw 192 0.0000 0.0000
-vdw 193 3.2500 0.1700
-vdw 194 3.7500 0.1050
-vdw 195 2.9600 0.2100
-vdw 196 0.0000 0.0000
-vdw 197 2.5000 0.0200
-vdw 198 3.5000 0.0660
-vdw 199 3.5000 0.0660
-vdw 200 3.5000 0.0660
-vdw 201 3.5000 0.0660
-vdw 202 3.5500 0.0700
-vdw 203 3.6500 0.1500
-vdw 204 3.2000 0.1700
-vdw 205 3.5500 0.0700
-vdw 206 3.4000 0.3000
-vdw 207 3.2500 0.1700
-vdw 208 3.5500 0.0700
-vdw 209 3.7500 0.1050
-vdw 210 2.9600 0.2100
-vdw 211 3.0000 0.1700
-vdw 212 0.0000 0.0000
-vdw 213 3.7500 0.1050
-vdw 214 2.9600 0.2100
-vdw 215 3.5000 0.0660
-vdw 216 3.5000 0.0660
-vdw 217 3.5000 0.0660
-vdw 218 3.5000 0.0660
-vdw 219 3.7500 0.1050
-vdw 220 2.9600 0.2100
-vdw 221 2.4200 0.0150
-vdw 222 3.7500 0.1050
-vdw 223 2.9600 0.2100
-vdw 224 2.4200 0.0150
-vdw 225 3.5000 0.0660
-vdw 226 3.5000 0.0660
-vdw 227 3.5000 0.0660
-vdw 228 3.5000 0.0660
-vdw 229 3.2500 0.1700
-vdw 230 3.2500 0.1700
-vdw 231 3.2500 0.1700
-vdw 232 0.0000 0.0000
-vdw 233 0.0000 0.0000
-vdw 234 3.5000 0.0660
-vdw 235 3.5000 0.0660
-vdw 236 3.5000 0.0660
-vdw 237 3.5000 0.0660
-vdw 238 3.5000 0.0660
-vdw 239 3.5000 0.0660
-vdw 240 3.5000 0.0660
-vdw 241 3.5000 0.0660
-vdw 242 3.5000 0.0660
-vdw 243 3.2500 0.1700
-vdw 244 0.0000 0.0000
-vdw 245 3.5500 0.0500
-vdw 246 3.2500 0.1700
-vdw 247 0.0000 0.0000
-vdw 248 3.5000 0.0660
-vdw 249 3.5000 0.0660
-vdw 250 3.5000 0.0660
-vdw 251 3.5000 0.0660
-vdw 252 3.2500 0.1700
-vdw 253 0.0000 0.0000
-vdw 254 3.2500 0.1700
-vdw 255 3.5000 0.0800
-vdw 256 3.2500 0.1700
-vdw 257 0.0000 0.0000
-vdw 258 3.5000 0.0800
-vdw 259 2.5000 0.0500
-vdw 260 3.5000 0.0800
-vdw 261 2.5000 0.0500
-vdw 262 3.2500 0.1700
-vdw 263 3.7500 0.1050
-vdw 264 3.2500 0.1700
-vdw 265 3.7500 0.1050
-vdw 266 3.5000 0.0800
-vdw 267 3.5000 0.0800
-vdw 268 0.0000 0.0000
-vdw 269 2.9600 0.2100
-vdw 270 0.0000 0.0000
-vdw 271 2.9600 0.2100
-vdw 272 2.5000 0.0500
-vdw 273 2.5000 0.0500
-vdw 274 3.5000 0.0800
-vdw 275 2.5000 0.0500
-vdw 276 3.2500 0.1700
-vdw 277 3.7500 0.1050
-vdw 278 3.2500 0.1700
-vdw 279 3.5000 0.0800
-vdw 280 3.5000 0.0800
-vdw 281 3.5000 0.0800
-vdw 282 0.0000 0.0000
-vdw 283 2.9600 0.2100
-vdw 284 3.2500 0.1700
-vdw 285 0.0000 0.0000
-vdw 286 0.0000 0.0000
-vdw 287 2.5000 0.0500
-vdw 288 2.5000 0.0500
-vdw 289 3.2500 0.1700
-vdw 290 3.5000 0.0800
-vdw 291 3.2500 0.1700
-vdw 292 3.5000 0.0800
-vdw 293 3.5000 0.0800
-vdw 294 3.5000 0.0800
-vdw 295 3.2500 0.1700
-vdw 296 3.5000 0.0800
-vdw 297 3.2500 0.1700
-vdw 298 2.5000 0.0500
-vdw 299 3.2500 0.1700
-vdw 300 0.0000 0.0000
-vdw 301 0.0000 0.0000
-vdw 302 2.5000 0.0500
-vdw 303 0.0000 0.0000
-vdw 304 3.2500 0.1700
-vdw 305 3.5000 0.0800
-vdw 306 3.2500 0.1700
-vdw 307 3.5000 0.0800
-vdw 308 3.5000 0.0800
-vdw 309 3.7500 0.1050
-vdw 310 0.0000 0.0000
-vdw 311 3.2500 0.1700
-vdw 312 0.0000 0.0000
-vdw 313 2.9600 0.2100
-vdw 314 3.5000 0.0800
-vdw 315 2.5000 0.0500
-vdw 316 3.5000 0.0800
-vdw 317 2.5000 0.0500
-vdw 318 3.5000 0.0800
-vdw 319 2.5000 0.0500
-vdw 320 3.2500 0.1700
-vdw 321 3.7500 0.1050
-vdw 322 3.2500 0.1700
-vdw 323 3.5000 0.0800
-vdw 324 3.5000 0.0800
-vdw 325 3.5000 0.0800
-vdw 326 0.0000 0.0000
-vdw 327 2.9600 0.2100
-vdw 328 0.0000 0.0000
-vdw 329 3.2500 0.1700
-vdw 330 0.0000 0.0000
-vdw 331 0.0000 0.0000
-vdw 332 2.5000 0.0500
-vdw 333 2.5000 0.0500
-vdw 334 3.5000 0.0800
-vdw 335 2.5000 0.0500
-vdw 336 3.7400 0.2000
-vdw 337 2.9600 0.2100
-vdw 338 3.0000 0.1700
-vdw 339 3.5500 0.0660
-vdw 340 3.5000 0.0800
-vdw 341 3.4000 0.3000
-vdw 342 3.5500 0.0760
-vdw 343 3.0500 0.7100
-vdw 344 4.0200 0.7100
-vdw 345 4.2800 0.7100
-vdw 346 4.8100 0.7100
-vdw 347 5.3400 0.0005
-vdw 348 2.8700 0.0005
-vdw 349 4.0700 0.0005
-vdw 350 5.1700 0.0005
-vdw 351 5.6000 0.0005
-vdw 352 6.2000 0.0005
-vdw 353 1.644471 0.875044
-vdw 354 2.412031 0.449657
-vdw 355 3.102688 0.118226
-vdw 356 3.816610 0.047096
-vdw 357 4.2000 0.3000
-vdw 358 2.5000 0.0500
-vdw 359 4.2500 0.5000
-vdw 360 4.2000 0.3000
-vdw 361 2.5000 0.0500
-vdw 362 3.1500 0.2500
-vdw 363 4.2000 0.3000
-vdw 364 2.5000 0.0500
-vdw 365 3.6500 0.1500
-vdw 366 3.4000 0.2500
-vdw 367 4.2000 0.3000
-vdw 368 2.5000 0.0500
-vdw 369 3.4000 0.2500
-vdw 370 2.5000 0.0500
-vdw 371 4.2000 0.3000
-vdw 372 2.5000 0.0500
-vdw 373 4.2000 0.3000
-vdw 374 2.5000 0.0500
-vdw 375 0.0000 0.0000
-vdw 376 3.2000 0.2500
-vdw 377 0.0000 0.0000
-vdw 378 2.81524 0.4000
-vdw 379 3.11815 0.2000
-vdw 380 2.9000 0.1400
-vdw 381 3.7400 0.2000
-vdw 382 3.1500 0.2000
-vdw 383 2.9000 0.1400
-vdw 384 3.5000 0.0660
-vdw 385 2.5000 0.0300
-vdw 386 3.7400 0.2000
-vdw 387 3.1500 0.2000
-vdw 388 2.9000 0.1400
-vdw 389 3.5000 0.0660
-vdw 390 2.5000 0.0300
-vdw 391 3.7400 0.2000
-vdw 392 3.1500 0.2000
-vdw 393 2.9000 0.1400
-vdw 394 3.5000 0.0660
-vdw 395 2.5000 0.0300
-vdw 396 3.5000 0.0660
-vdw 397 2.5000 0.0300
-vdw 398 3.5500 0.0700
-vdw 399 3.5000 0.0660
-vdw 400 2.5000 0.0300
-vdw 401 3.5500 0.0700
-vdw 402 3.5000 0.0660
-vdw 403 2.5000 0.0300
-vdw 404 3.5500 0.0700
-vdw 405 3.5000 0.0660
-vdw 406 3.7500 0.1050
-vdw 407 2.9600 0.2100
-vdw 408 3.0000 0.1700
-vdw 409 3.5000 0.0660
-vdw 410 2.4200 0.0150
-vdw 411 3.7500 0.1050
-vdw 412 3.7500 0.1050
-vdw 413 3.5500 0.0700
-vdw 414 3.0000 0.1700
-vdw 415 3.5500 0.2500
-vdw 416 2.9600 0.1700
-vdw 417 3.5000 0.0660
-vdw 418 2.5000 0.0300
-vdw 419 3.2500 0.1700
-vdw 420 0.0000 0.0000
-vdw 421 3.2500 0.1700
-vdw 422 0.0000 0.0000
-vdw 423 3.5000 0.0660
-vdw 424 2.5000 0.0300
-vdw 425 3.5000 0.0660
-vdw 426 2.5000 0.0300
-vdw 427 3.5000 0.0660
-vdw 428 2.5000 0.0300
-vdw 429 3.5500 0.0700
-vdw 430 3.5500 0.0700
-vdw 431 3.5000 0.0660
-vdw 432 3.5000 0.0660
-vdw 433 3.5000 0.0660
-vdw 434 3.5500 0.2500
-vdw 435 2.9600 0.1700
-vdw 436 3.5600 0.3950
-vdw 437 3.5600 0.3950
-vdw 438 2.9300 0.2800
-vdw 439 3.5000 0.0660
-vdw 440 3.5000 0.0660
-vdw 441 3.5500 0.0700
-vdw 442 3.5500 0.0700
-vdw 443 3.5500 0.0700
-vdw 444 3.2500 0.1700
-vdw 445 0.0000 0.0000
-vdw 446 3.5000 0.0660
-vdw 447 3.5500 0.0700
-vdw 448 3.5500 0.0700
-vdw 449 3.5500 0.0700
-vdw 450 3.5500 0.0700
-vdw 451 3.5500 0.0700
-vdw 452 3.2500 0.1700
-vdw 453 3.2500 0.1700
-vdw 454 0.0000 0.0000
-vdw 455 3.5500 0.0700
-vdw 456 3.5000 0.0660
-vdw 457 3.5000 0.0660
-vdw 458 3.5500 0.0760
-vdw 459 3.5500 0.0760
-vdw 460 3.5500 0.0700
-vdw 461 3.2500 0.1700
-vdw 462 3.5500 0.0700
-vdw 463 3.5500 0.0700
-vdw 464 3.5500 0.0700
-vdw 465 2.4200 0.0300
-vdw 466 2.4200 0.0300
-vdw 467 2.4200 0.0300
-vdw 468 3.2500 0.1700
-vdw 469 3.5500 0.0700
-vdw 470 2.4200 0.0300
-vdw 471 3.2500 0.1700
-vdw 472 3.5500 0.0700
-vdw 473 3.5500 0.0700
-vdw 474 3.5500 0.0700
-vdw 475 2.4200 0.0300
-vdw 476 2.4200 0.0300
-vdw 477 2.4200 0.0300
-vdw 478 3.2500 0.1700
-vdw 479 3.5500 0.0700
-vdw 480 3.5500 0.0700
-vdw 481 2.4200 0.0300
-vdw 482 2.4200 0.0300
-vdw 483 3.2500 0.1700
-vdw 484 3.5500 0.0700
-vdw 485 3.5500 0.0700
-vdw 486 0.0000 0.0000
-vdw 487 2.4200 0.0300
-vdw 488 2.4200 0.0300
-vdw 489 3.2500 0.1700
-vdw 490 3.2500 0.1700
-vdw 491 3.5500 0.0700
-vdw 492 3.5500 0.0700
-vdw 493 3.5500 0.0700
-vdw 494 0.0000 0.0000
-vdw 495 2.4200 0.0300
-vdw 496 2.4200 0.0300
-vdw 497 2.4200 0.0300
-vdw 498 3.2500 0.1700
-vdw 499 3.5500 0.0700
-vdw 500 3.2500 0.1700
-vdw 501 3.5500 0.0700
-vdw 502 3.5500 0.0700
-vdw 503 0.0000 0.0000
-vdw 504 2.4200 0.0300
-vdw 505 2.4200 0.0300
-vdw 506 2.4200 0.0300
-vdw 507 2.9000 0.1400
-vdw 508 3.5500 0.0700
-vdw 509 3.5500 0.0760
-vdw 510 2.4200 0.0300
-vdw 511 2.4200 0.0300
-vdw 512 2.9000 0.1400
-vdw 513 3.5500 0.0700
-vdw 514 3.2500 0.1700
-vdw 515 3.5500 0.0700
-vdw 516 3.5500 0.0700
-vdw 517 2.4200 0.0300
-vdw 518 2.4200 0.0300
-vdw 519 2.4200 0.0300
-vdw 520 2.9000 0.1400
-vdw 521 3.2500 0.1700
-vdw 522 3.5500 0.0700
-vdw 523 3.5500 0.0700
-vdw 524 3.5500 0.0700
-vdw 525 2.4200 0.0300
-vdw 526 2.4200 0.0300
-vdw 527 2.4200 0.0300
-vdw 528 3.2500 0.1700
-vdw 529 3.5500 0.0700
-vdw 530 3.5500 0.0700
-vdw 531 3.5500 0.0700
-vdw 532 3.5500 0.0700
-vdw 533 3.5500 0.0700
-vdw 534 3.5500 0.0700
-vdw 535 3.5500 0.0700
-vdw 536 3.5500 0.0700
-vdw 537 0.0000 0.0000
-vdw 538 2.4200 0.0300
-vdw 539 2.4200 0.0300
-vdw 540 2.4200 0.0300
-vdw 541 2.4200 0.0300
-vdw 542 2.4200 0.0300
-vdw 543 2.4200 0.0300
-vdw 544 3.2500 0.1700
-vdw 545 3.5500 0.0700
-vdw 546 3.5500 0.0700
-vdw 547 3.5500 0.0700
-vdw 548 3.5500 0.0700
-vdw 549 3.5500 0.0700
-vdw 550 3.5500 0.0700
-vdw 551 3.5500 0.0700
-vdw 552 3.5500 0.0700
-vdw 553 3.5500 0.0700
-vdw 554 2.4200 0.0300
-vdw 555 2.4200 0.0300
-vdw 556 2.4200 0.0300
-vdw 557 2.4200 0.0300
-vdw 558 2.4200 0.0300
-vdw 559 2.4200 0.0300
-vdw 560 2.4200 0.0300
-vdw 561 3.2500 0.1700
-vdw 562 3.5500 0.0700
-vdw 563 3.2500 0.1700
-vdw 564 3.5500 0.0700
-vdw 565 3.5500 0.0700
-vdw 566 3.5500 0.0700
-vdw 567 3.2500 0.1700
-vdw 568 3.5500 0.0700
-vdw 569 3.2500 0.1700
-vdw 570 2.4200 0.0300
-vdw 571 2.4200 0.0300
-vdw 572 2.4200 0.0300
-vdw 573 0.0000 0.0000
-vdw 574 3.5500 0.2500
-vdw 575 3.5500 0.0700
-vdw 576 3.2500 0.1700
-vdw 577 3.5500 0.0700
-vdw 578 3.5500 0.0700
-vdw 579 2.4200 0.0300
-vdw 580 2.4200 0.0300
-vdw 581 2.4200 0.0300
-vdw 582 3.2500 0.1700
-vdw 583 3.5500 0.0700
-vdw 584 2.4200 0.0300
-vdw 585 3.5500 0.0700
-vdw 586 3.5000 0.0660
-vdw 587 3.2500 0.1700
-vdw 588 3.5500 0.0700
-vdw 589 3.5500 0.0700
-vdw 590 3.5500 0.0700
-vdw 591 3.5500 0.0700
-vdw 592 3.5500 0.0700
-vdw 593 3.5500 0.0700
-vdw 594 2.4200 0.0300
-vdw 595 2.4200 0.0300
-vdw 596 2.4200 0.0300
-vdw 597 2.4200 0.0300
-vdw 598 3.2500 0.1700
-vdw 599 3.5500 0.0700
-vdw 600 3.2500 0.1700
-vdw 601 3.5500 0.0700
-vdw 602 3.5500 0.0700
-vdw 603 3.5000 0.0660
-vdw 604 2.4200 0.0300
-vdw 605 2.4200 0.0300
-vdw 606 2.4200 0.0300
-vdw 607 2.5000 0.0300
-vdw 608 3.5000 0.0660
-vdw 609 3.5000 0.0660
-vdw 610 3.5000 0.0660
-vdw 611 3.5000 0.0660
-vdw 612 3.5000 0.0660
-vdw 613 3.5000 0.0660
-vdw 614 3.5000 0.0660
-vdw 615 3.5000 0.0660
-vdw 616 3.5000 0.0660
-vdw 617 3.5000 0.0660
-vdw 618 3.5000 0.0660
-vdw 619 3.5000 0.0660
-vdw 620 3.5000 0.0660
-vdw 621 3.5000 0.0660
-vdw 622 3.5000 0.0660
-vdw 623 3.5500 0.2500
-vdw 624 0.0000 0.0000
-vdw 625 3.5500 0.0700
-vdw 626 3.7500 0.1050
-vdw 627 3.2500 0.1700
-vdw 628 3.5000 0.0660
-vdw 629 3.5000 0.0660
-vdw 630 3.5000 0.0660
-vdw 631 3.5500 0.0700
-vdw 632 3.5500 0.0700
-vdw 633 3.5500 0.0700
-vdw 634 3.5500 0.0700
-vdw 635 3.5500 0.0700
-vdw 636 3.5500 0.0700
-vdw 637 3.5500 0.2500
-vdw 638 3.4730 0.0540
-vdw 639 3.3000 0.0500
-vdw 640 3.3000 0.0500
-vdw 641 3.5500 0.0760
-vdw 642 3.5000 0.0660
-vdw 643 2.5000 0.0300
-vdw 644 3.7500 0.0600
-vdw 645 3.4730 0.0540
-vdw 646 3.3000 0.0500
-vdw 647 3.3000 0.0500
-vdw 648 2.9500 0.0400
-vdw 649 3.5500 0.0760
-vdw 650 3.4000 0.3000
-vdw 651 2.4200 0.0300
-vdw 652 3.5000 0.0660
-vdw 653 3.5000 0.0660
-vdw 654 3.5000 0.0660
-vdw 655 3.5500 0.0700
-vdw 656 2.4200 0.0300
-vdw 657 3.5500 0.0700
-vdw 658 2.4200 0.0300
-vdw 659 3.5500 0.0700
-vdw 660 2.8500 0.0610
-vdw 661 3.5500 0.0700
-vdw 662 2.8500 0.0610
-vdw 663 3.4700 0.4700
-vdw 664 3.9050 0.1180
-vdw 665 3.5500 0.0700
-vdw 666 3.2500 0.0620
-vdw 667 2.9400 0.0610
-vdw 668 3.5500 0.0700
-vdw 669 2.8500 0.0610
-vdw 670 3.5500 0.0700
-vdw 671 3.4700 0.4700
-vdw 672 3.5500 0.0700
-vdw 673 3.7500 0.6000
-vdw 674 3.5000 0.0660
-vdw 675 3.5500 0.2500
-vdw 676 3.5500 0.0700
-vdw 677 3.5500 0.0700
-vdw 678 3.5500 0.0700
-vdw 679 3.5500 0.0700
-vdw 680 3.5500 0.0700
-vdw 681 2.4200 0.0300
-vdw 682 2.4200 0.0300
-vdw 683 3.5500 0.0500
-vdw 684 3.2500 0.1700
-vdw 685 0.0000 0.0000
-vdw 686 0.0000 0.0000
-vdw 687 2.4200 0.0300
-vdw 688 3.5000 0.0660
-vdw 689 3.5000 0.0660
-vdw 690 3.2500 0.1700
-vdw 691 3.2500 0.1700
-vdw 692 3.2500 0.1700
-vdw 693 3.5500 0.0500
-vdw 694 3.2000 0.1700
-vdw 695 3.3000 0.0660
-vdw 696 3.3000 0.0660
-vdw 697 3.3000 0.0660
-vdw 698 3.3000 0.0660
-vdw 699 3.3000 0.0660
-vdw 700 2.5000 0.0150
-vdw 701 3.2500 0.1200
-vdw 702 2.9600 0.1700
-vdw 703 3.5000 0.0660
-vdw 704 2.5000 0.0150
-vdw 705 3.5000 0.0660
-vdw 706 3.5000 0.0660
-vdw 707 3.5000 0.0660
-vdw 708 3.2500 0.1200
-vdw 709 3.5500 0.0700
-vdw 710 3.3000 0.0660
-vdw 711 3.2500 0.1700
-vdw 712 2.9600 0.2100
-vdw 713 3.7500 0.1050
-vdw 714 3.0000 0.1700
-vdw 715 3.5000 0.0660
-vdw 716 3.5000 0.0660
-vdw 717 3.5000 0.0660
-vdw 718 2.4200 0.0150
-vdw 719 2.4200 0.0150
-vdw 720 2.4200 0.0150
-vdw 721 2.9000 0.1400
-vdw 722 3.7400 0.2000
-vdw 723 3.5000 0.0660
-vdw 724 3.5000 0.0660
-vdw 725 2.5000 0.0300
-vdw 726 3.7400 0.2000
-vdw 727 3.1181 0.0610
-vdw 728 3.1500 0.1700
-vdw 729 2.8600 0.2100
-vdw 730 3.3000 0.1700
-vdw 731 3.3000 0.1700
-vdw 732 3.3000 0.1700
-vdw 733 3.5000 0.0660
-vdw 734 3.5000 0.0660
-vdw 735 3.5000 0.0660
-vdw 736 3.5000 0.0660
-vdw 737 3.5000 0.0660
-vdw 738 3.5000 0.0660
-vdw 739 0.0000 0.0000
-vdw 740 0.0000 0.0000
-vdw 741 2.5000 0.0150
-vdw 742 3.5000 0.0660
-vdw 743 3.5000 0.0660
-vdw 744 3.5000 0.0660
-vdw 745 3.5000 0.0660
-vdw 746 3.5500 0.0700
-vdw 747 3.5500 0.0700
-vdw 748 3.5500 0.0700
-vdw 749 3.5000 0.0660
-vdw 750 3.5000 0.0660
-vdw 751 3.5000 0.0660
-vdw 752 3.5000 0.0660
-vdw 753 3.5000 0.0660
-vdw 754 3.5000 0.0660
-vdw 755 3.3000 0.0860
-vdw 756 2.4200 0.0150
-vdw 757 3.3000 0.2100
-vdw 758 3.3000 0.1350
-vdw 759 3.3000 0.1000
-vdw 760 2.5000 0.0150
-vdw 761 3.5000 0.0660
-vdw 762 3.5000 0.0660
-vdw 763 3.5000 0.0660
-vdw 764 3.1200 0.1700
-vdw 765 0.0000 0.0000
-vdw 766 3.2500 0.1700
-vdw 767 3.2500 0.1700
-vdw 768 3.2500 0.1700
-vdw 769 3.3000 0.2100
-vdw 770 3.2500 0.1700
-vdw 771 0.0000 0.0000
-vdw 772 3.5000 0.0660
-vdw 773 3.5000 0.0660
-vdw 774 3.5000 0.0660
-vdw 775 3.5000 0.0660
-vdw 776 3.5500 0.0700
-vdw 777 3.5500 0.0760
-vdw 778 3.5500 0.0700
-vdw 779 3.5500 0.0700
-vdw 780 2.5000 0.0300
-vdw 781 3.5000 0.0660
-vdw 782 3.7500 0.1050
-vdw 783 3.2500 0.1700
-vdw 784 2.9600 0.2100
-vdw 785 0.0000 0.0000
-vdw 786 2.9400 0.0610
-vdw 787 3.5000 0.0660
-vdw 788 2.5000 0.0300
-vdw 789 3.5000 0.0660
-vdw 790 3.5000 0.0660
-vdw 791 3.5000 0.0660
-vdw 792 3.5000 0.0660
-vdw 793 3.5000 0.0660
-vdw 794 3.5000 0.0970
-vdw 795 2.9500 0.0530
-vdw 796 3.2500 0.0620
-vdw 797 2.5000 0.0300
-vdw 798 3.5000 0.0660
-vdw 799 3.5000 0.0660
-vdw 800 3.4000 0.3000
-vdw 801 3.5000 0.0660
-vdw 802 2.5000 0.0300
-vdw 803 3.5000 0.0660
-vdw 804 3.5000 0.0660
-vdw 805 3.4700 0.4700
-vdw 806 3.5000 0.0660
-vdw 807 2.5000 0.0300
-vdw 808 3.5000 0.0660
-vdw 809 3.5000 0.0660
-vdw 810 2.9400 0.0610
-vdw 811 3.4000 0.3000
-vdw 812 3.4700 0.4700
-vdw 813 3.5500 0.0700
-vdw 814 2.9000 0.1400
-vdw 815 3.5000 0.0660
-vdw 816 2.9000 0.0600
-vdw 817 3.2500 0.1700
-vdw 818 3.5500 0.0700
-vdw 819 3.5000 0.0660
-vdw 820 3.7500 0.1050
-vdw 821 3.7500 0.1050
-vdw 822 2.9600 0.2100
-vdw 823 3.2500 0.1700
-vdw 824 0.0000 0.0000
-vdw 825 3.1200 0.1700
-vdw 826 0.0000 0.0000
-vdw 827 3.5000 0.0660
-vdw 828 3.5000 0.0660
-vdw 829 3.5500 0.0700
-vdw 830 3.5500 0.0700
-vdw 831 3.5500 0.0700
-vdw 832 3.5500 0.0700
-vdw 833 3.5500 0.0700
-vdw 834 1.9600 0.0125
-vdw 835 3.5000 0.0660
-vdw 836 3.5000 0.0660
-vdw 837 3.5000 0.0660
-vdw 838 3.7500 0.6000
-vdw 839 2.5000 0.0300
-vdw 840 3.2500 0.1700
-vdw 841 3.5500 0.0700
-vdw 842 3.5500 0.0700
-vdw 843 3.2500 0.1700
-vdw 844 3.5500 0.0700
-vdw 845 3.7500 0.1050
-vdw 846 2.9600 0.2100
-vdw 847 3.2500 0.1700
-vdw 848 3.5000 0.0660
-vdw 849 3.5000 0.0660
-vdw 850 3.5000 0.0660
-vdw 851 3.5000 0.0660
-vdw 852 2.4200 0.0150
-vdw 853 3.7500 0.1050
-vdw 854 2.9600 0.2100
-vdw 855 2.4200 0.0150
-vdw 856 3.5000 0.0660
-vdw 857 3.5000 0.0660
-vdw 858 3.5000 0.0660
-vdw 859 3.5000 0.0660
-vdw 860 3.5000 0.0660
-vdw 861 3.5000 0.0660
-vdw 862 3.5000 0.0660
-vdw 863 3.5000 0.0660
-vdw 864 3.5000 0.0660
-vdw 865 3.5000 0.0660
-vdw 866 4.0000 0.1000
-vdw 867 4.0000 0.1000
-vdw 868 4.0000 0.1000
-vdw 869 4.0000 0.1000
-vdw 870 2.5000 0.0300
-vdw 871 3.5000 0.0660
-vdw 872 3.5000 0.0660
-vdw 873 3.5000 0.0660
-vdw 874 3.5000 0.0660
-vdw 875 3.0800 0.7200
-vdw 876 4.1800 0.11779
-vdw 877 4.5100 0.0900
-vdw 878 5.1500 0.0700
-vdw 879 2.7000 0.018279
-vdw 880 3.3500 0.002772
-vdw 881 4.0600 0.000328
-vdw 882 4.3200 0.000171
-vdw 883 4.8200 0.000081
-vdw 884 2.9100 0.875044
-vdw 885 3.4700 0.449657
-vdw 886 3.8200 0.118226
-vdw 887 4.1800 0.047096
-vdw 888 3.5000 0.0660
-vdw 889 3.5000 0.0660
-vdw 890 3.5000 0.0660
-vdw 891 3.5000 0.0660
-vdw 892 2.5000 0.0300
-vdw 893 3.2500 0.1700
-vdw 894 3.5500 0.0700
-vdw 895 3.2500 0.1700
-vdw 896 3.5500 0.0700
-vdw 897 3.5500 0.0760
-vdw 898 3.5500 0.0760
-vdw 899 2.4200 0.0300
-vdw 900 3.3000 0.0860
-vdw 901 3.3000 0.0860
-vdw 902 3.3000 0.0860
-vdw 903 3.3000 0.0860
-vdw 904 3.3000 0.0860
-vdw 905 2.9600 0.2100
-vdw 906 3.5000 0.0660
-
-
- ##################################
- ## ##
- ## Bond Stretching Parameters ##
- ## ##
- ##################################
-
-
-bond 1 2 367.00 1.3800
-bond 1 3 420.00 1.3570
-bond 1 13 367.00 1.3600
-bond 1 19 450.00 1.2790
-bond 1 25 300.00 0.3000
-bond 1 47 420.00 1.3400
-bond 1 48 420.00 1.3540
-bond 1 82 420.00 1.3540
-bond 1 83 420.00 1.3540
-bond 1 84 420.00 1.3540
-bond 1 87 420.00 1.3540
-bond 1 88 420.00 1.3540
-bond 1 108 461.00 1.5700
-bond 2 2 260.00 1.5260
-bond 2 3 317.00 1.5220
-bond 2 5 386.00 1.4250
-bond 2 6 260.00 1.5260
-bond 2 10 260.00 1.5260
-bond 2 11 317.00 1.5000
-bond 2 12 317.00 1.5100
-bond 2 13 260.00 1.5260
-bond 2 14 317.00 1.5000
-bond 2 15 222.00 1.8100
-bond 2 16 222.00 1.8100
-bond 2 20 320.00 1.4250
-bond 2 24 337.00 1.4490
-bond 2 44 382.00 1.4480
-bond 2 48 317.00 1.5100
-bond 2 51 260.00 1.5260
-bond 2 53 367.00 1.4710
-bond 2 55 337.00 1.4630
-bond 2 80 317.00 1.4950
-bond 3 3 350.00 1.5100
-bond 3 4 570.00 1.2290
-bond 3 5 450.00 1.3640
-bond 3 6 317.00 1.5220
-bond 3 10 317.00 1.5220
-bond 3 12 469.00 1.4000
-bond 3 13 317.00 1.5220
-bond 3 19 400.00 1.4440
-bond 3 20 214.00 1.3270
-bond 3 21 300.00 1.7900
-bond 3 24 490.00 1.3350
-bond 3 44 317.00 1.5220
-bond 3 46 340.00 1.0900
-bond 3 47 410.00 1.4440
-bond 3 48 400.00 1.4900
-bond 3 50 385.00 1.4600
-bond 3 52 656.00 1.2500
-bond 3 56 457.00 1.3580
-bond 3 57 418.00 1.3880
-bond 3 60 447.00 1.4190
-bond 3 65 300.00 1.9800
-bond 3 84 400.00 1.4900
-bond 3 86 385.00 1.4600
-bond 3 105 424.00 1.3830
-bond 3 107 490.00 1.3350
-bond 4 25 553.00 0.3000
-bond 4 64 525.00 1.4800
-bond 4 89 570.00 1.2290
-bond 4 110 700.00 1.1710
-bond 5 6 386.00 1.4250
-bond 5 7 553.00 0.9450
-bond 5 10 386.00 1.4250
-bond 5 13 320.00 1.4100
-bond 5 20 250.00 1.4700
-bond 5 24 400.00 1.3800
-bond 5 25 340.00 0.3000
-bond 5 44 320.00 1.4500
-bond 5 47 450.00 1.3700
-bond 5 48 450.00 1.3640
-bond 5 51 320.00 1.3800
-bond 5 64 230.00 1.6100
-bond 5 79 450.00 1.6700
-bond 5 106 94.00 1.8000
-bond 5 108 374.00 1.6400
-bond 6 6 260.00 1.5260
-bond 6 10 260.00 1.5260
-bond 6 11 317.00 1.5000
-bond 6 13 260.00 1.5260
-bond 6 14 317.00 1.5000
-bond 6 15 222.00 1.8100
-bond 6 16 222.00 1.8100
-bond 6 20 320.00 1.4250
-bond 6 24 337.00 1.4490
-bond 6 44 382.00 1.4480
-bond 6 47 317.00 1.5100
-bond 6 51 260.00 1.5260
-bond 6 53 367.00 1.4710
-bond 6 55 337.00 1.4630
-bond 6 79 222.00 1.8100
-bond 6 105 337.00 1.4750
-bond 7 20 553.00 0.9450
-bond 7 25 340.00 0.1000
-bond 9 9 530.00 1.3400
-bond 9 11 530.00 1.3400
-bond 9 14 530.00 1.3400
-bond 10 10 260.00 1.5260
-bond 10 11 317.00 1.5000
-bond 10 14 317.00 1.5000
-bond 10 20 320.00 1.4250
-bond 10 24 337.00 1.4490
-bond 10 44 382.00 1.4480
-bond 10 105 337.00 1.4750
-bond 11 11 530.00 1.3400
-bond 11 13 317.00 1.5000
-bond 11 14 530.00 1.3400
-bond 11 79 222.00 1.7600
-bond 12 12 469.00 1.4000
-bond 12 48 469.00 1.4000
-bond 12 60 469.00 1.4000
-bond 12 81 469.00 1.4000
-bond 13 13 268.00 1.5290
-bond 13 14 317.00 1.5000
-bond 13 15 222.00 1.8100
-bond 13 16 222.00 1.8100
-bond 13 18 390.00 1.4300
-bond 13 19 390.00 1.4700
-bond 13 20 320.00 1.4100
-bond 13 21 245.00 1.7810
-bond 13 22 340.00 1.7900
-bond 13 24 337.00 1.4490
-bond 13 25 340.00 0.3000
-bond 13 44 382.00 1.4480
-bond 13 46 340.00 1.0900
-bond 13 47 317.00 1.5100
-bond 13 48 317.00 1.5100
-bond 13 50 317.00 1.5100
-bond 13 51 268.00 1.5290
-bond 13 53 367.00 1.4710
-bond 13 55 337.00 1.4630
-bond 13 56 337.00 1.4490
-bond 13 57 337.00 1.4750
-bond 13 60 317.00 1.5100
-bond 13 64 212.00 1.8430
-bond 13 65 245.00 1.9450
-bond 13 66 200.00 2.1900
-bond 13 79 340.00 1.7700
-bond 13 80 317.00 1.4950
-bond 13 83 317.00 1.5040
-bond 13 84 317.00 1.5040
-bond 13 85 317.00 1.5040
-bond 13 87 317.00 1.4950
-bond 13 90 337.00 1.4490
-bond 13 91 280.00 1.5100
-bond 13 95 532.80 1.4600
-bond 13 101 382.00 1.4480
-bond 13 102 375.00 1.4900
-bond 13 104 212.00 1.8200
-bond 13 105 337.00 1.4750
-bond 13 107 337.00 1.4490
-bond 13 108 187.00 1.8600
-bond 13 109 317.00 1.5100
-bond 14 14 530.00 1.3400
-bond 15 17 274.00 1.3360
-bond 15 48 250.00 1.7400
-bond 16 16 166.00 2.0380
-bond 16 19 300.00 1.6850
-bond 16 24 250.00 1.7300
-bond 16 25 340.00 0.5000
-bond 16 47 250.00 1.7600
-bond 16 48 250.00 1.7600
-bond 16 61 250.00 1.7300
-bond 16 82 250.00 1.7600
-bond 16 84 250.00 1.7400
-bond 16 91 222.00 1.8100
-bond 16 108 144.00 2.1500
-bond 17 25 340.00 0.1000
-bond 18 18 550.00 1.1200
-bond 18 19 650.00 1.1570
-bond 18 48 400.00 1.4100
-bond 18 56 550.00 1.2400
-bond 19 19 1150.00 1.2100
-bond 19 21 330.00 1.6370
-bond 19 46 420.00 1.0800
-bond 19 47 400.00 1.4260
-bond 19 48 400.00 1.4510
-bond 19 50 400.00 1.4260
-bond 19 65 330.00 1.7840
-bond 19 88 400.00 1.4510
-bond 19 91 400.00 1.4510
-bond 20 20 250.00 1.4700
-bond 20 21 200.00 1.6900
-bond 20 24 320.00 1.4500
-bond 20 25 340.00 0.3000
-bond 20 44 320.00 1.4500
-bond 20 47 450.00 1.3700
-bond 20 48 450.00 1.3640
-bond 20 51 320.00 1.3800
-bond 20 60 340.00 1.3600
-bond 20 61 462.00 1.3990
-bond 20 64 230.00 1.6100
-bond 20 82 462.00 1.3570
-bond 20 84 340.00 1.3600
-bond 20 108 374.00 1.6400
-bond 21 25 300.00 0.3000
-bond 21 47 300.00 1.7250
-bond 21 48 300.00 1.7250
-bond 21 82 300.00 1.7250
-bond 21 83 300.00 1.7250
-bond 21 84 300.00 1.7250
-bond 21 87 300.00 1.7250
-bond 21 88 300.00 1.7250
-bond 21 108 223.00 2.0200
-bond 22 23 700.00 1.5300
-bond 22 25 340.00 0.5000
-bond 23 25 340.00 0.3000
-bond 23 79 700.00 1.4400
-bond 24 25 367.00 0.3000
-bond 24 45 434.00 1.0100
-bond 24 48 427.00 1.3810
-bond 24 59 427.00 1.3810
-bond 24 79 434.00 1.6700
-bond 24 84 427.00 1.3810
-bond 24 88 427.00 1.3810
-bond 24 91 337.00 1.4490
-bond 24 103 500.00 1.2700
-bond 24 106 40.00 2.0500
-bond 25 25 340.00 0.3000
-bond 25 44 340.00 0.3000
-bond 25 45 340.00 0.1000
-bond 25 46 340.00 0.3000
-bond 25 47 340.00 0.3000
-bond 25 48 367.00 0.3000
-bond 25 49 340.00 0.3000
-bond 25 53 340.00 0.3000
-bond 25 56 367.00 0.3000
-bond 25 61 367.00 0.3000
-bond 25 65 300.00 0.3000
-bond 25 103 340.00 0.1000
-bond 31 32 600.00 0.9572
-bond 31 33 900.00 0.1500
-bond 31 106 40.00 2.0500
-bond 34 35 529.60 0.9572
-bond 36 37 600.00 0.9572
-bond 36 38 900.00 0.1750
-bond 39 40 600.00 0.9572
-bond 39 41 900.00 0.7000
-bond 42 43 600.00 1.0000
-bond 44 44 350.00 1.4450
-bond 44 45 434.00 1.0100
-bond 44 48 481.00 1.3400
-bond 44 79 340.00 1.7700
-bond 44 91 382.00 1.4480
-bond 44 108 266.00 1.7400
-bond 45 53 434.00 1.0100
-bond 45 55 434.00 1.0100
-bond 45 56 434.00 1.0100
-bond 45 57 434.00 1.0100
-bond 45 101 434.00 1.0100
-bond 45 105 434.00 1.0100
-bond 45 108 166.00 1.4800
-bond 46 47 340.00 1.0800
-bond 46 50 340.00 1.0800
-bond 46 51 340.00 1.0900
-bond 46 80 340.00 1.0800
-bond 46 91 340.00 1.0880
-bond 46 95 532.80 1.0840
-bond 46 108 166.00 1.4800
-bond 46 109 340.00 1.0800
-bond 47 47 549.00 1.3400
-bond 47 48 427.00 1.4330
-bond 47 50 549.00 1.3400
-bond 47 57 448.00 1.3650
-bond 47 58 367.00 1.0800
-bond 47 65 300.00 1.9000
-bond 47 66 250.00 2.0800
-bond 47 86 385.00 1.4600
-bond 47 91 317.00 1.5100
-bond 47 105 448.00 1.3650
-bond 47 110 700.00 1.3050
-bond 48 48 469.00 1.4000
-bond 48 49 367.00 1.0800
-bond 48 50 427.00 1.4330
-bond 48 53 400.00 1.4500
-bond 48 55 481.00 1.3400
-bond 48 56 483.00 1.3390
-bond 48 57 427.00 1.3810
-bond 48 60 469.00 1.4040
-bond 48 61 414.00 1.3910
-bond 48 64 220.00 1.7800
-bond 48 65 300.00 1.8700
-bond 48 66 250.00 2.0800
-bond 48 79 340.00 1.7700
-bond 48 81 469.00 1.4000
-bond 48 84 546.00 1.3670
-bond 48 86 469.00 1.4000
-bond 48 88 469.00 1.4210
-bond 48 91 317.00 1.4900
-bond 48 101 382.00 1.3850
-bond 48 102 400.00 1.4600
-bond 48 109 427.00 1.4330
-bond 49 59 367.00 1.0800
-bond 49 62 340.00 1.0800
-bond 49 82 367.00 1.0800
-bond 49 83 367.00 1.0800
-bond 49 84 367.00 1.0800
-bond 49 85 367.00 1.0800
-bond 49 87 367.00 1.0800
-bond 49 88 367.00 1.0800
-bond 50 50 385.00 1.4600
-bond 50 56 457.00 1.2900
-bond 50 84 549.00 1.3650
-bond 50 109 385.00 1.4600
-bond 51 105 337.00 1.4750
-bond 52 64 525.00 1.4800
-bond 53 54 434.00 1.0100
-bond 54 55 434.00 1.0100
-bond 55 59 481.00 1.3400
-bond 55 82 481.00 1.3400
-bond 56 56 500.00 1.3200
-bond 56 59 502.00 1.3240
-bond 56 60 461.00 1.3540
-bond 56 82 461.00 1.3540
-bond 56 86 483.00 1.3390
-bond 56 103 550.00 1.2100
-bond 56 109 457.00 1.2900
-bond 57 60 436.00 1.3740
-bond 57 61 400.00 1.3490
-bond 57 62 440.00 1.3710
-bond 57 81 428.00 1.3800
-bond 57 82 477.00 1.3430
-bond 57 84 427.00 1.3810
-bond 57 85 427.00 1.3810
-bond 57 86 385.00 1.4400
-bond 58 83 367.00 1.0800
-bond 58 84 367.00 1.0800
-bond 59 63 367.00 1.0800
-bond 60 60 520.00 1.3700
-bond 60 61 414.00 1.3910
-bond 60 80 388.00 1.4590
-bond 60 81 447.00 1.4190
-bond 60 87 469.00 1.4240
-bond 60 105 436.00 1.3740
-bond 61 61 400.00 1.2800
-bond 61 62 529.00 1.3040
-bond 61 82 488.00 1.3350
-bond 61 83 410.00 1.3940
-bond 61 84 410.00 1.3940
-bond 61 88 410.00 1.3200
-bond 62 63 367.00 1.0800
-bond 62 105 440.00 1.3710
-bond 63 82 367.00 1.0800
-bond 64 108 108.00 2.2500
-bond 65 82 300.00 1.8700
-bond 65 83 300.00 1.8700
-bond 65 84 300.00 1.8700
-bond 65 87 300.00 1.8700
-bond 65 88 300.00 1.8700
-bond 65 108 151.00 2.1900
-bond 66 82 250.00 2.0800
-bond 66 83 250.00 2.0800
-bond 66 84 250.00 2.0800
-bond 66 87 250.00 2.0800
-bond 66 88 250.00 2.0800
-bond 66 108 108.00 2.4400
-bond 77 78 500.00 1.8000
-bond 80 84 546.00 1.3520
-bond 82 86 385.00 1.4600
-bond 82 87 520.00 1.3700
-bond 83 84 520.00 1.3700
-bond 83 86 385.00 1.4600
-bond 84 84 512.00 1.3750
-bond 84 86 385.00 1.4600
-bond 84 87 546.00 1.3670
-bond 84 88 520.00 1.3700
-bond 85 85 520.00 1.3700
-bond 86 86 385.00 1.4600
-bond 86 87 385.00 1.4600
-bond 86 88 385.00 1.4600
-bond 87 87 469.00 1.4240
-bond 87 88 469.00 1.4240
-bond 89 90 490.00 1.3350
-bond 89 91 317.00 1.5220
-bond 90 91 337.00 1.4490
-bond 91 91 260.00 1.5200
-bond 102 103 550.00 1.2250
-bond 108 108 94.00 2.3200
-bond 109 109 549.00 1.3450
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 25 1 25 33.00 109.47
-angle 1 2 2 50.00 109.50
-angle 2 2 2 63.00 112.40
-angle 2 2 3 63.00 112.40
-angle 2 2 5 80.00 109.50
-angle 2 2 6 63.00 112.40
-angle 6 2 6 63.00 112.40
-angle 5 2 6 80.00 109.50
-angle 2 2 10 63.00 112.40
-angle 3 2 10 63.00 112.40
-angle 6 2 10 63.00 112.40
-angle 10 2 10 63.00 112.40
-angle 5 2 10 80.00 109.50
-angle 10 2 12 63.00 114.00
-angle 6 2 13 63.00 112.40
-angle 10 2 15 50.00 108.60
-angle 2 2 16 50.00 114.70
-angle 10 2 16 50.00 114.70
-angle 2 2 20 80.00 109.50
-angle 6 2 20 80.00 109.50
-angle 10 2 20 80.00 109.50
-angle 3 2 24 80.00 110.30
-angle 2 2 24 80.00 111.20
-angle 2 2 44 56.20 109.47
-angle 6 2 44 56.20 109.47
-angle 10 2 44 56.20 109.47
-angle 13 2 44 56.20 109.47
-angle 3 2 44 80.00 111.20
-angle 2 2 48 63.00 112.40
-angle 10 2 48 63.00 114.00
-angle 2 2 51 63.00 112.40
-angle 6 2 51 63.00 112.40
-angle 2 2 53 80.00 111.20
-angle 2 2 55 80.00 111.20
-angle 10 2 80 63.00 115.60
-angle 2 3 4 80.00 120.40
-angle 1 3 4 80.00 121.00
-angle 3 3 4 80.00 121.40
-angle 4 3 4 80.00 126.00
-angle 4 3 5 80.00 121.00
-angle 4 3 6 80.00 120.40
-angle 5 3 10 70.00 115.00
-angle 4 3 10 80.00 120.40
-angle 5 3 12 70.00 120.00
-angle 12 3 12 85.00 120.00
-angle 5 3 13 70.00 108.00
-angle 13 3 13 70.00 116.00
-angle 1 3 13 80.00 111.00
-angle 3 3 13 80.00 117.20
-angle 4 3 13 80.00 120.40
-angle 10 3 20 81.00 111.40
-angle 13 3 20 81.00 111.40
-angle 4 3 20 83.00 123.40
-angle 13 3 21 75.00 109.00
-angle 4 3 21 75.00 119.00
-angle 24 3 24 70.00 114.20
-angle 2 3 24 70.00 116.60
-angle 3 3 24 70.00 116.60
-angle 6 3 24 70.00 116.60
-angle 10 3 24 70.00 116.60
-angle 13 3 24 70.00 116.60
-angle 4 3 24 80.00 122.90
-angle 20 3 24 81.00 111.40
-angle 13 3 44 70.00 116.00
-angle 4 3 44 80.00 120.40
-angle 13 3 46 35.00 115.00
-angle 46 3 46 35.00 115.00
-angle 4 3 46 35.00 123.00
-angle 24 3 46 40.00 114.00
-angle 5 3 46 40.00 115.00
-angle 20 3 46 40.00 115.00
-angle 24 3 47 70.00 115.50
-angle 4 3 47 80.00 125.30
-angle 46 3 48 35.00 115.00
-angle 24 3 48 70.00 115.50
-angle 13 3 48 70.00 116.00
-angle 5 3 48 70.00 120.00
-angle 4 3 48 80.00 120.40
-angle 20 3 48 81.00 111.40
-angle 48 3 48 85.00 120.00
-angle 13 3 50 70.00 116.00
-angle 46 3 50 80.00 116.00
-angle 4 3 50 80.00 124.00
-angle 10 3 52 65.00 117.00
-angle 2 3 52 70.00 117.00
-angle 6 3 52 70.00 117.00
-angle 13 3 52 70.00 117.00
-angle 48 3 52 70.00 117.00
-angle 4 3 52 80.00 126.00
-angle 52 3 52 80.00 126.00
-angle 46 3 56 35.00 116.00
-angle 46 3 56 35.00 122.00
-angle 4 3 56 80.00 122.50
-angle 47 3 57 70.00 114.10
-angle 56 3 57 70.00 118.60
-angle 57 3 57 70.00 118.60
-angle 4 3 57 80.00 120.60
-angle 24 3 60 70.00 111.30
-angle 57 3 60 70.00 111.30
-angle 4 3 60 80.00 128.80
-angle 13 3 65 75.00 109.00
-angle 4 3 65 75.00 119.00
-angle 44 3 84 70.00 116.00
-angle 4 3 84 80.00 120.40
-angle 4 3 87 80.00 128.20
-angle 57 3 105 70.00 115.40
-angle 56 3 105 70.00 118.60
-angle 4 3 105 80.00 120.90
-angle 13 3 107 70.00 116.60
-angle 4 3 107 80.00 122.90
-angle 25 4 25 10.00 117.00
-angle 3 4 25 35.00 113.00
-angle 3 5 7 35.00 113.00
-angle 2 5 7 55.00 108.50
-angle 6 5 7 55.00 108.50
-angle 7 5 10 55.00 108.50
-angle 7 5 13 55.00 108.50
-angle 7 5 24 49.00 105.40
-angle 25 5 25 5.00 109.47
-angle 7 5 25 10.00 109.47
-angle 13 5 25 10.00 109.47
-angle 7 5 47 35.00 109.00
-angle 25 5 48 10.00 109.47
-angle 7 5 48 35.00 113.00
-angle 7 5 51 55.00 108.50
-angle 7 5 64 55.00 108.50
-angle 13 5 64 100.00 120.50
-angle 7 5 79 74.00 110.00
-angle 7 5 106 100.00 126.00
-angle 5 7 25 10.00 109.47
-angle 25 7 25 33.00 109.47
-angle 2 10 2 63.00 112.40
-angle 2 10 3 63.00 111.10
-angle 2 10 5 80.00 109.50
-angle 3 10 6 63.00 111.10
-angle 6 10 6 63.00 111.50
-angle 2 10 6 63.00 112.40
-angle 5 10 6 80.00 109.50
-angle 3 10 10 63.00 111.10
-angle 2 10 10 63.00 111.50
-angle 6 10 10 63.00 111.50
-angle 10 10 10 63.00 111.50
-angle 5 10 10 80.00 109.50
-angle 2 10 20 80.00 109.50
-angle 6 10 20 80.00 109.50
-angle 10 10 20 80.00 109.50
-angle 3 10 24 63.00 110.10
-angle 6 10 24 80.00 109.50
-angle 2 10 24 80.00 109.70
-angle 10 10 24 80.00 109.70
-angle 2 10 44 56.20 109.47
-angle 6 10 44 56.20 109.47
-angle 10 10 44 56.20 109.47
-angle 13 10 44 56.20 109.47
-angle 3 10 44 80.00 109.70
-angle 2 10 48 63.00 112.40
-angle 20 10 48 80.00 109.50
-angle 2 10 105 80.00 109.50
-angle 10 10 105 80.00 109.50
-angle 20 10 105 80.00 109.50
-angle 2 11 2 70.00 124.00
-angle 2 11 6 70.00 124.00
-angle 6 11 6 70.00 124.00
-angle 2 11 9 70.00 118.00
-angle 6 11 9 70.00 118.00
-angle 9 11 10 70.00 118.00
-angle 2 11 10 70.00 124.00
-angle 6 11 10 70.00 124.00
-angle 10 11 10 70.00 124.00
-angle 2 11 11 70.00 118.00
-angle 6 11 11 70.00 118.00
-angle 9 11 11 70.00 118.00
-angle 10 11 11 70.00 118.00
-angle 11 11 11 70.00 118.00
-angle 9 11 13 70.00 118.00
-angle 11 11 13 70.00 118.00
-angle 2 11 13 70.00 124.00
-angle 6 11 13 70.00 124.00
-angle 10 11 13 70.00 124.00
-angle 13 11 13 70.00 124.00
-angle 9 11 14 70.00 118.00
-angle 11 11 14 70.00 118.00
-angle 9 11 79 70.00 118.00
-angle 2 12 12 70.00 120.00
-angle 3 12 12 85.00 120.00
-angle 12 12 12 85.00 120.00
-angle 12 12 48 85.00 120.00
-angle 12 12 60 85.00 120.00
-angle 12 12 81 85.00 120.00
-angle 1 13 1 77.00 109.10
-angle 2 13 2 40.00 109.50
-angle 1 13 3 50.00 109.50
-angle 2 13 3 63.00 111.10
-angle 3 13 3 63.00 111.10
-angle 2 13 6 40.00 109.50
-angle 6 13 6 40.00 109.50
-angle 3 13 6 63.00 109.50
-angle 1 13 13 50.00 109.50
-angle 5 13 13 50.00 109.50
-angle 13 13 13 58.35 112.70
-angle 3 13 13 63.00 111.10
-angle 13 13 15 50.00 108.60
-angle 13 13 16 50.00 114.70
-angle 13 13 19 58.35 112.70
-angle 3 13 20 50.00 109.50
-angle 13 13 20 50.00 109.50
-angle 3 13 21 69.00 109.80
-angle 13 13 21 69.00 109.80
-angle 21 13 21 78.00 111.70
-angle 13 13 22 50.00 108.60
-angle 20 13 24 50.00 109.50
-angle 3 13 24 63.00 110.10
-angle 2 13 24 80.00 109.70
-angle 13 13 24 80.00 109.70
-angle 16 13 44 50.00 114.70
-angle 2 13 44 56.20 109.47
-angle 6 13 44 56.20 109.47
-angle 10 13 44 56.20 109.47
-angle 13 13 44 56.20 109.47
-angle 3 13 44 80.00 111.20
-angle 46 13 46 33.00 107.80
-angle 18 13 46 35.00 108.50
-angle 19 13 46 35.00 108.50
-angle 2 13 46 35.00 109.50
-angle 3 13 46 35.00 109.50
-angle 5 13 46 35.00 109.50
-angle 15 13 46 35.00 109.50
-angle 16 13 46 35.00 109.50
-angle 20 13 46 35.00 109.50
-angle 22 13 46 35.00 109.50
-angle 24 13 46 35.00 109.50
-angle 44 13 46 35.00 109.50
-angle 13 13 46 37.50 110.70
-angle 1 13 46 40.00 107.00
-angle 21 13 46 51.00 107.60
-angle 46 13 47 35.00 109.50
-angle 1 13 47 50.00 109.50
-angle 13 13 47 63.00 111.10
-angle 47 13 47 63.00 112.40
-angle 46 13 48 35.00 109.50
-angle 47 13 48 40.00 109.50
-angle 48 13 48 40.00 109.50
-angle 1 13 48 50.00 109.50
-angle 5 13 48 50.00 109.50
-angle 20 13 48 50.00 109.50
-angle 16 13 48 50.00 114.70
-angle 3 13 48 63.00 112.00
-angle 2 13 48 63.00 114.00
-angle 13 13 48 63.00 114.00
-angle 44 13 48 80.00 111.20
-angle 46 13 50 35.00 109.50
-angle 46 13 51 37.50 110.70
-angle 5 13 51 50.00 109.50
-angle 13 13 51 58.35 112.70
-angle 46 13 53 35.00 109.50
-angle 3 13 53 80.00 111.20
-angle 13 13 53 80.00 111.20
-angle 46 13 55 35.00 109.50
-angle 13 13 55 80.00 111.20
-angle 46 13 56 35.00 109.50
-angle 3 13 56 63.00 110.10
-angle 13 13 56 65.00 109.00
-angle 46 13 57 35.00 109.50
-angle 48 13 57 80.00 111.20
-angle 46 13 60 35.00 109.50
-angle 13 13 60 63.00 114.00
-angle 46 13 64 41.00 109.50
-angle 13 13 64 43.00 109.50
-angle 48 13 64 43.00 109.50
-angle 46 13 65 51.00 107.60
-angle 3 13 65 69.00 109.80
-angle 13 13 65 69.00 110.00
-angle 48 13 65 69.00 110.00
-angle 65 13 65 78.00 111.70
-angle 46 13 66 75.00 111.00
-angle 13 13 66 75.00 112.00
-angle 46 13 79 35.00 109.50
-angle 13 13 79 50.00 108.60
-angle 1 13 79 50.00 109.50
-angle 46 13 80 35.00 109.50
-angle 13 13 80 63.00 115.60
-angle 46 13 83 35.00 109.50
-angle 13 13 83 63.00 114.00
-angle 46 13 84 35.00 109.50
-angle 16 13 84 50.00 114.70
-angle 13 13 84 63.00 114.00
-angle 46 13 85 35.00 109.50
-angle 13 13 85 63.00 114.00
-angle 46 13 87 35.00 109.50
-angle 13 13 87 63.00 115.60
-angle 46 13 90 35.00 109.50
-angle 13 13 90 80.00 110.00
-angle 3 13 90 80.00 113.00
-angle 46 13 91 37.50 110.70
-angle 46 13 95 35.00 105.00
-angle 13 13 95 63.00 105.00
-angle 46 13 101 35.00 109.50
-angle 13 13 101 80.00 111.20
-angle 46 13 102 35.00 105.00
-angle 13 13 102 63.00 111.10
-angle 46 13 104 41.00 109.50
-angle 13 13 104 43.00 109.50
-angle 46 13 105 35.00 109.50
-angle 13 13 105 50.00 109.50
-angle 20 13 105 50.00 109.50
-angle 46 13 107 35.00 109.50
-angle 13 13 107 80.00 109.70
-angle 46 13 108 35.00 109.50
-angle 13 13 108 60.00 112.00
-angle 2 14 2 70.00 124.00
-angle 2 14 6 70.00 124.00
-angle 6 14 6 70.00 124.00
-angle 2 14 9 70.00 118.00
-angle 6 14 9 70.00 118.00
-angle 9 14 10 70.00 118.00
-angle 2 14 10 70.00 124.00
-angle 6 14 10 70.00 124.00
-angle 10 14 10 70.00 124.00
-angle 2 14 11 70.00 118.00
-angle 6 14 11 70.00 118.00
-angle 9 14 11 70.00 118.00
-angle 10 14 11 70.00 118.00
-angle 11 14 11 70.00 118.00
-angle 9 14 13 70.00 118.00
-angle 11 14 13 70.00 118.00
-angle 2 14 13 70.00 124.00
-angle 6 14 13 70.00 124.00
-angle 10 14 13 70.00 124.00
-angle 13 14 13 70.00 124.00
-angle 2 14 14 70.00 118.00
-angle 6 14 14 70.00 118.00
-angle 9 14 14 70.00 118.00
-angle 10 14 14 70.00 118.00
-angle 11 14 14 70.00 118.00
-angle 13 14 14 70.00 118.00
-angle 14 14 14 70.00 118.00
-angle 17 15 17 35.00 92.07
-angle 2 15 17 44.00 96.00
-angle 6 15 17 44.00 96.00
-angle 13 15 17 44.00 96.00
-angle 25 15 25 5.00 109.47
-angle 13 15 25 10.00 109.47
-angle 33 15 33 10.00 160.00
-angle 2 15 33 150.00 96.70
-angle 6 15 33 150.00 96.70
-angle 13 15 33 150.00 96.70
-angle 17 15 33 150.00 96.70
-angle 17 15 48 50.00 96.00
-angle 2 16 6 62.00 98.90
-angle 13 16 13 62.00 98.90
-angle 2 16 16 68.00 103.70
-angle 6 16 16 68.00 103.70
-angle 13 16 16 68.00 103.70
-angle 13 16 19 65.00 100.00
-angle 25 16 25 5.00 109.47
-angle 13 16 25 10.00 109.47
-angle 33 16 33 10.00 160.00
-angle 2 16 33 150.00 96.70
-angle 6 16 33 150.00 96.70
-angle 13 16 33 150.00 96.70
-angle 16 16 33 150.00 96.70
-angle 13 16 48 62.00 104.20
-angle 47 16 48 62.00 104.20
-angle 24 16 60 74.00 92.40
-angle 25 16 61 10.00 130.00
-angle 25 16 82 10.00 130.00
-angle 60 16 82 74.00 97.00
-angle 25 16 84 10.00 130.00
-angle 82 16 84 74.00 90.00
-angle 60 16 84 74.00 97.00
-angle 84 16 84 74.00 97.00
-angle 13 16 91 62.00 94.00
-angle 15 17 25 10.00 109.47
-angle 25 17 25 33.00 109.47
-angle 13 18 19 150.00 180.00
-angle 19 18 48 170.00 180.00
-angle 18 18 56 100.00 180.00
-angle 13 19 18 150.00 180.00
-angle 16 19 19 140.00 180.00
-angle 13 19 19 150.00 180.00
-angle 18 19 25 10.00 90.00
-angle 19 19 46 112.00 180.00
-angle 18 19 47 150.00 180.00
-angle 19 19 47 160.00 180.00
-angle 18 19 48 150.00 180.00
-angle 19 19 48 160.00 180.00
-angle 19 19 50 160.00 180.00
-angle 18 19 55 150.00 180.00
-angle 18 19 88 150.00 180.00
-angle 2 20 2 100.00 111.80
-angle 2 20 3 83.00 116.90
-angle 3 20 6 83.00 116.90
-angle 2 20 6 100.00 111.80
-angle 2 20 7 55.00 108.50
-angle 7 20 10 55.00 108.50
-angle 3 20 10 83.00 116.90
-angle 10 20 10 100.00 111.80
-angle 13 20 13 60.00 109.50
-angle 3 20 13 83.00 116.90
-angle 25 20 25 5.00 109.47
-angle 13 20 25 10.00 109.47
-angle 13 20 47 75.00 111.00
-angle 25 20 48 10.00 109.47
-angle 13 20 48 75.00 111.00
-angle 47 20 48 75.00 111.00
-angle 48 20 48 75.00 111.00
-angle 3 20 48 83.00 116.90
-angle 2 20 48 100.00 111.80
-angle 13 20 51 60.00 109.50
-angle 2 20 51 100.00 113.00
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-angle 10 48 48 70.00 120.00
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-angle 15 48 48 70.00 120.00
-angle 19 48 48 70.00 120.00
-angle 20 48 48 70.00 120.00
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-angle 1 48 48 80.00 120.00
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-angle 55 48 55 70.00 120.00
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-angle 50 48 56 70.00 121.50
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-angle 21 48 56 75.00 120.00
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-angle 49 48 60 35.00 120.00
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-angle 2 48 60 70.00 128.60
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-angle 48 48 65 75.00 120.00
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-angle 25 50 50 2.00 90.00
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-angle 2 51 20 80.00 109.50
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-angle 48 53 54 35.00 109.50
-angle 54 53 54 35.00 109.50
-angle 25 53 82 10.00 100.00
-angle 13 55 13 50.00 118.00
-angle 45 55 45 35.00 113.00
-angle 13 55 45 35.00 118.40
-angle 45 55 48 35.00 120.00
-angle 2 55 48 50.00 123.20
-angle 6 55 48 50.00 123.20
-angle 13 55 48 50.00 123.20
-angle 2 55 54 35.00 118.40
-angle 13 55 54 35.00 118.40
-angle 48 55 54 35.00 120.00
-angle 54 55 54 35.00 120.00
-angle 45 55 59 35.00 120.00
-angle 3 56 13 70.00 120.50
-angle 13 56 18 70.00 120.00
-angle 25 56 48 5.00 120.00
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-angle 13 56 48 50.00 118.00
-angle 48 56 48 70.00 117.00
-angle 3 56 48 70.00 120.50
-angle 13 56 56 70.00 117.00
-angle 48 56 56 70.00 117.00
-angle 25 56 59 5.00 119.80
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-angle 59 56 59 70.00 118.60
-angle 59 56 60 70.00 111.00
-angle 48 56 60 70.00 112.20
-angle 59 56 82 70.00 111.00
-angle 48 56 86 70.00 117.00
-angle 13 56 103 70.00 114.00
-angle 3 57 3 70.00 126.40
-angle 3 57 45 35.00 116.80
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-angle 3 57 47 70.00 121.60
-angle 45 57 48 35.00 118.00
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-angle 48 57 48 70.00 125.20
-angle 45 57 60 30.00 125.80
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-angle 60 57 61 56.00 113.10
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-angle 60 57 84 70.00 109.80
-angle 82 57 84 70.00 109.80
-angle 84 57 84 70.00 109.80
-angle 81 57 84 70.00 111.60
-angle 45 57 85 35.00 120.00
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-angle 24 59 55 70.00 116.00
-angle 49 59 56 35.00 115.45
-angle 13 59 56 70.00 115.50
-angle 55 59 56 70.00 119.30
-angle 24 59 56 70.00 123.30
-angle 56 59 56 70.00 129.10
-angle 56 59 63 35.00 115.45
-angle 13 60 48 70.00 120.00
-angle 48 60 48 85.00 134.90
-angle 56 60 57 70.00 126.20
-angle 57 60 60 70.00 106.20
-angle 20 60 60 70.00 110.60
-angle 16 60 60 70.00 111.00
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-angle 56 60 60 70.00 127.70
-angle 48 60 60 85.00 117.30
-angle 3 60 60 85.00 119.20
-angle 60 60 61 70.00 111.00
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-angle 3 60 61 70.00 130.00
-angle 48 60 61 70.00 132.40
-angle 12 60 80 85.00 134.90
-angle 48 60 80 85.00 134.90
-angle 80 60 81 85.00 108.80
-angle 12 60 81 85.00 116.20
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-angle 3 60 84 70.00 130.00
-angle 60 60 87 70.00 107.30
-angle 57 60 87 70.00 107.70
-angle 81 60 87 85.00 108.80
-angle 12 60 87 85.00 134.90
-angle 48 60 87 85.00 134.90
-angle 60 60 105 70.00 106.20
-angle 56 60 105 70.00 126.20
-angle 48 61 48 70.00 125.20
-angle 25 61 57 10.00 125.00
-angle 25 61 61 10.00 125.00
-angle 60 61 62 70.00 103.80
-angle 25 61 82 10.00 125.00
-angle 61 61 82 70.00 109.00
-angle 60 61 82 70.00 110.00
-angle 82 61 83 70.00 110.00
-angle 57 61 84 70.00 104.10
-angle 82 61 84 70.00 110.00
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-angle 20 61 88 70.00 105.30
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-angle 61 62 63 35.00 123.05
-angle 49 62 105 35.00 120.00
-angle 63 62 105 35.00 123.05
-angle 61 62 105 70.00 113.90
-angle 5 64 5 45.00 102.60
-angle 4 64 5 100.00 108.23
-angle 4 64 13 45.00 109.50
-angle 5 64 20 45.00 102.60
-angle 20 64 20 45.00 102.60
-angle 13 64 20 45.00 109.50
-angle 4 64 20 100.00 108.23
-angle 4 64 48 45.00 109.50
-angle 5 64 48 45.00 109.50
-angle 20 64 48 45.00 109.50
-angle 5 64 52 45.00 108.23
-angle 13 64 52 45.00 109.50
-angle 20 64 52 100.00 108.23
-angle 52 64 52 140.00 119.90
-angle 25 65 25 33.00 109.47
-angle 25 66 25 33.00 109.47
-angle 78 77 78 150.00 180.00
-angle 6 79 11 62.00 98.90
-angle 13 79 13 62.00 102.00
-angle 5 79 13 75.00 96.40
-angle 5 79 23 74.00 108.70
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-angle 23 79 23 104.00 119.00
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-angle 5 79 48 75.00 96.40
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-angle 46 80 60 35.00 126.80
-angle 2 80 60 70.00 128.60
-angle 13 80 60 70.00 128.60
-angle 46 80 84 35.00 126.80
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-angle 60 80 84 85.00 106.40
-angle 12 81 57 70.00 132.80
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-angle 61 82 79 70.00 120.00
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-angle 56 82 87 70.00 127.70
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-angle 61 83 84 70.00 111.00
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-angle 3 84 57 85.00 120.00
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-angle 49 84 80 35.00 120.00
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-angle 4 89 90 80.00 134.00
-angle 90 89 91 70.00 91.00
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-angle 89 90 91 50.00 94.00
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-angle 16 91 46 37.50 108.00
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-angle 16 91 90 55.00 109.00
-angle 91 91 91 30.00 79.20
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-angle 89 91 91 63.00 85.00
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-angle 90 91 91 80.00 89.00
-angle 13 95 13 172.80 120.00
-angle 13 95 46 144.00 120.00
-angle 13 101 45 35.00 109.50
-angle 45 101 45 43.60 106.40
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-angle 13 102 103 80.00 117.50
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-angle 103 102 103 80.00 125.00
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-angle 25 103 102 10.00 109.50
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-angle 10 105 60 70.00 125.80
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-angle 51 105 62 70.00 128.80
-angle 4 106 24 20.00 109.50
-angle 24 106 24 20.00 109.50
-angle 13 107 13 50.00 118.00
-angle 3 107 13 50.00 121.90
-angle 1 108 13 35.00 110.50
-angle 13 108 13 60.00 110.00
-angle 13 108 20 60.00 100.00
-angle 20 108 20 60.00 110.00
-angle 13 108 21 35.00 110.50
-angle 45 108 45 35.00 109.50
-angle 13 108 45 35.00 110.50
-angle 46 108 46 35.00 109.50
-angle 13 108 46 35.00 110.50
-angle 13 108 65 35.00 110.50
-angle 13 108 66 35.00 110.50
-angle 13 108 108 50.00 112.00
-angle 46 109 48 35.00 123.30
-angle 46 109 50 35.00 120.00
-angle 13 109 50 70.00 124.00
-angle 46 109 109 35.00 120.00
-angle 13 109 109 70.00 124.00
-angle 50 109 109 70.00 124.00
-angle 48 109 109 85.00 117.00
-angle 4 110 47 160.00 180.00
-angle 47 110 47 160.00 180.00
-
-
- ################################
- ## ##
- ## Urey-Bradley Parameters ##
- ## ##
- ################################
-
-
-ureybrad 35 34 35 38.25 1.5537
-
-
- #####################################
- ## ##
- ## Improper Torsional Parameters ##
- ## ##
- #####################################
-
-
-imptors 0 0 3 4 21.000 180.0 2
-imptors 0 0 3 52 21.000 180.0 2
-imptors 0 0 24 0 5.000 180.0 2
-imptors 0 0 47 0 30.000 180.0 2
-imptors 0 0 48 0 5.000 180.0 2
-
-
- ############################
- ## ##
- ## Torsional Parameters ##
- ## ##
- ############################
-
-
- ###################################################################
- ## ##
- ## Alternative Torsional Parameter Values for Use with OPLS-AA ##
- ## ##
- ## For some torsions, OPLS-AA has multiple possible parameter ##
- ## values; the list below shows functional groups for which ##
- ## these alternate (commented) values should be preferred; the ##
- ## values are in the same order as in the full parameter list ##
- ## ##
- ## 4 3 3 36 generic (default) ##
- ## 4 3 3 36 dicarbonyls ##
- ## 36 3 3 36 hydrocarbon (default) ##
- ## 36 3 3 36 dicarbonyls ##
- ## 13 3 5 7 carboxylic acid (default) ##
- ## 13 3 5 7 1,2-diacid monoanion ##
- ## 4 3 13 13 peptide (default) ##
- ## 4 3 13 13 propanamide ##
- ## 4 3 13 13 carboxylic acid ##
- ## 4 3 13 13 dicarboxylic acid ##
- ## 4 3 13 13 aldyhyde, ketone, acyl halide ##
- ## 4 3 13 13 1,2-diacid monoanion ##
- ## 5 3 13 13 carboxylic acid (default) ##
- ## 5 3 13 13 dicarboxylic acid ##
- ## 35 3 13 13 peptide psi' (default) ##
- ## 35 3 13 13 propanamide ##
- ## 35 3 13 13 beta-3-peptide, last psi ##
- ## 4 3 29 13 esters (default) ##
- ## 4 3 29 13 benzoic esters ##
- ## 7 5 13 13 alcohols (default) ##
- ## 7 5 13 13 trifluoroethanol ##
- ## 7 5 13 13 hexopyranoses ##
- ## 7 5 13 36 alcohols (default) ##
- ## 7 5 13 36 axial cyclohexanol ##
- ## 7 5 13 36 trifluoroethanol ##
- ## 0 13 13 13 alcohols, ethers (default) ##
- ## 0 13 13 13 hexopyranoses ##
- ## 3 13 13 3 dicarboxylic acid (default) ##
- ## 3 13 13 3 1,2-diacid monoanion ##
- ## 3 13 13 13 butanamide (default) ##
- ## 3 13 13 13 carboxylate ion ##
- ## 3 13 13 13 aldyhyde, ketone, acyl halide ##
- ## 3 13 13 36 all carbonyls (default) ##
- ## 3 13 13 36 dicarboxylic acid ##
- ## 3 13 13 36 aldehyde, ketone, acyl halide ##
- ## 5 13 13 5 diols only (default) ##
- ## 5 13 13 5 triols only ##
- ## 5 13 13 5 hexopyranoses ##
- ## 13 13 13 13 hydrocarbon (default) ##
- ## 13 13 13 13 perfluoroalkane ##
- ## 13 13 13 35 peptide chi-1 (default) ##
- ## 13 13 13 35 N-propylformamide ##
- ## 36 13 13 69 generic (default) ##
- ## 36 13 13 69 sulfone ##
- ## 13 13 33 13 amine (default) ##
- ## 13 13 33 13 exocyclic amine ##
- ## 13 13 33 13 exocyclic 1,4-diamine ##
- ## 13 13 33 34 amine (default) ##
- ## 13 13 33 34 azetidine, 4-ring ##
- ## 13 13 33 34 pyrrolidine, 5-ring ##
- ## 13 13 33 34 cyclic amine ##
- ## 13 13 33 34 cyclic 1,4-diamine ##
- ## 13 13 35 3 peptide phi' (default) ##
- ## 13 13 35 3 N-ethylformamide ##
- ## 13 13 35 3 beta-3-peptide, first theta tors ##
- ## 13 13 35 13 proline, CD-N-CA-CB (default) ##
- ## 13 13 35 13 proline, CG-CD-N-CA ##
- ## 36 13 35 3 peptide phi'' (default) ##
- ## 36 13 35 3 N-methylformamide ##
- ## 13 13 47 0 imidazole, indole, purine (default) ##
- ## 13 13 47 0 nucleoside chi ##
- ## 13 13 47 52 nucleoside (default) ##
- ## 13 13 47 52 imidazole, indole, purine ##
- ## 29 13 47 0 imidazole, indole, purine (default) ##
- ## 29 13 47 0 nucleoside chi ##
- ## 29 13 95 52 nucleoside (default) ##
- ## 29 13 95 52 imidazole, indole, purine ##
- ## 13 13 97 13 generic (default) ##
- ## 13 13 97 13 generic ##
- ## 17 15 38 0 aromatic thiol (default) ##
- ## 17 15 38 0 aromatic thiol, N-C-S-H ##
- ## 13 29 54 42 phosphonates (default) ##
- ## 13 29 54 42 dimethyl phosphate ##
- ## 34 35 72 16 diaryl amine (default) ##
- ## 34 35 72 16 aniline-like ##
- ## 34 35 72 29 diaryl amine (default) ##
- ## 34 35 72 29 aniline-like ##
- ## 13 40 40 37 diene (default) ##
- ## 13 40 40 37 2-methyl-1,3-butadiene ##
- ## 0 46 72 0 generic (default) ##
- ## 0 46 72 0 generic ##
- ## 0 47 72 0 generic (default) ##
- ## 0 47 72 0 generic ##
- ## 0 47 74 0 generic (default) ##
- ## 0 47 74 0 generic ##
- ## 0 47 74 0 generic ##
- ## 0 51 72 0 generic (default) ##
- ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ##
- ## 0 72 77 0 generic (default) ##
- ## 0 72 77 0 biphenyl-like, N-C-C-C ##
- ## ##
- ###################################################################
-
-
-torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3
-torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3
-torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3
-torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3
-torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3
-torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3
-torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3
-torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3
-torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3
-torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3
-torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3
-torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3
-torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3
-torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3
-torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3
-torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3
-torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3
-#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3
-torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3
-torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3
-#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3
-#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3
-#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3
-#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3
-torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3
-torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3
-#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3
-torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3
-torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3
-torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3
-torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3
-torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3
-#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3
-#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3
-torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3
-torsion 24 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 48 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3
-torsion 52 3 13 13 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 52 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 52 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 65 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 65 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3
-torsion 107 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 20 13 0.000 0.0 1 5.124 180.0 2 0.000 0.0 3
-#torsion 4 3 29 13 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 4 3 20 48 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 13 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3
-torsion 13 3 20 48 1.500 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 24 3 20 13 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 46 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3
-torsion 48 3 20 13 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 3 3 24 13 0.400 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 3 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 3 24 5 0.000 0.0 1 6.603 180.0 2 0.000 0.0 3
-torsion 4 3 24 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 3 24 47 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 3 24 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 3 24 91 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 5 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 5 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 13 3 24 5 4.542 0.0 1 6.603 180.0 2 1.045 0.0 3
-torsion 13 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 13 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 13 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 20 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 20 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 24 3 24 3 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 24 3 24 13 4.600 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 46 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 46 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 47 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 48 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 48 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 48 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 48 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 84 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 84 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 84 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 87 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 87 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 87 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 87 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 0 3 47 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3
-torsion 4 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 47 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3
-torsion 5 3 47 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 24 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 107 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 107 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 5 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 13 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 20 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 24 3 48 48 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3
-torsion 46 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3
-torsion 0 3 50 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3
-torsion 4 3 50 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3
-torsion 5 3 50 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 13 3 50 47 0.800 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 13 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 3 56 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 3 56 45 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 0 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3
-torsion 4 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3
-torsion 4 3 82 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 3 82 57 2.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 4 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 82 3 82 57 -2.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 82 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3
-torsion 4 3 84 20 -0.750 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 4 3 84 87 0.750 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 84 3 84 20 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 84 3 84 87 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3
-torsion 48 3 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 3 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 4 3 87 84 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 4 3 87 87 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3
-torsion 24 3 87 84 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3
-torsion 24 3 87 87 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3
-torsion 4 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 13 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 3 109 109 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3
-torsion 5 3 109 109 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3
-torsion 0 4 106 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 10 2 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3
-torsion 7 5 10 6 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3
-torsion 7 5 13 2 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3
-torsion 7 5 13 6 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3
-torsion 7 5 13 13 -0.356 0.0 1 -0.174 180.0 2 0.492 0.0 3
-#torsion 7 5 13 13 4.478 0.0 1 -2.175 180.0 2 0.000 0.0 3
-#torsion 7 5 13 13 2.674 0.0 1 -2.883 180.0 2 1.026 0.0 3
-torsion 7 5 13 46 0.000 0.0 1 0.000 180.0 2 0.352 0.0 3
-#torsion 7 5 13 36 -2.589 0.0 1 -1.123 180.0 2 0.270 0.0 3
-#torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.476 0.0 3
-torsion 7 5 13 47 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 13 48 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 13 50 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 44 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 7 5 44 45 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 7 5 24 3 5.519 0.0 1 -6.700 180.0 2 0.581 0.0 3
-torsion 7 5 24 45 2.722 0.0 1 -5.154 180.0 2 0.000 0.0 3
-torsion 7 5 47 47 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3
-torsion 7 5 48 48 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3
-torsion 7 5 51 20 -1.257 0.0 1 -1.806 180.0 2 0.003 0.0 3
-torsion 7 5 56 3 3.000 0.0 1 3.000 180.0 2 0.000 0.0 3
-torsion 7 5 64 4 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 64 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 79 13 -0.750 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 79 23 0.750 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 7 5 79 48 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 13 13 3 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3
-torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3
-#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 13 13 24 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3
-torsion 1 13 13 1 -2.500 0.0 1 0.000 180.0 2 0.250 0.0 3
-torsion 1 13 13 5 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3
-torsion 1 13 13 13 0.300 0.0 1 -0.400 180.0 2 0.400 0.0 3
-torsion 1 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3
-torsion 3 13 13 3 -0.550 0.0 1 0.000 180.0 2 1.000 0.0 3
-#torsion 3 13 13 3 0.800 0.0 1 0.000 180.0 2 0.900 0.0 3
-torsion 3 13 13 5 -6.180 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 13 13 13 -2.060 0.0 1 -0.313 180.0 2 0.315 0.0 3
-#torsion 3 13 13 13 -3.185 0.0 1 -0.825 180.0 2 0.493 0.0 3
-#torsion 3 13 13 13 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 15 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3
-torsion 3 13 13 16 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3
-torsion 3 13 13 24 -9.000 0.0 1 2.000 180.0 2 0.800 0.0 3
-torsion 3 13 13 46 0.000 0.0 1 0.000 180.0 2 -0.100 0.0 3
-#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 0.074 0.0 3
-#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.076 0.0 3
-torsion 3 13 13 48 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 80 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 5 13 13 5 9.508 0.0 1 0.000 180.0 2 0.000 0.0 3
-#torsion 5 13 13 5 12.234 0.0 1 0.000 180.0 2 0.000 0.0 3
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-torsion 0 61 82 49 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3
-torsion 83 61 82 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 88 61 82 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 88 61 82 20 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 61 83 0 0.000 0.0 1 4.800 180.0 2 0.000 0.0 3
-torsion 82 61 83 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 82 61 83 84 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 61 84 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3
-torsion 0 61 88 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 82 61 88 84 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 80 84 0 0.000 0.0 1 13.050 180.0 2 0.000 0.0 3
-torsion 0 82 84 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 16 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 20 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 57 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 61 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 82 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-#torsion 0 72 77 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 83 84 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 0 83 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 49 83 84 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 49 83 84 16 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 49 83 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 61 83 84 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 61 83 84 20 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 61 83 84 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 83 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 61 83 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 61 83 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 84 83 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 84 84 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 0 84 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 16 84 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 49 84 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 0 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 16 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 20 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 57 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 84 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 84 87 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 84 87 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 84 88 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 16 84 88 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-torsion 16 84 88 61 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 20 84 88 61 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 84 88 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 49 84 88 61 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 48 86 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 48 86 86 56 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 48 86 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 48 86 88 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 48 86 88 61 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 56 86 88 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 87 87 20 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 87 87 57 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 0 87 87 87 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3
-torsion 49 87 87 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 4 89 90 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 89 90 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 4 89 90 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 4 89 90 91 0.000 0.0 1 20.000 180.0 2 0.000 0.0 3
-torsion 91 89 90 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 91 89 90 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3
-torsion 91 89 90 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 91 89 90 91 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3
-torsion 0 89 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 89 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 4 89 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 90 89 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 90 89 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 90 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 90 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 90 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 91 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 91 91 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 91 91 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 91 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 91 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 46 91 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 91 91 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 0 109 109 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 13 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 46 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 48 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 50 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 50 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3
-torsion 109 109 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3
-
-
- ################################################################
- ## ##
- ## Additional Torsional Parameter Values Used with OPLS-AA ##
- ## ##
- ## The torsions listed below were added to official OPLS-AA ##
- ## to complete the set needed for proteins; the values were ##
- ## obtained by analogy from the closest OPLS-AA torsions; ##
- ## most of the added values are for HIP or N-terminal AAs; ##
- ## ##
- ################################################################
-
-
-torsion 24 3 13 53 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3
-torsion 52 3 13 24 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3
-torsion 3 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 13 13 83 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 84 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 3 13 13 85 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3
-torsion 5 13 13 53 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3
-torsion 15 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3
-torsion 16 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3
-torsion 13 13 13 55 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3
-torsion 24 13 13 83 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 53 13 13 83 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 13 13 84 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 53 13 13 84 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 24 13 13 85 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3
-torsion 46 13 13 85 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3
-torsion 53 13 13 85 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 3 13 53 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3
-torsion 3 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3
-torsion 13 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3
-torsion 46 13 55 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 13 85 57 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3
-torsion 46 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 55 48 55 54 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3
-torsion 0 48 81 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3
-torsion 0 57 85 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3
-torsion 0 85 85 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3
-
-
- ################################################################
- ## ##
- ## Additional Torsional Parameter Values Used with OPLS-AA ##
- ## ##
- ## The torsions listed below were added to official OPLS-AA ##
- ## to complete the values needed for selected organics ##
- ## ##
- ################################################################
-
-
-torsion 13 13 13 20 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 1 -0.2200
-charge 2 0.2200
-charge 3 0.5500
-charge 4 -0.5000
-charge 5 -0.5800
-charge 6 0.0800
-charge 7 0.4500
-charge 8 0.0000
-charge 9 0.0000
-charge 10 0.0000
-charge 11 0.0000
-charge 12 0.0000
-charge 13 0.0000
-charge 14 0.0000
-charge 15 0.0000
-charge 16 0.0000
-charge 17 0.0000
-charge 18 0.0000
-charge 19 0.0000
-charge 20 -0.7000
-charge 21 0.4350
-charge 22 0.2650
-charge 23 0.2650
-charge 24 -0.4700
-charge 25 -0.4500
-charge 26 -0.4700
-charge 27 -0.3000
-charge 28 0.2350
-charge 29 0.2700
-charge 30 0.1800
-charge 31 0.1800
-charge 32 0.2350
-charge 33 0.2350
-charge 34 0.3000
-charge 35 0.3000
-charge 36 -0.4300
-charge 37 0.2800
-charge 38 0.1500
-charge 39 0.2650
-charge 40 0.2650
-charge 41 -0.5000
-charge 42 0.2500
-charge 43 0.2500
-charge 44 0.5000
-charge 45 -0.2500
-charge 46 0.4200
-charge 47 -0.1400
-charge 48 0.2480
-charge 49 -0.0620
-charge 50 0.1390
-charge 51 -0.4590
-charge 52 0.1600
-charge 53 -0.5000
-charge 54 -0.5700
-charge 55 0.5000
-charge 56 0.2850
-charge 57 0.0000
-charge 58 0.0000
-charge 59 0.0000
-charge 60 0.0000
-charge 61 0.0000
-charge 62 0.0000
-charge 63 -0.8340
-charge 64 0.4170
-charge 65 0.0000
-charge 66 0.5200
-charge 67 -1.0400
-charge 68 -0.8220
-charge 69 0.4110
-charge 70 0.0000
-charge 71 0.5110
-charge 72 -1.0220
-charge 73 0.0000
-charge 74 0.2410
-charge 75 -0.2410
-charge 76 -0.8200
-charge 77 0.4100
-charge 78 -1.0200
-charge 79 0.3400
-charge 80 -0.1800
-charge 81 -0.1200
-charge 82 -0.0600
-charge 83 -0.2400
-charge 84 0.0000
-charge 85 0.0600
-charge 86 0.0000
-charge 87 -0.1150
-charge 88 -0.2300
-charge 89 0.1150
-charge 90 -0.1150
-charge 91 0.1150
-charge 92 0.0000
-charge 93 -0.0650
-charge 94 -0.0050
-charge 95 -0.1150
-charge 96 -0.6830
-charge 97 0.4180
-charge 98 0.0400
-charge 99 0.1450
-charge 100 0.2050
-charge 101 0.2650
-charge 102 0.1263
-charge 103 0.5323
-charge 104 -0.6351
-charge 105 0.4286
-charge 106 -0.2057
-charge 107 0.0825
-charge 108 0.1500
-charge 109 -0.5850
-charge 110 0.4350
-charge 111 -0.7000
-charge 112 0.4350
-charge 113 -0.7300
-charge 114 0.4650
-charge 115 0.1450
-charge 116 0.2050
-charge 117 0.2650
-charge 118 0.0600
-charge 119 -0.1700
-charge 120 0.0000
-charge 121 -0.2850
-charge 122 -0.4000
-charge 123 0.1100
-charge 124 0.1400
-charge 125 0.1700
-charge 126 0.2000
-charge 127 0.0300
-charge 128 -0.4000
-charge 129 -0.7000
-charge 130 0.4350
-charge 131 0.2000
-charge 132 0.1000
-charge 133 0.2650
-charge 134 0.1000
-charge 135 0.3000
-charge 136 0.1000
-charge 137 0.3650
-charge 138 0.1000
-charge 139 0.4000
-charge 140 0.4650
-charge 141 0.0850
-charge 142 -0.3350
-charge 143 -0.4700
-charge 144 -0.4350
-charge 145 -0.2175
-charge 146 0.1550
-charge 147 0.2350
-charge 148 0.0600
-charge 149 0.1200
-charge 150 0.1800
-charge 151 0.0375
-charge 152 0.0975
-charge 153 0.1575
-charge 154 0.2175
-charge 155 0.0375
-charge 156 0.0975
-charge 157 0.1575
-charge 158 0.2175
-charge 159 0.0000
-charge 160 0.2000
-charge 161 0.2600
-charge 162 0.3200
-charge 163 -0.0550
-charge 164 -0.3200
-charge 165 0.0800
-charge 166 0.1400
-charge 167 0.2000
-charge 168 -0.1200
-charge 169 0.0050
-charge 170 0.1025
-charge 171 0.1400
-charge 172 0.2000
-charge 173 0.7000
-charge 174 0.5650
-charge 175 0.5850
-charge 176 0.6150
-charge 177 0.5000
-charge 178 -0.5000
-charge 179 -0.7600
-charge 180 -0.5000
-charge 181 -0.1400
-charge 182 0.3800
-charge 183 0.3000
-charge 184 0.0200
-charge 185 -0.1100
-charge 186 0.0800
-charge 187 -0.0500
-charge 188 0.0100
-charge 189 0.1420
-charge 190 -0.3900
-charge 191 -0.5420
-charge 192 0.3330
-charge 193 -0.4900
-charge 194 0.4200
-charge 195 -0.4200
-charge 196 0.3700
-charge 197 0.0600
-charge 198 -0.1200
-charge 199 -0.0600
-charge 200 0.0000
-charge 201 0.0600
-charge 202 0.0350
-charge 203 0.3950
-charge 204 -0.4300
-charge 205 0.1800
-charge 206 -0.1800
-charge 207 -0.3850
-charge 208 0.0850
-charge 209 0.5200
-charge 210 -0.4400
-charge 211 -0.5300
-charge 212 0.4500
-charge 213 0.7000
-charge 214 -0.8000
-charge 215 -0.2800
-charge 216 -0.2200
-charge 217 -0.1600
-charge 218 -0.1000
-charge 219 0.4500
-charge 220 -0.4500
-charge 221 0.0000
-charge 222 0.4700
-charge 223 -0.4700
-charge 224 0.0600
-charge 225 0.0400
-charge 226 -0.0200
-charge 227 0.1000
-charge 228 -0.0900
-charge 229 -0.4000
-charge 230 -0.3000
-charge 231 0.0000
-charge 232 0.3500
-charge 233 0.3300
-charge 234 0.1300
-charge 235 0.1900
-charge 236 0.2500
-charge 237 0.3100
-charge 238 0.2300
-charge 239 0.1700
-charge 240 0.1100
-charge 241 0.0900
-charge 242 0.1500
-charge 243 -0.8000
-charge 244 0.4600
-charge 245 0.6400
-charge 246 -0.7000
-charge 247 0.4400
-charge 248 0.2000
-charge 249 -0.1100
-charge 250 0.1900
-charge 251 -0.0500
-charge 252 -0.2000
-charge 253 0.3100
-charge 254 -0.4600
-charge 255 0.3600
-charge 256 -0.8500
-charge 257 0.3700
-charge 258 -0.1500
-charge 259 0.1000
-charge 260 -0.0400
-charge 261 0.1000
-charge 262 -0.6000
-charge 263 0.5000
-charge 264 -0.5100
-charge 265 0.4500
-charge 266 -0.0700
-charge 267 0.0800
-charge 268 0.4100
-charge 269 -0.4000
-charge 270 0.3600
-charge 271 -0.4200
-charge 272 0.1000
-charge 273 0.1000
-charge 274 -0.1400
-charge 275 0.0800
-charge 276 -0.5600
-charge 277 0.5500
-charge 278 -0.5400
-charge 279 0.4600
-charge 280 -0.0600
-charge 281 0.1000
-charge 282 0.3800
-charge 283 -0.4800
-charge 284 -0.7900
-charge 285 0.3850
-charge 286 0.3550
-charge 287 0.1000
-charge 288 0.1000
-charge 289 -0.5300
-charge 290 0.2200
-charge 291 -0.5500
-charge 292 0.3800
-charge 293 0.1500
-charge 294 0.4400
-charge 295 -0.4900
-charge 296 0.2000
-charge 297 -0.5000
-charge 298 0.2000
-charge 299 -0.8100
-charge 300 0.3850
-charge 301 0.3550
-charge 302 0.2000
-charge 303 0.3500
-charge 304 -0.5600
-charge 305 0.4600
-charge 306 -0.5100
-charge 307 0.3400
-charge 308 0.1200
-charge 309 0.5200
-charge 310 0.3800
-charge 311 -0.8000
-charge 312 0.4000
-charge 313 -0.5100
-charge 314 -0.0100
-charge 315 0.1200
-charge 316 -0.0100
-charge 317 0.1400
-charge 318 -0.0100
-charge 319 0.1300
-charge 320 -0.6400
-charge 321 0.6500
-charge 322 -0.7400
-charge 323 0.6600
-charge 324 -0.0600
-charge 325 0.1000
-charge 326 0.4900
-charge 327 -0.3000
-charge 328 0.4800
-charge 329 -0.8100
-charge 330 0.4600
-charge 331 0.4300
-charge 332 0.1400
-charge 333 0.1400
-charge 334 0.0100
-charge 335 0.1600
-charge 336 0.7800
-charge 337 -0.6600
-charge 338 -0.4300
-charge 339 0.2000
-charge 340 0.1800
-charge 341 -0.0600
-charge 342 0.1200
-charge 343 -1.0000
-charge 344 -1.0000
-charge 345 -1.0000
-charge 346 -1.0000
-charge 347 1.0000
-charge 348 1.0000
-charge 349 1.0000
-charge 350 1.0000
-charge 351 1.0000
-charge 352 1.0000
-charge 353 2.0000
-charge 354 2.0000
-charge 355 2.0000
-charge 356 2.0000
-charge 357 -0.4000
-charge 358 0.1000
-charge 359 -0.9000
-charge 360 -0.2000
-charge 361 0.0600
-charge 362 -0.9800
-charge 363 -1.0700
-charge 364 0.1900
-charge 365 0.5100
-charge 366 -0.8200
-charge 367 -0.3000
-charge 368 0.0700
-charge 369 -1.3100
-charge 370 0.4000
-charge 371 -0.4000
-charge 372 0.0800
-charge 373 0.0000
-charge 374 0.0700
-charge 375 -0.9800
-charge 376 -1.3000
-charge 377 0.3000
-charge 378 2.5000
-charge 379 -0.2500
-charge 380 -0.8650
-charge 381 1.6200
-charge 382 -0.9200
-charge 383 -0.6000
-charge 384 0.3000
-charge 385 -0.0300
-charge 386 1.9200
-charge 387 -1.1200
-charge 388 -0.7000
-charge 389 0.4400
-charge 390 -0.1000
-charge 391 1.6200
-charge 392 -0.9700
-charge 393 -0.6300
-charge 394 0.2800
-charge 395 -0.0200
-charge 396 -0.5100
-charge 397 0.0800
-charge 398 -0.1400
-charge 399 0.3200
-charge 400 0.0200
-charge 401 -0.0400
-charge 402 -0.4700
-charge 403 0.1200
-charge 404 0.1400
-charge 405 0.2400
-charge 406 0.5100
-charge 407 -0.4300
-charge 408 -0.3300
-charge 409 0.1600
-charge 410 0.0300
-charge 411 0.6350
-charge 412 0.6250
-charge 413 0.1350
-charge 414 -0.2150
-charge 415 1.4800
-charge 416 -0.6800
-charge 417 -0.5400
-charge 418 0.1800
-charge 419 -1.0000
-charge 420 0.4400
-charge 421 -0.8000
-charge 422 0.4100
-charge 423 0.1800
-charge 424 0.0300
-charge 425 0.3900
-charge 426 -0.0600
-charge 427 -0.1800
-charge 428 0.0600
-charge 429 0.0000
-charge 430 0.0300
-charge 431 0.1900
-charge 432 0.2200
-charge 433 0.2500
-charge 434 1.3740
-charge 435 -0.6870
-charge 436 0.2450
-charge 437 0.1300
-charge 438 -0.4200
-charge 439 -0.0350
-charge 440 0.0250
-charge 441 0.0750
-charge 442 -0.0550
-charge 443 0.1300
-charge 444 -0.5700
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-
-
- ########################################
- ## ##
- ## Biopolymer Atom Type Conversions ##
- ## ##
- ########################################
-
-
-biotype 1 N "Glycine" 180
-biotype 2 CA "Glycine" 165
-biotype 3 C "Glycine" 177
-biotype 4 HN "Glycine" 183
-biotype 5 O "Glycine" 178
-biotype 6 HA "Glycine" 85
-biotype 7 N "Alanine" 180
-biotype 8 CA "Alanine" 166
-biotype 9 C "Alanine" 177
-biotype 10 HN "Alanine" 183
-biotype 11 O "Alanine" 178
-biotype 12 HA "Alanine" 85
-biotype 13 CB "Alanine" 80
-biotype 14 HB "Alanine" 85
-biotype 15 N "Valine" 180
-biotype 16 CA "Valine" 166
-biotype 17 C "Valine" 177
-biotype 18 HN "Valine" 183
-biotype 19 O "Valine" 178
-biotype 20 HA "Valine" 85
-biotype 21 CB "Valine" 82
-biotype 22 HB "Valine" 85
-biotype 23 CG1 "Valine" 80
-biotype 24 HG1 "Valine" 85
-biotype 25 CG2 "Valine" 80
-biotype 26 HG2 "Valine" 85
-biotype 27 N "Leucine" 180
-biotype 28 CA "Leucine" 166
-biotype 29 C "Leucine" 177
-biotype 30 HN "Leucine" 183
-biotype 31 O "Leucine" 178
-biotype 32 HA "Leucine" 85
-biotype 33 CB "Leucine" 81
-biotype 34 HB "Leucine" 85
-biotype 35 CG "Leucine" 82
-biotype 36 HG "Leucine" 85
-biotype 37 CD1 "Leucine" 80
-biotype 38 HD1 "Leucine" 85
-biotype 39 CD2 "Leucine" 80
-biotype 40 HD2 "Leucine" 85
-biotype 41 N "Isoleucine" 180
-biotype 42 CA "Isoleucine" 166
-biotype 43 C "Isoleucine" 177
-biotype 44 HN "Isoleucine" 183
-biotype 45 O "Isoleucine" 178
-biotype 46 HA "Isoleucine" 85
-biotype 47 CB "Isoleucine" 82
-biotype 48 HB "Isoleucine" 85
-biotype 49 CG1 "Isoleucine" 80
-biotype 50 HG1 "Isoleucine" 85
-biotype 51 CG2 "Isoleucine" 81
-biotype 52 HG2 "Isoleucine" 85
-biotype 53 CD "Isoleucine" 80
-biotype 54 HD "Isoleucine" 85
-biotype 55 N "Serine" 180
-biotype 56 CA "Serine" 166
-biotype 57 C "Serine" 177
-biotype 58 HN "Serine" 183
-biotype 59 O "Serine" 178
-biotype 60 HA "Serine" 85
-biotype 61 CB "Serine" 99
-biotype 62 HB "Serine" 85
-biotype 63 OG "Serine" 96
-biotype 64 HG "Serine" 97
-biotype 65 N "Threonine" 180
-biotype 66 CA "Threonine" 166
-biotype 67 C "Threonine" 177
-biotype 68 HN "Threonine" 183
-biotype 69 O "Threonine" 178
-biotype 70 HA "Threonine" 85
-biotype 71 CB "Threonine" 100
-biotype 72 HB "Threonine" 85
-biotype 73 OG1 "Threonine" 96
-biotype 74 HG1 "Threonine" 97
-biotype 75 CG2 "Threonine" 80
-biotype 76 HG2 "Threonine" 85
-biotype 77 N "Cysteine (SH)" 180
-biotype 78 CA "Cysteine (SH)" 166
-biotype 79 C "Cysteine (SH)" 177
-biotype 80 HN "Cysteine (SH)" 183
-biotype 81 O "Cysteine (SH)" 178
-biotype 82 HA "Cysteine (SH)" 85
-biotype 83 CB "Cysteine (SH)" 148
-biotype 84 HB "Cysteine (SH)" 85
-biotype 85 SG "Cysteine (SH)" 142
-biotype 86 HG "Cysteine (SH)" 146
-biotype 87 N "Cystine (SS)" 180
-biotype 88 CA "Cystine (SS)" 166
-biotype 89 C "Cystine (SS)" 177
-biotype 90 HN "Cystine (SS)" 183
-biotype 91 O "Cystine (SS)" 178
-biotype 92 HA "Cystine (SS)" 85
-biotype 93 CB "Cystine (SS)" 156
-biotype 94 HB "Cystine (SS)" 85
-biotype 95 SG "Cystine (SS)" 145
-biotype 96 N "Cysteine (S-)" -1
-biotype 97 CA "Cysteine (S-)" -1
-biotype 98 C "Cysteine (S-)" -1
-biotype 99 HN "Cysteine (S-)" -1
-biotype 100 O "Cysteine (S-)" -1
-biotype 101 HA "Cysteine (S-)" -1
-biotype 102 CB "Cysteine (S-)" -1
-biotype 103 HB "Cysteine (S-)" -1
-biotype 104 SG "Cysteine (S-)" -1
-biotype 105 N "Proline" 181
-biotype 106 CA "Proline" 188
-biotype 107 C "Proline" 177
-biotype 108 O "Proline" 178
-biotype 109 HA "Proline" 85
-biotype 110 CB "Proline" 81
-biotype 111 HB "Proline" 85
-biotype 112 CG "Proline" 81
-biotype 113 HG "Proline" 85
-biotype 114 CD "Proline" 187
-biotype 115 HD "Proline" 85
-biotype 116 N "Phenylalanine" 180
-biotype 117 CA "Phenylalanine" 166
-biotype 118 C "Phenylalanine" 177
-biotype 119 HN "Phenylalanine" 183
-biotype 120 O "Phenylalanine" 178
-biotype 121 HA "Phenylalanine" 85
-biotype 122 CB "Phenylalanine" 94
-biotype 123 HB "Phenylalanine" 85
-biotype 124 CG "Phenylalanine" 90
-biotype 125 CD "Phenylalanine" 90
-biotype 126 HD "Phenylalanine" 91
-biotype 127 CE "Phenylalanine" 90
-biotype 128 HE "Phenylalanine" 91
-biotype 129 CZ "Phenylalanine" 90
-biotype 130 HZ "Phenylalanine" 91
-biotype 131 N "Tyrosine" 180
-biotype 132 CA "Tyrosine" 166
-biotype 133 C "Tyrosine" 177
-biotype 134 HN "Tyrosine" 183
-biotype 135 O "Tyrosine" 178
-biotype 136 HA "Tyrosine" 85
-biotype 137 CB "Tyrosine" 94
-biotype 138 HB "Tyrosine" 85
-biotype 139 CG "Tyrosine" 90
-biotype 140 CD "Tyrosine" 90
-biotype 141 HD "Tyrosine" 91
-biotype 142 CE "Tyrosine" 90
-biotype 143 HE "Tyrosine" 91
-biotype 144 CZ "Tyrosine" 108
-biotype 145 OH "Tyrosine" 109
-biotype 146 HH "Tyrosine" 110
-biotype 147 N "Tyrosine (O-)" -1
-biotype 148 CA "Tyrosine (O-)" -1
-biotype 149 C "Tyrosine (O-)" -1
-biotype 150 HN "Tyrosine (O-)" -1
-biotype 151 O "Tyrosine (O-)" -1
-biotype 152 HA "Tyrosine (O-)" -1
-biotype 153 CB "Tyrosine (O-)" -1
-biotype 154 HB "Tyrosine (O-)" -1
-biotype 155 CG "Tyrosine (O-)" -1
-biotype 156 CD "Tyrosine (O-)" -1
-biotype 157 HD "Tyrosine (O-)" -1
-biotype 158 CE "Tyrosine (O-)" -1
-biotype 159 HE "Tyrosine (O-)" -1
-biotype 160 CZ "Tyrosine (O-)" -1
-biotype 161 OH "Tyrosine (O-)" -1
-biotype 162 N "Tryptophan" 180
-biotype 163 CA "Tryptophan" 166
-biotype 164 C "Tryptophan" 177
-biotype 165 HN "Tryptophan" 183
-biotype 166 O "Tryptophan" 178
-biotype 167 HA "Tryptophan" 85
-biotype 168 CB "Tryptophan" 81
-biotype 169 HB "Tryptophan" 85
-biotype 170 CG "Tryptophan" 441
-biotype 171 CD1 "Tryptophan" 455
-biotype 172 HD1 "Tryptophan" 91
-biotype 173 CD2 "Tryptophan" 442
-biotype 174 NE1 "Tryptophan" 444
-biotype 175 HE1 "Tryptophan" 445
-biotype 176 CE2 "Tryptophan" 443
-biotype 177 CE3 "Tryptophan" 90
-biotype 178 HE3 "Tryptophan" 91
-biotype 179 CZ2 "Tryptophan" 90
-biotype 180 HZ2 "Tryptophan" 91
-biotype 181 CZ3 "Tryptophan" 90
-biotype 182 HZ3 "Tryptophan" 91
-biotype 183 CH2 "Tryptophan" 90
-biotype 184 HH2 "Tryptophan" 91
-biotype 185 N "Histidine (+)" 180
-biotype 186 CA "Histidine (+)" 166
-biotype 187 C "Histidine (+)" 177
-biotype 188 HN "Histidine (+)" 183
-biotype 189 O "Histidine (+)" 178
-biotype 190 HA "Histidine (+)" 85
-biotype 191 CB "Histidine (+)" 446
-biotype 192 HB "Histidine (+)" 85
-biotype 193 CG "Histidine (+)" 451
-biotype 194 ND1 "Histidine (+)" 453
-biotype 195 HD1 "Histidine (+)" 454
-biotype 196 CD2 "Histidine (+)" 451
-biotype 197 HD2 "Histidine (+)" 91
-biotype 198 CE1 "Histidine (+)" 450
-biotype 199 HE1 "Histidine (+)" 91
-biotype 200 NE2 "Histidine (+)" 453
-biotype 201 HE2 "Histidine (+)" 454
-biotype 202 N "Histidine (HD)" 180
-biotype 203 CA "Histidine (HD)" 166
-biotype 204 C "Histidine (HD)" 177
-biotype 205 HN "Histidine (HD)" 183
-biotype 206 O "Histidine (HD)" 178
-biotype 207 HA "Histidine (HD)" 85
-biotype 208 CB "Histidine (HD)" 446
-biotype 209 HB "Histidine (HD)" 85
-biotype 210 CG "Histidine (HD)" 449
-biotype 211 ND1 "Histidine (HD)" 444
-biotype 212 HD1 "Histidine (HD)" 445
-biotype 213 CD2 "Histidine (HD)" 448
-biotype 214 HD2 "Histidine (HD)" 91
-biotype 215 CE1 "Histidine (HD)" 447
-biotype 216 HE1 "Histidine (HD)" 91
-biotype 217 NE2 "Histidine (HD)" 452
-biotype 218 N "Histidine (HE)" 180
-biotype 219 CA "Histidine (HE)" 166
-biotype 220 C "Histidine (HE)" 177
-biotype 221 HN "Histidine (HE)" 183
-biotype 222 O "Histidine (HE)" 178
-biotype 223 HA "Histidine (HE)" 85
-biotype 224 CB "Histidine (HE)" 446
-biotype 225 HB "Histidine (HE)" 85
-biotype 226 CG "Histidine (HE)" 448
-biotype 227 ND1 "Histidine (HE)" 452
-biotype 228 CD2 "Histidine (HE)" 449
-biotype 229 HD2 "Histidine (HE)" 91
-biotype 230 CE1 "Histidine (HE)" 447
-biotype 231 HE1 "Histidine (HE)" 91
-biotype 232 NE2 "Histidine (HE)" 444
-biotype 233 HE2 "Histidine (HE)" 445
-biotype 234 N "Aspartic Acid" 180
-biotype 235 CA "Aspartic Acid" 166
-biotype 236 C "Aspartic Acid" 177
-biotype 237 HN "Aspartic Acid" 183
-biotype 238 O "Aspartic Acid" 178
-biotype 239 HA "Aspartic Acid" 85
-biotype 240 CB "Aspartic Acid" 216
-biotype 241 HB "Aspartic Acid" 85
-biotype 242 CG "Aspartic Acid" 213
-biotype 243 OD "Aspartic Acid" 214
-biotype 244 N "Aspartic Acid (COOH)" -1
-biotype 245 CA "Aspartic Acid (COOH)" -1
-biotype 246 C "Aspartic Acid (COOH)" -1
-biotype 247 HN "Aspartic Acid (COOH)" -1
-biotype 248 O "Aspartic Acid (COOH)" -1
-biotype 249 HA "Aspartic Acid (COOH)" -1
-biotype 250 CB "Aspartic Acid (COOH)" -1
-biotype 251 HB "Aspartic Acid (COOH)" -1
-biotype 252 CG "Aspartic Acid (COOH)" -1
-biotype 253 OD1 "Aspartic Acid (COOH)" -1
-biotype 254 OD2 "Aspartic Acid (COOH)" -1
-biotype 255 HD2 "Aspartic Acid (COOH)" -1
-biotype 256 N "Asparagine" 180
-biotype 257 CA "Asparagine" 166
-biotype 258 C "Asparagine" 177
-biotype 259 HN "Asparagine" 183
-biotype 260 O "Asparagine" 178
-biotype 261 HA "Asparagine" 85
-biotype 262 CB "Asparagine" 81
-biotype 263 HB "Asparagine" 85
-biotype 264 CG "Asparagine" 177
-biotype 265 OD1 "Asparagine" 178
-biotype 266 ND2 "Asparagine" 179
-biotype 267 HD2 "Asparagine" 182
-biotype 268 N "Glutamic Acid" 180
-biotype 269 CA "Glutamic Acid" 166
-biotype 270 C "Glutamic Acid" 177
-biotype 271 HN "Glutamic Acid" 183
-biotype 272 O "Glutamic Acid" 178
-biotype 273 HA "Glutamic Acid" 85
-biotype 274 CB "Glutamic Acid" 81
-biotype 275 HB "Glutamic Acid" 85
-biotype 276 CG "Glutamic Acid" 216
-biotype 277 HG "Glutamic Acid" 85
-biotype 278 CD "Glutamic Acid" 213
-biotype 279 OE "Glutamic Acid" 214
-biotype 280 N "Glutamic Acid (COOH)" -1
-biotype 281 CA "Glutamic Acid (COOH)" -1
-biotype 282 C "Glutamic Acid (COOH)" -1
-biotype 283 HN "Glutamic Acid (COOH)" -1
-biotype 284 O "Glutamic Acid (COOH)" -1
-biotype 285 HA "Glutamic Acid (COOH)" -1
-biotype 286 CB "Glutamic Acid (COOH)" -1
-biotype 287 HB "Glutamic Acid (COOH)" -1
-biotype 288 CG "Glutamic Acid (COOH)" -1
-biotype 289 HG "Glutamic Acid (COOH)" -1
-biotype 290 CD "Glutamic Acid (COOH)" -1
-biotype 291 OE1 "Glutamic Acid (COOH)" -1
-biotype 292 OE2 "Glutamic Acid (COOH)" -1
-biotype 293 HE2 "Glutamic Acid (COOH)" -1
-biotype 294 N "Glutamine" 180
-biotype 295 CA "Glutamine" 166
-biotype 296 C "Glutamine" 177
-biotype 297 HN "Glutamine" 183
-biotype 298 O "Glutamine" 178
-biotype 299 HA "Glutamine" 85
-biotype 300 CB "Glutamine" 81
-biotype 301 HB "Glutamine" 85
-biotype 302 CG "Glutamine" 81
-biotype 303 HG "Glutamine" 85
-biotype 304 CD "Glutamine" 177
-biotype 305 OE1 "Glutamine" 178
-biotype 306 NE2 "Glutamine" 179
-biotype 307 HE2 "Glutamine" 182
-biotype 308 N "Methionine" 180
-biotype 309 CA "Methionine" 166
-biotype 310 C "Methionine" 177
-biotype 311 HN "Methionine" 183
-biotype 312 O "Methionine" 178
-biotype 313 HA "Methionine" 85
-biotype 314 CB "Methionine" 81
-biotype 315 HB "Methionine" 85
-biotype 316 CG "Methionine" 152
-biotype 317 HG "Methionine" 85
-biotype 318 SD "Methionine" 144
-biotype 319 CE "Methionine" 151
-biotype 320 HE "Methionine" 85
-biotype 321 N "Lysine" 180
-biotype 322 CA "Lysine" 166
-biotype 323 C "Lysine" 177
-biotype 324 HN "Lysine" 183
-biotype 325 O "Lysine" 178
-biotype 326 HA "Lysine" 85
-biotype 327 CB "Lysine" 81
-biotype 328 HB "Lysine" 85
-biotype 329 CG "Lysine" 81
-biotype 330 HG "Lysine" 85
-biotype 331 CD "Lysine" 81
-biotype 332 HD "Lysine" 85
-biotype 333 CE "Lysine" 235
-biotype 334 HE "Lysine" 85
-biotype 335 NZ "Lysine" 230
-biotype 336 HZ "Lysine" 233
-biotype 337 N "Lysine (NH2)" -1
-biotype 338 CA "Lysine (NH2)" -1
-biotype 339 C "Lysine (NH2)" -1
-biotype 340 HN "Lysine (NH2)" -1
-biotype 341 O "Lysine (NH2)" -1
-biotype 342 HA "Lysine (NH2)" -1
-biotype 343 CB "Lysine (NH2)" -1
-biotype 344 HB "Lysine (NH2)" -1
-biotype 345 CG "Lysine (NH2)" -1
-biotype 346 HG "Lysine (NH2)" -1
-biotype 347 CD "Lysine (NH2)" -1
-biotype 348 HD "Lysine (NH2)" -1
-biotype 349 CE "Lysine (NH2)" -1
-biotype 350 HE "Lysine (NH2)" -1
-biotype 351 NZ "Lysine (NH2)" -1
-biotype 352 HZ "Lysine (NH2)" -1
-biotype 353 N "Arginine" 180
-biotype 354 CA "Arginine" 166
-biotype 355 C "Arginine" 177
-biotype 356 HN "Arginine" 183
-biotype 357 O "Arginine" 178
-biotype 358 HA "Arginine" 85
-biotype 359 CB "Arginine" 81
-biotype 360 HB "Arginine" 85
-biotype 361 CG "Arginine" 251
-biotype 362 HG "Arginine" 85
-biotype 363 CD "Arginine" 250
-biotype 364 HD "Arginine" 85
-biotype 365 NE "Arginine" 246
-biotype 366 HE "Arginine" 247
-biotype 367 CZ "Arginine" 245
-biotype 368 NH "Arginine" 243
-biotype 369 HH "Arginine" 244
-biotype 370 N "Ornithine" 180
-biotype 371 CA "Ornithine" 166
-biotype 372 C "Ornithine" 177
-biotype 373 HN "Ornithine" 183
-biotype 374 O "Ornithine" 178
-biotype 375 HA "Ornithine" 85
-biotype 376 CB "Ornithine" 81
-biotype 377 HB "Ornithine" 85
-biotype 378 CG "Ornithine" 81
-biotype 379 HG "Ornithine" 85
-biotype 380 CD "Ornithine" 235
-biotype 381 HD "Ornithine" 85
-biotype 382 NE "Ornithine" 230
-biotype 383 HE "Ornithine" 233
-biotype 384 N "MethylAlanine (AIB)" 180
-biotype 385 CA "MethylAlanine (AIB)" 167
-biotype 386 C "MethylAlanine (AIB)" 177
-biotype 387 HN "MethylAlanine (AIB)" 183
-biotype 388 O "MethylAlanine (AIB)" 178
-biotype 389 CB "MethylAlanine (AIB)" 80
-biotype 390 HB "MethylAlanine (AIB)" 85
-biotype 391 N "Pyroglutamic Acid" 180
-biotype 392 CA "Pyroglutamic Acid" 166
-biotype 393 C "Pyroglutamic Acid" 177
-biotype 394 HN "Pyroglutamic Acid" 183
-biotype 395 O "Pyroglutamic Acid" 178
-biotype 396 HA "Pyroglutamic Acid" 85
-biotype 397 CB "Pyroglutamic Acid" 81
-biotype 398 HB "Pyroglutamic Acid" 85
-biotype 399 CG "Pyroglutamic Acid" 216
-biotype 400 HG "Pyroglutamic Acid" 85
-biotype 401 CD "Pyroglutamic Acid" 177
-biotype 402 OE "Pyroglutamic Acid" 178
-biotype 403 N "N-Terminal GLY" 230
-biotype 404 CA "N-Terminal GLY" 235
-biotype 405 C "N-Terminal GLY" 177
-biotype 406 HN "N-Terminal GLY" 233
-biotype 407 O "N-Terminal GLY" 178
-biotype 408 HA "N-Terminal GLY" 85
-biotype 409 N "N-Terminal ALA" 230
-biotype 410 CA "N-Terminal ALA" 236
-biotype 411 C "N-Terminal ALA" 177
-biotype 412 HN "N-Terminal ALA" 233
-biotype 413 O "N-Terminal ALA" 178
-biotype 414 HA "N-Terminal ALA" 85
-biotype 415 N "N-Terminal VAL" 230
-biotype 416 CA "N-Terminal VAL" 236
-biotype 417 C "N-Terminal VAL" 177
-biotype 418 HN "N-Terminal VAL" 233
-biotype 419 O "N-Terminal VAL" 178
-biotype 420 HA "N-Terminal VAL" 85
-biotype 421 N "N-Terminal LEU" 230
-biotype 422 CA "N-Terminal LEU" 236
-biotype 423 C "N-Terminal LEU" 177
-biotype 424 HN "N-Terminal LEU" 233
-biotype 425 O "N-Terminal LEU" 178
-biotype 426 HA "N-Terminal LEU" 85
-biotype 427 N "N-Terminal ILE" 230
-biotype 428 CA "N-Terminal ILE" 236
-biotype 429 C "N-Terminal ILE" 177
-biotype 430 HN "N-Terminal ILE" 233
-biotype 431 O "N-Terminal ILE" 178
-biotype 432 HA "N-Terminal ILE" 85
-biotype 433 N "N-Terminal SER" 230
-biotype 434 CA "N-Terminal SER" 236
-biotype 435 C "N-Terminal SER" 177
-biotype 436 HN "N-Terminal SER" 233
-biotype 437 O "N-Terminal SER" 178
-biotype 438 HA "N-Terminal SER" 85
-biotype 439 N "N-Terminal THR" 230
-biotype 440 CA "N-Terminal THR" 236
-biotype 441 C "N-Terminal THR" 177
-biotype 442 HN "N-Terminal THR" 233
-biotype 443 O "N-Terminal THR" 178
-biotype 444 HA "N-Terminal THR" 85
-biotype 445 N "N-Terminal CYS (SH)" 230
-biotype 446 CA "N-Terminal CYS (SH)" 236
-biotype 447 C "N-Terminal CYS (SH)" 177
-biotype 448 HN "N-Terminal CYS (SH)" 233
-biotype 449 O "N-Terminal CYS (SH)" 178
-biotype 450 HA "N-Terminal CYS (SH)" 85
-biotype 451 N "N-Terminal CYX (SS)" 230
-biotype 452 CA "N-Terminal CYX (SS)" 236
-biotype 453 C "N-Terminal CYX (SS)" 177
-biotype 454 HN "N-Terminal CYX (SS)" 233
-biotype 455 O "N-Terminal CYX (SS)" 178
-biotype 456 HA "N-Terminal CYX (SS)" 85
-biotype 457 N "N-Terminal CYD (S-)" -1
-biotype 458 CA "N-Terminal CYD (S-)" -1
-biotype 459 C "N-Terminal CYD (S-)" -1
-biotype 460 HN "N-Terminal CYD (S-)" -1
-biotype 461 O "N-Terminal CYD (S-)" -1
-biotype 462 HA "N-Terminal CYD (S-)" -1
-biotype 463 N "N-Terminal PRO" 252
-biotype 464 CA "N-Terminal PRO" 238
-biotype 465 C "N-Terminal PRO" 177
-biotype 466 HN "N-Terminal PRO" 253
-biotype 467 O "N-Terminal PRO" 178
-biotype 468 HA "N-Terminal PRO" 85
-biotype 469 CD "N-Terminal PRO" 239
-biotype 470 HD "N-Terminal PRO" 85
-biotype 471 N "N-Terminal PHE" 230
-biotype 472 CA "N-Terminal PHE" 236
-biotype 473 C "N-Terminal PHE" 177
-biotype 474 HN "N-Terminal PHE" 233
-biotype 475 O "N-Terminal PHE" 178
-biotype 476 HA "N-Terminal PHE" 85
-biotype 477 N "N-Terminal TYR" 230
-biotype 478 CA "N-Terminal TYR" 236
-biotype 479 C "N-Terminal TYR" 177
-biotype 480 HN "N-Terminal TYR" 233
-biotype 481 O "N-Terminal TYR" 178
-biotype 482 HA "N-Terminal TYR" 85
-biotype 483 N "N-Terminal TYD (O-)" -1
-biotype 484 CA "N-Terminal TYD (O-)" -1
-biotype 485 C "N-Terminal TYD (O-)" -1
-biotype 486 HN "N-Terminal TYD (O-)" -1
-biotype 487 O "N-Terminal TYD (O-)" -1
-biotype 488 HA "N-Terminal TYD (O-)" -1
-biotype 489 N "N-Terminal TRP" 230
-biotype 490 CA "N-Terminal TRP" 236
-biotype 491 C "N-Terminal TRP" 177
-biotype 492 HN "N-Terminal TRP" 233
-biotype 493 O "N-Terminal TRP" 178
-biotype 494 HA "N-Terminal TRP" 85
-biotype 495 N "N-Terminal HIS (+)" 230
-biotype 496 CA "N-Terminal HIS (+)" 236
-biotype 497 C "N-Terminal HIS (+)" 177
-biotype 498 HN "N-Terminal HIS (+)" 233
-biotype 499 O "N-Terminal HIS (+)" 178
-biotype 500 HA "N-Terminal HIS (+)" 85
-biotype 501 N "N-Terminal HIS (HD)" 230
-biotype 502 CA "N-Terminal HIS (HD)" 236
-biotype 503 C "N-Terminal HIS (HD)" 177
-biotype 504 HN "N-Terminal HIS (HD)" 233
-biotype 505 O "N-Terminal HIS (HD)" 178
-biotype 506 HA "N-Terminal HIS (HD)" 85
-biotype 507 N "N-Terminal HIS (HE)" 230
-biotype 508 CA "N-Terminal HIS (HE)" 236
-biotype 509 C "N-Terminal HIS (HE)" 177
-biotype 510 HN "N-Terminal HIS (HE)" 233
-biotype 511 O "N-Terminal HIS (HE)" 178
-biotype 512 HA "N-Terminal HIS (HE)" 85
-biotype 513 N "N-Terminal ASP" 230
-biotype 514 CA "N-Terminal ASP" 236
-biotype 515 C "N-Terminal ASP" 177
-biotype 516 HN "N-Terminal ASP" 233
-biotype 517 O "N-Terminal ASP" 178
-biotype 518 HA "N-Terminal ASP" 85
-biotype 519 N "N-Terminal ASH (COOH)" -1
-biotype 520 CA "N-Terminal ASH (COOH)" -1
-biotype 521 C "N-Terminal ASH (COOH)" -1
-biotype 522 HN "N-Terminal ASH (COOH)" -1
-biotype 523 O "N-Terminal ASH (COOH)" -1
-biotype 524 HA "N-Terminal ASH (COOH)" -1
-biotype 525 N "N-Terminal ASN" 230
-biotype 526 CA "N-Terminal ASN" 236
-biotype 527 C "N-Terminal ASN" 177
-biotype 528 HN "N-Terminal ASN" 233
-biotype 529 O "N-Terminal ASN" 178
-biotype 530 HA "N-Terminal ASN" 85
-biotype 531 N "N-Terminal GLU" 230
-biotype 532 CA "N-Terminal GLU" 236
-biotype 533 C "N-Terminal GLU" 177
-biotype 534 HN "N-Terminal GLU" 233
-biotype 535 O "N-Terminal GLU" 178
-biotype 536 HA "N-Terminal GLU" 85
-biotype 537 N "N-Terminal GLH (COOH)" -1
-biotype 538 CA "N-Terminal GLH (COOH)" -1
-biotype 539 C "N-Terminal GLH (COOH)" -1
-biotype 540 HN "N-Terminal GLH (COOH)" -1
-biotype 541 O "N-Terminal GLH (COOH)" -1
-biotype 542 HA "N-Terminal GLH (COOH)" -1
-biotype 543 N "N-Terminal GLN" 230
-biotype 544 CA "N-Terminal GLN" 236
-biotype 545 C "N-Terminal GLN" 177
-biotype 546 HN "N-Terminal GLN" 233
-biotype 547 O "N-Terminal GLN" 178
-biotype 548 HA "N-Terminal GLN" 85
-biotype 549 N "N-Terminal MET" 230
-biotype 550 CA "N-Terminal MET" 236
-biotype 551 C "N-Terminal MET" 177
-biotype 552 HN "N-Terminal MET" 233
-biotype 553 O "N-Terminal MET" 178
-biotype 554 HA "N-Terminal MET" 85
-biotype 555 N "N-Terminal LYS" 230
-biotype 556 CA "N-Terminal LYS" 236
-biotype 557 C "N-Terminal LYS" 177
-biotype 558 HN "N-Terminal LYS" 233
-biotype 559 O "N-Terminal LYS" 178
-biotype 560 HA "N-Terminal LYS" 85
-biotype 561 N "N-Terminal LYD (NH2)" -1
-biotype 562 CA "N-Terminal LYD (NH2)" -1
-biotype 563 C "N-Terminal LYD (NH2)" -1
-biotype 564 HN "N-Terminal LYD (NH2)" -1
-biotype 565 O "N-Terminal LYD (NH2)" -1
-biotype 566 HA "N-Terminal LYD (NH2)" -1
-biotype 567 N "N-Terminal ARG" 230
-biotype 568 CA "N-Terminal ARG" 236
-biotype 569 C "N-Terminal ARG" 177
-biotype 570 HN "N-Terminal ARG" 233
-biotype 571 O "N-Terminal ARG" 178
-biotype 572 HA "N-Terminal ARG" 85
-biotype 573 N "N-Terminal ORN" 230
-biotype 574 CA "N-Terminal ORN" 236
-biotype 575 C "N-Terminal ORN" 177
-biotype 576 HN "N-Terminal ORN" 233
-biotype 577 O "N-Terminal ORN" 178
-biotype 578 HA "N-Terminal ORN" 85
-biotype 579 N "N-Terminal AIB" 230
-biotype 580 CA "N-Terminal AIB" 237
-biotype 581 C "N-Terminal AIB" 177
-biotype 582 HN "N-Terminal AIB" 233
-biotype 583 O "N-Terminal AIB" 178
-biotype 584 N "C-Terminal GLY" 180
-biotype 585 CA "C-Terminal GLY" 226
-biotype 586 C "C-Terminal GLY" 213
-biotype 587 HN "C-Terminal GLY" 183
-biotype 588 OXT "C-Terminal GLY" 214
-biotype 589 HA "C-Terminal GLY" 85
-biotype 590 N "C-Terminal ALA" 180
-biotype 591 CA "C-Terminal ALA" 225
-biotype 592 C "C-Terminal ALA" 213
-biotype 593 HN "C-Terminal ALA" 183
-biotype 594 OXT "C-Terminal ALA" 214
-biotype 595 HA "C-Terminal ALA" 85
-biotype 596 N "C-Terminal VAL" 180
-biotype 597 CA "C-Terminal VAL" 225
-biotype 598 C "C-Terminal VAL" 213
-biotype 599 HN "C-Terminal VAL" 183
-biotype 600 OXT "C-Terminal VAL" 214
-biotype 601 HA "C-Terminal VAL" 85
-biotype 602 N "C-Terminal LEU" 180
-biotype 603 CA "C-Terminal LEU" 225
-biotype 604 C "C-Terminal LEU" 213
-biotype 605 HN "C-Terminal LEU" 183
-biotype 606 OXT "C-Terminal LEU" 214
-biotype 607 HA "C-Terminal LEU" 85
-biotype 608 N "C-Terminal ILE" 180
-biotype 609 CA "C-Terminal ILE" 225
-biotype 610 C "C-Terminal ILE" 213
-biotype 611 HN "C-Terminal ILE" 183
-biotype 612 OXT "C-Terminal ILE" 214
-biotype 613 HA "C-Terminal ILE" 85
-biotype 614 N "C-Terminal SER" 180
-biotype 615 CA "C-Terminal SER" 225
-biotype 616 C "C-Terminal SER" 213
-biotype 617 HN "C-Terminal SER" 183
-biotype 618 OXT "C-Terminal SER" 214
-biotype 619 HA "C-Terminal SER" 85
-biotype 620 N "C-Terminal THR" 180
-biotype 621 CA "C-Terminal THR" 225
-biotype 622 C "C-Terminal THR" 213
-biotype 623 HN "C-Terminal THR" 183
-biotype 624 OXT "C-Terminal THR" 214
-biotype 625 HA "C-Terminal THR" 85
-biotype 626 N "C-Terminal CYS (SH)" 180
-biotype 627 CA "C-Terminal CYS (SH)" 225
-biotype 628 C "C-Terminal CYS (SH)" 213
-biotype 629 HN "C-Terminal CYS (SH)" 183
-biotype 630 OXT "C-Terminal CYS (SH)" 214
-biotype 631 HA "C-Terminal CYS (SH)" 85
-biotype 632 N "C-Terminal CYX (SS)" 180
-biotype 633 CA "C-Terminal CYX (SS)" 225
-biotype 634 C "C-Terminal CYX (SS)" 213
-biotype 635 HN "C-Terminal CYX (SS)" 183
-biotype 636 OXT "C-Terminal CYX (SS)" 214
-biotype 637 HA "C-Terminal CYX (SS)" 85
-biotype 638 N "C-Terminal CYD (S-)" -1
-biotype 639 CA "C-Terminal CYD (S-)" -1
-biotype 640 C "C-Terminal CYD (S-)" -1
-biotype 641 HN "C-Terminal CYD (S-)" -1
-biotype 642 OXT "C-Terminal CYD (S-)" -1
-biotype 643 HA "C-Terminal CYD (S-)" -1
-biotype 644 N "C-Terminal PRO" 181
-biotype 645 CA "C-Terminal PRO" 228
-biotype 646 C "C-Terminal PRO" 213
-biotype 647 OXT "C-Terminal PRO" 214
-biotype 648 HA "C-Terminal PRO" 85
-biotype 649 N "C-Terminal PHE" 180
-biotype 650 CA "C-Terminal PHE" 225
-biotype 651 C "C-Terminal PHE" 213
-biotype 652 HN "C-Terminal PHE" 183
-biotype 653 OXT "C-Terminal PHE" 214
-biotype 654 HA "C-Terminal PHE" 85
-biotype 655 N "C-Terminal TYR" 180
-biotype 656 CA "C-Terminal TYR" 225
-biotype 657 C "C-Terminal TYR" 213
-biotype 658 HN "C-Terminal TYR" 183
-biotype 659 OXT "C-Terminal TYR" 214
-biotype 660 HA "C-Terminal TYR" 85
-biotype 661 N "C-Terminal TYD (O-)" -1
-biotype 662 CA "C-Terminal TYD (O-)" -1
-biotype 663 C "C-Terminal TYD (O-)" -1
-biotype 664 HN "C-Terminal TYD (O-)" -1
-biotype 665 OXT "C-Terminal TYD (O-)" -1
-biotype 666 HA "C-Terminal TYD (O-)" -1
-biotype 667 N "C-Terminal TRP" 180
-biotype 668 CA "C-Terminal TRP" 225
-biotype 669 C "C-Terminal TRP" 213
-biotype 670 HN "C-Terminal TRP" 183
-biotype 671 OXT "C-Terminal TRP" 214
-biotype 672 HA "C-Terminal TRP" 85
-biotype 673 N "C-Terminal HIS (+)" 180
-biotype 674 CA "C-Terminal HIS (+)" 225
-biotype 675 C "C-Terminal HIS (+)" 213
-biotype 676 HN "C-Terminal HIS (+)" 183
-biotype 677 OXT "C-Terminal HIS (+)" 214
-biotype 678 HA "C-Terminal HIS (+)" 85
-biotype 679 N "C-Terminal HIS (HD)" 180
-biotype 680 CA "C-Terminal HIS (HD)" 225
-biotype 681 C "C-Terminal HIS (HD)" 213
-biotype 682 HN "C-Terminal HIS (HD)" 183
-biotype 683 OXT "C-Terminal HIS (HD)" 214
-biotype 684 HA "C-Terminal HIS (HD)" 85
-biotype 685 N "C-Terminal HIS (HE)" 180
-biotype 686 CA "C-Terminal HIS (HE)" 225
-biotype 687 C "C-Terminal HIS (HE)" 213
-biotype 688 HN "C-Terminal HIS (HE)" 183
-biotype 689 OXT "C-Terminal HIS (HE)" 214
-biotype 690 HA "C-Terminal HIS (HE)" 85
-biotype 691 N "C-Terminal ASP" 180
-biotype 692 CA "C-Terminal ASP" 225
-biotype 693 C "C-Terminal ASP" 213
-biotype 694 HN "C-Terminal ASP" 183
-biotype 695 OXT "C-Terminal ASP" 214
-biotype 696 HA "C-Terminal ASP" 85
-biotype 697 N "C-Terminal ASH (COOH)" -1
-biotype 698 CA "C-Terminal ASH (COOH)" -1
-biotype 699 C "C-Terminal ASH (COOH)" -1
-biotype 700 HN "C-Terminal ASH (COOH)" -1
-biotype 701 OXT "C-Terminal ASH (COOH)" -1
-biotype 702 HA "C-Terminal ASH (COOH)" -1
-biotype 703 N "C-Terminal ASN" 180
-biotype 704 CA "C-Terminal ASN" 225
-biotype 705 C "C-Terminal ASN" 213
-biotype 706 HN "C-Terminal ASN" 183
-biotype 707 OXT "C-Terminal ASN" 214
-biotype 708 HA "C-Terminal ASN" 85
-biotype 709 N "C-Terminal GLU" 180
-biotype 710 CA "C-Terminal GLU" 225
-biotype 711 C "C-Terminal GLU" 213
-biotype 712 HN "C-Terminal GLU" 183
-biotype 713 OXT "C-Terminal GLU" 214
-biotype 714 HA "C-Terminal GLU" 85
-biotype 715 N "C-Terminal GLH (COOH)" -1
-biotype 716 CA "C-Terminal GLH (COOH)" -1
-biotype 717 C "C-Terminal GLH (COOH)" -1
-biotype 718 HN "C-Terminal GLH (COOH)" -1
-biotype 719 OXT "C-Terminal GLH (COOH)" -1
-biotype 720 HA "C-Terminal GLH (COOH)" -1
-biotype 721 N "C-Terminal GLN" 180
-biotype 722 CA "C-Terminal GLN" 225
-biotype 723 C "C-Terminal GLN" 213
-biotype 724 HN "C-Terminal GLN" 183
-biotype 725 OXT "C-Terminal GLN" 214
-biotype 726 HA "C-Terminal GLN" 85
-biotype 727 N "C-Terminal MET" 180
-biotype 728 CA "C-Terminal MET" 225
-biotype 729 C "C-Terminal MET" 213
-biotype 730 HN "C-Terminal MET" 183
-biotype 731 OXT "C-Terminal MET" 214
-biotype 732 HA "C-Terminal MET" 85
-biotype 733 N "C-Terminal LYS" 180
-biotype 734 CA "C-Terminal LYS" 225
-biotype 735 C "C-Terminal LYS" 213
-biotype 736 HN "C-Terminal LYS" 183
-biotype 737 OXT "C-Terminal LYS" 214
-biotype 738 HA "C-Terminal LYS" 85
-biotype 739 N "C-Terminal LYD (NH2)" -1
-biotype 740 CA "C-Terminal LYD (NH2)" -1
-biotype 741 C "C-Terminal LYD (NH2)" -1
-biotype 742 HN "C-Terminal LYD (NH2)" -1
-biotype 743 OXT "C-Terminal LYD (NH2)" -1
-biotype 744 HA "C-Terminal LYD (NH2)" -1
-biotype 745 N "C-Terminal ARG" 180
-biotype 746 CA "C-Terminal ARG" 225
-biotype 747 C "C-Terminal ARG" 213
-biotype 748 HN "C-Terminal ARG" 183
-biotype 749 OXT "C-Terminal ARG" 214
-biotype 750 HA "C-Terminal ARG" 85
-biotype 751 N "C-Terminal ORN" 180
-biotype 752 CA "C-Terminal ORN" 225
-biotype 753 C "C-Terminal ORN" 213
-biotype 754 HN "C-Terminal ORN" 183
-biotype 755 OXT "C-Terminal ORN" 214
-biotype 756 HA "C-Terminal ORN" 85
-biotype 757 N "C-Terminal AIB" 180
-biotype 758 CA "C-Terminal AIB" 227
-biotype 759 C "C-Terminal AIB" 213
-biotype 760 HN "C-Terminal AIB" 183
-biotype 761 OXT "C-Terminal AIB" 214
-biotype 762 N "Deprotonated N-Terminus" -1
-biotype 763 H "Deprotonated N-Terminus" -1
-biotype 764 C "Formyl N-Terminus" 177
-biotype 765 H "Formyl N-Terminus" 221
-biotype 766 O "Formyl N-Terminus" 178
-biotype 767 CH3 "Acetyl N-Terminus" 80
-biotype 768 H "Acetyl N-Terminus" 85
-biotype 769 C "Acetyl N-Terminus" 177
-biotype 770 O "Acetyl N-Terminus" 178
-biotype 771 C "Protonated C-Terminus" -1
-biotype 772 O "Protonated C-Terminus" -1
-biotype 773 OH "Protonated C-Terminus" -1
-biotype 774 HO "Protonated C-Terminus" -1
-biotype 775 N "Amide C-Terminus" 179
-biotype 776 HN "Amide C-Terminus" 182
-biotype 777 N "N-MeAmide C-Terminus" 180
-biotype 778 HN "N-MeAmide C-Terminus" 183
-biotype 779 CH3 "N-MeAmide C-Terminus" 184
-biotype 780 H "N-MeAmide C-Terminus" 85
-biotype 2001 O "Water" 63
-biotype 2002 H "Water" 64
-biotype 2003 NA "Sodium Ion" -1
-biotype 2004 K "Potassium Ion" -1
-biotype 2005 MG "Magnesium Ion" -1
-biotype 2006 CA "Calcium Ion" -1
-biotype 2007 CL "Chloride Ion" -1
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt
deleted file mode 100644
index fae58d65c..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt
+++ /dev/null
@@ -1,21 +0,0 @@
-import "ethylene.lt" # <- defines the "Ethylene" molecule type.
-import "benzene.lt" # <- defines the "Benzene" molecule type.
-
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 80.00 xlo xhi
- 0.0 80.00 ylo yhi
- 0.0 80.00 zlo zhi
-}
-
-
-# Create 1000 ethylenes and 500 benzenes
-# List them in the same order they appear in the PACKMOL .inp file(s).
-
-ethylenes = new Ethylene[1000]
-benzenes = new Benzene[500]
-
-# Note: We can omit the .move() and .rot() commands which normally appear
-# after the "new" command because we will be using a separate program
-# (PACKMOL) to generate the coordinates of these molecules.
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz
deleted file mode 100644
index d64a95504..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz
+++ /dev/null
@@ -1,12002 +0,0 @@
- 12000
- Built with Packmol
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- H12 21.853441 24.847475 12.153636
- H21 23.368835 23.791678 9.786690
- H22 21.706418 24.187550 9.779599
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- C2 20.874880 11.369561 61.571491
- H11 22.444012 10.040471 61.925867
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- H21 21.410694 12.237834 61.482003
- H22 19.866271 11.506692 61.457888
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- C2 51.118136 2.597830 3.083817
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- H21 51.018302 3.537459 2.688679
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- H12 69.548565 36.556544 16.558353
- H21 70.464670 36.504504 13.699751
- H22 71.406555 35.997391 15.032448
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- H22 51.854112 34.525510 62.858323
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- H11 37.327390 27.117487 79.281648
- H12 37.193735 28.821168 79.282692
- H21 39.629821 27.298648 78.410353
- H22 39.496167 29.002329 78.411398
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- H22 59.611548 24.676976 48.987247
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- H21 47.642426 38.555209 77.634528
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- C2 49.629489 31.508662 60.288103
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- H12 49.908290 29.499731 60.778719
- H21 49.011589 32.226121 59.897648
- H22 50.533418 31.880547 60.594072
- C1 70.285207 40.468345 63.514615
- C2 69.451519 39.423750 63.596504
- H11 69.973795 41.443456 63.549032
- H12 71.299829 40.374340 63.411125
- H21 68.436897 39.517755 63.699994
- H22 69.762931 38.448639 63.562087
- C1 74.639200 8.945741 65.383745
- C2 74.083871 8.050095 64.557700
- H11 75.439088 9.531374 65.126417
- H12 74.307728 9.115576 66.337833
- H21 74.415344 7.880259 63.603611
- H22 73.283984 7.464462 64.815028
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- C2 38.962281 73.109074 27.495972
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- H12 40.082557 71.365257 27.737466
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- H22 39.694946 73.802244 27.674077
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- C2 64.680569 70.650896 17.811711
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- H12 65.782184 71.766880 19.188396
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- H12 20.928637 5.235394 54.331099
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- C1 65.365438 56.864613 2.461825
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- H21 63.388614 56.196483 2.463985
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- H22 12.051537 18.899062 21.286840
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- H22 29.767588 25.259256 58.538712
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- H12 14.639678 38.367870 22.704909
- H21 14.219862 41.173102 21.721044
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- H12 59.158969 46.393594 7.709961
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- H12 52.236160 75.670011 13.390730
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- H12 67.270311 46.605221 29.472832
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- C1 39.859387 42.060831 18.536824
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- H22 63.567271 3.154778 22.365609
- C1 48.128009 8.095819 43.506441
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- H11 48.518708 9.042482 43.520126
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- C2 63.888360 29.106168 50.860900
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- C2 35.278751 76.374641 14.167369
- C3 34.928335 76.335689 12.812532
- C4 35.782970 75.726983 11.885579
- C5 36.988214 75.158206 12.313380
- C6 37.338630 75.197158 13.668217
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- H31 33.998203 76.774380 12.482774
- H41 35.512780 75.697539 10.840613
- H51 37.647963 74.689093 11.598254
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- H41 43.021648 77.603401 78.097931
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- H41 25.088572 53.187503 52.467714
- H51 24.464119 55.471463 51.730435
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- C1 26.197950 69.277423 8.235662
- C2 27.259753 69.918617 7.586590
- C3 28.327724 69.167228 7.081869
- C4 28.333892 67.774644 7.226220
- C5 27.272677 67.133782 7.876030
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- H21 27.254836 70.992943 7.474602
- H31 29.146266 69.661944 6.580290
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- H51 27.277594 66.059456 7.988018
- H61 25.385575 67.390124 8.881593
- C1 67.455021 39.524735 72.123171
- C2 68.519078 40.144181 71.456897
- C3 69.110328 39.521178 70.351374
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- C5 67.574272 37.659067 70.578947
- C6 66.983022 38.282069 71.684470
- H11 66.999317 40.005102 72.976046
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- H31 69.930512 39.999658 69.836890
- H41 69.094033 37.798145 69.059798
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- C1 4.772877 61.080316 30.441400
- C2 5.330659 61.713812 29.324524
- C3 5.046592 63.060692 29.069354
- C4 4.204744 63.774076 29.931060
- C5 3.646374 63.140317 31.047172
- C6 3.930440 61.793437 31.302342
- H11 4.991693 60.041417 30.637927
- H21 5.980663 61.163728 28.659961
- H31 5.477780 63.549507 28.208264
- H41 3.985340 64.812711 29.733769
- H51 2.996370 63.690401 31.711735
- H61 3.499841 61.304886 32.164196
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- C4 76.640487 25.480795 40.873603
- C5 75.615163 26.431378 40.808507
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- H11 76.271807 27.724133 37.729847
- H21 78.088983 26.040509 37.845059
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- H41 76.743689 24.856807 41.748710
- H51 74.926514 26.540431 41.633498
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- C1 47.762159 7.110335 60.494537
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- C4 48.700688 5.190416 58.685493
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- H31 49.268333 4.059474 60.428429
- H41 49.062174 4.449662 57.988044
- H51 48.025265 6.540563 57.149630
- H61 47.194514 8.241277 58.751601
- C1 23.350138 77.181586 56.994509
- C2 23.602396 78.262954 57.847071
- C3 24.637143 79.159069 57.553528
- C4 25.419632 78.973817 56.407423
- C5 25.167923 77.892067 55.555604
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- H41 26.217999 79.664755 56.181503
- H51 25.771932 77.748664 54.671665
- H61 23.938818 76.161611 55.191128
- C1 61.748925 34.659583 28.793291
- C2 62.183774 34.457279 30.108521
- C3 61.303398 34.666471 31.176729
- C4 59.988173 35.077966 30.929707
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- H21 63.198272 34.139213 30.299225
- H31 61.638735 34.509385 32.191229
- H41 59.309497 35.239787 31.753744
- H51 58.539311 35.599177 29.424014
- H61 60.098363 35.228164 27.531769
- C1 20.424924 22.860619 14.405888
- C2 19.964320 21.541982 14.311586
- C3 20.787183 20.482828 14.712808
- C4 22.070651 20.742310 15.208332
- C5 22.531401 22.060691 15.301678
- C6 21.708538 23.119845 14.900456
- H11 19.790381 23.677427 14.096059
- H21 18.973906 21.341673 13.929881
- H31 20.431312 19.465711 14.640932
- H41 22.705340 19.925247 15.517205
- H51 23.521815 22.261000 15.683383
- H61 22.064263 24.137217 14.973288
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.TXT
deleted file mode 100644
index f0e39ec90..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.TXT
+++ /dev/null
@@ -1,5 +0,0 @@
-You can use packmol to create a file containing the atomic coordinates
-for a system of ethylene mixed with benzene using this command:
-
-packmol < mix_ethylene+benzene.inp
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz
deleted file mode 100644
index 1a727ff40..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz
+++ /dev/null
@@ -1,14 +0,0 @@
-12
- Benzene
-C1 5.274 1.999 -8.568
-C2 6.627 2.018 -8.209
-C3 7.366 0.829 -8.202
-C4 6.752 -0.379 -8.554
-C5 5.399 -0.398 -8.912
-C6 4.660 0.791 -8.919
-H11 4.704 2.916 -8.573
-H21 7.101 2.950 -7.938
-H31 8.410 0.844 -7.926
-H41 7.322 -1.296 -8.548
-H51 4.925 -1.330 -9.183
-H61 3.616 0.776 -9.196
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz
deleted file mode 100644
index 35326fe81..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz
+++ /dev/null
@@ -1,8 +0,0 @@
-6
- Ethylene
-C1 -0.6695 0.000000 0.000000
-C2 0.6695 0.000000 0.000000
-H11 -1.234217 -0.854458 0.000000
-H12 -1.234217 0.854458 0.000000
-H21 1.234217 -0.854458 0.000000
-H22 1.234217 0.854458 0.000000
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp
deleted file mode 100644
index 76202ebf3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp
+++ /dev/null
@@ -1,31 +0,0 @@
-#
-# A mixture of ethylene and benzene
-#
-
-# All the atoms from diferent molecules will be separated at least 2.0
-# Anstroms at the solution.
-
-tolerance 2.0
-
-# The file type of input and output files is XYZ
-
-filetype xyz
-
-# The name of the output file
-
-output system.xyz
-
-# 1000 water molecules and 500 urea molecules will be put in a box
-# defined by the minimum coordinates x, y and z = 0. 0. 0. and maximum
-# coordinates 80. 80. 80. That is, they will be put in a cube of side
-# 80. (the keyword "inside cube 0. 0. 0. 80.") could be used as well.
-
-structure ethylene.xyz
- number 1000
- inside box 0. 0. 0. 80. 80. 80.
-end structure
-
-structure benzene.xyz
- number 500
- inside box 0. 0. 0. 80. 80. 80.
-end structure
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt
deleted file mode 100644
index 1066f810d..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt
+++ /dev/null
@@ -1,58 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# OPLSAA atom charges are stored in a separate file.
-# Load that file now:
-
-include "system.in.charges"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# -- simulation protocol --
-
-timestep 1.0
-
-print "---------------------------------------------------------------------------"
-print "First, use Langevin dynamics to randomize the initial shape of the molecules"
-print "(This is not really necessary, but it seems to speed up equilibration.)"
-print "---------------------------------------------------------------------------"
-
-fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K
-fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr
-run 2000
-unfix fxlan
-unfix fxnph
-
-print "---------------------------------------------------------------------------"
-print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---"
-print "---------------------------------------------------------------------------"
-dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
-# temperature: 300 K, pressure: 50 barr
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0
-thermo 100
-#thermo_modify flush yes
-
-run 200000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt
deleted file mode 100644
index 2f3b81c18..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt
+++ /dev/null
@@ -1,51 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# OPLSAA atom charges are stored in a separate file.
-# Load that file now:
-
-include "system.in.charges"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 200000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README.TXT
deleted file mode 100644
index eceba67ef..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README.TXT
+++ /dev/null
@@ -1,43 +0,0 @@
-This example is a simple simulation of many long alkane chains (hexadecane) in a
-box at room temperature and atmospheric pressure. Please read "WARNING.TXT".
-
-NOTE: This particular example uses the OPLSAA force-field
- However, moltemplate is not limited to OPLSAA.
-
-1) Create the "system.data", "system.in.init", and "system.in.settings"
-files which LAMMPS will read by running:
-
-moltemplate.sh system.lt
-
-
-2) Run LAMMPS in this order:
-
-lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before...
-lmp_mpi -i run.in.npt # running the simulation at constant pressure
-lmp_mpi -i run.in.nvt # running the simulation at constant temperature
-
-(The name of the LAMMPS executable, eg "lmp_mpi", may vary.)
-
----- Details ----
-
-The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains
-use the OPLSAA force-field. This means that when we define these molecules,
-we only specify the atom names, bond list, and coordinates.
-We do not have to list the atom charges, angles, dihedrals, or impropers.
-The rules for creating atomic charge and angle topology are contained in
-the "loplsaa.lt" file created by step 3) above. The "ch2group.lt",
-"ch3group.lt", and "hexadecane.lt" files all refer to "loplsaa.lt",
-(as well as the "OPLSAA" force-field object which it defines). Excerpt:
-
-import "loplsaa.lt"
-CH2 inherits OPLSAA { ...
-CH3 inherits OPLSAA { ...
-Hexadecane inherits OPLSAA { ...
-
-Alternatively, you can manually define a list of angles, dihedrals, and
-improper interactions in these files, instead of asking the force-field
-to generate them for you. You can also specify some of the angles and
-dihedrals explicitly, and let the force-field handle the rest.
-(Many of the examples which come with moltemplate do this.)
-
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_run.sh
deleted file mode 100755
index 5f8286664..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_setup.sh
deleted file mode 100755
index 33b505dbb..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_setup.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/WARNING.TXT b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/WARNING.TXT
deleted file mode 100644
index c92b2592a..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/WARNING.TXT
+++ /dev/null
@@ -1,15 +0,0 @@
-# -------- WARNING: --------
-
-This software is experimental, and the force-fields and equilbration protocols
-have not been tested carefully by me. There is no gaurantee that the simulation
-will reproduce the behavior of real hexadecane molecules,
-(or even of hexadecane molecules simulated using AMBER, which should
- be using the same force-field).
-
-# -------- REQUEST FOR HELP: --------
-
-However, if you notice a problem with this example, please report it.
-Peer-review is the only way to improve this software (or any software).
-Other suggestions are also welcome!
-
-(Contact jewett.aij@gmail.com, 2014-12-16)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
deleted file mode 100644
index b0d31f884..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
deleted file mode 100644
index f7c13d098..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg
deleted file mode 100644
index 3ad353dbb..000000000
Binary files a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt
deleted file mode 100644
index 510b7e111..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt
+++ /dev/null
@@ -1,82 +0,0 @@
-# This file contains a definition for the "CH2" molecular subunit.
-
-# First, load the OPLS force field parameters we will need.
-# These 2 files are located in the "src/moltemplate_force_fields/" subdirectory:
-
-import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field
-import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from
- # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459
- # To use the ordinary OPLSAA force field parameters,
- # (instead of the Sui et al. parameters), change the
- # atom types below from "@atom:81L","@atom:85LCH2" to
- # "@atom:81" and "@atom:85" (defined in "oplsaa.lt")
-
-
-
-# Then define "CH2":
-
-
-CH2 inherits OPLSAA {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:C $mol:... @atom:81L 0.0 0.000000 0.000000 0.000000
- $atom:H1 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 0.892431
- $atom:H2 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 -0.892431
- }
-
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- }
-
- # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt",
- # which is usually located in the "src/moltemplate_force_fields/" subdirectory
- # @atom:80L "Alkane CH3- (LOPLS CT_CH3)"
- # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)"
- # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)"
- # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)"
- # In this example, atomic charges are generated by atom type (according to the
- # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now.
- # The "..." in "$mol:..." tells moltemplate that this molecule may be part
- # of a larger molecule, and (if so) to use the larger parent object's
- # molecule id number as it's own.
-
-} # CH2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-# Optional: Shift all the coordinates in the +Y direction by 0.4431163.
-# This way, the carbon atom is no longer located at 0,0,0, but the
-# axis of an alkane chain containing this monomer is at 0,0,0.
-# (This makes it more convenient to construct a polymer later.
-# If this is confusing, then simply add 0.4431163 to the Y
-# coordinates in the "Data Atoms" section above.)
-
-CH2.move(0,0.4431163,0)
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163
-# DeltaZh = Lch*sin(theta/2) # = 0.892431
-# DeltaYh = Lch*cos(theta/2) # = 0.631044
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt
deleted file mode 100644
index b01c8c0cd..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt
+++ /dev/null
@@ -1,83 +0,0 @@
-# This file contains a definition for the "CH3" molecular subunit.
-
-# First, load the OPLS force field parameters we will need.
-# These 2 files are located in the "src/moltemplate_force_fields/" subdirectory:
-
-import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field
-import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from
- # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459
- # To use the ordinary OPLSAA force field parameters,
- # (instead of the Sui et al. parameters), change the
- # atom types below from "@atom:80L","@atom:85LCH3" to
- # "@atom:80" and "@atom:85" (defined in "oplsaa.lt")
-
-
-
-# Then define "CH3":
-
-
-CH3 inherits OPLSAA {
-
- # atom-id mol-id atom-type charge x y z
-
- write("Data Atoms") {
- $atom:C $mol:... @atom:80L 0.0 0.000000 0.000000 0.000000
- $atom:H1 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 0.892431
- $atom:H2 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 -0.892431
- $atom:H3 $mol:... @atom:85LCH3 0.0 -0.892431 -0.631044 0.000000
- }
-
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- $bond:CH3 $atom:C $atom:H3
- }
-
- # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt",
- # @atom:80L "Alkane CH3- (LOPLS CT_CH3)"
- # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)"
- # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)"
- # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)"
- # In this example, atomic charges are generated by atom type (according to the
- # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now.
- # The "..." in "$mol:..." tells moltemplate that this molecule may be part
- # of a larger molecule, and (if so) to use the larger parent object's
- # molecule id number as it's own.
-
-} # CH3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-# Optional: Shift all the coordinates in the +Y direction by 0.4431163.
-# This way, the carbon atom is no longer located at 0,0,0, but the
-# axis of an alkane chain containing this monomer is at 0,0,0.
-# (This makes it more convenient to construct a polymer later.
-# If this is confusing, then simply add 0.4431163 to the Y
-# coordinates in the "Data Atoms" section above.)
-
-CH3.move(0,0.4431163,0)
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163
-# DeltaZh = Lch*sin(theta/2) # = 0.892431
-# DeltaYh = Lch*cos(theta/2) # = 0.631044
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt
deleted file mode 100644
index 96e9e6b4b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt
+++ /dev/null
@@ -1,79 +0,0 @@
-# This example looks complicated because I split the
-# hexadecane molecule into individual CH2 and CH3 monomers.
-#
-# I defined it this way so that you can easily modify
-# it to change the length of the alkane chain.
-
-
-import "oplsaa.lt" # load the "OPLSAA" force-field information
-import "ch2group.lt" # load the definition of the "CH2" object
-import "ch3group.lt" # load the definition of the "CH3" object
-
-
-
-Hexadecane inherits OPLSAA {
-
-
- create_var {$mol} # optional:force all monomers to share the same molecule-ID
-
-
- # Now create an array of 16 "CH2" objects distributed along the X axis
-
- monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0)
-
- # Each monomer is rotated 180 degrees with respect to the previous
- # monomer, and then moved 1.2533223 Angstroms down the X axis.
-
- # ---- Now, modify the ends: ---
- # Delete the CH2 groups at the beginning and end, and replace them with CH3.
-
- delete monomers[0]
- delete monomers[15]
-
- monomers[0] = new CH3
- monomers[15] = new CH3
-
- # Move the CH3 groups to the correct location at either end of the chain:
-
- monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0)
- # Note: 18.7998345 = (16-1) * 1.2533223
-
-
- # Now add a list of bonds connecting the carbon atoms together:
-
- write('Data Bond List') {
- $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C
- $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C
- $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C
- $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C
- $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C
- $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C
- $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C
- $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C
- $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C
- $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C
- $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C
- $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C
- $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C
- $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C
- $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C
- }
-
-} # Hexadecane
-
-
-
-
-
-
-
-
-######### (scratchwork calculations for the atomic coordinates) #########
-# Lcc = 1.5350 # length of the C-C bond (Sp3)
-# Lch = 1.0930 # length of the C-H bond
-# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
-# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
-# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
-# # 0.5*DeltaYc = 0.4431163316030377
-# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
-# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index 5b6e32d84..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,108 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the
-"ethylene" example. (However, these instructions should work
-for other molecules too.)
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with ethylene, you would delete every line
-beginning with the word "atom", except for these two lines:
-
-
-atom 80 13 CT "Alkane CH3-" 6 12.011 4
-atom 81 13 CT "Alkane -CH2-" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "88", "89", "47", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "ethyelene.lt":
-
-import "oplsaa.lt"
-Ethylene inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Jason Lambert and Andrew Jewett
-December 14 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index 1260acdbd..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,151 +0,0 @@
-# This file is a heavily redacted version of the "oplsaa.prm" file distributed
-# with TINKER (Downloaded April, 2014). This version only contains information
-# relevant to alkane chains. The complete version of that file works with most
-# small organic molecules and you can use that file with moltemplate too.
-# Unfortunately, I do not own or have permission to distribute that file.
-# You can download the latest complete version of that file here:
-#
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-#
-# When building your own molecules, you should download this file, and delete
-# only the lines from the "atoms" section which you don't need. (But leave the
-# rest of that file alone. I deleted other sections of this file here in order
-# to reduce the file size, but this is not necessary.)
-#
-# Rename the resulting file "oplsaa_subset.prm"
-#
-# Then you can create an oplsaa.lt file (which moltemplate.sh needs) this way:
-# oplsaa_moltemplate.py oplsaa_subset.prm
-#
-# Then copy the newly created "oplsa.lt" file to the directory where you
-# plan to run moltemplate, and run moltemplate:
-# moltemplate system.lt
-
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-
-atom 80 13 CT "Alkane CH3-" 6 12.011 4
-atom 81 13 CT "Alkane -CH2-" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 80 3.5000 0.0660
-vdw 81 3.5000 0.0660
-vdw 85 2.5000 0.0300
-
-
-bond 13 13 268.00 1.5290
-bond 13 46 340.00 1.0900
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 13 13 13 58.35 112.70
-angle 46 13 46 33.00 107.80
-angle 13 13 46 37.50 110.70
-
-
- ############################
- ## ##
- ## Torsional Parameters ##
- ## ##
- ############################
-
-
- ###################################################################
- ## ##
- ## Alternative Torsional Parameter Values for Use with OPLS-AA ##
- ## ##
- ## For some torsions, OPLS-AA has multiple possible parameter ##
- ## values; the list below shows functional groups for which ##
- ## these alternate (commented) values should be preferred; the ##
- ## values are in the same order as in the full parameter list ##
- ## ##
- ## 13 13 13 13 hydrocarbon (default) ##
- ## 13 13 13 13 perfluoroalkane ##
- ## ##
- ###################################################################
-
-
-torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3
-#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3
-torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3
-#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4
-torsion 13 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-torsion 46 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3
-
-
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 80 -0.1800
-charge 81 -0.1200
-charge 85 0.0600
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt
deleted file mode 100644
index 4e0cfaec6..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt
+++ /dev/null
@@ -1,18 +0,0 @@
-import "hexadecane.lt" # <- defines the "Hexadecane" molecule type.
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 62.4 xlo xhi
- 0.0 62.4 ylo yhi
- 0.0 62.4 zlo zhi
-}
-
-molecules = new Hexadecane [12].move(0, 0, 5.2)
- [12].move(0, 5.2, 0)
- [2].move(31.2, 0, 0)
-
-
-# NOTE: The spacing between molecules is large. There should be extra room to
-# move during the initial stages of equilibration. However, you will have to
-# run the simulation at NPT conditions later to compress the system to a
-# more realistic density.
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/run.in.npt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/run.in.npt
deleted file mode 100644
index 1b1a28fab..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/run.in.npt
+++ /dev/null
@@ -1,87 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-include system.in.charges
-
-# ------------------------------- Run Section -------------------------------
-
-# To avoid explosions, I have a 4-step equilibraion process (expand, minimize,
-# reorient, compress). The system (as defined in the "system.data" file)
-# is already expanded. That means there are 3 steps left:
-
-dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz
-thermo 50
-
-# -- Equilibration: part 1: initial minimization --
-
-# Note: In general, it's always a good idea to minimize the system at first.
-
-minimize 1.0e-5 1.0e-7 100000 400000
-undump dumpeq1
-
-write_data system_after_eq1_min.data
-
-# -- Equilibration part 2: reorienting the molecules (NVT) --
-
-timestep 1.0
-dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz
-
-# Run the system at high temperature (at constant volume) to reorient the
-# the molecules (which would otherwise be pointing in the same direction).
-
-# To speed it up, I randomize the atomic positions for a few thousand steps
-# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover).
-# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.)
-
-
-fix fxlan all langevin 900.0 900.0 120 48279
-fix fxnve all nve
-
-run 4000
-
-unfix fxlan
-unfix fxnve
-# Now continue the simulation at high temperature using fix nvt (Nose-Hoover).
-fix fxnvt all nvt temp 900.0 900.0 100.0
-
-run 50000
-undump dumpeq2
-
-
-write_data system_after_eq2_reorient.data
-
-unfix fxnvt
-
-# -- equilibration part 3: Equilibrating the density (NPT) --
-
-# Originally, the simulation box (in "system.data" and "system.lt") was
-# unrealistically large. The spacing between the molecules was large also.
-# I did this to enable the molecules to move freely and reorient themselves.
-# After doing that, we should run the simulation under NPT conditions to
-# allow the simulation box to contract to it's natural size. We do that here:
-# We begin the simulation at 100 barr (a relatively low pressure), and
-# slowly decrease it to 1 barr, maintianing the temperature at 300K.
-
-dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 900.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0
-
-timestep 1.0
-run 100000
-
-write_data system_after_eq3_npt.data
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/run.in.nvt
deleted file mode 100644
index 38815745c..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/hexadecane/run.in.nvt
+++ /dev/null
@@ -1,44 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_eq3_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-include system.in.charges
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1
-thermo 100
-#thermo_modify flush yes
-
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/methane/README.TXT
deleted file mode 100644
index 9f9e9d099..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/README.TXT
+++ /dev/null
@@ -1,24 +0,0 @@
-This example demonstrates how to build a simulation containing a box of methane.
-(Not a very interesting example.)
-
----- Details ----
-
-The methane molecules in this example use the OPLSAA force-field.
-This means that the database of force-field parameters in "oplsaa.lt"
-will be used to generate angles, dihedrals, and impropers.
-The "moltemplate_files/methane.lt" file
-contains these lines which refer to OPLSAA:
-
-import "oplsaa.lt"
-Methane inherits OPLSAA { ...
-
--------- Instructions: ---------
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step 2)
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/methane/README_run.sh
deleted file mode 100755
index 5f8286664..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/methane/README_setup.sh
deleted file mode 100755
index 6aa6c06f4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/README_setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/methane/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/methane.lt b/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/methane.lt
deleted file mode 100644
index bb8f0469c..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/methane.lt
+++ /dev/null
@@ -1,32 +0,0 @@
-import "oplsaa.lt"
-
-# Atom type numbers are from the "oplsaa_subset.prm"
-# file used to generate "oplsaa.lt".
-
-# atom 83 13 CT "Methane CH4"
-# atom 85 46 HC "Alkane H-C"
-
-Methane inherits OPLSAA {
-
- # atomID molID atomTyle charge X Y Z
- write('Data Atoms') {
- $atom:C $mol:. @atom:83 0.0 0.000000 0.000000 0.000000
- $atom:H1 $mol:. @atom:85 0.0 0.000000 0.000000 1.089000
- $atom:H2 $mol:. @atom:85 0.0 1.026719 0.000000 -0.363000
- $atom:H3 $mol:. @atom:85 0.0 -0.513360 -0.889165 -0.363000
- $atom:H4 $mol:. @atom:85 0.0 -0.513360 0.889165 -0.363000
- }
-
- # Charges will be assigned by OPLSAA, so we leave them 0.0 here.
- #
- # (The "." in "$mol:." refers to this molecule-object's molecule-ID number.
- # The "." simply means this molecule is not a part of a larger molecule.)
-
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- $bond:CH3 $atom:C $atom:H3
- $bond:CH4 $atom:C $atom:H4
- }
-
-} # Methane
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index 3336341da..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,108 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the "Methane"
-molecule. (However, these instructions should work for other molecules too.)
-
---- Instructions ---
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with methane, you would delete every line
-beginning with the word "atom", except for these two lines:
-
-
-atom 83 13 CT "Methane CH4" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "83", "85", "46", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "methane.lt":
-
-import "oplsaa.lt"
-Methane inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Andrew Jewett and Jason Lambert
-May, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index 5f982059b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,115 +0,0 @@
-# This is a modified version of the file "oplsaa.prm" distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# In this version, all of the lines beginning with "atom" have been deleted
-# except for the atom types we will be using in this simulation
-# (I also deleted some other lines from that file data to reduce the file size,
-# but doing that is not necessary.)
-#
-# If you use this file, please also cite the software this file comes from:
-#
-# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024
-# "An efficient newton‐like method for molecular mechanics energy
-# minimization of large molecules."
-#
-# Ponder, J. W, (2004)
-# "TINKER: Software tools for molecular design"
-# http://dasher.wustl.edu/tinker/
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-# Note:
-# In this example, I am only using OPLSAA to lookup force-field parameters
-# for methane. (The water molecules in this example do not need OPLSAA.)
-# So I deleted all of the lines beginning with "atom" except these two:
-
-atom 83 13 CT "Methane CH4" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 83 3.5000 0.0660
-vdw 85 2.5000 0.0300
-
-
- ##################################
- ## ##
- ## Bond Stretching Parameters ##
- ## ##
- ##################################
-
-
-bond 13 46 340.00 1.0900
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 46 13 46 33.00 107.80
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 83 -0.2400
-charge 85 0.0600
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/system.lt
deleted file mode 100644
index 7c846cd93..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/moltemplate_files/system.lt
+++ /dev/null
@@ -1,15 +0,0 @@
-import "methane.lt" # <- defines the "Methane" molecule type (uses OPLSAA)
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 103.5 xlo xhi
- 0.0 103.5 ylo yhi
- 0.0 103.5 zlo zhi
-}
-
-# Now add methane molecules:
-
-methanes = new Methane [10].move(0, 0, 10.35)
- [10].move(0, 10.35, 0)
- [10].move(10.35, 0, 0)
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/run.in.npt b/tools/moltemplate/examples/force_field_OPLSAA/methane/run.in.npt
deleted file mode 100644
index 208d4b681..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/run.in.npt
+++ /dev/null
@@ -1,51 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-#
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# (The "fShakeSPCE" fix was defined in system.in.settings.
-# It is incompatible with "minimize", so we disable it first.)
-#unfix fShakeSPCE
-thermo 500
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# Now read "system.in.settings" in order to enable fShakeSPCE again:
-#include system.in.settings
-
-# Optional: write the coordinates after minimization
-write_data system_after_min.data
-
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 2500 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-
-run 500000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/methane/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/methane/run.in.nvt
deleted file mode 100644
index a4f382118..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/methane/run.in.nvt
+++ /dev/null
@@ -1,42 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# (The "write_restart" and "reagd_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 50000
-
-write_restart system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README.TXT
deleted file mode 100644
index 5ad3a04b5..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README.TXT
+++ /dev/null
@@ -1,30 +0,0 @@
-This example contains a mixture of water(SPCE) and methane.
-The methane molecules use OPLSAA force-field, but the water molecules do not.
-
----- Details ----
-
-The methane molecules in this example use the OPLSAA force-field.
-This means that the database of force-field parameters in "oplsaa.lt"
-will be used to generate angles, dihedrals, and impropers.
-The "moltemplate_files/methane.lt" file
-contains these lines which refer to OPLSAA:
-
-import "oplsaa.lt"
-Methane inherits OPLSAA { ...
-
-However the "SPCE" (water) molecules does NOT use a database to look up the
-force-field parameters for this tiny molecule.
-Instead, the "moltemplate_files/spce.lt" file declares all of the angle
-interactions, atom properties and force-field parameters for water explicitly.
-(Consequently, it makes no mention of "oplsaa.lt" or "OPLSAA".)
-
--------- Instructions: ---------
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step 2)
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh
deleted file mode 100755
index 5f8286664..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh
deleted file mode 100755
index 6aa6c06f4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt
deleted file mode 100644
index bb8f0469c..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt
+++ /dev/null
@@ -1,32 +0,0 @@
-import "oplsaa.lt"
-
-# Atom type numbers are from the "oplsaa_subset.prm"
-# file used to generate "oplsaa.lt".
-
-# atom 83 13 CT "Methane CH4"
-# atom 85 46 HC "Alkane H-C"
-
-Methane inherits OPLSAA {
-
- # atomID molID atomTyle charge X Y Z
- write('Data Atoms') {
- $atom:C $mol:. @atom:83 0.0 0.000000 0.000000 0.000000
- $atom:H1 $mol:. @atom:85 0.0 0.000000 0.000000 1.089000
- $atom:H2 $mol:. @atom:85 0.0 1.026719 0.000000 -0.363000
- $atom:H3 $mol:. @atom:85 0.0 -0.513360 -0.889165 -0.363000
- $atom:H4 $mol:. @atom:85 0.0 -0.513360 0.889165 -0.363000
- }
-
- # Charges will be assigned by OPLSAA, so we leave them 0.0 here.
- #
- # (The "." in "$mol:." refers to this molecule-object's molecule-ID number.
- # The "." simply means this molecule is not a part of a larger molecule.)
-
- write('Data Bond List') {
- $bond:CH1 $atom:C $atom:H1
- $bond:CH2 $atom:C $atom:H2
- $bond:CH3 $atom:C $atom:H3
- $bond:CH4 $atom:C $atom:H4
- }
-
-} # Methane
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index 0bc46d88c..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,111 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the "Methane"
-molecule. (However, these instructions should work for other molecules too.)
-Note that the "SPCE" (water) molecules in this example, do NOT use the OPLSAA
-database to look up the force-field parameters, so I did not include water
-atom types in the "oplsaa_subset.prm".
-
---- Instructions ---
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with methane, you would delete every line
-beginning with the word "atom", except for these two lines:
-
-
-atom 83 13 CT "Methane CH4" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "83", "85", "46", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "methane.lt":
-
-import "oplsaa.lt"
-Methane inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Andrew Jewett and Jason Lambert
-May, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index fee34956b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,126 +0,0 @@
-# This is a modified version of the file "oplsaa.prm" distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# In this version, all of the lines beginning with "atom" have been deleted
-# except for the atom types we will be using in this simulation.
-# (I also deleted some other lines from that file data to reduce the file size,
-# but doing that is not necessary.)
-#
-# If you use this file, please also cite the software this file comes from:
-#
-# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024
-# "An efficient newton‐like method for molecular mechanics energy
-# minimization of large molecules."
-#
-# Ponder, J. W, (2004)
-# "TINKER: Software tools for molecular design"
-# http://dasher.wustl.edu/tinker/
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-# Note:
-# In this example, I am only using OPLSAA to lookup force-field parameters
-# for methane. (The water molecules in this example do not need OPLSAA.)
-# So I deleted all of the lines beginning with "atom" except these two:
-
-atom 83 13 CT "Methane CH4" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-# NOTE: You can use the OPLSAA force field to look up SPC water parameters as
-# In that case, you could do this by uncommenting these next two lines:
-# atom 76 42 OW "SPC Water O" 8 15.999 2
-# atom 77 43 HW "SPC Water H" 1 1.008 1
-
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 83 3.5000 0.0660
-vdw 85 2.5000 0.0300
-
-
- ##################################
- ## ##
- ## Bond Stretching Parameters ##
- ## ##
- ##################################
-
-
-bond 13 46 340.00 1.0900
-bond 42 43 600.00 1.0000
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 46 13 46 33.00 107.80
-angle 43 42 43 75.00 109.47
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 76 -0.8200
-charge 77 0.4100
-charge 83 -0.2400
-charge 85 0.0600
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt
deleted file mode 100644
index fdf6172a4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt
+++ /dev/null
@@ -1,52 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-SPCE {
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
- $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 600.0 1.0
- angle_coeff @angle:HOH harmonic 75.0 109.47
- pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166
- pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 0.0
- group spce type @atom:O @atom:H
- fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeSPCE during minimization.)
- }
-
- write_once("In Init") {
- # -- Default styles (for solo "SPCE" water) --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/cut/coul/long 10.0 10.0
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED!
- }
-
-} # end of definition of "SPCE" water molecule type
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt
deleted file mode 100644
index 3957d08eb..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt
+++ /dev/null
@@ -1,26 +0,0 @@
-import "spce.lt" # <- defines the "SPCE" (water) molecule type.
-import "methane.lt" # <- defines the "Methane" molecule type (uses OPLSAA)
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 41.50 xlo xhi
- 0.0 41.50 ylo yhi
- 0.0 41.50 zlo zhi
-}
-
-# The next command generates a (rather dense) cubic lattice with
-# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
-
-waters = new SPCE [12].move(0.00, 0.00, 3.45)
- [12].move(0.00, 3.45, 0.00)
- [12].move(3.45, 0.00, 0.00)
-
-# Now add methane molecules:
-
-methanes = new Methane [4].move(0, 0, 10.35)
- [4].move(0, 10.35, 0)
- [4].move(10.35, 0, 0)
-
-# Move the methane molecules slightly to reduce overlap with the water
-methanes[*][*][*].move(1.725, 1.725, 1.725)
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/run.in.npt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/run.in.npt
deleted file mode 100644
index df9c1f95f..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/run.in.npt
+++ /dev/null
@@ -1,52 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-#
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# (The "fShakeSPCE" fix was defined in system.in.settings.
-# It is incompatible with "minimize", so we disable it first.)
-unfix fShakeSPCE
-thermo 50
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# Now read "system.in.settings" in order to enable fShakeSPCE again:
-include system.in.settings
-
-# Optional: write the coordinates after minimization
-write_data system_after_min.data
-
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-thermo 100
-
-run 2000000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/run.in.nvt
deleted file mode 100644
index 9652779bb..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/run.in.nvt
+++ /dev/null
@@ -1,42 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README.TXT
deleted file mode 100644
index 292d9d0ec..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README.TXT
+++ /dev/null
@@ -1,18 +0,0 @@
-The purpose of this example is to test the density of water
-constructed using the OPLSAA force-field. (I think this is SPC water, not SPCE)
-
-I just wanted some kind of sanity check to make sure we are converting
-the OPLSAA parameters into moltemplate/LAMMPS format correctly.
-
-The "TEST_density_estimate.txt" contains the results of that test.
-
--------- Instructions: ---------
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step 2)
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh
deleted file mode 100755
index 71a18b0ab..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-# --- Running LAMMPS ---
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # simulation at constant volume
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh
deleted file mode 100755
index 6aa6c06f4..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
-
-
-
-
-# Optional:
-# Note: The system.data and system.in.settings files contain extra information
-# for atoms defined in OPLSAA which you are not using in this simulation. This
-# is harmless, but if you to delete this information from your
-# system.in.settings and system.in.data files, follow the instructions in
-# this script: "optional_cleanup/README_remove_irrelevant_info.sh"
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt
deleted file mode 100644
index 9dc50b389..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-This system contains 1728 water molecules
-(This is SPC water I think.)
-
-Then I ran a short simulation for 170000 timesteps at 300Kelvin and 1 atm.
-(that's when it crashed. I'll worry about why later...)
-
-Anyway, the average volume was 52149.8 (in Angstroms^3)
-(for the last 80000 timesteps, after it had equilibrated)
-
-Given that the mass of water is 18.0154 grams per mole, I'm getting
-this value for the density:
-
-density = (1728*18.0154/6.02214129e23) / (52149.8*1e-30*1e6)
- = 0.991 (in grams per mL)
-
-I'm only looking for gross errors in the OPLSAA force-field.
-So I'm satisfied with a 1% error.
-But I realize this is not a particularly rigorous test.
-
-Andrew 2014-5-21
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
deleted file mode 100644
index d5e469af3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-
-OPLSAA force-field conversion tools provided by Jason Lambert.
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT
deleted file mode 100644
index 8ae373d71..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT
+++ /dev/null
@@ -1,115 +0,0 @@
-This directory contains instructions for creating a a moltemplate file
-("oplsaa.lt") containing force-field definitions relevant to the "Methane"
-molecule. (However, these instructions should work for other molecules too.)
-Note that the "SPCE" (water) molecules in this example, do NOT use the OPLSAA
-database to look up the force-field parameters, so I did not include water
-atom types in the "oplsaa_subset.prm".
-
---- Instructions ---
-
-First, check and see if there is an "oplsaa_subset.prm" file present.
-If not, then download this file:
-
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- This file is also available here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below for details). Then run the opls_moltemplate.py script this way:
-
-
-oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then move this file to wherever you plan to run moltemplate. For example:
-
-mv -f oplsaa.lt ..
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with methane and SPC water, you would delete every line
-beginning with the word "atom", except for these two lines:
-
-
-atom 76 42 OW "SPC Water O" 8 15.999 2
-atom 77 43 HW "SPC Water H" 1 1.008 1
-atom 83 13 CT "Methane CH4" 6 12.011 4
-atom 85 46 HC "Alkane H-C" 1 1.008 1
-
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "83", "85", "46", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "methane.lt":
-
-import "oplsaa.lt"
-Methane inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 1 charge -0.82
-set type 2 charge 0.41
-set type 3 charge -0.42
-set type 4 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because these examples use the "oplsaa.prm" file which
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Andrew Jewett and Jason Lambert
-May, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
deleted file mode 100644
index 60bf1d855..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
+++ /dev/null
@@ -1,112 +0,0 @@
-# This is a modified version of the file "oplsaa.prm" distributed with TINKER
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# In this version, all of the lines beginning with "atom" have been deleted
-# except for the atom types we will be using in this simulation.
-# (That's all you need to do, but in this version, I also deleted
-# everything else we don't need to reduce the file size.)
-#
-# If you use this file, please also cite the software this file comes from:
-#
-# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024
-# "An efficient newton‐like method for molecular mechanics energy
-# minimization of large molecules."
-#
-# Ponder, J. W, (2004)
-# "TINKER: Software tools for molecular design"
-# http://dasher.wustl.edu/tinker/
-
- ##############################
- ## ##
- ## Force Field Definition ##
- ## ##
- ##############################
-
-
-forcefield OPLS-AA
-
-vdwindex TYPE
-vdwtype LENNARD-JONES
-radiusrule GEOMETRIC
-radiustype SIGMA
-radiussize DIAMETER
-epsilonrule GEOMETRIC
-torsionunit 0.5
-imptorunit 0.5
-vdw-14-scale 2.0
-chg-14-scale 2.0
-electric 332.06
-dielectric 1.0
-
-
- #############################
- ## ##
- ## Literature References ##
- ## ##
- #############################
-
-
-The parameters supplied with TINKER are from "OPLS All-Atom Parameters
-for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as
-provided by W. L. Jorgensen, Yale University during June 2009. These
-parameters are taken from those distributed with BOSS Version 4.8.
-
-Note that "atom type" numbers and not "atom class" numbers are used
-to index van der Waals parameters, see the "vdwindex" keyword above
-
-The atom types with (UA) in the description are "united atom" values,
-ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their
-attached atoms. All other parameters are "all-atom", OPLS-AA, including
-explicit hydrogen atoms.
-
-
- #############################
- ## ##
- ## Atom Type Definitions ##
- ## ##
- #############################
-
-
-atom 76 42 OW "SPC Water O" 8 15.999 2
-atom 77 43 HW "SPC Water H" 1 1.008 1
-
-
- ################################
- ## ##
- ## Van der Waals Parameters ##
- ## ##
- ################################
-
-
-vdw 76 3.16557 0.1554
-vdw 77 0.0000 0.0000
-
-
- ##################################
- ## ##
- ## Bond Stretching Parameters ##
- ## ##
- ##################################
-
-
-bond 42 43 600.00 1.0000
-
-
- ################################
- ## ##
- ## Angle Bending Parameters ##
- ## ##
- ################################
-
-
-angle 43 42 43 75.00 109.47
-
-
- ########################################
- ## ##
- ## Atomic Partial Charge Parameters ##
- ## ##
- ########################################
-
-
-charge 76 -0.8200
-charge 77 0.4100
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt
deleted file mode 100644
index e7f3d6d84..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt
+++ /dev/null
@@ -1,86 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-
-import "oplsaa.lt"
-
-SPC inherits OPLSAA {
-
- # Atom types from "oplsaa_lt_generator/oplsaa_subset.prm"
- # @atom:76 <--> OW "SPC Water O"
- # @atom:77 <--> HW "SPC Water H"
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:76 -0.8200 0.0000000 0.0000 0.000000
- $atom:H1 $mol:. @atom:77 0.4100 0.8164904 0.0000 0.577359
- $atom:H2 $mol:. @atom:77 0.4100 -0.8164904 0.0000 0.577359
- }
-
- write("Data Bond List") {
- $bond:OH1 $atom:O $atom:H1
- $bond:OH2 $atom:O $atom:H2
- }
-
-} # end of definition of "SPC" water molecule type
-
-
-
-
-
-
-
-
-
-
-
-###################### old version (SPCE) ######################
-#
-#SPCE {
-#
-# write("Data Atoms") {
-# $atom:O $mol:. @atom:O -0.8476 0.0000000 0.0000 0.000000
-# $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.0000 0.577359
-# $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.0000 0.577359
-# }
-#
-# write_once("Data Masses") {
-# @atom:O 15.9994
-# @atom:H 1.008
-# }
-#
-# write("Data Bonds") {
-# $bond:OH1 @bond:OH $atom:O $atom:H1
-# $bond:OH2 @bond:OH $atom:O $atom:H2
-# }
-#
-# write("Data Angles") {
-# $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
-# }
-#
-# write_once("In Settings") {
-# bond_coeff @bond:OH harmonic 1000.0 1.0
-# angle_coeff @angle:HOH harmonic 1000.0 109.47
-# pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166
-# pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058
-# group spce type @atom:O @atom:H
-# fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
-# # (Remember to "unfix" fShakeSPCE during minimization.)
-# }
-#
-# write_once("In Init") {
-# # -- Default styles (for solo "SPCE" water) --
-# units real
-# atom_style full
-# # (Hybrid force fields were not necessary but are used for portability.)
-# pair_style hybrid lj/cut/coul/long 10.0
-# bond_style hybrid harmonic
-# angle_style hybrid harmonic
-# kspace_style pppm 0.0001
-# pair_modify shift yes
-# }
-#
-#} SPCE
-###################################################################
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt
deleted file mode 100644
index 5dd56c116..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt
+++ /dev/null
@@ -1,16 +0,0 @@
-import "spc.lt" # <- defines the "SPC" (water) molecule type (uses OPLSAA)
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 41.40 xlo xhi
- 0.0 41.40 ylo yhi
- 0.0 41.40 zlo zhi
-}
-
-# The next command generates a (rather dense) cubic lattice with
-# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
-
-waters = new SPC [12].move(0.00, 0.00, 3.45)
- [12].move(0.00, 3.45, 0.00)
- [12].move(3.45, 0.00, 0.00)
-
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt
deleted file mode 100644
index 642880af2..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt
+++ /dev/null
@@ -1,52 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-#
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# (The "fShakeSPCE" fix was defined in system.in.settings.
-# It is incompatible with "minimize", so we disable it first.)
-#unfix fShakeSPCE
-thermo 50
-minimize 1.0e-4 1.0e-6 100000 400000
-
-# Now read "system.in.settings" in order to enable fShakeSPCE again:
-#include system.in.settings
-
-# Optional: write the coordinates after minimization
-write_data system_after_min.data
-
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 2500 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-thermo 100
-
-run 2000000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt
deleted file mode 100644
index 9652779bb..000000000
--- a/tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt
+++ /dev/null
@@ -1,42 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data "system_after_npt.data"
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-#thermo_modify flush yes
-
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README.TXT b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README.TXT
deleted file mode 100644
index 036c6e756..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README.TXT
+++ /dev/null
@@ -1,21 +0,0 @@
-This example was contributed by Yue Chun Chiu (Chinese University of Hong Kong)
-(Thanks!)
-
-This is a simulation of propane using the OPLSUA force-field.
-(It uses the OPLSUA force field even though the file names begin with "oplsaa")
-
-IMPORTANT: This is NOT an all-atom simulation.
- OPLSUA is a united-atom force-field.
- Hydrogen atoms are not represented explicitly.
- The force-field has been adjusted accordingly.
-
--------- Instructions: ---------
-
-More detailed instructions on how to build LAMMPS input files and
-run a short simulation are provided in other README files.
-
-step 1)
-README_setup.sh
-
-step 2)
-README_run.sh
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_run.sh b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_run.sh
deleted file mode 100755
index 5f8286664..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_run.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-# --- Running LAMMPS ---
-#
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation might be ignored when beginning the simulation at constant
-# volume. (This is because restart files in LAMMPS don't always work,
-# and I was spending a lot of time trying to convince people it was a
-# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
-# Read the "run.in.nvt" file to find out how to use the "read_restart"
-# command to load the results of the pressure-equilibration simulation,
-# before beginning a constant-volume run.
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_setup.sh b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_setup.sh
deleted file mode 100755
index 412634dfe..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_setup.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- ######################### WEIRD LAMMPS QUIRK:###############################
- # The default pair_style used with the OPLSAA forcefield requires that SOME
- # atoms have non-zero charge. Unfortunately, in this example none of them do.
- # (This does not happen very often.)
- # Since you don't need long-range coulombics in this example, LAMMPS will
- # print out an error message and tell you to use a more efficient pair_style.
- # To get around this AFTER RUNNING MOLTEMPLATE, run these commands in the
- # shell:
-
- echo "pair_style hybrid lj/cut 10.0" >> system.in.init
- sed -i 's/lj\/cut\/coul\/long/lj\/cut/g' system.in.settings
- sed -i 's/kspace_style/#kspace_style/g' system.in.init
-
- # This will override the pair_style and pair_coeff commands in the
- # system.in.init and system.in.settings files (created by moltemplate):
-
- # Moltemplate generates various files with names ending in *.in* and *.data.
- # Move them to the directory where you plan to run LAMMPS (in this case "../")
- mv -f system.data system.in* ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_visualize.txt b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt
deleted file mode 100644
index d82d8cfd9..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt
+++ /dev/null
@@ -1,31 +0,0 @@
-import "oplsaa.lt"
-
-
-Propane inherits OPLSAA {
-
- # atomID molID atomTyle charge X Y Z
- write('Data Atoms') {
- $atom:CH3a $mol:. @atom:10 0.0 -0.748 -0.015 0.024
- $atom:CH2 $mol:. @atom:13 0.0 0.558 0.420 -0.278
- $atom:CH3b $mol:. @atom:10 0.0 0.716 1.404 0.137
- }
-
- write('Data Bond List') {
- $bond:CC1 $atom:CH3a $atom:CH2
- $bond:CC2 $atom:CH2 $atom:CH3b
- }
-
- # These atom types are defined in the "oplsaa.lt" file
- # (usually located in the "src/moltemplate_force_fields/" subdirectory)
- # @atom:10 "N-Alkane CH3- (UA)"
- # @atom:13 "Alkanes -CH2- (UA)"
- #
- # NOTE: UA means united atom (no explicit hydrogens).
- # The first 56 atoms in the "oplsaa.lt" file are united atoms
- #
- # NOTE: Charges will be assigned by OPLSAA, so we leave them 0.0 here.
- #
- # (The "." in "$mol:." refers to this molecule-object's molecule-ID number.
- # The "." simply means this molecule is not a part of a larger molecule.)
-
-}
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt
deleted file mode 100644
index 6f266aac3..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt
+++ /dev/null
@@ -1,37 +0,0 @@
-import "propane.lt"
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 36.0 xlo xhi
- 0.0 36.0 ylo yhi
- 0.0 36.0 zlo zhi
-}
-
-# Now add methane molecules:
-
-propanes = new Propane [6].move(0, 0, 6)
- [6].move(0, 6, 0)
- [6].move(6, 0, 0)
-
-propanes[*][*][*].move(2.0, 2.0, 2.0)
-
-
-
-
-
-
-
-######################### WEIRD LAMMPS QUIRK:###############################
-# The default pair_style used with the OPLSAA forcefield requires that SOME
-# atoms have non-zero charge. Unfortunately, in this example none of them do.
-# (This does not happen very often.)
-# Since you don't need long-range coulombics in this example, LAMMPS will
-# terminate with an error message and ask you to use a more efficient pair_style
-# To get around this AFTER RUNNING MOLTEMPLATE, run these commands in the shell
-#
-# echo "pair_style hybrid lj/cut 10.0" >> system.in.init
-# sed -i 's/lj\/cut\/coul\/long/lj\/cut/g' system.in.settings
-# sed -i 's/kspace_style/#kspace_style/g' system.in.init
-#
-# This will override the pair_style and pair_coeff commands in the
-# system.in.init and system.in.settings files (created by moltemplate):
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.npt b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.npt
deleted file mode 100644
index c1115f67b..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.npt
+++ /dev/null
@@ -1,43 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-#
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data "system.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-thermo 500
-thermo_style custom step temp etotal press vol
-minimize 6.0e-5 1.0e-6 500 400000
-
-write_data system_after_min.data
-
-# -- simulation protocol --
-
-reset_timestep 0
-timestep 1.0
-dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz element
-velocity all create 200.0 4928459 rot yes mom yes dist gaussian
-fix fxnpt all npt temp 200.0 200.0 100.0 iso 1.0 1.0 1000.0
-neigh_modify delay 5 every 1 check yes
-
-run 100000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.nvt b/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.nvt
deleted file mode 100644
index 115bfe527..000000000
--- a/tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.nvt
+++ /dev/null
@@ -1,39 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (Follow the instructions in README_setup.sh,
-# or run the file as a script using ./README_setup.sh)
-#
-# ------------------------------- Initialization Section --------------------
-
-include "system.in.init"
-
-# ------------------------------- Atom Definition Section -------------------
-
-#read_data "system.data"
-read_data "system_after_npt.data"
-
-# ------------------------------- Settings Section --------------------------
-
-include "system.in.settings"
-include "system.in.charges"
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- simulation protocol --
-
-reset_timestep 0
-timestep 2.0
-thermo 500
-thermo_style custom step temp etotal press
-dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz element type
-dump_modify 1 element "C" "C"
-velocity all create 200.0 4928459 rot yes mom yes dist gaussian
-fix fxnvt all nvt temp 200.0 200.0 100.0
-neigh_modify delay 5 every 1 check yes
-
-run 1000000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README.TXT b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README.TXT
deleted file mode 100644
index 115c1fab3..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README.TXT
+++ /dev/null
@@ -1,54 +0,0 @@
-NOTE: This example requires the "Al99.eam.alloy" file.
- (It was not included in this directory because if its large size.)
- As of 2012-11, I was able to obtain it here:
- http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
- Copy it to the directory containing this README file.
-------------------------------------------------------------------------
-This example shows an alternative way to setup the
-aluminum crystal loading simulation described here:
-http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression
-by Mark Tschopp and Nathan R. Rhodes
-For additional backgroumd information, please consult that web page.
-
-In this example, I use moltemplate to build a "DATA" file for this system.
-(I can't think of a compelling reason to do this for simple simulations like
-this. But this approach might be useful if you want to artificially create
-unusual structures out of aluminum crystals, or mix them with other molecules.
-I created this example in response to a user request.)
-
-
- --- To build the system ---
-
-Carry out the instructions in README_setup.sh,
-to generate the LAMMPS DATA file and input scripts you need:
-system.data, system.in.init, system.in.settings.
-(The run.in script contains references to these files.)
-
-
- --- To run LAMMPS, try a command like: ---
-
-lmp_mpi -i run.in
-
- or (if you have mpi installed)
-
-mpirun -np 4 lmp_mpi -i run.in
-
-This will create an ordinary LAMMPS dump file you can visualize with VMD
-traj.lammpstrj (See README_visualize.txt)
-
-It will also create a number of other files, such as:
-dump.comp_0.cfg
-dump.comp_500.cfg
-dump.comp_20000.cfg
-Al_comp_100.def1.txt
-
-The dump.comp_*.cfg files can be visualized using
-AtomEye if you have AtomEye and ImageJ installed.
-The procedure for doing this is explained in the original tutorial at:
-http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression
-
-The "Al_comp_100.def1.txt" file is a four-column text file containing:
-column 1: v_strain = (lx - v_L0)/v_L0
-column 2: -pxx/10000 (diagonal components of the stress tensor)
-column 3: -pyy/10000
-column 4: -pzz/10000
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README_setup.sh b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README_setup.sh
deleted file mode 100755
index 22eb8c435..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README_setup.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -atomstyle full system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # We will also need the "Al99.eam.alloy" file:
- #cp -f Al99.eam.alloy ../
- # This file was (can be) downloaded from:
- # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
-
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README_visualize.txt b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCell_LR.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCell_LR.jpg
deleted file mode 100644
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg
deleted file mode 100644
index 8650cf5cb..000000000
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg
deleted file mode 100644
index 582cf5fe6..000000000
Binary files a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/README.sh b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/README.sh
deleted file mode 100755
index 64f350f64..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/README.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-# This example shows an alternative way to setup the
-# aluminum crystal loading simulation described here:
-# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression
-# by Mark Tschopp and Nathan R. Rhodes
-# For additional backgroumd information, please consult that web page.
-#
-# In this example, I use moltemplate to build a "DATA" file for this system.
-# (I can't think of a compelling reason to do this for simple simulations like
-# this. But this approach might be useful if you want to artificially create
-# unusual structures out of aluminum crystals, or mix them with other molecules.
-# I created this example in response to a user request.)
-#
-# Use these commands to generate the LAMMPS input script and data file:
-
-moltemplate.sh system.lt
-
-# This will generate system.data, system.in.init, system.in.settings.
-# In addition to will need to download "Al99.eam.alloy" file.
-# (It was not included in this directory because if its large size.)
-# As of 2012-11, I was able to obtain it here:
-# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/al_cell.lt
deleted file mode 100644
index 3054a45e0..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/al_cell.lt
+++ /dev/null
@@ -1,64 +0,0 @@
-# "AlCell" defines the 4-atom FCC unit cell
-# of Aluminum (with a 4.05 angstrom spacing)
-
-AlCell {
-
- # AtomID MolID(IGNORE!) AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000
- $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025
- $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025
- $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000
- }
-
- write_once("In Init") {
- units metal
- atom_style full # <- Requires each atom has a MolID and Charge.
- # This is not necessary. (Why use "full"?
- # The "full" atom style is useful if you want to
- # mix the aluminum with other molecules later.
- # Otherwise, just use "atom_style atomic", and
- # and remove the 2nd and 4th columns above.)
- pair_style eam/alloy
- }
-
- write_once("In Settings") {
- pair_coeff * * Al99.eam.alloy Al
- }
-
- write_once("Data Masses") {
- @atom:Al 27.0
- }
-
-} # AlCell
-
-
-
-
-
-# Here is an alternate way to define AlCell
-# using "scale(4.05)" to select the lattice spacing:
-#
-#FccCell {
-# write("Data Atoms") {
-# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0
-# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5
-# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5
-# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0
-# }
-# write_once("Data Masses") {
-# @atom:Al 27.0
-# }
-# write_once("In Init") {
-# units metal
-# atom_style full
-# pair_style eam/alloy
-# }
-# write_once("In Settings") {
-# pair_coeff * * Al99.eam.alloy Al
-# }
-#}
-#
-#AlCell = FccCell.scale(4.05)
-#
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/system.lt
deleted file mode 100644
index f813c6f66..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/system.lt
+++ /dev/null
@@ -1,35 +0,0 @@
-
-import "al_cell.lt" # <- this defines the unit cell for aluminum
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 40.50 xlo xhi
- 0.0 40.50 ylo yhi
- 0.0 40.50 zlo zhi
-}
-
-# The next command generates an array of 10x10x10 AlCell unit cells with
-# spacing 4.05 Angstroms.
-
-unitcells = new AlCell [10].move(0.00, 0.00, 4.05)
- [10].move(0.00, 4.05, 0.00)
- [10].move(4.05, 0.00, 0.00)
-
-
-
-
-
-
-
-
-
-
-
-
-################################################################
-# The next command is not necessary:
-#
- create_var { $mol } # <-This forces all of the Al atoms in the crystal
-# # to share the same molecule ID number.
-# # Molecule ID numbers are not necessary. Ignore this.
-#
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/run.in b/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/run.in
deleted file mode 100644
index 677cc60ca..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/aluminum_crystal_strain/run.in
+++ /dev/null
@@ -1,76 +0,0 @@
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-#
-# The run-settings below were stolen from:
-#
-# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression
-
-
-compute csym all centro/atom fcc
-compute peratom all pe/atom
-
-# EQUILIBRATION
-reset_timestep 0
-timestep 0.001
-velocity all create 300 12345 mom yes rot no
-fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1
-
-# Set thermo output
-thermo 1000
-thermo_style custom step lx ly lz press pxx pyy pzz pe temp
-
-# Run for at least 10 picosecond (assuming 1 fs timestep)
-run 20000
-unfix 1
-
-# Store final cell length for strain calculations
-variable tmp equal "lx"
-variable L0 equal ${tmp}
-print "Initial Length, L0: ${L0}"
-
-######################################
-# DEFORMATION
-reset_timestep 0
-
-fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1
-variable srate equal 1.0e10
-variable srate1 equal "-v_srate / 1.0e12"
-fix 2 all deform 1 x erate ${srate1} units box remap x
-
-# Output strain and stress info to file
-# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
-# p2, p3, p4 are in GPa
-variable strain equal "(lx - v_L0)/v_L0"
-variable p1 equal "v_strain"
-variable p2 equal "-pxx/10000"
-variable p3 equal "-pyy/10000"
-variable p4 equal "-pzz/10000"
-fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Al_comp_100.def1.txt screen no
-
-# Use cfg for AtomEye
-dump dAtomEye all cfg 250 dump.comp_*.cfg id type xs ys zs c_csym c_peratom fx fy fz
-dump_modify dAtomEye element Al
-
-# For users without AtomEye (like me), I decided to create a regular dump file:
-dump dCoords all custom 250 traj.lammpstrj id type x y z ix iy iz
-
-# Display thermo
-thermo 1000
-thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press
-
-run 20000
-
-######################################
-# SIMULATION DONE
-print "All done"
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_run.sh b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_run.sh
deleted file mode 100755
index 4a1e13064..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_run.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-
-# to be followed by
-
-lmp_mpi -i run.in.nvt # simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation are ignored when beginning the simulation at constant volume.
-# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-# or
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_setup.sh b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_setup.sh
deleted file mode 100755
index 3a0821269..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -atomstyle full system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_visualize.txt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_visualize.txt
deleted file mode 100644
index 73358e55d..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 500 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg
deleted file mode 100644
index 2cdc08b31..000000000
Binary files a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/images/ice_rect8_unitcell.png b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/images/ice_rect8_unitcell.png
deleted file mode 100644
index 5bd6057e1..000000000
Binary files a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/images/ice_rect8_unitcell.png and /dev/null differ
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt
deleted file mode 100644
index 2b550b630..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt
+++ /dev/null
@@ -1,52 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-SPCE {
-
- write_once("In Init") {
- # -- Default styles (for solo "SPCE" water) --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- pair_modify mix arithmetic
- }
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
- $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 1000.0 1.0
- angle_coeff @angle:HOH harmonic 1000.0 109.47
- pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166
- pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058
- group spce type @atom:O @atom:H
- fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fSHAKE during minimization.)
- }
-
-} # end of definition of "SPCE" water molecule type
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect16.lt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect16.lt
deleted file mode 100644
index fb431cede..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect16.lt
+++ /dev/null
@@ -1,81 +0,0 @@
-# This ice (1h) unit cell is rectangular and contains 16 water molecules.
-# (Coordinates and cell dimensions converted were from a PDB file.)
-# The dimensions of the unit cell (in Angstroms) are: 9.043 7.832 7.361
-
-
-import "spce.lt" # <-- define the "SPCE" molecule
-
-SpceIceRect16 {
-
- # Create a 3-dimensional array of 16 water molecules
-
- wat = new SPCE[4][2][2]
-
- # Array indices will be correlated with position [xindex][yindex][zindex]
-
- # You can overwrite coordinates of atoms after they were created this way:
- # (Order is not important)
- # atom-ID molecule-ID atomType charge newX newY newZ
-
- write("Data Atoms") {
- $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
- $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970
- $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 3.545 1.970
- $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
- $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711
- $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.371 1.711
- $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300
- $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970
- $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 2.611 3.291
- $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381
- $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711
- $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 1.305 0.390
- $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
- $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711
- $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 5.221 0.390
- $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
- $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970
- $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291
- $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381
- $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711
- $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 4.287 1.711
- $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300
- $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970
- $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970
- $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
- $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391
- $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 2.611 4.070
- $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
- $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651
- $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.972
- $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061
- $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391
- $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 3.545 5.391
- $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981
- $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651
- $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 0.371 5.651
- $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
- $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651
- $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 4.287 5.651
- $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
- $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391
- $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391
- $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981
- $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651
- $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 5.221 6.972
- $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061
- $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391
- $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070
- }
-} # SpceIceRect16
-
-# Credit goes to Martin Chaplin.
-# These coordinates were orignally downloaded from Martin Chaplin's
-# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
-# ... and then they were stretched independently in the xy and z
-# directions in order to match the lattice parameters measured by
-# Rottger et al.,
-# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
-# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
-# I am using the lattice constants measured at temperature 265K
-# (and pressure=100Torr).
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect32.lt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect32.lt
deleted file mode 100644
index 7ddcb0adf..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect32.lt
+++ /dev/null
@@ -1,129 +0,0 @@
-# This ice (1h) unit cell is rectangular and contains 32 water molecules.
-# (Coordinates and cell dimensions converted were from a PDB file.)
-# The dimensions of the unit cell (in Angstroms) are: 9.043 15.663 7.361
-
-
-import "spce.lt" # <-- define the "SPCE" molecule
-
-SpceIceRect32 {
-
- # Create a 3-dimensional array of 32 water molecules
-
- wat = new SPCE[4][4][2]
-
- # Array indices will be correlated with position [xindex][yindex][zindex]
-
- # You can overwrite coordinates of atoms after they were created this way:
- # (Order is not important)
- # atom-ID molecule-ID atomType charge newX newY newZ
-
- write("Data Atoms") {
- $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
- $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970
- $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.291
- $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
- $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711
- $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 1.305 0.390
- $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300
- $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970
- $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 3.545 1.970
- $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381
- $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711
- $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 0.371 1.711
- $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
- $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711
- $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.287 1.711
- $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
- $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970
- $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291
- $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381
- $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711
- $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 5.221 0.390
- $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300
- $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970
- $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970
- $atom:wat[0][2][0]/O $mol:wat[0][2][0] @atom:SPCE/O -0.8476 1.131 10.443 2.300
- $atom:wat[0][2][0]/H1 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 0.322 9.976 1.970
- $atom:wat[0][2][0]/H2 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 1.131 11.377 1.970
- $atom:wat[1][2][0]/O $mol:wat[1][2][0] @atom:SPCE/O -0.8476 3.391 9.137 1.381
- $atom:wat[1][2][0]/H1 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 2.582 9.604 1.711
- $atom:wat[1][2][0]/H2 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 3.391 8.203 1.711
- $atom:wat[2][2][0]/O $mol:wat[2][2][0] @atom:SPCE/O -0.8476 5.652 10.443 2.300
- $atom:wat[2][2][0]/H1 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 4.843 9.976 1.970
- $atom:wat[2][2][0]/H2 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 5.652 10.443 3.291
- $atom:wat[3][2][0]/O $mol:wat[3][2][0] @atom:SPCE/O -0.8476 7.912 9.137 1.381
- $atom:wat[3][2][0]/H1 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.103 9.604 1.711
- $atom:wat[3][2][0]/H2 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.912 9.137 0.390
- $atom:wat[0][3][0]/O $mol:wat[0][3][0] @atom:SPCE/O -0.8476 1.131 13.053 1.381
- $atom:wat[0][3][0]/H1 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.940 13.520 1.711
- $atom:wat[0][3][0]/H2 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.131 13.053 0.390
- $atom:wat[1][3][0]/O $mol:wat[1][3][0] @atom:SPCE/O -0.8476 3.391 14.358 2.300
- $atom:wat[1][3][0]/H1 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 4.200 13.891 1.970
- $atom:wat[1][3][0]/H2 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 3.391 15.292 1.970
- $atom:wat[2][3][0]/O $mol:wat[2][3][0] @atom:SPCE/O -0.8476 5.652 13.053 1.381
- $atom:wat[2][3][0]/H1 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 6.461 13.520 1.711
- $atom:wat[2][3][0]/H2 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 5.652 12.119 1.711
- $atom:wat[3][3][0]/O $mol:wat[3][3][0] @atom:SPCE/O -0.8476 7.912 14.358 2.300
- $atom:wat[3][3][0]/H1 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 8.721 13.891 1.970
- $atom:wat[3][3][0]/H2 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 7.912 14.358 3.291
- $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
- $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391
- $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.545 5.391
- $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
- $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651
- $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 0.371 5.651
- $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061
- $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391
- $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 2.611 4.070
- $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981
- $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651
- $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 1.305 6.972
- $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
- $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651
- $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.972
- $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
- $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391
- $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391
- $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981
- $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651
- $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 4.287 5.651
- $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061
- $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391
- $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070
- $atom:wat[0][2][1]/O $mol:wat[0][2][1] @atom:SPCE/O -0.8476 1.131 10.443 5.061
- $atom:wat[0][2][1]/H1 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.940 9.976 5.391
- $atom:wat[0][2][1]/H2 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.131 10.443 4.070
- $atom:wat[1][2][1]/O $mol:wat[1][2][1] @atom:SPCE/O -0.8476 3.391 9.137 5.981
- $atom:wat[1][2][1]/H1 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 4.200 9.604 5.651
- $atom:wat[1][2][1]/H2 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 3.391 9.137 6.972
- $atom:wat[2][2][1]/O $mol:wat[2][2][1] @atom:SPCE/O -0.8476 5.652 10.443 5.061
- $atom:wat[2][2][1]/H1 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 6.461 9.976 5.391
- $atom:wat[2][2][1]/H2 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 5.652 11.377 5.391
- $atom:wat[3][2][1]/O $mol:wat[3][2][1] @atom:SPCE/O -0.8476 7.912 9.137 5.981
- $atom:wat[3][2][1]/H1 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 8.721 9.604 5.651
- $atom:wat[3][2][1]/H2 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 7.912 8.203 5.651
- $atom:wat[0][3][1]/O $mol:wat[0][3][1] @atom:SPCE/O -0.8476 1.131 13.053 5.981
- $atom:wat[0][3][1]/H1 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 0.322 13.520 5.651
- $atom:wat[0][3][1]/H2 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 1.131 12.119 5.651
- $atom:wat[1][3][1]/O $mol:wat[1][3][1] @atom:SPCE/O -0.8476 3.391 14.358 5.061
- $atom:wat[1][3][1]/H1 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 2.582 13.891 5.391
- $atom:wat[1][3][1]/H2 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 3.391 14.358 4.070
- $atom:wat[2][3][1]/O $mol:wat[2][3][1] @atom:SPCE/O -0.8476 5.652 13.053 5.981
- $atom:wat[2][3][1]/H1 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 4.843 13.520 5.651
- $atom:wat[2][3][1]/H2 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 5.652 13.053 6.972
- $atom:wat[3][3][1]/O $mol:wat[3][3][1] @atom:SPCE/O -0.8476 7.912 14.358 5.061
- $atom:wat[3][3][1]/H1 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.103 13.891 5.391
- $atom:wat[3][3][1]/H2 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.912 15.292 5.391
- }
-} # SpceIceRect32
-
-# Credit goes to Martin Chaplin.
-# These coordinates were orignally downloaded from Martin Chaplin's
-# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
-# ... and then they were stretched independently in the xy and z
-# directions in order to match the lattice parameters measured by
-# Rottger et al.,
-# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
-# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
-# I am using the lattice constants measured at temperature 265K
-# (and pressure=100Torr).
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect8.lt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect8.lt
deleted file mode 100644
index 2d716540a..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect8.lt
+++ /dev/null
@@ -1,57 +0,0 @@
-# This ice (1h) unit cell is rectangular and contains 8 water molecules.
-# (Coordinates and cell dimensions converted were from a PDB file.)
-# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362
-
-
-import "spce.lt" # <-- define the "SPCE" molecule
-
-SpceIceRect8 {
-
- # Create a 3-dimensional array of 8 water molecules
-
- wat = new SPCE[2][2][2]
-
- # Array indices will be correlated with position [xindex][yindex][zindex]
-
- # You can overwrite coordinates of atoms after they were created this way:
- # (Order is not important)
- # atom-ID molecule-ID atomType charge newX newY newZ
-
- write("Data Atoms") {
- $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
- $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289
- $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971
- $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
- $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710
- $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710
- $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
- $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710
- $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710
- $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
- $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289
- $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971
- $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
- $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391
- $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391
- $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
- $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970
- $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652
- $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
- $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970
- $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652
- $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
- $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391
- $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391
- }
-} # SpceIceRect8
-
-# Credit goes to Martin Chaplin.
-# These coordinates were orignally downloaded from Martin Chaplin's
-# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
-# ... and then they were stretched independently in the xy and z
-# directions in order to match the lattice parameters measured by
-# Rottger et al.,
-# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
-# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
-# I am using the lattice constants measured at temperature 265K
-# (and pressure=100Torr).
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/system.lt
deleted file mode 100644
index b4f22f9dc..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/moltemplate_files/system.lt
+++ /dev/null
@@ -1,11 +0,0 @@
-import "spce_ice_rect8.lt"
-
-cells = new SpceIceRect8 [3].move(4.521, 0.0, 0.0)
- [2].move( 0.0, 7.832, 0.0)
- [2].move( 0.0, 0.0, 7.362)
-
-write_once("Data Boundary") {
- 0 13.563 xlo xhi
- 0 15.664 ylo yhi
- 0 14.724 zlo zhi
-}
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/run.in.npt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/run.in.npt
deleted file mode 100644
index c10893b41..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/run.in.npt
+++ /dev/null
@@ -1,48 +0,0 @@
-# You can run LAMMPS this way
-# lmp_linux -i run.in.npt
-# (Assuming your LAMMPS binary is named "lmp_linux")
-#
-# PREREQUISITES:
-# You will need these files (created by moltemplate.sh):
-# system.data, system.in.init, system.in.settings
-# (See README_setup.sh for details)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# fSHAKE was defined in system.in.settings. It is incompatible with "minimize".
-unfix fSHAKE
-minimize 1.0e-5 1.0e-7 100000 400000
-# Now read "system.in.settings" in order to redefine fSHAKE again:
-include system.in.settings
-
-# -- simulation protocol --
-
-
-timestep 2.0
-dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 400.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-
-thermo 100
-
-#restart 10000 restart_npt
-
-run 20000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/run.in.nvt b/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/run.in.nvt
deleted file mode 100644
index 1815e1da7..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/ice_crystal/run.in.nvt
+++ /dev/null
@@ -1,45 +0,0 @@
-# You can run LAMMPS this way
-# lmp_linux -i run.in.nvt
-# (Assuming your LAMMPS binary is named "lmp_linux")
-#
-# PREREQUISITES:
-# You will need these files (created by moltemplate.sh):
-# system.in.init, system.in.settings (See README_setup.sh)
-# You will also need this file: system_after_npt.data
-# This file is created by running LAMMPS on the run.in.npt file.
-#
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates after pressure equilibration
-read_data system_after_npt.data
-
-# (Or, if you prefer, you can read the original coordinates using
-# read_data system.data)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-timestep 2.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-
-
-thermo 500
-
-
-#restart 10000 restart_nvt
-
-
-run 50000
-
-write_data system_after_nvt.data
-
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README.TXT b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README.TXT
deleted file mode 100644
index 83b4ad80b..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README.TXT
+++ /dev/null
@@ -1,51 +0,0 @@
-This is a small version of a carbon-nanotube, water capillary system.
-It was inspired by this paper:
-
- Laurent Joly, J. Chem. Phys. 135(21):214705 (2011)
-
--------- Requirements: -------
-To run this system at constant pressure, it might help to compile LAMMPS
-with the optional RIGID package, and use "fix rigid" on the carbon.
-(The use of fix rigid is controversial.) Running at NVT does not require this.
-------------------------------
-
-Note: To investigate the behavior from that paper, it might be a good
- idea to increase the size of the water reservoir, the spacing between
- the walls, and the size of the system in the X and Y directions.
-
-Note: Explicit carbon-carbon bonds:
- In the graphene and nanotube structures, I did not try to connect the
- carbon atoms together with bonds. Instead we will hold these structures
- rigid by not integrating their equations of motion.
- (If you want to simulate movement of the carbon atoms at high
- temperatures or tension, LAMMPS has 3-body/many-body LAMMPS force-fields
- available for simulating the behaviour of carbon in graphite. I know
- that you don't need to specify bonds to use these force fields. I do
- not know know if these force fields work for nanotubes or graphene.)
-
-Note: Other modeling tools:
- If you need explicit bonds between carbon atoms, then you must add them
- yourself or use a different tool. Currently (2012-10-20), moltemplate does
- not generate bonds automatically. The "Nanotube Builder" and "topotools"
- plugins for for VMD can generate a nanotube with bonds in LAMMPS data
- format. You can then convert this data file to .LT format using the
- ltemplify.py utility and then import it into another .LT file and play
- with it later. (In the "cnad-cnt" example, the carbon nanotube was built
- using "Nanotube Builder" and topotools, and processed with ltemplify.py)
-
-
-# WARNING: THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION.
-# A real junction would be curved and deformed near the boundary,
-# (not 90 degrees) and it would not be built entirely from hexagons.
-# (This is not a problem in this example because the carbon atoms
-# are immobilized.) If you want to simulate the behavior of
-# real graphene or nanotube junctions, you must be more careful.
-# To solve this problem:
-# Moltemplate allows you to move, customize or delete individual
-# atoms near the boundary. You can move atoms by overwriting their
-# coordinates using additional write("Data Atoms") statements (after
-# the walls and tube are created). You can also change their charge.
-# Alternately, you could start with the structure provided here, and
-# relax/minimize the coordinates of the carbon atoms using LAMMPS
-# before using it in other simulations.
-# Or you could do both (customization & minimization).
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_realistic_junctions.txt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_realistic_junctions.txt
deleted file mode 100644
index 432a7b7ad..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_realistic_junctions.txt
+++ /dev/null
@@ -1,22 +0,0 @@
- WARNING: A reader has emailed me to point out:
-
- THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION.
- A real junction would likely be curved near the boundary,
- not a 90 degree junction. (Although both graphene and nanotubes
- consist of hexagons of carbon atoms, you would need 6 heptagons
- near the junction between the nanotube and the graphene
- to account for the negative Gaussian curvature there).
-
- To solve this problem:
- Moltemplate allows you to move, add, customize or delete individual
- atoms near the boundary. You can move atoms by overwriting their
- coordinates using additional write("Data Atoms") statements (after
- the walls and tube are created). You can also adjust their partial charge.
-
- Alternately, you could start with the structure provided here, add or delete
- atoms if necessary, and relax/minimize the coordinates of the carbon
- atoms using LAMMPS. You could also run a high temperature annealing
- simulation to relax their positions. If it helps, the AIREBO
- force-field has used in LAMMPS to simulate carbon nanotubes breaking:
- http://scitation.aip.org/content/aip/journal/jcp/134/20/10.1063/1.3594197
- http://lammps.sandia.gov/pictures.html#cnt
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_run.sh b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_run.sh
deleted file mode 100755
index ee5e5665a..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_run.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
- # (WARNING: The "run.in.npt" example has not been
- # rigorously tested and may fail.)
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_setup.sh b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_setup.sh
deleted file mode 100755
index acc5fbbaa..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_visualize.txt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_visualize.txt
deleted file mode 100644
index 206db9903..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_visualize.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- To shift the box by a fraction in the x direction (for example)
- do this:
-
- pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 }
- pbc box -shiftcenterrel {-0.50 -0.52 0.0 }
-
- # Alternately if you have a solute whose atoms are all of type 1,
- # then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/images/graphene_unit_cell.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/images/graphene_unit_cell.jpg
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh
deleted file mode 100755
index 1cc480669..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-# This is a small version of a carbon-nanotube, water capillary system.
-# It was inspired by this paper:
-#
-# Laurent Joly, J. Chem. Phys. 135(21):214705 (2011)
-#
-# Note: To investigate the behavior from that paper, you would have to increase
-# the spacing between the two graphene sheets to prevent the water from
-# making contact with the lower graphene wall.
-#
-# Requirements: 1) Set your $MOLTEMPLATE_PATH variable
-# 2) The "RIGID" LAMMPS package may be needed later
-# To run this system at constant pressure, it might help to compile LAMMPS with
-# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.)
-#
-# Also, if you have not yet done this set your MOLTEMPLATE_PATH environment
-# variable to access it. (See installation instructions.)
-# Most likely some of the files in this example (like graphene.lt, tip3p2004.lt)
-# are not in this directory, but are in the "src/moltemplate_force_fields/"
-# subdirectory.
-#
-# -----------------------------------------------------------
-#
-# To run moltemplate, use:
-
-moltemplate.sh system.lt
-
-# If you have VMD installed, you can run it this way to visualize the system:
-#
-# moltemplate.sh -vmd system.lt
-#
-# Either way, this will generate the following files (which LAMMPS reads):
-# system.data, system.in, system.in.init, system.in.settings
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt
deleted file mode 100644
index c54a380f6..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt
+++ /dev/null
@@ -1,55 +0,0 @@
-# The minimal unit cell for graphine contains only 2 atoms:
-# (which I arbitrarily named "C1" and "C2")
-
-Graphene {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0000
- $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0000
- }
-
- # Now define the "C" atom type
- write_once("Data Masses") {
- @atom:C 12.0
- }
- write_once("In Settings") {
- # i j epsilon sigma
- pair_coeff @atom:C @atom:C lj/cut/coul/long 0.068443 3.407
-
- # These Lennard-Jones parameters come from
- # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
- # Chem Phys Lett, 348:187 (2001)
-
- # Define a group consisting of only carbon atoms in graphene molecules
- group Cgraphene type @atom:C
- }
- write_once("In Init") {
- # -- Default styles (used in this file for graphene carbon) --
- units real
- atom_style full #(full enables you to to add other molecules later)
- pair_style hybrid lj/cut/coul/long 10.0
- }
-} # Graphene
-
-
-
-
-# This is a 2-dimensional hexagonal unit cell. The unit vectors are:
-#
-# (2.4595121467478, 0, 0)
-# (1.2297560733739, 2.13, 0)
-#
-# You can create a sheet of single-layer graphene this way:
-#
-# small_crystal = new Graphene [3].move(2.45951214, 0, 0)
-# [3].move(1.229756, 2.13, 0)
-#
-# For thicker sheets, follow the instructions in the "graphite.lt" file.
-#
-# Note: The length of each carbon-carbon bond is currently 1.42 Angstroms.
-# To increase it to 1.422 Angstroms, uncomment the following line:
-#
-# Graphene.scale(1.0014084507042254) # 1.0014084507042254 = 1.422 / 1.42
-#
-# You will have to change the unit cell lattice vectors (see above) accordingly
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt
deleted file mode 100644
index 888b9cce8..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt
+++ /dev/null
@@ -1,57 +0,0 @@
-
-import "graphene.lt"
-
-# -------------- graphene sheet -----------------
-
-# Notes:
-# Hexagonal lattice with:
-# d = length of each hexagonal side = 1.42 Angstroms
-# L = length of each hexagon = 2*d = 2.84 Angstroms
-# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478 Angstroms
-# w = width of hexagon rows = 1.5*d = 2.13 Angstroms
-
-Wall {
- unitcells = new Graphene [14].move(1.2297560733739, 2.13, 0)
- [13].move(2.4595121467478, 0, 0)
-
- unitcells[*][*].move(-24.595121467478, -14.91, 0.000)
-
- # Now cut a hole in the graphene sheet roughly where the nanotube is located
- delete unitcells[5][7-8] # delete 2 unit cells (2 atoms each, 4 atoms total)
- delete unitcells[6][6-8] # delete 3 unit cells (2 atoms each, 6 atoms total)
- delete unitcells[7][5-8] # delete 4 unit cells (2 atoms each, 8 atoms total)
- delete unitcells[8][5-7] # delete 3 unit cells (2 atoms each, 6 atoms total)
- delete unitcells[9][5-6] # delete 2 unit cells (2 atoms each, 4 atoms total)
- # Optional fine tuning: delete a few additional atoms around the edges
- delete unitcells[5][6]/C2 # delete a single atom
- delete unitcells[6][5]/C2 # delete a single atom
- delete unitcells[6][9]/C1 # delete a single atom
- delete unitcells[8][4]/C2 # delete a single atom
- delete unitcells[8][8]/C1 # delete a single atom
- delete unitcells[9][7]/C1 # delete a single atom
-}
-
-# Make two copies of the wall, and place them on either end of the nanotube
-
-wall1 = new Wall.move(0, 0, 32.0)
-wall2 = new Wall.move(0, 0, 58.26)
-
-# WARNING: A reader has pointed out :
-# THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION.
-# A real junction would likely be curved near the boundary,
-# not a 90 degree junction. (Although both graphene and nanotubes
-# consist of hexagons of carbon atoms, you would need 6 heptagons
-# near the junction between the nanotube and the graphene
-# to account for the negative Gaussian curvature there).
-# To solve this problem:
-# Moltemplate allows you to move, add, customize or delete individual
-# atoms near the boundary. You can move atoms by overwriting their
-# coordinates using additional write("Data Atoms") statements (after
-# the walls and tube are created). You can also adjust their partial charge.
-# Alternately, you could start with the structure provided here, add or delete
-# atoms if necessary, and relax/minimize the coordinates of the carbon
-# atoms using LAMMPS. You could also run a high temperature annealing
-# simulation to relax their positions. If it helps, the AIREBO
-# force-field has used in LAMMPS to simulate carbon nanotubes breaking:
-# http://scitation.aip.org/content/aip/journal/jcp/134/20/10.1063/1.3594197
-# http://lammps.sandia.gov/pictures.html#cnt
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt
deleted file mode 100644
index 49fb49fb0..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt
+++ /dev/null
@@ -1,61 +0,0 @@
-import "graphene.lt" # defines "Graphene"
-
-
-# ------------ Graphite -----------
-#
-# Note: For graphite: sheets stacked in the Z direction are separated by a
-# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction
-# by a distance of d (1.42 Angstroms). To add additional graphene layers
-# you could use:
-# sheet2 = new Graphene [10].move(2.4595121467478,0,0)
-# [10].move(1.2297560733739,2.13,0)
-# sheet2[*][*].move(0, 1.42, 3.35)
-# sheet3 = new Graphene [10].move(2.4595121467478,0,0)
-# [10].move(1.2297560733739,2.13,0)
-# sheet3[*][*].move(0, -1.42, 6.70)
-# etc...
-#
-# This should work fine.
-# However, to build a thick sheet of graphite, it may be less trouble
-# to use a 4-atom unit cell which includes two graphene layers.
-# Here is one way to do that:
-
-Graphite inherits Graphene {
-
- # This allows us to access access the "@atom:C" carbon atom type
- # whose properties are defined in the "Graphene" object (see "graphene.lt").
- # That atom is NOT globally defined. It belongs to the "Graphene" object.
- # This is one way to access it. Alternately, you could redefine it here
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0
- $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0
- $atom:C3 $mol:... @atom:C 0.0 -0.61487803668695 1.065 3.35
- $atom:C4 $mol:... @atom:C 0.0 0.61487803668695 1.775 3.35
- }
-
- # Note: The first two lines in the "Data Atoms" section override the positions
- # of the $atom:C1 and $atom:C2 atoms previously defined in "Graphene"
- # (which this object inherits). This is okay.
-
-} # Graphite
-
-
-
-
-
-
-# This is a 3-dimensional hexagonal unit cell. The unit vectors are:
-#
-# (2.4595121467478, 0, 0 )
-# (1.2297560733739, 2.13, 0 )
-# ( 0, 0, 6.70)
-
-# Then you could create a thick sheet of graphite this way:
-#
-# graphite = new Graphite [10].move(2.4595121467478,0,0)
-# [10].move(1.2297560733739,2.13,0)
-# [5].move(0,0,6.70)
-#
-# (Your graphite slab will contain an even number of graphene sheets.)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt
deleted file mode 100644
index 06a5e9433..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt
+++ /dev/null
@@ -1,101 +0,0 @@
-import "graphene.lt"
-
-# The "Graphene" unit cell defined in "graphene.lt" lies in the XY plane.
-# In the next line, we will create a new version of the graphene unit cell
-# which lies in the XZ plane, by rotating Graphene 90 degrees around the X axis:
-
-GrapheneXZ = Graphene.rot(90,1,0,0)
-
-# ------------------ nanotube ---------------
-
-# Now use this to build a simple ("zigzag") nanotube where the long-axis of each
-# hexagon is aligned with the tube axis (along the Z direction). If the
-# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of
-# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon
-# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms
-# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms.
-
-
-
-nanotube = new GrapheneXZ.move(0, 5.457193512764, 0) # 5.45 = R
- [14].rot(25.7142857,0,0,1) #25.7=360/14
- [12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14
- #2.13= d*1.5
-
-
- # Note: The length is 12 hexegons, the circumference is
- # 14 hexegons (~=25.56 and 34.43 Angstroms, respectively).
-
-
-# Move all of the unit-cells in the nanotube between the two graphene sheets.
-
-nanotube[*][*].move(0, 0, 33.42)
-
-
-
-
-
-# ---------- BUILDING CHIRAL NANOTUBES USING EXTERNAL SOFTWARE -------------
-#
-# The approach shown here works well for "zig-zag" nanotubes.
-# Nanotubes with other chiralities are more difficult to make this way
-# (because the tube axis is no longer perpendicular to graphene basis vectors).
-# For those nanotubes, I recommend using an external program to generate
-# a LAMMPS data file for the nanotube. If you want to combine the tube
-# with other molecules created by moltemplate, you can then import it into
-# moltemplate as a molecule object using the "ltemplify.py" utility. Details:
-#
-# --- VMD plugins (by Axel Kohlmeyer and Robert R. Johnson) ---
-#
-# The nanotube-builder for VMD can generate nanotubes (with smooth tips)
-# for any chirality. These tubes also have explicit bonds between carbons:
-# http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
-#
-# The resulting nanotube can be converted to a data file using topotools:
-# https://sites.google.com/site/akohlmey/software/topotools
-# To do that, select the "Extensions"->"Tk Console" menu and enter
-#
-# topo writelammpsdata nanotube.data full
-#
-# --- ltemplify.py ---
-#
-# That data file can be converted to moltemplate format (an .LT file)
-# using the "ltemplify.py" utility.
-#
-# The first step is to create a short input script containing the atom_style
-# command (ltemplify.py will read this script. Presumably atom_style is "full").
-#
-# echo "atom_style full" > nanotube.in
-#
-# Then run ltemplify to convert nanotube.data into a moltemplate file:
-# ltemplify.py -name Nanotube nanotube.in nanotube.data > nanotube.lt
-#
-# You will need to edit the "nanotube.lt" file to replace all of the
-# "@atom:type1" atoms types file to match the carbon atom types in the other lt
-# files (ie "@atom:../C"). If you don't plan on defining bonded interactions
-# between carbon atoms, then be sure to remove the write("Data Bonds") section
-# of the "nanotube.lt" file (if it is present).
-#
-# Finally make sure the "system.lt" contains these lines:
-#
-# import "nanotube.lt"
-# nanotube = new Nanotube.move(?,?,?)
-#
-# (Replace ?,?,? with the location where you want the nanotube to go.
-# You can also rotate it using .rot(angle,axisx,axisy,axiz).)
-#
-# ... and then run moltemplate the normal way
-#
-# Let me know if you run into trouble with this approach,
-# and I will make note of that in this file.
-#
-# --- links ---
-# Note: there are numerous programs for specifying the coordinates
-# of the atoms in a nanotube, some of which are below.
-# http://www.nanotube.msu.edu/tubeASP/
-# http://turin.nss.udel.edu/research/tubegenonline.html
-# http://www.ugr.es/~gmdm/java/contub/contub.html
-# (You can load coordinates into moltemplate using the "-xyz" or "-pdb"
-# arguments. However currently (2013-12-01), the file must contain coordinates
-# for all of the atoms in your sytem, not just the nanotube.)
-# -------------------------------------------------------------------------
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt
deleted file mode 100644
index e1bf2390a..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt
+++ /dev/null
@@ -1,52 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-SPCE {
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
- $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 600.0 1.0
- angle_coeff @angle:HOH harmonic 75.0 109.47
- pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166
- pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058
- group spce type @atom:O @atom:H
- fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeSPCE during minimization.)
- }
-
- write_once("In Init") {
- # -- Default styles (for solo "SPCE" water) --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/cut/coul/long 9.0
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED!
- }
-
-} # end of definition of "SPCE" water molecule type
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt
deleted file mode 100644
index d7c610fc0..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt
+++ /dev/null
@@ -1,29 +0,0 @@
-# This is a small version of a carbon-nanotube, water capillary system. It was
-# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011)
-
-import "graphene_walls.lt"
-
-import "nanotube.lt"
-
-import "water_box.lt"
-
-
-# ------------ boundary conditions ------------
-
-write_once("Data Boundary") {
- -15.98682895386 15.98682895386 xlo xhi
- -14.91 14.91 ylo yhi
- -31.0 31.00 zlo zhi
-}
-
-# ---------------------------------------------
-
-write_once("In Settings") {
- # --- We must eventually specify the interactions between the atoms ---
- # --- in different molecule types (graphene-water interactions). ---
- # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details
-
- pair_coeff @atom:Graphene/C @atom:SPCE/O lj/cut/coul/long 0.114 3.28
- pair_coeff @atom:Graphene/C @atom:SPCE/H lj/cut/coul/long 0.0 3.28
-}
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt
deleted file mode 100644
index c825276f5..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt
+++ /dev/null
@@ -1,20 +0,0 @@
-import "spce.lt"
-
-# --------------- water ------------------
-
-# Create a rhombohedral box of water. (A rectangular box works also.)
-
-wat = new SPCE [9].move(3.5526287, 0, 0 )
- [9].move(1.77631435, 3.3133, 0 )
- [6].move( 0, 0, 3.45)
-
-# Optional: Center the water box at the origin. (Not really necessary.)
-
-wat[*][*][*].move(-23.9802437, -14.90985, 11.47)
-
-# --------------- Note: -----------------
-# The spacing between water molecules does not matter much as long as it is
-# reasonable. (I adjusted the spacing try to insure that the waters are spread
-# uniformly throughout the box. We do not want bubles to form if there are
-# gaps near the XY periodic boundaries.) We will have to equilibrate it later.
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt
deleted file mode 100644
index c7aaecebb..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt
+++ /dev/null
@@ -1,54 +0,0 @@
-# This file stores LAMMPS data for the "mW" water model.
-# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016)
-#
-# In this model, each water molecule is represented by a single "mW" particle.
-# These particles interact with their neighbors via 3-body Stillinger-Weber
-# forces whose parameters are tuned to mimic directional hydrogen-bonding
-# in liquid water (as well as hexagonal ice, type II ice, and
-# low-density super-cooled liquid/amorphous water phases).
-
-WatMW {
- write("Data Atoms") {
- $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:mW 18.02
- }
-
- write_once("system.in.sw") {
- mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0
- }
-
- write_once("In Init") {
- # -- Default styles for "WatMW" --
- units real
- pair_style sw
- }
-
- write_once("In Settings") {
- # --Now indicate which atom type(s) are simulated using the "sw" pair style
- # -- In this case only one of the atom types is used (the mW water "atom").
-
- pair_coeff * * sw system.in.sw mW NULL NULL NULL
-
- # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
- # -- the atoms are identified by order in the list, not by name. (The "mW"
- # -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
- # -- This command says that the first atom type corresponds to the "mW"
- # -- atom in system.in.sw, and to ignore the remaining three atom types
- # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
- # -- We don't want to use the "sw" force field for interactions involving
- # -- these atom types, so we put "NULL" there.)
- # -- Note: For this to work, you should probably run moltemplate this way:
- # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
- # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom)
- }
-
- # -- optional --
-
- write_once("In Settings") {
- group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group)
- }
-
-} # WatMW
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.npt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.npt
deleted file mode 100644
index 2728a1f5a..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.npt
+++ /dev/null
@@ -1,147 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (You do not need to run LAMMPS to equilibrate the system before
-# using this file.)
-#
-# Requirements:
-# To run this system at constant pressure, it might help to compile LAMMPS with
-# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.)
-# The use of fix rigid is controversial. This method is demonstrated below.
-# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. This simulation may fail.
-# (However the "run.in.nvt" example in this directory should work.)
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# Use "neigh_modify" to turn off calculation of interactions between immobilized
-# atoms. (Note: group "cGraphene" was defined in the file "system.insettings")
-neigh_modify exclude group Cgraphene Cgraphene
-
-# ------------------------------- Run Section -------------------------------
-
-
-# Only the Cgraphene atoms are immobile.
-group mobile subtract all Cgraphene
-
-# (Note: The "Cgraphene" group was defined in system.in.settings.)
-
-
-# Unfortunately you can not use the LAMMPS "minimize" command on this system
-# because there is no way to immobilize the carbon graphene & nanotube atoms
-# during minimization. Instead, we can use langevin dynamics with a fast
-# damping parameter and a small timestep.
-
-print "--------- beginning minimization (using fix langevin) ---------"
-
-timestep 0.1
-fix fxlan mobile langevin 1.0 1.0 100.0 48279
-fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation)
-thermo 100
-run 2500
-
-unfix fxlan
-unfix fxnve
-
-# -- simulation protocol --
-
-print "--------- beginning simulation (using fix nvt) ---------"
-
-dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
-thermo 200 # time interval for printing out "thermo" data
-
-
-
-
-
-# ------------------------- NPT ---------------------------
-
-
-# ------ QUESTIONABLE (see below): ------
-
-fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off
-
-# Comment:
-# The use of "fix rigid" to immobilize an object is somewhat controversial.
-# Feel free to omit it.
-# (Neither Trung or Steve Plimpton use fix rigid for immobilizing
-# molecules, but I noticed that at NPT, it does a better job of maintaining
-# the correct volume. However "fix rigid" has changed since then (2011),
-# so this may no longer be true. Please use this example with caution.)
-
-
-
-# Thermostat+Barostat
-# Set temp=300K, pressure=200bar, and equilibrate volume only in the z direction
-
-fix fxMoveStuff mobile npt temp 300 300 100 z 200 200 1000.0 dilate mobile drag 2.0
-
-# ----------------------------------------
-
-# The next two lines recalculate the temperature using
-# only the mobile degrees of freedom (ie. water atom velocities):
-
-compute tempMobile mobile temp
-compute pressMobile all pressure tempMobile
-
-thermo_style custom step c_tempMobile c_pressMobile temp press vol
-
-fix_modify fxMoveStuff temp tempMobile
-
-reset_timestep 0
-
-timestep 0.25
-
-run 100000
-
-timestep 0.5
-
-run 200000
-
-# Hopefully the barostat is no longer oscillating. Increase the timestep and
-# also get get rid of "drag 2.0". (A non-zero drag parameter will result in
-# unrealistic fluctuations of volume under NPT conditions.)
-# drag 2.0 <-- commenting out
-#
-# Set temp=300K, pressure=0bar, and equilibrate volume only in the z direction
-unfix fxMoveStuff
-fix fxMoveStuff mobile npt temp 300 300 100 z 0 0 1000.0 dilate mobile
-fix_modify fxMoveStuff temp tempMobile
-
-timestep 0.5
-
-run 1000000
-
-write_data system_after_npt.data
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also.)
-
-
-
-
-
-
-
-# ----- Comment: Avoid using fix rigid/npt on large single rigid objects -----
-#
-# Use of the following is not recommended:
-#
-# fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 200 200 1000.0 force * off off off torque * off off off dilate mobile
-# (temp=300K, pressure=200bar, and equilibrate volume only in the z direction)
-#
-# In my experience, the system becomes unstable when applying "fix rigid/npt"
-# to the immobile atoms, while also applying "fix npt" on the solvent atoms.
-# (It is probably a bad idea to use two barostats simultaneously.)
-# ----------------------------------------------------------------------------
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.nvt b/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.nvt
deleted file mode 100644
index 86253c45b..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.nvt
+++ /dev/null
@@ -1,78 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (You do not need to run LAMMPS to equilibrate the system before
-# using this file.)
-
-# ----------------------------- Initialization Section --------------------
-
-include system.in.init
-
-
-# ----------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-
-# ----------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# Use "neigh_modify" to turn off calculation of interactions between immobilized
-# atoms. (Note: group "cGraphene" was defined in the file "system.insettings")
-neigh_modify exclude group Cgraphene Cgraphene
-
-# ----------------------------- Run Section -------------------------------
-
-
-
-# Only the Cgraphene atoms are immobile.
-group mobile subtract all Cgraphene
-
-# (Note: The "Cgraphene" group was defined in system.in.settings.)
-
-
-
-# -- minimization protocol --
-
-# Unfortunately you can not use the LAMMPS "minimize" command on this system
-# because there is no way to immobilize the carbon graphene & nanotube atoms
-# during minimization. Instead, we can use langevin dynamics with a fast
-# damping parameter and a small timestep.
-
-print "--------- beginning minimization (using fix langevin) ---------"
-
-timestep 0.1
-fix fxlan mobile langevin 1.0 1.0 100.0 48279
-fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation)
-thermo 100
-run 2500
-
-unfix fxlan
-unfix fxnve
-
-# -- simulation protocol --
-
-print "--------- beginning simulation (using fix nvt) ---------"
-
-dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
-
-thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed
-thermo 500 # time interval for printing out "thermo" data
-
-# Integrate the equations of motion:
-fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0
-
-# The next two lines recalculate the temperature
-# using only the mobile degrees of freedom:
-
-compute tempMobile mobile temp
-fix_modify fxMoveStuff temp tempMobile
-
-
-timestep 2.0
-run 5000000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh
deleted file mode 100755
index 70c34bd6f..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# --- Running LAMMPS ---
-# -- Prerequisites: --
-# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
-# input scripts which link to the input scripts and data files
-# you hopefully have created earlier with moltemplate.sh:
-# system.in.init, system.in.settings, system.data
-# If not, carry out the instructions in "README_setup.sh".
-#
-# -- Instructions: --
-# If "lmp_mpi" is the name of the command you use to invoke lammps,
-# then you would run lammps on these files this way:
-
-
-lmp_mpi -i run.in.npt # minimization and simulation at constant pressure
-
-# or
-
-lmp_mpi -i run.in.nvt # minimization and simulation at constant volume
-
-#(Note: The constant volume simulation lacks pressure equilibration. These are
-# completely separate simulations. The results of the constant pressure
-# simulation are ignored when beginning the simulation at constant volume.
-# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
-
-
-
-
-
-# If you have compiled the MPI version of lammps, you can run lammps in parallel
-#mpirun -np 4 lmp_mpi -i run.in.npt
-# or
-#mpirun -np 4 lmp_mpi -i run.in.nvt
-# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh
deleted file mode 100755
index 3a0821269..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -atomstyle full system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Cl.jpg
deleted file mode 100644
index 5261bedc2..000000000
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deleted file mode 100644
index 78c4056f8..000000000
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/wat.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/wat.jpg
deleted file mode 100644
index 60aaf90b9..000000000
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
deleted file mode 100644
index 2c34754c4..000000000
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg
deleted file mode 100644
index 220a71727..000000000
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diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt
deleted file mode 100644
index 8d3634125..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt
+++ /dev/null
@@ -1,67 +0,0 @@
-# We define two molecule classes to represent Na+ and Cl- ions, respectively.
-# This may seem like overkill since they both only consist of one atom each.
-
-
-# Note: Monovalent ion parameters for Ewald and SPC/E water
-# are from: Joung & Cheatham JPCB (2008)
-# These Lennard Jones parameters match the parameters for ions
-# in SPC/E water in the "frcmod.ionsjc_spce" file distributed
-# with Amber (the 2010 version).
-
-
-NaIon {
-
- # The epsilong & sigma parameters from that paper were 0.3526418 & 1.212.
- # However sigma must be divided by 2^(1/6), because they use the alternate
- # Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and
- # pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6)
- # (Note: This change does not effect the epsilon parameter.)
-
- write_once("In Settings") {
- pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.079769246386
- }
-
- write_once("Data Masses") {
- @atom:Na 22.9898
- }
-
- # assumes "full" atom style
- write("Data Atoms") {
- $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000
- }
-} # NaIon
-
-
-ClIon {
- write_once("In Settings") {
- pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711
- }
-
- write_once("Data Masses") {
- @atom:Cl 35.453
- }
-
- # assumes "full" atom style
- write("Data Atoms") {
- $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000
- }
-} # ClIon
-
-
-write_once("In Init") {
- # -- Default styles for ions --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- kspace_style pppm 0.0001
- pair_modify mix arithmetic
-}
-
-# Optional: Define a group named "ions" consisting of either Na or Cl ions.
-write_once("In Settings") {
- group ionNa type @atom:NaIon/Na @atom:NaIon/Na
- group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl
- group ions type @atom:NaIon/Na @atom:ClIon/Cl
-}
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt
deleted file mode 100644
index 019911c19..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt
+++ /dev/null
@@ -1,52 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-SPCE {
-
- write_once("In Init") {
- # -- Default styles (for solo "SPCE" water) --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- pair_modify mix arithmetic
- }
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
- $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 1000.0 1.0
- angle_coeff @angle:HOH harmonic 1000.0 109.47
- pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166
- pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058
- group spce type @atom:O @atom:H
- fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeSPCE during minimization.)
- }
-
-} # end of definition of "SPCE" water molecule type
-
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt
deleted file mode 100644
index 639222d18..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt
+++ /dev/null
@@ -1,49 +0,0 @@
-import "spce.lt" # <- This defines the SPCE water molecule. This file is
- # located in the "src/moltemplate_force_fields" directory.
-
-import "ions.lt" # <- This defines the ions "NaIon" and "ClIon".
-
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 34.50 xlo xhi
- 0.0 34.50 ylo yhi
- 0.0 34.50 zlo zhi
-}
-
-
-# The next command generates a (rather dense) cubic lattice with
-# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
-
-wat = new SPCE [10].move(0.00, 0.00, 3.45)
- [10].move(0.00, 3.45, 0.00)
- [10].move(3.45, 0.00, 0.00)
-
-# We now create a 2x2x2 lattice of Na+ and Cl- ions:
-
-na = new NaIon [2].move(0,0,17.25)
- [2].move(0,17.25,0)
- [2].move(17.25,0,0)
-
-
-cl = new ClIon [2].move(0,0,17.25)
- [2].move(0,17.25,0)
- [2].move(17.25,0,0)
-
-na[*][*][*].move(5.175,5.175,5.6)
-cl[*][*][*].move(12.075,12.075,12.5)
-
-# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts
-# prevent the Na and Cl ions from overlapping
-# with the water molecules or each other.)
-
-
-# Comment: Fortunately the ions and the water in this example share the
-# same force-field styles (so their was no need to use "hybrid" styles).
-# If this were not the case, you might need to add something like this.
-#
-# write_once("In Init") {
-# # -- Styles for the combined system (overrides earlier settings) --
-# pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 NEWPAIRSTYLE
-# bond_style hybrid harmonic NEWBONDSTYLE
-# angle_style hybrid harmonic NEWANGLESTYLE
-# }
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt
deleted file mode 100644
index 9bd2f15f4..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt
+++ /dev/null
@@ -1,48 +0,0 @@
-# PREREQUISITES:
-#
-# You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-
-# Note: The minimization step is not necessary in this example. However
-# in general, it's always a good idea to minimize the system beforehand.
-# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
-unfix fShakeSPCE
-minimize 1.0e-3 1.0e-5 100000 400000
-# Now read "system.in.settings" in order to redefine fShakeSPCE again:
-include system.in.settings
-
-# -- simulation protocol --
-
-
-timestep 1.0
-dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-thermo 100
-
-run 10000
-
-# Now that the system's temperature has become more equilibrated,
-# we can increase the timestep:
-
-timestep 2.0
-run 50000
-
-write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt
deleted file mode 100644
index fb0642332..000000000
--- a/tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt
+++ /dev/null
@@ -1,58 +0,0 @@
-# PREREQUISITES:
-#
-# 1) You must use moltemplate.sh to create 3 files:
-# system.data system.in.init system.in.settings
-# (See README_setup.sh for details.)
-# 2) You must equilibrate the system beforehand using "run.in.npt".
-# This will create the file "system_after_npt.data" which this file reads.
-# (Note: I have not verified that this equilibration protocol works well.)
-
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-# Read the coordinates generated by an earlier NPT simulation
-
-read_data system_after_npt.data
-
-
-# (The "write_restart" and "read_restart" commands were buggy in 2012,
-# but they should work also. I prefer "write_data" and "read_data".)
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-
-
-# -- minimization protocol --
-# Note: If you are reading the restart file instead of the data file,
-# then you should not need to minimize the system beforehand..
-# fShakeSPCE was defined in system.in.settings.
-# (It is incompatible with "minimize".)
-unfix fShakeSPCE
-minimize 1.0e-5 1.0e-7 100000 400000
-# Now read "system.in.settings" in order to redefine fShakeSPCE again:
-include system.in.settings
-
-# -- simulation protocol --
-
-
-
-timestep 1.0
-dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-thermo 500
-
-run 10000
-
-# Now that the system's temperature has become more equilibrated,
-# we can increase the timestep:
-
-timestep 2.0
-run 50000
-
-write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT b/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT
deleted file mode 100644
index 4d3a9d2f8..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT
+++ /dev/null
@@ -1,45 +0,0 @@
-NOTE: This example requires the "Al99.eam.alloy" file.
- (It was not included in this directory because if its large size.)
- As of 2012-11, I was able to obtain it here:
- http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
- Copy it to the directory containing this README file.
-------------------------------------------------------------------------
-3D fractal test
-
-Moltemplate is useful for building larger molecular structures from
-smaller pieces. Although this simulation is of no scientific value, thiss
-example illustrates how to build large (many-level) heirarchical objects
-(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".)
-
-The files in this directory demonstrate a way to build a periodic lattice of
-3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity).
-
-In this example, the basic indivisible units are 4-atoms of Aluminum
-(arranged in a cubic FCC unit-cell for bulk Aluminum).
-This was an arbitrary choice. The resulting construct is not stable.
-(But it makes pretty movies while collapsing.)
-
-To understand what is going on with this example, look at this file:
-
-./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt
-
-(This approach uses too much memory to be practical for large simulaions.
-The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt)
-
- --- To build the system ---
-
-Carry out the instructions in README_setup.sh,
-to generate the LAMMPS DATA file and input scripts you need:
-system.data, system.in.init, system.in.settings.
-(The run.in script contains references to these files.)
-
- --- To run LAMMPS, try a command like: ---
-
-lmp_mpi -i run.in
-
- or (if you have mpi installed)
-
-mpirun -np 4 lmp_mpi -i run.in
-
-This will create an ordinary LAMMPS dump file you can visualize with VMD
-traj.lammpstrj (See README_visualize.txt)
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh b/tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh
deleted file mode 100755
index 2af3d7372..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh -atomstyle full system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # We will also need the "Al99.eam.alloy" file:
- #cp -f Al99.eam.alloy ../
- # This file was downloaded from:
- # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
-
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README_visualize.txt b/tools/moltemplate/examples/misc_examples/menger_sponge/README_visualize.txt
deleted file mode 100644
index 019afc144..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/README_visualize.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- Sometimes the solvent or membrane obscures the view of the solute.
- It can help to shift the location of the periodic boundary box
- To shift the box in the y direction (for example) do this:
-
- pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
- pbc box -shiftcenterrel {0.0 0.15 0.0}
-
- Distances are measured in units of box-length fractions, not Angstroms.
-
- Alternately if you have a solute whose atoms are all of type 1,
- then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4)
- You should check if your periodic boundary conditions are too small.
- To do that:
- select Graphics->Representations menu option
- click on the "Periodic" tab, and
- click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
-
-5) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/AlCell_LR.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/AlCell_LR.jpg
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diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/al_cell.lt
deleted file mode 100644
index 3054a45e0..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/al_cell.lt
+++ /dev/null
@@ -1,64 +0,0 @@
-# "AlCell" defines the 4-atom FCC unit cell
-# of Aluminum (with a 4.05 angstrom spacing)
-
-AlCell {
-
- # AtomID MolID(IGNORE!) AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000
- $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025
- $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025
- $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000
- }
-
- write_once("In Init") {
- units metal
- atom_style full # <- Requires each atom has a MolID and Charge.
- # This is not necessary. (Why use "full"?
- # The "full" atom style is useful if you want to
- # mix the aluminum with other molecules later.
- # Otherwise, just use "atom_style atomic", and
- # and remove the 2nd and 4th columns above.)
- pair_style eam/alloy
- }
-
- write_once("In Settings") {
- pair_coeff * * Al99.eam.alloy Al
- }
-
- write_once("Data Masses") {
- @atom:Al 27.0
- }
-
-} # AlCell
-
-
-
-
-
-# Here is an alternate way to define AlCell
-# using "scale(4.05)" to select the lattice spacing:
-#
-#FccCell {
-# write("Data Atoms") {
-# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0
-# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5
-# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5
-# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0
-# }
-# write_once("Data Masses") {
-# @atom:Al 27.0
-# }
-# write_once("In Init") {
-# units metal
-# atom_style full
-# pair_style eam/alloy
-# }
-# write_once("In Settings") {
-# pair_coeff * * Al99.eam.alloy Al
-# }
-#}
-#
-#AlCell = FccCell.scale(4.05)
-#
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/al_cell.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/al_cell.lt
deleted file mode 100644
index 3054a45e0..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/al_cell.lt
+++ /dev/null
@@ -1,64 +0,0 @@
-# "AlCell" defines the 4-atom FCC unit cell
-# of Aluminum (with a 4.05 angstrom spacing)
-
-AlCell {
-
- # AtomID MolID(IGNORE!) AtomType Charge X Y Z
-
- write("Data Atoms") {
- $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000
- $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025
- $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025
- $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000
- }
-
- write_once("In Init") {
- units metal
- atom_style full # <- Requires each atom has a MolID and Charge.
- # This is not necessary. (Why use "full"?
- # The "full" atom style is useful if you want to
- # mix the aluminum with other molecules later.
- # Otherwise, just use "atom_style atomic", and
- # and remove the 2nd and 4th columns above.)
- pair_style eam/alloy
- }
-
- write_once("In Settings") {
- pair_coeff * * Al99.eam.alloy Al
- }
-
- write_once("Data Masses") {
- @atom:Al 27.0
- }
-
-} # AlCell
-
-
-
-
-
-# Here is an alternate way to define AlCell
-# using "scale(4.05)" to select the lattice spacing:
-#
-#FccCell {
-# write("Data Atoms") {
-# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0
-# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5
-# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5
-# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0
-# }
-# write_once("Data Masses") {
-# @atom:Al 27.0
-# }
-# write_once("In Init") {
-# units metal
-# atom_style full
-# pair_style eam/alloy
-# }
-# write_once("In Settings") {
-# pair_coeff * * Al99.eam.alloy Al
-# }
-#}
-#
-#AlCell = FccCell.scale(4.05)
-#
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/menger_cubes.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/menger_cubes.lt
deleted file mode 100644
index afafd46e9..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/menger_cubes.lt
+++ /dev/null
@@ -1,34 +0,0 @@
-import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell
-
-# This approach uses the "delete" command.
-# It works and it is elegant, but because the majority of atoms will be
-# deleted, (and because memory is allocated for all atoms, including
-# deleted atoms) this approach is not very memory efficient.
-
-MengerCubeLvl1 {
- cells = new AlCell [3].move(0.00, 0.00, 4.05)
- [3].move(0.00, 4.05, 0.00)
- [3].move(4.05, 0.00, 0.00)
- delete cells[*][1][1]
- delete cells[1][*][1]
- delete cells[1][1][*]
-}
-
-MengerCubeLvl2 {
- cells = new MengerCubeLvl1 [3].move(0.00, 0.00, 12.15)
- [3].move(0.00, 12.15, 0.00)
- [3].move(12.15, 0.00, 0.00)
- delete cells[*][1][1]
- delete cells[1][*][1]
- delete cells[1][1][*]
-}
-
-MengerCubeLvl3 {
- cells = new MengerCubeLvl2 [3].move(0.00, 0.00, 36.45)
- [3].move(0.00, 36.45, 0.00)
- [3].move(36.45, 0.00, 0.00)
- delete cells[*][1][1]
- delete cells[1][*][1]
- delete cells[1][1][*]
-}
-
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/system.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/system.lt
deleted file mode 100644
index 8da5f2d9c..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version/system.lt
+++ /dev/null
@@ -1,34 +0,0 @@
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 218.7 xlo xhi
- 0.0 218.7 ylo yhi
- 0.0 218.7 zlo zhi
-}
-
-import "menger_cubes.lt"
-
-cube_at_000 = new MengerCubeLvl3.move(0.0000, 0.0000, 0.0000)
-cube_at_100 = new MengerCubeLvl3.move(109.35, 0.0000, 0.0000)
-cube_at_010 = new MengerCubeLvl3.move(0.0000, 109.35, 0.0000)
-cube_at_001 = new MengerCubeLvl3.move(0.0000, 0.0000, 109.35)
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-################################################################
-# The next command is not necessary:
-#
- create_var { $mol } # <-This forces all of the Al atoms in the crystal
-# # to share the same molecule ID number.
-# # Molecule ID numbers are not necessary. Ignore this.
-#
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/menger_cubes.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/menger_cubes.lt
deleted file mode 100644
index 0d2922d41..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/menger_cubes.lt
+++ /dev/null
@@ -1,66 +0,0 @@
-import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell
-
-# A Menger cube is a fractal which resembles a 3x3x3 Rubik's-cube. It has a
-# cube in each central face (and in the interior) removed. There are 3x3x3-7=20
-# remaining sub-cubes. Each of these 20 sub-cubes is a smaller MengerCube.
-# To build a MengerCube, you can list all 20 sub-cubes, or you can fill a
-# 3x3x3 cube with sub-cubes and delete the interior sub-cubes. (The later
-# approach is used in file "elegant_inefficient_version/menger_cubes.lt")
-
-
-
-MengerCubeLvl1 {
- # Again, a Menger-cube is constructed of 20 smaller cube-shaped objects.
- # Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt").
- # I could list out the positions of all 20 AlCells, (and this would be clearer
- # for the reader). However instead I built it from a combination of
- # two-dimensional and three-dimensional arrays of AlCells (explained below).
-
- # The next command creates 12 AlCells (2x2x3) at:
- # (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1)
- # (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1)
- # (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1)
-
- cells_z = new AlCell [2].move(8.10, 0.00, 0.00)
- [2].move(0.00, 8.10, 0.00)
- [3].move(0.00, 0.00, 4.05)
-
- # The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0),
- # (0, 4.05, 8.1), (8.1, 4.05, 8.1)
-
- cells_xz = new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 )
- [2].move(0.0, 0.0, 8.10)
-
- # The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0),
- # (4.05, 0, 8.1), (4.05, 8.1, 8.1)
-
- cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 )
- [2].move(0.0, 0.0, 8.10)
-}
-
-
-
-MengerCubeLvl2 {
- # Identical arrangement to MengerCube1 (with 3x larger length scales)
- cells_z = new MengerCubeLvl1 [2].move(24.3, 0.00, 0.00)
- [2].move(0.00, 24.3, 0.00)
- [3].move(0.00, 0.00, 12.15)
- cells_xz= new MengerCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 )
- [2].move(0.0, 0.0, 24.3)
- cells_yz= new MengerCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 )
- [2].move(0.0, 0.0, 24.3)
-}
-
-
-
-MengerCubeLvl3 {
- # Identical arrangement to MengerCube2 (with 3x larger length scales)
- cells_z = new MengerCubeLvl2 [2].move(72.9, 0.00, 0.00)
- [2].move(0.00, 72.9, 0.00)
- [3].move(0.00, 0.00, 36.45)
- cells_xz= new MengerCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 )
- [2].move(0.0, 0.0, 72.9)
- cells_yz= new MengerCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 )
- [2].move(0.0, 0.0, 72.9)
-}
-
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/system.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/system.lt
deleted file mode 100644
index 8da5f2d9c..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/system.lt
+++ /dev/null
@@ -1,34 +0,0 @@
-# Periodic boundary conditions:
-write_once("Data Boundary") {
- 0.0 218.7 xlo xhi
- 0.0 218.7 ylo yhi
- 0.0 218.7 zlo zhi
-}
-
-import "menger_cubes.lt"
-
-cube_at_000 = new MengerCubeLvl3.move(0.0000, 0.0000, 0.0000)
-cube_at_100 = new MengerCubeLvl3.move(109.35, 0.0000, 0.0000)
-cube_at_010 = new MengerCubeLvl3.move(0.0000, 109.35, 0.0000)
-cube_at_001 = new MengerCubeLvl3.move(0.0000, 0.0000, 109.35)
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-################################################################
-# The next command is not necessary:
-#
- create_var { $mol } # <-This forces all of the Al atoms in the crystal
-# # to share the same molecule ID number.
-# # Molecule ID numbers are not necessary. Ignore this.
-#
diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/run.in b/tools/moltemplate/examples/misc_examples/menger_sponge/run.in
deleted file mode 100644
index 6b9ad17e6..000000000
--- a/tools/moltemplate/examples/misc_examples/menger_sponge/run.in
+++ /dev/null
@@ -1,38 +0,0 @@
-# ------------------------------- Initialization Section --------------------
-
-include system.in.init
-
-# ------------------------------- Atom Definition Section -------------------
-
-read_data system.data
-
-# ------------------------------- Settings Section --------------------------
-
-include system.in.settings
-
-# ------------------------------- Run Section -------------------------------
-#
-# Some of the run-settings below were stolen from:
-#
-# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression
-
-# EQUILIBRATION
-reset_timestep 0
-timestep 0.001
-velocity all create 300 12345 mom yes rot no
-fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1
-
-# Output files
-thermo 100
-thermo_style custom step ke pe press
-dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz
-
-run 20000
-
-# Run for at least 10 picosecond (assuming 1 fs timestep)
-run 10000
-
-
-######################################
-# SIMULATION DONE
-print "All done"
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT
deleted file mode 100644
index 68f7c2ab0..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT
+++ /dev/null
@@ -1,23 +0,0 @@
- Description:
-
-This is a simulation of pyramid-shaped objects resting on an immobile surface
-(resembling graphene). Each pyramid is built from spherical particles stacked
-like cannon-balls (or fruit). Ordinarily, the stack does not move
-because the particles at the ground layer are immobilized. However,
-given an initial (small) perturbation the pyramids collapse in an avalanche.
-
-(In this example, the perturbation is due to shock because we (intentionally)
- did not minimize the system before starting the simulation. This shock
- causes an avalanche to begin approximately 5000 timesteps later.)
-
-The particles roll down the pyramid and bounce off the "ground". The bouncing
-is due to a repulsive external force which is added artificially.
-(See the "run.in" file.) The simulation looks weird without something
-to bounce off of. So I added a graphene surface at the bottom as scenery.
-(It does not exert any force on the atoms.)
-
-(Random comment: This could be a fun example to illustrate the Boltzmann
- distribution. Because there is no damping, in a small region, I'm guessing
- the particle heights should eventually approach the Boltzmann distribution
- for some temperature consistent with the initial potential energy of the
- system.)
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_VMD_graphene.txt b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_VMD_graphene.txt
deleted file mode 100644
index 096674f7f..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_VMD_graphene.txt
+++ /dev/null
@@ -1,28 +0,0 @@
- ------- A note on building the graphene sheet in VMD: ------
-
-Probably you can ignore these instructions.
-These instructions are not necessary for this example to run.
-
-This example contains several pyramid shaped objects resting on a surface
-made of graphene. The instructions in this file explain how to build the
-graphene (representing the "ground") using VMD instead of with moltemplate.
- Why do this?
-VMD can create graphene sheets with bonds connecting neighboring carbon atoms,
-(which looks more pretty). However, as of 2013-4-29, moltemplate currently
-can not generate these bonds. It does not matter physically in this case,
-because the graphene sheet used here does not move. It is only used as
-scenery, to graphically represent the ground surface.
-
-Select "Extensions"->"Modeling"->"Carbon Nanotube Builder"
- Build a graphene sheet of size 39.8 x 39.8 (units: nm)
- 400.3358398 399.876008
- (try to use a size compatible with the periodic boundaries)
-Select "Extensions"->"Tk Console", and type
- display backgroundgradient on
-
-Note: If you want to do this, before you run moltemplate, you may want to delete
- the sections of the "system.lt" file (located in "moltemplate_files")
- which define the graphene wall. Instead create the graphene data file
- in VMD. You will have to manually merge the data file for graphene
- with the data file for the pyramids created by moltemplate,
- (taking care to avoid overlapping atom-id numbers).
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_setup.sh b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_setup.sh
deleted file mode 100755
index acc5fbbaa..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_setup.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-# Use these commands to generate the LAMMPS input script and data file
-# (and other auxilliary files):
-
-
-# Create LAMMPS input files this way:
-cd moltemplate_files
-
- # run moltemplate
-
- moltemplate.sh system.lt
-
- # This will generate various files with names ending in *.in* and *.data.
- # These files are the input files directly read by LAMMPS. Move them to
- # the parent directory (or wherever you plan to run the simulation).
-
- mv -f system.in* system.data ../
-
- # Optional:
- # The "./output_ttree/" directory is full of temporary files generated by
- # moltemplate. They can be useful for debugging, but are usually thrown away.
- rm -rf output_ttree/
-
-cd ../
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_visualize.txt b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_visualize.txt
deleted file mode 100644
index 10198fc92..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_visualize.txt
+++ /dev/null
@@ -1,76 +0,0 @@
- ------- To view a lammps trajectory in VMD --------
-
-
-1) Build a PSF file for use in viewing with VMD.
-
-This step works with VMD 1.9 and topotools 1.2.
-(Older versions, like VMD 1.8.6, don't support this.)
-
-
-a) Start VMD
-b) Menu Extensions->Tk Console
-c) Enter:
-
-(I assume that the the DATA file is called "system.data")
-
- topo readlammpsdata system.data full
- animate write psf system.psf
-
-2)
-
-Later, to Load a trajectory in VMD:
-
- Start VMD
- Select menu: File->New Molecule
- -Browse to select the PSF file you created above, and load it.
- (Don't close the window yet.)
- -Browse to select the trajectory file.
- If necessary, for "file type" select: "LAMMPS Trajectory"
- Load it.
-
- ---- A note on trajectory format: -----
-If the trajectory is a DUMP file, then make sure the it contains the
-information you need for pbctools (see below. I've been using this
-command in my LAMMPS scripts to create the trajectories:
-
- dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
-
-It's a good idea to use an atom_style which supports molecule-ID numbers
-so that you can assign a molecule-ID number to each atom. (I think this
-is needed to wrap atom coordinates without breaking molecules in half.)
-
-Of course, you don't have to save your trajectories in DUMP format,
-(other formats like DCD work fine) I just mention dump files
-because these are the files I'm familiar with.
-
-3) ----- Wrap the coordinates to the unit cell
- (without cutting the molecules in half)
-
-a) Start VMD
-b) Load the trajectory in VMD (see above)
-c) Menu Extensions->Tk Console
-d) Try entering these commands:
-
- pbc wrap -compound res -all
- pbc box
-
- ----- Optional ----
- To shift the box by a fraction in the x direction (for example)
- do this:
-
- pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 }
- pbc box -shiftcenterrel {-0.50 -0.52 0.0 }
-
- # Alternately if you have a solute whose atoms are all of type 1,
- # then you can also try this to center the box around it:
-
- pbc wrap -sel type=1 -all -centersel type=2 -center com
-
-4) Optional: If you like, change the atom types in the PSF file so
- that VMD recognizes the atom types, use something like:
-
-sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
-sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
-sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
-
-(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg
deleted file mode 100644
index dc010258f..000000000
Binary files a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg and /dev/null differ
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg
deleted file mode 100644
index 53dc98f3e..000000000
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diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg
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diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/README.sh b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/README.sh
deleted file mode 100755
index 365ab9fb0..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/README.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-# This directory contains moltemplate files for the "Pyramids of Giza" example.
-# (Note: the ground lattice work that appears in some images was not generated
-# by moltemplate. Moltemplate can not currently create bonded periodic
-# structures as of 2013-4-04. Those were generated by topotools.)
-#
-# To run moltemplate, use:
-
-moltemplate.sh system.lt
-
-# This will generate:system.data, system.in, system.in.init, system.in.settings
-#
-# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds"
-# which contain the corresponding structures of the system.data file.
-# (This might make it slightly easier to combine them with atom data and
-# bond data generated by other programs, such as topotools, for example.)
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/graphene.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/graphene.lt
deleted file mode 100644
index 3b3e21333..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/graphene.lt
+++ /dev/null
@@ -1,61 +0,0 @@
-# This file contains a unit cell for building graphene and nanotubes
-#
-#
-# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell
-# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg")
-# Surfaces constructed with this unit cell can be flat or curved into tubes.
-# The distance between nearest-neighbor carbon atoms (ie the length of a
-# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms.
-#
-# d = length of each hexagon's side = 1.42 Angstroms
-# L = length of each hexagon = 2*d = 2.84 Angstroms
-# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms
-# 2w = width of hexagon rows = 3*l = 4.26 Angstroms
-#
-# Consequently, the Lattice-cell vectors for singe-layer graphene are:
-# (2.4595121467478, 0, 0) (aligned with X axis)
-# (0, 4.26, 0) (aligned with Y axis)
-# So, to build a sheet of graphite, you could use:
-# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0)
-# [10].move(0, 4.26, 0)
-
-
-
-
-Graphene {
-
- 4AtomRectCellXY
- {
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0
- $atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0
- $atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0
- $atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0
- }
- }
-
- # Now define properties of the Carbon graphene atom
-
- write_once("In Init") {
- pair_style hybrid lj/cut 9.0
- }
-
- write_once("Data Masses") {
- @atom:C 12.0
- }
-
- write_once("In Settings") {
- # i j epsilon sigma
- pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407
-
- # These Lennard-Jones parameters come from
- # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
- # Chem Phys Lett, 348:187 (2001)
-
- # Define a group consisting of only carbon atoms in graphene molecules
- group gGraphene type @atom:C
- }
-
-} # Graphene
-
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt
deleted file mode 100644
index 759f0f5d0..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt
+++ /dev/null
@@ -1,21 +0,0 @@
-import "graphene.lt"
-
-# -------------- graphene sheet -----------------
-
-# Notes:
-# Hexagonal lattice with:
-# l = length of each hexagonal side = 1.42 Angstroms
-# L = length of each hexagon = 2*l = 2.84 Angstroms
-# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms
-# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms
-
-
-GrapheneWall {
-
- unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0)
- [94].move(0, 4.254, 0)
-
- # (Note: I fudged the spacing slightly to make it line up better with the
- # lattice spacing for graphene generated by VMD's graphene builder.)
-}
-
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/pyramids.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/pyramids.lt
deleted file mode 100644
index 84c2b6f6d..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/pyramids.lt
+++ /dev/null
@@ -1,283 +0,0 @@
-# Brick is a very simple molecule containing one "atom".
-# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are
-# given different atom types. (This makes it easier to put them in
-# different groups and apply different LAMMPS "fixes" to them.)
-
-Brick {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom $mol @atom 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom 1.0
- }
-
- write_once("In Settings") {
- # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6)
- #
- # i j eps sig
- pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393
- }
-
- write_once("In Settings") {
- group gMobile type @atom
- # (Atoms of this type belong to the "gMobile" group)
- }
-
- write_once("In Init") {
- atom_style full
- units lj
- pair_style lj/cut 1.0
- }
-}
-
-
-
-#We want to stack "Brick"s the same way a green-grocer sometimes stack apples:
-#Place the apples at the base an square lattice of apples at the base.
-#The apples in the next layer up are placed in between the 4 apples beneath them.
-#Each new layer is smaller and placed above the previous layer at a height
-#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick".
-#We will artificially hold the apples at the base in place
-#(to keep the entire stack from collapsing).
-#
-# The lines below were generated from the following python loop:
-#
-#from math import *
-#N=50
-#s=1.0
-#for i in range(0,N):
-# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+
-# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+
-# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)")
-
-
-PyramidKhufu {
- layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0)
- layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0)
- layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0)
- layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0)
- layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0)
- layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0)
- layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0)
- layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0)
- layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0)
- layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0)
- layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0)
- layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0)
- layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0)
- layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0)
- layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0)
- layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0)
- layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0)
- layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0)
- layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0)
- layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0)
- layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0)
- layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0)
- layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0)
- layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0)
- layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0)
- layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0)
- layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0)
- layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0)
- layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0)
- layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0)
- layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0)
- layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0)
- layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0)
- layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0)
- layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0)
- layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0)
- layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0)
- layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0)
- layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0)
- layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0)
- layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0)
- layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0)
- layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0)
- layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0)
- layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0)
- layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0)
- layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0)
- layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0)
- layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0)
- layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0)
-}
-
-
-PyramidKhafre {
- layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0)
- layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0)
- layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0)
- layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0)
- layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0)
- layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0)
- layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0)
- layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0)
- layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0)
- layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0)
- layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0)
- layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0)
- layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0)
- layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0)
- layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0)
- layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0)
- layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0)
- layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0)
- layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0)
- layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0)
- layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0)
- layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0)
- layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0)
- layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0)
- layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0)
- layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0)
- layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0)
- layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0)
- layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0)
- layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0)
- layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0)
- layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0)
- layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0)
- layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0)
- layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0)
- layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0)
- layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0)
- layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0)
- layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0)
- layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0)
- layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0)
- layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0)
- layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0)
- layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0)
- layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0)
- layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0)
- layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0)
- layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0)
-}
-
-
-PyramidMenkaure {
- layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0)
- layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0)
- layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0)
- layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0)
- layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0)
- layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0)
- layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0)
- layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0)
- layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0)
- layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0)
- layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0)
- layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0)
- layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0)
- layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0)
- layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0)
- layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0)
- layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0)
- layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0)
- layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0)
-}
-
-PyramidQueens1 {
- layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0)
- layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0)
- layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0)
- layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0)
- layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0)
- layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0)
-}
-
-PyramidQueens2 {
- layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0)
- layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0)
- layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0)
- layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0)
- layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0)
- layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0)
-}
-
-PyramidQueens3 {
- layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0)
- layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0)
- layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0)
- layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0)
- layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0)
- layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0)
- layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0)
- layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0)
-}
-
-
-
-
-# "ImmobileBrick"s are identical to "Brick"s,
-# except that they have a different atom type.
-# We can define groups based on atom type
-# and apply fixes to them.
-
-ImmobileBrick {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom $mol @atom 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom 1.0
- }
-
- write_once("In Settings") {
- # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6)
- #
- # i j eps sig
- pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393
- }
-
- write_once("In Settings") {
- group gImmobile type @atom
- # (Atoms of this type belong to the "gImmobile" group)
- }
-
- write_once("In Init") {
- atom_style full
- units lj
- pair_style hybrid lj/cut 1.0
- }
-}
-
-
-
-GoldBrick {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom $mol @atom 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom 1.0
- }
-
- write_once("In Settings") {
- # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6)
- #
- # i j eps sig
- pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393
- }
-
- write_once("In Settings") {
- group gMobile type @atom
- # (Atoms of this type belong to the "gMobile" group)
- }
-
- write_once("In Init") {
- atom_style full
- units lj
- pair_style lj/cut 1.0
- }
-}
-
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/system.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/system.lt
deleted file mode 100644
index 0c9c50ae9..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files/system.lt
+++ /dev/null
@@ -1,80 +0,0 @@
-# Description.
-# This is a simulation of pyramid-like objects made of particles stacked
-# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack
-# does not collapse because the particles at the ground layer are immobilized.
-# However given an initial perterbation the pyramids collapse in an avalanche.
-# (This can happen, for example when you do not minimize the system beforehand.)
-# The particles roll down the pyramid and bounce off the "ground". The bouncing
-# is due to a repulsive external force which is added artificially.
-# (See the "run.in" file.) The simulation looks weird without something
-# to bounce off of. So I added a graphene surface at the bottom as scenery.
-# The ground does not serve any purpose except to look pretty.
-#
-# (Because there is no damping, I suspect that the distribution of heights of
-# the particles in a small area should approach the Boltzmann distribution,
-# if you run the simulation long enough.)
-
-
-# ----------------- Pyramids: -----------------
-
-import "pyramids.lt"
-
-# Move the pyramids into their locations in Giza (approximate)
-
-pyramidKhufu = new PyramidKhufu.move(210, 215, 1)
-pyramidKhafre = new PyramidKhafre.move(150, 150, 1)
-pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1)
-PyramidQueens1 = new PyramidQueens1.move(089, 059, 1)
-PyramidQueens2 = new PyramidQueens2.move(100, 059, 1)
-PyramidQueens3 = new PyramidQueens3.move(111, 059, 1)
-
-
-# --------------- Scenery: --------------------
-
-import "graphene_wall.lt"
-
-graphene_wall = new GrapheneWall
-
-write_once("In Settings") {
- # Turn off all interactions with the graphene atoms by setting epsilon to 0.
- # (We will use a different repulsive barrier to represent the ground instead.)
- # These atoms are just "for show". epsilon sigma
- pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407
-
- # Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them
- group gImmobile type @atom:Graphene/C
-}
-
-# Unfortunately, the ground still looks kind of ugly because moltemplate does
-# not yet know how to automatically connect nearby carbon atoms with C-C bonds
-# (based on distance). (As of 2013-4-29, moltemplate is not good at
-# generating crystalline objects containing explicit bonds.)
-# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin"
-# (which creates data files with bonds) and then merge the two data files
-# manually later. (This is not done here.)
-
-
-# -------- override earlier settings ----------
-
-write_once("In Init") {
- # Override any earlier style settings
- atom_style full
- units lj
- pair_style hybrid lj/cut 1.0
- bond_style none
- angle_style none
- dihedral_style none
- improper_style none
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 0.0
-}
-
-# ------------ boundary conditions ------------
-
-write_once("Data Boundary") {
- -1.842033 398.493813 xlo xhi
- -0.708994 399.167013 ylo yhi
- 0.0 400.0 zlo zhi
-}
-# ---------------------------------------------
-
diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/run.in b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/run.in
deleted file mode 100644
index a99dfda28..000000000
--- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/run.in
+++ /dev/null
@@ -1,68 +0,0 @@
-# -- Init Section --
-
-include system.in.init
-boundary p p f
-
-# -- Atom Definition Section --
-
-read_data system.data
-
-# -- Settings Section --
-
-include system.in.settings
-
-# -- Run Section --
-
-
-timestep 0.0025
-dump 1 all custom 200 traj.lammpstrj id mol type x y z ix iy iz
-
-thermo_style custom step temp pe etotal
-thermo 100 # time interval for printing out "thermo" data
-
-# ---- Set up the physical environment ----
-
-# Add gravity:
-fix fxGrav gMobile gravity 0.05 vector 0 0 -1
-
-# Create a "ground" surface.
-# This is a repulsive "wall" which particles can bounce off of:
-
-fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0
-
-
-# ---- Evolve the system: ----
-
-# Evolve the (mobile) atoms using ordinary Newton's laws (NVE)
-
-fix fxNVE gMobile nve
-
-
-# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE:
-#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279
-# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve"
-# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
-# This was not tested.
-
-# OPTIONAL:
-# For efficient simulation in parallel, try using "fix balance":
-# (This will adjust the spatial decomposition as the distribution of
-# particles changes over time.)
-# http://lammps.sandia.gov/doc/fix_balance.html
-# fix fxBalance gMobile balance 1000 1.1 shift 1000 xy 20 1.1
-# Alternatiely, try this:
-#fix fxBalance gMobile balance 1000 1.2 rcb
-
-
-# OPTIONAL: Improve efficiency by omitting the calcuation of interactions
-# between immobile atoms:
-
-neigh_modify exclude group gImmobile gImmobile
-
-
-restart 50000 restart_nvt
-
-run 200000
-
-write_data system_after_nvt.data
-
diff --git a/tools/moltemplate/moltemplate_manual.pdf b/tools/moltemplate/moltemplate_manual.pdf
deleted file mode 100644
index 14246f155..000000000
Binary files a/tools/moltemplate/moltemplate_manual.pdf and /dev/null differ
diff --git a/tools/moltemplate/src/bonds_by_type.py b/tools/moltemplate/src/bonds_by_type.py
deleted file mode 100644
index 919cfa51a..000000000
--- a/tools/moltemplate/src/bonds_by_type.py
+++ /dev/null
@@ -1,370 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2011, Regents of the University of California
-# All rights reserved.
-
-"""
- bonds_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS)
- data file containing bonded many-body interactions by atom type
- (and bond type), and generates a list of additional interactions
- in LAMMPS format consistent with those type (to the standard out).
-
- Typical Usage:
-
- bonds_by_type.py -atoms atoms.data \\
- -bonds bonds.data \\
- -bondsbytype bonds_by_type.data \\
- > new_bonds.data
-
-"""
-
-# -bonds-ids-atom-pairs bonds_ids_atom_pairs.data \\
-
-import sys
-#from extract_lammps_data import *
-#from nbody_by_type_lib import GenInteractions_str
-import ttree_lex
-#from ttree_lex import *
-from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid
-
-
-
-def LookupBondTypes(bond_types,
- bond_ids,
- bond_pairs,
- lines_atoms,
- lines_bonds,
- lines_bondsbytype,
- atom_style,
- section_name,
- prefix='',
- suffix='',
- bond_ids_offset=0):
- #report_progress = False):
- """
- LookupBondTypes() looks up bond types.
-
- Output:
- ...It looks up the corresponding type of each bond and store it in the
- "bond_types" list. (If the bond_ids were not specified by the user,
- generate them and store them in the bond_ids list.)
-
-
- Input (continued):
- This function requires:
- ...a list of bonded pairs of atoms
- stored in the lines_bonds variable (from the "Data Bond List"
- or "Data Bonds AtomId AtomId" sections)
- ...and a list of atom types
- stored in the lines_atoms variable (from the "Data Atoms" section)
- ...and a list of bond-types-as-a-function-of-atom-types
- stored in the lines_bondsbytype (from the "Data Bonds By Type" section)
-
- Generated bond_ids (if applicable) are of the form
- prefix + str(number) + suffix
- (where "number" begins at bond_ids_offset+1)
-
- """
-
- column_names = AtomStyle2ColNames(atom_style)
- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
-
- atomids = []
- atomtypes = []
- atomids2types = {}
-
- for iv in range(0, len(lines_atoms)):
- line = lines_atoms[iv].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = ttree_lex.SplitQuotedString(line)
- if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
- sys.stderr.write("\""+line+"\"\n")
- raise(ttree_lex.InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.'))
- tokens = ttree_lex.SplitQuotedString(line)
- atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid])
- atomids.append(atomid)
- atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype])
- atomtypes.append(atomtype)
- atomids2types[atomid] = atomtype
-
-
- assert(isinstance(bond_ids, list))
- assert(isinstance(bond_types, list))
- assert(isinstance(bond_pairs, list))
- del bond_ids[:]
- del bond_types[:]
- del bond_pairs[:]
-
- for ie in range(0, len(lines_bonds)):
-
- line = lines_bonds[ie].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
-
- if len(line) == 0:
- continue
-
- tokens = ttree_lex.SplitQuotedString(line)
-
- if section_name == "Data Bonds AtomId AtomId":
- if len(tokens) == 2:
- bondid_n = bond_ids_offset + len(bond_ids) + 1
- bond_ids.append(prefix+str(bondid_n)+suffix)
- bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]),
- ttree_lex.EscCharStrToChar(tokens[1])) )
- else:
- raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
-
- elif section_name == "Data Bond List":
- if len(tokens) == 3:
- bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
- bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]),
- ttree_lex.EscCharStrToChar(tokens[2])) )
- else:
- raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
-
- else:
- raise(ttree_lex.InputError('Internal Error ('+g_program_name+'): Unknown section name: \"'+section_name+'\"'))
-
-
- assert(len(bond_types) == 0)
- typepattern_to_coefftypes = []
-
- for i in range(0, len(lines_bondsbytype)):
- line = lines_bondsbytype[i].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = ttree_lex.SplitQuotedString(line)
-
- if (len(tokens) != 3):
- raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Bonds By Type\" section of data file.\n'
- 'Offending line:\n'+
- '\"'+line+'\"\n'
- 'Expected 3 columns\n'))
-
- coefftype = ttree_lex.EscCharStrToChar(tokens[0])
- typepattern = []
-
- for typestr in tokens[1:]:
- if ((len(typestr) >= 2) and
- (typestr[0] == '/') and (typestr[-1] == '/')):
- regex_str = typestr[1:-1]
- typepattern.append( re.compile(regex_str) )
- else:
- typepattern.append(ttree_lex.EscCharStrToChar(typestr))
-
- typepattern_to_coefftypes.append([typepattern, coefftype])
-
-
-
- assert(len(bond_ids) == len(bond_pairs))
-
- for ie in range(0,len(bond_ids)):
- bond_types.append(None)
-
- for ie in range(0, len(bond_ids)):
- bondid = bond_ids[ie]
- (atomid1, atomid2) = bond_pairs[ie]
-
- if atomid1 not in atomids2types:
- raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n'
- ' This usually happens when the user mistypes one of the names of the\n'
- ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
- ' To find out where the mistake occured, search the \n'
- ' \"ttree_assignments.txt\" file for:\n'
- ' \"'+atomid1+'\"\n')
-
- if atomid2 not in atomids2types:
- raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n'
- ' This usually happens when the user mistypes one of the names of the\n'
- ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
- ' To find out where the mistake occured, search the \n'
- ' \"ttree_assignments.txt\" file for:\n'
- ' \"'+atomid2+'\"\n')
-
- atomtype1 = atomids2types[atomid1]
- atomtype2 = atomids2types[atomid2]
-
- for typepattern, coefftype in typepattern_to_coefftypes:
-
- # use string comparisons to check if atom types match the pattern
- if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or
- ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)):
- # ("MatchesAll()" defined in "ttree_lex.py")
-
- bond_types[ie] = coefftype
-
- for ie in range(0, len(bond_ids)):
- if not bond_types[ie]:
- (atomid1, atomid2) = bond_pairs[ie]
- atomtype1 = atomids2types[atomid1]
- atomtype2 = atomids2types[atomid2]
- raise ttree_lex.InputError('Error: No bond types defined for the bond between\n'
- ' atoms '+atomid1+' (type '+atomtype1+')\n'
- ' and '+atomid2+' (type '+atomtype2+')\n')
-
-
-
-
-if __name__ == "__main__":
-
- g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py'
- g_date_str = '2015-11-09'
- g_version_str = '0.11'
-
- ####### Main Code Below: #######
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
- if sys.version < '3':
- sys.stderr.write(' (python version < 3)\n')
- else:
- sys.stderr.write('\n')
-
- try:
- fname_atoms = None
- fname_bond_list = None
- fname_bondsbytype = None
- section_name = 'Data Bond List' # (This will be replaced later.)
- atom_style = 'full'
- prefix=''
- suffix=''
- bond_lack_types = False
-
- argv = [arg for arg in sys.argv]
-
-
- # Loop over the remaining arguments not processed yet.
- # These arguments are specific to the lttree.py program
- # and are not understood by ttree.py:
- i = 1
- while i < len(argv):
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
- if ((argv[i].lower() == '-?') or
- (argv[i].lower() == '--?') or
- (argv[i].lower() == '-help') or
- (argv[i].lower() == '-help')):
- if i+1 >= len(argv):
- sys.stdout.write(man_page_text+'\n')
- sys.exit(0)
-
- elif argv[i].lower() == '-atoms':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- ' text which might appear in the "Atoms" section of a LAMMPS data file.\n')
- fname_atoms = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-bonds':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- ' text which might appear in the "Bonds" section of a LAMMPS data file.\n')
- fname_bond_list = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-bond-list':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
- #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- # ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n')
- fname_bond_list = argv[i+1]
- section_name = "Data Bond List"
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-bondsbytype':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
-
- #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n'
- # ' text which might appear in the "'+section_name+' By Type" section\n'
- # ' of a LAMMPS data file.\n')
- fname_bondsbytype = argv[i+1]
- del(argv[i:i+2])
-
- elif ((argv[i].lower() == '-atom-style') or
- (argv[i].lower() == '-atom_style')):
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n'
- ' (Or single quoted string which includes a space-separated\n'
- ' list of column names.)\n')
- atom_style = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-prefix':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a prefix string\n'
- ' (a string you want to appear to the left of the integer\n'
- ' which counts the bonded interactions you have generated.)\n')
- prefix = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-suffix':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a suffix string\n'
- ' (a string you want to appear to the right of the integer\n'
- ' which counts the bonded interactions you have generated.)\n')
- prefix = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i][0] == '-':
- raise ttree_lex.InputError('Error('+g_program_name+'):\n'
- 'Unrecognized command line argument \"'+argv[i]+'\"\n')
- else:
- i += 1
-
- if len(argv) != 1:
- # if there are more than 2 remaining arguments,
- problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
- raise ttree_lex.InputError('Syntax Error('+g_program_name+'):\n\n'
- ' Problem with argument list.\n'
- ' The remaining arguments are:\n\n'
- ' '+(' '.join(problem_args))+'\n\n'
- ' (The actual problem may be earlier in the argument list.)\n')
-
- bond_types = []
- bond_ids = []
- bond_pairs = []
-
- fatoms = open(fname_atoms, 'r')
- fbonds = open(fname_bond_list, 'r')
- fbondsbytype = open(fname_bondsbytype, 'r')
- lines_atoms = fatoms.readlines()
- lines_bonds = fbonds.readlines()
- lines_bondsbytype = fbondsbytype.readlines()
- fatoms.close()
- fbonds.close()
- fbondsbytype.close()
-
- LookupBondTypes(bond_types,
- bond_ids,
- bond_pairs,
- lines_atoms,
- lines_bonds,
- lines_bondsbytype,
- atom_style,
- section_name,
- prefix='',
- suffix='')
-
- assert(len(bond_types) == len(bond_ids) == len(bond_pairs))
-
- ie=0
- N = len(bond_types)
- for ie in range(0, N):
- sys.stdout.write(bond_ids[ie] + ' ' +
- bond_types[ie] + ' ' +
- bond_pairs[ie][0] + ' ' +
- bond_pairs[ie][1] + '\n')
-
-
- except (ValueError, ttree_lex.InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/chargepairs_by_type.py b/tools/moltemplate/src/chargepairs_by_type.py
deleted file mode 100644
index 3de813114..000000000
--- a/tools/moltemplate/src/chargepairs_by_type.py
+++ /dev/null
@@ -1,389 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2011, Regents of the University of California
-# All rights reserved.
-
-"""
- chargepairs_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS)
- data file containing bonded many-body interactions by atom type
- (and bond type), and generates a list of atom charges in LAMMPS input
- script format consistent with those types (to the standard out).
-
- Typical Usage:
-
- chargepairs_by_type.py -atoms atoms.data \\
- -bonds bonds.data \\
- -chargepairsbytype chargepairs_by_type.data \\
- > list_of_atom_charges.in
-
-"""
-
-# -bonds-ids-atom-pairs bonds_ids_atom_pairs.data \\
-
-import sys
-from collections import defaultdict
-#from extract_lammps_data import *
-#from nbody_by_type_lib import GenInteractions_str
-import ttree_lex
-#from ttree_lex import *
-from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid
-
-
-
-def LookupChargePairs(chargebyatomid,
- #bond_ids,
- #bond_pairs,
- lines_atoms,
- lines_bonds,
- lines_bond_list,
- lines_chargepairsbytype,
- atom_style,
- section_name,
- prefix='',
- suffix=''):
- #bond_ids_offset=0):
- #report_progress = False):
- """
- LookupChargePairs() looks up partial-charge pair contributions from the
- types of atoms participating in a bond.
-
- Output:
- ...It looks up the corresponding change in the partial charges for
- each pair of atoms and stores this in the "chargebyatomid" dictionary.
-
- Input (continued):
- This function requires:
- ...a list of bonded pairs of atoms
- stored in the lines_bonds variable (from the "Data Bond List"
- or "Data Bonds AtomId AtomId" sections)
- ...and a list of atom types
- stored in the lines_atoms variable (from the "Data Atoms" section)
-
- ...and a list of charge-pairs-as-a-function-of-atom-types
- stored in the lines_chargepairsbytype (from the "Data Bonds By Type" section)
-
- """
-
- column_names = AtomStyle2ColNames(atom_style)
- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
-
- atomids = []
- atomtypes = []
- atomids2types = {}
-
- for iv in range(0, len(lines_atoms)):
- line = lines_atoms[iv].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = ttree_lex.SplitQuotedString(line)
- if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
- sys.stderr.write("\""+line+"\"\n")
- raise(ttree_lex.InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.'))
- tokens = ttree_lex.SplitQuotedString(line)
- atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid])
- atomids.append(atomid)
- atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype])
- atomtypes.append(atomtype)
- atomids2types[atomid] = atomtype
-
-
- #assert(isinstance(bond_ids, list))
- #assert(isinstance(bond_types, list))
- #assert(isinstance(bond_pairs, list))
- #del bond_ids[:]
- #del bond_types[:]
- #del bond_pairs[:]
- bond_pairs = []
-
- for ie in range(0, len(lines_bond_list)):
- line = lines_bond_list[ie].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) == 0:
- continue
- tokens = ttree_lex.SplitQuotedString(line)
- if len(tokens) == 3:
- #bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
- bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]),
- ttree_lex.EscCharStrToChar(tokens[2])) )
- else:
- raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
-
-
- for ie in range(0, len(lines_bonds)):
- line = lines_bonds[ie].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) == 0:
- continue
- tokens = ttree_lex.SplitQuotedString(line)
- if len(tokens) == 4:
- #bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
- #bond_types.append(ttree_lex.EscCharStrToChar(tokens[1]))
- bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[2]),
- ttree_lex.EscCharStrToChar(tokens[3])) )
- else:
- raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
-
-
-
- #for ie in range(0, len(lines_bonds_atomid_atomid)):
- # line = lines_bonds_atomid_atomid[ie].strip()
- # if '#' in line:
- # icomment = line.find('#')
- # line = (line[:icomment]).strip()
- # if len(line) == 0:
- # continue
- # tokens = ttree_lex.SplitQuotedString(line)
- # if len(tokens) == 2:
- # #bondid_n = bond_ids_offset + len(bond_ids) + 1
- # #bond_ids.append(prefix+str(bondid_n)+suffix)
- # bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]),
- # ttree_lex.EscCharStrToChar(tokens[1])) )
- # else:
- # raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
-
-
-
- assert(len(bond_types) == 0)
- typepattern_to_chargepairs = []
- warning_unassigned_chargepairs = None
-
- for i in range(0, len(lines_chargepairsbytype)):
- line = lines_chargepairsbytype[i].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = ttree_lex.SplitQuotedString(line)
-
- if (len(tokens) != 4):
- raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Charge Pairs By Type\" section of data file.\n'
- 'Offending line:\n'+
- '\"'+line+'\"\n'
- 'Expected 4 columns\n'))
-
- chargepair = (float(tokens[2]),
- float(tokens[3]))
-
- typepattern = []
-
- for typestr in tokens[:2]:
- if ((len(typestr) >= 2) and
- (typestr[0] == '/') and (typestr[-1] == '/')):
- regex_str = typestr[1:-1]
- typepattern.append( re.compile(regex_str) )
- else:
- typepattern.append(ttree_lex.EscCharStrToChar(typestr))
-
- typepattern_to_chargepairs.append([typepattern, chargepair])
-
-
- for atomid1, atomid2 in bond_pairs:
-
- if atomid1 not in atomids2types:
- raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n'
- ' This usually happens when the user mistypes one of the names of the\n'
- ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
- ' To find out where the mistake occured, search the \n'
- ' \"ttree_assignments.txt\" file for:\n'
- ' \"'+atomid1+'\"\n')
-
- if atomid2 not in atomids2types:
- raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n'
- ' This usually happens when the user mistypes one of the names of the\n'
- ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
- ' To find out where the mistake occured, search the \n'
- ' \"ttree_assignments.txt\" file for:\n'
- ' \"'+atomid2+'\"\n')
-
-
- atomtype1 = atomids2types[atomid1]
- atomtype2 = atomids2types[atomid2]
-
- for typepattern, chargepair in typepattern_to_chargepairs:
- # use string comparisons to check if atom types match the pattern
- if ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern):
- # ("MatchesAll()" defined in "ttree_lex.py")
- chargebyatomid[atomid1] += chargepair[0]
- chargebyatomid[atomid2] += chargepair[1]
- elif ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern):
- chargebyatomid[atomid1] += chargepair[1]
- chargebyatomid[atomid2] += chargepair[0]
- else:
- if not warning_unassigned_chargepairs:
- warning_unassigned_chargepairs = (atomid1, atomid2)
-
-
- if warning_unassigned_chargepairs:
- sys.stderr.write('---------------------------------------------------------------------------\n'
- 'Warning: bonds found between atoms with no partial-charge rules.\n'
- ' This means that somewhere you are using a force-field\n'
- ' which assigns atomic charge according to the bonds these atoms\n'
- ' participate in, AND at least one pair of bonded atoms does NOT have\n'
- ' a rule defined to assign charges to that pair of atoms.\n'
- ' This can happen if there is a problem with the force-field file\n'
- ' OR if you are defining the charges for these atoms manually\n'
- ' In the later case, it is not a problem.\n'
- ' The first bond with this problem is between this pair of atoms:\n'
- ' '+str(warning_unassigned_chargepairs[0])+'\n'
- ' '+str(warning_unassigned_chargepairs[1])+'\n'
- '---------------------------------------------------------------------------\n')
-
-
-
-
-
-if __name__ == "__main__":
-
- g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py'
- g_date_str = '2016-10-16'
- g_version_str = '0.11'
-
- ####### Main Code Below: #######
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
- if sys.version < '3':
- sys.stderr.write(' (python version < 3)\n')
- else:
- sys.stderr.write('\n')
-
- try:
- fname_atoms = None
- fname_bonds = None
- fname_bond_list = None
- fname_chargepairsbytype = None
- section_name = 'Data Bond List' # (This will be replaced later.)
- atom_style = 'full'
- prefix=''
- suffix=''
- bond_lack_types = False
-
- argv = [arg for arg in sys.argv]
-
-
- # Loop over the remaining arguments not processed yet.
- # These arguments are specific to the lttree.py program
- # and are not understood by ttree.py:
- i = 1
- while i < len(argv):
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
- if ((argv[i].lower() == '-?') or
- (argv[i].lower() == '--?') or
- (argv[i].lower() == '-help') or
- (argv[i].lower() == '-help')):
- if i+1 >= len(argv):
- sys.stdout.write(man_page_text+'\n')
- sys.exit(0)
-
- elif argv[i].lower() == '-atoms':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- ' text which might appear in the "Atoms" section of a LAMMPS data file.\n')
- fname_atoms = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-bonds':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- ' text which might appear in the "Bonds" section of a LAMMPS data file.\n')
- fname_bonds = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-bond-list':
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
- #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- # ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n')
- fname_bond_list = argv[i+1]
- section_name = "Data Bond List"
- del(argv[i:i+2])
-
- elif ((argv[i].lower() == '-chargepairsbytype') or
- (argv[i].lower() == '-chargepairs-by-type') or
- (argv[i].lower() == '-charge-pairs-by-type')):
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
-
- #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n'
- # ' text which might appear in the "'+section_name+' By Type" section\n'
- # ' of a LAMMPS data file.\n')
- fname_chargepairsbytype = argv[i+1]
- del(argv[i:i+2])
-
- elif ((argv[i].lower() == '-atom-style') or
- (argv[i].lower() == '-atom_style')):
- if i+1 >= len(argv):
- raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n'
- ' (Or single quoted string which includes a space-separated\n'
- ' list of column names.)\n')
- atom_style = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i][0] == '-':
- raise ttree_lex.InputError('Error('+g_program_name+'):\n'
- 'Unrecognized command line argument \"'+argv[i]+'\"\n')
- else:
- i += 1
-
- if len(argv) != 1:
- # if there are more than 2 remaining arguments,
- problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
- raise ttree_lex.InputError('Syntax Error('+g_program_name+'):\n\n'
- ' Problem with argument list.\n'
- ' The remaining arguments are:\n\n'
- ' '+(' '.join(problem_args))+'\n\n'
- ' (The actual problem may be earlier in the argument list.)\n')
-
- bond_types = []
- fatoms = open(fname_atoms, 'r')
- lines_bonds = []
- lines_bond_list = []
- fbonds = fbond_list = None
- try:
- if fname_bonds != None:
- fbonds = open(fname_bonds, 'r')
- lines_bonds = fbonds.readlines()
- fbonds.close()
- except IOError:
- pass
- try:
- if fname_bond_list != None:
- fbond_list = open(fname_bond_list, 'r')
- lines_bond_list = fbond_list.readlines()
- fbond_list.close()
- except IOError:
- pass
- if ((len(lines_bonds) == 0) and (len(lines_bond_list) == 0)):
- sys.stderr.write('Error('+g_program_name+'): No bonds defined for this system\n'
- ' (This error may be a bug in moltemplate.)\n')
- fchargepairsbytype = open(fname_chargepairsbytype, 'r')
- lines_atoms = fatoms.readlines()
-
- lines_chargepairsbytype = fchargepairsbytype.readlines()
- fatoms.close()
- fchargepairsbytype.close()
- chargebyatomid = defaultdict(float)
-
- LookupChargePairs(chargebyatomid,
- lines_atoms,
- lines_bonds,
- lines_bond_list,
- lines_chargepairsbytype,
- atom_style,
- section_name)
-
- for atomid, charge in chargebyatomid.items():
- sys.stdout.write(' set atom ' + str(atomid) +
- ' charge ' + str(charge) + '\n')
-
- except (ValueError, ttree_lex.InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py
deleted file mode 100644
index 25c73219d..000000000
--- a/tools/moltemplate/src/dump2data.py
+++ /dev/null
@@ -1,1290 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""
-dump2data.py
-
-Extract dynamical degrees of freedom from a lammps DUMP file (from the stdin)
-and construct a new DATA file (to the stdout).
-A reference DATA file is needed (argument).
-
- basic usage
-./dump2data.py orig_file.data < dump.lammpstrj > new_file.data
- (This extract last frame, uses "full" atom_style.)
-
- options:
-./dump2data.py [-t t -atomstyle style] orig.data < dump.lammpstrj > new.data
-
-"""
-
-# Authors: Andrew Jewett
-# License: New BSD License
-# Copyright (c) 2014
-# All rights reserved.
-
-
-import sys
-from collections import defaultdict
-from operator import itemgetter, attrgetter
-
-
-class InputError(Exception):
- def __init__(self, err_msg):
- self.err_msg = err_msg
- def __str__(self):
- return self.err_msg
-
-
-def ErrorLeader(infile, lineno):
- return '\"'+infile+'\", line '+str(lineno)+': '
-
-
-class MiscSettings(object):
- def __init__(self):
- self.tstart = None
- self.tstop = None
- self.timestep_str = ''
- self.last_frame = False
- self.center_frame = False
- self.output_format = 'data'
- self.input_format = 'dump'
- self.multi = True
- self.skip_interval = 1
- self.scale = None
-
-
-class AtomStyleSettings(object):
- def __init__(self):
- # The following new member data indicate which columns store
- # LAMMPS-specific information.
- # The next 6 members store keep track of the different columns
- # of the "Atoms" section of a LAMMPS data file:
- self.column_names = [] #<--A list of column names (optional)
- self.i_coords=[] #<--A triplet of integers indicating which columns store coordinate data
- #self.ii_coords= [] #<--A list of triplets of column indexes storing coordinate data
- self.ii_vects=[] #<--A list of triplets of column indexes storing directional data
- # (such as dipole or ellipsoid orientations)
- self.i_atomid=None #<--An integer indicating which column has the atomid
- self.i_atomtype=None #<--An integer indicating which column has the atomtype
- self.i_molid=None #<--An integer indicating which column has the molid, if applicable
-
-
-
-class DataSettings(AtomStyleSettings):
- def __init__(self):
- AtomStyleSettings.__init__(self)
- self.contents = ''
- self.file_name = ''
-
-
-
-# Atom Styles in LAMMPS as of 2011-7-29
-g_style_map = {'angle': ['atom-ID','molecule-ID','atom-type','x','y','z'],
- 'atomic': ['atom-ID','atom-type','x','y','z'],
- 'bond': ['atom-ID','molecule-ID','atom-type','x','y','z'],
- 'charge': ['atom-ID','atom-type','q','x','y','z'],
- 'colloid': ['atom-ID','atom-type','x','y','z'],
- 'dipole': ['atom-ID','atom-type','q','x','y','z','mux','muy','muz'],
- 'electron': ['atom-ID','atom-type','q','spin','eradius','x','y','z'],
- 'ellipsoid':['atom-ID','atom-type','x','y','z','quatw','quati','quatj','quatk'],
- 'full': ['atom-ID','molecule-ID','atom-type','q','x','y','z'],
- 'granular': ['atom-ID','atom-type','diameter','density','x','y','z'],
- 'molecular':['atom-ID','molecule-ID','atom-type','x','y','z'],
- 'peri': ['atom-ID','atom-type','volume','density','x','y','z'],
- 'hybrid': ['atom-ID','atom-type','x','y','z']}
-
-
-
-
-def AtomStyle2ColNames(atom_style_string):
-
- atom_style_string = atom_style_string.strip()
- if len(atom_style_string) == 0:
- raise InputError('Error(dump2data): Invalid atom_style\n'
- ' (The atom_style command was followed by an empty string.)\n')
- atom_style_args = atom_style_string.split()
- atom_style = atom_style_args[0]
-
- hybrid_args = atom_style_args[1:]
- if (atom_style not in g_style_map):
- if (len(atom_style_args) >= 2):
- # If the atom_style_string includes at least 2 words, then we
- # interpret this as a list of the individual column names
- return atom_style_args
- else:
- raise InputError('Error(dump2data): Unrecognized atom_style: \"'+atom_style+'\"\n')
-
- if (atom_style != 'hybrid'):
- return g_style_map[atom_style]
- else:
- column_names = ['atom-ID','atom-type','x','y','z']
- if (len(hybrid_args)==0):
- raise InputError('Error(dump2data): atom_style hybrid must be followed by a sub_style.\n')
- for sub_style in hybrid_args:
- if (sub_style not in g_style_map):
- raise InputError('Error(dump2data): Unrecognized atom_style: \"'+sub_style+'\"\n')
- for cname in g_style_map[sub_style]:
- if cname not in column_names:
- column_names.append(cname)
-
- return column_names
-
-
-def ColNames2AidAtypeMolid(column_names):
- # Because of the diversity of ways that these
- # numbers are referred to in the LAMMPS documentation,
- # we have to be flexible and allow the user to refer
- # to these quantities in a variety of ways.
- # Hopefully this covers everything:
-
- i_atomid = None
- if 'atom-ID' in column_names:
- i_atomid = column_names.index('atom-ID')
- elif 'atom−ID' in column_names: # (− is the character used in the manual)
- i_atomid = column_names.index('atom−ID')
- elif 'atomID' in column_names:
- i_atomid = column_names.index('atomID')
- elif 'atomid' in column_names:
- i_atomid = column_names.index('atomid')
- elif 'id' in column_names:
- i_atomid = column_names.index('id')
- elif 'atom' in column_names:
- i_atomid = column_names.index('atom')
- elif '$atom' in column_names:
- i_atomid = column_names.index('$atom')
- else:
- raise InputError('Error(dump2data): List of column names lacks an \"atom-ID\"\n')
-
- i_atomtype = None
- if 'atom-type' in column_names:
- i_atomtype = column_names.index('atom-type')
- elif 'atom−type' in column_names: # (− hyphen character used in manual)
- i_atomtype = column_names.index('atom−type')
- elif 'atomtype' in column_names:
- i_atomtype = column_names.index('atomtype')
- elif 'type' in column_names:
- i_atomtype = column_names.index('type')
- elif '@atom' in column_names:
- i_atomtype = column_names.index('@atom')
- else:
- raise InputError('Error(dump2data): List of column names lacks an \"atom-type\"\n')
-
- i_molid = None
- if 'molecule-ID' in column_names:
- i_molid = column_names.index('molecule-ID')
- elif 'molecule−ID' in column_names: # (− hyphen character used in manual)
- i_molid = column_names.index('molecule−ID')
- elif 'moleculeID' in column_names:
- i_molid = column_names.index('moleculeID')
- elif 'moleculeid' in column_names:
- i_molid = column_names.index('moleculeid')
- elif 'molecule' in column_names:
- i_molid = column_names.index('molecule')
- elif 'molID' in column_names:
- i_molid = column_names.index('molID')
- elif 'molid' in column_names:
- i_molid = column_names.index('molid')
- elif 'mol' in column_names:
- i_molid = column_names.index('mol')
- elif '$mol' in column_names:
- i_molid = column_names.index('$mol')
- else:
- pass # some atom_types do not have a valid molecule-ID
-
- return i_atomid, i_atomtype, i_molid
-
-
-
-def ColNames2Coords(column_names):
- """ Which of the columns correspond to coordinates
- which must be transformed using rigid-body
- (affine: rotation + translation) transformations?
- This function outputs a list of lists of triplets of integers.
-
- """
- i_x = None
- i_y = None
- i_z = None
- if 'x' in column_names:
- i_x = column_names.index('x')
- if 'y' in column_names:
- i_y = column_names.index('y')
- if 'z' in column_names:
- i_z = column_names.index('z')
- if (((i_x != None) != (i_y != None)) or
- ((i_y != None) != (i_z != None)) or
- ((i_z != None) != (i_x != None))):
- raise InputError('Error(dump2data): columns must include \"x\", \"y\", and \"z\".\n')
- return [[i_x, i_y, i_z]]
-
-
-def ColNames2Vects(column_names):
- """ Which of the columns correspond to coordinates
- which must be transformed using rotations?
- Some coordinates like dipole moments and
- ellipsoid orientations should only be rotated
- (not translated).
- This function outputs a list of lists of triplets of integers.
-
- """
- vects = []
- i_mux = None
- i_muy = None
- i_muz = None
- if 'mux' in column_names:
- i_mux = column_names.index('mux')
- if 'muy' in column_names:
- i_muy = column_names.index('muy')
- if 'muz' in column_names:
- i_muz = column_names.index('muz')
- if (((i_mux != None) != (i_muy != None)) or
- ((i_muy != None) != (i_muz != None)) or
- ((i_muz != None) != (i_mux != None))):
- raise InputError('Error(dump2data): custom atom_style list must define mux, muy, and muz or none.\n')
- if i_mux != None:
- vects.append([i_mux, i_muy, i_muz])
- i_quati = None
- i_quatj = None
- i_quatk = None
- if 'quati' in column_names:
- i_quati = column_names.index('quati')
- if 'quatj' in column_names:
- i_quatj = column_names.index('quatj')
- if 'quatk' in column_names:
- i_quatk = column_names.index('quatk')
- if (((i_quati != None) != (i_quatj != None)) or
- ((i_quatj != None) != (i_quatk != None)) or
- ((i_quatk != None) != (i_quati != None))):
- raise InputError('Error(dump2data): custom atom_style list must define quati, quatj, and quatk or none.\n')
- if i_quati != None:
- vects.append([i_quati, i_quatj, i_quatk])
- return vects
-
-
-
-
-
-def ParseArgs(argv,
- misc_settings,
- data_settings,
- warning_strings=None):
-
- # Loop over the remaining arguments not processed yet.
- # These arguments are specific to the lttree.py program
- # and are not understood by this program.
- i = 1
- while i < len(argv):
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
- if ((argv[i].lower() == '-atomstyle') or
- (argv[i].lower() == '-atom_style') or
- (argv[i].lower() == '-atom-style')):
- in_init = []
- if i+1 >= len(argv):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by a an atom_style name.\n'
- ' (Or single quoted string which includes a space-separated\n'
- ' list of column names.)\n')
- data_settings.column_names = AtomStyle2ColNames(argv[i+1])
- sys.stderr.write(' \"Atoms\" column format:\n')
- sys.stderr.write(' '+(' '.join(data_settings.column_names))+'\n')
-
- # ColNames2Coords() and ColNames2Vects() generate lists of
- # triplets of integers, storing the column numbers containing
- # x, y, and z coordinate values, and vx,vy,vz direction vectors.
- data_settings.ii_vects = ColNames2Vects(data_settings.column_names)
- ii_coords = ColNames2Coords(data_settings.column_names)
- # This program assumes that there is only one coordinate triplet
- # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1
- assert(len(ii_coords) == 1)
- data_settings.i_coords = ii_coords[0]
-
- # Now figure out which columns correspond to atomid, atomtype, molid
- data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names)
- del(argv[i:i+2])
-
- elif (argv[i].lower() == '-icoord'):
- if i+1 >= len(argv):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n'
- ' corresponding to column numbers for coordinates in\n'
- ' the \"Atoms\" section of a LAMMPS data file.\n')
- ilist = argv[i+1].split()
- if (len(ilist) % 3) != 0:
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n'
- ' This is usually a list of 3 intebers, but it can contain more.\n'
- ' The number of cooridnate columns must be divisible by 3,\n'
- ' (even if the simulation is in 2 dimensions)\n')
-
- #ii_coords = []
- #for i in range(0, len(ilist)/3):
- # cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1]
- # ii_coords.append(cols)
- #if ((len(ii_coords) != 0) or (len(ii_coords[0]) != 3)):
- # raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n')
-
- data_settings.i_coords = ilist
- if (len(i_coords) != 3):
- raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n')
-
- data_settings.i_coords = ii_coords[0]
-
- del(argv[i:i+2])
-
- elif (argv[i].lower() == '-ivect'):
- if i+1 >= len(argv):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n'
- ' corresponding to column numbers for direction vectors in\n'
- ' the \"Atoms\" section of a LAMMPS data file.\n')
- ilist = argv[i+1].split()
- if (len(ilist) % 3) != 0:
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n'
- ' This is usually a list of 3 intebers, but it can contain more.\n'
- ' The number of cooridnate columns must be divisible by 3,\n'
- ' (even if the simulation is in 2 dimensions)\n')
-
- data_settings.ii_vects = []
- for i in range(0, len(ilist)/3):
- cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1]
- setting.ii_vects.append(cols)
- # This should override any earlier settings as a result of the
- # -atomstyle argument. So you can specify a custom list of column
- # names using -atomstyle "list of column names", and then afterwards
- # specify which of these columns correspond to direction vectors
- # using the "-ivect" command line argument later on.
- # This way, in theory you should be able to read columns from
- # new custom atom-styles that have not been invented yet.
- # (Although I haven't tested this.)
-
- del(argv[i:i+2])
- # i_atomid is not really needed for this program, but I load it anyway
- elif ((argv[i].lower() == '-iatomid') or
- (argv[i].lower() == '-iid') or
- (argv[i].lower() == '-iatom-id')):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n'
- ' (>=1) indicating which column in the \"Atoms\" section of a\n'
- ' LAMMPS data file contains the atom id number (typically 1).\n'
- ' (This argument is unnecessary if you use the -atomstyle argument.)\n')
- i_atomid = int(argv[i+1])-1
- del(argv[i:i+2])
- # i_atomtype is not really needed for this program, but I load it anyway
- elif ((argv[i].lower() == '-iatomtype') or
- (argv[i].lower() == '-itype') or
- (argv[i].lower() == '-iatom-type')):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n'
- ' (>=1) indicating which column in the \"Atoms\" section of a\n'
- ' LAMMPS data file contains the atom type.\n'
- ' (This argument is unnecessary if you use the -atomstyle argument.)\n')
- i_atomtype = int(argv[i+1])-1
- del(argv[i:i+2])
- # i_molid is not really needed for this program, but I load it anyway
- elif ((argv[i].lower() == '-imolid') or
- (argv[i].lower() == '-imol') or
- (argv[i].lower() == '-imol-id') or
- (argv[i].lower() == '-imoleculeid') or
- (argv[i].lower() == '-imolecule-id')):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n'
- ' (>=1) indicating which column in the \"Atoms\" section of a\n'
- ' LAMMPS data file contains the molecule id number.\n'
- ' (This argument is unnecessary if you use the -atomstyle argument.)\n')
- del(argv[i:i+2])
- # Which frame do we want?
- elif (argv[i].lower() == '-t'):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n'
- ' the frame you want to extract from the dump file (trajectory).\n'
- ' This integer should match the timestep corresponding to the frame\n'
- ' whose coordinates you wish to extract.\n')
- misc_settings.timestep_str = argv[i+1]
- del(argv[i:i+2])
- misc_settings.multi = False
- misc_settings.last_frame = False
-
- elif (argv[i].lower() == '-tstart'):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n'
- ' the first frame you want to extract from the dump file (trajectory).\n'
- ' This integer should match the timestep corresponding to the frame\n'
- ' (after which) you wish to extract coordinates.\n')
- misc_settings.tstart = float(argv[i+1])
- del(argv[i:i+2])
- misc_settings.multi = True
-
- elif (argv[i].lower() == '-tstop'):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an number indicating\n'
- ' the first frame you want to extract from the dump file (trajectory).\n'
- ' Frames after this timestep will be ignored.\n')
- misc_settings.tstop = float(argv[i+1])
- del(argv[i:i+2])
- misc_settings.multi = True
-
- elif (argv[i].lower() == '-center'):
- misc_settings.center_frame = True
- del(argv[i:i+1])
-
- elif ((argv[i].lower() == '-raw') or (argv[i].lower() == '-rawout')):
- misc_settings.output_format = 'raw'
- del(argv[i:i+1])
-
- elif (argv[i].lower() == '-rawin'):
- misc_settings.input_format = 'raw'
- misc_settings.multi = False
- del(argv[i:i+1])
-
- elif ((argv[i].lower() == '-xyz') or (argv[i].lower() == '-xyzout')):
- misc_settings.output_format = 'xyz'
- del(argv[i:i+1])
-
- elif (argv[i].lower() == '-xyzin'):
- misc_settings.input_format = 'xyz'
- misc_settings.multi = False
- del(argv[i:i+1])
-
- elif (argv[i].lower() == '-multi'):
- misc_settings.multi = True
- del(argv[i:i+1])
-
- elif (argv[i].lower() == '-last'):
- misc_settings.last_frame = True
- misc_settings.multi = False
- del(argv[i:i+1])
-
- elif (argv[i].lower() == '-interval'):
- misc_settings.skip_interval = int(argv[i+1])
- del(argv[i:i+2])
-
- elif (argv[i].lower() == '-scale'):
- misc_settings.scale = float(argv[i+1])
- del(argv[i:i+2])
-
- elif ((argv[i][0] == '-') and (__name__ == "__main__")):
- raise InputError('Error(dump2data): Unrecognized command line argument \"'+argv[i]+'\"\n')
- else:
- i += 1
-
- usage_examples = \
-""" Typical usage:
-dump2data.py orig_file.data < dump.lammpstrj > new_file.data
- (This extracts last frame, uses "full" atom_style.)
- Additional options:
-dump2data.py -t t -atomstyle style orig.data < dump.lammpstrj > new.data
-"""
-
- #if __name__ == "__main__":
-
- if (len(argv) > 2):
- # if there are more than 2 remaining arguments,
- # AND
- # no other function will process the remaining argument list
- # (ie. if __name__ == "__main__")
- # THEN
- raise InputError(' ----\n'
- 'ERROR(dump2data): You have too many arguments (or unrecognized arguments):\n'
- ' \"'+(' '.join(argv))+'\"\n'
- ' ----\n'
- +usage_examples)
- elif (len(argv) < 2):
- if misc_settings.output_format == 'data':
- raise InputError(' ----\n'
- 'ERROR(dump2data): Problem with argument list:\n'
- ' Expected a LAMMPS .data file as an argument.\n'
- ' ----\n'
- +usage_examples)
- else:
- in_data_file = open(argv[1], 'r')
- data_settings.file_name = argv[1];
- data_settings.contents = in_data_file.readlines()
- in_data_file.close()
-
- #end of if-then statement for "if __name__ == "__main__""
-
- if len(data_settings.i_coords) == 0:
- if warning_strings != None:
- warning_strings.append('WARNING(dump2data): atom_style unknown. (Use -atomstyle style. Assuming \"full\")')
- warn_atom_style_unspecified = True
- # The default atom_style is "full"
- data_settings.column_names = AtomStyle2ColNames('full')
- ii_coords = ColNames2Coords(data_settings.column_names)
- # This program assumes that there is only one coordinate triplet
- # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1
- assert(len(ii_coords) == 1)
- data_settings.i_coords = ii_coords[0]
- data_settings.ii_vects = ColNames2Vects(data_settings.column_names)
- data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names)
-
- ### sys.stderr.write('########################################################\n'
- ### '## WARNING: atom_style unspecified ##\n'
- ### '## --> \"Atoms\" column data has an unknown format. ##\n'
- ### '## Assuming atom_style = \"full\" ##\n'
- ### '########################################################\n'
- ### '## To specify the \"Atoms\" column format you can: ##\n'
- ### '## 1) Use the -atom_style \"STYLE\" argument ##\n'
- ### '## where \"STYLE\" is a string indicating a LAMMPS ##\n'
- ### '## atom_style, including hybrid styles.(Standard ##\n'
- ### '## atom styles defined in 2011 are supported.) ##\n'
- ### '## 2) Use the -atom_style \"COL_LIST\" argument ##\n'
- ### '## where \"COL_LIST" is a quoted list of strings ##\n'
- ### '## indicating the name of each column. ##\n'
- ### '## Names \"x\",\"y\",\"z\" are interpreted as ##\n'
- ### '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n'
- ### '## and \"quati\",\"quatj\",\"quatk\" are ##\n'
- ### '## interpreted as direction vectors. ##\n'
- ### '## 3) Use the -icoord \"cx cy cz...\" argument ##\n'
- ### '## where \"cx cy cz\" is a list of integers ##\n'
- ### '## indicating the column numbers for the x,y,z ##\n'
- ### '## coordinates of each atom. ##\n'
- ### '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n'
- ### '## where \"cmux cmuy cmuz...\" is a list of ##\n'
- ### '## integers indicating the column numbers for ##\n'
- ### '## the vector that determines the direction of a ##\n'
- ### '## dipole or ellipsoid (ie. a rotateable vector).##\n'
- ### '## (More than one triplet can be specified. The ##\n'
- ### '## number of entries must be divisible by 3.) ##\n'
- ### '## 5) Include a ##\n'
- ### '## write(\"in_init.txt\"){atom_style ...} ##\n'
- ### '## statement in your .ttree file. ##\n'
- ### '########################################################\n')
-
-
-
-
-def GetIntAtomID(pair):
- return int(pair[0])
-
-
-
-def WriteFrameToData(out_file,
- descr_str,
- misc_settings,
- data_settings,
- natoms,
- coords,
- coords_ixiyiz,
- vects,
- velocities,
- atomtypes,
- molids,
- xlo_str, xhi_str,
- ylo_str, yhi_str,
- zlo_str, zhi_str,
- xy_str, xz_str, yz_str):
-
- """
- Open a data file. Read the LAMMPS DATA file line by line.
- When the line contains information which is also in the dump file,
- replace that information with information from the dump file.
- (Information from a dump file is stored in the arguments to this function.)
- The resulting file also has LAMMPS DATA format.
-
- """
-
- section = ''
- firstline = True
- for line in data_settings.contents:
- ic = line.find('#')
- if ic != -1:
- line = line[:ic]
- line = line.strip()
-
- if firstline: # Construct a new descriptive header line:
- if descr_str != None:
- line = descr_str
- firstline = False
-
- if (len(line) > 0):
- # The initial section (section='') is assumed to be
- # the "LAMMPS Description" section. This is where the
- # box boundaries are specified.
- if section == '':
- tokens = line.split()
- if ((len(tokens) >= 2) and
- ((tokens[-2] == 'xlo') and (tokens[-1] == 'xhi')) and
- ((xlo_str != None) and (xhi_str != None))):
- tokens[0] = xlo_str
- tokens[1] = xhi_str
- line = ' '.join(tokens)
- elif ((len(tokens) >= 2) and
- ((tokens[-2] == 'ylo') and (tokens[-1] == 'yhi')) and
- ((ylo_str != None) and (yhi_str != None))):
- tokens[0] = ylo_str
- tokens[1] = yhi_str
- line = ' '.join(tokens)
- elif ((len(tokens) >= 2) and
- ((tokens[-2] == 'zlo') and (tokens[-1] == 'zhi')) and
- ((zlo_str != None) and (zhi_str != None))):
- tokens[0] = zlo_str
- tokens[1] = zhi_str
- line = ' '.join(tokens)
- elif ((len(tokens) >= 3) and
- ((tokens[-3] == 'xy') and
- (tokens[-2] == 'xz') and
- (tokens[-1] == 'yz')) and
- ((xy_str != None) and
- (xz_str != None) and
- (yz_str != None))):
- tokens[0] = xy_str
- tokens[1] = xz_str
- tokens[2] = yz_str
- line = ' '.join(tokens)
- if (line in set(['Masses', 'Velocities', 'Atoms',
- 'Bond Coeffs', 'Angle Coeffs',
- 'Dihedral Coeffs', 'Improper Coeffs',
- 'Bonds', 'Angles', 'Dihedrals', 'Impropers'])):
- section = line
- else:
- if (section == 'Atoms'):
- tokens = line.split()
- atomid = tokens[0]
-
- # update the atomtype and molID
- # (which may change during the simulation)
- if atomtypes:
- tokens[data_settings.i_atomtype] = atomtypes[atomid]
- if molids and data_settings.i_molid:
- tokens[data_settings.i_molid] = molids[atomid]
-
- if atomid in coords:
- # Loop over all of the vector degrees of
- # freedom of the particle, excluding coords
- # (for example: mu_x, mu_y, mu_z,
- # or quat_i, quat_j, quat_k)
- # In principle, depending on the atom_style,
- # there could be multiple vectors per atom.
- for I in range(0,len(data_settings.ii_vects)):
- vxvyvz = vects[atomid][I]
- i_vx = data_settings.ii_vects[I][0]
- i_vy = data_settings.ii_vects[I][1]
- i_vz = data_settings.ii_vects[I][2]
- if ((i_vx >= len(tokens)) or
- (i_vy >= len(tokens)) or
- (i_vz >= len(tokens))):
- raise InputError('Error(dump2data): Atom style incompatible with data file.\n'
- ' Specify the atom_style using -atomstyle style.\n')
- if ((vxvyvz == None) or
- (type(vxvyvz) is not tuple)):
- assert(data_settings.column_names[i_vx] not in dump_column_names)
- raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"'+data_settings.column_names[i_vx]+'\"\n'
- ' However there are no columns with this name in your DUMP file\n'
- ' (or the column was not in the expected place).\n'
- ' Hence, the atom styles in the dump and data files do not match.')
-
- # Replace the vector components with numbers
- # from the dump file
- tokens[i_vx] = vxvyvz[0]
- tokens[i_vy] = vxvyvz[1]
- tokens[i_vz] = vxvyvz[2]
-
- # Now loop over the coordinates of each atom.
- #for I in range(0,len(data_settings.ii_coords)):
- # xyz = coords[atomid][I]
- # THIS LOOP IS SILLY.
- # EACH ATOM ONLY HAS ONE SET OF X,Y,Z
- # COORDINATES. COMMENTING OUT THIS LOOP:
- # i_x = data_settings.ii_coords[I][0]
- # i_y = data_settings.ii_coords[I][1]
- # i_z = data_settings.ii_coords[I][2]
- # USING THIS INSTEAD:
-
- xyz = coords[atomid]
- i_x = data_settings.i_coords[0]
- i_y = data_settings.i_coords[1]
- i_z = data_settings.i_coords[2]
- if ((i_x >= len(tokens)) or
- (i_y >= len(tokens)) or
- (i_z >= len(tokens))):
- raise InputError('Error(dump2data): Atom style incompatible with data file.\n'
- ' Specify the atom_style using -atomstyle style.\n')
- # Replace the coordinates with coordinates from
- # the dump file into tokens[i_x]...
- tokens[i_x] = str(xyz[0])
- tokens[i_y] = str(xyz[1])
- tokens[i_z] = str(xyz[2])
-
- # Are there there any integer coords
- # (ix, iy, iz) in the dump file?
- if coords_ixiyiz[atomid]:
- assert(len(coords_ixiyiz[atomid]) == 3)
- # Integer coords stored in the DATA file too?
- if len(tokens)==(len(data_settings.column_names)+3):
- # Then replace the last 3 columns of the
- # line in the data file with: ix iy iz
- tokens[-3] = coords_ixiyiz[atomid][0]
- tokens[-2] = coords_ixiyiz[atomid][1]
- tokens[-1] = coords_ixiyiz[atomid][2]
- else:
- if (not misc_settings.center_frame):
- # Append them to the end of the line:
- tokens.append(coords_ixiyiz[atomid][0])
- tokens.append(coords_ixiyiz[atomid][1])
- tokens.append(coords_ixiyiz[atomid][2])
-
- # Now finally paste all the tokens together:
- line = ' '.join(tokens)
-
-
- elif (section == 'Velocities'):
- tokens = line.split()
- atomid = tokens[0]
- if atomid in velocities:
-
- vxvyvz = velocities[atomid]
- if len(tokens) < 4:
- raise InputError('Error(dump2data): Not enough columns in the \"Velocities\" file.\n')
- # Replace the coordinates with coordinates from
- # the dump file into tokens[i_x]...
- tokens[1] = str(vxvyvz[0])
- tokens[2] = str(vxvyvz[1])
- tokens[3] = str(vxvyvz[2])
-
- # Now finally paste all the tokens together:
- line = ' '.join(tokens)
-
-
- out_file.write(line+'\n')
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-if __name__ == "__main__":
-
- g_program_name = 'dump2data.py'
- g_date_str = '2015-8-11'
- g_version_str = 'v0.51'
-
- ####### Main Code Below: #######
- sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str+' ')
- #if sys.version < '3':
- # sys.stderr.write(' (python version < 3)\n')
- #else:
- sys.stderr.write('\n')
-
- try:
- data_settings = DataSettings()
- misc_settings = MiscSettings()
- warning_strings = []
- ParseArgs(sys.argv,
- misc_settings,
- data_settings,
- warning_strings)
-
- # Open the lammps dump file (trajectory file)
- # Skip to the line containing the correct frame/timestep.
- # (this is the last frame by default).
- # Read the "BOX BOUNDS" and the "ATOMS" sections.
- # Store the x,y,z coordinates in the "coords" associative array
- # (indexed by atom id, which could be non-numeric in general).
-
- section = ''
-
- #coords = defaultdict(list)
- #coords_ixiyiz = defaultdict(list)
- #vects = defaultdict(list)
- #xlo_str = xhi_str = ylo_str = yhi_str = zlo_str = zhi_str = None
- #xy_str = xz_str = yz_str = None
- #natoms = -1
- #timestep_str = ''
-
- frame_coords = defaultdict(list)
- frame_coords_ixiyiz = defaultdict(list)
- frame_vects = defaultdict(list)
- frame_velocities = defaultdict(list)
- frame_atomtypes = defaultdict(list)
- frame_molid = defaultdict(list)
- frame_xlo_str = frame_xhi_str = None
- frame_ylo_str = frame_yhi_str = None
- frame_zlo_str = frame_zhi_str = None
- frame_xy_str = frame_xz_str = frame_yz_str = None
- frame_natoms = -1
- frame_timestep_str = ''
- i_atomid = i_atomtype = i_molid = -1
- i_x = i_y = i_z = i_xu = i_yu = i_zu = -1
- i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1
-
- dump_column_names = []
-
- #num_frames_in = -1
- num_frames_out = 0
- finished_reading_frame = False
- read_last_frame = False
-
- #in_coord_file = open('traj_nvt.lammpstrj','r')
- #in_coord_file = open('deleteme.lammpstrj','r')
- in_coord_file = sys.stdin
-
- while True:
-
- line = in_coord_file.readline()
- if line == '': # if EOF
- if len(frame_coords) > 0:
- finished_reading_frame = True
- read_last_frame = True
-
- line = line.strip()
- if (line.find('ITEM:') == 0):
- section = line
- if (section.find('ITEM: ATOMS ') == 0):
- dump_column_names = line[12:].split()
- i_atomid, i_atomtype, i_molid = \
- ColNames2AidAtypeMolid(dump_column_names)
- #ii_coords = ColNames2Coords(dump_column_names)
-
- x_already_unwrapped = False
- y_already_unwrapped = False
- z_already_unwrapped = False
-
- if 'x' in dump_column_names:
- i_x = dump_column_names.index('x')
- elif 'xu' in dump_column_names:
- i_xu = dump_column_names.index('xu')
- x_already_unwrapped = True
- elif 'xs' in dump_column_names:
- i_xs = dump_column_names.index('xs')
- elif 'xsu' in dump_column_names:
- i_xsu = dump_column_names.index('xsu')
- x_already_unwrapped = True
- else:
- raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"x\" column.\n'+
- ' (excerpt below)\n' + line)
-
- if 'y' in dump_column_names:
- i_y = dump_column_names.index('y')
- elif 'yu' in dump_column_names:
- i_yu = dump_column_names.index('yu')
- y_already_unwrapped = True
- elif 'ys' in dump_column_names:
- i_ys = dump_column_names.index('ys')
- elif 'ysu' in dump_column_names:
- i_ysu = dump_column_names.index('ysu')
- y_already_unwrapped = True
- else:
- raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"y\" column.\n'+
- ' (excerpt below)\n' + line)
-
- if 'z' in dump_column_names:
- i_z = dump_column_names.index('z')
- elif 'zu' in dump_column_names:
- i_zu = dump_column_names.index('zu')
- z_already_unwrapped = True
- elif 'zs' in dump_column_names:
- i_zs = dump_column_names.index('zs')
- elif 'zsu' in dump_column_names:
- i_zsu = dump_column_names.index('zsu')
- z_already_unwrapped = True
- else:
- raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"z\" column.\n'+
- ' (excerpt below)\n' + line)
-
-
-
-
-
- ii_vects = ColNames2Vects(dump_column_names)
- if (len(ii_vects) != len(data_settings.ii_vects)):
- raise InputError('Error(dump2data): atom styles in data and dump files differ.\n'
- ' Some needed columns from the atom_styles are missing in the dump file.')
-
- i_ix = i_iy = i_iz = -1
- if 'ix' in dump_column_names:
- i_ix = dump_column_names.index('ix')
- if 'iy' in dump_column_names:
- i_iy = dump_column_names.index('iy')
- if 'iz' in dump_column_names:
- i_iz = dump_column_names.index('iz')
-
-
- i_vx = i_vy = i_vz = -1
- if 'vx' in dump_column_names:
- i_vx = dump_column_names.index('vx')
- if 'vy' in dump_column_names:
- i_vy = dump_column_names.index('vy')
- if 'vz' in dump_column_names:
- i_vz = dump_column_names.index('vz')
-
- elif (section.find('ITEM: BOX BOUNDS') == 0):
- avec=[1.0, 0.0, 0.0]
- bvec=[0.0, 1.0, 0.0]
- cvec=[0.0, 0.0, 1.0]
-
- elif (section.find('ITEM: TIMESTEP') == 0):
- if len(frame_coords) > 0:
- finished_reading_frame = True
-
- elif ((len(line) > 0) and (line[0] != '#')):
- if (section.find('ITEM: TIMESTEP') == 0):
- finished_reading_frame = False
- frame_timestep_str = line
- frame_coords = defaultdict(list)
- frame_coords_ixiyiz = defaultdict(list)
- frame_vects = defaultdict(list)
- frame_velocities = defaultdict(list)
- frame_atomtypes = defaultdict(list)
- frame_molids = defaultdict(list)
- frame_xlo_str = frame_xhi_str = None
- frame_ylo_str = frame_yhi_str = None
- frame_zlo_str = frame_zhi_str = None
- frame_xy_str = frame_xz_str = frame_yz_str = None
-
- elif (section == 'ITEM: NUMBER OF ATOMS'):
- frame_natoms = int(line)
-
- elif (section.find('ITEM: BOX BOUNDS') == 0):
- is_triclinic = (section.find('xy xz yz') == 0)
-
- tokens = line.split()
- if not frame_xlo_str:
- assert(not frame_xhi_str)
- frame_xlo_str = tokens[0]
- frame_xhi_str = tokens[1]
- avec[0] = float(frame_xhi_str) - float(frame_xlo_str)
- if (is_triclinic and (len(tokens) > 2)):
- frame_xy_str = tokens[2]
- bvec[0] = float(frame_xy_str)
- #See http://lammps.sandia.gov/doc/Section-howto.html#howto_12
- #sys.stderr.write('avec='+str(avec)+'\n')
-
- elif not frame_ylo_str:
- assert(not frame_yhi_str)
- frame_ylo_str = tokens[0]
- frame_yhi_str = tokens[1]
- bvec[1] = float(frame_yhi_str) - float(frame_ylo_str)
- if (is_triclinic and (len(tokens) > 2)):
- frame_xz_str = tokens[2]
- cvec[0] = float(frame_xz_str)
- #See http://lammps.sandia.gov/doc/Section-howto.html#howto_12
- #sys.stderr.write('bvec='+str(bvec)+'\n')
-
- elif not frame_zlo_str:
- assert(not frame_zhi_str)
- frame_zlo_str = tokens[0]
- frame_zhi_str = tokens[1]
- cvec = [0.0, 0.0, float(frame_zhi_str) - float(frame_zlo_str)]
- if (is_triclinic and (len(tokens) > 2)):
- frame_yz_str = tokens[2]
- cvec[1] = float(frame_yz_str)
- #See http://lammps.sandia.gov/doc/Section-howto.html#howto_12
- #sys.stderr.write('cvec='+str(cvec)+'\n')
-
- elif (section.find('ITEM: ATOMS') == 0):
- tokens = line.split()
- atomid = tokens[i_atomid]
- atomtype = tokens[i_atomtype]
- frame_atomtypes[atomid] = atomtype
- if i_molid:
- molid = tokens[i_molid]
- frame_molids[atomid] = molid
-
- if ((i_x != -1) and (i_y != -1) and (i_z != -1)):
- x = float(tokens[i_x]) #i_x determined above
- y = float(tokens[i_y])
- z = float(tokens[i_z])
-
- elif ((i_xu != -1) and (i_yu != -1) and (i_zu != -1)):
- x = float(tokens[i_xu]) #i_x determined above
- y = float(tokens[i_yu])
- z = float(tokens[i_zu])
-
- elif ((i_xs != -1) and (i_ys != -1) and (i_zs != -1)):
- xs = float(tokens[i_xs]) #i_xs determined above
- ys = float(tokens[i_ys])
- zs = float(tokens[i_zs])
-
- x = float(xlo_str) + xs*avec[0] + ys*bvec[0] + zs*cvec[0]
- y = float(ylo_str) + xs*avec[1] + ys*bvec[1] + zs*cvec[1]
- z = float(zlo_str) + xs*avec[2] + ys*bvec[2] + zs*cvec[2]
-
- # avec, bvec, cvec described here:
- #http://lammps.sandia.gov/doc/Section-howto.html#howto_12
-
- elif ((i_xsu != -1) and (i_ysu != -1) and (i_zsu != -1)):
- xsu = float(tokens[i_xsu]) #i_xs determined above
- ysu = float(tokens[i_ysu])
- zsu = float(tokens[i_zsu])
-
- x = float(xlo_str) + xsu*avec[0] + ysu*bvec[0] + zsu*cvec[0]
- y = float(ylo_str) + xsu*avec[1] + ysu*bvec[1] + zsu*cvec[1]
- z = float(zlo_str) + xsu*avec[2] + ysu*bvec[2] + zsu*cvec[2]
-
- # Now deal with ix, iy, iz
- if (i_ix != -1) and (not x_already_unwrapped):
- ix = int(tokens[i_ix])
- if (misc_settings.center_frame or
- (misc_settings.output_format != 'data')):
- #sys.stderr.write('atomid='+str(atomid)+', ix = '+str(ix)+', avec='+str(avec)+'\n')
- x += ix*avec[0]
- y += ix*avec[1]
- z += ix*avec[2]
- else:
- if atomid not in frame_coords_ixiyiz:
- frame_coords_ixiyiz[atomid] = ["0", "0", "0"]
- frame_coords_ixiyiz[atomid][0] = str(ix)
-
- if (i_iy != -1) and (not y_already_unwrapped):
- iy = int(tokens[i_iy])
- if (misc_settings.center_frame or
- (misc_settings.output_format != 'data')):
- #sys.stderr.write('atomid='+str(atomid)+', iy = '+str(iy)+', bvec='+str(bvec)+'\n')
- x += iy*bvec[0]
- y += iy*bvec[1]
- z += iy*bvec[2]
- else:
- if atomid not in frame_coords_ixiyiz:
- frame_coords_ixiyiz[atomid] = ["0", "0", "0"]
- frame_coords_ixiyiz[atomid][1] = str(iy)
-
- if (i_iz != -1) and (not z_already_unwrapped):
- iz = int(tokens[i_iz])
- if (misc_settings.center_frame or
- (misc_settings.output_format != 'data')):
- #sys.stderr.write('atomid='+str(atomid)+', iz = '+str(iz)+', cvec='+str(cvec)+'\n')
- x += iz*cvec[0]
- y += iz*cvec[1]
- z += iz*cvec[2]
- else:
- if atomid not in frame_coords_ixiyiz:
- frame_coords_ixiyiz[atomid] = ["0", "0", "0"]
- frame_coords_ixiyiz[atomid][2] = str(iz)
-
- #frame_coords[atomid] = [str(x), str(y), str(z)]
- frame_coords[atomid] = [x, y, z]
-
- vx = 0.0
- vy = 0.0
- vz = 0.0
- if i_vx != -1:
- vx = float(tokens[i_vx])
- if i_vy != -1:
- vy = float(tokens[i_vy])
- if i_vz != -1:
- vz = float(tokens[i_vz])
-
- frame_velocities[atomid] = [vx, vy, vz]
-
- # Ugly detail:
- # There can be multiple "vects" associated with each atom
- # (for example, dipole moments, ellipsoid directions, etc..)
-
- if atomid not in frame_vects:
- frame_vects[atomid] = [None for I in range(0,len(ii_vects))]
-
- for I in range(0, len(ii_vects)):
- i_vx = ii_vects[I][0]
- i_vy = ii_vects[I][1]
- i_vz = ii_vects[I][2]
- vx_str = tokens[i_vx]
- vy_str = tokens[i_vy]
- vz_str = tokens[i_vz]
-
- # Now the annoying part:
- # Which vect is it (mux,muy,muz) or (quati,quatj,quatk)?
- # The columns could be listed in a different order
- # in the data file and in the dump file.
- # Figure out which vector it is in the data file (stored
- # in the integer "I_data") so that column names match.
- name_vx = dump_column_names[i_vx]
- name_vy = dump_column_names[i_vy]
- name_vz = dump_column_names[i_vz]
- i_vx_data = 0
- I_data = -1
- # This code is ugly and inneficient.
- # I never want to touch this code again. (Hope it works)
- while i_vx_data < len(data_settings.column_names):
- if name_vx == data_settings.column_names[i_vx_data]:
- I_data = 0
- while I_data < len(data_settings.ii_vects):
- if ii_vects[I] == data_settings.ii_vects[I_data]:
- break
- I_data += 1
-
- if (0<I_data) and (I_data < len(data_settings.ii_vects)):
- break
-
- i_vx_data += 1
-
- if (0 <= I_data) and (I_data < len(data_settings.ii_vects)):
- frame_vects[atomid][I_data] = (vx_str,vy_str,vz_str)
- else:
- raise InputError('Error(dump2data): You have a vector coordinate in your dump file named \"'+name_vx+'\"\n'
- ' However there are no columns with this name in your data file\n'
- ' (or the column was not in the expected place).\n'
- ' Hence, the atom styles in the dump and data files do not match.')
-
-
- if finished_reading_frame:
-
- if misc_settings.scale != None:
- for atomid in frame_coords:
- for d in range(0,3):
- crd = float(frame_coords[atomid][d])
- frame_coords[atomid][d] = str(crd*misc_settings.scale)
-
- if len(frame_coords) != frame_natoms:
- err_msg = 'Number of lines in \"ITEM: ATOMS\" section disagrees with\n' \
- + ' \"ITEM: NUMBER OF ATOMS\" declared earlier in this file.\n'
- raise InputError(err_msg)
-
- if misc_settings.center_frame:
- cm = [0.0, 0.0, 0.0]
- for atomid in frame_coords:
- for d in range(0,3):
- cm[d] += float(frame_coords[atomid][d])
- for d in range(0,3):
- cm[d] /= float(len(frame_coords))
- for atomid in frame_coords:
- for d in range(0,3):
- frame_coords[atomid][d] = "%.7g" % (float(frame_coords[atomid][d]) - cm[d])
- frame_coords_ixiyiz[atomid] = ["0","0","0"]
-
- if misc_settings.output_format != 'data':
- frame_coords_ixiyiz[atomid] = ["0","0","0"]
-
-
-
- #if (num_frames_in == -1):
- # if (misc_settings.timestep_str != ''):
- # if (float(frame_timestep_str) >=
- # float(misc_settings.timestep_str)):
- # num_frames_in = 1
- # if not misc_settings.multi:
- # read_last_frame = True
- # else:
- # num_frames_in = 1
-
-
-
- # Should we write out the coordinates in this frame?
- write_this_frame = False
-
- if misc_settings.multi:
-
- write_this_frame = True
- if (misc_settings.tstart and
- (int(frame_timestep_str) < misc_settings.tstart)):
- write_this_frame = False
- if (misc_settings.tstop and
- (int(frame_timestep_str) > misc_settings.tstop)):
- write_this_frame = False
- read_last_frame = True
-
- if misc_settings.tstart:
- tstart = misc_settings.tstart
- else:
- tstart = 0
-
- if ((int(frame_timestep_str) - tstart)
- %
- misc_settings.skip_interval) != 0:
- write_this_frame = False
-
- else:
- if misc_settings.last_frame:
- if read_last_frame:
- write_this_frame = True
- else:
- assert(misc_settings.timestep_str)
- if (int(frame_timestep_str) >=
- int(misc_settings.timestep_str)):
- write_this_frame = True
- read_last_frame = True
-
-
- if write_this_frame:
-
- num_frames_out += 1
-
- sys.stderr.write(' (writing frame '+str(num_frames_out)+
- ' at timestep '+frame_timestep_str+')\n')
-
-
- # Print the frame
- # First check which format to output the data:
- if misc_settings.output_format == 'raw':
- # Print out the coordinates in simple 3-column text format
- for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)):
- if misc_settings.scale == None:
- sys.stdout.write(str(xyz[0])+' '+str(xyz[1])+' '+str(xyz[2])+'\n')
- else:
- # Only convert to float and back if misc_settings.scale != None
- sys.stdout.write(str(misc_settings.scale*float(xyz[0]))+' '+
- str(misc_settings.scale*float(xyz[1]))+' '+
- str(misc_settings.scale*float(xyz[2]))+'\n')
- sys.stdout.write('\n')
-
- elif misc_settings.output_format == 'xyz':
- # Print out the coordinates in simple 3-column text format
- sys.stdout.write(str(len(frame_coords))+'\n')
- descr_str = 'LAMMPS data from timestep '+frame_timestep_str
- sys.stdout.write(descr_str+'\n')
- for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)):
- if misc_settings.scale == None:
- sys.stdout.write(str(atomid)+' '+
- str(xyz[0])+' '+
- str(xyz[1])+' '+
- str(xyz[2])+'\n')
- else:
- # Only convert to float and back if misc_settings.scale != None
- sys.stdout.write(str(atomid)+' '+
- str(misc_settings.scale*float(xyz[0]))+' '+
- str(misc_settings.scale*float(xyz[1]))+' '+
- str(misc_settings.scale*float(xyz[2]))+'\n')
-
- else:
- # Parse the DATA file specified by the user
- # and replace appropriate lines or fields with
- # the corresponding text from the DUMP file.
- descr_str = 'LAMMPS data from timestep '+frame_timestep_str
- if misc_settings.multi and (misc_settings.output_format == 'data'):
- out_file_name = data_settings.file_name + '.'\
- + str(num_frames_out)
- sys.stderr.write(' (creating file \"'+out_file_name+'\")\n')
- out_file = open(out_file_name, 'w')
- else:
- out_file = sys.stdout
-
- WriteFrameToData(out_file,
- descr_str,
- misc_settings,
- data_settings,
- frame_natoms,
- frame_coords,
- frame_coords_ixiyiz,
- frame_vects,
- frame_velocities,
- frame_atomtypes,
- frame_molids,
- frame_xlo_str, frame_xhi_str,
- frame_ylo_str, frame_yhi_str,
- frame_zlo_str, frame_zhi_str,
- frame_xy_str, frame_xz_str, frame_yz_str)
-
- #if misc_settings.multi:
- # out_file.close()
-
-
- #if num_frames_in >= 0:
- # num_frames_in += 1
-
-
- if read_last_frame:
- exit(0)
-
-
- for warning_str in warning_strings:
- sys.stderr.write(warning_str+'\n')
-
-
-
- except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py
deleted file mode 100644
index 4fe3ec743..000000000
--- a/tools/moltemplate/src/extract_lammps_data.py
+++ /dev/null
@@ -1,119 +0,0 @@
-#!/usr/bin/env python
-
-lammps_data_sections = set(['Atoms',
- 'Masses',
- 'Bonds',
- 'Bond Coeffs',
- 'Angles',
- 'Angle Coeffs',
- 'Dihedrals',
- 'Dihedral Coeffs',
- 'Impropers',
- 'Improper Coeffs',
- 'BondBond Coeffs', # class2 angles
- 'BondAngle Coeffs', # class2 angles
- 'MiddleBondTorsion Coeffs', # class2 dihedrals
- 'EndBondTorsion Coeffs', # class2 dihedrals
- 'AngleTorsion Coeffs', # class2 dihedrals
- 'AngleAngleTorsion Coeffs', # class2 dihedrals
- 'BondBond13 Coeffs', # class2 dihedrals
- 'AngleAngle Coeffs', # class2 impropers
- 'Angles By Type', # new. not standard LAMMPS
- 'Dihedrals By Type',# new. not standard LAMMPS
- 'Angles By Type']) # new. not standard LAMMPS
-
-
-def DeleteComments(string,
- escape='\\',
- comment_char='#'):
- escaped_state = False
- for i in range(0,len(string)):
- if string[i] in escape:
- if escaped_state:
- escaped_state = False
- else:
- escaped_state = True
- elif string[i] == comment_char:
- if not escaped_state:
- return string[0:i]
- return string
-
-
-
-def ExtractDataSection(f,
- section_name,
- comment_char = '#',
- include_section_name = False,
- return_line_nums = False):
-
- inside_section = False
- if section_name in ('header','Header'): #"Header" section includes beginning
- inside_section = True
-
- nonblank_encountered = False
- nonheader_encountered = False
-
- i = 0
- for line_orig in f:
- return_this_line = False
- line = DeleteComments(line_orig).strip()
- if line in lammps_data_sections:
- nonheader_encountered = True
- if section_name in ('header', 'Header'):
- # The "header" section includes all lines at the beginning of the
- # before any other section is encountered.
- if nonheader_encountered:
- return_this_line = False
- else:
- return_this_line = True
- elif line == section_name:
- inside_section = True
- nonblank_encountered = False
- if include_section_name:
- return_this_line = True
- # A block of blank lines (which dont immediately follow
- # the section_name) signal the end of a section:
- elif len(line) == 0:
- if inside_section and include_section_name:
- return_this_line = True
- if nonblank_encountered:
- inside_section = False
- elif line[0] != comment_char:
- if inside_section:
- nonblank_encountered = True
- return_this_line = True
-
- if return_this_line:
- if return_line_nums:
- yield i
- else:
- yield line_orig
-
- i += 1
-
-
-
-if __name__ == "__main__":
-
- import sys
- lines = sys.stdin.readlines()
- exclude_sections = False
- if sys.argv[1] == '-n':
- exclude_sections = True
- del sys.argv[1]
-
- if not exclude_sections:
- for section_name in sys.argv[1:]:
- for line in ExtractDataSection(lines, section_name):
- sys.stdout.write(line)
- else:
- line_nums_exclude = set([])
- for section_name in sys.argv[1:]:
- for line_num in ExtractDataSection(lines,
- section_name,
- include_section_name=True,
- return_line_nums=True):
- line_nums_exclude.add(line_num)
- for i in range(0, len(lines)):
- if i not in line_nums_exclude:
- sys.stdout.write(lines[i])
diff --git a/tools/moltemplate/src/ltemplify.py b/tools/moltemplate/src/ltemplify.py
deleted file mode 100644
index 3ce6cb8e7..000000000
--- a/tools/moltemplate/src/ltemplify.py
+++ /dev/null
@@ -1,3361 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-"""
-ltemplify.py
-
-The "ltemplify.py" script can be used to convert existing LAMMPS
-input script and data files into a single .lt file
-(which includes both topology and force-field information
- for a single molecule in your system).
-
-Example:
-
- ltemplify.py -name Mol file.in file.data > mol.lt
-
-This creates a template for a new type of molecule (named "Mol"),
-consisting of all the atoms in the lammps files you included,
-and saves this data in a single ttree file ("mol.lt").
-This file can be used with moltemplate (ttree) to
-define large systems containing this molecule.
-
-"""
-
-import sys
-from ttree_lex import *
-from lttree_styles import *
-
-
-
-def Intify(s):
- if s.isdigit():
- return int(s)
- elif s[0:2] == 'id':
- return int(s[2:])
- elif s[0:4] == 'type':
- return int(s[4:])
- else:
- return s
-
-
-def IsNumber(s):
- try:
- float(s)
- return True
- except ValueError, TypeError:
- return False
-
-def StringToInterval(sel_str, slice_delim='*'):
- # Split a string into 1-3 tokens using the slice_delim and convert to int.
- # What a mess. I should rewrite this function
-
- i_slice = sel_str.find(slice_delim)
-
- if i_slice == -1:
- a = sel_str
- b = sel_str
- c = ''
- else:
- a = sel_str[:i_slice]
- bc = sel_str[i_slice+len(slice_delim):]
- b = ''
- c = ''
- i_slice = bc.find(slice_delim)
- if i_slice == -1:
- b = bc
- c = ''
- else:
- b = bc[:i_slice]
- c = bc[i_slice+len(slice_delim):]
-
- if a == '':
- a = None
- elif a.isdigit():
- a = int(a)
- else:
- raise InputError('Error: invalid selection string \"'+
- sel_str+'\"\n')
-
- if b == '':
- b = None
- elif b.isdigit():
- b = int(b)
- else:
- raise InputError('Error: invalid selection string \"'+
- sel_str+'\"\n')
-
- if c == '':
- c = None
- elif c.isdigit():
- c = int(c)
- else:
- raise InputError('Error: invalid selection string \"'+
- sel_str+'\"\n')
-
- if c == None:
- return (a,b)
- else:
- return (a,b,c)
-
-
-
-# Selections are simply lists of 2-tuples (pairs)
-
-def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '):
-
- """
- This function converts a string such as "1*4 6 9*12 50*70*10" into
- a list of tuples, for example: [(1,4), (6,6), (9,12), (50,50), (60,60), (70,70)]
- In general, the of intervals has the form:
- [(a1,b1), (a2,b2), (a3,b3), ... ]
-
- An atom is considered to belong to this selection
- if it happens to lie within the closed interval [a,b]
- for any pair of a,b values in the list of intervals.
- If for a given pair a,b, either a or b is "None", then that a or b
- value is not used to disqualify membership in the interval.
- (Similar to -infinity or +infinity. In other words if a is set to None,
- then to belong to the interval it is enough to be less than b.)
-
- """
- selection_list = []
- #tokens = sel_str.split(or_delim) <-- Not what we want when len(or_delim)>1
- tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False)
- for token in tokens:
- token = token.strip()
- interval = StringToInterval(token, slice_delim)
-
- if len(interval)==2:
- # Normally, "interval" should be a tuple containing 2 entries
- selection_list.append(interval)
- else:
- assert(len(interval)==3)
- # Handle 1000:2000:10 notation
- # (corresponding to 1000, 1010, 1020, 1030, ..., 1990, 2000)
- a=interval[0]
- b=interval[1]
- incr=interval[2]
- i=a
- while i<=b:
- selection_list.append((i,i))
- i += incr
-
- return selection_list
-
-
-def IntervalListToMinMax(interval_list):
- min_a = None
- max_b = None
- for (a,b) in interval_list:
- if ((not (type(a) is int)) or (not (type(b) is int))):
- return None,None #only integer min/max makes sense. otherwise skip
-
- if (min_a == None) or (a < min_a):
- min_a = a
- if (max_b == None) or (b > max_b):
- max_b = b
- return min_a, max_b
-
-
-def MergeIntervals(interval_list):
- """
- A crude simple function that merges consecutive intervals in the list
- whenever they overlap. (This function does not bother to compare
- non-consecutive entries in the interval_list.)
-
- """
- i = 1
- while i < len(interval_list):
- if ((interval_list[i-1][1] == None) or
- (interval_list[i-1][1]+1 >= interval_list[i][0])):
- interval_list[i-1] = (interval_list[i-1][0], interval_list[i][1])
- del interval_list[i]
- else:
- i += 1
-
-
-def BelongsToSel(i, sel):
- if (i == None) or (sel == None) or (len(sel) == 0):
- # If the user has not specified a selection for this category,
- # then by default all objects are accepted
- return True
-
- elif (type(i) is str):
- if i.isdigit():
- i = int(i)
- else:
- return True
-
- belongs = False
- for interval in sel:
- assert(len(interval) == 2)
- if interval[0]:
- if i >= interval[0]:
- if (interval[1] == None) or (i <= interval[1]):
- belongs = True
- break
- elif interval[1]:
- if i <= interval[1]:
- belongs = True
- break
- else:
- # In that case, the user entered something like "*"
- # which covers all possible numbers
- belongs = True
- break
-
- return belongs
-
-
-
-try:
-
- g_program_name = __file__.split('/')[-1] # = 'ltemplify.py'
- g_version_str = '0.51'
- g_date_str = '2015-10-27'
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
-
- non_empty_output = False
- no_warnings = True
- indent = 2
- cindent = 0
- atomid_selection = []
- atomtype_selection = []
- molid_selection = []
- mol_name = ''
-
- min_sel_atomid = None
- min_sel_atomtype = None
- min_sel_bondid = None
- min_sel_bondtype = None
- min_sel_angleid = None
- min_sel_angletype = None
- min_sel_dihedralid = None
- min_sel_dihedraltype = None
- min_sel_improperid = None
- min_sel_impropertype = None
-
- max_sel_atomid = None
- max_sel_atomtype = None
- max_sel_bondid = None
- max_sel_bondtype = None
- max_sel_angleid = None
- max_sel_angletype = None
- max_sel_dihedralid = None
- max_sel_dihedraltype = None
- max_sel_improperid = None
- max_sel_impropertype = None
-
- needed_atomids = set([])
- needed_atomtypes = set([])
- needed_molids = set([])
- needed_bondids = set([])
- needed_bondtypes = set([])
- needed_angleids = set([])
- needed_angletypes = set([])
- needed_dihedralids = set([])
- needed_dihedraltypes = set([])
- needed_improperids = set([])
- needed_impropertypes = set([])
-
- min_needed_atomtype = None
- max_needed_atomtype = None
- min_needed_bondtype = None
- max_needed_bondtype = None
- min_needed_angletype = None
- max_needed_angletype = None
- min_needed_dihedraltype = None
- max_needed_dihedraltype = None
- min_needed_impropertype = None
- max_needed_impropertype = None
-
- min_needed_atomid = None
- max_needed_atomid = None
- min_needed_molid = None
- max_needed_molid = None
- min_needed_bondid = None
- max_needed_bondid = None
- min_needed_angleid = None
- max_needed_angleid = None
- min_needed_dihedralid = None
- max_needed_dihedralid = None
- min_needed_improperid = None
- max_needed_improperid = None
-
-
- # To process the selections, we need to know the atom style:
- atom_style_undefined = True
-
- i_atomid = None
- i_atomtype = None
- i_molid = None
- i_x = None
- i_y = None
- i_z = None
-
- l_in_init = []
- l_in_settings = []
- l_in_masses = []
- l_in_pair_coeffs = []
- l_in_bond_coeffs = []
- l_in_angle_coeffs = []
- l_in_dihedral_coeffs = []
- l_in_improper_coeffs = []
- l_in_group = []
- l_in_fix_shake = []
- l_in_fix_rigid = []
- l_in_fix_poems = []
- l_in_fix_qeq = []
- l_in_fix_qmmm = []
- l_data_masses = []
- l_data_bond_coeffs = []
- l_data_angle_coeffs = []
- l_data_dihedral_coeffs = []
- l_data_improper_coeffs = []
- l_data_pair_coeffs = []
- l_data_pairij_coeffs = []
- l_data_atoms = []
- l_data_velocities = []
- l_data_bonds = []
- l_data_angles = []
- l_data_dihedrals = []
- l_data_impropers = []
-
- # class2 force fields
- #l_in_bondbond_coeffs = [] <--not needed, included in l_in_angle_coeff
- #l_in_bondangle_coeffs = [] <--not needed, included in l_in_angle_coeff
- #l_in_middlebondtorsion_coeffs = [] not needed, included in l_in_dihedral_coeff
- #l_in_endbondtorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff
- #l_in_angletorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff
- #l_in_angleangletorsion_coeffs = [] not needed, included in l_in_dihedral_coeff
- #l_in_bondbond13_coeffs = [] <--not needed, included in l_in_dihedral_coeff
- #l_in_angleangle_coeffs = [] <--not needed, included in l_in_improper_coeff
- l_data_bondbond_coeffs = []
- l_data_bondangle_coeffs = []
- l_data_middlebondtorsion_coeffs = []
- l_data_endbondtorsion_coeffs = []
- l_data_angletorsion_coeffs = []
- l_data_angleangletorsion_coeffs = []
- l_data_bondbond13_coeffs = []
- l_data_angleangle_coeffs = []
-
- # non-point-like particles:
- l_data_ellipsoids = []
- l_data_lines = []
- l_data_triangles = []
-
- # automatic generation of bonded interactions by type:
- l_data_angles_by_type = []
- l_data_dihedrals_by_type = []
- l_data_impropers_by_type = []
-
- atoms_already_read = False
- some_pair_coeffs_read = False
- complained_atom_style_mismatch = False
- infer_types_from_comments = False
- remove_coeffs_from_data_file = True
-
- argv = [arg for arg in sys.argv]
-
- i = 1
-
- while i < len(argv):
-
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
-
- if argv[i] == '-columns':
- if i+1 >= len(argv):
- raise InputError('Error: the \"'+argv[i]+'\" argument should be followed by a quoted\n'
- ' string which contains a space-delimited list of the names of\n'
- ' of columns in the \"Atoms\" section of the LAMMPS data file.\n'
- ' If the list contains the symbols:\n'
- ' \"atom-ID\" or \"atomid\", they are interpreted\n'
- ' as unique atom ID numbers, and columns named\n'
- ' \"atom-type\" or \"atomtype\" are interpreted\n'
- ' as atom types. Finally, columns named\n'
- ' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n'
- ' are interpreted as unique molecule id numbers.\n'
- 'Example:\n'
- ' '+argv[i]+' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n'
- ' defines a custom atom_style containing the properties\n'
- ' atom-ID atom-type q polarizability molecule-ID x y z\n'
- ' Make sure you enclose the entire list in quotes.\n');
- column_names = argv[i+1].strip('\"\'').strip().split()
- del argv[i:i+2]
-
- elif (argv[i] == '-ignore-comments'):
- infer_types_from_comments = False
- del argv[i:i+1]
-
- elif (argv[i] == '-infer-comments'):
- infer_types_from_comments = True
- del argv[i:i+1]
-
- elif ((argv[i] == '-name') or
- (argv[i] == '-molname') or
- (argv[i] == '-molecule-name') or
- (argv[i] == '-molecule_name')):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a a molecule type name.\n')
- cindent = 2
- indent += cindent
- mol_name = argv[i+1]
- del argv[i:i+2]
-
- elif ((argv[i].lower() == '-atomstyle') or
- (argv[i].lower() == '-atom_style') or
- (argv[i].lower() == '-atom-style')):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n'
- ' (or single quoted string which includes a space-separated\n'
- ' list of column names).\n')
- atom_style_undefined = False
- column_names = AtomStyle2ColNames(argv[i+1])
- if (argv[i+1].strip().split()[0] in g_style_map):
- l_in_init.append((' '*indent) + 'atom_style ' + argv[i+1] + '\n')
- sys.stderr.write('\n \"Atoms\" column format:\n')
- sys.stderr.write(' '+(' '.join(column_names))+'\n')
- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
- # Which columns contain the coordinates?
- ii_coords = ColNames2Coords(column_names)
- assert(len(ii_coords) == 1)
- i_x = ii_coords[0][0]
- i_y = ii_coords[0][1]
- i_z = ii_coords[0][2]
-
- if i_molid:
- sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n')
- else:
- sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n')
- del argv[i:i+2]
-
- elif ((argv[i].lower() == '-id') or
- #(argv[i].lower() == '-a') or
- #(argv[i].lower() == '-atoms') or
- (argv[i].lower() == '-atomid') or
- #(argv[i].lower() == '-atomids') or
- (argv[i].lower() == '-atom-id')
- #(argv[i].lower() == '-atom-ids') or
- #(argv[i].lower() == '-$atom') or
- #(argv[i].lower() == '-$atoms')
- ):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n'
- ' (or strings). These identify the group of atoms you want to\n'
- ' to include in the template you are creating.\n')
- atomid_selection += LammpsSelectToIntervals(argv[i+1])
- min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection)
- del argv[i:i+2]
- elif ((argv[i].lower() == '-datacoeffs') or
- (argv[i].lower() == '-datacoeff') or
- (argv[i].lower() == '-Coeff') or
- (argv[i].lower() == '-Coeffs')):
- remove_coeffs_from_data_file = False
- del argv[i:i+1]
- elif ((argv[i].lower() == '-type') or
- #(argv[i].lower() == '-t') or
- (argv[i].lower() == '-atomtype') or
- (argv[i].lower() == '-atom-type')
- #(argv[i].lower() == '-atomtypes') or
- #(argv[i].lower() == '-atom-types') or
- #(argv[i].lower() == '-@atom') or
- #(argv[i].lower() == '-@atoms') or
- #(argv[i].lower() == '-@atomtype') or
- #(argv[i].lower() == '-@atomtypes')
- ):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n'
- ' (or strings). These identify the group of atom types you want to\n'
- ' to include in the template you are creating.\n')
- atomtype_selection += LammpsSelectToIntervals(argv[i+1])
- min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection)
- del argv[i:i+2]
- elif ((argv[i].lower() == '-mol') or
- #(argv[i].lower() == '-m') or
- (argv[i].lower() == '-molid') or
- #(argv[i].lower() == '-molids') or
- (argv[i].lower() == '-mol-id') or
- #(argv[i].lower() == '-mol-ids') or
- #(argv[i].lower() == '-molecule') or
- (argv[i].lower() == '-moleculeid') or
- (argv[i].lower() == '-molecule-id')
- #(argv[i].lower() == '-molecules') or
- #(argv[i].lower() == '-molecule-ids') or
- #(argv[i].lower() == '-$mol') or
- #(argv[i].lower() == '-$molecule')
- ):
- if i+1 >= len(argv):
- sys.stderr.write('Error: '+argv[i]+' flag should be followed by a list of integers.\n'
- ' (or strings). These identify the group of molecules you want to\n'
- ' include in the template you are creating.\n')
- molid_selection += LammpsSelectToIntervals(argv[i+1])
- del argv[i:i+2]
- else:
- i += 1
-
- # We might need to parse the simulation boundary-box.
- # If so, use these variables. (None means uninitialized.)
- boundary_xlo = None
- boundary_xhi = None
- boundary_ylo = None
- boundary_yhi = None
- boundary_zlo = None
- boundary_zhi = None
- boundary_xy = None
- boundary_yz = None
- boundary_xz = None
-
- # atom type names
- atomtypes_name2int = {}
- atomtypes_int2name = {}
- #atomids_name2int = {} not needed
- atomids_int2name = {}
- atomids_by_type = {}
-
-
- if atom_style_undefined:
- # The default atom_style is "full"
- column_names = AtomStyle2ColNames('full')
- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
- # Which columns contain the coordinates?
- ii_coords = ColNames2Coords(column_names)
- assert(len(ii_coords) == 1)
- i_x = ii_coords[0][0]
- i_y = ii_coords[0][1]
- i_z = ii_coords[0][2]
-
- #---------------------------------------------------------
- #-- The remaining arguments are files that the user wants
- #-- us to read and convert. It is typical to have
- #-- multiple input files, because LAMMPS users often
- #-- store their force field parameters in either the LAMMPS
- #-- data files and input script files, or both.
- #-- We want to search all of the LAMMPS input files in
- #-- order to make sure we extracted all the force field
- #-- parameters (coeff commands).
- #---------------------------------------------------------
-
- for i_arg in range(1,len(argv)):
- fname = argv[i_arg]
- try:
- lammps_file = open(fname, 'r')
- except IOError:
- raise InputError('Error: unrecognized argument (\"'+fname+'\"),\n'
- ' OR unable to open file:\n'
- '\n'
- ' \"'+fname+'\"\n'
- ' for reading.\n'
- '\n'
- ' (If you were not trying to open a file with this name,\n'
- ' then there is a problem in your argument list.)\n')
-
- sys.stderr.write('reading file \"'+fname+'\"\n')
-
- atomid2type = {}
- atomid2mol = {}
- data_file_header_names = set(['LAMMPS Description',
- 'Atoms', 'Masses', 'Velocities', 'Bonds',
- 'Angles', 'Dihedrals', 'Impropers',
- 'Pair Coeffs',
- 'Bond Coeffs', 'Angle Coeffs',
- 'Dihedral Coeffs', 'Improper Coeffs',
- #class2 force fields:
- 'BondBond Coeffs', 'BondAngle Coeffs',
- 'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs',
- 'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs',
- 'BondBond13 Coeffs',
- 'AngleAngle Coeffs',
- # non-point-like particles:
- 'Ellipsoids', 'Triangles', 'Lines',
- #specifying bonded interactions by type:
- 'Angles By Type', 'Dihedrals By Type', 'Impropers By Type'
- ])
-
- lex=LineLex(lammps_file, fname)
- lex.source_triggers = set(['include','import'])
- # set up lex to accept most characters in file names:
- lex.wordterminators = '(){}' + lex.whitespace
- # set up lex to understand the "include" statement:
- lex.source = 'include'
- lex.escape = '\\'
-
- while lex:
- infile = lex.infile
- lineno = lex.lineno
- line = lex.ReadLine()
- if (lex.infile != infile):
- infile = lex.infile
- lineno = lex.lineno
-
- #sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n')
-
- if line == '':
- break
-
- tokens = line.strip().split()
- if (len(tokens) > 0):
- if ((tokens[0] == 'atom_style') and
- atom_style_undefined):
-
- sys.stderr.write(' Atom Style found. Processing: \"'+line.strip()+'\"\n')
- if atoms_already_read:
- raise InputError('Error: The file containing the \"atom_style\" command must\n'
- ' come before the data file in the argument list.\n'
- ' (The templify program needs to know the atom style before reading\n'
- ' the data file. Either change the order of arguments so that the\n'
- ' LAMMPS input script file is processed before the data file, or use\n'
- ' the \"-atom_style\" command line argument to specify the atom_style.)\n')
-
- column_names = AtomStyle2ColNames(line.split()[1])
- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
- # Which columns contain the coordinates?
- ii_coords = ColNames2Coords(column_names)
- assert(len(ii_coords) == 1)
- i_x = ii_coords[0][0]
- i_y = ii_coords[0][1]
- i_z = ii_coords[0][2]
-
- sys.stderr.write('\n \"Atoms\" column format:\n')
- sys.stderr.write(' '+(' '.join(column_names))+'\n')
- if i_molid:
- sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n')
- else:
- sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n\n')
- l_in_init.append((' '*indent)+line.lstrip())
-
- elif (tokens[0] in set(['units',
- 'angle_style',
- 'bond_style',
- 'dihedral_style',
- 'improper_style',
- 'min_style',
- 'pair_style',
- 'pair_modify',
- 'special_bonds',
- 'kspace_style',
- 'kspace_modify'])):
- l_in_init.append((' '*indent)+line.lstrip())
-
- #if (line.strip() == 'LAMMPS Description'):
- # sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- # # skip over this section
- # while lex:
- # line = lex.ReadLine()
- # if line.strip() in data_file_header_names:
- # lex.push_raw_text(line) # <- Save line for later
- # break
-
- elif (line.strip() == 'Atoms'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- atoms_already_read = True
-
- # Before attempting to read atomic coordinates, first find
- # the lattice vectors of the simulation's boundary box:
- # Why do we care about the Simulation Boundary?
- # Some LAMMPS data files store atomic coordinates in a
- # complex format with 6 numbers, 3 floats, and 3 integers.
- # The 3 floats are x,y,z coordinates. Any additional numbers
- # following these are integers which tell LAMMPS which cell
- # the particle belongs to, (in case it has wandered out of
- # the original periodic boundary box). In order to find
- # the true location of the particle, we need to offset that
- # particle's position with the unit-cell lattice vectors:
- # avec, bvec, cvec (or multiples thereof)
- # avec, bvec, cvec are the axis of the parallelepiped which
- # define the simulation's boundary. They are described here:
- #http://lammps.sandia.gov/doc/Section_howto.html#howto-12
- if ((boundary_xlo==None) or (boundary_xhi==None) or
- (boundary_ylo==None) or (boundary_yhi==None) or
- (boundary_zlo==None) or (boundary_zhi==None)):
-
- raise InputError('Error: Either DATA file lacks a boundary-box header, or it is in the wrong\n'
- ' place. At the beginning of the file, you need to specify the box size:\n'
- ' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n'
- ' These numbers should appear BEFORE the other sections in the data file\n'
- ' (such as the \"Atoms\", \"Masses\", \"Bonds\", \"Pair Coeffs\" sections)\n'
- '\n'
- ' Use this format (example):\n'
- ' -100.0 100.0 xhi xlo\n'
- ' 0.0 200.0 yhi ylo\n'
- ' -25.0 50.0 zhi zlo\n'
- '\n'
- 'For details, see http://lammps.sandia.gov/doc/read_data.html\n'
- '\n'
- ' (NOTE: If the atom coordinates are NOT followed by integers, then\n'
- ' these numbers are all ignored, however you must still specify\n'
- ' xlo, xhi, ylo, yhi, zlo, zhi. You can set them all to 0.0.)\n')
-
- if not (boundary_xy and boundary_yz and boundary_xz):
- # Then use a simple rectangular boundary box:
- avec = (boundary_xhi-boundary_xlo, 0.0, 0.0)
- bvec = (0.0, boundary_yhi-boundary_ylo, 0.0)
- cvec = (0.0, 0.0, boundary_zhi-boundary_zlo)
- else:
- # Triclinic geometry in LAMMPS is explained here:
- # http://lammps.sandia.gov/doc/Section_howto.html#howto-12
- # http://lammps.sandia.gov/doc/read_data.html
- avec = (boundary_xhi-boundary_xlo, 0.0, 0.0)
- bvec = (boundary_xy, boundary_yhi-boundary_ylo, 0.0)
- cvec = (boundary_xz, boundary_yz, boundary_zhi-boundary_zlo)
-
-
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if ((len(tokens) <= i_atomid) or
- (len(tokens) <= i_atomtype) or
- ((i_molid != None) and
- (len(tokens) <= i_molid))):
- raise InputError('Error: The number of columns in the \"Atoms\" section does\n'
- ' not match the atom_style (see column name list above).\n')
- elif ((len(tokens) != len(column_names)) and
- (len(tokens) != len(column_names)+3) and
- (not complained_atom_style_mismatch)):
- complained_atom_style_mismatch = True
- sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n'
- ' not match the atom_style (see column name list above).\n')
- # this is not a very serious warning.
- #no_warnings = False <--no need. commenting out
-
-
- atomid = Intify(tokens[i_atomid])
- atomtype = Intify(tokens[i_atomtype])
-
- molid = None
- if i_molid:
- molid = Intify(tokens[i_molid])
-
- atomid2type[atomid] = atomtype
- if i_molid:
- atomid2mol[atomid] = molid
-
-
- if (BelongsToSel(atomid, atomid_selection) and
- BelongsToSel(atomtype, atomtype_selection) and
- BelongsToSel(molid, molid_selection)):
-
- tokens[i_atomid] = '$atom:id'+tokens[i_atomid]
- #tokens[i_atomid] = '$atom:'+atomids_int2name[atomid]
- # fill atomtype_int2str[] with a default name (change later):
- #tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype]
- atomtype_name = 'type'+tokens[i_atomtype]
- atomtypes_int2name[atomtype] = atomtype_name
- tokens[i_atomtype] = '@atom:'+atomtype_name
-
- # Interpreting unit-cell counters
- # If present, then unit-cell "flags" must be
- # added to the x,y,z coordinates.
- #
- # For more details on unit-cell "flags", see:
- # http://lammps.sandia.gov/doc/read_data.html
- # "In the data file, atom lines (all lines or
- # none of them) can optionally list 3 trailing
- # integer values (nx,ny,nz), which are used to
- # initialize the atom’s image flags.
- # If nx,ny,nz values are not listed in the
- # data file, LAMMPS initializes them to 0.
- # Note that the image flags are immediately
- # updated if an atom’s coordinates need to
- # wrapped back into the simulation box."
-
- if (len(tokens) == len(column_names)+3):
- nx = int(tokens[-3])
- ny = int(tokens[-2])
- nz = int(tokens[-1])
- x = float(tokens[i_x]) + nx*avec[0]+ny*bvec[0]+nz*cvec[0]
- y = float(tokens[i_y]) + nx*avec[1]+ny*bvec[1]+nz*cvec[1]
- z = float(tokens[i_z]) + nx*avec[2]+ny*bvec[2]+nz*cvec[2]
- tokens[i_x] = str(x)
- tokens[i_y] = str(y)
- tokens[i_z] = str(z)
- # Now get rid of them:
- del tokens[-3:]
-
-
-
- # I can't use atomids_int2name or atomtypes_int2name yet
- # because they probably have not been defined yet.
- # (Instead assign these names in a later pass.)
-
- if i_molid:
- tokens[i_molid] = '$mol:id'+tokens[i_molid]
- l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n'))
- needed_atomids.add(atomid)
-
- needed_atomtypes.add(atomtype)
- # Not all atom_styles have molids.
- # Check for this before adding.
- if molid != None:
- needed_molids.add(molid)
-
- for atomtype in needed_atomtypes:
- assert(type(atomtype) is int)
- if ((min_needed_atomtype == None) or
- (min_needed_atomtype > atomtype)):
- min_needed_atomtype = atomtype
- if ((max_needed_atomtype == None) or
- (max_needed_atomtype < atomtype)):
- max_needed_atomtype = atomtype
-
- for atomid in needed_atomids:
- assert(type(atomid) is int)
- if ((min_needed_atomid == None) or
- (min_needed_atomid > atomid)):
- min_needed_atomid = atomid
- if ((max_needed_atomid == None) or
- (max_needed_atomid < atomid)):
- max_needed_atomid = atomid
- for molid in needed_molids:
- assert(type(molid) is int)
- if ((min_needed_molid == None) or
- (min_needed_molid > molid)):
- min_needed_molid = molid
- if ((max_needed_molid == None) or
- (max_needed_molid < molid)):
- max_needed_molid = molid
-
- elif (line.strip() == 'Masses'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- # Read the next line of text but don't skip comments
- comment_char_backup = lex.commenters
- lex.commenters = ''
- line = lex.ReadLine()
- lex.commenters = comment_char_backup
-
- comment_text = ''
- ic = line.find('#')
- if ic != -1:
- line = line[:ic]
- comment_text = line[ic+1:].strip()
- line = line.rstrip()
-
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
-
- tokens = line.strip().split()
- if len(tokens) > 0:
- atomtype = Intify(tokens[0])
- atomtype_name = str(atomtype)
-
- if comment_text != '':
- comment_tokens = comment_text.split()
- # Assume the first word after the # is the atom type name
- atomtype_name = comment_tokens[0]
-
- if BelongsToSel(atomtype, atomtype_selection):
- #tokens[0] = '@atom:type'+tokens[0]
- l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n'))
- # infer atom type names from comment strings?
- if infer_types_from_comments:
- if atomtype_name in atomtypes_name2int:
- raise InputError('Error: duplicate atom type names in mass section: \"'+atomtype_name+'\"\n'
- ' (By default '+g_program_name+' attempts to infer atom type names from\n'
- ' comments which appear in the \"Masses\" section of your data file.)\n'
- ' You can avoid this error by adding the \"-ignore-comments\" argument.\n')
- atomtypes_name2int[atomtype_name] = atomtype
- atomtypes_int2name[atomtype] = atomtype_name
- else:
- atomtypes_int2name[atomtype] = 'type'+str(atomtype)
-
-
- elif (line.strip() == 'Velocities'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- atomid = Intify(tokens[0])
- atomtype = None
- if atomid in atomid2type:
- atomtype = atomid2type[atomid]
- moldid = None
- if atomid in atomid2mol:
- molid = atomid2mol[atomid]
- if (BelongsToSel(atomid, atomid_selection) and
- BelongsToSel(atomtype, atomtype_selection) and
- BelongsToSel(molid, molid_selection)):
- tokens[0] = '$atom:id'+tokens[0]
- #tokens[0] = '$atom:'+atomids_int2name[atomid]
- #NOTE:I can't use "atomids_int2name" yet because
- # they probably have not been defined yet.
- # (Instead assign these names in a later pass.)
- l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- # non-point-like-particles:
- elif (line.strip() == 'Ellipsoids'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- atomid = Intify(tokens[0])
- atomtype = None
- if atomid in atomid2type:
- atomtype = atomid2type[atomid]
- moldid = None
- if atomid in atomid2mol:
- molid = atomid2mol[atomid]
- if (BelongsToSel(atomid, atomid_selection) and
- BelongsToSel(atomtype, atomtype_selection) and
- BelongsToSel(molid, molid_selection)):
- tokens[0] = '$atom:id'+tokens[0]
- #tokens[0] = '$atom:'+atomids_int2name[atomid]
- #NOTE:I can't use "atomids_int2name" yet because
- # they probably have not been defined yet.
- # (Instead assign these names in a later pass.)
- l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (line.strip() == 'Lines'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- atomid = Intify(tokens[0])
- atomtype = None
- if atomid in atomid2type:
- atomtype = atomid2type[atomid]
- moldid = None
- if atomid in atomid2mol:
- molid = atomid2mol[atomid]
- if (BelongsToSel(atomid, atomid_selection) and
- BelongsToSel(atomtype, atomtype_selection) and
- BelongsToSel(molid, molid_selection)):
- tokens[0] = '$atom:id'+tokens[0]
- #tokens[0] = '$atom:'+atomids_int2name[atomid]
- #NOTE:I can't use "atomids_int2name" yet because
- # they probably have not been defined yet.
- # (Instead assign these names in a later pass.)
- l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (line.strip() == 'Triangles'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- atomid = Intify(tokens[0])
- atomtype = None
- if atomid in atomid2type:
- atomtype = atomid2type[atomid]
- moldid = None
- if atomid in atomid2mol:
- molid = atomid2mol[atomid]
- if (BelongsToSel(atomid, atomid_selection) and
- BelongsToSel(atomtype, atomtype_selection) and
- BelongsToSel(molid, molid_selection)):
- tokens[0] = '$atom:id'+tokens[0]
- #tokens[0] = '$atom:'+atomids_int2name[atomid]
- #NOTE:I can't use "atomids_int2name" yet because
- # they probably have not been defined yet.
- # (Instead assign these names in a later pass.)
- l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Bonds'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if (len(tokens) < 4):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical line in Bonds section:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[0] = '$bond:id'+tokens[0]
- #tokens[1] = '@bond:type'+tokens[1]
- atomids = [None, None]
- atomtypes = [None, None]
- molids = [None, None]
- in_selections = True
- some_in_selection = False
- for n in range(0,2):
- atomids[n] = Intify(tokens[2+n])
- if atomids[n] in atomid2type:
- atomtypes[n] = atomid2type[atomids[n]]
- if atomids[n] in atomid2mol:
- molids[n] = atomid2mol[atomids[n]]
- if (BelongsToSel(atomids[n], atomid_selection) and
- BelongsToSel(atomtypes[n], atomtype_selection) and
- BelongsToSel(molids[n], molid_selection)):
- #tokens[2+n] = '$atom:id'+tokens[2+n]
- #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
- some_in_selection = True
- else:
- in_selections = False
- if in_selections:
- l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif some_in_selection:
- sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n')
- sys.stderr.write(' (between atom ids: ')
-
- for n in range(0,2):
- sys.stderr.write(str(atomids[n])+' ')
- sys.stderr.write(')\n'
- ' The atoms you selected are bonded\n'
- ' to other atoms you didn\'t select.\n'
- ' Are you sure you selected the correct atoms?\n')
- no_warnings = False
-
-
-
- elif (line.strip() == 'Angles'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line == '':
- break
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if (len(tokens) < 5):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical line in Angles section:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[0] = '$angle:id'+tokens[0]
- #tokens[1] = '@angle:type'+tokens[1]
- atomids = [None, None, None]
- atomtypes = [None, None, None]
- molids = [None, None, None]
- in_selections = True
- some_in_selection = False
- for n in range(0,3):
- atomids[n] = Intify(tokens[2+n])
- if atomids[n] in atomid2type:
- atomtypes[n] = atomid2type[atomids[n]]
- if atomids[n] in atomid2mol:
- molids[n] = atomid2mol[atomids[n]]
- if (BelongsToSel(atomids[n], atomid_selection) and
- BelongsToSel(atomtypes[n], atomtype_selection) and
- BelongsToSel(molids[n], molid_selection)):
- #tokens[2+n] = '$atom:id'+tokens[2+n]
- #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
- some_in_selection = True
- else:
- in_selections = False
- if in_selections:
- l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif some_in_selection:
- sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n')
- sys.stderr.write(' (between atom ids: ')
- for n in range(0,3):
- sys.stderr.write(str(atomids[n])+' ')
- sys.stderr.write(')\n'
- ' The atoms you selected participate in 3-body \"Angle\"\n'
- ' interactions with other atoms you didn\'t select.\n'
- ' (They will be ignored.)\n'
- ' Are you sure you selected the correct atoms?\n')
- no_warnings = False
-
-
- elif (line.strip() == 'Dihedrals'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if (len(tokens) < 6):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical line in Dihedrals section:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[0] = '$dihedral:id'+tokens[0]
- #tokens[1] = '@dihedral:type'+tokens[1]
- atomids = [None, None, None, None]
- atomtypes = [None, None, None, None]
- molids = [None, None, None, None]
- in_selections = True
- some_in_selection = False
- for n in range(0,4):
- atomids[n] = Intify(tokens[2+n])
- if atomids[n] in atomid2type:
- atomtypes[n] = atomid2type[atomids[n]]
- if atomids[n] in atomid2mol:
- molids[n] = atomid2mol[atomids[n]]
- if (BelongsToSel(atomids[n], atomid_selection) and
- BelongsToSel(atomtypes[n], atomtype_selection) and
- BelongsToSel(molids[n], molid_selection)):
- #tokens[2+n] = '$atom:id'+tokens[2+n]
- #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
- some_in_selection = True
- else:
- in_selections = False
- if in_selections:
- l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif some_in_selection:
- sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n')
- sys.stderr.write(' (between atom ids: ')
- for n in range(0,4):
- sys.stderr.write(str(atomids[n])+' ')
- sys.stderr.write(')\n'
- ' The atoms you selected participate in 4-body \"Dihedral\"\n'
- ' interactions with other atoms you didn\'t select.\n'
- ' (They will be ignored.)\n'
- ' Are you sure you selected the correct atoms?\n')
- no_warnings = False
-
-
- elif (line.strip() == 'Impropers'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if (len(tokens) < 6):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical line in Impropers section:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[0] = '$improper:id'+tokens[0]
- #tokens[1] = '@improper:type'+tokens[1]
- atomids = [None, None, None, None]
- atomtypes = [None, None, None, None]
- molids = [None, None, None, None]
- in_selections = True
- some_in_selection = False
- for n in range(0,4):
- atomids[n] = Intify(tokens[2+n])
- if atomids[n] in atomid2type:
- atomtypes[n] = atomid2type[atomids[n]]
- if atomids[n] in atomid2mol:
- molids[n] = atomid2mol[atomids[n]]
- if (BelongsToSel(atomids[n], atomid_selection) and
- BelongsToSel(atomtypes[n], atomtype_selection) and
- BelongsToSel(molids[n], molid_selection)):
- #tokens[2+n] = '$atom:id'+tokens[2+n]
- #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
- some_in_selection = True
- else:
- in_selections = False
- if in_selections:
- l_data_impropers.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif some_in_selection:
- sys.stderr.write('WARNING: SELECTION BREAKS IMPROPERS\n')
- sys.stderr.write(' (between atom ids: ')
- for n in range(0,4):
- sys.stderr.write(str(atomids[n])+' ')
- sys.stderr.write(')\n'
- ' The atoms you selected participate in 4-body \"Improper\"\n'
- ' interactions with other atoms you didn\'t select.\n'
- ' (They will be ignored.)\n'
- ' Are you sure you selected the correct atoms?\n')
- no_warnings = False
-
-
- elif (line.strip() == 'Bond Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@bond:type'+tokens[0]
- l_data_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Angle Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@angle:type'+tokens[0]
- l_data_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Dihedral Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@dihedral:type'+tokens[0]
- l_data_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Improper Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@improper:type'+tokens[0]
- l_data_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Pair Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- some_pair_coeffs_read = True
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if (len(tokens) < 2):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical line in Pair Coeffs section:\n'
- ' \"'+line.strip()+'\"\n')
- atomtype_i_str = tokens[0]
- if '*' in atomtype_i_str:
- raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n'
- ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n'
- ' character in the \"Pair Coeffs\" section.\n')
- else:
- i = int(atomtype_i_str)
- if ((not i) or
- BelongsToSel(i, atomtype_selection)):
- i_str = '@atom:type'+str(i)
- tokens[0] = i_str
- l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'PairIJ Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- some_pair_coeffs_read = True
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- if (len(tokens) < 2):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical line in Pair Coeffs section:\n'
- ' \"'+line.strip()+'\"\n')
- atomtype_i_str = tokens[0]
- atomtype_j_str = tokens[1]
- if (('*' in atomtype_i_str) or ('*' in atomtype_j_str)):
- raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n'
- ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n'
- ' character in the \"PairIJ Coeffs\" section.\n')
- else:
- i = int(atomtype_i_str)
- j = int(atomtype_j_str)
- if (((not i) or BelongsToSel(i, atomtype_selection)) and
- ((not j) or BelongsToSel(j, atomtype_selection))):
- i_str = '@atom:type'+str(i)
- j_str = '@atom:type'+str(j)
- tokens[0] = i_str
- tokens[1] = j_str
- l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (tokens[0] == 'pair_coeff'):
- some_pair_coeffs_read = True
- if (len(tokens) < 3):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical pair_coeff command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_pair_coeffs.append(' '*indent+line.strip())
-
- elif (tokens[0] == 'mass'):
- some_pair_coeffs_read = True
- if (len(tokens) < 3):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical \"mass\" command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_masses.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (tokens[0] == 'bond_coeff'):
- if (len(tokens) < 2):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical bond_coeff command:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[1] = '@bond:type'+tokens[1]
- l_in_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (tokens[0] == 'angle_coeff'):
- if (len(tokens) < 2):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical angle_coeff command:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[1] = '@angle:type'+tokens[1]
- l_in_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (tokens[0] == 'dihedral_coeff'):
- if (len(tokens) < 2):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical dihedral_coeff command:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[1] = '@dihedral:type'+tokens[1]
- l_in_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (tokens[0] == 'improper_coeff'):
- if (len(tokens) < 2):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical improper_coeff command:\n'
- ' \"'+line.strip()+'\"\n')
- #tokens[1] = '@improper:type'+tokens[1]
- l_in_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
-
- # -- class2 force fields --
- elif (line.strip() == 'BondBond Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@angle:type'+tokens[0]
- l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'BondAngle Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@angle:type'+tokens[0]
- l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'MiddleBondTorsion Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@dihedral:type'+tokens[0]
- l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'EndBondTorsion Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@dihedral:type'+tokens[0]
- l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'AngleTorsion Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@dihedral:type'+tokens[0]
- l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'AngleAngleTorsion Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@dihedral:type'+tokens[0]
- l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'BondBond13 Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@dihedral:type'+tokens[0]
- l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'AngleAngle Coeffs'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- #tokens[0] = '@improper:type'+tokens[0]
- l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Angles By Type'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- tokens[0] = '@angle:type'+tokens[0]
- l_data_angles_by_type.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Dihedrals By Type'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- tokens[0] = '@dihedral:type'+tokens[0]
- l_data_dihedrals_by_type.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif (line.strip() == 'Impropers By Type'):
- sys.stderr.write(' reading \"'+line.strip()+'\"\n')
- while lex:
- line = lex.ReadLine()
- if line.strip() in data_file_header_names:
- lex.push_raw_text(line) # <- Save line for later
- break
- tokens = line.strip().split()
- if len(tokens) > 0:
- tokens[0] = '@improper:type'+tokens[0]
- l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n'))
-
-
- # Figure out the size of the simulation box boundary:
- elif ((len(tokens)==4) and
- (tokens[2] == 'xlo') and
- (tokens[3] == 'xhi') and
- IsNumber(tokens[0]) and
- IsNumber(tokens[1])):
- boundary_xlo = float(tokens[0])
- boundary_xhi = float(tokens[1])
-
- elif ((len(tokens)==4) and
- (tokens[2] == 'ylo') and
- (tokens[3] == 'yhi') and
- IsNumber(tokens[0]) and
- IsNumber(tokens[1])):
- boundary_ylo = float(tokens[0])
- boundary_yhi = float(tokens[1])
-
- elif ((len(tokens)==4) and
- (tokens[2] == 'zlo') and
- (tokens[3] == 'zhi') and
- IsNumber(tokens[0]) and
- IsNumber(tokens[1])):
- boundary_zlo = float(tokens[0])
- boundary_zhi = float(tokens[1])
-
- elif ((len(tokens)==6) and
- (tokens[3] == 'xy') and
- (tokens[4] == 'xz') and
- (tokens[5] == 'yz') and
- IsNumber(tokens[0]) and
- IsNumber(tokens[1]) and
- IsNumber(tokens[2])):
- boundary_xy = float(tokens[0])
- boundary_xz = float(tokens[1])
- boundary_yz = float(tokens[2])
-
- elif (tokens[0] == 'group'):
- if (len(tokens) < 3):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical group command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_group.append((' '*indent)+(' '.join(tokens)+'\n'))
-
- elif ((tokens[0] == 'fix') and (len(tokens) >= 4)):
- if (tokens[3].find('rigid') == 0):
- if (len(tokens) < 6):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_fix_rigid.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (tokens[3].find('shake') == 0):
- if (len(tokens) < 7):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_fix_shake.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (tokens[3].find('poems') == 0):
- if (len(tokens) < 4):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_fix_poems.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (tokens[3].find('qeq') == 0):
- if (len(tokens) < 8):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_fix_qeq.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (tokens[3].find('qmmm') == 0):
- if (len(tokens) < 8):
- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
- ' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
- ' \"'+line.strip()+'\"\n')
- l_in_fix_qmmm.append((' '*indent)+(' '.join(tokens)+'\n'))
- elif (tokens[3].find('restrain') == 0):
- sys.stderr('WARNING: fix \"'+tokens[3]+'\" commands are NOT understood by '+g_program_name+'.\n'
- ' If you need restraints, add them to your final .LT file (eg. \"system.lt\"),\n'
- ' (And be sure to use unique (full, long) moltemplate names for each $atom:.)\n'
- ' Ignoring line \"'+line.strip()+'\"\n')
-
- else:
- sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n')
-
- sys.stderr.write('\n\n')
-
- sys.stderr.write(' processing \"Atoms\" section (')
-
- # post-processing:
-
- if len(l_data_masses) == 0:
- infer_types_from_comments = False
-
- # Pass 1 through l_data_atoms:
- # Now do a second-pass throught the "l_data_atoms" section, and
- # finish dealing with "infer_types_from_comments".
- # During this pass, peplace the atomtype names and atomid names with
- # atom type names which were inferred from comments read earlier.
-
- sys.stderr.write('pass1')
- for i in range(0, len(l_data_atoms)):
- tokens = l_data_atoms[i].split()
- atomid = tokens[i_atomid]
- if atomid.find('$atom:') == 0:
- atomid = atomid[6:]
- # convert to an integer
- atomid = Intify(atomid)
-
- if infer_types_from_comments:
- atomtype = tokens[i_atomtype]
- # remove the "@atom:" prefix (we will put it back later)
- if atomtype.find('@atom:') == 0:
- atomtype = atomtype[6:]
- # convert to an integer
- atomtype = Intify(atomtype)
- atomtype_name = atomtypes_int2name[atomtype]
- if atomtype in atomids_by_type:
- l_atomids = atomids_by_type[atomtype]
- prev_count = len(l_atomids)
- # lookup the most recently added atom of this type:
- #prev_atomid_name = l_atomids[-1]
- #ic = prev_atomid_name.rfind('_')
- #prev_count = int(prev_atomid_name[ic+1:])
- atomid_name = atomtype_name+'_'+str(prev_count+1)
- atomids_by_type[atomtype].append(atomid)
- else:
- atomids_by_type[atomtype] = [atomid]
- atomid_name = atomtype_name+'_1'
- atomids_int2name[atomid] = atomid_name
- #atomids_name2str[atomid_name] = atomid
- else:
- atomids_int2name[atomid] = 'id'+str(atomid)
-
- sys.stderr.write(', pass2')
- # Pass 2: If any atom types only appear once, simplify their atomid names.
- for i in range(0, len(l_data_atoms)):
- tokens = l_data_atoms[i].split()
-
- # remove the "@atom:" prefix (we will put it back later)
- atomtype = tokens[i_atomtype]
- if atomtype.find('@atom:') == 0:
- atomtype = atomtype[6:]
- atomtype = Intify(atomtype)
- if infer_types_from_comments:
- if len(atomids_by_type[atomtype]) == 1:
- atomid = tokens[i_atomid]
- if atomid.find('$atom:') == 0:
- atomid = atomid[6:]
- atomid = Intify(atomid)
- atomtype_name = atomtypes_int2name[atomtype]
- atomids_int2name[atomid] = atomtype_name
-
- sys.stderr.write(', pass3')
- # Pass 3: substitute the atomid names and atom type names into l_data_atoms
- for i in range(0, len(l_data_atoms)):
- tokens = l_data_atoms[i].split()
- atomid = tokens[i_atomid]
- if atomid.find('$atom:') == 0:
- atomid = atomid[6:]
- # convert to an integer
- atomid = Intify(atomid)
- atomtype = tokens[i_atomtype]
- if atomtype.find('@atom:') == 0:
- atomtype = atomtype[6:]
- atomtype = Intify(atomtype)
- tokens = l_data_atoms[i].split()
- tokens[i_atomid] = '$atom:'+atomids_int2name[atomid]
- tokens[i_atomtype] = '@atom:'+atomtypes_int2name[atomtype]
- l_data_atoms[i] = (' '*indent)+(' '.join(tokens)+'\n')
- sys.stderr.write(')\n')
-
-
- if len(l_data_atoms) == 0:
- raise InputError('Error('+g_program_name+'): You have no atoms in you selection!\n'
- '\n'
- ' Either you have chosen a set of atoms, molecules, or atom types which\n'
- ' does not exist, or there is a problem with (the format of) your\n'
- ' arguments. Check the documentation and examples.\n')
-
-
- # --- Now delete items that were not selected from the other lists ---
-
- # --- MASSES ---
-
- # delete masses for atom types we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_masses):
- line = l_data_masses[i_line]
- tokens = line.strip().split()
- atomtype = Intify(tokens[0])
- if ((not (atomtype in needed_atomtypes)) and
- (not ((len(atomtype_selection) > 0) and
- BelongsToSel(atomtype, atomtype_selection)))):
- del l_data_masses[i_line]
- else:
- atomtype_name = atomtypes_int2name[atomtype]
- tokens[0] = '@atom:'+atomtype_name
- l_data_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
-
-
- # --- PAIR COEFFS ---
-
- # delete data_pair_coeffs for atom types we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_pair_coeffs):
- line = l_data_pair_coeffs[i_line]
- tokens = line.strip().split()
- assert(len(tokens) > 0)
- split_colon = tokens[0].split(':')
- assert(len(split_colon) == 2)
- atomtype = Intify(split_colon[1])
- if ((not (atomtype in needed_atomtypes)) and
- (not ((len(atomtype_selection) > 0) and
- BelongsToSel(atomtype, atomtype_selection)))):
- del l_data_pair_coeffs[i_line]
- else:
- i_line += 1
-
- # delete data_pairij_coeffs for atom types we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_pairij_coeffs):
- line = l_data_pairij_coeffs[i_line]
- tokens = line.strip().split()
- assert(len(tokens) > 0)
- split_colon_I = tokens[0].split(':')
- assert(len(split_colon_I) == 2)
- atomtype_I = Intify(split_colon_I[1])
- split_colon_J = tokens[1].split(':')
- assert(len(split_colon_J) == 2)
- atomtype_J = Intify(split_colon_J[1])
- if (((not (atomtype_I in needed_atomtypes)) and
- (not ((len(atomtype_selection) > 0) and
- BelongsToSel(atomtype_I, atomtype_selection))))
- or
- ((not (atomtype_J in needed_atomtypes)) and
- (not ((len(atomtype_selection) > 0) and
- BelongsToSel(atomtype_J, atomtype_selection))))):
- del l_data_pairij_coeffs[i_line]
- else:
- i_line += 1
-
- # delete in_pair_coeffs for atom we don't care about anymore:
- i_line = 0
- while i_line < len(l_in_pair_coeffs):
- line = l_in_pair_coeffs[i_line]
- tokens = line.strip().split()
- atomtype_i_str = tokens[1]
- atomtype_j_str = tokens[2]
- #if (('*' in atomtype_i_str) or
- # ('*' in atomtype_j_str)):
- # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n'
- # ' pair_coeff command contains a \"*\" character.\n'
- # ' Keep in mind that using moltemplate.sh you can manually change the\n'
- # ' numbers assigned to each atom type (when using -a or -b). Make sure\n'
- # ' nor to accidentally change the order of atom types in one of these\n'
- # ' pair_coeff commands. For example, commands like\n'
- # ' pair_coeff 10*4 20*10 0.15 3.6\n'
- # ' can be generated by moltemplate.sh, however\n'
- # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n'
- # ' pair_coeff 4*10 10*20 0.15 3.6)\n'
- # ' Later on, you may want to check to make sure moltemplate.sh\n'
- # ' is not doing this. (Fortunately you never have to worry unless\n'
- # ' you are using the -a or -b arguments with moltemplate.sh)\n')
-
- if ('*' in atomtype_i_str):
- atomtype_i_tokens = atomtype_i_str.split('*')
-
- if atomtype_i_tokens[0] == '':
- if (min_sel_atomtype and
- (min_sel_atomtype < min_needed_atomtype)):
- i_a = min_sel_atomtype
- else:
- i_a = min_needed_atomtype
- else:
- i_a = Intify(atomtype_i_tokens[0])
-
- if atomtype_i_tokens[1] == '':
- if (max_sel_atomtype and
- (max_sel_atomtype > max_needed_atomtype)):
- i_b = max_sel_atomtype
- else:
- i_b = max_needed_atomtype
- else:
- i_b = Intify(atomtype_i_tokens[1])
-
- else:
- i_a = i_b = Intify(atomtype_i_str)
-
- i_a_final = None
- i_b_final = None
- for i in range(i_a, i_b+1):
- if ((i in needed_atomtypes) or (min_sel_atomtype <= i)):
- i_a_final = i
- break
- for i in reversed(range(i_a, i_b+1)):
- if ((i in needed_atomtypes) or (max_sel_atomtype >= i)):
- i_b_final = i
- break
-
- #if i_a_final and i_b_final:
- # if i_a_final == i_b_final:
- # i_str = '@atom:type'+str(i_a_final)
- # tokens[1] = i_str
- # else:
- # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}'
-
-
-
- if ('*' in atomtype_j_str):
- atomtype_j_tokens = atomtype_j_str.split('*')
-
- if atomtype_j_tokens[0] == '':
- if (min_sel_atomtype and
- (min_sel_atomtype < min_needed_atomtype)):
- j_a = min_sel_atomtype
- else:
- j_a = min_needed_atomtype
- else:
- j_a = Intify(atomtype_j_tokens[0])
-
- if atomtype_j_tokens[1] == '':
- if (max_sel_atomtype and
- (max_sel_atomtype > max_needed_atomtype)):
- j_b = max_sel_atomtype
- else:
- j_b = max_needed_atomtype
- else:
- j_b = Intify(atomtype_j_tokens[1])
-
- else:
- j_a = j_b = Intify(atomtype_j_str)
-
- j_a_final = None
- j_b_final = None
- for j in range(j_a, j_b+1):
- if ((j in needed_atomtypes) or (min_sel_atomtype <= j)):
- j_a_final = j
- break
- for j in reversed(range(j_a, j_b+1)):
- if ((j in needed_atomtypes) or (max_sel_atomtype >= j)):
- j_b_final = j
- break
-
- #if j_a_final and j_b_final:
- # if j_a_final == j_b_final:
- # j_str = '@atom:type'+str(j_a_final)
- # tokens[1] = j_str
- # else:
- # j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}'
-
-
-
- if not (i_a_final and i_b_final and j_a_final and j_b_final):
- del l_in_pair_coeffs[i_line]
- elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)):
- del l_in_pair_coeffs[i_line]
- for i in range(i_a_final, i_b_final+1):
- for j in range(j_a_final, j_b_final+1):
- if j >= i:
- #tokens[1] = '@atom:type'+str(i)
- #tokens[2] = '@atom:type'+str(j)
- tokens[1] = '@atom:'+atomtypes_int2name[i]
- tokens[2] = '@atom:'+atomtypes_int2name[j]
- l_in_pair_coeffs.insert(i_line,
- (' '*indent)+(' '.join(tokens)+'\n'))
- i_line += 1
- else:
- #tokens[1] = '@atom:type'+tokens[1]
- #tokens[2] = '@atom:type'+tokens[2]
- tokens[1] = '@atom:'+atomtypes_int2name[int(tokens[1])]
- tokens[2] = '@atom:'+atomtypes_int2name[int(tokens[2])]
- l_in_pair_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
-
-
-
- # delete mass commands for atom types we don't care about anymore:
- i_line = 0
- while i_line < len(l_in_masses):
- line = l_in_masses[i_line]
- tokens = line.strip().split()
- atomtype_i_str = tokens[1]
- #if (('*' in atomtype_i_str) or
- # ('*' in atomtype_j_str)):
- # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n'
- # ' pair_coeff command contains a \"*\" character.\n'
- # ' Keep in mind that using moltemplate.sh you can manually change the\n'
- # ' numbers assigned to each atom type (when using -a or -b). Make sure\n'
- # ' nor to accidentally change the order of atom types in one of these\n'
- # ' pair_coeff commands. For example, commands like\n'
- # ' pair_coeff 10*4 20*10 0.15 3.6\n'
- # ' can be generated by moltemplate.sh, however\n'
- # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n'
- # ' pair_coeff 4*10 10*20 0.15 3.6)\n'
- # ' Later on, you may want to check to make sure moltemplate.sh\n'
- # ' is not doing this. (Fortunately you never have to worry unless\n'
- # ' you are using the -a or -b arguments with moltemplate.sh)\n')
-
- if ('*' in atomtype_i_str):
- atomtype_i_tokens = atomtype_i_str.split('*')
-
- if atomtype_i_tokens[0] == '':
- if (min_sel_atomtype and
- (min_sel_atomtype < min_needed_atomtype)):
- i_a = min_sel_atomtype
- else:
- i_a = min_needed_atomtype
- else:
- i_a = Intify(atomtype_i_tokens[0])
-
- if atomtype_i_tokens[1] == '':
- if (max_sel_atomtype and
- (max_sel_atomtype > max_needed_atomtype)):
- i_b = max_sel_atomtype
- else:
- i_b = max_needed_atomtype
- else:
- i_b = Intify(atomtype_i_tokens[1])
-
- else:
- i_a = i_b = Intify(atomtype_i_str)
-
- i_a_final = None
- i_b_final = None
- for i in range(i_a, i_b+1):
- if ((i in needed_atomtypes) or (min_sel_atomtype <= i)):
- i_a_final = i
- break
- for i in reversed(range(i_a, i_b+1)):
- if ((i in needed_atomtypes) or (max_sel_atomtype >= i)):
- i_b_final = i
- break
- #if i_a_final and i_b_final:
- # if i_a_final == i_b_final:
- # i_str = '@atom:type'+str(i_a_final)
- # tokens[1] = i_str
- # else:
- # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}'
-
- if not (i_a_final and i_b_final and j_a_final and j_b_final):
- del l_in_masses[i_line]
- elif ('*' in atomtype_i_str):
- del l_in_masses[i_line]
- for i in range(i_a_final, i_b_final+1):
- #tokens[1] = '@atom:type'+str(i)
- tokens[1] = '@atom:'+atomtypes_int2name[i]
- # CONTINUEHERE: CHECK THAT THIS IS WORKING
- l_in_masses.insert(i_line, (' '*indent)+(' '.join(tokens)+'\n'))
- i_line += 1
- else:
- assert(i_a == i_b)
- #tokens[1] = '@atom:type'+str(i_a)
- tokens[1] = '@atom:'+atomtypes_int2name[i_a]
- # CONTINUEHERE: CHECK THAT THIS IS WORKING
- l_in_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
-
-
-
- # --- BONDS AND BOND COEFFS ---
-
- # delete lines from data_bonds if they involve atoms we don't care about
- i_line = 0
- while i_line < len(l_data_bonds):
- line = l_data_bonds[i_line]
- tokens = line.strip().split()
- assert(len(tokens) == 4)
-
- bondid = Intify(tokens[0])
- bondtype = Intify(tokens[1])
- atomid1 = Intify(tokens[2])
- atomid2 = Intify(tokens[3])
- #if ((atomid1 in needed_atomids) and
- # (atomid2 in needed_atomids)):
- tokens[0] = '$bond:id'+str(bondid)
- tokens[1] = '@bond:type'+str(bondtype)
- #tokens[2] = '$atom:id'+str(atomid1)
- #tokens[3] = '$atom:id'+str(atomid2)
- tokens[2] = '$atom:'+atomids_int2name[atomid1]
- tokens[3] = '$atom:'+atomids_int2name[atomid2]
- needed_bondids.add(bondid)
- needed_bondtypes.add(bondtype)
- l_data_bonds[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- #else:
- # del l_data_bonds[i_line]
-
- # delete data_bond_coeffs for bondtypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_bond_coeffs):
- line = l_data_bond_coeffs[i_line]
- tokens = line.strip().split()
- bondtype = Intify(tokens[0])
- if (not (bondtype in needed_bondtypes)):
- del l_data_bond_coeffs[i_line]
- else:
- tokens[0] = '@bond:type'+str(bondtype)
- l_data_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
- # delete in_bond_coeffs for bondtypes we don't care about anymore:
- for bondtype in needed_bondtypes:
- assert(type(bondtype) is int)
- if ((min_needed_bondtype == None) or
- (min_needed_bondtype > bondtype)):
- min_needed_bondtype = bondtype
- if ((max_needed_bondtype == None) or
- (max_needed_bondtype < bondtype)):
- max_needed_bondtype = bondtype
- for bondid in needed_bondids:
- assert(type(bondid) is int)
- if ((min_needed_bondid == None) or
- (min_needed_bondid > bondid)):
- min_needed_bondid = bondid
- if ((max_needed_bondid == None) or
- (max_needed_bondid < bondid)):
- max_needed_bondid = bondid
-
-
- i_line = 0
- while i_line < len(l_in_bond_coeffs):
- line = l_in_bond_coeffs[i_line]
- tokens = line.strip().split()
- bondtype_str = tokens[1]
-
- if ('*' in bondtype_str):
- bondtype_tokens = bondtype_str.split('*')
-
- if bondtype_tokens[0] == '':
- i_a = min_needed_bondtype
- else:
- i_a = Intify(bondtype_tokens[0])
-
- if bondtype_tokens[1] == '':
- i_b = max_needed_bondtype
- else:
- i_b = Intify(bondtype_tokens[1])
-
- else:
- i_a = Intify(bondtype_str)
- i_b = i_a
-
- if i_a < min_needed_bondtype:
- i_a = min_needed_bondtype
- if i_b > max_needed_bondtype:
- i_b = max_needed_bondtype
-
- #if i_a == i_b:
- # i_str = '@bond:type'+str(i_a)
- # tokens[1] = i_str
- #else:
- # i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}'
-
- if ('*' in bondtype_str):
- del l_in_bond_coeffs[i_line]
- for i in range(i_a, i_b+1):
- if (i in needed_bondtypes):
- tokens[1] = '@bond:type'+str(i)
- l_in_bond_coeffs.insert(i_line,
- (' '*indent)+(' '.join(tokens)+'\n'))
- i_line += 1
- else:
- if i_a < i_b:
- raise InputError('Error: number of bond types in data file is not consistent with the\n'
- ' number of bond types you have define bond_coeffs for.\n')
- if (i_a == i_b) and (i_a in needed_bondtypes):
- tokens[1] = '@bond:type'+str(i_a)
- l_in_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- else:
- del l_in_bond_coeffs[i_line]
-
-
-
-
-
- # --- ANGLES AND ANGLE COEFFS ---
-
- # delete lines from data_angles if they involve atoms we don't care about
- i_line = 0
- while i_line < len(l_data_angles):
- line = l_data_angles[i_line]
- tokens = line.strip().split()
- assert(len(tokens) == 5)
-
- angleid = Intify(tokens[0])
- angletype = Intify(tokens[1])
- atomid1 = Intify(tokens[2])
- atomid2 = Intify(tokens[3])
- atomid3 = Intify(tokens[4])
- #if ((atomid1 in needed_atomids) and
- # (atomid2 in needed_atomids)):
- tokens[0] = '$angle:id'+str(angleid)
- tokens[1] = '@angle:type'+str(angletype)
- #tokens[2] = '$atom:id'+str(atomid1)
- #tokens[3] = '$atom:id'+str(atomid2)
- #tokens[4] = '$atom:id'+str(atomid3)
- tokens[2] = '$atom:'+atomids_int2name[atomid1]
- tokens[3] = '$atom:'+atomids_int2name[atomid2]
- tokens[4] = '$atom:'+atomids_int2name[atomid3]
- needed_angleids.add(angleid)
- needed_angletypes.add(angletype)
- l_data_angles[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- #else:
- # del l_data_angles[i_line]
-
- # delete data_angle_coeffs for angletypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_angle_coeffs):
- line = l_data_angle_coeffs[i_line]
- tokens = line.strip().split()
- angletype = Intify(tokens[0])
- if (not (angletype in needed_angletypes)):
- del l_data_angle_coeffs[i_line]
- else:
- tokens[0] = '@angle:type'+str(angletype)
- l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
- # --- class2specific ----
- # Do the same for BondBond and BondAngle Coeffs:
- # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by:
- # angle_coeff, dihedral_coeff, and improper_coeff commands.
- # THERE ARE NO bondbond_coeff commands, or bondangle_coeff commands,
- # etc..., so we dont have to worry about l_in_bondbond_coeffs,...
- # delete data_bondbond_coeffs for angletypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_bondbond_coeffs):
- line = l_data_bondbond_coeffs[i_line]
- tokens = line.strip().split()
- angletype = Intify(tokens[0])
- if (not (angletype in needed_angletypes)):
- del l_data_bondbond_coeffs[i_line]
- else:
- tokens[0] = '@angle:type'+str(angletype)
- l_data_bondbond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # delete data_bondangle_coeffs for angletypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_bondangle_coeffs):
- line = l_data_bondangle_coeffs[i_line]
- tokens = line.strip().split()
- angletype = Intify(tokens[0])
- if (not (angletype in needed_angletypes)):
- del l_data_bondangle_coeffs[i_line]
- else:
- tokens[0] = '@angle:type'+str(angletype)
- l_data_bondangle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # --- end of class2specific ----
-
-
- # delete in_angle_coeffs for angletypes we don't care about anymore:
- for angletype in needed_angletypes:
- assert(type(angletype) is int)
- if ((min_needed_angletype == None) or
- (min_needed_angletype > angletype)):
- min_needed_angletype = angletype
- if ((max_needed_angletype == None) or
- (max_needed_angletype < angletype)):
- max_needed_angletype = angletype
- for angleid in needed_angleids:
- assert(type(angleid) is int)
- if ((min_needed_angleid == None) or
- (min_needed_angleid > angleid)):
- min_needed_angleid = angleid
- if ((max_needed_angleid == None) or
- (max_needed_angleid < angleid)):
- max_needed_angleid = angleid
-
- i_line = 0
- while i_line < len(l_in_angle_coeffs):
- line = l_in_angle_coeffs[i_line]
- tokens = line.strip().split()
- angletype_str = tokens[1]
-
- if ('*' in angletype_str):
- angletype_tokens = angletype_str.split('*')
-
- if angletype_tokens[0] == '':
- i_a = min_needed_angletype
- else:
- i_a = Intify(angletype_tokens[0])
-
- if angletype_tokens[1] == '':
- i_b = max_needed_angletype
- else:
- i_b = Intify(angletype_tokens[1])
-
- else:
- i_a = i_b = Intify(angletype_str)
-
- if i_a < min_needed_angletype:
- i_a = min_needed_angletype
- if i_b > max_needed_angletype:
- i_b = max_needed_angletype
-
- #if i_a == i_b:
- # i_str = '@angle:type'+str(i_a)
- # tokens[1] = i_str
- #else:
- # i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}'
-
- if ('*' in angletype_str):
- del l_in_angle_coeffs[i_line]
- for i in range(i_a, i_b+1):
- if (i in needed_angletypes):
- tokens[1] = '@angle:type'+str(i)
- l_in_angle_coeffs.insert(i_line,
- (' '*indent)+(' '.join(tokens)+'\n'))
- i_line += 1
- else:
- if i_a < i_b:
- raise InputError('Error: number of angle types in data file is not consistent with the\n'
- ' number of angle types you have define angle_coeffs for.\n')
- if (i_a == i_b) and (i_a in needed_angletypes):
- tokens[1] = '@angle:type'+str(i_a)
- l_in_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- else:
- del l_in_angle_coeffs[i_line]
-
-
-
-
- # --- DIHEDRALS AND DIHEDRAL COEFFS ---
-
- # delete lines from data_dihedrals if they involve atoms we don't care about
- i_line = 0
- while i_line < len(l_data_dihedrals):
- line = l_data_dihedrals[i_line]
- tokens = line.strip().split()
- assert(len(tokens) == 6)
-
- dihedralid = Intify(tokens[0])
- dihedraltype = Intify(tokens[1])
- atomid1 = Intify(tokens[2])
- atomid2 = Intify(tokens[3])
- atomid3 = Intify(tokens[4])
- atomid4 = Intify(tokens[5])
- #if ((atomid1 in needed_atomids) and
- # (atomid2 in needed_atomids)):
- tokens[0] = '$dihedral:id'+str(dihedralid)
- tokens[1] = '@dihedral:type'+str(dihedraltype)
- #tokens[2] = '$atom:id'+str(atomid1)
- #tokens[3] = '$atom:id'+str(atomid2)
- #tokens[4] = '$atom:id'+str(atomid3)
- #tokens[5] = '$atom:id'+str(atomid4)
- tokens[2] = '$atom:'+atomids_int2name[atomid1]
- tokens[3] = '$atom:'+atomids_int2name[atomid2]
- tokens[4] = '$atom:'+atomids_int2name[atomid3]
- tokens[5] = '$atom:'+atomids_int2name[atomid4]
-
- needed_dihedralids.add(dihedralid)
- needed_dihedraltypes.add(dihedraltype)
- l_data_dihedrals[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- #else:
- # del l_data_dihedrals[i_line]
-
- # delete data_dihedral_coeffs for dihedraltypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_dihedral_coeffs):
- line = l_data_dihedral_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype = Intify(tokens[0])
- if (not (dihedraltype in needed_dihedraltypes)):
- del l_data_dihedral_coeffs[i_line]
- else:
- tokens[0] = '@dihedral:type'+str(dihedraltype)
- l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
- # --- class2specific ----
- # Do the same for MiddleBondTorsion, EndBondTorsion, AngleTorsion,
- # AngleAngleTorsion, and BondBond13 Coeffs
- # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by:
- # angle_coeff, dihedral_coeff, and improper_coeff commands.
- # THERE ARE NO "middlebondtorsion_coeff" commands, etc...so we don't
- # have to worry about dealing with "l_in_middlebondtorsion_coeffs",...
- # delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_middlebondtorsion_coeffs):
- line = l_data_middlebondtorsion_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype = Intify(tokens[0])
- if (not (dihedraltype in needed_dihedraltypes)):
- del l_data_middlebondtorsion_coeffs[i_line]
- else:
- tokens[0] = '@dihedral:type'+str(dihedraltype)
- l_data_middlebondtorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # delete data_endbondtorsion_coeffs for dihedraltypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_endbondtorsion_coeffs):
- line = l_data_endbondtorsion_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype = Intify(tokens[0])
- if (not (dihedraltype in needed_dihedraltypes)):
- del l_data_endbondtorsion_coeffs[i_line]
- else:
- tokens[0] = '@dihedral:type'+str(dihedraltype)
- l_data_endbondtorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # delete data_angletorsion_coeffs for dihedraltypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_angletorsion_coeffs):
- line = l_data_angletorsion_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype = Intify(tokens[0])
- if (not (dihedraltype in needed_dihedraltypes)):
- del l_data_angletorsion_coeffs[i_line]
- else:
- tokens[0] = '@dihedral:type'+str(dihedraltype)
- l_data_angletorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # delete data_angleangletorsion_coeffs for dihedraltypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_angleangletorsion_coeffs):
- line = l_data_angleangletorsion_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype = Intify(tokens[0])
- if (not (dihedraltype in needed_dihedraltypes)):
- del l_data_angleangletorsion_coeffs[i_line]
- else:
- tokens[0] = '@dihedral:type'+str(dihedraltype)
- l_data_angleangletorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # delete data_bondbond13_coeffs for dihedraltypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_bondbond13_coeffs):
- line = l_data_bondbond13_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype = Intify(tokens[0])
- if (not (dihedraltype in needed_dihedraltypes)):
- del l_data_bondbond13_coeffs[i_line]
- else:
- tokens[0] = '@dihedral:type'+str(dihedraltype)
- l_data_bondbond13_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # --- end of class2specific ----
-
-
- # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore:
- for dihedraltype in needed_dihedraltypes:
- assert(type(dihedraltype) is int)
- if ((min_needed_dihedraltype == None) or
- (min_needed_dihedraltype > dihedraltype)):
- min_needed_dihedraltype = dihedraltype
- if ((max_needed_dihedraltype == None) or
- (max_needed_dihedraltype < dihedraltype)):
- max_needed_dihedraltype = dihedraltype
- for dihedralid in needed_dihedralids:
- assert(type(dihedralid) is int)
- if ((min_needed_dihedralid == None) or
- (min_needed_dihedralid > dihedralid)):
- min_needed_dihedralid = dihedralid
- if ((max_needed_dihedralid == None) or
- (max_needed_dihedralid < dihedralid)):
- max_needed_dihedralid = dihedralid
-
- i_line = 0
- while i_line < len(l_in_dihedral_coeffs):
- line = l_in_dihedral_coeffs[i_line]
- tokens = line.strip().split()
- dihedraltype_str = tokens[1]
-
- if ('*' in dihedraltype_str):
- dihedraltype_tokens = dihedraltype_str.split('*')
-
- if dihedraltype_tokens[0] == '':
- i_a = min_needed_dihedraltype
- else:
- i_a = Intify(dihedraltype_tokens[0])
-
- if dihedraltype_tokens[1] == '':
- i_b = max_needed_dihedraltype
- else:
- i_b = Intify(dihedraltype_tokens[1])
-
- else:
- i_a = i_b = Intify(dihedraltype_str)
-
- if i_a < min_needed_dihedraltype:
- i_a = min_needed_dihedraltype
- if i_b > max_needed_dihedraltype:
- i_b = max_needed_dihedraltype
-
- #if i_a == i_b:
- # i_str = '@dihedral:type'+str(i_a)
- # tokens[1] = i_str
- #else:
- # i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}'
-
- if ('*' in dihedraltype_str):
- del l_in_dihedral_coeffs[i_line]
- for i in range(i_a, i_b+1):
- if (i in needed_dihedraltypes):
- tokens[1] = '@dihedral:type'+str(i)
- l_in_dihedral_coeffs.insert(i_line,
- (' '*indent)+(' '.join(tokens)+'\n'))
- i_line += 1
- else:
- if i_a < i_b:
- raise InputError('Error: number of dihedral types in data file is not consistent with the\n'
- ' number of dihedral types you have define dihedral_coeffs for.\n')
- if (i_a == i_b) and (i_a in needed_dihedraltypes):
- tokens[1] = '@dihedral:type'+str(i_a)
- l_in_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- else:
- del l_in_dihedral_coeffs[i_line]
-
-
-
- # --- IMPROPERS AND IMPROPER COEFFS ---
-
- # delete lines from data_impropers if they involve atoms we don't care about
- i_line = 0
- while i_line < len(l_data_impropers):
- line = l_data_impropers[i_line]
- tokens = line.strip().split()
- assert(len(tokens) == 6)
-
- improperid = Intify(tokens[0])
- impropertype = Intify(tokens[1])
- atomid1 = Intify(tokens[2])
- atomid2 = Intify(tokens[3])
- atomid3 = Intify(tokens[4])
- atomid4 = Intify(tokens[5])
- #if ((atomid1 in needed_atomids) and
- # (atomid2 in needed_atomids)):
- tokens[0] = '$improper:id'+str(improperid)
- tokens[1] = '@improper:type'+str(impropertype)
- #tokens[2] = '$atom:id'+str(atomid1)
- #tokens[3] = '$atom:id'+str(atomid2)
- #tokens[4] = '$atom:id'+str(atomid3)
- #tokens[5] = '$atom:id'+str(atomid4)
- tokens[2] = '$atom:'+atomids_int2name[atomid1]
- tokens[3] = '$atom:'+atomids_int2name[atomid2]
- tokens[4] = '$atom:'+atomids_int2name[atomid3]
- tokens[5] = '$atom:'+atomids_int2name[atomid4]
-
- needed_improperids.add(improperid)
- needed_impropertypes.add(impropertype)
- l_data_impropers[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- #else:
- # del l_data_impropers[i_line]
-
- # delete data_improper_coeffs for impropertypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_improper_coeffs):
- line = l_data_improper_coeffs[i_line]
- tokens = line.strip().split()
- impropertype = Intify(tokens[0])
- if (not (impropertype in needed_impropertypes)):
- del l_data_improper_coeffs[i_line]
- else:
- tokens[0] = '@improper:type'+str(impropertype)
- l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
-
- # --- class2specific ----
- # Do the same for AngleAngle Coeffs
- # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by:
- # angle_coeff, dihedral_coeff, and improper_coeff commands.
- # THERE ARE NO "angleangle_coeff" commands, etc...so we don't
- # have to worry about dealing with "l_in_angleangle_coeffs",...
- # delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore:
- # delete data_angleangle_coeffs for impropertypes we don't care about anymore:
- i_line = 0
- while i_line < len(l_data_angleangle_coeffs):
- line = l_data_angleangle_coeffs[i_line]
- tokens = line.strip().split()
- impropertype = Intify(tokens[0])
- if (not (impropertype in needed_impropertypes)):
- del l_data_angleangle_coeffs[i_line]
- else:
- tokens[0] = '@improper:type'+str(impropertype)
- l_data_angleangle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- # --- end of class2specific ----
-
-
- # delete in_improper_coeffs for impropertypes we don't care about anymore:
- for impropertype in needed_impropertypes:
- assert(type(impropertype) is int)
- if ((min_needed_impropertype == None) or
- (min_needed_impropertype > impropertype)):
- min_needed_impropertype = impropertype
- if ((max_needed_impropertype == None) or
- (max_needed_impropertype < impropertype)):
- max_needed_impropertype = impropertype
- for improperid in needed_improperids:
- assert(type(improperid) is int)
- if ((min_needed_improperid == None) or
- (min_needed_improperid > improperid)):
- min_needed_improperid = improperid
- if ((max_needed_improperid == None) or
- (max_needed_improperid < improperid)):
- max_needed_improperid = improperid
-
- i_line = 0
- while i_line < len(l_in_improper_coeffs):
- line = l_in_improper_coeffs[i_line]
- tokens = line.strip().split()
- impropertype_str = tokens[1]
-
- if ('*' in impropertype_str):
- impropertype_tokens = impropertype_str.split('*')
-
- if impropertype_tokens[0] == '':
- i_a = min_needed_impropertype
- else:
- i_a = Intify(impropertype_tokens[0])
-
- if impropertype_tokens[1] == '':
- i_b = max_needed_impropertype
- else:
- i_b = Intify(impropertype_tokens[1])
-
- else:
- i_a = i_b = Intify(impropertype_str)
-
- if i_a < min_needed_impropertype:
- i_a = min_needed_impropertype
- if i_b > max_needed_impropertype:
- i_b = max_needed_impropertype
-
- #if i_a == i_b:
- # i_str = '@improper:type'+str(i_a)
- # tokens[1] = i_str
- #else:
- # i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}'
-
- if ('*' in impropertype_str):
- del l_in_improper_coeffs[i_line]
- for i in range(i_a, i_b+1):
- if (i in needed_impropertypes):
- tokens[1] = '@improper:type'+str(i)
- l_in_improper_coeffs.insert(i_line,
- (' '*indent)+(' '.join(tokens)+'\n'))
- i_line += 1
- else:
- if i_a < i_b:
- raise InputError('Error: number of improper types in data file is not consistent with the\n'
- ' number of improper types you have define improper_coeffs for.\n')
- if (i_a == i_b) and (i_a in needed_impropertypes):
- tokens[1] = '@improper:type'+str(i_a)
- l_in_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
- i_line += 1
- else:
- del l_in_improper_coeffs[i_line]
-
- # --- GROUPS ---
-
- # Now parse through all of the "group" commands and try and figure
- # out if any of these groups contain any of the atoms we are keeping.
- # If so, then save the group and write it out.
- # (I hate trying to parse this kind of text.)
-
- #if len(l_in_group) > 0:
- # sys.stderr.write('\n'
- # ' --groups-- Attempting to parse \"group\" commands.\n'
- # ' This may cause '+g_program_name+' to crash.\n'
- # ' If so, comment out all group commands in your input script(s), and\n'
- # ' try again. (And please report the error. -Andrew 2014-10-30)\n')
-
- i_line = 0
- groups_needed = set(['all'])
- while i_line < len(l_in_group):
- line = l_in_group[i_line]
- tokens = line.strip().split()
- delete_this_command = False
- explicit_definition = False
- if len(tokens) < 3:
- delete_this_command = True
- group_name = tokens[1]
- specifier_style = tokens[2]
- str_logical = ''
- str_selection = ''
- if specifier_style[0:4] == 'type':
- str_logical+=specifier_style[4:]
- explicit_definition = True
- specifier_style = 'type'
- elif specifier_style == 'id':
- str_logical+=specifier_style[2:]
- explicit_definition = True
- specifier_style = 'id'
- elif specifier_style == 'molecule':
- str_logical+=specifier_style[8:]
- specifier_style = 'molecule'
- explicit_definition = True
-
- if explicit_definition:
- i_token_sel_min = 3
- if len(tokens) <= i_token_sel_min:
- sys.stderr.write('WARNING: possible syntax error on this line:\n'
- +' '+l_in_group[i_line]+'\n')
- delete_this_command = True
- if str_logical == '':
- str_logical = tokens[i_token_sel_min]
- if not str_logical[0].isdigit():
- i_token_sel_min += 1
- if len(tokens) <= i_token_sel_min:
- tokens.append('')
- else:
- tokens.insert(i_token_sel_min, str_logical)
-
- i_token_sel_max = len(tokens)-1
-
- for i in range(i_token_sel_min, len(tokens)):
- if tokens[i].isdigit():
- break
- else:
- i_token_sel_max = i
-
- assert(len(tokens) > i_token_sel_min)
-
- if str_logical[0:2] in ('<=','>=','==','!=','<>'):
- tokens[i_token_sel_min] = str_logical[2:] + tokens[i_token_sel_min]
- str_logical = str_logical[0:2]
- if str_logical == '<=':
- l_group_selection = [ (None,int(tokens[i_token_sel_min])) ]
- elif str_logical == '>=':
- l_group_selection = [ (int(tokens[i_token_sel_min]),None) ]
- elif str_logical == '==':
- l_group_selection = [ (int(tokens[i_token_sel_min]),
- int(tokens[i_token_sel_min])) ]
- elif str_logical == '!=':
- l_group_selection = [ (None,int(tokens[i_token_sel_min])-1),
- (int(tokens[i_token_sel_min])+1,None)]
- elif str_logical == '<>':
- l_group_selection = [ (int(tokens[i_token_sel_min]),
- int(tokens[i_token_sel_max])) ]
-
- elif str_logical[0:1] in ('<','>'):
- tokens[i_token_sel_min] = str_logical[1:] + tokens[i_token_sel_min]
- str_logical = str_logical[0:1]
- if str_logical == '<':
- l_group_selection = [(None,int(tokens[i_token_sel_min])-1)]
- elif str_logical == '>':
- l_group_selection = [(int(tokens[i_token_sel_min])+1,None)]
- else:
- str_selection = ' '.join(tokens[i_token_sel_min:i_token_sel_max+1])
- l_group_selection = LammpsSelectToIntervals(str_selection,
- slice_delim=':',
- or_delim=' ')
-
- mn, mx = IntervalListToMinMax(l_group_selection)
- if mn == None:
- mn = 1
- filtered_selection=[]
- if specifier_style == 'type':
- if mx == None:
- mx = max_needed_atomtype
- for i in range(mn, mx+1):
- if (BelongsToSel(i, l_group_selection)
- and (i in needed_atomtypes)):
- filtered_selection.append((i,i))
- elif specifier_style == 'id':
- if mx == None:
- mx = max_needed_atomid
- for i in range(mn, mx+1):
- if (BelongsToSel(i, l_group_selection)
- and (i in needed_atomids)):
- filtered_selection.append((i,i))
- elif specifier_style == 'molecule':
- if mx == None:
- mx = max_needed_molid
- for i in range(mn, mx+1):
- if (BelongsToSel(i, l_group_selection)
- and (i in needed_molids)):
- filtered_selection.append((i,i))
-
-
- MergeIntervals(filtered_selection)
-
-
- if len(filtered_selection) > 0:
-
- tokens = ['group', group_name, specifier_style]
- for interval in filtered_selection:
- a = interval[0]
- b = interval[1]
-
- if specifier_style == 'type':
- if a == b:
- tokens.append('@atom:type'+str(a))
- else:
- tokens.append('@{atom:type'+str(a)+
- '}:@{atom:type'+str(b)+'}')
-
- if specifier_style == 'id':
- if a == b:
- tokens.append('$atom:id'+str(a))
- else:
- tokens.append('${atom:id'+str(a)
- +'}:${atom:id'+str(b)+'}')
-
- if specifier_style == 'molecule':
- if a == b:
- tokens.append('$mol:id'+str(a))
- else:
- tokens.append('${mol:id'+str(a)+
- '}:${mol:id'+str(b)+'}')
-
-
- # Commenting out next two lines. (This is handled later.)
- #l_in_group[i_line] = ' '.join(tokens)
- #groups_needed.add(group_name)
-
- else:
- delete_this_command = True
-
-
- else:
- if len(tokens) > 3:
- if tokens[2] == 'union':
- i_token = 3
- while i_token < len(tokens):
- if not (tokens[i_token] in groups_needed):
- del tokens[i_token]
- else:
- i_token += 1
- # if none of the groups contain atoms we need,
- # then delete the entire command
- if len(tokens) <= 3:
- delete_this_command = True
- elif tokens[2] == 'intersect':
- i_token = 3
- while i_token < len(tokens):
- if not (tokens[i_token] in groups_needed):
- # if any of the groups we need are empty
- # then delete the command
- delete_this_command = True
- break
- i_token += 1
- elif (tokens[2] == 'subtract') and (len(tokens) >= 5):
- if not (tokens[3] in groups_needed):
- delete_this_command = True
- i_token = 4
- while i_token < len(tokens):
- if not (tokens[i_token] in groups_needed):
- del tokens[i_token]
- else:
- i_token += 1
- else:
- # Otherwise I don't recongize the syntax of this
- # group command. In that case, I just delete it.
- delete_this_command = True
-
- elif tokens[2] == 'clear':
- pass
- elif tokens[2] == 'delete':
- pass
- else:
- delete_this_command = True
- if delete_this_command:
- sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_group[i_line].rstrip()+'\"\n')
- del l_in_group[i_line]
- else:
- groups_needed.add(group_name)
- l_in_group[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
- i_line += 1
-
-
-
- # --- fix rigid ---
-
- i_line = 0
- while i_line < len(l_in_fix_rigid):
- line = l_in_fix_rigid[i_line]
- tokens = line.strip().split()
- if len(tokens) < 4:
- break
- fixid = tokens[1]
- group_name = tokens[2]
- delete_this_command = True
- assert(tokens[3].find('rigid') == 0)
- if group_name in groups_needed:
- delete_this_command = False
-
- if delete_this_command:
- sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_rigid[i_line].rstrip()+'\"\n')
- del l_in_fix_rigid[i_line]
- else:
- l_in_fix_rigid[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
- i_line += 1
-
-
-
- # --- fix shake ---
-
- i_line = 0
- while i_line < len(l_in_fix_shake):
- line = l_in_fix_shake[i_line]
- tokens = line.strip().split()
- if len(tokens) < 4:
- break
- fixid = tokens[1]
- group_name = tokens[2]
- delete_this_command = True
- assert(tokens[3].find('shake') == 0)
-
- # parse the list of angle types
- #i_token = tokens.index('a')
- for i_token in range(0, len(tokens)):
- if tokens[i_token] == 'a':
- break
- if i_token != len(tokens):
- i_token += 1
- while (i_token < len(tokens)) and tokens[i_token].isdigit():
- # delete angle types from the list which
- # do not belong to the selection
- btype=int(tokens[i_token])
- if int(tokens[i_token]) in needed_angletypes:
- tokens[i_token] = '@angle:type'+tokens[i_token]
- i_token += 1
- delete_this_command = False
- else:
- del tokens[i_token]
-
- # parse the list of bond types
- #i_token = tokens.index('b')
- for i_token in range(0, len(tokens)):
- if tokens[i_token] == 'b':
- break
- if i_token != len(tokens):
- i_token += 1
- while (i_token < len(tokens)) and tokens[i_token].isdigit():
- # delete bond types from the list which
- # do not belong to the selection
- btype=int(tokens[i_token])
- if int(tokens[i_token]) in needed_bondtypes:
- tokens[i_token] = '@bond:type'+tokens[i_token]
- i_token += 1
- delete_this_command = False
- else:
- del tokens[i_token]
-
- # parse the list of atom types
- # i_token = tokens.index('t')
- for i_token in range(0, len(tokens)):
- if tokens[i_token] == 't':
- break
- if i_token != len(tokens):
- i_token += 1
- while (i_token < len(tokens)) and tokens[i_token].isdigit():
- # delete atom types from the list which
- # do not belong to the selection
- btype=int(tokens[i_token])
- if int(tokens[i_token]) in needed_atomtypes:
- tokens[i_token] = '@atom:type'+tokens[i_token]
- i_token += 1
- delete_this_command = False
- else:
- del tokens[i_token]
-
-
- # Selecting atoms by mass feature should still work, so we
- # don't need to delete or ignore these kinds of commands.
- #for i_token in range(0, len(tokens)):
- # if tokens[i_token] == 'm':
- # break
- #if i_token != len(tokens):
- # delete_this_command = True
-
- if 'mol' in tokens:
- delete_this_command = True
-
- if not (group_name in groups_needed):
- delete_this_command = True
-
- if delete_this_command:
- sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_shake[i_line].rstrip()+'\"\n')
- del l_in_fix_shake[i_line]
- else:
- l_in_fix_shake[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
- i_line += 1
-
-
- # --- fix poems ---
-
- i_line = 0
- while i_line < len(l_in_fix_poems):
- line = l_in_fix_poems[i_line]
- tokens = line.strip().split()
- if len(tokens) < 4:
- break
- fixid = tokens[1]
- group_name = tokens[2]
- delete_this_command = True
- assert(tokens[3].find('poems') == 0)
- if group_name in groups_needed:
- delete_this_command = False
- if tokens[4] != 'molecule':
- delete_this_command = True
- sys.stderr.write('WARNING: '+g_program_name+' ONLY supports \"fix poems\" commands\n'
- ' which use the \"molecule\" keyword.\n')
- if tokens[4] == 'file':
- sys.stderr.write(' If you want use external files with fix poems, then you will have to\n'
- ' generate the file yourself. You ask use moltemplate to generate\n'
- ' this file for you, by manually adding a section at the end of your\n'
- ' final .LT file (eg. \"system.lt\") which resembles the following:\n\n'
- 'write(\"poems_file.txt\") {\n'
- ' 1 1 $atom:idname1a $atom:idname2a $atom:idname3a ...\n'
- ' 2 1 $atom:idname1b $atom:idname2b $atom:idname3b ...\n'
- ' 3 1 $atom:idname1c $atom:idname2c $atom:idname3c ...\n'
- ' : : etc...\n'
- '}\n\n'
- ' ...where $atom:idname1a, $atom:idname2a, ... are moltemplate-compatible\n'
- ' unique (full,long) id-names for the atoms in each rigid body.\n'
- ' This will insure the atom-id numbers in this file are correct.\n'
-
- ' See the documentation for fix poems for details.\n')
-
-
- if delete_this_command:
- sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_poems[i_line].rstrip()+'\"\n')
- del l_in_fix_poems[i_line]
- else:
- l_in_fix_poems[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
- i_line += 1
-
-
-
- # --- fix qeq ---
-
- i_line = 0
- while i_line < len(l_in_fix_qeq):
- line = l_in_fix_qeq[i_line]
- tokens = line.strip().split()
- if len(tokens) < 4:
- break
- fixid = tokens[1]
- group_name = tokens[2]
- delete_this_command = True
- assert(tokens[3].find('qeq') == 0)
- if group_name in groups_needed:
- delete_this_command = False
-
- if delete_this_command:
- sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_qeq[i_line].rstrip()+'\"\n')
- del l_in_fix_qeq[i_line]
- else:
- l_in_fix_qeq[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
- i_line += 1
-
-
-
- # --- fix qmmm ---
-
- i_line = 0
- while i_line < len(l_in_fix_qmmm):
- line = l_in_fix_qmmm[i_line]
- tokens = line.strip().split()
- if len(tokens) < 4:
- break
- fixid = tokens[1]
- group_name = tokens[2]
- delete_this_command = True
- assert(tokens[3].find('qmmm') == 0)
- if group_name in groups_needed:
- delete_this_command = False
-
- if delete_this_command:
- sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_qmmm[i_line].rstrip()+'\"\n')
- del l_in_fix_qmmm[i_line]
- else:
- l_in_fix_qmmm[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
- i_line += 1
-
-
-
-
-
-
- ########################################
- ### Now begin writing the template. ###
- ########################################
-
- if not some_pair_coeffs_read:
- sys.stderr.write('Warning: No \"pair coeffs\" set.\n'
- ' (No interactions between non-bonded atoms defined.)\n')
- no_warnings = False
-
- #sys.stderr.write('Writing ttree data to standard out.\n'
- # ' You can redirect this to a file using:\n'+
- # ' '+' '.join(sys.argv)+' > filename.ttree\n'
- # ' ----------------------\n')
-
- if mol_name != '':
- sys.stdout.write(mol_name + ' {\n')
-
- if len(l_in_init) > 0:
- sys.stdout.write('\n### LAMMPS commands for initialization\n'
- '### (These can be overridden later.)\n\n')
- l_in_init.insert(0, (' '*cindent)+'write_once(\"'+in_init+'\") {\n')
- l_in_init.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_init))
- if len(l_in_settings) > 0:
- sys.stdout.write('\n### LAMMPS commands for settings\n'
- '### (These can be overridden later.)\n\n')
- l_in_settings.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_settings.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_settings))
- non_empty_output = True
- if len(l_in_masses) > 0:
- l_in_masses.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_masses.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_masses))
- non_empty_output = True
-
-
- if remove_coeffs_from_data_file:
- if len(l_data_pair_coeffs) > 0:
- for line in l_data_pair_coeffs:
- tokens = line.strip().split()
- atomtype_str = tokens[0]
- l_in_pair_coeffs.append((' '*cindent)+' pair_coeff '+atomtype_str+' '+atomtype_str+' '+' '.join(tokens[1:])+'\n')
- l_data_pair_coeffs = []
- if len(l_data_pairij_coeffs) > 0:
- for line in l_data_pairij_coeffs:
- l_in_pair_coeffs.append((' '*cindent)+' pair_coeff '+line.strip()+'\n')
- l_data_pairij_coeffs = []
- if len(l_in_pair_coeffs) > 0:
- l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_pair_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_pair_coeffs))
- non_empty_output = True
-
-
- if (remove_coeffs_from_data_file and (len(l_data_bond_coeffs) > 0)):
- for line in l_data_bond_coeffs:
- l_in_bond_coeffs.append((' '*cindent)+' bond_coeff '+line.strip()+'\n')
- l_data_bond_coeffs = []
- if len(l_in_bond_coeffs) > 0:
- l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_bond_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_bond_coeffs))
- non_empty_output = True
-
- if (remove_coeffs_from_data_file and (len(l_data_angle_coeffs) > 0)):
- for line in l_data_angle_coeffs:
- l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+line.strip()+'\n')
- l_data_angle_coeffs = []
- for line in l_data_bondbond_coeffs:
- tokens = line.strip().split()
- l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+tokens[0]+' bb '+' '.join(tokens[1:])+'\n')
- l_data_bondbond_coeffs = []
- for line in l_data_bondangle_coeffs:
- tokens = line.strip().split()
- l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+tokens[0]+' ba '+' '.join(tokens[1:])+'\n')
- l_data_bondangle_coeffs = []
- if len(l_in_angle_coeffs) > 0:
- l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_angle_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_angle_coeffs))
- non_empty_output = True
-
- if (remove_coeffs_from_data_file and (len(l_data_dihedral_coeffs) > 0)):
- for line in l_data_dihedral_coeffs:
- l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+line.strip()+'\n')
- l_data_dihedral_coeffs = []
-
- for line in l_data_middlebondtorsion_coeffs:
- tokens = line.strip().split()
- l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' mbt '+' '.join(tokens[1:])+'\n')
- l_data_middlebondtorsion_coeffs = []
-
- for line in l_data_endbondtorsion_coeffs:
- tokens = line.strip().split()
- l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' ebt '+' '.join(tokens[1:])+'\n')
- l_data_endbondtorsion_coeffs = []
-
- for line in l_data_angletorsion_coeffs:
- tokens = line.strip().split()
- l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' at '+' '.join(tokens[1:])+'\n')
- l_data_angletorsion_coeffs = []
-
- for line in l_data_angleangletorsion_coeffs:
- tokens = line.strip().split()
- l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' aat '+' '.join(tokens[1:])+'\n')
- l_data_angleangletorsion_coeffs = []
-
- for line in l_data_bondbond13_coeffs:
- tokens = line.strip().split()
- l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' bb13 '+' '.join(tokens[1:])+'\n')
- l_data_bondbond13_coeffs = []
-
- if len(l_in_dihedral_coeffs) > 0:
- l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_dihedral_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_dihedral_coeffs))
- non_empty_output = True
-
- if (remove_coeffs_from_data_file and (len(l_data_improper_coeffs) > 0)):
- for line in l_data_improper_coeffs:
- l_in_improper_coeffs.append((' '*cindent)+' improper_coeff '+line.strip()+'\n')
- l_data_improper_coeffs = []
-
- for line in l_data_angleangle_coeffs:
- tokens = line.strip().split()
- l_in_improper_coeffs.append((' '*cindent)+' improper_coeff '+tokens[0]+' aa '+' '.join(tokens[1:])+'\n')
- l_data_angleangle_coeffs = []
-
- if len(l_in_improper_coeffs) > 0:
- l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
- l_in_improper_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_improper_coeffs))
- non_empty_output = True
-
- if non_empty_output:
- sys.stdout.write('\n\n### DATA sections\n\n')
-
- if len(l_data_masses) > 0:
- l_data_masses.insert(0, (' '*cindent)+'write_once(\"'+data_masses+'\") {\n')
- l_data_masses.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_masses))
- non_empty_output = True
- if len(l_data_bond_coeffs) > 0:
- l_data_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bond_coeffs+'\") {\n')
- l_data_bond_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_bond_coeffs))
- non_empty_output = True
- if len(l_data_angle_coeffs) > 0:
- l_data_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angle_coeffs+'\") {\n')
- l_data_angle_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_angle_coeffs))
- non_empty_output = True
- if len(l_data_dihedral_coeffs) > 0:
- l_data_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_dihedral_coeffs+'\") {\n')
- l_data_dihedral_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_dihedral_coeffs))
- non_empty_output = True
- if len(l_data_improper_coeffs) > 0:
- l_data_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_improper_coeffs+'\") {\n')
- l_data_improper_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_improper_coeffs))
- non_empty_output = True
- if len(l_data_pair_coeffs) > 0:
- l_data_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pair_coeffs+'\") {\n')
- l_data_pair_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_pair_coeffs))
- non_empty_output = True
- if len(l_data_pairij_coeffs) > 0:
- l_data_pairij_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pairij_coeffs+'\") {\n')
- l_data_pairij_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_pairij_coeffs))
- non_empty_output = True
-
- # class2 force fields:
- if len(l_data_bondbond_coeffs) > 0:
- l_data_bondbond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond_coeffs+'\") {\n')
- l_data_bondbond_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_bondbond_coeffs))
- non_empty_output = True
- if len(l_data_bondangle_coeffs) > 0:
- l_data_bondangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondangle_coeffs+'\") {\n')
- l_data_bondangle_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_bondangle_coeffs))
- non_empty_output = True
- if len(l_data_middlebondtorsion_coeffs) > 0:
- l_data_middlebondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_middlebondtorsion_coeffs+'\") {\n')
- l_data_middlebondtorsion_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs))
- non_empty_output = True
- if len(l_data_endbondtorsion_coeffs) > 0:
- l_data_endbondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_endbondtorsion_coeffs+'\") {\n')
- l_data_endbondtorsion_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_endbondtorsion_coeffs))
- non_empty_output = True
- if len(l_data_angletorsion_coeffs) > 0:
- l_data_angletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angletorsion_coeffs+'\") {\n')
- l_data_angletorsion_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_angletorsion_coeffs))
- non_empty_output = True
- if len(l_data_angleangletorsion_coeffs) > 0:
- l_data_angleangletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangletorsion_coeffs+'\") {\n')
- l_data_angleangletorsion_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_angleangletorsion_coeffs))
- non_empty_output = True
- if len(l_data_bondbond13_coeffs) > 0:
- l_data_bondbond13_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond13_coeffs+'\") {\n')
- l_data_bondbond13_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_bondbond13_coeffs))
- non_empty_output = True
- if len(l_data_angleangle_coeffs) > 0:
- l_data_angleangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangle_coeffs+'\") {\n')
- l_data_angleangle_coeffs.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_angleangle_coeffs))
- non_empty_output = True
-
- # automatic generation of bonded interactions by type:
- if len(l_data_angles_by_type) > 0:
- l_data_angles_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_angles_by_type+'\") {\n')
- l_data_angles_by_type.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_angles_by_type))
- non_empty_output = True
- if len(l_data_dihedrals_by_type) > 0:
- l_data_dihedrals_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_dihedrals_by_type+'\") {\n')
- l_data_dihedrals_by_type.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_dihedrals_by_type))
- non_empty_output = True
- if len(l_data_impropers_by_type) > 0:
- l_data_impropers_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_impropers_by_type+'\") {\n')
- l_data_impropers_by_type.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_impropers_by_type))
- non_empty_output = True
-
- if len(l_data_atoms) > 0:
- l_data_atoms.insert(0, (' '*cindent)+'write(\"'+data_atoms+'\") {\n')
- l_data_atoms.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_atoms))
- non_empty_output = True
- else:
- sys.stderr.write('Warning: missing \"Atoms\" section.\n'
- ' (Did you include a LAMMPS data file in your argument list?)\n')
- no_warnings = False
-
- # non-point-like particles
- if len(l_data_ellipsoids) > 0:
- l_data_ellipsoids.insert(0, (' '*cindent)+'write(\"'+data_ellipsoids+'\") {\n')
- l_data_ellipsoids.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_ellipsoids))
- if len(l_data_lines) > 0:
- l_data_lines.insert(0, (' '*cindent)+'write(\"'+data_lines+'\") {\n')
- l_data_lines.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_lines))
- if len(l_data_triangles) > 0:
- l_data_triangles.insert(0, (' '*cindent)+'write(\"'+data_triangles+'\") {\n')
- l_data_triangles.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_triangles))
-
- # DO NOT WRITE OUT VELOCITY DATA
- # (Why: because it makes it difficult to combine this molecular template
- # with molecule templates from other sources which lack velocity data.
- # LAMMPS (and topotools) will crash if the number of entries in the
- # Velocities section of a data file does not match the number of atoms.)
- # COMMENTING OUT:
- #if len(l_data_velocities) > 0:
- # l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n')
- # l_data_velocities.append((' '*cindent)+'}\n')
- # sys.stdout.write('\n')
- # sys.stdout.write(''.join(l_data_velocities))
- if len(l_data_bonds) > 0:
- l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n')
- l_data_bonds.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_bonds))
- non_empty_output = True
- if len(l_data_angles) > 0:
- l_data_angles.insert(0, (' '*cindent)+'write(\"'+data_angles+'\") {\n')
- l_data_angles.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_angles))
- non_empty_output = True
- if len(l_data_dihedrals) > 0:
- l_data_dihedrals.insert(0, (' '*cindent)+'write(\"'+data_dihedrals+'\") {\n')
- l_data_dihedrals.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_dihedrals))
- non_empty_output = True
- if len(l_data_impropers) > 0:
- l_data_impropers.insert(0, (' '*cindent)+'write(\"'+data_impropers+'\") {\n')
- l_data_impropers.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_data_impropers))
- non_empty_output = True
-
- if len(l_in_group) > 0:
- no_warnings = False
- l_in_group.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
- l_in_group.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_group))
- #sys.stderr.write('######################################################\n'
- # 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n'
- # ' Please check to make sure that the group(s) generated by\n'
- # ' '+g_program_name+' contain the correct atoms. (-Andrew 2014-10-30)\n'
- # '######################################################\n')
- assert(non_empty_output)
-
- if len(l_in_fix_rigid) > 0:
- no_warnings = False
- l_in_fix_rigid.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
- l_in_fix_rigid.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_fix_rigid))
- sys.stderr.write('WARNING: \"fix rigid\" style command(s) applied to selected atoms.\n'
- ' Please make sure that the fix group(s) are defined correctly.\n'
- '######################################################\n')
- assert(non_empty_output)
-
- if len(l_in_fix_shake) > 0:
- no_warnings = False
- l_in_fix_shake.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
- l_in_fix_shake.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_fix_shake))
- sys.stderr.write('WARNING: \"fix shake\" style command(s) applied to selected atoms.\n'
- ' Please check to make sure that the fix group(s) are defined correctly,\n'
-
- ' and also check that the atom, bond, and angle types are correct.\n'
- '######################################################\n')
- assert(non_empty_output)
-
- if len(l_in_fix_poems) > 0:
- no_warnings = False
- l_in_fix_poems.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
- l_in_fix_poems.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_fix_poems))
- sys.stderr.write('WARNING: \"fix poems\" style command(s) applied to selected atoms.\n'
- ' Please make sure that the fix group(s) are defined correctly.\n'
- '######################################################\n')
- assert(non_empty_output)
-
- if len(l_in_fix_qeq) > 0:
- no_warnings = False
- l_in_fix_qeq.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
- l_in_fix_qeq.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_fix_qeq))
- sys.stderr.write('WARNING: \"fix qeq\" style command(s) applied to selected atoms.\n'
- ' Please make sure that the fix group(s) are defined correctly.\n'
- '######################################################\n')
- assert(non_empty_output)
-
- if len(l_in_fix_qmmm) > 0:
- no_warnings = False
- l_in_fix_qmmm.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
- l_in_fix_qmmm.append((' '*cindent)+'}\n')
- sys.stdout.write('\n')
- sys.stdout.write(''.join(l_in_fix_qmmm))
- sys.stderr.write('WARNING: \"fix qmmm\" style command(s) applied to selected atoms.\n'
- ' Please make sure that the fix group(s) are defined correctly.\n'
- '######################################################\n')
- assert(non_empty_output)
-
-
-
- if mol_name != '':
- sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n')
-
-
-
- #if non_empty_output and no_warnings:
- if non_empty_output:
- sys.stderr.write('WARNING: The '+g_program_name+' script has not been rigorously tested.\n'
- ' Exotic (many-body) pair-styles and pair-styles with\n'
- ' unusual syntax (such hbond/dreiding) are not understood\n'
- ' by '+g_program_name+' (...although they are supported by moltemplate).\n'
- ' Please look over the resulting LT file and check for errors.\n'
- ' Convert any remaining atom, bond, angle, dihedral, or improper id\n'
- ' or type numbers to the corresponding $ or @-style counter variables.\n'
- ' Feel free to report any bugs you find. (-Andrew Jewett 2015-8-02)\n')
-
-
-
-except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py
deleted file mode 100644
index 743419eb2..000000000
--- a/tools/moltemplate/src/lttree.py
+++ /dev/null
@@ -1,744 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2011, Regents of the University of California
-# All rights reserved.
-
-"""
-lttree.py
-
-lttree.py is an extension of the generic ttree.py program.
-This version can understand and manipulate ttree-style templates which
-are specialized for storing molecule-specific data for use in LAMMPS.
-
-The main difference between lttree.py and ttree.py is:
-Unlike ttree.py, lttree.py understands rigid-body movement commands like
-"rot()" and "move()" which allows it to reorient and move each copy
-of a molecule to a new location. (ttree.py just ignores these commands.
-Consequently LAMMPS input file (fragments) created with ttree.py have
-invalid (overlapping) atomic coordinates and must be modified or aguemted
-later (by loading atomic coordinates from a PDB file or an XYZ file).
-lttree.py understands the "Data Atoms" section of a LAMMPS
-data file (in addition to the various "atom_styles" which effect it).
-
-Additional LAMMPS-specific features may be added in the future.
-
-"""
-
-import sys
-from ttree import *
-from lttree_styles import *
-from ttree_matrix_stack import *
-
-try:
- unicode
-except NameError:
- # Python 3
- basestring = unicode = str
-
-
-
-
-class LttreeSettings(BasicUISettings):
- def __init__(self,
- user_bindings_x=None,
- user_bindings=None,
- order_method='by_command'):
-
- BasicUISettings.__init__(self,
- user_bindings_x,
- user_bindings,
- order_method)
-
- # The following new member data indicate which columns store
- # LAMMPS-specific information.
- # The next 6 members store keep track of the different columns
- # of the "Data Atoms" section of a LAMMPS data file:
- self.column_names = [] #<--A list of column names (optional)
- self.ii_coords=[] #<--A list of triplets of column indexes storing coordinate data
- self.ii_vects=[] #<--A list of triplets of column indexes storing directional data
- # (such as dipole or ellipsoid orientations)
- self.i_atomid=None #<--An integer indicating which column has the atomid
- self.i_atomtype=None #<--An integer indicating which column has the atomtype
- self.i_molid=None #<--An integer indicating which column has the molid, if applicable
- self.infile=None # Name of the outermost file. This is the file
- # which was read at the moment parsing begins.
-
-
-
-
-def LttreeParseArgs(argv, settings):
-
- BasicUIParseArgs(argv, settings)
-
- # Loop over the remaining arguments not processed yet.
- # These arguments are specific to the lttree.py program
- # and are not understood by ttree.py:
- i = 1
- while i < len(argv):
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
- if ((argv[i].lower() == '-atomstyle') or
- (argv[i].lower() == '-atom-style') or
- (argv[i].lower() == '-atom_style')):
- if i+1 >= len(argv):
- raise InputError('Error('+g_program_name+'): The '+argv[i]+' flag should be followed by a LAMMPS\n'
- ' atom_style name (or single quoted string containing a space-separated\n'
- ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n')
- settings.column_names = AtomStyle2ColNames(argv[i+1])
- sys.stderr.write('\n \"'+data_atoms+'\" column format:\n')
- sys.stderr.write(' '+(' '.join(settings.column_names))+'\n\n')
- settings.ii_coords = ColNames2Coords(settings.column_names)
- settings.ii_vects = ColNames2Vects(settings.column_names)
- settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names)
- del(argv[i:i+2])
- elif (argv[i].lower() == '-icoord'):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n'
- ' corresponding to column numbers for coordinates in\n'
- ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n')
- ilist = argv[i+1].split()
- if (len(ilist) % 3) != 0:
- raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n'
- ' This is usually a list of 3 integers, but it can contain more.\n'
- ' The number of cooridnate columns must be divisible by 3,\n'
- ' (even if the simulation is in 2 dimensions)\n')
- settings.iaffinevects = []
- for i in range(0, len(ilist)/3):
- cols = [int(ilist[3*i])+1,
- int(ilist[3*i+1])+1,
- int(ilist[3*i+2])+1]
- settings.iaffinevects.append(cols)
- del(argv[i:i+2])
- elif (argv[i].lower() == '-ivect'):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n'
- ' corresponding to column numbers for direction vectors in\n'
- ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n')
- ilist = argv[i+1].split()
- if (len(ilist) % 3) != 0:
- raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n'
- ' This is usually a list of 3 integers, but it can contain more.\n'
- ' The number of cooridnate columns must be divisible by 3,\n'
- ' (even if the simulation is in 2 dimensions)\n')
- settings.ivects = []
- for i in range(0, len(ilist)/3):
- cols = [int(ilist[3*i])+1,
- int(ilist[3*i+1])+1,
- int(ilist[3*i+2])+1]
- settings.ivects.append(cols)
- del(argv[i:i+2])
- elif ((argv[i].lower() == '-iatomid') or
- (argv[i].lower() == '-iid') or
- (argv[i].lower() == '-iatom-id')):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n'
- ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n'
- ' LAMMPS data file contains the atom id number (typically 1).\n'
- ' (This argument is unnecessary if you use the -atomstyle argument.)\n')
- i_atomid = int(argv[i+1])-1
- del(argv[i:i+2])
- elif ((argv[i].lower() == '-iatomtype') or
- (argv[i].lower() == '-itype') or
- (argv[i].lower() == '-iatom-type')):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n'
- ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n'
- ' LAMMPS data file contains the atom type.\n'
- ' (This argument is unnecessary if you use the -atomstyle argument.)\n')
- i_atomtype = int(argv[i+1])-1
- del(argv[i:i+2])
- elif ((argv[i].lower() == '-imolid') or
- (argv[i].lower() == '-imol') or
- (argv[i].lower() == '-imol-id') or
- (argv[i].lower() == '-imoleculeid') or
- (argv[i].lower() == '-imolecule-id')):
- if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
- raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n'
- ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n'
- ' LAMMPS data file contains the molecule id number.\n'
- ' (This argument is unnecessary if you use the -atomstyle argument.)\n')
- i_molid = int(argv[i+1])-1
- del(argv[i:i+2])
-
- elif ((argv[i][0] == '-') and (__name__ == "__main__")):
- #elif (__name__ == "__main__"):
- raise InputError('Error('+g_program_name+'):\n'
- 'Unrecognized command line argument \"'+argv[i]+'\"\n')
- else:
- i += 1
-
-
- if __name__ == "__main__":
-
- # Instantiate the lexer we will be using.
- # (The lexer's __init__() function requires an openned file.
- # Assuming __name__ == "__main__", then the name of that file should
- # be the last remaining (unprocessed) argument in the argument list.
- # Otherwise, then name of that file will be determined later by the
- # python script which imports this module, so we let them handle it.)
-
- if len(argv) == 1:
- raise InputError('Error: This program requires at least one argument\n'
- ' the name of a file containing ttree template commands\n')
- elif len(argv) == 2:
- try:
- settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file
- except IOError:
- sys.stderr.write('Error: unable to open file\n'
- ' \"'+argv[1]+'\"\n'
- ' for reading.\n')
- sys.exit(1)
- del(argv[1:2])
-
- else:
- # if there are more than 2 remaining arguments,
- problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
- raise InputError('Syntax Error('+g_program_name+'):\n\n'
- ' Problem with argument list.\n'
- ' The remaining arguments are:\n\n'
- ' '+(' '.join(problem_args))+'\n\n'
- ' (The actual problem may be earlier in the argument list.\n'
- ' If these arguments are source files, then keep in mind\n'
- ' that this program can not parse multiple source files.)\n'
- ' Check the syntax of the entire argument list.\n')
-
-
-
- if len(settings.ii_coords) == 0:
- sys.stderr.write('########################################################\n'
- '## WARNING: atom_style unspecified ##\n'
- '## --> \"'+data_atoms+'\" column data has an unknown format ##\n'
- '## Assuming atom_style = \"full\" ##\n'
- # '########################################################\n'
- # '## To specify the \"'+data_atoms+'\" column format you can: ##\n'
- # '## 1) Use the -atomstyle \"STYLE\" argument ##\n'
- # '## where \"STYLE\" is a string indicating a LAMMPS ##\n'
- # '## atom_style, including hybrid styles.(Standard ##\n'
- # '## atom styles defined in 2011 are supported.) ##\n'
- # '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n'
- # '## where \"COL_LIST" is a quoted list of strings ##\n'
- # '## indicating the name of each column. ##\n'
- # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n'
- # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n'
- # '## are interpreted as direction vectors. ##\n'
- # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n'
- # '## where \"cx cy cz\" is a list of integers ##\n'
- # '## indicating the column numbers for the x,y,z ##\n'
- # '## coordinates of each atom. ##\n'
- # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n'
- # '## where \"cmux cmuy cmuz...\" is a list of ##\n'
- # '## integers indicating the column numbers for ##\n'
- # '## the vector that determines the direction of a ##\n'
- # '## dipole or ellipsoid (ie. a rotateable vector).##\n'
- # '## (More than one triplet can be specified. The ##\n'
- # '## number of entries must be divisible by 3.) ##\n'
- '########################################################\n')
-
- # The default atom_style is "full"
- settings.column_names = AtomStyle2ColNames('full')
- settings.ii_coords = ColNames2Coords(settings.column_names)
- settings.ii_vects = ColNames2Vects(settings.column_names)
- settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names)
-
-
-
-
-
-
-
-
-
-def TransformAtomText(text, matrix):
- """ Apply transformations to the coordinates and other vector degrees
- of freedom stored in the \"Data Atoms\" section of a LAMMPS data file.
- This is the \"text\" argument.
- The \"matrix\" stores the aggregate sum of combined transformations
- to be applied.
-
- """
-
- #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n')
-
- lines = text.split('\n')
-
- for i in range(0, len(lines)):
- line_orig = lines[i]
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- comment = ' '+line_orig[ic:].rstrip('\n')
- else:
- line = line_orig.rstrip('\n')
- comment = ''
-
- columns = line.split()
- if len(columns) > 0:
- if len(columns) == len(settings.column_names)+3:
- raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n'
- ' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n'
- ' Instead please add the appropriate offsets (these offsets\n'
- ' should be multiples of the cell size) to the atom coordinates\n'
- ' in the data file, and eliminate the extra columns. Then try again.\n'
- ' (If you get this message often, email me and I\'ll fix this limitation.)')
- if len(columns) < len(settings.column_names):
- raise InputError('Error: The number of columns in your data file does not\n'
- ' match the LAMMPS atom_style you selected.\n'
- ' Use the -atomstyle <style> command line argument.\n')
- x0 = [0.0, 0.0, 0.0]
- x = [0.0, 0.0, 0.0]
- # Atomic coordinates transform using "affine" transformations
- # (translations plus rotations [or other linear transformations])
- for cxcycz in settings.ii_coords:
- for d in range(0,3):
- x0[d] = float(columns[cxcycz[d]])
- AffineTransform(x, matrix, x0) # x = matrix * x0 + b
- for d in range(0,3): #("b" is part of "matrix")
- columns[cxcycz[d]] = str(x[d])
- # Dipole moments and other direction-vectors
- # are not effected by translational movement
- for cxcycz in settings.ii_vects:
- for d in range(0,3):
- x0[d] = float(columns[cxcycz[d]])
- LinearTransform(x, matrix, x0) # x = matrix * x0
- for d in range(0,3):
- columns[cxcycz[d]] = str(x[d])
- lines[i] = ' '.join(columns) + comment
- return '\n'.join(lines)
-
-
-
-def CalcCM(text_Atoms,
- text_Masses=None,
- settings=None):
- types2masses = None
- # Loop through the "Masses" section: what is the mass of each atom type?
- if text_Masses != None:
- types2masses = {}
- lines = text_Masses.split('\n')
- for i in range(0, len(lines)):
- line = lines[i]
- columns = line.split()
- if len(columns) == 2:
- atomtype = columns[0]
- m = float(columns[1])
- types2masses[atomtype] = m
-
- lines = text_Atoms.split('\n')
- # Pass 1 through the "Data Atoms" section: Determine each atom's mass
- if text_Masses != None:
- assert(settings != None)
- for i in range(0, len(lines)):
- line = lines[i]
- columns = line.split()
- atomid = columns[settings.i_atomid]
- atomtype = columns[settings.i_atomtype]
- if atomtype not in types2masses[atomtype]:
- raise InputError('Error(lttree): You have neglected to define the mass of atom type: \"'+atomtype+'\"\n'
- 'Did you specify the mass of every atom type using write(\"Masses\"){}?')
- atomid2mass[atomid] = atomtype2mass[atomtype]
-
- # Pass 2 through the "Data Atoms" section: Find the center of mass.
- for i in range(0, len(lines)):
- line = lines[i]
- columns = line.split()
- if len(columns) > 0:
- if len(columns) == len(settings.column_names)+3:
- raise InputError('Error: lttree.py does not yet support integer unit-cell counters (ix, iy, iz)\n'
- ' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n'
- ' Instead please add the appropriate offsets (these offsets\n'
- ' should be multiples of the cell size) to the atom coordinates\n'
- ' in the data file, and eliminate the extra columns. Then try again.\n'
- ' (If you get this message often, email me and I\'ll fix this limitation.)')
- if len(columns) != len(settings.column_names):
- raise InputError('Error: The number of columns in your data file does not\n'
- ' match the LAMMPS atom_style you selected.\n'
- ' Use the -atomstyle <style> command line argument.\n')
- x = [0.0, 0.0, 0.0]
- if atomids2masses != None:
- m = atomids2masses[atomid]
- else:
- m = 1.0
- tot_m += m
- for cxcycz in settings.ii_coords:
- for d in range(0,3):
- x[d] = float(columns[cxcycz[d]])
- tot_x[d] += x[d]
- # Note: dipole moments and other direction vectors don't effect
- # the center of mass. So I commented out the loop below.
- #for cxcycz in settings.ii_vects:
- # for d in range(0,3):
- # v[d] = float(columns[cxcycz[d]])
- lines[i] = ' '.join(columns)
-
- xcm = [0.0, 0.0, 0.0]
- for d in range(0,3):
- xcm[d] = tot_x[d] / tot_m
- return xcm
-
-
-
-def _ExecCommands(command_list,
- index,
- global_files_content,
- settings,
- matrix_stack,
- current_scope_id=None,
- substitute_vars=True):
- """
- _ExecCommands():
- The argument "commands" is a nested list of lists of
- "Command" data structures (defined in ttree.py).
-
- Carry out the write() and write_once() commands (which
- write out the contents of the templates contain inside them).
- Instead of writing the files, save their contents in a string.
-
- The argument "global_files_content" should be of type defaultdict(list)
- It is an associative array whose key is a string (a filename)
- and whose value is a lists of strings (of rendered templates).
-
- """
- files_content = defaultdict(list)
- postprocessing_commands = []
-
- while index < len(command_list):
- command = command_list[index]
- index += 1
-
- # For debugging only
- if ((not isinstance(command, StackableCommand)) and
- (not isinstance(command, ScopeCommand)) and
- (not isinstance(command, WriteFileCommand))):
- sys.stderr.write(str(command)+'\n')
-
-
- if isinstance(command, PopCommand):
- assert(current_scope_id != None)
- if command.context_node == None:
- command.context_node = current_scope_id
- if isinstance(command, PopRightCommand):
- matrix_stack.PopRight(which_stack = command.context_node)
- elif isinstance(command, PopLeftCommand):
- matrix_stack.PopLeft(which_stack = command.context_node)
- else:
- assert(False)
-
- elif isinstance(command, PushCommand):
- assert(current_scope_id != None)
- if command.context_node == None:
- command.context_node = current_scope_id
- # Some commands are post-processing commands, and must be
- # carried out AFTER all the text has been rendered. For example
- # the "movecm(0,0,0)" waits until all of the coordinates have
- # been rendered, calculates the center-of-mass, and then applies
- # a translation moving the center of mass to the origin (0,0,0).
- # We need to figure out which of these commands need to be
- # postponed, and which commands can be carried out now.
- # ("now"=pushing transformation matrices onto the matrix stack).
- # UNFORTUNATELY POSTPONING SOME COMMANDS MAKES THE CODE UGLY
- transform_list = command.contents.split('.')
- transform_blocks = []
- i_post_process = -1
- # Example: Suppose:
- #command.contents = '.rot(30,0,0,1).movecm(0,0,0).rot(45,1,0,0).scalecm(2.0).move(-2,1,0)'
- # then
- #transform_list = ['rot(30,0,0,1)', 'movecm(0,0,0)', 'rot(45,1,0,0)', 'scalecm(2.0)', 'move(-2,1,0)']
- # Note: the first command 'rot(30,0,0,1)' is carried out now.
- # The remaining commands are carried out during post-processing,
- # (when processing the "ScopeEnd" command.
- #
- # We break up the commands into "blocks" separated by center-
- # of-mass transformations ('movecm', 'rotcm', or 'scalecm')
- #
- # transform_blocks = ['.rot(30,0,0,1)',
- # '.movecm(0,0,0).rot(45,1,0,0)',
- # '.scalecm(2.0).move(-2,1,0)']
-
- i = 0
- while i < len(transform_list):
- transform_block = ''
- while i < len(transform_list):
- transform = transform_list[i]
- i += 1
- if transform != '':
- transform_block += '.' + transform
- transform = transform.split('(')[0]
- if ((transform == 'movecm') or
- (transform == 'rotcm') or
- (transform == 'scalecm')):
- break
- transform_blocks.append(transform_block)
-
- if len(postprocessing_commands) == 0:
- # The first block (before movecm, rotcm, or scalecm)
- # can be executed now by modifying the matrix stack.
- if isinstance(command, PushRightCommand):
- matrix_stack.PushCommandsRight(transform_blocks[0].strip('.'),
- command.srcloc,
- which_stack=command.context_node)
- elif isinstance(command, PushLeftCommand):
- matrix_stack.PushCommandsLeft(transform_blocks[0].strip('.'),
- command.srcloc,
- which_stack=command.context_node)
- # Everything else must be saved for later.
- postprocessing_blocks = transform_blocks[1:]
- else:
- # If we already encountered a "movecm" "rotcm" or "scalecm"
- # then all of the command blocks must be handled during
- # postprocessing.
- postprocessing_blocks = transform_blocks
-
- for transform_block in postprocessing_blocks:
- assert(isinstance(block, basestring))
- if isinstance(command, PushRightCommand):
- postprocessing_commands.append(PushRightCommand(transform_block,
- command.srcloc,
- command.context_node))
- elif isinstance(command, PushLeftCommand):
- postprocessing_commands.append(PushLeftCommand(transform_block,
- command.srcloc,
- command.context_node))
-
-
- elif isinstance(command, WriteFileCommand):
-
- # --- Throw away lines containin references to deleted variables:---
-
- # First: To edit the content of a template,
- # you need to make a deep local copy of it
- tmpl_list = []
- for entry in command.tmpl_list:
- if isinstance(entry, TextBlock):
- tmpl_list.append(TextBlock(entry.text,
- entry.srcloc)) #, entry.srcloc_end))
- else:
- tmpl_list.append(entry)
-
-
- # Now throw away lines with deleted variables
-
- DeleteLinesWithBadVars(tmpl_list)
-
- # --- Now render the text ---
- text = Render(tmpl_list,
- substitute_vars)
-
- # ---- Coordinates of the atoms, must be rotated
- # and translated after rendering.
- # In addition, other vectors (dipoles, ellipsoid orientations)
- # must be processed.
- # This requires us to re-parse the contents of this text
- # (after it has been rendered), and apply these transformations
- # before passing them on to the caller.
- if command.filename == data_atoms:
- text = TransformAtomText(text, matrix_stack.M)
-
- files_content[command.filename].append(text)
-
-
- elif isinstance(command, ScopeBegin):
-
- if isinstance(command.node, InstanceObj):
- if ((command.node.children != None) and
- (len(command.node.children) > 0)):
- matrix_stack.PushStack(command.node)
-
- # "command_list" is a long list of commands.
- # ScopeBegin and ScopeEnd are (usually) used to demarcate/enclose
- # the commands which are issued for a single class or
- # class instance. _ExecCommands() carries out the commands for
- # a single class/instance. If we reach a ScopeBegin(),
- # then recursively process the commands belonging to the child.
- index = _ExecCommands(command_list,
- index,
- files_content,
- settings,
- matrix_stack,
- command.node,
- substitute_vars)
-
- elif isinstance(command, ScopeEnd):
- if data_atoms in files_content:
- for ppcommand in postprocessing_commands:
- if data_masses in files_content:
- xcm = CalcCM(files_content[data_atoms],
- files_content[data_masses],
- settings)
- else:
- xcm = CalcCM(files_content[data_atoms])
- if isinstance(ppcommand, PushRightCommand):
- matrix_stack.PushCommandsRight(ppcommand.contents,
- ppcommand.srcloc,
- xcm,
- which_stack=command.context_node)
- elif isinstance(ppcommand, PushLeftCommand):
- matrix_stack.PushCommandsLeft(ppcommand.contents,
- ppcommand.srcloc,
- xcm,
- which_stack=command.context_node)
- files_content[data_atoms] = \
- TransformAtomText(files_content[data_atoms],
- matrix_stack.M)
-
- for ppcommand in postprocessing_commands:
- matrix_stack.Pop(which_stack = command.context_node)
- #(same as PopRight())
-
- if isinstance(command.node, InstanceObj):
- if ((command.node.children != None) and
- (len(command.node.children) > 0)):
- matrix_stack.PopStack()
-
- # "ScopeEnd" means we're done with this class/instance.
- break
-
- else:
- assert(False)
- # no other command types allowed at this point
-
-
- # After processing the commands in this list,
- # merge the templates with the callers template list
- for filename, tmpl_list in files_content.items():
- global_files_content[filename] += \
- files_content[filename]
-
- return index
-
-
-
-def ExecCommands(commands,
- files_content,
- settings,
- substitute_vars=True):
-
- matrix_stack = MultiAffineStack()
-
- index = _ExecCommands(commands,
- 0,
- files_content,
- settings,
- matrix_stack,
- None,
- substitute_vars)
- assert(index == len(commands))
-
-
-
-
-def WriteFiles(files_content, suffix='', write_to_stdout=True):
- for filename, str_list in files_content.items():
- if filename != None:
- out_file = None
- if filename == '':
- if write_to_stdout:
- out_file = sys.stdout
- else:
- out_file = open(filename+suffix, 'a')
- if out_file != None:
- out_file.write(''.join(str_list))
- if filename != '':
- out_file.close()
-
-
-
-
-if __name__ == "__main__":
-
- """
- This is is a "main module" wrapper for invoking lttree.py
- as a stand alone program. This program:
-
- 1)reads a ttree file,
- 2)constructs a tree of class definitions (g_objectdefs)
- 3)constructs a tree of instantiated class objects (g_objects),
- 4)automatically assigns values to the variables,
- 5)and carries out the "write" commands to write the templates a file(s).
-
- """
- g_program_name = __file__.split('/')[-1] # ='lttree.py'
- g_date_str = '2014-12-19'
- g_version_str = '0.75'
-
- ####### Main Code Below: #######
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
- sys.stderr.write('\n(python version '+str(sys.version)+')\n')
- if sys.version < '2.6':
- raise InputError('Error: Alas, you must upgrade to a newer version of python.')
-
- try:
-
- #settings = BasicUISettings()
- #BasicUIParseArgs(sys.argv, settings)
- settings = LttreeSettings()
- LttreeParseArgs(sys.argv, settings)
-
- # Data structures to store the class definitionss and instances
- g_objectdefs = StaticObj('', None) # The root of the static tree
- # has name '' (equivalent to '/')
- g_objects = InstanceObj('', None) # The root of the instance tree
- # has name '' (equivalent to '/')
-
- # A list of commands to carry out
- g_static_commands = []
- g_instance_commands = []
-
-
- BasicUI(settings,
- g_objectdefs,
- g_objects,
- g_static_commands,
- g_instance_commands)
-
- # Interpret the the commands. (These are typically write() or
- # write_once() commands, rendering templates into text.
- # This step also handles coordinate transformations and delete commands.
- # Coordinate transformations can be applied to the rendered text
- # as a post-processing step.
-
- sys.stderr.write(' done\nbuilding templates...')
-
- files_content = defaultdict(list)
-
- ExecCommands(g_static_commands,
- files_content,
- settings,
- False)
- ExecCommands(g_instance_commands,
- files_content,
- settings,
- False)
-
- # Finally: write the rendered text to actual files.
-
- # Erase the files that will be written to:
- sys.stderr.write(' done\nwriting templates...')
- EraseTemplateFiles(g_static_commands)
- EraseTemplateFiles(g_instance_commands)
-
- # Write the files as templates
- # (with the original variable names present)
- WriteFiles(files_content, suffix=".template", write_to_stdout=False)
-
- # Write the files with the variables substituted by values
- sys.stderr.write(' done\nbuilding and rendering templates...')
- files_content = defaultdict(list)
- ExecCommands(g_static_commands, files_content, settings, True)
- ExecCommands(g_instance_commands, files_content, settings, True)
- sys.stderr.write(' done\nwriting rendered templates...\n')
- WriteFiles(files_content)
- sys.stderr.write(' done\n')
-
- # Now write the variable bindings/assignments table.
- sys.stderr.write('writing \"ttree_assignments.txt\" file...')
- open('ttree_assignments.txt', 'w').close() # <-- erase previous version.
- WriteVarBindingsFile(g_objectdefs)
- WriteVarBindingsFile(g_objects)
- sys.stderr.write(' done\n')
-
- except (ValueError, InputError) as err:
- sys.stderr.write('\n\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/lttree_check.py b/tools/moltemplate/src/lttree_check.py
deleted file mode 100644
index 78b84b8ca..000000000
--- a/tools/moltemplate/src/lttree_check.py
+++ /dev/null
@@ -1,2222 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2011, Regents of the University of California
-# All rights reserved.
-
-"""
-lttree_check.py
-
-The original template file format supports any variable types or file names.
-However if you plan to process template files using lttree.py to create
-LAMMPS-readable input/data files, then variables and file names obey certain
-naming conventions. This code attempts to insure these conventions are obeyed
-and to make sure that necessary variables are defined.
-
- -- This code checks static variables (@) and basic LAMMPS syntax --
-
-This program makes an attempt to check that the variables and file names
-which appear in an "lttree" file are not mispelled (or miscapitlised).
-
-It also attempts to check that LAMMPS syntax conventions are obeyed.
-(It checks that the appropriate type of variable is located in each column).
-
-It also attempts to check that all of the needed coeffs are defined.
-
- -- This code does NOT check instance variables ($) --
-
-This code does not check to make sure that all references to instance variables
-(such as $atom, $bond, $angle, $dihedral, $improper or $mol variables) are valid
-This means a user's input script command (like the "group" command) could refer
-to an $atom or $mol which was never defined, and this code would not detect it.
-(Why: Checking for instance variables requires building the entire instance tree
- and checking references uses up additional memory after that. I do not do this
- because memory is often very scarce after building the instance tree.)
-Instead, we could check for these kinds of errors when post-processing of
-the files generated by lttree.py or moltemplate.sh.
-
- -- This is not the pretiest code I've ever written. --
-
-"""
-
-
-import sys
-#from ttree import *
-from lttree_styles import *
-from lttree import *
-from ttree_lex import InputError
-
-if sys.version < '2.6':
- raise InputError('Error: Alas, you must upgrade to a newer version of python.')
-
-
-#g_no_check_msg = \
-# "(If this error message is wrong, and/or you would like to continue anyway,\n"+\
-# "try running moltemplate again using the \"-nocheck\" command-line-argument.)\n"
-
-g_no_check_msg = \
- '(To continue anyway, run moltemplate using the \"-nocheck\" argument.)\n'
-
-
-
-
-def CheckCommonVarNames(prefix, descr_str, suffix, srcloc):
- """ Check the name of variables in a lttree-file to confirm
- that they follow the conventions used by lttree.
- Almost any variable/category name is permitted, except for
- names which closely match those reserved by lttree.
-
- """
-
- cat_name, cat_ptkns, leaf_ptkns = \
- DescrToCatLeafPtkns(descr_str,
- srcloc)
-
- if (cat_name.lower()=='mol'):
- if (cat_name != 'mol'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Perhaps you meant \"mol\"?')
-
- elif (cat_name.lower()=='group'):
- if (cat_name != 'group'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Perhaps you meant \"group\"?')
- elif (cat_name.lower()=='fix'):
- if (cat_name != 'fix'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Use \"fix\" instead.')
- elif (cat_name.lower()=='atom'):
- if (cat_name != 'atom'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Illegal lttree variable category: \"'+cat_name+'\"\n'+
- 'Use \"atom\" instead.')
- elif (cat_name.lower()=='bond'):
- if (cat_name != 'bond'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Use \"bond\" instead.')
- elif (cat_name.lower()=='angle'):
- if (cat_name != 'angle'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Use \"angle\" instead.')
- elif (cat_name.lower()=='dihedral'):
- if (cat_name != 'dihedral'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Use \"dihedral\" instead.')
- elif (cat_name.lower()=='improper'):
- if (cat_name != 'improper'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
- 'closely with a reserved lttree variable category.\n'
- 'Use \"improper\" instead.')
- else:
- sys.stderr.write('-----------------------------------------------------\n'+
- 'WARNING: in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- ' Unrecognised template variable category: \"'+cat_name+'\"\n'+
- '-----------------------------------------------------\n')
-
-
-
-
-
-
-def CheckDataFileNames(filename,
- srcloc,
- write_command,
- fnames_found):
- N_data_prefix = len(data_prefix)
- #data_prefix_no_space = data_prefix.rstrip()
- N_data_prefix_no_space = len(data_prefix)
-
- section_name = filename[N_data_prefix:]
-
- if ((section_name.lower() == 'atom') or
- (section_name.lower() == 'atoms')):
- if (filename != data_atoms):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_atoms+'\"?')
-
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
-
- elif ((section_name.lower() == 'velocities') or
- (section_name.lower() == 'velocity')):
- if (filename != data_velocities):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_velocities+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
-
- elif ((section_name.lower() == 'mass') or
- (section_name.lower() == 'masses')):
- if (filename != data_masses):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_masses+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'ellipsoids') or
- (section_name.lower() == 'ellipsoid') or
- (section_name.lower() == 'elipsoids') or
- (section_name.lower() == 'elipsoid')):
- if (filename != data_ellipsoids):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_ellipsoids+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'triangle') or
- (section_name.lower() == 'triangles')):
- if (filename != data_triangles):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_triangles+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'line') or
- (section_name.lower() == 'lines')):
- if (filename != data_lines):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_lines+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('pair coef') == 0) or
- (section_name.lower().find('pair_coef') == 0) or
- (section_name.lower().find('paircoef') == 0) or
- (section_name.lower().find('pair by type') == 0) or
- (section_name.lower().find('pair bytype') == 0) or
- (section_name.lower().find('pair_by_type') == 0) or
- (section_name.lower().find('pair_bytype') == 0) or
- (section_name.lower().find('pairbytype') == 0)):
- if (filename != data_pair_coeffs):
- err_msg = 'Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+\
- 'Output file name (\"'+filename+'\") does not match,\n'+\
- 'yet overlaps closely with reserved lttree-file name.\n'+\
- 'Perhaps you meant \"'+data_pair_coeffs+'\"?'
- if ((section_name.lower().find('by type') != -1) or
- (section_name.lower().find('by_type') != -1) or
- (section_name.lower().find('bytype') != -1)):
- err_msg += '\n (Note: "pair" parameters are always assigned by type.\n'+\
- ' There\'s no need to specify \"by type\")'
- raise InputError(err_msg)
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('bond coef') == 0) or
- (section_name.lower().find('bond_coef') == 0) or
- (section_name.lower().find('bondcoef') == 0)):
- if (filename != data_bond_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bond_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('angle coef') == 0) or
- (section_name.lower().find('angle_coef') == 0) or
- (section_name.lower().find('anglecoef') == 0)):
- if (filename != data_angle_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_angle_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('dihedral coef') == 0) or
- (section_name.lower().find('dihedral_coef') == 0) or
- (section_name.lower().find('dihedralcoef') == 0)):
- if (filename != data_dihedral_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_dihedral_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('improper coef') == 0) or
- (section_name.lower().find('improper_coef') == 0) or
- (section_name.lower().find('impropercoef') == 0)):
- if (filename != data_improper_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_improper_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
-
- # -- class2 data sections --
- elif ((section_name.lower().find('bondbond coef') == 0) or
- (section_name.lower().find('bondbond_coef') == 0) or
- (section_name.lower().find('bondbondcoef') == 0)):
- if (filename != data_bondbond_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bondbond_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('bondangle coef') == 0) or
- (section_name.lower().find('bondangle_coef') == 0) or
- (section_name.lower().find('bondanglecoef') == 0)):
- if (filename != data_bondangle_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bondangle_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('middlebondtorsion coef') == 0) or
- (section_name.lower().find('middlebondtorsion_coef') == 0) or
- (section_name.lower().find('middlebondtorsioncoef') == 0) or
- (section_name.lower().find('middlebondtorision coef') == 0) or
- (section_name.lower().find('middlebondtorision_coef') == 0) or
- (section_name.lower().find('middlebondtorisioncoef') == 0)):
- if (filename != data_middlebondtorsion_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_middlebondtorsion_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('endbondtorsion coef') == 0) or
- (section_name.lower().find('endbondtorsion_coef') == 0) or
- (section_name.lower().find('endbondtorsioncoef') == 0) or
- (section_name.lower().find('endbondtorision coef') == 0) or
- (section_name.lower().find('endbondtorision_coef') == 0) or
- (section_name.lower().find('endbondtorisioncoef') == 0)):
- if (filename != data_endbondtorsion_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_endbondtorsion_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('angletorsion coef') == 0) or
- (section_name.lower().find('angletorsion_coef') == 0) or
- (section_name.lower().find('angletorsioncoef') == 0) or
- (section_name.lower().find('angletorision coef') == 0) or
- (section_name.lower().find('angletorision_coef') == 0) or
- (section_name.lower().find('angletorisioncoef') == 0)):
- if (filename != data_angletorsion_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_angletorsion_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('angleangletorsion coef') == 0) or
- (section_name.lower().find('angleangletorsion_coef') == 0) or
- (section_name.lower().find('angleangletorsioncoef') == 0) or
- (section_name.lower().find('angleangletorision coef') == 0) or
- (section_name.lower().find('angleangletorision_coef') == 0) or
- (section_name.lower().find('angleangletorisioncoef') == 0)):
- if (filename != data_angleangletorsion_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_angleangletorsion_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('bondbond13 coef') == 0) or
- (section_name.lower().find('bondbond13_coef') == 0) or
- (section_name.lower().find('bondbond13coef') == 0)):
- if (filename != data_bondbond13_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bondbond13_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('angleangle coef') == 0) or
- (section_name.lower().find('angleangle_coef') == 0) or
- (section_name.lower().find('angleanglecoef') == 0)):
- if (filename != data_angleangle_coeffs):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_angleangle_coeffs+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
-
- elif ((section_name.lower() == 'bonds by type') or
- (section_name.lower() == 'bonds bytype') or
- (section_name.lower() == 'bonds_by_type') or
- (section_name.lower() == 'bonds_bytype') or
- (section_name.lower() == 'bondsbytype') or
- (section_name.lower() == 'bond by type') or
- (section_name.lower() == 'bond bytype') or
- (section_name.lower() == 'bond_by_type') or
- (section_name.lower() == 'bond_bytype') or
- (section_name.lower() == 'bondbytype')):
- if (filename != data_bonds_by_type):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bonds_by_type+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
-
-
- elif ((section_name.lower() == 'angles by type') or
- (section_name.lower() == 'angles bytype') or
- (section_name.lower() == 'angles_by_type') or
- (section_name.lower() == 'angles_bytype') or
- (section_name.lower() == 'anglesbytype') or
- (section_name.lower() == 'angle by type') or
- (section_name.lower() == 'angle bytype') or
- (section_name.lower() == 'angle_by_type') or
- (section_name.lower() == 'angle_bytype') or
- (section_name.lower() == 'anglebytype')):
- if (filename != data_angles_by_type):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_angles_by_type+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'dihedrals by type') or
- (section_name.lower() == 'dihedrals bytype') or
- (section_name.lower() == 'dihedrals_by_type') or
- (section_name.lower() == 'dihedrals_bytype') or
- (section_name.lower() == 'dihedralsbytype') or
- (section_name.lower() == 'dihedral by type') or
- (section_name.lower() == 'dihedral bytype') or
- (section_name.lower() == 'dihedral_by_type') or
- (section_name.lower() == 'dihedral_bytype') or
- (section_name.lower() == 'dihedralbytype')):
- if (filename != data_dihedrals_by_type):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_dihedrals_by_type+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'impropers by type') or
- (section_name.lower() == 'impropers bytype') or
- (section_name.lower() == 'impropers_by_type') or
- (section_name.lower() == 'impropers_bytype') or
- (section_name.lower() == 'impropersbytype') or
- (section_name.lower() == 'improper by type') or
- (section_name.lower() == 'improper bytype') or
- (section_name.lower() == 'improper_by_type') or
- (section_name.lower() == 'improper_bytype') or
- (section_name.lower() == 'improperbytype')):
- if (filename != data_impropers_by_type):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_impropers_by_type+'\"?')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
-
-
-
- elif ((section_name.lower() == 'bonds') or
- (section_name.lower() == 'bond')):
- if (filename != data_bonds):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bonds+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower().find('bond list') == 0) or
- (section_name.lower().find('bonds list') == 0) or
- (section_name.lower().find('bond_list') == 0) or
- (section_name.lower().find('bonds_list') == 0)):
- if (filename != data_bond_list):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_bonds_by_type+'\"?')
- elif (write_command != 'write'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
-
- elif ((section_name.lower() == 'angles') or
- (section_name.lower() == 'angle')):
- if (filename != data_angles):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_angles+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'dihedrals') or
- (section_name.lower() == 'dihedral')):
- if (filename != data_dihedrals):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_dihedrals+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'impropers') or
- (section_name.lower() == 'improper')):
- if (filename != data_impropers):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_impropers+'\"?')
- elif (write_command == 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write(\"'+filename+'\") instead.\n')
-
- elif ((section_name.lower() == 'box boundaries') or
- (section_name.lower() == 'box boundary') or
- (section_name.lower() == 'boundaries') or
- (section_name.lower() == 'boundary') or
- (section_name.lower() == 'boundary conditions') or
- (section_name.lower() == 'periodic boundaries') or
- (section_name.lower() == 'periodic boundary conditions') or
- (section_name.lower() == 'periodic_boundaries') or
- (section_name.lower() == 'periodic_boundary_conditions') or
- (section_name.lower() == 'pbc')):
- if ((filename != data_boundary) and
- (filename != data_pbc)):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_boundary+'\"?\n'
- '(Specify periodic boundary conditions this way.)')
- elif (write_command != 'write_once'):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- 'You should probably use write_once(\"'+filename+'\") instead.\n')
- elif (filename == data_pbc):
- sys.stderr.write('WARNING: write_once(\"'+data_pbc+'\") is depreciated.\n'
- ' Use write_once(\"'+data_boundary+'\") instead.\n')
-
-
-
-
-def CheckCommonFileNames(filename,
- srcloc,
- write_command,
- filenames_found):
- """
- Check the write() or write_once() statements in a
- lttree-file to make sure that the files being written
- follow the conventions used by lttree.
- Almost any file name is permitted, except for file names
- which closely match those reserved by lttree.
-
- """
-
- filenames_found.add(filename)
-
- N_data_prefix = len(data_prefix)
- #data_prefix_no_space = data_prefix.rstrip()
- N_data_prefix_no_space = len(data_prefix_no_space)
-
- if ((filename[:N_data_prefix].lower() == data_prefix.lower()) and
- (filename[:N_data_prefix] != data_prefix)):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'The beginning of output file (\"'+filename+'\")\n'
- 'does not match yet overlaps closely with a reserved lttree-file name prefix.\n'
- '(\"'+data_prefix+'\"). Perhaps you meant \"'+data_prefix+filename[N_data_prefix:]+'\"?')
-
- # check did they forget the space?
- if (filename[:N_data_prefix_no_space] == data_prefix_no_space):
- if (filename[:N_data_prefix] == data_prefix):
-
- CheckDataFileNames(filename,
- srcloc,
- write_command,
- filenames_found)
-
- else:
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'The beginning of output file (\"'+filename+'\")\n'
- 'does not match yet overlaps closely with a reserved lttree-file name prefix.\n'
- '(\"'+data_prefix+'\"). Perhaps you meant \"'+data_prefix+filename[N_data_prefix_no_space:]+'\"?')
-
-
- elif ((filename.lower() == 'box boundaries') or
- (filename.lower() == 'box boundary') or
- (filename.lower() == 'boundaries') or
- (filename.lower() == 'boundary') or
- (filename.lower() == 'boundary conditions') or
- (filename.lower() == 'periodic boundaries') or
- (filename.lower() == 'periodic boundary conditions') or
- (filename.lower() == 'periodic_boundaries') or
- (filename.lower() == 'periodic_boundary_conditions') or
- (filename.lower() == 'pbc')):
- # In that case (for one thing) they forgot the data_prefix
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+data_boundary+'\"?\n'
- '(Specify periodic boundary conditions this way.)')
-
-
-
- elif ((filename.lower() == 'init') or
- (filename.lower() == 'in init') or
- (filename.lower() == 'ininit') or
- (filename.lower() == 'initialize') or
- (filename.lower() == 'in initialize') or
- (filename.lower() == 'ininitialize')):
- if (filename != in_init):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+in_init+'\"?')
- #elif (write_command != 'write_once'):
- # raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- # 'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
- # 'want to use the '+write_command+'() command with \"'+filename+'\".\n'
- # 'You should probably use write_once(\"'+filename+'\") instead.\n')
-
- elif ((filename.lower() == 'settings') or
- (filename.lower() == 'in settings') or
- (filename.lower() == 'insettings')):
-
- if (filename != in_settings):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+in_settings+'\"?')
-
- elif ((filename.lower() == 'set_coords') or
- (filename.lower() == 'set coords') or
- (filename.lower() == 'setcoords') or
- (filename.lower() == 'in set_coords') or
- (filename.lower() == 'in set coords') or
- (filename.lower() == 'in setcoords')):
- if (filename != in_set_coords):
- raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
- 'Output file name (\"'+filename+'\") does not match,\n'
- 'yet overlaps closely with reserved lttree-file name.\n'
- 'Perhaps you meant \"'+in_set_coords+'\"?')
-
-
-
-
-
-
-
-def CheckSyntaxCheap(lex):
-
- """ Parse() builds a static tree of StaticObjs by parsing text file.
- -The "lex" argument is afile or input stream which has been converted
- to a "TemplateLexer" object (similar to the python's built-in shlex lexer).
- """
-
- fnames_found = set([])
- prematurely_read_token = None
-
- while True:
-
- if prematurely_read_token == None:
- command = lex.get_token()
- else:
- command = prematurely_read_token
- prematurely_read_token = None
-
- #print('Parse(): token = \"'+command+'\", '+lex.error_leader())
-
- if command == lex.eof:
- #print('Parse(): EOF encountered\n')
- break
-
- if ((command == 'write') or (command == 'write_once')):
- open_paren = lex.get_token()
-
- #print('Parse(): open_paren=\"'+open_paren+'\"')
-
- if open_paren=='{':
- # ..then the user neglected to specify the "filename" file-name
- # argument. In that case, supply the default, ''.
- # (which is shorthand for the standard out in this case)
- open_curly = open_paren[0]
- open_paren = ''
- close_paren = ''
- filename = ''
- srcloc = lex.GetSrcLoc()
- else:
- filename = lex.get_token()
- if filename == ')':
- filename == ''
- close_paren = ')'
- else:
- close_paren = lex.get_token()
- open_curly = lex.get_token()
- srcloc = lex.GetSrcLoc()
-
- if ((open_curly != '{') or
- ((open_paren == '') and (close_paren != '')) or
- ((open_paren == '(') and (close_paren != ')'))):
- raise InputError('Error: in '+lex.error_leader()+'\n\n'
- 'Syntax error at beginning of '+command+' command.')
-
- filename = RemoveOuterQuotes(filename, lex.quotes)
- # The previous line is similar to:
- #filename = filename.strip(lex.quotes)
-
-
- CheckCommonFileNames(filename, lex.GetSrcLoc(), command, fnames_found)
-
-
- tmpl_contents = lex.ReadTemplate()
- StaticObj.CleanupReadTemplate(tmpl_contents, lex)
-
-
- for entry in tmpl_contents:
- if (type(entry) is VarRef):
-
- CheckCommonVarNames(entry.prefix,
- entry.descr_str,
- entry.suffix,
- entry.srcloc)
-
-
- #if (data_velocities not in fnames_found):
- # sys.stderr.write('-------------------------------------------------\n'
- # 'WARNING: \"'+data_velocities+'\" file not found\n'
- # '-------------------------------------------------\n')
- #if (data_pair_coeffs not in fnames_found):
- # sys.stderr.write('-------------------------------------------------\n'
- # 'WARNING: \"'+data_pair_coeffs+'\" file not found\n'
- # '-------------------------------------------------\n')
- if (data_atoms not in fnames_found):
- sys.stderr.write('WARNING: \"'+data_atoms+'\" file not found\n')
- if (data_masses not in fnames_found):
- sys.stderr.write('WARNING: \"'+data_masses+'\" file not found\n')
- #if (data_bonds not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_bonds+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_angles not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_angles+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_dihedrals not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_dihedrals+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_impropers not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_impropers+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_bond_coeffs not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_bond_coeffs+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_angle_coeffs not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_angle_coeffs+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_dihedral_coeffs not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_dihedral_coeffs+'\" file not found\n'
- # '--------------------------------------------------\n')
- #if (data_improper_coeffs not in fnames_found):
- # sys.stderr.write('--------------------------------------------------\n'
- # 'WARNING: \"'+data_imrpoper_coeffs+'\" file not found\n'
- # '--------------------------------------------------\n')
- if (in_init not in fnames_found):
- sys.stderr.write('WARNING: \"'+in_init+'\" file not found\n')
-
- if (in_settings not in fnames_found):
- sys.stderr.write('WARNING: \"'+in_settings+'\" file not found\n')
-
-
-
-
-
-def CheckSyntaxStatic(context_node,
- root_node,
- atom_column_names,
- data_pair_coeffs_defined,
- data_bond_coeffs_defined,
- data_angle_coeffs_defined,
- data_dihedral_coeffs_defined,
- data_improper_coeffs_defined,
- in_pair_coeffs_defined,
- in_bond_coeffs_defined,
- in_angle_coeffs_defined,
- in_dihedral_coeffs_defined,
- in_improper_coeffs_defined,
- search_instance_commands):
-
- if search_instance_commands:
- assert(isinstance(context_node, StaticObj))
- commands = context_node.instance_commands
- else:
- # Note: Leaf nodes contain no commands, so skip them
- if (not hasattr(context_node, 'commands')):
- return
- # Otherwise process their commands
- commands = context_node.commands
-
- for command in commands:
- if isinstance(command, WriteFileCommand):
-
- filename = command.filename
-
- if filename == None: # (The "create_var" command causes this)
- pass
- elif (filename.find(in_prefix) == 0): #if filename begins with "In "
- CheckInFileSyntax(command.tmpl_list,
- root_node,
- in_pair_coeffs_defined,
- in_bond_coeffs_defined,
- in_angle_coeffs_defined,
- in_dihedral_coeffs_defined,
- in_improper_coeffs_defined)
-
- elif filename == 'Data Atoms':
- table = TableFromTemplate(command.tmpl_list,
- [[' ', '\t', '\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
-
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) == 0:
- pass # skip blank lines
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass # skip comment lines
- else:
- syntax_err = False
-
- if len(table[i]) < len(atom_column_names):
- syntax_err = True
- else:
- syntax_err = False
- for j in range(0, len(atom_column_names)):
- if ((atom_column_names[j].lower() == 'atom-id') and
- (not ((j < len(table[i])) and
- isinstance(table[i][j], VarRef) and
- (table[i][j].prefix in ('$','${')) and
- (ExtractCatName(table[i][j].descr_str) == 'atom')))):
- syntax_err = True
- elif ((atom_column_names[j].lower() == 'molecule-id') and
- (not ((j < len(table[i])) and
- isinstance(table[i][j], VarRef) and
- (table[i][j].prefix in ('$','${')) and
- (ExtractCatName(table[i][j].descr_str) == 'mol')))):
- syntax_err = True
- elif ((atom_column_names[j].lower() == 'atom-type') and
- (not ((j < len(table[i])) and
- (isinstance(table[i][j], VarRef)) and
- (table[i][j].prefix in ('@', '@{')) and
- (table[i][j].nptr.cat_name == 'atom') and
- (table[i][j].nptr.cat_node == root_node)))):
- syntax_err = True
-
- if syntax_err:
- correct_rows_list = [s for s in atom_column_names]
- for j in range(0, len(correct_rows_list)):
- if correct_rows_list[j].lower() == 'atom-id':
- correct_rows_list[j] = '$atom:id'
- elif correct_rows_list[j].lower() == 'atom-type':
- correct_rows_list[j] = '@atom:type'
- elif correct_rows_list[j].lower() == 'molecule-id':
- correct_rows_list[j] = '$mol:id'
- correct_rows_msg = ' '.join(correct_rows_list)
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Invalid "Data Atoms" syntax.\n'+
- 'Each line of the \"Data Atoms\" section should have this format:\n\n'
- ' '+correct_rows_msg+'\n\n'
- 'You may have forgotten to specify the LAMMPS atom_style.\n'+
- '(You can do this running moltemplate with the -atom-style _style_ argument.)\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- elif filename == 'Data Bonds':
- table = TableFromTemplate(command.tmpl_list,
- [[' ', '\t', '\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- syntax_err = False
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) > 0:
- if ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass
- else:
- if len(table[i]) < 4:
- syntax_err = True
- table_entry = table[i][0]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'bond'))):
- syntax_err = True
- if len(table[i]) > 1:
- table_entry = table[i][1]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('@', '@{')) and
- (table_entry.nptr.cat_name == 'bond') and
- (table_entry.nptr.cat_node == root_node))):
- syntax_err = True
- if len(table[i]) > 2:
- table_entry = table[i][2]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 3:
- table_entry = table[i][3]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
-
- if syntax_err:
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Bonds" syntax.\n'+
- 'Each line of the \"Data Bonds\" section should have this format:\n\n'
- ' $bond:id @bond:type $atom:id1 $atom:id2\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
- elif filename == 'Data Bond List':
- table = TableFromTemplate(command.tmpl_list,
- [[' ', '\t', '\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- syntax_err = False
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) > 0:
- if ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass
- else:
- if len(table[i]) < 3:
- syntax_err = True
- table_entry = table[i][0]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'bond'))):
- syntax_err = True
- if len(table[i]) > 1:
- table_entry = table[i][1]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 2:
- table_entry = table[i][2]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
-
- if syntax_err:
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Bond List" syntax.\n'+
- 'Each lines in this section should have this format:\n\n'
- ' $bond:id $atom:id1 $atom:id2\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
- elif filename == 'Data Angles':
- table = TableFromTemplate(command.tmpl_list,
- [[' ', '\t', '\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- syntax_err = False
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) > 0:
- if ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass
- else:
- if len(table[i]) < 5:
- syntax_err = True
- table_entry = table[i][0]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'angle'))):
- syntax_err = True
- if len(table[i]) > 1:
- table_entry = table[i][1]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('@', '@{')) and
- (table_entry.nptr.cat_name == 'angle') and
- (table_entry.nptr.cat_node == root_node))):
- syntax_err = True
- if len(table[i]) > 2:
- table_entry = table[i][2]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 3:
- table_entry = table[i][3]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 4:
- table_entry = table[i][4]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
-
- if syntax_err:
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Angles" syntax.\n'+
- 'Each line of the \"Data Angles\" section should have this format:\n\n'
- ' $angle:id @angle:type $atom:id1 $atom:id2 $atom:id3\n'+
- '----------------------------------------------------\n\n'+
- g_no_check_msg)
-
- elif filename == 'Data Dihedrals':
- table = TableFromTemplate(command.tmpl_list,
- [[' ', '\t', '\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- syntax_err = False
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) > 0:
- if ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass
- else:
- if len(table[i]) < 6:
- syntax_err = True
- table_entry = table[i][0]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'dihedral'))):
- syntax_err = True
- if len(table[i]) > 1:
- table_entry = table[i][1]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('@', '@{')) and
- (table_entry.nptr.cat_name == 'dihedral') and
- (table_entry.nptr.cat_node == root_node))):
- syntax_err = True
- if len(table[i]) > 2:
- table_entry = table[i][2]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 3:
- table_entry = table[i][3]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 4:
- table_entry = table[i][4]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 5:
- table_entry = table[i][5]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
-
- if syntax_err:
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Dihedrals" syntax.\n'+
- 'Each line of the \"Data Dihedrals\" section should have this format:\n\n'
- ' $dihedral:id @dihedral:type $atom:id1 $atom:id2 $atom:id3 $atom:id4\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- elif filename == 'Data Impropers':
- table = TableFromTemplate(command.tmpl_list,
- [[' ', '\t', '\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- syntax_err = False
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) > 0:
- if ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass
- else:
- if len(table[i]) < 6:
- syntax_err = True
- table_entry = table[i][0]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'improper'))):
- syntax_err = True
- if len(table[i]) > 1:
- table_entry = table[i][1]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('@', '@{')) and
- (table_entry.nptr.cat_name == 'improper') and
- (table_entry.nptr.cat_node == root_node))):
- syntax_err = True
- if len(table[i]) > 2:
- table_entry = table[i][2]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 3:
- table_entry = table[i][3]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 4:
- table_entry = table[i][4]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
- if len(table[i]) > 5:
- table_entry = table[i][5]
- if (not ((isinstance(table_entry, VarRef)) and
- (table_entry.prefix in ('$','${')) and
- (ExtractCatName(table_entry.descr_str) == 'atom'))):
- syntax_err = True
-
- if syntax_err:
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Impropers" syntax.\n'+
- 'Each line of the \"Data Impropers\" section should have this format:\n\n'
- ' $improper:id @improper:type $atom:id1 $atom:id2 $atom:id3 $atom:id4\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
-
- # A simple wildcard is the character "*" on its own.
- # These are okay.
- # A "compound" wildcard expression is something like
- # 5*7 or
- # 5* or
- # *7 or
- # @{bond:A}*@bond:B or
- # @{bond:A}* or
- # *@bond:B
- # LAMMPS allows this but in moltemplate this causes
- # unintended side-effects. Check for these now.
- if filename in set(['Data Bond Coeffs',
- 'Data Angle Coeffs',
- 'Data Dihedral Coeffs',
- 'Data Improper Coeffs',
- 'Data Pair Coeffs']):
- table = TableFromTemplate(command.tmpl_list,
- [[' ','\t','\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- assert(hasattr(table[i], '__len__'))
- if len(table[i]) > 0:
- if (isinstance(table[i][0], TextBlock) and
- table[i][0].text == '*'):
- if filename == 'Data Bond Coeffs':
- data_bond_coeffs_defined.add('*')
- elif filename == 'Data Angle Coeffs':
- data_angle_coeffs_defined.add('*')
- elif filename == 'Data Dihedral Coeffs':
- data_dihedral_coeffs_defined.add('*')
- elif filename == 'Data Improper Coeffs':
- data_improper_coeffs_defined.add('*')
- elif filename == 'Data Pair Coeffs':
- data_pair_coeffs_defined.add(('*','*'))
- else:
- compound_wildcard = False
- if (len(table[i]) > 1):
- if hasattr(table[i][0],'__len__'):
- ltmpl = table[i][0]
- else:
- ltmpl = [table[i][0]]
- for entry in ltmpl:
- if (isinstance(entry, TextBlock) and
- ('*' in entry.text)):
- compound_wildcard = True
- elif (isinstance(entry, VarRef) and
- ('*' in entry.descr_str)):
- compound_wildcard = True
- if compound_wildcard:
- raise InputError('--- Paranoid checking: ---\n'
- ' Possible error near '+
- ErrorLeader(entry.srcloc.infile,
- entry.srcloc.lineno)+'\n'
- 'The wildcard symbol, \"*\", is not recommended within \"'+filename+'\".\n'
- 'It is safer to specify the parameters for each type explicitly.\n'
- 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n'
- 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n')
-
-
- if filename == 'Data Bond Coeffs':
- # Commenting the next line out. We did this already:
- #table = TableFromTemplate(command.tmpl_list,
- # [[' ','\t','\r'], '\n'],
- # [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (table[i][0].text == '*')):
- pass # we dealt with this case earlier
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not (isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'bond') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Bond Coeffs" syntax.\n'
- ' Each line of the \"Data Bond Coeffs\" section\n'
- ' should have the following syntax:\n\n'+
- ' @bond:type list-of-parameters...\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
- else:
- data_bond_coeffs_defined.add(table[i][0].binding)
-
-
- elif filename == 'Data Angle Coeffs':
- # Commenting the next line out. We did this already:
- #table = TableFromTemplate(command.tmpl_list,
- # [[' ','\t','\r'], '\n'],
- # [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (table[i][0].text == '*')):
- pass # we dealt with this case earlier
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not (isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'angle') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Angle Coeffs" syntax.\n'
- ' Each line of the \"Data Angle Coeffs\" section\n'
- ' should have the following syntax:\n\n'+
- ' @angle:type list-of-parameters...\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
- else:
- data_angle_coeffs_defined.add(table[i][0].binding)
-
-
- elif filename == 'Data Dihedral Coeffs':
- # Commenting the next line out. We did this already:
- #table = TableFromTemplate(command.tmpl_list,
- # [[' ','\t','\r'], '\n'],
- # [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (table[i][0].text == '*')):
- pass # we dealt with this case earlier
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not (isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'dihedral') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Dihedral Coeffs" syntax.\n'
- ' Each line of the \"Data Dihedral Coeffs\" section\n'
- ' should have the following syntax:\n\n'+
- ' @dihedral:type list-of-parameters...\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
- else:
- data_dihedral_coeffs_defined.add(table[i][0].binding)
-
-
- elif filename == 'Data Improper Coeffs':
- # Commenting the next line out. We did this already:
- #table = TableFromTemplate(command.tmpl_list,
- # [[' ','\t','\r'], '\n'],
- # [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (table[i][0].text == '*')):
- pass # we dealt with this case earlier
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not (isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'improper') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Improper Coeffs" syntax.\n'
- ' Each line of the \"Data Improper Coeffs\" section\n'
- ' should have the following syntax:\n\n'+
- ' @improper:type list-of-parameters...\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
- else:
- data_improper_coeffs_defined.add(table[i][0].binding)
-
-
- elif filename == 'Data Pair Coeffs':
- # Commenting the next line out. We did this already:
- #table = TableFromTemplate(command.tmpl_list,
- # [[' ','\t','\r'], '\n'],
- # [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 0) and
- isinstance(table[i][0], TextBlock) and
- (table[i][0].text == '*')):
- pass # we dealt with this case earlier
- elif ((len(table[i]) > 0) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not ((len(table[i]) > 0) and
- isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'atom') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect "Data Pair Coeffs" syntax.\n'
- ' Each line of the \"Data Pair Coeffs\" section\n'
- ' should have the following syntax:\n\n'+
- ' @atom:type list-of-parameters...\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
- else:
- data_pair_coeffs_defined.add((table[i][0].binding,
- table[i][0].binding))
-
-
- elif filename == 'Data Bonds By Type':
- table = TableFromTemplate(command.tmpl_list,
- [[' ','\t','\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not ((len(table[i]) >= 3) and
- isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'bond') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect \"Data Bonds By Type\" syntax.\n'
- ' Each line of the \"Data Bonds By Type\" section should begin with an\n'
- ' @bond:type variable followed by 2 atom types.\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
- elif filename == 'Data Angles By Type':
- table = TableFromTemplate(command.tmpl_list,
- [[' ','\t','\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not ((len(table[i]) >= 4) and
- isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'angle') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect \"Data Angles By Type\" syntax.\n'
- ' Each line of the \"Data Angles By Type\" section should begin with an\n'
- ' @angle:type variable followed by 3 atom types (and 2 optional bond types).\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
- elif filename == 'Data Dihedrals By Type':
- table = TableFromTemplate(command.tmpl_list,
- [[' ','\t','\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not ((len(table[i]) >= 5) and
- isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'dihedral') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect \"Data Dihedrals By Type\" syntax.\n'
- ' Each line of the \"Data Dihedrals By Type\" section should begin with a\n\n'
- ' @dihedral:type variable followed by 4 atom types (and 3 optional bond types).\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
- elif filename == 'Data Impropers By Type':
- table = TableFromTemplate(command.tmpl_list,
- [[' ','\t','\r'], '\n'],
- [True, False])
- for i in range(0, len(table)):
- if len(table[i]) == 0:
- pass
- elif ((len(table[i]) > 1) and
- isinstance(table[i][0], TextBlock) and
- (len(table[i][0].text) > 0) and
- (table[i][0].text == '#')):
- pass #Ignore comment lines (postprocessing removes them)
- elif (not ((len(table[i]) >= 5) and
- isinstance(table[i][0], VarRef) and
- (table[i][0].prefix in ('@', '@{')) and
- (table[i][0].nptr.cat_name == 'improper') and
- (table[i][0].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Incorrect \"Data Impropers By Type\" syntax.\n'
- ' Each line of the \"Data Impropers By Type\" section should begin with an\n\n'
- ' @improper:type variable followed by 4 atom types (and 3 optional bond types).\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
-
- # Recursively invoke AssignVarPtrs() on all (non-leaf) child nodes:
- for child in context_node.children.values():
- CheckSyntaxStatic(child,
- root_node,
- atom_column_names,
- data_pair_coeffs_defined,
- data_bond_coeffs_defined,
- data_angle_coeffs_defined,
- data_dihedral_coeffs_defined,
- data_improper_coeffs_defined,
- in_pair_coeffs_defined,
- in_bond_coeffs_defined,
- in_angle_coeffs_defined,
- in_dihedral_coeffs_defined,
- in_improper_coeffs_defined,
- search_instance_commands)
-
-
-
-
-
-def CheckInFileSyntax(tmpl_list,
- root_node,
- pair_coeffs_defined,
- bond_coeffs_defined,
- angle_coeffs_defined,
- dihedral_coeffs_defined,
- improper_coeffs_defined):
-
- table = TableFromTemplate(tmpl_list,
- [[' ','\t','\r'], '\n'],
- [True, False])
-
- for i in range(0, len(table)):
- assert(hasattr(table[i], '__len__'))
-
- if len(table[i]) > 0:
- if ((isinstance(table[i][0], TextBlock)) and
- (table[i][0].text in set(['bond_coeff',
- 'angle_coeff',
- 'dihedral_coeff',
- 'improper_coeff']))):
- if len(table[i]) > 1: # if not deal with error later
- if (isinstance(table[i][1], TextBlock) and
- table[i][1].text == '*'):
- if table[i][0].text == 'bond_coeff':
- bond_coeffs_defined.add('*')
- elif table[i][0].text == 'angle_coeff':
- angle_coeffs_defined.add('*')
- elif table[i][0].text == 'dihedral_coeff':
- dihedral_coeffs_defined.add('*')
- elif table[i][0].text == 'improper_coeff':
- improper_coeffs_defined.add('*')
- else:
- compound_wildcard = False
- if (len(table[i]) > 1):
- if hasattr(table[i][1], '__len__'):
- ltmpl = table[i][1]
- else:
- ltmpl = [table[i][1]]
- for entry in ltmpl:
- if (isinstance(entry, TextBlock) and
- ('*' in entry.text)):
- compound_wildcard = True
- elif (isinstance(entry, VarRef) and
- ('*' in entry.descr_str)):
- compound_wildcard = True
- if compound_wildcard:
- raise InputError('---- Paranoid checking: ---\n'
- ' Possible error near '+
- ErrorLeader(entry.srcloc.infile,
- entry.srcloc.lineno)+'\n'
- 'The wildcard symbol, \"*\", is not recommended within a \"'+table[i][0].text+'\".\n'
- 'command. It is safer to specify the parameters for each bond type explicitly.\n'
- 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n'
- 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n')
-
-
-
- if ((isinstance(table[i][0], TextBlock)) and
- ((table[i][0].text.lower() == 'bondcoeff') or
- (table[i][0].text.lower() == 'bond_coeff'))):
- if table[i][0].text != 'bond_coeff':
- raise InputError('----------------------------------------------------\n'+
- ' Spelling error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Use \"bond_coeff\", not \"'+table[i][0].text+'\"\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- if ((len(table[i]) > 1) and
- isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*')):
- pass # we dealt with this case earlier
- elif (not ((len(table[i]) > 1) and
- (isinstance(table[i][1], VarRef)) and
- (table[i][1].prefix in ('@', '@{')) and
- (table[i][1].nptr.cat_name == 'bond') and
- (table[i][1].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Invalid \"bond_coeff\" command.\n\n'+
- ' Each \"bond_coeff\" command should have the following syntax:\n\n'+
- ' bond_coeff @bond:type [optional style] list-of-parameters...\n'+
- '----------------------------------------------------\n\n'+
- g_no_check_msg)
- else:
- bond_coeffs_defined.add(table[i][1].binding)
-
-
- if ((isinstance(table[i][0], TextBlock)) and
- ((table[i][0].text.lower() == 'anglecoeff') or
- (table[i][0].text.lower() == 'angle_coeff'))):
- if table[i][0].text != 'angle_coeff':
- raise InputError('----------------------------------------------------\n'+
- ' Spelling error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Use \"angle_coeff\", not \"'+table[i][0].text+'\"\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- if ((len(table[i]) > 1) and
- isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*')):
- pass # we dealt with this case earlier
- elif (not ((len(table[i]) > 1) and
- (isinstance(table[i][1], VarRef)) and
- (table[i][1].prefix in ('@', '@{')) and
- (table[i][1].nptr.cat_name == 'angle') and
- (table[i][1].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Invalid \"angle_coeff\" command.\n\n'+
- ' Each \"angle_coeff\" command should have the following syntax:\n\n'+
- ' angle_coeff @angle:type [optional style] list-of-parameters...\n'+
- '----------------------------------------------------\n\n'+
- g_no_check_msg)
- else:
- angle_coeffs_defined.add(table[i][1].binding)
-
-
- if ((isinstance(table[i][0], TextBlock)) and
- ((table[i][0].text.lower() == 'dihedralcoeff') or
- (table[i][0].text.lower() == 'dihedral_coeff'))):
- if table[i][0].text != 'dihedral_coeff':
- raise InputError('----------------------------------------------------\n'+
- ' Spelling error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Use \"dihedral_coeff\", not \"'+table[i][0].text+'\"\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- if ((len(table[i]) > 1) and
- isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*')):
- pass # we dealt with this case earlier
- elif (not ((len(table[i]) > 1) and
- (isinstance(table[i][1], VarRef)) and
- (table[i][1].prefix in ('@', '@{')) and
- (table[i][1].nptr.cat_name == 'dihedral') and
- (table[i][1].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Invalid \"dihedral_coeff\" command.\n\n'+
- ' Each \"dihedral_coeff\" command should have the following syntax:\n\n'+
- ' dihedral_coeff @dihedral:type [optional style] list-of-parameters...\n'+
- '----------------------------------------------------\n\n'+
- g_no_check_msg)
- else:
- dihedral_coeffs_defined.add(table[i][1].binding)
-
-
- if ((isinstance(table[i][0], TextBlock)) and
- ((table[i][0].text.lower() == 'impropercoeff') or
- (table[i][0].text.lower() == 'improper_coeff'))):
- if table[i][0].text != 'improper_coeff':
- raise InputError('----------------------------------------------------\n'+
- ' Spelling error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Use \"improper_coeff\", not \"'+table[i][0].text+'\"\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- if ((len(table[i]) > 1) and
- isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*')):
- pass # we dealt with this case earlier
- elif (not ((len(table[i]) > 1) and
- (isinstance(table[i][1], VarRef)) and
- (table[i][1].prefix in ('@', '@{')) and
- (table[i][1].nptr.cat_name == 'improper') and
- (table[i][1].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Invalid \"improper_coeff\" command.\n\n'+
- ' Each \"improper_coeff\" command should have the following syntax:\n\n'+
- ' improper_coeff @improper:type [optional style] list-of-parameters...\n'+
- '----------------------------------------------------\n\n'+
- g_no_check_msg)
- else:
- improper_coeffs_defined.add(table[i][1].binding)
-
-
- elif ((isinstance(table[i][0], TextBlock)) and
- ((table[i][0].text.lower() == 'paircoeff') or
- (table[i][0].text.lower() == 'pair_coeff'))):
- if table[i][0].text != 'pair_coeff':
- raise InputError('----------------------------------------------------\n'+
- ' Spelling error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Use \"pair_coeff\", not \"'+table[i][0].text+'\"\n'+
- '----------------------------------------------------\n'+
- g_no_check_msg)
-
- if len(table[i]) > 2: # if not, deal with error later
- if ((isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*')) and
- (isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*'))):
- pair_coeffs_defined.add(('*','*'))
- else:
- compound_wildcard = False
- assert(len(table[i]) > 1)
-
- if hasattr(table[i][1], '__len__'):
- ltmpl = table[i][1]
- else:
- ltmpl = [table[i][1]]
- for entry in ltmpl:
- if (isinstance(entry, TextBlock) and
- ('*' in entry.text)):
- compound_wildcard = True
- elif (isinstance(entry, VarRef) and
- ('*' in entry.descr_str)):
- compound_wildcard = True
-
- if hasattr(table[i][2], '__len__'):
- ltmpl = table[i][2]
- else:
- ltmpl = [table[i][2]]
- for entry in ltmpl:
- if (isinstance(entry, TextBlock) and
- ('*' in entry.text)):
- compound_wildcard = True
- elif (isinstance(entry, VarRef) and
- ('*' in entry.descr_str)):
- compound_wildcard = True
-
- if compound_wildcard:
- raise InputError('---- Paranoid checking: ---\n'
- ' Possible error near '+
- ErrorLeader(entry.srcloc.infile,
- entry.srcloc.lineno)+'\n'
- 'The wildcard symbol, \"*\", is not recommended within a \"pair_coeff\" command.\n'
- 'It is safer to specify the parameters for each bond type explicitly.\n'
- 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n'
- 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n')
-
-
- if ((len(table[i]) > 2) and
- (isinstance(table[i][1], TextBlock) and
- (table[i][1].text == '*')) and
- (isinstance(table[i][2], TextBlock) and
- (table[i][2].text == '*'))):
- pass # we dealt with this case earlier
-
- elif (not ((len(table[i]) > 2) and
- (isinstance(table[i][1], VarRef)) and
- (table[i][1].prefix in ('@', '@{')) and
- (table[i][1].nptr.cat_name == 'atom') and
- (table[i][1].nptr.cat_node == root_node) and
- (isinstance(table[i][2], VarRef)) and
- (table[i][2].prefix in ('@', '@{')) and
- (table[i][2].nptr.cat_name == 'atom') and
- (table[i][2].nptr.cat_node == root_node))):
- raise InputError('----------------------------------------------------\n'+
- ' Syntax error near '+
- ErrorLeader(table[i][0].srcloc.infile,
- table[i][0].srcloc.lineno)+'\n'
- ' Invalid \"pair_coeff\" command.\n\n'+
- ' Each \"pair_coeff\" command should have the following syntax:\n\n'+
- ' pair_coeff @atom:typeI @atom:typeJ [optional style] list-of-parameters...\n'+
- '----------------------------------------------------\n\n'+
- g_no_check_msg)
- else:
- pair_coeffs_defined.add((table[i][1].binding, table[i][2].binding))
-
-
-
-
-def LttreeCheckParseArgs(argv, settings):
-
- LttreeParseArgs(argv, settings)
-
- if __name__ == "__main__":
- # Instantiate the lexer we will be using.
- # (The lexer's __init__() function requires an openned file.
- # Assuming __name__ == "__main__", then the name of that file should
- # be the last remaining (unprocessed) argument in the argument list.)
- if len(argv) == 1:
- raise InputError('Error: This program requires at least one argument\n'
- ' the name of a file containing ttree template commands\n')
- elif len(argv) == 2:
- settings.infile = argv[1]
- try:
- settings.lex = TemplateLexer(open(settings.infile, 'r'),
- settings.infile) # Parse text from file
- except IOError:
- sys.stderr.write('Error: unable to open file\n'
- ' \"'+settings.infile+'\"\n'
- ' for reading.\n')
- sys.exit(1)
- del(argv[1:2])
-
- else:
- # if there are more than 2 remaining arguments,
- problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
- raise InputError('Syntax Error('+g_program_name+'):\n\n'
- ' Unrecognized argument.\n'
- ' (That or there is some other problem with the argument list.)\n'
- ' The problem begins with these arguments:\n'
- ' '+(' '.join(problem_args))+'\n\n'
- ' (The actual problem may be earlier in the argument list.\n'
- ' If these arguments are source files, then keep in mind\n'
- ' that this program can not parse multiple source files.)\n'
- ' Check the syntax of the entire argument list.\n')
-
-
-
-
-
-####### control flow begins here: #######
-
-
-if __name__ == "__main__":
-
- g_program_name = __file__.split('/')[-1] # = 'lttree_check.py'
- g_version_str = '0.76'
- g_date_str = '2014-12-19'
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
-
- try:
- # Parse the argument list and instantiate the lexer we will be using:
-
- #settings = BasicUISettings()
- #BasicUIParseArgs(sys.argv, settings)
- settings = LttreeSettings()
- LttreeCheckParseArgs(sys.argv, settings)
-
- # Invoke syntax checker pass:
- # This first check only checks for very simple mistakes
- # (mispelled versions of standard files or variable names).
- CheckSyntaxCheap(settings.lex)
- settings.lex.instream.close()
- # Now read the file again.
- # This time parse it using StaticObj.ReadTemplate().
- # (This will allow us to check for deeper problems.)
- del settings.lex
- settings.lex = TemplateLexer(open(settings.infile, 'r'),
- settings.infile)
- static_tree_root = StaticObj('', None) # The root of the static tree
- # has name '' (equivalent to '/')
- sys.stderr.write(g_program_name+': parsing the class definitions...')
- static_tree_root.Parse(settings.lex)
-
- sys.stderr.write(' done\n'+g_program_name+': looking up classes...')
- static_tree_root.LookupStaticRefs()
- sys.stderr.write(' done\n'+g_program_name+': looking up @variables...')
- AssignStaticVarPtrs(static_tree_root,
- search_instance_commands=False)
- replace_var_pairs = {}
- FindReplacementVarPairs(static_tree_root, replace_var_pairs)
- ReplaceVars(static_tree_root, replace_var_pairs,
- search_instance_commands=False)
- AssignStaticVarPtrs(static_tree_root,
- search_instance_commands=True)
- ReplaceVars(static_tree_root, replace_var_pairs,
- search_instance_commands=True)
- sys.stderr.write(' done\n')
- #sys.stderr.write(' done\n\nclass_def_tree = ' + str(static_tree_root) + '\n\n')
-
- data_pair_coeffs_defined = set([])
- data_bond_coeffs_defined = set([])
- data_angle_coeffs_defined = set([])
- data_dihedral_coeffs_defined = set([])
- data_improper_coeffs_defined = set([])
- in_pair_coeffs_defined = set([])
- in_bond_coeffs_defined = set([])
- in_angle_coeffs_defined = set([])
- in_dihedral_coeffs_defined = set([])
- in_improper_coeffs_defined = set([])
-
- # Now check the static syntax
- # Here we check the contents of the the "write_once()" commands:
- CheckSyntaxStatic(static_tree_root,
- static_tree_root,
- settings.column_names,
- data_pair_coeffs_defined,
- data_bond_coeffs_defined,
- data_angle_coeffs_defined,
- data_dihedral_coeffs_defined,
- data_improper_coeffs_defined,
- in_pair_coeffs_defined,
- in_bond_coeffs_defined,
- in_angle_coeffs_defined,
- in_dihedral_coeffs_defined,
- in_improper_coeffs_defined,
- search_instance_commands=False)
- # Here we check the contents of the the "write()" commands:
- CheckSyntaxStatic(static_tree_root,
- static_tree_root,
- settings.column_names,
- data_pair_coeffs_defined,
- data_bond_coeffs_defined,
- data_angle_coeffs_defined,
- data_dihedral_coeffs_defined,
- data_improper_coeffs_defined,
- in_pair_coeffs_defined,
- in_bond_coeffs_defined,
- in_angle_coeffs_defined,
- in_dihedral_coeffs_defined,
- in_improper_coeffs_defined,
- search_instance_commands=True)
-
-
- if 'bond' in static_tree_root.categories:
-
- if ((len(data_bond_coeffs_defined) > 0) and
- (len(in_bond_coeffs_defined) > 0)):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: You can EITHER use \"bond_coeff\" commands\n'+
- ' OR you can have a \"Data Bond Coeffs\" section.\n'+
- ' LAMMPS will not allow both (...as of late 2012)\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
- #' If this is no longer true, to override this error message you must\n'+
- #' disable error checking by running moltemplate with the -nocheck option.\n')
- if len(data_bond_coeffs_defined) > 0:
- bond_coeffs_defined = data_bond_coeffs_defined
- else:
- bond_coeffs_defined = in_bond_coeffs_defined
-
- bond_bindings = static_tree_root.categories['bond'].bindings
- for nd,bond_binding in bond_bindings.items():
- if not nd.IsDeleted():
- if ((not (bond_binding in bond_coeffs_defined)) and
- (not HasWildCard(bond_binding.full_name)) and
- (not ('*' in bond_coeffs_defined))):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: Missing bond coeff.\n\n'+
- ' No coeffs for the \"'+bond_binding.full_name+'\" bond type have been\n'+
- 'defined, but a reference to that bond type was discovered\n'+
- 'near '+ErrorLeader(bond_binding.refs[0].srcloc.infile,
- bond_binding.refs[0].srcloc.lineno)+'. Check this file and also check\n'
- 'your \"bond_coeff\" commands or your \"Data Bond Coeffs" section.\n'
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
-
-
-
- if 'angle' in static_tree_root.categories:
-
- if ((len(data_angle_coeffs_defined) > 0) and
- (len(in_angle_coeffs_defined) > 0)):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: You can EITHER use \"angle_coeff\" commands\n'+
- ' OR you can have a \"Data Angle Coeffs\" section.\n'+
- ' LAMMPS will not allow both (...as of late 2012)\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
- #' If this is no longer true, to override this error message you must\n'+
- #' disable error checking by running moltemplate with the -nocheck option.\n')
- if len(data_angle_coeffs_defined) > 0:
- angle_coeffs_defined = data_angle_coeffs_defined
- else:
- angle_coeffs_defined = in_angle_coeffs_defined
-
- angle_bindings = static_tree_root.categories['angle'].bindings
- for nd,angle_binding in angle_bindings.items():
- if not nd.IsDeleted():
- if ((not (angle_binding in angle_coeffs_defined)) and
- #(not HasWildCard(angle_binding.full_name)) and
- (not ('*' in angle_coeffs_defined))):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: Missing angle coeff.\n\n'+
- ' No coeffs for the \"'+angle_binding.full_name+'\" angle type have been\n'+
- 'defined, but a reference to that angle type was discovered\n'+
- 'near '+ErrorLeader(angle_binding.refs[0].srcloc.infile,
- angle_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
- 'also check your \"angle_coeff\" commands or your \"Data Angle Coeffs" section.\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
-
-
-
- if 'dihedral' in static_tree_root.categories:
-
- if ((len(data_dihedral_coeffs_defined) > 0) and
- (len(in_dihedral_coeffs_defined) > 0)):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: You can EITHER use \"dihedral_coeff\" commands\n'+
- ' OR you can have a \"Data Dihedral Coeffs\" section.\n'+
- ' LAMMPS will not allow both (...as of late 2012)\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
- #' If this is no longer true, to override this error message you must\n'+
- #' disable error checking by running moltemplate with the -nocheck option.\n')
- if len(data_dihedral_coeffs_defined) > 0:
- dihedral_coeffs_defined = data_dihedral_coeffs_defined
- else:
- dihedral_coeffs_defined = in_dihedral_coeffs_defined
-
- dihedral_bindings = static_tree_root.categories['dihedral'].bindings
- for nd,dihedral_binding in dihedral_bindings.items():
- if not nd.IsDeleted():
- if ((not (dihedral_binding in dihedral_coeffs_defined)) and
- #(not HasWildCard(dihedral_binding.full_name)) and
- (not ('*' in dihedral_coeffs_defined))):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: Missing dihedral coeff.\n\n'+
- ' No coeffs for the \"'+dihedral_binding.full_name+'\" dihedral type have been\n'+
- 'defined, but a reference to that dihedral type was discovered\n'+
- 'near '+ErrorLeader(dihedral_binding.refs[0].srcloc.infile,
- dihedral_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
- 'also check your \"dihedral_coeff\" commands or your \"Data Dihedral Coeffs" section.\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
-
-
- if 'improper' in static_tree_root.categories:
-
- if ((len(data_improper_coeffs_defined) > 0) and
- (len(in_improper_coeffs_defined) > 0)):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: You can EITHER use \"improper_coeff\" commands\n'+
- ' OR you can have a \"Data Improper Coeffs\" section.\n'+
- ' LAMMPS will not allow both (...as of late 2012)\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
- #' If this is no longer true, to override this error message you must\n'+
- #' disable error checking by running moltemplate with the -nocheck option.\n')
- if len(data_improper_coeffs_defined) > 0:
- improper_coeffs_defined = data_improper_coeffs_defined
- else:
- improper_coeffs_defined = in_improper_coeffs_defined
-
- improper_bindings = static_tree_root.categories['improper'].bindings
- for nd,improper_binding in improper_bindings.items():
- if not nd.IsDeleted():
- if ((not (improper_binding in improper_coeffs_defined)) and
- #(not HasWildCard(improper_binding.full_name)) and
- (not ('*' in improper_coeffs_defined))):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: Missing improper coeff.\n\n'+
- ' No coeffs for the \"'+improper_binding.full_name+'\" improper type have been\n'+
- 'defined, but a reference to that improper type was discovered\n'+
- 'near '+ErrorLeader(improper_binding.refs[0].srcloc.infile,
- improper_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
- 'also check your \"improper_coeff\" commands or your \"Data Improper Coeffs" section.\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
-
-
- if 'atom' in static_tree_root.categories:
-
- if ((len(data_pair_coeffs_defined) > 0) and
- (len(in_pair_coeffs_defined) > 0)):
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: You can EITHER use \"pair_coeff\" commands\n'+
- ' OR you can have a \"Data Pair Coeffs\" section.\n'+
- ' LAMMPS will not allow both (...as of late 2012)\n'+
- '---------------------------------------------------------------------\n'+
- g_no_check_msg)
- #' If this is no longer true, to override this error message you must\n'+
- #' disable error checking by running moltemplate with the -nocheck option.\n')
-
- if len(data_pair_coeffs_defined) > 0:
- pair_coeffs_defined = data_pair_coeffs_defined
- else:
- pair_coeffs_defined = in_pair_coeffs_defined
-
- atom_bindings = static_tree_root.categories['atom'].bindings
- for nd,atom_binding in atom_bindings.items():
- if not nd.IsDeleted():
- if ((not ((atom_binding,atom_binding)
- in
- pair_coeffs_defined)) and
- (not HasWildCard(atom_binding.full_name)) and
- (not (('*','*') in pair_coeffs_defined)) and
- (not (atom_binding.nptr.cat_name,
- atom_binding.nptr.cat_node,
- atom_binding.nptr.leaf_node)
- in replace_var_pairs)):
-
- raise InputError('---------------------------------------------------------------------\n'+
- ' Syntax error: Missing pair coeff.\n\n'+
- ' No pair coeffs for the \"'+atom_binding.full_name+'\" atom type have been\n'+
- 'defined, but a reference to that atom type was discovered\n'+
- 'near '+ErrorLeader(atom_binding.refs[0].srcloc.infile,
- atom_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
- 'also check your \"pair_coeff\" commands or your \"Data Pair Coeffs" section.\n\n'+
- g_no_check_msg)
- #else:
- # raise InputError('Error: No atom types (@atom) have been defined.\n')
-
- sys.stderr.write(g_program_name+': -- No errors detected. --\n')
- exit(0)
-
- except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(1)
-
diff --git a/tools/moltemplate/src/lttree_postprocess.py b/tools/moltemplate/src/lttree_postprocess.py
deleted file mode 100644
index 793752aac..000000000
--- a/tools/moltemplate/src/lttree_postprocess.py
+++ /dev/null
@@ -1,335 +0,0 @@
-#!/usr/bin/env python
-
-"""
- lttree_postprocess.py
- This is a stand-alone python script which checks the files created by
- lttree.py to insure that the standard instance-variables ($variables)
- have all been defined. This script performs a task which is very similar
- to the task performed by lttree_check.py. This script attempts to detect
- mistakes in the names of $atom, $bond, $angle, $dihedral, $improper, & $mol
- variables.
-
-"""
-
-import sys
-from lttree_styles import *
-from ttree_lex import ExtractCatName
-
-g_program_name = __file__.split('/')[-1] # = 'lttree_postprocess.py'
-g_version_str = '0.4'
-g_date_str = '2012-12-12'
-atom_style = 'full'
-ttree_assignments_fname = 'ttree_assignments.txt'
-defined_mols = set([])
-defined_atoms = set([])
-defined_bonds = set([])
-defined_angles = set([])
-defined_dihedrals = set([])
-defined_impropers = set([])
-
-g_no_check_msg = \
- '(To override this error, run moltemplate using the \"-nocheck\" argument.)\n'
-
-if len(sys.argv) > 1:
- for i in range(0,len(sys.argv)):
- if ((sys.argv[i].lower() == '-atomstyle') or
- (sys.argv[i].lower() == '-atom-style') or
- (sys.argv[i].lower() == '-atom_style')):
- if i+1 >= len(sys.argv):
- raise InputError('Error('+g_program_name+'): The '+sys.argv[i]+' flag should be followed by a LAMMPS\n'
- ' atom_style name (or single quoted string containing a space-separated\n'
- ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n')
-
- atom_style = sys.argv[i+1]
- elif ((sys.argv[i].lower() == '-ttreeassignments') or
- (sys.argv[i].lower() == '-ttree-assignments') or
- (sys.argv[i].lower() == '-ttree_assignments')):
- if i+1 >= len(sys.argv):
- raise InputError('Error('+g_program_name+'): The '+sys.argv[i]+' flag should be followed by \n'
- ' a file containing the variable bindings created by ttree/moltemplate.\n')
- ttree_assignments_fname = sys.argv[i+1]
- else:
- pass # ignore other arguments (they are intended for lttree.py)
-
-
-atom_column_names = AtomStyle2ColNames(atom_style)
-i_atomid = 0
-i_molid = -1
-for i in range(0,len(atom_column_names)):
- if atom_column_names[i].lower() == 'atom-id':
- i_atomid = i
- elif atom_column_names[i].lower() == 'molecule-id':
- i_molid = i
-i_max_column = max(i_atomid, i_molid)
-
-
-# The following variables are defined in "lttree_styles.py"
-#data_atoms="Data Atoms"
-#data_masses="Data Masses"
-#data_velocities="Data Velocities"
-#data_bonds="Data Bonds"
-#data_angles="Data Angles"
-#data_dihedrals="Data Dihedrals"
-#data_impropers="Data Impropers"
-
-
-sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
-
-try:
- # ------------ defined_atoms ------------
- try:
- f = open(data_atoms+'.template', 'r')
- except:
- raise InputError('Error('+g_program_name+'): Unable to open file\n'+
- '\"'+data_atoms+'.template\"\n'
- ' for reading. (Do your files lack a \"'+data_atoms+'\" section?)\n'
- +g_no_check_msg+'\n')
-
- for line_orig in f:
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- else:
- line = line_orig.rstrip('\n')
-
- tokens = line.strip().split()
- if len(tokens) == 0:
- pass
- elif len(tokens) <= i_max_column:
- raise InputError('Error('+g_program_name+'): The following line from\n'
- ' "\"'+data_atoms+'.template\" has bad format:\n\n'
- +line_orig+'\n'
- ' This my probably an internal error. (Feel free to contact the developer.)\n'
- +g_no_check_msg+'\n')
- else:
- defined_atoms.add(tokens[i_atomid])
- if i_molid != -1:
- defined_mols.add(tokens[i_molid])
-
- f.close()
-
-
- # ------------ defined_bonds ------------
- try:
- f = open(data_bonds+'.template', 'r')
-
- for line_orig in f:
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- else:
- line = line_orig.rstrip('\n')
-
- tokens = line.strip().split()
- if len(tokens) == 0:
- pass
- elif len(tokens) < 4:
- raise InputError('Error('+g_program_name+'): The following line from\n'
- ' "\"'+data_bonds+'.template\" has bad format:\n\n'
- +line_orig+'\n'
- ' This my probably an internal error. (Feel free to contact the developer.)\n'
- +g_no_check_msg+'\n')
- else:
- defined_bonds.add(tokens[0])
- f.close()
- except:
- pass # Defining bonds (stored in the data_bonds file) is optional
-
-
- # ------------ defined_angles ------------
- try:
- f = open(data_angles+'.template', 'r')
- for line_orig in f:
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- else:
- line = line_orig.rstrip('\n')
-
- tokens = line.strip().split()
- if len(tokens) == 0:
- pass
- elif len(tokens) < 5:
- raise InputError('Error('+g_program_name+'): The following line from\n'
- ' "\"'+data_angles+'.template\" has bad format:\n\n'
- +line_orig+'\n'
- ' This my probably an internal error. (Feel free to contact the developer.)\n'
- +g_no_check_msg+'\n')
- else:
- defined_angles.add(tokens[0])
- f.close()
- except:
- pass # Defining angles (stored in the data_angles file) is optional
-
-
- # ------------ defined_dihedrals ------------
- try:
- f = open(data_dihedrals+'.template', 'r')
- for line_orig in f:
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- else:
- line = line_orig.rstrip('\n')
-
- tokens = line.strip().split()
- if len(tokens) == 0:
- pass
- elif len(tokens) < 6:
- raise InputError('Error('+g_program_name+'): The following line from\n'
- ' "\"'+data_dihedrals+'.template\" has bad format:\n\n'
- +line_orig+'\n'
- ' This my probably an internal error. (Feel free to contact the developer.)\n'
- +g_no_check_msg+'\n')
- else:
- defined_dihedrals.add(tokens[0])
- f.close()
- except:
- pass #Defining dihedrals (stored in the data_dihedrals file) is optional
-
-
- # ------------ defined_impropers ------------
- try:
- f = open(data_impropers+'.template', 'r')
-
- for line_orig in f:
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- else:
- line = line_orig.rstrip('\n')
-
- tokens = line.strip().split()
- if len(tokens) == 0:
- pass
- elif len(tokens) < 6:
- raise InputError('Error('+g_program_name+'): The following line from\n'
- ' "\"'+data_impropers+'.template\" has bad format:\n\n'
- +line_orig+'\n'
- ' This my probably an internal error. (Feel free to contact the developer.)\n'
- +g_no_check_msg+'\n')
- else:
- defined_impropers.add(tokens[0])
- f.close()
- except:
- pass #Defining impropers (stored in the data_impropers file) is optional
-
-
-
-
- # ---- Check ttree_assignments to make sure variables are defined ----
-
- try:
- f = open(ttree_assignments_fname, 'r')
- except:
- raise InputError('Error('+g_program_name+'): Unable to open file\n'+
- '\"'+ttree_assignments_fname+'\"\n'
- ' for reading. (Do your files lack a \"'+data_atoms+'\" section?)\n'
- +g_no_check_msg+'\n')
-
- for line_orig in f:
-
- ic = line_orig.find('#')
- if ic != -1:
- line = line_orig[:ic]
- usage_location_str = 'near ' + line_orig[ic+1:]
- else:
- line = line_orig.rstrip('\n')
- usage_location_str = ''
-
- tokens = line.strip().split()
- if len(tokens) == 0:
- pass
- if len(tokens) > 0:
- # This file contains a list of variables of the form:
- #
- # @/atom:MoleculeType1:C 1
- # @/atom:MoleculeType1:H 2
- # @/atom:MoleculeType2:N 3
- # $/atom:molecule1:N1 1
- # $/atom:molecule1:C1 2
- # :
- # $/atom:molecule1141:CH 13578
- # $/atom:molecule1142:N3 13579
- # :
- # We only care about instance variables (which use the '$' prefix)
- # Lines corresponding to static variables (which use the '@' prefix)
- # are ignored during this pass.
- i_prefix = tokens[0].find('$')
- if i_prefix != -1:
- descr_str = tokens[0][i_prefix+1:]
- cat_name = ExtractCatName(descr_str)
-
- if ((cat_name == 'atom') and
- (tokens[0] not in defined_atoms)):
- raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
- ' Reference to undefined $atom:\n\n'
- ' '+tokens[0]+' (<--full name)\n\n'+
- ' (If that atom belongs to a molecule (or other subunit), make sure that\n'+
- ' you specified the correct path which leads to it (using / and ..))\n\n'+
- g_no_check_msg)
-
- elif ((cat_name == 'bond') and
- (tokens[0] not in defined_bonds)):
- raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
- ' Reference to undefined $bond:\n\n'
- ' '+tokens[0]+' (<--full name)\n\n'+
- ' (If that bond belongs to a molecule (or other subunit), make sure that\n'+
- ' you specified the correct path which leads to it (using / and ..))\n\n'+
- g_no_check_msg)
-
- elif ((cat_name == 'angle') and
- (tokens[0] not in defined_angles)):
- raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
- ' Reference to undefined $angle:\n\n'+
- ' '+tokens[0]+' (<--full name)\n\n'+
- ' (If that angle belongs to a molecule (or other subunit), make sure that\n'+
- ' you specified the correct path which leads to it (using / and ..))\n\n'+
- g_no_check_msg)
-
- elif ((cat_name == 'dihedral') and
- (tokens[0] not in defined_dihedrals)):
- raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n\n'+
- ' Reference to undefined $dihedral:\n\n'
- ' '+tokens[0]+' (<--full name)\n\n'+
- ' (If that dihedral belongs to a molecule (or other subunit), make sure that\n'+
- ' you specified the correct path which leads to it (using / and ..))\n\n'+
- g_no_check_msg)
-
- elif ((cat_name == 'improper') and
- (tokens[0] not in defined_impropers)):
- raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
- ' Reference to undefined $improper:\n\n'
- ' '+tokens[0]+' (<--full name)\n\n'+
- ' (If that improper belongs to a molecule (or other subunit), make sure that\n'+
- ' you specified the correct path which leads to it (using / and ..))\n\n'+
- g_no_check_msg)
-
- # I used to generate an error when a users defines a $mol
- # variable but does not associate any atoms with it (or if the
- # user systematically deletes all the atoms in that molecule),
- # but I stopped this practice.
- # I don't think there is any real need to complain if some
- # molecule id numbers are undefined. LAMMPS does not care.
- #
- #elif ((cat_name == 'mol') and
- # (tokens[0] not in defined_mols)):
- # raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
- # ' Reference to undefined $mol (molecule-ID) variable:\n\n'
- # ' '+tokens[0]+' (<--full name)\n\n'+
- # ' (If that molecule is part of a larger molecule, then make sure that\n'+
- # ' you specified the correct path which leads to it (using / and ..))\n\n'+
- # g_no_check_msg)
-
-
- f.close()
-
- sys.stderr.write(g_program_name+': -- No errors detected. --\n')
- exit(0)
-
-
-
-except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(1)
-
diff --git a/tools/moltemplate/src/lttree_styles.py b/tools/moltemplate/src/lttree_styles.py
deleted file mode 100644
index ec9c9a034..000000000
--- a/tools/moltemplate/src/lttree_styles.py
+++ /dev/null
@@ -1,239 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-from ttree_lex import InputError
-
-
-# Users of lttree typically generate the following files:
-# The variable below refer to file names generated by
-# write() and write_once() commands in a lttree-file.
-# (I keep changing my mind what I want these names to be.)
-data_prefix="Data "
-data_prefix_no_space="Data"
-data_atoms="Data Atoms"
-data_masses="Data Masses"
-data_velocities="Data Velocities"
-data_bonds="Data Bonds"
-data_bond_list="Data Bond List"
-data_angles="Data Angles"
-data_dihedrals="Data Dihedrals"
-data_impropers="Data Impropers"
-data_bond_coeffs="Data Bond Coeffs"
-data_angle_coeffs="Data Angle Coeffs"
-data_dihedral_coeffs="Data Dihedral Coeffs"
-data_improper_coeffs="Data Improper Coeffs"
-data_pair_coeffs="Data Pair Coeffs"
-
-# interactions-by-type (not id. This is not part of the LAMMPS standard.)
-data_bonds_by_type="Data Bonds By Type"
-data_angles_by_type="Data Angles By Type"
-data_dihedrals_by_type="Data Dihedrals By Type"
-data_impropers_by_type="Data Impropers By Type"
-
-# class2 data sections
-data_bondbond_coeffs="Data BondBond Coeffs"
-data_bondangle_coeffs="Data BondAngle Coeffs"
-data_middlebondtorsion_coeffs="Data MiddleBondTorsion Coeffs"
-data_endbondtorsion_coeffs="Data EndBondTorsion Coeffs"
-data_angletorsion_coeffs="Data AngleTorsion Coeffs"
-data_angleangletorsion_coeffs="Data AngleAngleTorsion Coeffs"
-data_bondbond13_coeffs="Data BondBond13 Coeffs"
-data_angleangle_coeffs="Data AngleAngle Coeffs"
-
-# sections for non-point-like particles:
-data_ellipsoids="Data Ellipsoids"
-data_lines="Data Lines"
-data_triangles="Data Triangles"
-
-# periodic boundary conditions
-data_boundary="Data Boundary"
-# (for backward compatibility), an older version of this file was named:
-data_pbc="Data PBC"
-
-# The files are fragments of a LAMMPS data file (see "read_data").
-# In addition, moltemplate may also generate the following files:
-in_prefix="In "
-in_prefix_no_space="In"
-in_init="In Init"
-in_settings="In Settings"
-in_coords="In Coords"
-# These files represent different sections of the LAMMPS input script.
-
-
-
-# Atom Styles in LAMMPS as of 2011-7-29
-g_style_map = {'angle': ['atom-ID','molecule-ID','atom-type','x','y','z'],
- 'atomic': ['atom-ID','atom-type','x','y','z'],
- 'bond': ['atom-ID','molecule-ID','atom-type','x','y','z'],
- 'charge': ['atom-ID','atom-type','q','x','y','z'],
- 'dipole': ['atom-ID','atom-type','q','x','y','z','mux','muy','muz'],
- 'electron': ['atom-ID','atom-type','q','spin','eradius','x','y','z'],
- 'ellipsoid': ['atom-ID','atom-type','x','y','z','quatw','quati','quatj','quatk'],
- 'full': ['atom-ID','molecule-ID','atom-type','q','x','y','z'],
- 'line': ['atom-ID','molecule-ID','atom-type','lineflag','density','x','y','z'],
- 'meso': ['atom-ID','atom-type','rho','e','cv','x','y','z'],
- 'molecular': ['atom-ID','molecule-ID','atom-type','x','y','z'],
- 'peri': ['atom-ID','atom-type','volume','density','x','y','z'],
- 'sphere': ['atom-ID','atom-type','diameter','density','x','y','z'],
- 'tri': ['atom-ID','molecule-ID','atom-type','triangleflag','density','x','y','z'],
- 'wavepacket':['atom-ID','atom-type','charge','spin','eradius','etag','cs_re','cs_im','x','y','z'],
- 'hybrid': ['atom-ID','atom-type','x','y','z'],
- # The following styles were removed from LAMMPS as of 2012-3
- 'colloid': ['atom-ID','atom-type','x','y','z'],
- 'granular': ['atom-ID','atom-type','diameter','density','x','y','z']}
-
-
-
-
-def AtomStyle2ColNames(atom_style_string):
-
- atom_style_string = atom_style_string.strip()
- if len(atom_style_string) == 0:
- raise InputError('Error: Invalid atom_style\n'
- ' (The atom_style command was followed by an empty string.)\n')
- atom_style_args = atom_style_string.split()
- atom_style = atom_style_args[0]
-
- hybrid_args = atom_style_args[1:]
- if (atom_style not in g_style_map):
- if (len(atom_style_args) >= 2):
- # If the atom_style_string includes at least 2 words, then we
- # interpret this as a list of the individual column names
- return atom_style_args
- else:
- raise InputError('Error: Unrecognized atom_style: \"'+atom_style+'\"\n')
-
- if (atom_style != 'hybrid'):
- return g_style_map[atom_style]
- else:
- column_names = ['atom-ID','atom-type','x','y','z']
- if (len(hybrid_args)==0):
- raise InputError('Error: atom_style hybrid must be followed by a sub_style.\n')
- for sub_style in hybrid_args:
- if (sub_style not in g_style_map):
- raise InputError('Error: Unrecognized atom_style: \"'+sub_style+'\"\n')
- for cname in g_style_map[sub_style]:
- if cname not in column_names:
- column_names.append(cname)
-
- return column_names
-
-
-def ColNames2AidAtypeMolid(column_names):
- # Because of the diversity of ways that these
- # numbers are referred to in the LAMMPS documentation,
- # we have to be flexible and allow the user to refer
- # to these quantities in a variety of ways.
- # Hopefully this covers everything:
-
- if 'atom-ID' in column_names:
- i_atomid = column_names.index('atom-ID')
- elif 'atom−ID' in column_names: # (− is the character used in the manual)
- i_atomid = column_names.index('atom−ID')
- elif 'atomID' in column_names:
- i_atomid = column_names.index('atomID')
- elif 'atomid' in column_names:
- i_atomid = column_names.index('atomid')
- elif 'id' in column_names:
- i_atomid = column_names.index('id')
- elif 'atom' in column_names:
- i_atomid = column_names.index('atom')
- elif '$atom' in column_names:
- i_atomid = column_names.index('$atom')
- else:
- raise InputError('Error: List of column names lacks an \"atom-ID\"\n')
-
- if 'atom-type' in column_names:
- i_atomtype = column_names.index('atom-type')
- elif 'atom−type' in column_names: # (− hyphen character used in manual)
- i_atomtype = column_names.index('atom−type')
- elif 'atomtype' in column_names:
- i_atomtype = column_names.index('atomtype')
- elif 'type' in column_names:
- i_atomtype = column_names.index('type')
- elif '@atom' in column_names:
- i_atomtype = column_names.index('@atom')
- else:
- raise InputError('Error: List of column names lacks an \"atom-type\"\n')
-
- i_molid = None
- if 'molecule-ID' in column_names:
- i_molid = column_names.index('molecule-ID')
- elif 'molecule−ID' in column_names: # (− hyphen character used in manual)
- i_molid = column_names.index('molecule−ID')
- elif 'moleculeID' in column_names:
- i_molid = column_names.index('moleculeID')
- elif 'moleculeid' in column_names:
- i_molid = column_names.index('moleculeid')
- elif 'molecule' in column_names:
- i_molid = column_names.index('molecule')
- elif 'molID' in column_names:
- i_molid = column_names.index('molID')
- elif 'molid' in column_names:
- i_molid = column_names.index('molid')
- elif 'mol' in column_names:
- i_molid = column_names.index('mol')
- elif '$mol' in column_names:
- i_molid = column_names.index('$mol')
- else:
- pass # some atom_types do not have a valid molecule-ID
-
- return i_atomid, i_atomtype, i_molid
-
-
-
-def ColNames2Coords(column_names):
- """ Which of the columns correspond to coordinates
- which must be transformed using rigid-body
- (affine: rotation + translation) transformations?
- This function outputs a list of lists of triplets of integers.
-
- """
- i_x = None
- i_y = None
- i_z = None
- if 'x' in column_names:
- i_x = column_names.index('x')
- if 'y' in column_names:
- i_y = column_names.index('y')
- if 'z' in column_names:
- i_z = column_names.index('z')
- if (((i_x != None) != (i_y != None)) or
- ((i_y != None) != (i_z != None)) or
- ((i_z != None) != (i_x != None))):
- raise InputError('Error: custom atom_style list must define x, y, and z.\n')
- return [[i_x, i_y, i_z]]
-
-
-def ColNames2Vects(column_names):
- """ Which of the columns correspond to coordinates
- which must be transformed using rotations?
- Some coordinates like dipole moments and
- ellipsoid orientations should only be rotated
- (not translated).
- This function outputs a list of lists of triplets of integers.
-
- """
- vects = []
- i_mux = None
- i_muy = None
- i_muz = None
- if 'mux' in column_names:
- i_mux = column_names.index('mux')
- if 'muy' in column_names:
- i_muy = column_names.index('muy')
- if 'muz' in column_names:
- i_muz = column_names.index('muz')
- if (((i_mux != None) != (i_muy != None)) or
- ((i_muy != None) != (i_muz != None)) or
- ((i_muz != None) != (i_mux != None))):
- raise InputError('Error: custom atom_style list must define mux, muy, and muz or none.\n')
- if i_mux != None:
- vects.append([i_mux, i_muy, i_muz])
- return vects
diff --git a/tools/moltemplate/src/moltemplate.sh b/tools/moltemplate/src/moltemplate.sh
deleted file mode 100755
index d6f76a248..000000000
--- a/tools/moltemplate/src/moltemplate.sh
+++ /dev/null
@@ -1,2110 +0,0 @@
-#!/usr/bin/env bash
-# (note: Classic Bourne shell (#!/bin/sh) also worked at some point.)
-
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.moltemplate.org
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-G_PROGRAM_NAME="moltemplate.sh"
-G_VERSION="1.40"
-G_DATE="2016-10-19"
-
-echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
-echo "" >&2
-
-# Check for python:
-# I prefer python over python3 because python3 requires slightly
-# more memory. Use regular python (ie 2.7) when available.
-
-if which python > /dev/null; then
- PYTHON_COMMAND='python'
-elif which python3 > /dev/null; then
- PYTHON_COMMAND='python3'
-else
- echo "Error: $G_PROGRAM_NAME requires python or python3" >&2
- exit 1
-fi
-
-
-# First, determine the directory in which this shell script is located.
-# (The python script files should also be located here as well.)
-#SCRIPT_DIR=$(dirname $0)
-SCRIPT_DIR=`dirname "$0"`
-
-
-MSG_BAD_INSTALL=$(cat <<EOF
-
-INSTALLATION ERROR:
-Follow the instructions in the "Installation" chapter of the moltemplate manual.
-(Note: You may need to log out and log in again before the changes take effect.)
-
-EOF
-)
-
-
-ERR_BAD_INSTALL()
-{
- echo "$MSG_BAD_INSTALL" >&2
- exit 1
-}
-
-
-ERR_INTERNAL()
-{
- echo " !!!!!! Possible internal error !!!!!!" >&2
- echo "This could be a bug in moltemplate." >&2
- echo "Please report this error." >&2
- echo "(And please include the last few lines of moltemplate output preceding this.)" >&2
- echo " Thank you." >&2
- exit 100
-}
-
-
-MOLTEMPLATE_FILES_NEEDED=$(cat <<EOF
-ttree.py
-lttree.py
-lttree_check.py
-lttree_postprocess.py
-nbody_by_type.py
-nbody_fix_ttree_assignments.py
-nbody_reorder_atoms.py
-pdbsort.py
-postprocess_input_script.py
-remove_duplicate_atoms.py
-remove_duplicates_nbody.py
-renumber_DATA_first_column.py
-ttree_render.py
-dump2data.py
-raw2data.py
-EOF
-)
-
-
-
-OIFS=$IFS
-#IFS=$'\n'
-IFS="
-"
-
-for f in $MOLTEMPLATE_FILES_NEEDED; do
- if [ ! -s "${SCRIPT_DIR}/$f" ]; then
- echo "Error: Missing file \"${SCRIPT_DIR}/$f\"" >&2
- ERR_BAD_INSTALL
- fi
-done
-IFS=$OIFS
-
-
-
-# Directory moltemplate looks for popular force-fields files:
-#IMOLPATH=""
-#if [ -n "${MOLTEMPLATE_PATH}" ]; then
-# IMOLPATH="-importpath \"${MOLTEMPLATE_PATH}\""
-#fi
-if [ -d "${SCRIPT_DIR}/moltemplate_force_fields" ]; then
- IMOLPATH="-importpath \"${SCRIPT_DIR}/moltemplate_force_fields\""
-else
- IMOLPATH=""
-fi
-
-# command that invokes lttree.py
-LTTREE_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree.py\" ${IMOLPATH}"
-
-# command that invokes lttree_check.py
-LTTREE_CHECK_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree_check.py\" ${IMOLPATH}"
-
-# command that invokes lttree_postprocess.py
-LTTREE_POSTPROCESS_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree_postprocess.py\" ${IMOLPATH}"
-
-
-# -----------------------------------------------------------
-# If everything worked, then running ttree usually
-# generates the following files:
-#
-# Users of lttree typically generate the following files:
-# The variable below refer to file names generated by
-# write() and write_once() commands in a lttree-file.
-# (I keep changing my mind what I want these names to be.)
-data_prefix="Data "
-data_prefix_no_space="Data"
-data_header="Data Header"
-data_atoms="Data Atoms"
-data_masses="Data Masses"
-data_velocities="Data Velocities"
-data_bonds="Data Bonds"
-data_bond_list="Data Bond List"
-data_bonds_atomid_atomid="Data Bonds AtomId AtomId"
-data_angles="Data Angles"
-data_dihedrals="Data Dihedrals"
-data_impropers="Data Impropers"
-data_bond_coeffs="Data Bond Coeffs"
-data_angle_coeffs="Data Angle Coeffs"
-data_dihedral_coeffs="Data Dihedral Coeffs"
-data_improper_coeffs="Data Improper Coeffs"
-data_pair_coeffs="Data Pair Coeffs"
-data_pairij_coeffs="Data PairIJ Coeffs"
-
-# interactions-by-type (not id. This is not part of the LAMMPS standard.)
-data_chargepairs_by_type="Data Charge Pairs By Type"
-data_bonds_by_type="Data Bonds By Type"
-data_angles_by_type="Data Angles By Type"
-data_dihedrals_by_type="Data Dihedrals By Type"
-data_impropers_by_type="Data Impropers By Type"
-
-# class2 data sections
-data_bondbond_coeffs="Data BondBond Coeffs"
-data_bondangle_coeffs="Data BondAngle Coeffs"
-data_middlebondtorsion_coeffs="Data MiddleBondTorsion Coeffs"
-data_endbondtorsion_coeffs="Data EndBondTorsion Coeffs"
-data_angletorsion_coeffs="Data AngleTorsion Coeffs"
-data_angleangletorsion_coeffs="Data AngleAngleTorsion Coeffs"
-data_bondbond13_coeffs="Data BondBond13 Coeffs"
-data_angleangle_coeffs="Data AngleAngle Coeffs"
-
-# sections for non-point-like particles:
-data_ellipsoids="Data Ellipsoids"
-data_lines="Data Lines"
-data_triangles="Data Triangles"
-
-# periodic boundary conditions
-data_boundary="Data Boundary"
-# (for backward compatibility), an older version of this file was named:
-data_pbc="Data PBC"
-
-# ---------------------------------------------------------------
-# Note: The files above are fragments of a LAMMPS data file.
-# In addition, moltemplate will probably also generate the following files:
-# (These files represent different sections of the LAMMPS input script.)
-# ---------------------------------------------------------------
-
-in_prefix="In "
-in_prefix_no_space="In"
-in_init="In Init"
-in_settings="In Settings"
-in_coords="In Coords"
-in_charges="In Charges"
-
-# If present, the various "In " files contain commands which should be
-# included by the user in their LAMMPS input script. (This task is left
-# to the user.) However, the "Data " files are processed and pasted together
-# automatically in order to build a LAMMPS data file.
-# ---------------------------------------------------------------
-
-tmp_atom_coords="tmp_atom_coords.dat" #<-temporary file for storing coordinates
-
-
-
-MOLTEMPLATE_TEMP_FILES=$(cat <<EOF
-*.template
-ttree_assignments.txt
-$tmp_atom_coords
-$data_masses
-$data_pair_coeffs
-$data_pairij_coeffs
-$data_bond_coeffs
-$data_angle_coeffs
-$data_dihedral_coeffs
-$data_improper_coeffs
-$data_atoms
-$data_velocities
-$data_bonds
-$data_bond_list
-$data_angles
-$data_dihedrals
-$data_impropers
-$data_bondbond_coeffs
-$data_bondangle_coeffs
-$data_middlebondtorsion_coeffs
-$data_endbondtorsion_coeffs
-$data_angletorsion_coeffs
-$data_angleangletorsion_coeffs
-$data_bondbond13_coeffs
-$data_angleangle_coeffs
-$data_ellipsoids
-$data_lines
-$data_triangles
-$data_boundary
-$data_bonds_by_type*
-${data_angles_by_type}*
-${data_dihedrals_by_type}*
-${data_impropers_by_type}*
-$in_init
-$in_settings
-EOF
-)
-
-OIFS=$IFS
-#IFS=$'\n'
-IFS="
-"
-for f in $MOLTEMPLATE_TEMP_FILES; do
- #echo "removing [$f]"
- rm -f "$f"
-done
-IFS=$OIFS
-
-rm -rf output_ttree
-
-
-
-
-SYNTAX_MSG=$(cat <<EOF
-Syntax example:
-Usage:
-
-moltemplate.sh [-atomstyle style] \
- [-pdb/-xyz coord_file] \
- [-a assignments.txt] file.lt
-
-Optional arguments:
-
--atomstyle style By default, moltemplate.sh assumes you are using the "full"
- atom style in LAMMPS. You can change the atom style to "dipole"
- using -atomstyle dipole. If you are using a hybrid style,
- you must enclose the list of styles in quotes. For example:
- -atomstyle "hybrid full dipole"
- For custom atom styles, you can also specify the
- list of column names manually (enclosed in quotes):
- -atomstyle "molid x y z atomid atomtype mux muy muz"
-
--xyz xyz_file An optional xyz_file argument can be supplied as an argument
- following "-xyz".
- This file should contain the atomic coordinates in xyz format.
- (The atoms must appear in the same order in the data file.)
-
--pdb pdb_file An optional pdb_file argument can be supplied as an argument
- following "-pdb".
-
- This should be a PDB file (with ATOM or HETATM records) with
- the coordinates you wish to appear in the LAMMPS data file.
- (The atoms must appear in the same order in the data file.)
-
- If the PDB file contains periodic boundary box information
- (ie., a "CRYST1" record), this information is also copied
- to the LAMMPS data file.
- (Support for triclinic cells is experimental as of 2012-2-13.
- Other molecular structure formats may be supported later.)
--a "@atom:x 1"
--a assignments.txt
- The user can customize the numbers assigned to atom, bond,
- angle, dihedral, and improper types or id numbers by using
- -a "VARIABLE_NAME VALUE"
- for each variable you want to modify. If there are many
- variables you want to modify, you can save them in a file
- (one variable per line). For an example of the file format
- run moltemplat.sh once and search for a file named
- "ttree_assignments.txt". (This file is often located in
- the "output_ttree/" directory.) Once assigned, the remaining
- variables in the same category will be automatically assigned
- to values which do not overlap with your chosen values.
--b assignments.txt
- "-b" is similar to "-a". However, in this case, no attempt
- is made to assign exclusive (unique) values to each variable.
--nocheck
- Normally moltemplate.sh checks for common errors and typos and
- halts if it thinks it has found one. This forces the variables
- and categories as well as write(file) and write_once(file)
- commands to obey standard naming conventions. The "-nocheck"
- argument bypasses these checks and eliminates these restrictions.
-
--overlay-angles Normally, moltemplate.sh checks to see if multiple angle
--overlay-dihedrals interactions are defined for the same triplet of atoms.
--overlay-impropers If so, it deletes the redundant ones (keeping the last one).
--overlay-bonds (It does the same thing for bonds, dihedrals, and impropers.)
- Use these options to prevent that behavoir.
-
-EOF
-)
-
-# --- Periodic boundary box information (default) ---
-
-# We will determine these numbers later.
-TRICLINIC=""
-BOXSIZE_MINX=0.0
-BOXSIZE_MINY=0.0
-BOXSIZE_MINZ=0.0
-BOXSIZE_MAXX=""
-BOXSIZE_MAXY=""
-BOXSIZE_MAXZ=""
-BOXSIZE_XY=0.0
-BOXSIZE_XZ=0.0
-BOXSIZE_YZ=0.0
-
-
-
-if [ "$1" = "--help" ]; then
- echo "$SYNTAX_MSG" >&2
- exit 0
-fi
-
-
-
-# --- Did the user specify a file containing atomic coordinates?
-
-rm -f "$tmp_atom_coords"
-
-# Optional files containing atom coordinates:
-PDB_FILE=""
-XYZ_FILE=""
-RAW_FILE=""
-LT_FILE=""
-OUT_FILE_BASE="system"
-# REMOVE_DUPLICATE variables:
-# ...If true (default), then any duplicate entries in the lists of bonds
-# bonds, angles, dihedrals, or impropers in the LAMMPS DATA file
-# are removed, giving priority to the most recent entry in the list.
-# (This might not be necessary, but I want to be careful.)
-REMOVE_DUPLICATE_BONDS="true"
-REMOVE_DUPLICATE_ANGLES="true"
-REMOVE_DUPLICATE_DIHEDRALS="true"
-REMOVE_DUPLICATE_IMPROPERS="true"
-RUN_VMD_AT_END=""
-
-
-ARGC=0
-for A in "$@"; do
- A_FIRSTCHAR="$(echo $A| cut -c 1)"
- # (Note to self: this next line only works in bash, not classic sh.)
- if [ "$A_FIRSTCHAR" = "\$" ]; then
- A="\\$A" # put an extra slash in front to prevent expansion later
- fi
-
- ARGC=$((ARGC+1))
- eval ARGV${ARGC}=\"$A\"
-done
-
-TTREE_ARGS=""
-ATOM_STYLE=""
-ATOM_STYLE_ARG=""
-
-i=0
-while [ "$i" -lt "$ARGC" ]; do
- i=$((i+1))
- eval A=\${ARGV${i}}
-
- if [ "$A" = "-nocheck" ]; then
- # Disable syntax checking by undefining LTTREE_CHECK_COMMAND
- unset LTTREE_CHECK_COMMAND
- unset LTTREE_POSTPROCESS_COMMAND
- elif [ "$A" = "-overlay-bonds" ]; then
- # In that case, do not remove duplicate bond interactions
- unset REMOVE_DUPLICATE_BONDS
- elif [ "$A" = "-overlay-angles" ]; then
- # In that case, do not remove duplicate angle interactions
- unset REMOVE_DUPLICATE_ANGLES
- elif [ "$A" = "-overlay-dihedrals" ]; then
- # In that case, do not remove duplicate dihedral interactions
- unset REMOVE_DUPLICATE_DIHEDRALS
- elif [ "$A" = "-overlay-impropers" ]; then
- # In that case, do not remove duplicate improper interactions
- unset REMOVE_DUPLICATE_IMPROPERS
- elif [ "$A" = "-vmd" ]; then
- RUN_VMD_AT_END="true"
- elif [ "$A" = "-raw" ]; then
- if [ "$i" -eq "$ARGC" ]; then
- echo "$SYNTAX_MSG" >&2
- exit 7
- fi
- i=$((i+1))
- eval A=\${ARGV${i}}
- RAW_FILE=$A
- if [ ! -s "$RAW_FILE" ]; then
- echo "$SYNTAX_MSG" >&2
- echo "-----------------------" >&2
- echo "" >&2
- echo "Error: Unable to open RAW-file \"$RAW_FILE\"." >&2
- echo " (File is empty or does not exist.)" >&2
- exit 8
- fi
- #echo " (extracting coordinates from \"$RAW_FILE\")" >&2
- awk '{if (NF==3) {print $0}}' < "$RAW_FILE" > "$tmp_atom_coords"
-
- elif [ "$A" = "-xyz" ]; then
- if [ "$i" -eq "$ARGC" ]; then
- echo "$SYNTAX_MSG" >&2
- exit 7
- fi
- i=$((i+1))
- eval A=\${ARGV${i}}
- XYZ_FILE=$A
- if [ ! -s "$XYZ_FILE" ]; then
- echo "$SYNTAX_MSG" >&2
- echo "-----------------------" >&2
- echo "" >&2
- echo "Error: Unable to open XYZ-file \"$XYZ_FILE\"." >&2
- echo " (File is empty or does not exist.)" >&2
- exit 8
- fi
- #echo " (extracting coordinates from \"$XYZ_FILE\")" >&2
-
- # "isnum(x)" returns 1 or 0 depending upon whether or not
- # a string is numeric.
- #http://rosettacode.org/wiki/Determine_if_a_string_is_numeric#AWK
-
- awk 'function isnum(x){return(x==x+0)} BEGIN{targetframe=1;framecount=0} {if (isnum($0)) {framecount++} else{if (framecount==targetframe){ if (NF>0) { if ((NF==3) && isnum($1)) {print $1" "$2" "$3} else if ((NF==4) && isnum($2)) {print $2" "$3" "$4} }}}}' < "$XYZ_FILE" > "$tmp_atom_coords"
-
- elif [ "$A" = "-pdb" ]; then
- if [ "$i" -eq "$ARGC" ]; then
- echo "$SYNTAX_MSG" >&2
- exit 9
- fi
- i=$((i+1))
- eval A=\${ARGV${i}}
- PDB_FILE=$A
- if [ ! -s "$PDB_FILE" ]; then
- echo "$SYNTAX_MSG" >&2
- echo "-----------------------" >&2
- echo "" >&2
- echo "Error: Unable to open PDB-file \"$PDB_FILE\"." >&2
- echo " (File is empty or does not exist.)" >&2
- exit 10
- fi
- #echo " (extracting coordinates from \"$PDB_FILE\")" >&2
- if grep -q '^ATOM \|^HETATM' "$PDB_FILE"; then
- # Extract the coords from the "ATOM" records in the PDB file
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/pdbsort.py" < "$PDB_FILE" \
- | awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then
- ERR_INTERNAL
- fi
- else
- echo "$SYNTAX_MSG" >&2
- echo "-----------------------" >&2
- echo "" >&2
- echo "Error: File \"$PDB_FILE\" is not a valid PDB file." >&2
- exit 11
- fi
- # Now extract the periodic bounding-box informatio from the PDB file
- # The CRYST1 records are described at:
- # http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
- BOXSIZE_A=-1.0
- BOXSIZE_B=-1.0
- BOXSIZE_C=-1.0
- ALPHA=" 90.00" #Note: The space before the number in " 90.00" is intentional.
- BETA=" 90.00" # Later we will check to see if the system is triclinic
- GAMMA=" 90.00" # by comparing these strings for equality with " 90.00"
- if grep -qF "CRYST1" "$PDB_FILE"; then
- BOXSIZE_A=`awk '/CRYST1/{print substr($0,8,8)}' < "$PDB_FILE"`
- BOXSIZE_B=`awk '/CRYST1/{print substr($0,17,8)}' < "$PDB_FILE"`
- BOXSIZE_C=`awk '/CRYST1/{print substr($0,26,8)}' < "$PDB_FILE"`
- ALPHA=`awk '/CRYST1/{print substr($0,35,6)}' < "$PDB_FILE"`
- BETA=`awk '/CRYST1/{print substr($0,42,6)}' < "$PDB_FILE"`
- GAMMA=`awk '/CRYST1/{print substr($0,49,6)}' < "$PDB_FILE"`
- fi
- if [ `echo "$ALPHA!=90.0"|bc` -eq 1 ] || [ `echo "$BETA!=90.0"|bc` -eq 1 ] || [ `echo "$GAMMA!=90.0"|bc` -eq 1 ]; then
- # I transform the parameters from one format to the other by inverting
- # the transformation formula from the LAMMPS documentation (which matches
- # http://www.ccl.net/cca/documents/molecular-modeling/node4.html)
- # Disclaimer:
- # As of September 2012, I have not tested the code below. I think the
- # equations are correct, but I don't know if their are special cases
- # that require the coordinates to be rotated or processed beforehand.
- # This is an experimental feature.
- TRICLINIC="True"
- PI=3.1415926535897931
- BOXSIZE_X=$BOXSIZE_A
- BOXSIZE_Y=`awk "BEGIN{print $BOXSIZE_B*sin($GAMMA*$PI/180.0)}"`
- BOXSIZE_XY=`awk "BEGIN{print $BOXSIZE_B*cos($GAMMA*$PI/180.0)}"`
- BOXSIZE_XZ=`awk "BEGIN{print $BOXSIZE_C*cos($BETA*$PI/180.0)}"`
- BOXSIZE_YZ=`awk "BEGIN{ca=cos($ALPHA*$PI/180.0); cb=cos($BETA*$PI/180.0); cg=cos($GAMMA*$PI/180.0); sg=sin($GAMMA*$PI/180.0); c=$BOXSIZE_C; print c*(ca-(cg*cb))/sg}"`
- BOXSIZE_Z=`awk "BEGIN{print sqrt(($BOXSIZE_C**2)-(($BOXSIZE_XZ**2)+($BOXSIZE_YZ**2)))}"`
- else
- BOXSIZE_X=$BOXSIZE_A
- BOXSIZE_Y=$BOXSIZE_B
- BOXSIZE_Z=$BOXSIZE_C
- BOXSIZE_XY=0.0
- BOXSIZE_XZ=0.0
- BOXSIZE_YZ=0.0
- fi
- BOXSIZE_MINX=0.0
- BOXSIZE_MINY=0.0
- BOXSIZE_MINZ=0.0
- BOXSIZE_MAXX=$BOXSIZE_X
- BOXSIZE_MAXY=$BOXSIZE_Y
- BOXSIZE_MAXZ=$BOXSIZE_Z
-
- elif [ "$A" = "-atomstyle" ] || [ "$A" = "-atom-style" ] || [ "$A" = "-atom_style" ]; then
- if [ "$i" -eq "$ARGC" ]; then
- echo "$SYNTAX_MSG" >&2
- exit 7
- fi
- i=$((i+1))
- eval A=\${ARGV${i}}
- if [ -z "$A" ]; then
- echo "$SYNTAX_MSG" >&2
- echo "-----------------------" >&2
- echo "" >&2
- echo "Error: The \"-atomstyle\" argument should be followed by an atom style." >&2
- echo " (See the \"atom_style\" command in the LAMMPS documentation." >&2
- echo " Note: hybrid atom styles are allowed but should be enclosed in quotes.)" >&2
- exit 8
- fi
-
- #echo " (atom_style=\"$A\")" >&2
- #echo "" >&2
-
- ATOM_STYLE="$A"
- ATOM_STYLE_ARG="-atomstyle \"$A\""
-
- # (minor detail: $ATOM_STYLE_ARG should also be appended to TTREE_ARGS)
- if [ -z "$TTREE_ARGS" ]; then
- TTREE_ARGS="$ATOM_STYLE_ARG"
- else
- TTREE_ARGS="${TTREE_ARGS} $ATOM_STYLE_ARG"
- fi
-
-
- #else: If the arguments are not understood in this script, then
- # pass them on to "lttree.py"
- else
- A_FIRSTCHAR="$(echo $A| cut -c 1)"
-
- if [ "$A_FIRSTCHAR" = "\$" ]; then
- A="\\$A" # put an extra slash in front to prevent expansion later
- fi
-
- if [ -z "$TTREE_ARGS" ]; then
- TTREE_ARGS="\"$A\""
- else
- TTREE_ARGS="${TTREE_ARGS} \"$A\""
- fi
- # Check to see if this string ($A) ends in .lt or .LT
- # If so, then set the base name of the output files
- # to equal the base name of the .LT file being read.
- # (Being careful here.
- # Sometimes the last argument is not the .lt or .LT file.
- # Sometimes that file appears earlier in the argument list.
- # I want to supply a default value.)
- #
- # Note, in bash you can use:
- # if [ "${LAST_ARG/%.lt/}" -neq "$LAST_ARG" ]; then
- # OUT_FILE_BASE="${LAST_ARG/%.lt/}"
- # But in the original bourn shell (sh), this does not work.
- # Instead we use a hack involving basename and dirname:
-
- if [ "$A_FIRSTCHAR" != "-" ]; then
- DN=`dirname "$A"`
- if [ "$DN" = "." ]; then
- DN=""
- else
- DN="${DN}/"
- fi
-
- BN=`basename "$A" .lt`
- if [ "${DN}${BN}" != "$A" ]; then
- OUT_FILE_BASE="$BN"
- else
- BN=`basename "$A" .LT`
- if [ "${DN}${BN}" != "$A" ]; then
- OUT_FILE_BASE="$BN"
- fi
- fi
- fi
- fi
-done
-
-
-
-
-if [ -z "$ATOM_STYLE" ]; then
- #echo '########################################################' >&2
- #echo '## WARNING: atom_style unspecified ##' >&2
- #echo '## Assuming atom_style = \"full\" ##' >&2
- #echo '########################################################' >&2
- ATOM_STYLE="full"
-fi
-
-
-
-OUT_FILE_INPUT_SCRIPT="${OUT_FILE_BASE}.in"
-OUT_FILE_INIT="${OUT_FILE_BASE}.in.init"
-OUT_FILE_SETTINGS="${OUT_FILE_BASE}.in.settings"
-OUT_FILE_DATA="${OUT_FILE_BASE}.data"
-OUT_FILE_COORDS="${OUT_FILE_BASE}.in.coords"
-
-rm -f "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_INIT" "$OUT_FILE_SETTINGS" "$OUT_FILE_DATA" "$OUT_FILE_COORDS"
-
-
-
-
-
-# --------------------------------------------------------------------
-# --- Now run ttree/lttree to generate the file fragments we need. ---
-# ------ (Afterwards, we will paste these fragments together.) -----
-# --------------------------------------------------------------------
-
-
-
-
-
-# If checking is not disabled, then first check for common spelling errors.
-
-if [ -n "$LTTREE_CHECK_COMMAND" ]; then
- if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS; then
- exit 1
- fi
-fi
-
-
-# --- Run ttree. ---
-#
-# 3, 2, 1, ...
-
-if ! eval $LTTREE_COMMAND $TTREE_ARGS; then
- exit 2
-fi
-
-# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-# > Traceback (most recent call last):
-# > File "./lttree.py", line...
-# .-.
-# (0.0)
-# '=.|m|.='
-# .='`"``=.
-#
-# Hopefully this does not happen.
-# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-echo "" >&2
-
-
-
-
-# Attempt to remove any the DOS return-cairrage characters
-# from inside the standard LAMMPS files generated by the user:
-# (Users are free to put whatever weird characters they want in other
-# (custom) auxilliary files. But not in the standard LAMMPS files.)
-OIFS=$IFS
-#IFS=$'\n'
-IFS="
-"
-for file in $MOLTEMPLATE_TEMP_FILES; do
- if [ -e "$file" ]; then
- #dos2unix < "$file" > "$file.dos2unix"
- tr -d '\r' < "$file" > "$file.dos2unix"
- rm -f "$file" >/dev/null 2>&1 || true
- mv -f "$file.dos2unix" "$file"
- fi
-done
-IFS=$OIFS
-
-
-if [ -s "${data_atoms}" ]; then
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
- < "${data_atoms}" \
- > "${data_atoms}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_atoms}.tmp" "${data_atoms}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
- < "${data_atoms}.template" \
- > "${data_atoms}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_atoms}.tmp" "${data_atoms}.template"
-
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
- < "${data_atoms}" \
- > "${data_atoms}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_atoms}.tmp" "${data_atoms}"
-else
- echo "Error: There are no atoms in your system. Suggestions:" >&2
- echo "" >&2
- echo " Make sure that you have the correct number of curly parenthesis {}." >&2
- echo " (Extra \"}\" parenthesis can cause this error.)" >&2
- echo "" >&2
- echo " Your files must contain at least one" >&2
- echo " write(\"${data_atoms}\")" >&2
- echo " command. These commands are typically located somewhere in" >&2
- echo " one of the molecule object(s) you have defined." >&2
- echo "" >&2
- echo " This error often occurs if your input files lack \"new\" commands." >&2
- echo " Once you have defined a type of molecule, you must create a copy" >&2
- echo " of it using \"new\", if you want it to appear in your simulation." >&2
- echo " See the moltemplate manual or online tutorials for examples." >&2
- echo "" >&2
- echo " (This error also occurs if you instantiated an object using \"new\"" >&2
- echo " which you thought was a molecule, but it is actually only a" >&2
- echo " namespace, a force-field name or category containing only the" >&2
- echo " definitions of other molecules, lacking any atoms of its own.)" >&2
- echo "" >&2
- exit 200
-fi
-
-
-
-
-# ---------------- ChargePairs By Type ------------------
-# Assign atom charge according to who they are bonded to
-
-if [ -s "$data_chargepairs_by_type" ]; then
- echo "Looking up partial charge contributions from bonds" >&2
- #-- Generate a file containing bondid bondtype atomid1 atomid2 --
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/chargepairs_by_type.py" \
- -atom-style "$ATOM_STYLE" \
- -atoms "${data_atoms}.template" \
- -bonds "${data_bonds}.template" \
- -bond-list "${data_bond_list}.template" \
- -chargepairsbytype "${data_chargepairs_by_type}.template" \
- > gen_charges.template.tmp; then
- exit 4
- fi
-
- # ---- cleanup: ----
- # ---- Create or re-build the "${in_charges}.template" file ----
- # Instert these lines into the "${in_charges}.template" file which includes
- # the newly generated interactions. (Note: these are in .template format)
-
- cp gen_charges.template.tmp new_charges.template.tmp
- if [ -s "${in_charges}.template" ]; then
- # Then append existing "Bonds" to the end of the generated interactions
- # (Hopefully this way they will override those interactions.)
- cat "${in_charges}.template" >> new_charges.template.tmp
- fi
- mv -f new_charges.template.tmp "${in_charges}.template"
-
- # ---- Re-build (render) the "$in_charges" file ----
- # Now substitute these variable values (assignments) into the variable
- # names present in the .template file. (We want to convert the file from
- # a .template format into an ordinary (numeric) LAMMPS data-section format.)
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
- ttree_assignments.txt \
- < "${in_charges}.template" \
- >> "${in_charges}"; then
- exit 6
- fi
- echo "" >&2
-
- rm -f gen_charges.template.tmp new_charges.template.tmp
-
- echo "" >&2
-fi
-
-
-
-
-# ---------------- Interactions By Type -----------------
-# At the time of writing, bonded-interactions-by-atom-type were not
-# understood by LAMMPS. These features require auxilliary python scripts.
-# These data sections must be processed before everything else (because
-# they effect the other data sections, and the ttree_assignments.txt file.)
-# -------------------------------------------------------
-
-if [ -s "${data_bond_list}.template" ]; then
-
- if [ ! -s "$data_bonds_by_type" ]; then
- echo "Error: You have a \"Data Bond List\", section somewhere"
- echo " without a \"Data Bonds By Type\" section to support it."
- echo " (Did you mean to use \"Data Bonds\" instead?)"
- echo "Details:"
- echo " Unlike the \"Data Bonds\" section, the \"Data Bond List\" section"
- echo " allows the user to omit the bond types. Instead moltemplate attempts"
- echo " to infer the type of bond by considering the pair of atom types."
- echo " However you must define a \"Data Bonds By Type\" section"
- echo " to make this feature work (or use \"Data Bonds\" instead)."
-
- exit 15
- fi
- echo "Looking up bond types according to atom type" >&2
- #-- Generate a file containing bondid bondtype atomid1 atomid2 --
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/bonds_by_type.py" \
- -atom-style "$ATOM_STYLE" \
- -atoms "${data_atoms}.template" \
- -bond-list "${data_bond_list}.template" \
- -bondsbytype "${data_bonds_by_type}.template" \
- -prefix '$/bond:bytype' > gen_bonds.template.tmp; then
- exit 4
- fi
-
- # ---- cleanup: ----
- # ---- Create or re-build the "${data_bonds}.template" file ----
- # Instert these lines into the "${data_bonds}.template" file which includes
- # the newly generated interactions. (Note: these are in .template format)
-
- cp gen_bonds.template.tmp new_bonds.template.tmp
- if [ -s "${data_bonds}.template" ]; then
- # Then append existing "Bonds" to the end of the generated interactions
- # (Hopefully this way they will override those interactions.)
- cat "${data_bonds}.template" >> new_bonds.template.tmp
- fi
- mv -f new_bonds.template.tmp "${data_bonds}.template"
-
-
-
- # ------ THE NEXT STEP IS NOT CURRENTLY NEEDED ------
- # All of the $bond variables have already been created, they just lack types
- # However we will need to do this if the user wants to omits the bond-ids.
- # In case I plan to allow the user to omit bond-ids, I leave this code here.
- #
- #echo "(Repairing ttree_assignments.txt file after bonds added.)" >&2
- #
- ## ---- Repair the ttree_assignments.txt file ----
- ## The next 2 lines extract the variable names from data_new.template.tmp
- ## and instert them into the appropriate place in ttree_assignments.txt
- ## (renumbering the relevant variable-assignments to avoid clashes).
- #if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
- # '/bond' gen_bonds.template.tmp \
- # < ttree_assignments.txt \
- # > ttree_assignments.tmp; then
- # exit 5
- #fi
- #
- #echo "(Rendering ttree_assignments.tmp file after bonds added.)" >&2
- #mv -f ttree_assignments.tmp ttree_assignments.txt
- # ----------------------------------------------------
-
-
-
- # ---- Re-build (render) the "$data_bonds" file ----
- # Now substitute these variable values (assignments) into the variable
- # names present in the .template file. (We want to convert the file from
- # a .template format into an ordinary (numeric) LAMMPS data-section format.)
-
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
- ttree_assignments.txt \
- < "${data_bonds}.template" \
- > "$data_bonds"; then
- exit 6
- fi
-
- echo "" >&2
-
- rm -f gen_bonds.template.tmp new_bonds.template.tmp
-
- echo "" >&2
-
-fi
-
-
-
-
-
-
-
-
-
-
-
-for FILE in "$data_angles_by_type"*.template; do
-
- if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then
- break; # This handles with the special cases that occur when
- # 1) There are no bonds in your system
- # 2) "$data_angles_by_type"*.template matches nothing
- fi
-
- echo "Generating 3-body angle interactions by atom/bond type" >&2
-
- # Extract the text between parenthesis (if present, empty-str otherwise)
- # Example: FILE="Data Angles By Type (gaff_angle.py)"
- SUBGRAPH_SCRIPT=`echo "$FILE" | awk '/\(.*\)/ {print $0}' | cut -d'(' -f2-| cut -d')' -f 1`
- # Example: (continued) SUBGRAPH_SCRIPT should equal "gaff_angle.py"
-
- if [ -z "$SUBGRAPH_SCRIPT" ]; then
- SUBGRAPH_SCRIPT="nbody_Angles.py"
- else
- echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2
- if [ ! -s "${SCRIPT_DIR}/nbody_alternate_symmetry/$SUBGRAPH_SCRIPT" ]; then
- echo "Error: File \"$SUBGRAPH_SCRIPT\" not found." >&2
- echo " It should be located in this directory:" >&2
- echo " ${SCRIPT_DIR}/nbody_alternate_symmetry/" >&2
- exit 4
- fi
- fi
-
- #-- Generate a file containing the list of interactions on separate lines --
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
- -subgraph "${SUBGRAPH_SCRIPT}" \
- -section "Angles" \
- -sectionbytype "Angles By Type" \
- -atom-style "$ATOM_STYLE" \
- -atoms "${data_atoms}.template" \
- -bonds "${data_bonds}.template" \
- -nbodybytype "${FILE}" \
- -prefix '$/angle:bytype' > gen_angles.template.tmp; then
- exit 4
- #WARNING: DO NOT REPLACE THIS WITH
- #if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
- fi
-
- # ---- cleanup: ----
- # ---- Re-build the "${data_angles}.template" file ----
- # Instert these lines into the "${data_angles}.template" file which includes
- # the newly generated interactions. (Note: these are in .template format)
-
- cp gen_angles.template.tmp new_angles.template.tmp
- if [ -s "${data_angles}.template" ]; then
- # Then append existing "Angles" to the end of the generated interactions
- # (Hopefully this way they will override those interactions.)
- cat "${data_angles}.template" >> new_angles.template.tmp
- fi
- mv -f new_angles.template.tmp "${data_angles}.template"
-
- echo "(Repairing ttree_assignments.txt file after angles added.)" >&2
-
- # ---- Repair the ttree_assignments.txt file ----
- # The next 2 lines extract the variable names from data_new.template.tmp
- # and instert them into the appropriate place in ttree_assignments.txt
- # (renumbering the relevant variable-assignments to avoid clashes).
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
- '/angle' gen_angles.template.tmp \
- < ttree_assignments.txt \
- > ttree_assignments.tmp; then
- exit 5
- fi
-
- echo "(Rendering ttree_assignments.tmp file after angles added.)" >&2
-
- # ---- Re-build (render) the "$data_angles" file ----
- # Now substitute these variable values (assignments) into the variable
- # names present in the .template file. (We want to convert the file from
- # a .template format into an ordinary (numeric) LAMMPS data-section format.)
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
- ttree_assignments.tmp \
- < "${data_angles}.template" \
- > "$data_angles"; then
- exit 6
- fi
- echo "" >&2
-
- mv -f ttree_assignments.tmp ttree_assignments.txt
- rm -f gen_angles.template.tmp new_angles.template.tmp
-done
-
-
-
-
-
-
-FILE_dihedrals_by_type1=""
-FILE_dihedrals_by_type2=""
-for FILE in "$data_dihedrals_by_type"*.template; do
-
- if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then
- break; # This handles with the special cases that occur when
- # 1) There are no bonds in your system
- # 2) "$data_dihedrals_by_type"*.template matches nothing
- fi
-
- echo "Generating 4-body dihedral interactions by atom/bond type" >&2
-
- # Extract the text between parenthesis (if present, empty-str otherwise)
- # Example: FILE="Data Dihedrals By Type (gaff_dih.py)"
- SUBGRAPH_SCRIPT=`echo "$FILE" | awk '/\(.*\)/ {print $0}' | cut -d'(' -f2-| cut -d')' -f 1`
- # Example: (continued) SUBGRAPH_SCRIPT should equal "gaff_dih.py"
-
- if [ -z "$SUBGRAPH_SCRIPT" ]; then
- SUBGRAPH_SCRIPT="nbody_Dihedrals.py"
- else
- echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2
- if [ ! -s "${SCRIPT_DIR}/nbody_alternate_symmetry/$SUBGRAPH_SCRIPT" ]; then
- echo "Error: File \"$SUBGRAPH_SCRIPT\" not found." >&2
- echo " It should be located in this directory:" >&2
- echo " ${SCRIPT_DIR}/nbody_alternate_symmetry/" >&2
- exit 4
- fi
- fi
-
- FILE_dihedrals_by_type2="$FILE_impropers_by_type1"
- FILE_dihedrals_by_type1="$FILE"
-
- #-- Generate a file containing the list of interactions on separate lines --
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
- -subgraph "${SUBGRAPH_SCRIPT}" \
- -section "Dihedrals" \
- -sectionbytype "Dihedrals By Type" \
- -atom-style "$ATOM_STYLE" \
- -atoms "${data_atoms}.template" \
- -bonds "${data_bonds}.template" \
- -nbodybytype "${FILE}" \
- -prefix '$/dihedral:bytype' > gen_dihedrals.template.tmp; then
- exit 4
- #WARNING: DO NOT REPLACE THIS WITH
- #if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
- fi
-
- # ---- cleanup: ----
- # ---- Re-build the "${data_dihedrals}.template" file ----
- # Instert these lines into the "${data_dihedrals}.template" file which includes
- # the newly generated interactions. (Note: these are in .template format)
-
- cp gen_dihedrals.template.tmp new_dihedrals.template.tmp
- if [ -s "${data_dihedrals}.template" ]; then
- # Then append existing "Dihedrals" to the end of the generated interactions
- # (Hopefully this way they will override those interactions.)
- cat "${data_dihedrals}.template" >> new_dihedrals.template.tmp
- fi
- mv -f new_dihedrals.template.tmp "${data_dihedrals}.template"
-
- echo "(Repairing ttree_assignments.txt file after dihedrals added.)" >&2
-
- # ---- Repair the ttree_assignments.txt file ----
- # The next 2 lines extract the variable names from data_new.template.tmp
- # and instert them into the appropriate place in ttree_assignments.txt
- # (renumbering the relevant variable-assignments to avoid clashes).
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
- '/dihedral' gen_dihedrals.template.tmp \
- < ttree_assignments.txt \
- > ttree_assignments.tmp; then
- exit 5
- fi
-
- echo "(Rendering ttree_assignments.tmp file after dihedrals added.)" >&2
-
- # ---- Re-build (render) the "$data_dihedrals" file ----
- # Now substitute these variable values (assignments) into the variable
- # names present in the .template file. (We want to convert the file from
- # a .template format into an ordinary (numeric) LAMMPS data-section format.)
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
- ttree_assignments.tmp \
- < "${data_dihedrals}.template" \
- > "$data_dihedrals"; then
- exit 6
- fi
- echo "" >&2
-
- mv -f ttree_assignments.tmp ttree_assignments.txt
- rm -f gen_dihedrals.template.tmp new_dihedrals.template.tmp
-done
-
-
-
-
-
-FILE_impropers_by_type1=""
-FILE_impropers_by_type2=""
-for FILE in "$data_impropers_by_type"*.template; do
-
- if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then
- break; # This handles with the special cases that occur when
- # 1) There are no bonds in your system
- # 2) "$data_impropers_by_type"*.template matches nothing
- fi
-
- echo "Generating 4-body improper interactions by atom/bond type" >&2
-
- # Extract the text between parenthesis (if present, empty-str otherwise)
- # Example: FILE="Data Impropers By Type (gaff_impr.py)"
- SUBGRAPH_SCRIPT=`echo "$FILE" | awk '/\(.*\)/ {print $0}' | cut -d'(' -f2-| cut -d')' -f 1`
- # Example: (continued) SUBGRAPH_SCRIPT should equal "gaff_impr.py"
-
- if [ -z "$SUBGRAPH_SCRIPT" ]; then
- SUBGRAPH_SCRIPT="nbody_Impropers.py"
- else
- echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2
- if [ ! -s "${SCRIPT_DIR}/nbody_alternate_symmetry/$SUBGRAPH_SCRIPT" ]; then
- echo "Error: File \"$SUBGRAPH_SCRIPT\" not found." >&2
- echo " It should be located in this directory:" >&2
- echo " ${SCRIPT_DIR}/nbody_alternate_symmetry/" >&2
- exit 4
- fi
- fi
-
- FILE_impropers_by_type2="$FILE_impropers_by_type1"
- FILE_impropers_by_type1="$FILE"
-
- #-- Generate a file containing the list of interactions on separate lines --
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
- -subgraph "${SUBGRAPH_SCRIPT}" \
- -section "Impropers" \
- -sectionbytype "Impropers By Type" \
- -atom-style "$ATOM_STYLE" \
- -atoms "${data_atoms}.template" \
- -bonds "${data_bonds}.template" \
- -nbodybytype "${FILE}" \
- -prefix '$/improper:bytype' > gen_impropers.template.tmp; then
- exit 4
- #WARNING: DO NOT REPLACE THIS WITH
- #if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
- fi
-
- # ---- cleanup: ----
- # ---- Re-build the "${data_impropers}.template" file ----
- # Instert these lines into the "${data_impropers}.template" file which includes
- # the newly generated interactions. (Note: these are in .template format)
-
- cp gen_impropers.template.tmp new_impropers.template.tmp
- if [ -s "${data_impropers}.template" ]; then
- # Then append existing "Impropers" to the end of the generated interactions
- # (Hopefully this way they will override those interactions.)
- cat "${data_impropers}.template" >> new_impropers.template.tmp
- fi
- mv -f new_impropers.template.tmp "${data_impropers}.template"
-
- echo "(Repairing ttree_assignments.txt file after impropers added.)" >&2
-
- # ---- Repair the ttree_assignments.txt file ----
- # The next 2 lines extract the variable names from data_new.template.tmp
- # and instert them into the appropriate place in ttree_assignments.txt
- # (renumbering the relevant variable-assignments to avoid clashes).
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
- '/improper' gen_impropers.template.tmp \
- < ttree_assignments.txt \
- > ttree_assignments.tmp; then
- exit 5
- fi
-
- echo "(Rendering ttree_assignments.tmp file after impropers added.)" >&2
-
- # ---- Re-build (render) the "$data_impropers" file ----
- # Now substitute these variable values (assignments) into the variable
- # names present in the .template file. (We want to convert the file from
- # a .template format into an ordinary (numeric) LAMMPS data-section format.)
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
- ttree_assignments.tmp \
- < "${data_impropers}.template" \
- > "$data_impropers"; then
- exit 6
- fi
- echo "" >&2
-
- mv -f ttree_assignments.tmp ttree_assignments.txt
- rm -f gen_impropers.template.tmp new_impropers.template.tmp
-done
-
-
-
-
-if [ -n "$LTTREE_POSTPROCESS_COMMAND" ]; then
- echo "" >&2
- if ! eval $LTTREE_POSTPROCESS_COMMAND $TTREE_ARGS; then
- exit 3
- fi
- echo "" >&2
-fi
-
-
-# -------------------------------------------------------
-# If present, then remove duplicate bonds, angles, dihedrals, and impropers
-# (unless overridden by the user).
-# -------------------------------------------------------
-
-
-if [ -s "${data_masses}" ]; then
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
- < "${data_masses}" \
- > "${data_masses}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_masses}.tmp" "${data_masses}"
-fi
-
-
-if [ -s "${data_bonds}" ]; then
- if [ ! -z $REMOVE_DUPLICATE_BONDS ]; then
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
- Bonds \
- nbody_Bonds.py \
- < "${data_bonds}" \
- > "${data_bonds}.tmp"; then
- ERR_INTERNAL
- fi
- cp -f "${data_bonds}.tmp" "${data_bonds}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 2 \
- < "${data_bonds}" \
- > "${data_bonds}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_bonds}.tmp" "${data_bonds}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 2 \
- < "${data_bonds}.template" \
- > "${data_bonds}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_bonds}.tmp" "${data_bonds}.template"
- fi
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
- < "${data_bonds}" \
- > "${data_bonds}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_bonds}.tmp" "${data_bonds}"
-fi
-
-
-
-
-if [ -s "${data_angles}" ]; then
- if [ ! -z $REMOVE_DUPLICATE_ANGLES ]; then
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
- Angles \
- nbody_Angles.py \
- < "${data_angles}" \
- > "${data_angles}.tmp"; then
- ERR_INTERNAL
- fi
- cp -f "${data_angles}.tmp" "${data_angles}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 3 \
- < "${data_angles}" \
- > "${data_angles}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_angles}.tmp" "${data_angles}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 3 \
- < "${data_angles}.template" \
- > "${data_angles}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_angles}.tmp" "${data_angles}".template
- fi
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
- < "${data_angles}" \
- > "${data_angles}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_angles}.tmp" "${data_angles}"
-fi
-
-
-if [ -s "${data_dihedrals}" ]; then
- if [ ! -z $REMOVE_DUPLICATE_DIHEDRALS ]; then
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
- Dihedrals \
- nbody_Dihedrals.py \
- < "${data_dihedrals}" \
- > "${data_dihedrals}.tmp"; then
- ERR_INTERNAL
- fi
- cp -f "${data_dihedrals}.tmp" "${data_dihedrals}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
- < "${data_dihedrals}" \
- > "${data_dihedrals}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_dihedrals}.tmp" "${data_dihedrals}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
- < "${data_dihedrals}.template" \
- > "${data_dihedrals}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_dihedrals}.tmp" "${data_dihedrals}.template"
- fi
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
- < "${data_dihedrals}" \
- > "${data_dihedrals}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_dihedrals}.tmp" "${data_dihedrals}"
-
- if [ ! -z $FILE_dihedrals_by_type2 ]; then
- MSG_MULTIPLE_DIHEDRAL_RULES=$(cat <<EOF
-#############################################################################
-WARNING:
- It appears as though multiple conflicting rules were used to generate
-DIHEDRAL interactions. (This can occur when combining molecules built with
-different force-field rules). In your case, you are using rules defined here:
- "$FILE_dihedrals_by_type2"
- "$FILE_dihedrals_by_type1"
- (Files ending in .py are located here:
- $SCRIPT_DIR/nbody_alternate_symmetry/)
-If the molecules built using these two different force-field settings are not
-connected, AND if you do NOT override force-field dihedrals with explicitly
-defined dihedrals, then you can probably ignore this warning message. Otherwise
-please check the list of dihedral interactions to make sure they are correct!
-(It might help to build a much smaller system using the same molecule types.)
-#############################################################################
-
-EOF
-)
- echo "$MSG_MULTIPLE_DIHEDRAL_RULES" >&2
- fi
-fi
-
-
-if [ -s "${data_impropers}" ]; then
- if [ ! -z $REMOVE_DUPLICATE_IMPROPERS ]; then
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
- Impropers \
- nbody_Impropers.py \
- < "${data_impropers}" \
- > "${data_impropers}.tmp"; then
- ERR_INTERNAL
- fi
- cp -f "${data_impropers}.tmp" "${data_impropers}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
- < "${data_impropers}" \
- > "${data_impropers}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_impropers}.tmp" "${data_impropers}"
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
- < "${data_impropers}.template" \
- > "${data_impropers}.tmp"; then
- ERR_INTERNAL
- fi
- mv "${data_impropers}.tmp" "${data_impropers}.template"
- fi
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
- < "${data_impropers}" \
- > "${data_impropers}.tmp"; then
- ERR_INTERNAL
- fi
- mv -f "${data_impropers}.tmp" "${data_impropers}"
-
- if [ ! -z $FILE_impropers_by_type2 ]; then
- MSG_MULTIPLE_IMPROPER_RULES=$(cat <<EOF
-#############################################################################
-WARNING:
- It appears as though multiple conflicting rules were used to generate
-IMPROPER interactions. (This can occur when combining molecules built with
-different force-field rules.) In your case, you are using rules defined here:
- "$FILE_impropers_by_type2"
- "$FILE_impropers_by_type1"
- (Files ending in .py are located here:
- $SCRIPT_DIR/nbody_alternate_symmetry/)
-If the molecules built using these two different force-field settings are not
-connected, AND if you do NOT override force-field imrpopers with explicitly
-defined impropers, then you can probably ignore this warning message. Otherwise
-please check the list of improper interactions to make sure they are correct!
-(It might help to build a much smaller system using the same molecule types.)
-#############################################################################
-
-EOF
-)
- echo "$MSG_MULTIPLE_IMPROPER_RULES" >&2
- fi
-
-fi
-
-
-# -------------------------------------------------------
-
-
-NATOMTYPES=`awk '/^@\/atom:/{n++}END{print n}' < ttree_assignments.txt`
-NBONDTYPES=`awk '/^@\/bond:/{n++}END{print n}' < ttree_assignments.txt`
-NANGLETYPES=`awk '/^@\/angle:/{n++}END{print n}' < ttree_assignments.txt`
-NDIHEDRALTYPES=`awk '/^@\/dihedral:/{n++}END{print n}' < ttree_assignments.txt`
-NIMPROPERTYPES=`awk '/^@\/improper:/{n++}END{print n}' < ttree_assignments.txt`
-
-#NATOMS=`awk '/^\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
-#NBONDS=`awk '/^\$\/bond:/{n++}END{print n}' < ttree_assignments.txt`
-#NANGLES=`awk '/^\$\/angle:/{n++}END{print n}' < ttree_assignments.txt`
-#NDIHEDRALS=`awk '/^\$\/dihedral:/{n++}END{print n}' < ttree_assignments.txt`
-#NIMPROPERS=`awk '/^\$\/improper:/{n++}END{print n}' < ttree_assignments.txt`
-
-NATOMS="0"
-NBONDS="0"
-NANGLES="0"
-NDIHEDRALS="0"
-NIMPROPERS="0"
-
-if [ -s "${data_atoms}" ]; then
- NATOMS=`awk 'END{print NR}' < "${data_atoms}"`
-fi
-if [ -s "${data_bonds}" ]; then
- NBONDS=`awk 'END{print NR}' < "${data_bonds}"`
-fi
-if [ -s "${data_angles}" ]; then
- NANGLES=`awk 'END{print NR}' < "${data_angles}"`
-fi
-if [ -s "${data_dihedrals}" ]; then
- NDIHEDRALS=`awk 'END{print NR}' < "${data_dihedrals}"`
-fi
-if [ -s "${data_impropers}" ]; then
- NIMPROPERS=`awk 'END{print NR}' < "${data_impropers}"`
-fi
-
-
-
-rm -f "$OUT_FILE_DATA"
-
-
-echo "LAMMPS Description" > "$OUT_FILE_DATA"
-echo "" >> "$OUT_FILE_DATA"
-echo " $NATOMS atoms" >> "$OUT_FILE_DATA"
-if [ -n "$NBONDS" ]; then
- echo " $NBONDS bonds" >> "$OUT_FILE_DATA"
-fi
-if [ -n "$NANGLES" ]; then
- echo " $NANGLES angles" >> "$OUT_FILE_DATA"
-fi
-if [ -n "$NDIHEDRALS" ]; then
- echo " $NDIHEDRALS dihedrals" >> "$OUT_FILE_DATA"
-fi
-if [ -n "$NIMPROPERS" ]; then
- echo " $NIMPROPERS impropers" >> "$OUT_FILE_DATA"
-fi
-
-echo "" >> "$OUT_FILE_DATA"
-echo " $NATOMTYPES atom types" >> "$OUT_FILE_DATA"
-
-if [ -n "$NBONDTYPES" ]; then
- echo " $NBONDTYPES bond types" >> "$OUT_FILE_DATA"
-fi
-if [ -n "$NANGLETYPES" ]; then
- echo " $NANGLETYPES angle types" >> "$OUT_FILE_DATA"
-fi
-if [ -n "$NDIHEDRALTYPES" ]; then
- echo " $NDIHEDRALTYPES dihedral types" >> "$OUT_FILE_DATA"
-fi
-if [ -n "$NIMPROPERTYPES" ]; then
- echo " $NIMPROPERTYPES improper types" >> "$OUT_FILE_DATA"
-fi
-echo "" >> "$OUT_FILE_DATA"
-
-
-# --- PERIODIC BOUNDARY CONDITIONS ---
-
-# Note: If there is a "$data_boundary" file present, it overrides any settings
-# which may have been stored in a pdb file or other external file.
-
-if [ -s "$data_pbc" ] && [ ! -s "$data_boundary" ]; then
- mv -f "$data_pbc" "$data_boundary"
- echo "WARNING: write_once(\"$data_pbc\") is depreciated" >&2
- echo " Use write_once(\"$data_boundary\") instead" >&2
-fi
-
-if [ -s "$data_boundary" ]; then
- # Copy the boundary conditions from the "$data_boundary" file.
- # Don't assume there is only one line containing "xlo xhi", for example.
- # It's possible the user wrote the boundary conditions multiple times.
- # As always, the most recent setting overrides the earlier settings.
- BOXSIZE_MINX=`tr -d '\015' < "$data_boundary" | awk '{if ($3=="xlo") {xlo=$1}} END{print xlo}'`
- BOXSIZE_MAXX=`tr -d '\015' < "$data_boundary" | awk '{if ($4=="xhi") {xhi=$2}} END{print xhi}'`
-
- BOXSIZE_MINY=`tr -d '\015' < "$data_boundary" | awk '{if ($3=="ylo") {ylo=$1}} END{print ylo}'`
- BOXSIZE_MAXY=`tr -d '\015' < "$data_boundary" | awk '{if ($4=="yhi") {yhi=$2}} END{print yhi}'`
-
- BOXSIZE_MINZ=`tr -d '\015' < "$data_boundary" | awk '{if ($3=="zlo") {zlo=$1}} END{print zlo}'`
- BOXSIZE_MAXZ=`tr -d '\015' < "$data_boundary" | awk '{if ($4=="zhi") {zhi=$2}} END{print zhi}'`
-
- if [ -z "$BOXSIZE_MINX" ] || [ -z "$BOXSIZE_MAXX" ]; then
- echo "Error: Problem with box boundary format (\"xlo xhi\") in \"$data_boundary\"" >&2
- exit 12
- fi
- if [ -z "$BOXSIZE_MINY" ] || [ -z "$BOXSIZE_MAXY" ]; then
- echo "Error: Problem with box boundary format (\"ylo yhi\") in \"$data_boundary\"" >&2
- exit 12
- fi
- if [ -z "$BOXSIZE_MINZ" ] || [ -z "$BOXSIZE_MAXZ" ]; then
- echo "Error: Problem with box boundary format (\"zlo zhi\") in \"$data_boundary\"" >&2
- exit 12
- fi
-
- BOXSIZE_XY=`awk '{if ($4=="xy") {xy=$1}} END{print xy}' < "$data_boundary"`
- BOXSIZE_XZ=`awk '{if ($5=="xz") {xz=$2}} END{print xz}' < "$data_boundary"`
- BOXSIZE_YZ=`awk '{if ($6=="yz") {yz=$3}} END{print yz}' < "$data_boundary"`
-
- if [ -n "$BOXSIZE_XY" ] || [ -n "$BOXSIZE_XZ" ] || [ -n "$BOXSIZE_YZ" ]; then
- if [ -n "$BOXSIZE_XY" ] && [ -n "$BOXSIZE_XZ" ] && [ -n "$BOXSIZE_YZ" ]; then
- #echo "triclinic_parameters: XY XZ YZ = $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ" >&2
- TRICLINIC="True"
- else
- echo "Error: Problem with triclinic format (\"xy xz yz\") in \"$data_boundary\"" >&2
- exit 13
- fi
- fi
-fi
-
-
-
-
-if [ -z "$BOXSIZE_MINX" ] || [ -z "$BOXSIZE_MAXX" ] || [ -z "$BOXSIZE_MINY" ] || [ -z "$BOXSIZE_MAXY" ] || [ -z "$BOXSIZE_MINZ" ] || [ -z "$BOXSIZE_MAXZ" ]; then
- echo "Periodic boundary conditions unspecified. Attempting to generate automatically." >&2
-
- # By default, disable triclinic
- BOXSIZE_XY=""
- BOXSIZE_XZ=""
- BOXSIZE_YZ=""
- TRICLINIC=""
-
- if [ -s "$tmp_atom_coords" ]; then
- # Estimate the minimimum, maximum x,y,z values
- # from the coordinate data.
-
- MINMAX_BOUNDS=`awk 'BEGIN{first=1}{if (NF>=3){x=$1; y=$2; z=$3; if (first) {first=0; xmin=x; xmax=x; ymin=y; ymax=y; zmin=z; zmax=z;} else {if (x<xmin) xmin=x; if (x>xmax) xmax=x; if (y<ymin) ymin=y; if (y>ymax) ymax=y; if (z<zmin) zmin=z; if (z>zmax) zmax=z;}}} END{print xmin" "xmax" "ymin" "ymax" "zmin" "zmax;}' < "$tmp_atom_coords"`
-
- # ...and add a narrow margin (10%) around the boundaries:
- BOXSIZE_MINX=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$2-$1; print $1-0.5*margin*width}"`
- BOXSIZE_MAXX=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$2-$1; print $2+0.5*margin*width}"`
- BOXSIZE_MINY=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$4-$3; print $3-0.5*margin*width}"`
- BOXSIZE_MAXY=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$4-$3; print $4+0.5*margin*width}"`
- BOXSIZE_MINZ=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$6-$5; print $5-0.5*margin*width}"`
- BOXSIZE_MAXZ=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$6-$5; print $6+0.5*margin*width}"`
- else
- # By default, choose some reasonably large box:
- BOXSIZE_MINX="-100.0"
- BOXSIZE_MAXX="100.0"
- BOXSIZE_MINY="-100.0"
- BOXSIZE_MAXY="100.0"
- BOXSIZE_MINZ="-100.0"
- BOXSIZE_MAXZ="100.0"
- # ...and print message scolding the user for being lazy
- echo "----------------------------------------------------------------------" >&2
- echo "---- WARNING: Unable to determine periodic boundary conditions. ----" >&2
- echo "---- (A default cube of volume=(200.0)^3 was used. ----" >&2
- echo "---- This is probably not what you want!) ----" >&2
- echo "---- It is recommended that you specify your periodic boundary ----" >&2
- echo "---- by adding a write_once(\"Boundary\") command to your .lt file. ----" >&2
- echo "---- For example: ----" >&2
- #echo "----------------------------------------------------------------------" >&2
- echo "---- ----" >&2
- echo "---- write_once(\"Boundary\") { ----" >&2
- echo "---- 2.51 46.79 xlo xhi ----" >&2
- echo "---- -4.38 35.824 ylo yhi ----" >&2
- echo "---- 0.3601 42.95 zlo zhi ----" >&2
- echo "---- } ----" >&2
- echo "----------------------------------------------------------------------" >&2
- fi
-fi
-
-
-
-
-if [ -z "$TRICLINIC" ]; then
- echo " $BOXSIZE_MINX $BOXSIZE_MAXX xlo xhi" >> "$OUT_FILE_DATA"
- echo " $BOXSIZE_MINY $BOXSIZE_MAXY ylo yhi" >> "$OUT_FILE_DATA"
- echo " $BOXSIZE_MINZ $BOXSIZE_MAXZ zlo zhi" >> "$OUT_FILE_DATA"
-else
- echo "triclinic parameters: XY XZ YZ = $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ" >&2
- echo "" >&2
- # Otherwise, this is a triclinic (non orthoganal) crystal basis.
- # LAMMPS represents triclinic symmetry using a different set of parameters
- # (lx,ly,lz,xy,xz,yz) than the PDB file format (alpha,beta,gamma).
- echo " $BOXSIZE_MINX $BOXSIZE_MAXX xlo xhi" >> "$OUT_FILE_DATA"
- echo " $BOXSIZE_MINY $BOXSIZE_MAXY ylo yhi" >> "$OUT_FILE_DATA"
- echo " $BOXSIZE_MINZ $BOXSIZE_MAXZ zlo zhi" >> "$OUT_FILE_DATA"
- #echo " 0.000000 $BOXSIZE_X xlo xhi" >> "$OUT_FILE_DATA"
- #echo " 0.000000 $BOXSIZE_Y ylo yhi" >> "$OUT_FILE_DATA"
- #echo " 0.000000 $BOXSIZE_Z zlo zhi" >> "$OUT_FILE_DATA"
- echo " $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ xy xz yz" >> "$OUT_FILE_DATA"
- #echo "a,b,c,alpha,beta,gamma = $BOXSIZE_A,$BOXSIZE_B,$BOXSIZE_C,$ALPHA,$BETA,$GAMMA"
-fi
-echo "" >> "$OUT_FILE_DATA"
-
-
-
-
-if [ -s "$data_header" ]; then
- cat "$data_header" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-
-if [ -s "$data_masses" ]; then
- echo "Masses" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_masses" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-else
- echo "WARNING: missing file \"$data_masses\"" >&2
-fi
-
-if [ -s "$data_pair_coeffs" ]; then
- echo "Pair Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_pair_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- PAIR_COEFFS_IN_DATA="true"
-fi
-if [ -s "$data_pairij_coeffs" ]; then
- echo "PairIJ Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_pairij_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- PAIR_COEFFS_IN_DATA="true"
-fi
-if [ -n "$PAIR_COEFFS_IN_DATA" ]; then
- if [ ! -s "$in_settings" ] || (! grep -q pair_coeff "$in_settings"); then
- echo "WARNING: no pair coeffs have been set!" >&2
- fi
-fi
-
-
-if [ -s "$data_bond_coeffs" ]; then
- echo "Bond Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_bond_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-else
- if [ -n "$NBONDTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q bond_coeff "$in_settings") ); then
- echo "WARNING: no bond coeff have been set!" >&2
- fi
-fi
-
-
-if [ -s "$data_angle_coeffs" ]; then
- echo "Angle Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_angle_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-else
- if [ -n "$NANGLETYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q angle_coeff "$in_settings") ); then
- echo "WARNING: no angle coeffs have been set!" >&2
- fi
-fi
-
-if [ -s "$data_dihedral_coeffs" ]; then
- echo "Dihedral Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_dihedral_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-else
- if [ -n "$NDIHEDRALTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q dihedral_coeff "$in_settings") ); then
- echo "WARNING: no dihedral coeffs have been set!" >&2
- fi
-fi
-
-if [ -s "$data_improper_coeffs" ]; then
- echo "Improper Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_improper_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-else
- if [ -n "$NIMPROPERTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q improper_coeff "$in_settings") ); then
- echo "WARNING: no improper coeffs have been set!" >&2
- fi
-fi
-
-
-# data file sections specific to class2 force-fields:
-
-if [ -s "$data_bondbond_coeffs" ]; then
- echo "BondBond Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_bondbond_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_bondangle_coeffs" ]; then
- echo "BondAngle Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_bondangle_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_middlebondtorsion_coeffs" ]; then
- echo "MiddleBondTorsion Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_middlebondtorsion_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_endbondtorsion_coeffs" ]; then
- echo "EndBondTorsion Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_endbondtorsion_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_angletorsion_coeffs" ]; then
- echo "AngleTorsion Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_angletorsion_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_angleangletorsion_coeffs" ]; then
- echo "AngleAngleTorsion Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_angleangletorsion_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_bondbond13_coeffs" ]; then
- echo "BondBond13 Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_bondbond13_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_angleangle_coeffs" ]; then
- echo "AngleAngle Coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_angleangle_coeffs" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-
-if [ -s "$data_atoms" ]; then
- if [ -n "$ATOM_STYLE" ]; then
- echo "Atoms # $ATOM_STYLE" >> "$OUT_FILE_DATA"
- else
- echo "Atoms # full" >> "$OUT_FILE_DATA"
- fi
- #if [ -s "$tmp_atom_coords" ]; then
- # echo "# (Note: x,y,z coordinates may overlap and can be modified later.)" >> "$OUT_FILE_DATA"
- #else
- # echo "" >> "$OUT_FILE_DATA"
- #fi
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_atoms" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-else
- echo "WARNING: missing file \"$data_atoms\"" >&2
-fi
-
-if [ -s "$data_ellipsoids" ]; then
- echo "Ellipsoids" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_ellipsoids" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_triangles" ]; then
- echo "Triangles" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_triangles" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_lines" ]; then
- echo "Lines" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_lines" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_velocities" ]; then
- echo "Velocities" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_velocities" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-#else
-# echo "Velocities" >> "$OUT_FILE_DATA"
-# echo "" >> "$OUT_FILE_DATA"
-# awk '{print $1 " 0.0 0.0 0.0"}' < "$data_atoms" >> "$OUT_FILE_DATA"
-# echo "" >> "$OUT_FILE_DATA"
-fi
-
-if [ -s "$data_bonds" ]; then
- echo "Bonds" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_bonds" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-#else
-# echo "WARNING: missing file \"$data_bonds\"" >&2
-fi
-
-
-
-if [ -s "$data_angles" ]; then
- echo "Angles" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_angles" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-#else
-# echo "WARNING: missing file \"$data_angles\"" >&2
-fi
-
-if [ -s "$data_dihedrals" ]; then
- echo "Dihedrals" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_dihedrals" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-#else
-# echo "WARNING: missing file \"$data_dihedrals\"" >&2
-fi
-
-if [ -s "$data_impropers" ]; then
- echo "Impropers" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_impropers" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
-#else
-# echo "WARNING: missing file \"$data_impropers\"" >&2
-fi
-
-
-
-
-
-
-rm -f $OUT_FILE_INPUT_SCRIPT
-
-if [ -s "$in_init" ]; then
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- cp -f "$in_init" $OUT_FILE_INIT
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- echo "# ----------------- Init Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- echo "include \"$OUT_FILE_INIT\"" >> $OUT_FILE_INPUT_SCRIPT
- #echo "# \"$in_init\" typically contains various styles, dimensions, and units:" >> $OUT_FILE_INPUT_SCRIPT
- #echo "include \"$in_init\"" >> $OUT_FILE_INPUT_SCRIPT
- #cat "$in_init" >> $OUT_FILE_INPUT_SCRIPT
- echo "" >> $OUT_FILE_INPUT_SCRIPT
-fi
-
-
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-echo "# ----------------- Atom Definition Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-echo "read_data \"$OUT_FILE_DATA\"" >> $OUT_FILE_INPUT_SCRIPT
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-echo "# ----------------- Settings Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-
-
-if [ -s "$in_settings" ]; then
- #echo "# \"$in_settings\" typically contains coeffs, fixes, groups & modify commands:" >> $OUT_FILE_INPUT_SCRIPT
- #echo "include \"$in_settings\"" >> $OUT_FILE_INPUT_SCRIPT
- #cat "$in_settings" >> $OUT_FILE_INPUT_SCRIPT
- cp -f "$in_settings" $OUT_FILE_SETTINGS
- echo "include \"$OUT_FILE_SETTINGS\"" >> $OUT_FILE_INPUT_SCRIPT
- echo "" >> $OUT_FILE_INPUT_SCRIPT
-fi
-
-
-if [ -s "$tmp_atom_coords" ]; then
-
- NATOMS=`awk '/^\\\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
- NATOMCRDS=`awk '{if (NF>=3) natom+=1} END{print(natom)}' < "$tmp_atom_coords"`
- if [ $NATOMS -ne $NATOMCRDS ]; then
- echo "Error: Number of atoms in coordinate file provided by user ($NATOMCRDS)" >&2
- echo "does not match the number of atoms generated in ttree file ($NATOMS)" >&2
- exit 14
- fi
-
- # Copy the coordinates in $tmp_atom_coords into $OUT_FILE_DATA
- rm -f "$OUT_FILE_COORDS"
- if ! eval $PYTHON_COMMAND "${SCRIPT_DIR}/raw2data.py" $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then
- ERR_INTERNAL
- fi
- mv -f "$OUT_FILE_COORDS" "$OUT_FILE_DATA"
- echo "copied atomic coordinates into $OUT_FILE_DATA"
-
- # Previously, in earlier versions of moltemplate, we used to
- # create a new input script containing "set" commands which the
- # user was supposed to tell LAMMPS to read using an "include" command.
- # If for some reason, you want to go back to doing it that way, then
- # uncomment the following 6 lines:
- #
- #rm -f "$OUT_FILE_COORDS"
- #awk '{if (NF>=3) {natom++; print "set atom "natom" x "$1" y "$2" z "$3" image 0 0 0"}}' < "$tmp_atom_coords" >> "$OUT_FILE_COORDS"
- #echo "# Load the atom coordinates:" >> $OUT_FILE_INPUT_SCRIPT
- #echo "" >> $OUT_FILE_INPUT_SCRIPT
- #echo "include \"$OUT_FILE_COORDS\"" >> $OUT_FILE_INPUT_SCRIPT
- #echo "" >> $OUT_FILE_INPUT_SCRIPT
-
-else
- rm -f "$OUT_FILE_COORDS"
-# echo "Warning: (moltemplate.sh)" >&2
-# echo " Atomic coordinates were not supplied externally" >&2
-# echo " (for example using the \"-pdb\" or \"-xyz\" arguments)." >&2
-# echo " Hopefully you used rot(), trans() lttree commands to move" >&2
-# echo " molecules to non-overlapping positions." >&2
-fi
-
-
-
-# ############## CLEAN UP ################
-
-# A lot of files have been created along the way.
-# However only a few of them are actually useful.
-#
-# Optional: clean up some non-essential temporary
-# files created by running ttree
-# We move the non-essential files into a different directory
-# (but we don't delete them).
-
-if [ ! -d output_ttree ]; then
- mkdir output_ttree
-fi
-
-
-
-
-# Move temporary files into the "output_ttree/" directory:
-OIFS=$IFS
-#IFS=$'\n'
-IFS="
-"
-rm -f ttree_replacements.txt >/dev/null 2>&1 || true
-for file in $MOLTEMPLATE_TEMP_FILES; do
- if [ -e "$file" ]; then
- rm -f "output_ttree/$file" >/dev/null 2>&1 || true
- #echo "file=\"$file\""
- mv "$file" output_ttree/ >/dev/null 2>&1 || true
- fi
-done
-IFS=$OIFS
-
-
-
-
-
-# ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################
-
-
-# N_data_prefix=`expr length "$data_prefix"` <-- not posix compliant. AVOID
-N_data_prefix=${#data_prefix} #<-- works even if $data_prefix contains spaces
-ls "${data_prefix}"* 2> /dev/null | while read file_name; do
- #If using bash:
- #SECTION_NAME="${file_name:$N_data_prefix}"
- #If using sh:
- #SECTION_NAME=`expr substr "$file_name" $(($N_data_prefix+1)) 1000000` <-- not posix compliant. AVOID
- SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_data_prefix+1)),1000000)}"`
- # Create a new section in the data file
- # matching the portion of the name of
- # the file after the data_prefix.
- echo "" >> "$OUT_FILE_DATA"
- echo "$SECTION_NAME" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- cat "$file_name" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- mv -f "$file_name" output_ttree/
-done
-
-
-if [ -e "$data_prefix_no_space" ]; then
- echo "" >> "$OUT_FILE_DATA"
- cat "$data_prefix_no_space" >> "$OUT_FILE_DATA"
- echo "" >> "$OUT_FILE_DATA"
- mv -f "$data_prefix_no_space" output_ttree/
-fi
-
-
-
-if [ -e "$OUT_FILE_DATA" ]; then
- mv -f "$OUT_FILE_DATA" "$OUT_FILE_DATA.tmp" >/dev/null 2>&1 || true
- #dos2unix < "$OUT_FILE_DATA.tmp" > "$OUT_FILE_DATA"
- tr -d '\r' < "$OUT_FILE_DATA.tmp" > "$OUT_FILE_DATA"
- rm -f "$OUT_FILE_DATA.tmp" >/dev/null 2>&1 || true
-fi
-
-
-#N_in_prefix=`expr length "$in_prefix"` <-- not posix compliant. AVOID.
-N_in_prefix=${#in_prefix} #<-- works even if $in_prefix contains spaces
-ls "${in_prefix}"* 2> /dev/null | while read file_name; do
- #If using bash:
- #SECTION_NAME="${file_name:$N_in_prefix}"
- #If using sh:
- #SECTION_NAME=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000` <-- not posix compliant. AVOID
- SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_in_prefix+1)),1000000)}"`
- FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'`
- # Create a new section in the lammps input script
- # matching the portion of the name of
- # the file after the in_prefix.
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- echo "# ----------------- $SECTION_NAME Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
- cp -f "$file_name" ${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}
-
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- echo "include \"${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}\"" >> $OUT_FILE_INPUT_SCRIPT
- echo "" >> $OUT_FILE_INPUT_SCRIPT
-
- mv -f "$file_name" output_ttree/
-done
-
-if [ -e "$in_prefix_no_space" ]; then
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- cat "$in_prefix_no_space" >> $OUT_FILE_INPUT_SCRIPT
- echo "" >> $OUT_FILE_INPUT_SCRIPT
- mv -f "$in_prefix_no_space" output_ttree/
-fi
-
-
-# Swap the order of atom types I, J in all "pair_coeff I J ..." commands
-# whenever I > J. Do this for every input script file generated by moltemplate.
-# (Perhaps later I'll check to make sure the user did not specify contradictory
-# "pair_coeff I J ..." and "pair_coeff J I ..." commands, but I won't do it
-# here, because at this point we've thrown away the original atom type names,
-# so there's no easy way to explain the problem to the user if there is one.)
-
-echo "" > input_scripts_so_far.tmp
-
-for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; do
- if [ -s "$file_name" ]; then
- echo "postprocessing file \"$file_name\"" >&2
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name.tmp"; then
- ERR_INTERNAL
- fi
- echo "" >&2
- mv -f "$file_name.tmp" "$file_name"
- #cat "$file_name" >> input_scripts_so_far.tmp
- #dos2unix < "$file_name" >> input_scripts_so_far.tmp
- tr -d '\r' < "$file_name" >> input_scripts_so_far.tmp
-
- # Delete all "bond_style" statements when no bond types are defined
- if [ -z "$NBONDTYPES" ]; then
- awk '{if ($1!="bond_style") print $0}' < "$file_name" > "${file_name}.tmp"
- mv -f "$file_name.tmp" "$file_name"
- fi
- # Delete all "angle_style" statements when no angle types are defined
- if [ -z "$NANGLETYPES" ]; then
- awk '{if ($1!="angle_style") print $0}' < "$file_name" > "${file_name}.tmp"
- mv -f "$file_name.tmp" "$file_name"
- fi
- # Delete all "dihedral_style" statements when no dihedral types are defined
- if [ -z "$NDIHEDRALTYPES" ]; then
- awk '{if ($1!="dihedral_style") print $0}' < "$file_name" > "${file_name}.tmp"
- mv -f "$file_name.tmp" "$file_name"
- fi
- # Delete all "improper_style" statements when no improper types are defined
- if [ -z "$NIMPROPERTYPES" ]; then
- awk '{if ($1!="improper_style") print $0}' < "$file_name" > "${file_name}.tmp"
- mv -f "$file_name.tmp" "$file_name"
- fi
- fi
-done
-
-
-ls "${in_prefix}"* 2> /dev/null | while read file_name; do
- echo "postprocessing file \"$file_name\"" >&2
- if ! $PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp; then
- ERR_INTERNAL
- fi
- echo "" >&2
- mv "$file_name".tmp "$file_name"
- cat "$file_name" >> input_scripts_so_far.tmp
-done
-
-rm -f input_scripts_so_far.tmp
-
-
-
-# ############ Optional: Add a fake run section as an example ############
-
-
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-echo "# ----------------- Run Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-echo "# The lines above define the system you want to simulate." >> $OUT_FILE_INPUT_SCRIPT
-echo "# What you do next is up to you." >> $OUT_FILE_INPUT_SCRIPT
-echo "# Typically a user would minimize and equilibrate" >> $OUT_FILE_INPUT_SCRIPT
-echo "# the system using commands similar to the following:" >> $OUT_FILE_INPUT_SCRIPT
-echo "# ---- examples ----" >> $OUT_FILE_INPUT_SCRIPT
-echo "#" >> $OUT_FILE_INPUT_SCRIPT
-echo "# -- minimize --" >> $OUT_FILE_INPUT_SCRIPT
-echo "# minimize 1.0e-5 1.0e-7 1000 10000" >> $OUT_FILE_INPUT_SCRIPT
-echo "# (Note: Some fixes, for example \"shake\", interfere with the minimize command," >> $OUT_FILE_INPUT_SCRIPT
-echo "# You can use the \"unfix\" command to disable them before minimization.)" >> $OUT_FILE_INPUT_SCRIPT
-echo "# -- declare time step for normal MD --" >> $OUT_FILE_INPUT_SCRIPT
-echo "# timestep 1.0" >> $OUT_FILE_INPUT_SCRIPT
-echo "# -- run at constant pressure (Nose-Hoover)--" >> $OUT_FILE_INPUT_SCRIPT
-#echo "# timestep 1.0" >> $OUT_FILE_INPUT_SCRIPT
-echo "# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0">>$OUT_FILE_INPUT_SCRIPT
-echo "# -- ALTERNATELY, run at constant volume (Nose-Hoover) --" >> $OUT_FILE_INPUT_SCRIPT
-echo "# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1" >> $OUT_FILE_INPUT_SCRIPT
-echo "# -- ALTERNATELY, run at constant volume using Langevin dynamics. --" >> $OUT_FILE_INPUT_SCRIPT
-echo "# -- (This is good for sparse CG polymers in implicit solvent.) --" >> $OUT_FILE_INPUT_SCRIPT
-echo "# fix fxLAN all langevin 300.0 300.0 5000 48279" >> $OUT_FILE_INPUT_SCRIPT
-echo "# fix fxNVE all nve #(<--needed by fix langevin)" >> $OUT_FILE_INPUT_SCRIPT
-echo "# -- Now, finally run the simulation --" >> $OUT_FILE_INPUT_SCRIPT
-echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT
-#echo "# write_restart system_after_nvt.rst" >> $OUT_FILE_INPUT_SCRIPT
-#echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT
-#echo "# write_restart system_after_npt.rst" >> $OUT_FILE_INPUT_SCRIPT
-echo "# ---- (end of examples) ----">> $OUT_FILE_INPUT_SCRIPT
-#echo "# It is the responsibility of the user to learn LAMMPS and specify these">>$OUT_FILE_INPUT_SCRIPT
-#echo "# these commands." >> $OUT_FILE_INPUT_SCRIPT
-echo "" >> $OUT_FILE_INPUT_SCRIPT
-
-
-
-# Finally, if the -vmd argument was included, start up VMD and
-# view the system (using topotools to convert the
-
-if [ ! -z $RUN_VMD_AT_END ]; then
-
- echo "topo readlammpsdata $OUT_FILE_DATA full" > vmd_viz_moltemplate.tcl.tmp
- bn=`basename $OUT_FILE_DATA .data`
- echo "animate write psf $bn.psf" >> vmd_viz_moltemplate.tcl.tmp
- vmd -e vmd_viz_moltemplate.tcl.tmp
- rm -rf vmd_viz_moltemplate.tcl.tmp
-
-fi
diff --git a/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_dump2data.txt b/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_dump2data.txt
deleted file mode 100644
index 2a29ba38d..000000000
--- a/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_dump2data.txt
+++ /dev/null
@@ -1,121 +0,0 @@
- (Rough-draft documentation for dump2data.py and raw2data.py)
-
- ---- Description ----
-
-"dump2data.py" was originally designed to convert dump files into LAMMPS DATA format (for restarting a simulation from where it left off). However it also reads and writes .XYZ and .RAW (simple 3-column text format) files also.
-
- Comparison with pizza.py:
-This script duplicates some of the tools in pizza.py, but you don't have to learn python to use it. If you are willing to learn a little python, pizza.py, can handle more general dump files which might cause dump2data.py to crash (eg "atom_style tri"). Unlike "dump2data.py", pizza.py is maintained by the lammps team:
-http://pizza.sandia.gov/doc/Manual.html
-
- ----- General Usage -----
-
-General usage:
-
-dump2data.py [old_data_file -xyz -raw -last -t time -tstart ta -tstop tb -interval n -multi -center -scale x -atomstyle style] < DUMP_FILE > OUTPUT_FILE
-
- ----- examples -----
-
- If your LAMMPS dump file is named "traj.lammpstrj", you can
-extract the coordinates this way:
-
-dump2data.py -xyz < traj.lammpstrj > traj.xyz
-
-This generates a 3-column text file containing the xyz coordinates on each line of each atom (sorted by atomid). If there are multiple frames in the trajectory file, it will concatenate them together this way:
-
-8192
-LAMMPS data from timestep 50000
-1 -122.28 -19.2293 -7.93705
-2 -121.89 -19.2417 -8.85591
-3 -121.6 -19.2954 -7.20586
-: : : :
-8192
-LAMMPS data from timestep 100000
-1 -121.59 -20.3273 -2.0079
-2 -122.2 -19.8527 -2.64669
-3 -120.83 -19.7342 -2.2393
-
-(When using the "-raw" argument to create simple 3-column .RAW files, blank lines are used to delimit different frames in the trajectory.)
-
----- optional command line arguments ---
-
-If you want to select a particular frame from the trajectory, use:
-
-dump2data.py -xyz -t 10000 < traj.lammpstrj > coords.xyz
-
-To select the most recent (complete) frame, use:
-
-dump2data.py -xyz -last < traj.lammpstrj > coords.xyz
-
-(If the last frame is incomplete, this script will attempt to use the previous frame.)
-
-If you want to select multiple frames, but there are too many frames in your trajectory, you can run dump2data.py this way...
-
-dump2data.py -xyz -interval 10000 < traj.lammpstrj > traj.xyz
-
-...to indicate the desired interval between frames (it must be a multiple of
-the save interval). You can also use "-tstart 500000 and "-tstop 1000000" arguments to limit the output to a particular range of time. (500000-1000000 in this example).
-
---- creating DATA files ---
-
-"dump2data.py" can also create lammps DATA files. You must supply it with an existing DATA file containing the correct number of atoms and topology information.
-
-If your coordinates are stored in a DUMP file (eg "traj.lammpstrj"), you can create a new data file this way:
-
-dump2data.py -t 10000 data_file < traj.lammpstrj > new_file
-
-Again, in this example, "10000" is the timestep for the frame you have selected. You can use "-last" to select the last frame. If you do not specify the frame you want, multiple data files may be created...
-
-Creating multiple data files:
-The "-multi" command line argument tells "dump2data.py" to generate a new data file for each frame in the trajectory/dump-file. Those files will have names ending in ".1", ".2", ".3", ... (If you use the "-interval" argument, frames in the trajectory whose timestep is not a multiple of the interval will be discarded.) I can't remember if this behavior is switched on by default.
-
-Reading simple 3-column coordinate files:
-If you have a file containing only the coordinates of the atoms (in sorted order), you can use "raw2data.py" to create a data file with those atoms coordinates.
-
-raw2data.py -atomstyle ATOMSTYLE data_file < coords.raw > new_data_file
-
-(where ATOMSTYLE is a quoted string, such as "full" or "hybrid sphere dipole" discussed earlier. Warning: "raw2data.py" is not a stand-alone script. Make sure raw2data.py is located in the same directory with dump2data.py.)
-
---- scaling and centering coordinates ---
-
--center
- This will center the coordinates around the geometric center, so that the average position of the atoms in each frame is located at the origin. (This script attempts to pay attention to the periodic image flags. As such, I think this script works with triclinic cells, but I have not tested that feature carefully.)
-
--scale 1.6
- This will multiply the coordinates by a constant (eg "1.6") (Please email me if this fails with periodic image flags.)
-
----- limitations ----
-
-Speed.
-The program is somewhat slow, although it should be able to handle big trajectories. If speed is important to you, you probably should write your own custom script or use pizza.py which might be faster.
-
-triclinic cells
- Support for triclinic cells has been added, but not tested.
-
-exotic atom_styles
-
- This script was designed to work with point-like atoms, and it extracts the x,y,z (and if present vx,vy,vz velocity) degrees of freedom and (by default) copies it to the new data being created by this script.
-
-By default, this script assumes you are using "atom_style full".
-If you are using some other atom style (eg "hybrid bond dipole"), then you can try to run it this way:
-
-dump2data.py -t 10000 \
- -atomstyle "hybrid bond dipole" \
- old_data_file < traj.lammpstrj > new_data_file
-
-In general, the -atomstyle argument can be any of the atom styles listed in the
-table at:
-http://lammps.sandia.gov/doc/atom_style.html
-...such as "angle", "bond", "charge", "full", "molecular", "dipole", "ellipsoid", or any hybrid combination of these styles. (When using hybrid atom styles, you must enclose the argument in quotes, for example: "hybrid sphere dipole")
-Warning: I have not tested using dump2data.py with exotic (non-point-like) atom
-styles. (I suspect that the script will not crash, but the dipole orientations
-will not be updated.)
-
-You can also customize the order columns you want to appear in that file using -atomstyle ”molid x y z atomid atomtype mux muy muz”, but again, I don't think the mux, muy, muz information in the new data file will be accurate.
-
-I also strongly suspect that "dump2data.py" does not currently work with the "tri", "ellipsoid", and new "body" styles.
-
-Again, try using pizza.py if you are simulating systems with exotic data types.
-http://pizza.sandia.gov/doc/Manual.html
-
-I hope this is useful to someone.
diff --git a/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_extract_lammps_data.txt b/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_extract_lammps_data.txt
deleted file mode 100644
index 2b591d0fa..000000000
--- a/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_extract_lammps_data.txt
+++ /dev/null
@@ -1,60 +0,0 @@
-extract_lammps_data.py is a simple script which extracts sections of text from
-a LAMMPS data file. (Of coarse, you can accomplish the same thing with a text
-editor, but this script performs the task automatically.)
-
-
-Typical usage:
-
-extract_lammps_data.py SECTION_NAME < FILE.DATA > EXCERPT.TXT
-
-This extracts a section from a LAMMPS data file and saves it in EXCERPT.TXT.
-
-More general usage:
-
-extract_lammps_data.py [-n] SECTION_LIST < FILE.DATA > EXCERPT.TXT
-
-The SECTION_LIST is a list of sections you want in your output file
-(eg "EXCERPT.TXT"). Each section must be a quoted-string, and spaces
-(not commas) should separate each section name.
-
-The optional "-n" flag negates the selection. (Selecting instead, everything
-except the sections you listed.)
-
-Examples:
-
-extract_lammps_data.py "Atoms" < FILE.DATA > Atoms.txt
-extract_lammps_data.py "Header" < FILE.DATA > Header.txt
-extract_lammps_data.py -n "Header" < FILE.DATA > everything_except_Header.txt
-
-extract_lammps_data.py "Bonds" "Angles" "Dihedrals" "Impropers" \
- < FILE.DATA > topology.txt
-
-extract_lammps_data.py "Pair Coeffs" "Bond Coeffs" "Angle Coeffs" \
- "Dihedral Coeffs" "Improper Coeffs" \
- < FILE.DATA > force_field.txt
-
-
-The following section names are allowed:
-
-"Header" # The header section at the beginning of the file.
-"Atoms"
-"Masses"
-"Bonds"
-"Bond Coeffs"
-"Angles"
-"Angle Coeffs"
-"Dihedrals"
-"Dihedral Coeffs"
-"Impropers"
-"Improper Coeffs"
-"BondBond Coeffs" # class2 angles
-"BondAngle Coeffs" # class2 angles
-"MiddleBondTorsion Coeffs" # class2 dihedrals
-"EndBondTorsion Coeffs" # class2 dihedrals
-"AngleTorsion Coeffs" # class2 dihedrals
-"AngleAngleTorsion Coeffs" # class2 dihedrals
-"BondBond13 Coeffs" # class2 dihedrals
-"AngleAngle Coeffs" # class2 impropers
-"Angles By Type" # moltemplate-specific. (not standard LAMMPS)
-"Dihedrals By Type" # moltemplate-specific. (not standard LAMMPS)
-"Angles By Type' # moltemplate-specific. (not standard LAMMPS)
diff --git a/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_raw2data.txt b/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_raw2data.txt
deleted file mode 100644
index 0bcb951c8..000000000
--- a/tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_raw2data.txt
+++ /dev/null
@@ -1,56 +0,0 @@
-raw2data.py replaces the coordinates of a LAMMPS data file with new coordinates.
-
-
-Typical usage:
-
-raw2data.py -atomstyle ATOMSTYLE FILE_OLD.data < COORDS.raw > FILE_NEW.data
-
-
-This will create a new LAMMPS DATA file named "FILE_NEW.data" whose atom
-coordinates are copied from the COORDS.raw file, but is otherwise identical
-to the original DATA file (eg, "FILE_OLD.data"). The optional
--atomstyle ATOMSTYLE argument tells raw2data.py about the format of the DATA
-file. If not specified, the atom style is "full" by default.
-
-
-Arguments:
-
-ATOMSTYLE is a quoted string, such as "full" or "hybrid sphere dipole" indicating the format of the data file. It can be any of the atom styles listed in the table at:
-http://lammps.sandia.gov/doc/atom_style.html
-...such as "angle", "bond", "charge", "full", "molecular", "dipole", "ellipsoid"
-or any hybrid combination of these styles.
-
-FILE_OLD.data
-The second argument to raw2data.py is the name of a DATA file you want to read.
-raw2data.py will replace the coordinates in the "Atoms" section of this file,
-while preserving the rest of the data file.
-
-COORDS.raw is a simple 3-column ASCII file containing the coordinates of the
-atoms in your system. It has a very simple format:
--122.28 -19.2293 -7.93705
--121.89 -19.2417 -8.85591
--121.6 -19.2954 -7.20586
--121.59 -20.3273 -2.0079
--122.2 -19.8527 -2.64669
--120.83 -19.7342 -2.2393
- : : :
-
-The order of the atoms in this file should match the ATOM-ID number in the
-first column of the "Atoms" section of the FILE_OLD.data file.
-(...I THINK...
- To be on the safe side, use a DATA file with the atoms in sorted order.)
-
-Exotic atom styles:
- When using hybrid atom styles, you must enclose the argument in quotes,
-for example: "hybrid sphere dipole"
-
- Warning 1: I have not tested using raw2data.py with exotic (non-point-like)
-atom styles. (I suspect that the script will not crash, but dipole orientations
-and other internal degrees of freedom will not be updated.)
-
- Warning 2: "raw2data.py" is not a stand-alone script. Make sure dump2data.py is located in the same directory with raw2data.py.
-
- Note: I have not tested it, but I suspect many of the other arguments that work with "dump2data.py", such as "-scale", and "-xyz" also work with raw2data.py.
-
-Try using pizza.py if you are simulating systems with exotic data types.
-http://pizza.sandia.gov/doc/Manual.html
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/README.TXT b/tools/moltemplate/src/moltemplate_force_fields/amber/README.TXT
deleted file mode 100644
index 20b4d7ed2..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/README.TXT
+++ /dev/null
@@ -1,74 +0,0 @@
-This directory contains scripts used for converting AMBER parameter files
-into moltemplate (.LT) format. When a newer version of the AMBER parameters
-is eventually published, you can use these scripts to convert the new files
-again. (Some tinkering may be necessary.)
-
-The main bash script is a wrapper which simply splits up the parameter (".dat")
-file into fragments which (it thinks) correspond to the mass, pair, bond,
-angle, dihedral, and improper section of the original .dat file.
-(However sometimes it gets this wrong and you have to split it up manually!)
-
-Then this bash script invokes the relevant python script to convert
-each section into .LT format:
-amberparm_to_mass.py
-amberparm_to_pair.py
-amberparm_to_bond.py
-amberparm_to_angle.py
-amberparm_to_dihedral.py
-amberparm_to_improper.py
-In case this goes wrong, you may have to run these scripts manaully.
-
-
-Find out how to run this bash script by invoking it without any arguments:
-
-./amberparm2lt.sh
-
------------- IMPORTANT ------------
-
-BEFORE YOU RUN THIS SCRIPT, BE SURE TO CHANGE THE ORDER OF THE IMPROPER DIHEDRAL
-PARAMETERS SO THAT THE "SPECIFIC" IMPROPER DIHEDRALS APPEAR LAST, AND THE
-"GENERIC" IMPROPER DIHEDRALS APPEAR FIRST.
-
-For example replace these two lines:
-
-X -o -c -o 1.1 180. 2. JCC,7,(1986),230
-X -X -c -o 10.5 180. 2. JCC,7,(1986),230
-
-with these two lines:
-
-X -X -c -o 10.5 180. 2. JCC,7,(1986),230
-X -o -c -o 1.1 180. 2. JCC,7,(1986),230
-
-Why:
-This is the order that moltemplate expects: generic first. specific last.
-So far only the improper dihedral parameters in the gaff.dat file seem
-to violate this order. The bonds, angles and dihedrals seem to obey this,
-but check to make sure.
-
-
-There is a discussion of these parameters here:
-http://structbio.vanderbilt.edu/archives/amber-archive/2005/3444.php
-
-excerpt:
-
-> > In the parm99 file (for example), sometimes the wild-card is used, as it
-> > is done in the following example:
-> >
-> > X -X -C -O 10.5 180. 2. JCC,7,(1986),230
-> >
-> > The first example is the specific case while the second one is the generic
-> > case. In page # 257 of the AMBER Manual, it is talking about Dihedral
-> > Angle, and how these dihedral parameters are used to calculate the
-> > energies. I am wondering what the difference between generic and specific
-> > case is for improper torsions.
->
-> "specific" torsions are search for first, and used if a match is found. If
-> no match is found, then a search is made to see if a "generic" (aka wild-card)
-> torsion with match.
-> ...good luck...dac
-
-Good luck
-
--Andrew
-2014-4-19
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
deleted file mode 100755
index 92e7e2c42..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
+++ /dev/null
@@ -1,203 +0,0 @@
-#!/bin/sh
-
-SYNTAX_MSG=$(cat <<EOF
-Typical Usage:
-
-amberparm2lt.sh gaff.dat GAFF > gaff.lt
-
- You can also try:
-amberparm2lt.sh parm94.dat "AMBERFF94 inherits GAFF" > amberff94.lt
- (However, this later usage may not work.
- You may need to manually split the .dat file and run these scripts instead:
- amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...)
- Be sure that all of these .py files are in your PATH as well.)
-
-EOF
-)
-
-if [ "$#" != "2" ]; then
- echo "${SYNTAX_MSG}" >&2
- echo "" >&2
- echo "Error: This script requires two arguments," >&2
- echo " 1) the name of the amber parm file to be converted (eg \"gaff.dat\")" >&2
- echo " 2) the name of the moltemplate object to be created (eg \"GAFF\")" >&2
- echo " (This may include the \"inherits\" keyword and parent classes.)" >&2
- exit 1
-fi
-
-MOLTEMPLATE_USAGE_MSG=$(cat <<EOF
-# Background information and usage explanation:
-# This file contanis a list of atom types and rules for generating bonded
-# interactions between these atoms (hopefully) according to AMBER conventions.
-# By using the atom types shown below in your own molecules, bonds and angular
-# interactions will be automatically generated.
-# AMBER (GAFF) force-field parameters will also be assigned to each angle
-# interaction (according to these atom types).
-# One way to apply the GAFF force field to a particular type of molecule, is
-# to use the "inherits" keyword when you define that molecule. For example:
-# import("gaff.lt")
-# MoleculeType inherits GAFF {
-# write_once("Data Atoms") {
-# \$atom:C1 \$mol:... @atom:cx 0.0 4.183 3.194 13.285
-# \$atom:C2 \$mol:... @atom:cx 0.0 4.291 4.618 13.382
-# : : :
-# }
-# }
-#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.)
-EOF
-)
-# (Note that the full name of the atom type in this example is "@atom:/GAFF/cx"
-# You can always refer to atom types this way as well. Using "inherits GAFF"
-# allows you to use more conventient "@atom:cx" shorthand notation instead.)
-
-echo "####################################################################"
-echo "# To use this, LAMMPS currently must be compiled with the USER-MISC package."
-echo "# (Type \"make yes-user-misc\" into the shell before compiling LAMMPS.)"
-echo "####################################################################"
-echo "# This moltemplate (LT) file was generated automatically using"
-echo "# amberparm2lt.sh $1 $2"
-echo "####################################################################"
-echo "$MOLTEMPLATE_USAGE_MSG"
-echo "####################################################################"
-echo "# Moltemplate can not assign atom charge. You must assign atomic"
-echo "# charges yourself. (Moltemplate is only a simple text manipulation tool.)"
-echo "####################################################################"
-echo ""
-echo ""
-
-
-if ! which ./amberparm_mass_to_lt.py > /dev/null; then
- echo "\nError: \"amberparm_mass_to_lt.py\" not found.\n" >&2
- echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
- exit 2
-fi
-if ! which ./amberparm_pair_to_lt.py > /dev/null; then
- echo "\nError: \"amberparm_pair_to_lt.py\" not found.\n" >&2
- echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
- exit 2
-fi
-if ! which ./amberparm_bond_to_lt.py > /dev/null; then
- echo "\nError: \"amberparm_bond_to_lt.py\" not found.\n" >&2
- echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
- exit 2
-fi
-if ! which ./amberparm_angle_to_lt.py > /dev/null; then
- echo "\nError: \"amberparm_angle_to_lt.py\" not found.\n" >&2
- echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
- exit 2
-fi
-if ! which ./amberparm_dihedral_to_lt.py > /dev/null; then
- echo "\nError: \"amberparm_dihedral_to_lt.py\" not found.\n" >&2
- echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
- exit 2
-fi
-if ! which ./amberparm_improper_to_lt.py > /dev/null; then
- echo "\nError: \"amberparm_improper_to_lt.py\" not found. (Update your PATH?)\n" >&2
- echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
- exit 2
-fi
-
-
-#PARM_FILE='gaff.dat'
-PARM_FILE=$1
-
-# sections are separated by blank lines
-# some sections have comment lines at the beginning
-
-# The 1st section is the mass (note: skip the first line)
-tail -n +2 < "$PARM_FILE" | \
- awk -v n=1 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- > "${PARM_FILE}.mass"
-
-# The 2nd section has the list of 2-body bond force-field params
-awk -v n=2 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- < "$PARM_FILE" \
- | tail -n +2 \
- > "${PARM_FILE}.bond"
-
-# The 3rd section has the list of 3-body angle force-field params
-awk -v n=3 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- < "$PARM_FILE" \
- > "${PARM_FILE}.angle"
-
-# The 4th section has the list of 4-body dihedral force-field params
-awk -v n=4 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- < "$PARM_FILE" \
- > "${PARM_FILE}.dihedral"
-
-# The 5th section has the list of 4-body improper force-field params
-awk -v n=5 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- < "$PARM_FILE" \
- > "${PARM_FILE}.improper"
-
-# The 6th section has the hbond-parameters (no-longer used. ignore)
-awk -v n=6 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- < "$PARM_FILE" \
- > "${PARM_FILE}.hbond"
-
-# The 7th "section" is just a blank line. (skip that)
-
-# The 8th section has the list of non-bonded ("pair") force-field parameters
-awk -v n=8 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
- < "$PARM_FILE" \
- | tail -n +2 \
- > "${PARM_FILE}.pair"
-
-
-./amberparm_mass_to_lt.py < "${PARM_FILE}.mass" > "${PARM_FILE}.mass.lt"
-./amberparm_pair_to_lt.py < "${PARM_FILE}.pair" > "${PARM_FILE}.pair.lt"
-./amberparm_bond_to_lt.py < "${PARM_FILE}.bond" > "${PARM_FILE}.bond.lt"
-./amberparm_angle_to_lt.py < "${PARM_FILE}.angle" > "${PARM_FILE}.angle.lt"
-./amberparm_dihedral_to_lt.py \
- < "${PARM_FILE}.dihedral" > "${PARM_FILE}.dihedral.lt"
-./amberparm_improper_to_lt.py \
- < "${PARM_FILE}.improper" > "${PARM_FILE}.improper.lt"
-
-echo "$2 {"
-echo ""
-echo " # ----------------------------------------------------------------------"
-#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\""
-echo " # The basic atom nomenclature and conventions are explained here:"
-echo " # http://ambermd.org/antechamber/gaff.pdf"
-echo " # For reference, the original gaff.dat file and format documentation are here:"
-echo " # http://ambermd.org/AmberTools-get.html"
-echo " # http://ambermd.org/formats.html#parm.dat"
-echo " # ----------------------------------------------------------------------"
-echo ""
-
-cat "$PARM_FILE.mass.lt" \
- "$PARM_FILE.pair.lt" \
- "$PARM_FILE.bond.lt" \
- "$PARM_FILE.angle.lt" \
- "$PARM_FILE.dihedral.lt" \
- "$PARM_FILE.improper.lt"
-
-AMBER_STYLES_INIT=$(cat <<EOF
-
- write_once("In Init") {
- # Default styles and settings for AMBER based force-fields:
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid fourier
- improper_style hybrid cvff
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- kspace_style pppm 0.0001
-
- # NOTE: If you do not want to use long-range coulombic forces,
- # comment out the two lines above and uncomment this line:
- # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
-
- pair_modify mix arithmetic
- special_bonds amber
- }
-EOF
-)
-
-echo "$AMBER_STYLES_INIT"
-echo ""
-echo "}"
-echo ""
-echo ""
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_angle_to_lt.py b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_angle_to_lt.py
deleted file mode 100755
index 6072afe62..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_angle_to_lt.py
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-
-lines_gaff = sys.stdin.readlines()
-angle_style_name = 'harmonic'
-
-sys.stdout.write(' write_once("In Settings") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:8].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- atype3 = atypes[2].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- at3 = atype3.replace('X','*')
- angletype = '@angle:'+atype1+'-'+atype2+'-'+atype3
-
- tokens= line[8:].split()
- keq = tokens[0]
- req = tokens[1]
- comments=' '.join(tokens[2:])
- sys.stdout.write(' angle_coeff '+angletype+' '+angle_style_name+' '+keq+' '+req+' # '+comments+'\n')
-
-sys.stdout.write(' } # (end of angle_coeffs)\n')
-sys.stdout.write('\n')
-sys.stdout.write(' write_once("Data Angles By Type") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:8].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- atype3 = atypes[2].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- at3 = atype3.replace('X','*')
- angletype = '@angle:'+atype1+'-'+atype2+'-'+atype3
-
- #tokens= line[8:].split()
- #keq = tokens[0]
- #req = tokens[1]
- #comments=' '.join(tokens[2:])
- sys.stdout.write(' '+angletype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+'\n')
-
-sys.stdout.write(' } # (end of Angles By Type)\n')
-sys.stdout.write('\n')
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_bond_to_lt.py b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_bond_to_lt.py
deleted file mode 100755
index eabae17b5..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_bond_to_lt.py
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-
-lines_gaff = sys.stdin.readlines()
-bond_style_name = 'harmonic'
-
-sys.stdout.write(' write_once("In Settings") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- tokens= line.split()
- atypes = line[:6].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- bondtype = '@bond:'+atype1+'-'+atype2
-
- tokens= line[5:].split()
- keq = tokens[0]
- req = tokens[1]
- comments=' '.join(tokens[2:])
- sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req+' # '+comments+'\n')
-
-sys.stdout.write(' } # (end of bond_coeffs)\n')
-sys.stdout.write('\n')
-sys.stdout.write(' write_once("Data Bonds By Type") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:6].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- bondtype = '@bond:'+atype1+'-'+atype2
-
- #tokens= line[5:].split()
- #keq = tokens[0]
- #req = tokens[1]
- #comments=' '.join(tokens[2:])
- sys.stdout.write(' '+bondtype+' @atom:'+at1+' @atom:'+at2+'\n')
-
-sys.stdout.write(' } # (end of Bonds By Type)\n')
-sys.stdout.write('\n')
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_dihedral_to_lt.py b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_dihedral_to_lt.py
deleted file mode 100755
index 2e3b306e6..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_dihedral_to_lt.py
+++ /dev/null
@@ -1,157 +0,0 @@
-#!/usr/bin/env python
-
-# SOME UGLY CODE HERE
-
-import sys
-
-lines_gaff = sys.stdin.readlines()
-dihedral_style_name = 'fourier'
-in_dihedral_coeffs = []
-
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:11].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- atype3 = atypes[2].strip()
- atype4 = atypes[3].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- at3 = atype3.replace('X','*')
- at4 = atype4.replace('X','*')
- dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
-
- tokens= line[11:].split()
- npth = float(tokens[0])
- Kn = float(tokens[1])
- Kn /= npth # The coeff for each fourier term is Kn/npth
- # ...I THINK (?). (Very confusing. See documentation below...)
- dn = float(tokens[2])
- n = int(float(tokens[3]))
- comments=' # '+(' '.join(tokens[4:]))
- in_dihedral_coeffs.append([dihedraltype, Kn, n, dn, comments])
- #print(Kn, n, dn)
-
-#for entry in in_dihedral_coeffs:
-# print(entry)
-#exit()
-
-
-# ---- processing dihedral fourier series ----
-# ---- (negative "n" values means the
-# ---- Fourier series is not yet complete.
-
-i = 0
-while i < len(in_dihedral_coeffs):
- type_str = in_dihedral_coeffs[i][0]
- Kn = in_dihedral_coeffs[i][1]
- n = in_dihedral_coeffs[i][2]
- dn = in_dihedral_coeffs[i][3]
-
- #if (i>0):
- # sys.stderr.write('prev_n='+str(in_dihedral_coeffs[i-1][-3])+'\n')
- #sys.stderr.write('n='+str(n)+'\n')
-
- if ((i>0) and (in_dihedral_coeffs[i-1][-3] < 0)):
-
- #sys.stdout.write('interaction_before_append: '+str(in_dihedral_coeffs[i-1])+'\n')
- assert(in_dihedral_coeffs[i-1][0] == in_dihedral_coeffs[i][0])
- in_dihedral_coeffs[i-1][-3] = -in_dihedral_coeffs[i-1][-3]
- comments = in_dihedral_coeffs[i-1][-1]
- in_dihedral_coeffs[i-1][-1] = Kn
- in_dihedral_coeffs[i-1].append(n)
- in_dihedral_coeffs[i-1].append(dn)
- in_dihedral_coeffs[i-1].append(comments)
- #sys.stdout.write('interaction_after_append: '+str(in_dihedral_coeffs[i-1])+'\n')
- del in_dihedral_coeffs[i]
-
- #elif len(in_dihedral_coeffs) < 3:
- # del in_dihedral_coeffs[i]
- else:
- i += 1
-
-
-
-for i in range(0, len(in_dihedral_coeffs)):
- type_str = in_dihedral_coeffs[i][0]
- params = in_dihedral_coeffs[i][1:]
- params = map(str, params)
- num_fourier_terms = (len(params)-1)/3
- dihedral_coeff_str = 'dihedral_coeff '+type_str+' '+\
- dihedral_style_name+' '+ \
- str(num_fourier_terms)+' '+ \
- ' '.join(params)
- in_dihedral_coeffs[i] = dihedral_coeff_str
-
-# ---- finished processing dihedral fourier series ----
-
-
-sys.stdout.write(' write_once(\"In Settings\") {\n ')
-sys.stdout.write('\n '.join(in_dihedral_coeffs)+'\n')
-sys.stdout.write(' } # (end of dihedral_coeffs)\n')
-
-
-
-
-
-sys.stdout.write('\n')
-
-sys.stdout.write(' write_once("Data Dihedrals By Type") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:11].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- atype3 = atypes[2].strip()
- atype4 = atypes[3].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- at3 = atype3.replace('X','*')
- at4 = atype4.replace('X','*')
- dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
-
- sys.stdout.write(' '+dihedraltype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n')
-
-sys.stdout.write(' } # (end of Dihedrals By Type)\n')
-sys.stdout.write('\n')
-
-
-"""
- - 6 - ***** INPUT FOR DIHEDRAL PARAMETERS *****
-
- IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
-
- FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-
- IPT, ... The atom symbols for the atoms forming a dihedral
- angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then
- any dihedrals in the system involving the atoms "JPT" and
- and "KPT" are assigned the same parameters. This is
- called the general dihedral type and is of the form
- "X "-"JPT"-"KPT"-"X ".
-
- IDIVF The factor by which the torsional barrier is divided.
- Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
- details. Basically, the actual torsional potential is
-
- (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
-
- PK The barrier height divided by a factor of 2.
-
- PHASE The phase shift angle in the torsional function.
-
- The unit is degrees.
-
- PN The periodicity of the torsional barrier.
- NOTE: If PN .lt. 0.0 then the torsional potential
- is assumed to have more than one term, and the
- values of the rest of the terms are read from the
- next cards until a positive PN is encountered. The
- negative value of pn is used only for identifying
- the existence of the next term and only the
- absolute value of PN is kept.
-
- The input is terminated by a blank card.
-"""
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_improper_to_lt.py b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_improper_to_lt.py
deleted file mode 100755
index 742884e36..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_improper_to_lt.py
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-
-lines_gaff = sys.stdin.readlines()
-improper_style_name = 'cvff'
-
-sys.stdout.write(' write_once("In Settings") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:11].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- atype3 = atypes[2].strip()
- atype4 = atypes[3].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- at3 = atype3.replace('X','*')
- at4 = atype4.replace('X','*')
- impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
- #sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n')
- # Oops. This is incorrect.
- # In moltemplate, the central atom is the first atom,
- # In "gaff.dat", the central atom is the third atom
- # http://archive.ambermd.org/201307/0519.html
- #impropertype = '@improper:'+atype3+'-'+atype1+'-'+atype2+'-'+atype4
-
- tokens= line[11:].split()
- Kn = float(tokens[0])
- dn = float(tokens[1])
- n = int(float(tokens[2]))
- comments=' '.join(tokens[3:])
-
- if (dn < 0.001):
- sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+' # '+comments+'\n')
- elif (179.999 < abs(dn) < 180.001):
- sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+' # '+comments+'\n')
- else:
- sys.stderr.write('Error: Illegal bondImproper parameters:\n'
- ' As of 2013-8-03, LAMMPS doens hot have an improper style\n'
- ' which can handle impropers with gamma != 0 or 180\n')
- exit(-1)
-
-
-
-sys.stdout.write(' } # (end of improper_coeffs)\n')
-sys.stdout.write('\n')
-sys.stdout.write(' write_once("Data Impropers By Type (gaff_imp.py)") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- atypes = line[:11].split('-')
- atype1 = atypes[0].strip()
- atype2 = atypes[1].strip()
- atype3 = atypes[2].strip()
- atype4 = atypes[3].strip()
- at1 = atype1.replace('X','*')
- at2 = atype2.replace('X','*')
- at3 = atype3.replace('X','*')
- at4 = atype4.replace('X','*')
-
- impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
- sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n')
- # The improper-angle is the angle between the planes
- # defined by at1,at2,at3, and at2,at3,at3
- # and we list the atoms in this order.
- # NOTE: In "gaff.dat", the central atom is the third atom (at3)
- # so we have to take this into account when matching atom order.
- # http://archive.ambermd.org/201307/0519.html
-
-
-sys.stdout.write(' } # (end of Impropers By Type)\n')
-sys.stdout.write('\n')
-
-# NOTE: AMBER documentation is not clear how the improper angle is defined.
-# It's not clear if we should be using the dihedral angle between
-# planes I-J-K and J-K-L. As of 2014-4, improper_style cvff does this.
-# Even if we create improper interactions with the angle defined between
-# the wrong planes, at least the minima should be the same
-# (0 degrees or 180 degrees).
-# So I'm not too worried we are getting this detail wrong long as
-# we generate new impropers realizing that the 3rd atom (K) is the
-# central atom (according to AMBER conventions).
-#
-# http://structbio.vanderbilt.edu/archives/amber-archive/2007/0408.php
-#
-# Currently, we only apply improper torsional angles for atoms
-# in a planar conformations. Is it clear?
-# Junmei
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_mass_to_lt.py b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_mass_to_lt.py
deleted file mode 100755
index 818b1fa30..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_mass_to_lt.py
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-
-lines_gaff = sys.stdin.readlines()
-
-sys.stdout.write(' write_once(\"Data Masses\") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- tokens= line.split()
- atype = tokens[0]
- mass=tokens[1]
- # what is the next number? (the one in tokens[2]?)
- comments=' '.join(tokens[3:])
- sys.stdout.write(' @atom:'+atype+' '+mass+' # '+comments+'\n')
-
-sys.stdout.write(' } # (end of masses)\n')
-sys.stdout.write('\n')
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_pair_to_lt.py b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_pair_to_lt.py
deleted file mode 100755
index 209fd46c9..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_pair_to_lt.py
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-
-lines_gaff = sys.stdin.readlines()
-
-#pair_style = 'lj/charmm/coul/long'
-
- # NOTE: Long-range coulombic forces were disabled intentionally. (See below)
- # If you want to use long-range electrostatics, uncomment these lines:
- # Instead I use hybrid lj/charmm/coul/charmm by default, because
- # LAMMPS complains if you attempt to use lj/charmm/coul/long on a
- # system if it does not contain any charged particles.
- # Currently, moltemplate does not assign atomic charge,
- # so this problem occurs frequently.
-
-#pair_style = 'lj/charmm/coul/charmm'
-pair_style = 'lj/charmm/coul/long'
-
-sys.stdout.write(' write_once(\"In Settings\") {\n')
-
-for i in range(0, len(lines_gaff)):
- line = lines_gaff[i]
- tokens= line.split()
- atype = tokens[0]
-
- # UGGHHH
-
- # OLD CODE:
- #sig=tokens[1]
-
- # CORRECTION #1
- # It looks the number in this part of the file is an atom radii, not a
- # diameter. In other words, this number is 0.5*sigma instead of sigma.
- # So we multiply it by 2.0.
- #sig=str(2.0*float(tokens[1]))
- #
- # CORRECTION #2
- # It also appears as though they are using this convention for LennardJones
- # U(r)=epsilon*((s/r)^12-2*(s/r)^6) instead of 4*eps*((s/r)^12-(s/r)^6)
- # ...where "s" is shorthand for "sigma"..
- # This means we must ALSO multiply sigma in gaff.dat by 2**(-1.0/6)
- # (This change makes the two U(r) formulas equivalent.)
-
- # I had to figure this out by iterations of trial and error.
- # The official AMBER documentation is quite vague about the LJ parameters.
- # My apologies to everyone effected by this bug! -Andrew 2014-5-19
- # http://ambermd.org/formats.html#parm.dat
- # http://structbio.vanderbilt.edu/archives/amber-archive/2009/5072.php)
-
- sig=str(float(tokens[1])*2.0*pow(2.0, (-1.0/6.0)))
- eps=tokens[2]
- comments=' '.join(tokens[3:])
- sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n')
-
-sys.stdout.write(' } # (end of pair_coeffs)\n')
-sys.stdout.write('\n')
diff --git a/tools/moltemplate/src/moltemplate_force_fields/gaff.lt b/tools/moltemplate/src/moltemplate_force_fields/gaff.lt
deleted file mode 100644
index 683dbf4ee..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/gaff.lt
+++ /dev/null
@@ -1,11789 +0,0 @@
-# This is the 1.7 version of GAFF (from AmberTools15), downloaded 2015-8-17.
-# NOTE: Corrections were made to the amberparm2lt.sh converter on 2014-5-19, so
-# this version of gaff.lt differs from earlier versions using the same source
-####################################################################
-# To use this, LAMMPS currently must be compiled with the USER-MISC package.
-# (Type "make yes-user-misc" into the shell before compiling LAMMPS.)
-####################################################################
-# This moltemplate (LT) file was generated automatically using
-# amber/amberparm2lt.sh gaff.dat GAFF > gaff.lt
-####################################################################
-# Background information and usage explanation:
-# This file contanis a list of atom types and rules for generating bonded
-# interactions between these atoms (hopefully) according to AMBER conventions.
-# By using the atom types shown below in your own molecules, bonds and angular
-# interactions will be automatically generated.
-# AMBER (GAFF) force-field parameters will also be assigned to each angle
-# interaction (according to these atom types).
-# One way to apply the GAFF force field to a particular type of molecule, is
-# to use the "inherits" keyword when you define that molecule. For example:
-#
-# import("gaff.lt")
-# MoleculeType inherits GAFF {
-# write_once("Data Atoms") {
-# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285
-# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382
-# : : :
-# }
-# }
-#
-#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.)
-####################################################################
-# Moltemplate can not assign atom charge. You must assign atomic
-# charges yourself. (Moltemplate is only a simple text manipulation tool.)
-####################################################################
-
-
-
-
-
-
-
-GAFF {
-
- # ----------------------------------------------------------------------
- # The basic atom nomenclature and conventions are explained here:
- # http://ambermd.org/antechamber/gaff.pdf
- # For reference, the original gaff.dat file and format documentation are here:
- # http://ambermd.org/AmberTools-get.html
- # http://ambermd.org/formats.html#parm.dat
- # ----------------------------------------------------------------------
-
- write_once("Data Masses") {
- @atom:c 12.01 # Sp2 C carbonyl group
- @atom:c1 12.01 # Sp C
- @atom:c2 12.01 # Sp2 C
- @atom:c3 12.01 # Sp3 C
- @atom:ca 12.01 # Sp2 C in pure aromatic systems
- @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys.
- @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp
- @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems
- @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc
- @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems
- @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce
- @atom:cg 12.01 # Inner Sp carbons in conjugated systems
- @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg
- @atom:cx 12.01 # Sp3 carbons in triangle systems
- @atom:cy 12.01 # Sp3 carbons in square systems
- @atom:cu 12.01 # Sp2 carbons in triangle systems
- @atom:cv 12.01 # Sp2 carbons in square systems
- @atom:cz 12.01 # Sp2 carbon in guanidine group
- @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group
- @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group
- @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group
- @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group
- @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group
- @atom:ha 1.008 # H bonded to aromatic carbon
- @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group
- @atom:hn 1.008 # H bonded to nitrogen atoms
- @atom:ho 1.008 # Hydroxyl group
- @atom:hp 1.008 # H bonded to phosphate
- @atom:hs 1.008 # Hydrogen bonded to sulphur
- @atom:hw 1.008 # Hydrogen in water
- @atom:hx 1.008 # H bonded to C next to positively charged group
- @atom:f 19.00 # Fluorine
- @atom:cl 35.45 # Chlorine
- @atom:br 79.90 # Bromine
- @atom:i 126.9 # Iodine
- @atom:n 14.01 # Sp2 nitrogen in amide groups
- @atom:n1 14.01 # Sp N
- @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms
- @atom:n3 14.01 # Sp3 N with three connected atoms
- @atom:n4 14.01 # Sp3 N with four connected atoms
- @atom:na 14.01 # Sp2 N with three connected atoms
- @atom:nb 14.01 # Sp2 N in pure aromatic systems
- @atom:nc 14.01 # Sp2 N in non-pure aromatic systems
- @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc
- @atom:ne 14.01 # Inner Sp2 N in conjugated systems
- @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne
- @atom:nh 14.01 # Amine N connected one or more aromatic rings
- @atom:no 14.01 # Nitro N
- @atom:o 16.00 # Oxygen with one connected atom
- @atom:oh 16.00 # Oxygen in hydroxyl group
- @atom:os 16.00 # Ether and ester oxygen
- @atom:ow 16.00 # Oxygen in water
- @atom:p2 30.97 # Phosphate with two connected atoms
- @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3
- @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2
- @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3
- @atom:pb 30.97 # Sp2 P in pure aromatic systems
- @atom:pc 30.97 # Sp2 P in non-pure aromatic systems
- @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc
- @atom:pe 30.97 # Inner Sp2 P in conjugated systems
- @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe
- @atom:px 30.97 # Special p4 in conjugated systems
- @atom:py 30.97 # Special p5 in conjugated systems
- @atom:s 32.06 # S with one connected atom
- @atom:s2 32.06 # S with two connected atom, involved at least one double bond
- @atom:s4 32.06 # S with three connected atoms
- @atom:s6 32.06 # S with four connected atoms
- @atom:sh 32.06 # Sp3 S connected with hydrogen
- @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether
- @atom:sx 32.06 # Special s4 in conjugated systems
- @atom:sy 32.06 # Special s6 in conjugated systems
- } # (end of masses)
-
- write_once("In Settings") {
- pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0157 2.47135304412 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0157 2.29317330049 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0157 2.11499355687 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0150 2.51055258772 # Spellmeyer, one electrowithdr. neighbor
- pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0150 2.42146271591 # Spellmeyer, two electrowithdr. neighbor
- pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0150 2.59964245953 # Spellmeyer
- pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0157 2.64953278775 # OPLS
- pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0157 1.06907846177 # !Ferguson base pair geom.
- pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0000 0.0 # OPLS Jorgensen, JACS,110,(1988),1657
- pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0157 1.06907846177 # same to hs (be careful !)
- pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0157 1.06907846177 # W. Cornell CH3SH --> CH3OH FEP
- pair_coeff @atom:hw @atom:hw lj/charmm/coul/long 0.0000 0.0 # OPLS Jorgensen, JACS,110,(1988),1657
- pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0157 1.95997717991 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.2100 2.95992190115 # OPLS
- pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.2104 3.06647338784 # OPLS
- pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.1700 3.00001234347 # OPLS ether
- pair_coeff @atom:ow @atom:ow lj/charmm/coul/long 0.1520 3.15075240658 # TIP3P water model
- pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.2100 3.39966950842 # cp C DLM 11/2007 well depth from OPLS replacing 0.0860
- pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0860 3.39966950842 # sp2 atom in the middle of C=CD-CD=C
- pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1094 3.39966950842 # OPLS
- pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.2100 3.39966950842 # DLM 12/2007 as c1
- pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.2100 3.39966950842 # DLM 12/2007 as c1
- pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0860 3.39966950842 # OPLS
- pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.1700 3.24999852378 # OPLS
- pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230;
- pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.061 3.11814551349 # Gough et al. JCC 13,(1992),963.
- pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.265 3.47094140587 # Fox, JPCB,102,8070,(98),flex.mdl CHCl3
- pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.420 3.59923082129 # Junmei, 2010
- pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.50 3.830864488 # Junmei, 2010
- } # (end of pair_coeffs)
-
- write_once("In Settings") {
- bond_coeff @bond:ow-hw harmonic 553.0 0.9572 # TIP3P_Water 1
- bond_coeff @bond:hw-hw harmonic 553.0 1.5136 # TIP3P_Water 1
- bond_coeff @bond:br-br harmonic 123.2 2.5420 # SOURCE1 4 0.0000
- bond_coeff @bond:br-c1 harmonic 352.7 1.7870 # SOURCE2 4 0.0024
- bond_coeff @bond:br-c2 harmonic 278.7 1.8830 # SOURCE1 31 0.0000
- bond_coeff @bond:br-c harmonic 240.3 1.9460 # SOURCE2 2 0.0285
- bond_coeff @bond:br-c3 harmonic 229.5 1.9660 # SOURCE1 100 0.0000
- bond_coeff @bond:br-ca harmonic 269.6 1.8970 # SOURCE1 127 0.0058
- bond_coeff @bond:br-cc harmonic 277.6 1.8847 # SOURCE4 39 0.0068
- bond_coeff @bond:br-cx harmonic 261.4 1.9100 # SOURCE1 8 0.0000
- bond_coeff @bond:br-i harmonic 142.4 2.6710 # SOURCE1 2 0.0245
- bond_coeff @bond:br-n1 harmonic 330.4 1.8600 # SOUECE3 1
- bond_coeff @bond:br-n2 harmonic 219.0 2.0380 # SOURCE3 5 0.1082
- bond_coeff @bond:br-n harmonic 320.2 1.8730 # SOURCE3 4 0.0046
- bond_coeff @bond:br-n3 harmonic 265.9 1.9520 # SOURCE3 2 0.0000
- bond_coeff @bond:br-n4 harmonic 282.4 1.9260 # SOURCE3 3 0.0013
- bond_coeff @bond:br-na harmonic 237.3 2.0020 # SOURCE3 7 0.2156
- bond_coeff @bond:br-nh harmonic 270.9 1.9440 # SOURCE3 1 0.0000
- bond_coeff @bond:br-no harmonic 191.0 2.1010 # SOURCE3 1 0.0000
- bond_coeff @bond:br-o harmonic 278.9 1.8000 # SOUECE3 1
- bond_coeff @bond:br-oh harmonic 237.2 1.8660 # SOURCE3 1 0.0000
- bond_coeff @bond:br-os harmonic 225.6 1.8870 # SOURCE3 2 0.0000
- bond_coeff @bond:br-p2 harmonic 174.3 2.2100 # SOURCE3 9 0.0510
- bond_coeff @bond:br-p3 harmonic 167.0 2.2310 # SOURCE3 3 0.0101
- bond_coeff @bond:br-p4 harmonic 188.8 2.1710 # SOUECE3 1
- bond_coeff @bond:br-p5 harmonic 179.3 2.1960 # SOURCE3 3 0.0099
- bond_coeff @bond:br-s harmonic 170.6 2.2200 # SOUECE3 1
- bond_coeff @bond:br-s4 harmonic 134.3 2.3410 # SOURCE3 1 0.0000
- bond_coeff @bond:br-s6 harmonic 172.7 2.2140 # SOURCE3 3 0.0443
- bond_coeff @bond:br-sh harmonic 174.4 2.2090 # SOURCE3 1 0.0000
- bond_coeff @bond:br-ss harmonic 176.6 2.2030 # SOURCE3 3 0.0035
- bond_coeff @bond:c1-c1 harmonic 986.2 1.1810 # SOURCE1 265 0.0031
- bond_coeff @bond:c1-c2 harmonic 625.0 1.3070 # SOURCE1 18 0.0000
- bond_coeff @bond:c1-c3 harmonic 368.3 1.4700 # SOURCE1 215 0.0017
- bond_coeff @bond:c1-ca harmonic 404.1 1.4400 # SOUECE3 1
- bond_coeff @bond:c1-ce harmonic 607.4 1.3153 # SOURCE4 6 0.0086
- bond_coeff @bond:c1-cg harmonic 845.8 1.2220 # SOURCE3 22 0.0101
- bond_coeff @bond:c1-ch harmonic 845.8 1.2220 # SOURCE3 22 same_as_c1-cg
- bond_coeff @bond:c1-cl harmonic 419.7 1.6310 # SOURCE2 6 0.0050
- bond_coeff @bond:c1-cx harmonic 399.1 1.4440 # SOURCE1 38 0.0000
- bond_coeff @bond:c1-f harmonic 469.4 1.2700 # SOURCE2 2 0.0085
- bond_coeff @bond:c1-ha harmonic 375.9 1.0660 # SOURCE3 63 0.0035
- bond_coeff @bond:c1-hc harmonic 385.6 1.0600 # SOUECE3 1
- bond_coeff @bond:c1-i harmonic 318.8 1.9890 # SOURCE2 4 0.0032
- bond_coeff @bond:c1-n1 harmonic 1014.5 1.1380 # SOURCE1 170 0.0055
- bond_coeff @bond:c1-n2 harmonic 769.8 1.2100 # SOURCE3 5 0.0115
- bond_coeff @bond:c1-n3 harmonic 409.8 1.3920 # SOURCE2 1 0.0000
- bond_coeff @bond:c1-n4 harmonic 378.2 1.4170 # SOURCE3 3 0.0032
- bond_coeff @bond:c1-n harmonic 503.0 1.3300 # SOUECE3 1
- bond_coeff @bond:c1-na harmonic 452.0 1.3620 # SOURCE3 8 0.0034
- bond_coeff @bond:c1-ne harmonic 803.3 1.1986 # SOURCE4 10 0.0088
- bond_coeff @bond:c1-nf harmonic 803.3 1.1986 # SOURCE4 10 same_as_c1-ne
- bond_coeff @bond:c1-nh harmonic 485.0 1.3408 # SOURCE4 11 0.0037
- bond_coeff @bond:c1-no harmonic 393.0 1.4050 # SOURCE3 3 0.0005
- bond_coeff @bond:c1-o harmonic 777.0 1.1660 # SOURCE2 9 0.0052
- bond_coeff @bond:c1-oh harmonic 435.6 1.3260 # SOURCE3 1 0.0000
- bond_coeff @bond:c1-os harmonic 437.1 1.3250 # SOURCE3 3 0.0148
- bond_coeff @bond:c1-p2 harmonic 289.3 1.7700 # SOUECE3 1
- bond_coeff @bond:c1-p3 harmonic 275.1 1.7900 # SOUECE3 1
- bond_coeff @bond:c1-p4 harmonic 275.1 1.7900 # SOUECE3 1
- bond_coeff @bond:c1-p5 harmonic 302.2 1.7530 # SOURCE3 2 0.0000
- bond_coeff @bond:c1-s2 harmonic 410.0 1.5950 # SOURCE3 1 0.0000
- bond_coeff @bond:c1-s harmonic 371.8 1.6300 # SOURCE1 14 0.0000
- bond_coeff @bond:c1-s4 harmonic 272.9 1.7460 # SOURCE3 2 0.0000
- bond_coeff @bond:c1-s6 harmonic 290.4 1.7220 # SOURCE3 2 0.0000
- bond_coeff @bond:c1-sh harmonic 324.5 1.6800 # SOUECE3 1
- bond_coeff @bond:c1-ss harmonic 325.4 1.6790 # SOURCE1 10 0.0000
- bond_coeff @bond:c2-c2 harmonic 589.7 1.3240 # SOURCE1 974 0.0096
- bond_coeff @bond:c2-c3 harmonic 328.3 1.5080 # SOURCE1 2536 0.0021
- bond_coeff @bond:c2-ca harmonic 357.2 1.4800 # SOUECE3 1
- bond_coeff @bond:c2-cc harmonic 522.6 1.3600 # SOURCE1 771 0.0185
- bond_coeff @bond:c2-cd harmonic 522.6 1.3600 # SOURCE1 771 0.0185
- bond_coeff @bond:c2-ce harmonic 560.5 1.3390 # SOURCE3 62 0.0128
- bond_coeff @bond:c2-cf harmonic 560.5 1.3390 # SOURCE3 62 same_as_c2-ce
- bond_coeff @bond:c2-cl harmonic 328.8 1.7220 # SOURCE1 163 0.0098
- bond_coeff @bond:c2-cu harmonic 573.9 1.3320 # SOURCE2 1 0.0000
- bond_coeff @bond:c2-cx harmonic 353.3 1.4836 # SOURCE4 26 0.0064
- bond_coeff @bond:c2-cy harmonic 331.7 1.5046 # SOURCE4 9 0.0053
- bond_coeff @bond:c2-f harmonic 368.7 1.3400 # SOURCE1 34 0.0000
- bond_coeff @bond:c2-h4 harmonic 348.6 1.0840 # SOURCE3 40 0.0058
- bond_coeff @bond:c2-h5 harmonic 338.0 1.0915 # SOURCE4 42 0.0017
- bond_coeff @bond:c2-ha harmonic 344.3 1.0870 # SOURCE3 797 0.0046
- bond_coeff @bond:c2-hc harmonic 344.3 1.0870 # SOURCE3 789 0.0046
- bond_coeff @bond:c2-hx harmonic 350.1 1.0830 # SOURCE3 3 0.0008
- bond_coeff @bond:c2-i harmonic 223.2 2.1530 # SOURCE3 2 0.0000
- bond_coeff @bond:c2-n1 harmonic 546.0 1.3060 # SOURCE3 4 0.0161
- bond_coeff @bond:c2-n2 harmonic 581.1 1.2880 # SOURCE1 103 0.0100
- bond_coeff @bond:c2-n3 harmonic 486.3 1.3400 # SOUECE3 1
- bond_coeff @bond:c2-n harmonic 390.5 1.4070 # SOURCE3 9 0.0124
- bond_coeff @bond:c2-n4 harmonic 309.1 1.4820 # SOURCE3 5 0.0064
- bond_coeff @bond:c2-na harmonic 411.1 1.3910 # SOURCE3 31 0.0289
- bond_coeff @bond:c2-nc harmonic 533.0 1.3130 # SOURCE1 99 0.0095
- bond_coeff @bond:c2-nd harmonic 533.0 1.3130 # SOURCE1 99 same_as_c2-nc
- bond_coeff @bond:c2-ne harmonic 597.7 1.2800 # SOURCE3 37 0.0110
- bond_coeff @bond:c2-nf harmonic 597.7 1.2800 # SOURCE3 37 same_as_c2-ne
- bond_coeff @bond:c2-nh harmonic 462.6 1.3550 # SOURCE3 38 0.0413
- bond_coeff @bond:c2-no harmonic 345.6 1.4457 # SOURCE4 7 0.0087
- bond_coeff @bond:c2-o harmonic 623.6 1.2244 # SOURCE4 15 0.0036
- bond_coeff @bond:c2-oh harmonic 425.4 1.3330 # SOURCE1 53 0.0000
- bond_coeff @bond:c2-os harmonic 392.6 1.3570 # SOURCE1 315 0.0097
- bond_coeff @bond:c2-p2 harmonic 375.9 1.6700 # SOURCE3 62 0.0147
- bond_coeff @bond:c2-p3 harmonic 246.6 1.8340 # SOURCE3 5 0.0042
- bond_coeff @bond:c2-p4 harmonic 254.0 1.8220 # SOUECE3 1
- bond_coeff @bond:c2-p5 harmonic 228.2 1.8658 # SOURCE4 5 0.0025
- bond_coeff @bond:c2-pe harmonic 355.3 1.6910 # SOURCE3 52 0.0542
- bond_coeff @bond:c2-pf harmonic 355.3 1.6910 # SOURCE3 52 same_as_c2-pe
- bond_coeff @bond:c2-s2 harmonic 393.1 1.6100 # SOURCE2 1 0.0000
- bond_coeff @bond:c2-s harmonic 281.5 1.7340 # SOURCE3 4 0.0034
- bond_coeff @bond:c2-s4 harmonic 263.2 1.7600 # SOUECE3 1
- bond_coeff @bond:c2-s6 harmonic 263.2 1.7600 # SOUECE3 1
- bond_coeff @bond:c2-sh harmonic 252.0 1.7771 # SOURCE4 5 0.0037
- bond_coeff @bond:c2-ss harmonic 280.0 1.7360 # SOURCE1 209 0.0155
- bond_coeff @bond:c3-c3 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048
- bond_coeff @bond:c3-ca harmonic 323.5 1.5130 # SOURCE1 1813 0.0000
- bond_coeff @bond:c3-cc harmonic 337.3 1.4990 # SOURCE3 50 0.0096
- bond_coeff @bond:c3-cd harmonic 337.3 1.4990 # SOURCE3 50 0.0096
- bond_coeff @bond:c3-ce harmonic 331.3 1.5050 # SOURCE3 9 0.0024
- bond_coeff @bond:c3-cf harmonic 331.3 1.5050 # SOURCE3 9 same_as_c3-ce
- bond_coeff @bond:c3-cl harmonic 279.0 1.7860 # SOURCE1 267 0.0194
- bond_coeff @bond:c3-cu harmonic 359.4 1.4780 # SOURCE1 7 0.0000
- bond_coeff @bond:c3-cv harmonic 347.6 1.4890 # SOURCE1 11 0.0000
- bond_coeff @bond:c3-cx harmonic 322.5 1.5140 # SOURCE1 712 0.0045
- bond_coeff @bond:c3-cy harmonic 308.5 1.5290 # SOURCE1 376 0.0000
- bond_coeff @bond:c3-f harmonic 363.8 1.3440 # SOURCE1 617 0.0281
- bond_coeff @bond:c3-h1 harmonic 335.9 1.0930 # SOURCE3 2175 0.0082
- bond_coeff @bond:c3-h2 harmonic 326.4 1.1000 # SOURCE3 66 0.0280
- bond_coeff @bond:c3-h3 harmonic 333.4 1.0948 # SOURCE4 25 0.0026
- bond_coeff @bond:c3-hc harmonic 337.3 1.0920 # SOURCE3 2815 0.0059
- bond_coeff @bond:c3-hx harmonic 338.7 1.0910 # SOURCE3 146 0.0066
- bond_coeff @bond:c3-i harmonic 219.1 2.1620 # SOURCE1 15 0.0000
- bond_coeff @bond:c3-n1 harmonic 325.1 1.4700 # SOURCE3 0
- bond_coeff @bond:c3-n2 harmonic 313.8 1.4770 # SOURCE1 129 0.0138
- bond_coeff @bond:c3-n harmonic 330.6 1.4600 # SOURCE1 187 0.0079
- bond_coeff @bond:c3-n3 harmonic 320.6 1.4700 # SOURCE1 1678 0.0017
- bond_coeff @bond:c3-n4 harmonic 293.6 1.4990 # SOURCE1 1370 0.0000
- bond_coeff @bond:c3-na harmonic 334.7 1.4560 # SOURCE3 23 0.0119
- bond_coeff @bond:c3-nc harmonic 334.7 1.4560 # SOURCE3 9 0.0109
- bond_coeff @bond:c3-nd harmonic 334.7 1.4560 # SOURCE3 9 same_as_c3-nc
- bond_coeff @bond:c3-nh harmonic 332.7 1.4580 # SOURCE3 27 0.0085
- bond_coeff @bond:c3-no harmonic 265.4 1.5330 # SOURCE1 83 0.0212
- bond_coeff @bond:c3-o harmonic 449.9 1.3165 # SOURCE4 8 0.0193
- bond_coeff @bond:c3-oh harmonic 314.1 1.4260 # SOURCE1 914 0.0129
- bond_coeff @bond:c3-os harmonic 301.5 1.4390 # SOURCE1 3123 0.0126
- bond_coeff @bond:c3-p2 harmonic 234.3 1.8550 # SOURCE3 9 0.0125
- bond_coeff @bond:c3-p3 harmonic 240.6 1.8440 # SOURCE3 109 0.0107
- bond_coeff @bond:c3-p4 harmonic 247.2 1.8330 # SOURCE3 29 0.0138
- bond_coeff @bond:c3-p5 harmonic 259.7 1.8130 # SOURCE1 84 0.0000
- bond_coeff @bond:c3-px harmonic 252.7 1.8240 # SOURCE3 28 0.0098
- bond_coeff @bond:c3-py harmonic 259.7 1.8130 # SOURCE3 13 0.0163
- bond_coeff @bond:c3-s harmonic 212.9 1.8450 # SOURCE3 4 0.0185
- bond_coeff @bond:c3-s4 harmonic 233.8 1.8070 # SOURCE1 139 0.0023
- bond_coeff @bond:c3-s6 harmonic 254.0 1.7740 # SOURCE1 118 0.0103
- bond_coeff @bond:c3-sh harmonic 225.3 1.8220 # SOURCE3 12 0.0051
- bond_coeff @bond:c3-ss harmonic 225.8 1.8210 # SOURCE1 358 0.0075
- bond_coeff @bond:c3-sx harmonic 232.6 1.8090 # SOURCE3 30 0.0067
- bond_coeff @bond:c3-sy harmonic 248.9 1.7820 # SOURCE3 31 0.0039
- bond_coeff @bond:ca-ca harmonic 478.4 1.3870 # SOURCE1 6228 0.0147
- bond_coeff @bond:ca-cc harmonic 411.7 1.4340 # SOURCE1 80 0.0000
- bond_coeff @bond:ca-cd harmonic 411.7 1.4340 # SOURCE1 80 0.0000
- bond_coeff @bond:ca-ce harmonic 366.0 1.4720 # SOURCE1 71 0.0030
- bond_coeff @bond:ca-cf harmonic 366.0 1.4720 # SOURCE1 71 0.0030
- bond_coeff @bond:ca-cg harmonic 406.6 1.4380 # SOURCE1 71 0.0045
- bond_coeff @bond:ca-ch harmonic 406.6 1.4380 # SOURCE1 71 0.0045
- bond_coeff @bond:ca-cl harmonic 322.8 1.7290 # SOURCE1 704 0.0095
- bond_coeff @bond:ca-cp harmonic 461.8 1.3980 # CORR 28
- bond_coeff @bond:ca-cq harmonic 461.8 1.3980 # CORR 28
- bond_coeff @bond:ca-cx harmonic 350.8 1.4860 # SOURCE1 98 0.0118
- bond_coeff @bond:ca-cy harmonic 323.0 1.5135 # SOURCE4 8 0.0043
- bond_coeff @bond:ca-f harmonic 363.8 1.3440 # SOURCE1 205 0.0089
- bond_coeff @bond:ca-h4 harmonic 342.9 1.0880 # SOURCE3 57 0.0026
- bond_coeff @bond:ca-h5 harmonic 347.2 1.0850 # SOURCE3 15 0.0048
- bond_coeff @bond:ca-ha harmonic 344.3 1.0870 # SOURCE3 1496 0.0045
- bond_coeff @bond:ca-i harmonic 252.4 2.0950 # SOURCE1 51 0.0000
- bond_coeff @bond:ca-n1 harmonic 398.1 1.4000 # SOURCE3 0
- bond_coeff @bond:ca-n2 harmonic 551.6 1.3030 # SOURCE4 7 0.0058
- bond_coeff @bond:ca-n harmonic 372.3 1.4220 # SOURCE3 9 0.0098
- bond_coeff @bond:ca-n4 harmonic 325.6 1.4650 # SOURCE1 23 0.0000
- bond_coeff @bond:ca-na harmonic 470.3 1.3500 # SOURCE1 150 0.0103
- bond_coeff @bond:ca-nb harmonic 483.1 1.3420 # SOURCE3 104 0.0076
- bond_coeff @bond:ca-nc harmonic 492.9 1.3360 # SOURCE1 1826 0.0020
- bond_coeff @bond:ca-nd harmonic 492.9 1.3360 # SOURCE1 1826 0.0020
- bond_coeff @bond:ca-ne harmonic 361.8 1.4310 # SOURCE1 52 0.0000
- bond_coeff @bond:ca-nf harmonic 361.8 1.4310 # SOURCE1 52 0.0000
- bond_coeff @bond:ca-nh harmonic 449.0 1.3640 # SOURCE1 137 0.0085
- bond_coeff @bond:ca-no harmonic 322.6 1.4680 # SOURCE1 556 0.0000
- bond_coeff @bond:ca-o harmonic 610.0 1.2304 # SOURCE4 5 0.0026
- bond_coeff @bond:ca-oh harmonic 386.1 1.3620 # SOURCE1 551 0.0000
- bond_coeff @bond:ca-os harmonic 372.4 1.3730 # SOURCE1 1092 0.0071
- bond_coeff @bond:ca-p2 harmonic 243.0 1.8400 # SOUECE3 1
- bond_coeff @bond:ca-p3 harmonic 252.7 1.8240 # SOURCE1 145 0.0187
- bond_coeff @bond:ca-p4 harmonic 264.3 1.8060 # SOUECE3 1
- bond_coeff @bond:ca-p5 harmonic 271.6 1.7950 # SOURCE1 571 0.0028
- bond_coeff @bond:ca-pe harmonic 249.6 1.8290 # SOURCE3 10 0.0042
- bond_coeff @bond:ca-pf harmonic 249.6 1.8290 # SOURCE3 10 0.0042
- bond_coeff @bond:ca-px harmonic 252.1 1.8250 # SOURCE3 5 0.0168
- bond_coeff @bond:ca-py harmonic 268.3 1.7999 # SOURCE4 5 0.0072
- bond_coeff @bond:ca-s harmonic 277.9 1.7390 # SOURCE3 2 0.0000
- bond_coeff @bond:ca-s4 harmonic 245.2 1.7880 # SOURCE1 51 0.0048
- bond_coeff @bond:ca-s6 harmonic 263.9 1.7590 # SOURCE1 229 0.0036
- bond_coeff @bond:ca-sh harmonic 251.3 1.7783 # SOURCE4 12 0.0041
- bond_coeff @bond:ca-ss harmonic 256.6 1.7700 # SOURCE1 297 0.0041
- bond_coeff @bond:ca-sx harmonic 223.5 1.8252 # SOURCE4 24 0.0032
- bond_coeff @bond:ca-sy harmonic 247.7 1.7840 # SOURCE3 13 0.0094
- bond_coeff @bond:c-c1 harmonic 379.8 1.4600 # SOUECE3 1
- bond_coeff @bond:c-c2 harmonic 449.9 1.4060 # SOURCE3 2 0.0370
- bond_coeff @bond:c-c harmonic 290.1 1.5500 # SOURCE1 31 0.0100
- bond_coeff @bond:c-c3 harmonic 328.3 1.5080 # SOURCE1 2949 0.0060
- bond_coeff @bond:c-ca harmonic 349.7 1.4870 # SOURCE1 480 0.0055
- bond_coeff @bond:c-cc harmonic 377.4 1.4620 # SOURCE3 132 0.0210
- bond_coeff @bond:cc-cc harmonic 418.3 1.4290 # SOURCE1 740 0.0069
- bond_coeff @bond:cc-cd harmonic 504.0 1.3710 # SOURCE3 523 0.0217
- bond_coeff @bond:cc-ce harmonic 387.9 1.4532 # CORR 249
- bond_coeff @bond:cc-cf harmonic 511.3 1.3666 # CORR 70
- bond_coeff @bond:cc-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000
- bond_coeff @bond:cc-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000
- bond_coeff @bond:cc-cl harmonic 317.1 1.7359 # CORR 66
- bond_coeff @bond:cc-cx harmonic 366.6 1.4715 # CORR 24
- bond_coeff @bond:c-cd harmonic 377.4 1.4620 # SOURCE3 132 0.0210
- bond_coeff @bond:c-ce harmonic 363.8 1.4740 # SOURCE1 601 0.0105
- bond_coeff @bond:c-cf harmonic 363.8 1.4740 # SOURCE1 601 0.0105
- bond_coeff @bond:cc-f harmonic 368.6 1.3401 # SOURCE4 24 0.0034
- bond_coeff @bond:c-cg harmonic 389.3 1.4520 # SOURCE3 2 0.0000
- bond_coeff @bond:c-ch harmonic 389.3 1.4520 # SOURCE3 2 same_as_c-cg
- bond_coeff @bond:cc-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037
- bond_coeff @bond:cc-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051
- bond_coeff @bond:cc-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039
- bond_coeff @bond:c-cl harmonic 293.5 1.7660 # SOURCE3 6 0.0250
- bond_coeff @bond:cc-n2 harmonic 573.8 1.2917 # CORR 81
- bond_coeff @bond:cc-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109
- bond_coeff @bond:cc-n4 harmonic 299.0 1.4930 # SOURCE4 7 0.0148
- bond_coeff @bond:cc-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144
- bond_coeff @bond:cc-nc harmonic 431.6 1.3760 # SOURCE1 88 0.0000
- bond_coeff @bond:cc-nd harmonic 494.6 1.3350 # SOURCE3 203 0.0239
- bond_coeff @bond:cc-ne harmonic 427.4 1.3790 # SOURCE4 30 0.0126
- bond_coeff @bond:cc-nf harmonic 565.4 1.2960 # CORR 23
- bond_coeff @bond:cc-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040
- bond_coeff @bond:cc-no harmonic 367.4 1.4262 # SOURCE4 133 0.0061
- bond_coeff @bond:cc-oh harmonic 408.5 1.3451 # CORR 121
- bond_coeff @bond:cc-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192
- bond_coeff @bond:cc-pd harmonic 318.2 1.7330 # SOURCE3 84 0.0161
- bond_coeff @bond:cc-sh harmonic 257.9 1.7681 # SOURCE4 8 0.0027
- bond_coeff @bond:cc-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194
- bond_coeff @bond:cc-sx harmonic 231.3 1.8113 # SOURCE4 16 0.0050
- bond_coeff @bond:cc-sy harmonic 248.1 1.7834 # CORR 55
- bond_coeff @bond:c-cu harmonic 441.4 1.4120 # SOURCE2 1 0.0000
- bond_coeff @bond:c-cx harmonic 350.8 1.4860 # SOURCE1 105 0.0000
- bond_coeff @bond:c-cy harmonic 308.5 1.5290 # SOURCE1 18 0.0000
- bond_coeff @bond:cd-cd harmonic 418.3 1.4290 # SOURCE1 740 0.0069
- bond_coeff @bond:cd-ce harmonic 511.3 1.3666 # CORR 70
- bond_coeff @bond:cd-cf harmonic 387.9 1.4532 # CORR 249
- bond_coeff @bond:cd-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000
- bond_coeff @bond:cd-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000
- bond_coeff @bond:cd-cl harmonic 317.1 1.7359 # CORR 66
- bond_coeff @bond:cd-cx harmonic 366.6 1.4715 # CORR 24
- bond_coeff @bond:cd-cy harmonic 330.9 1.5054 # SOURCE4 10 0.0008
- bond_coeff @bond:cd-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037
- bond_coeff @bond:cd-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051
- bond_coeff @bond:cd-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039
- bond_coeff @bond:cd-n2 harmonic 573.8 1.2917 # CORR 81
- bond_coeff @bond:cd-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109
- bond_coeff @bond:cd-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144
- bond_coeff @bond:cd-nc harmonic 494.6 1.3350 # SOURCE3 203 0.0239
- bond_coeff @bond:cd-nd harmonic 431.6 1.3760 # SOURCE1 88 0.0000
- bond_coeff @bond:cd-ne harmonic 565.4 1.2960 # CORR 23
- bond_coeff @bond:cd-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040
- bond_coeff @bond:cd-oh harmonic 408.5 1.3451 # CORR 121
- bond_coeff @bond:cd-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192
- bond_coeff @bond:cd-pc harmonic 318.2 1.7330 # SOURCE3 84 same_as_cc-pd
- bond_coeff @bond:cd-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194
- bond_coeff @bond:cd-sy harmonic 248.1 1.7834 # CORR 55
- bond_coeff @bond:ce-ce harmonic 390.5 1.4510 # SOURCE1 66 0.0060
- bond_coeff @bond:ce-cf harmonic 562.4 1.3380 # SOURCE1 543 0.0045
- bond_coeff @bond:ce-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000
- bond_coeff @bond:ce-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000
- bond_coeff @bond:ce-cl harmonic 292.6 1.7671 # SOURCE4 24 0.0062
- bond_coeff @bond:ce-cx harmonic 337.0 1.4993 # SOURCE4 5 0.0066
- bond_coeff @bond:ce-cy harmonic 323.0 1.5135 # SOURCE4 17 0.0024
- bond_coeff @bond:ce-h4 harmonic 337.4 1.0919 # CORR 144
- bond_coeff @bond:ce-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056
- bond_coeff @bond:ce-n1 harmonic 536.1 1.3113 # CORR 13
- bond_coeff @bond:ce-n2 harmonic 599.8 1.2790 # SOURCE1 75 0.0000
- bond_coeff @bond:ce-n harmonic 368.9 1.4249 # CORR 136
- bond_coeff @bond:ce-na harmonic 373.8 1.4207 # SOURCE4 5 0.0051
- bond_coeff @bond:ce-ne harmonic 381.8 1.4140 # SOURCE3 7 0.0103
- bond_coeff @bond:ce-nf harmonic 574.0 1.2916 # CORR 42
- bond_coeff @bond:ce-nh harmonic 412.3 1.3901 # CORR 168
- bond_coeff @bond:ce-oh harmonic 402.9 1.3493 # CORR 37
- bond_coeff @bond:ce-os harmonic 372.8 1.3727 # CORR 45
- bond_coeff @bond:ce-p2 harmonic 259.1 1.8140 # SOUECE3 1
- bond_coeff @bond:ce-pe harmonic 256.5 1.8180 # SOURCE3 8 0.0108
- bond_coeff @bond:ce-px harmonic 254.6 1.8210 # SOURCE3 6 0.0046
- bond_coeff @bond:ce-py harmonic 272.3 1.7940 # SOURCE3 5 0.0045
- bond_coeff @bond:ce-s harmonic 324.5 1.6800 # SOUECE3 1
- bond_coeff @bond:ce-ss harmonic 243.6 1.7906 # SOURCE4 10 0.0064
- bond_coeff @bond:ce-sx harmonic 239.7 1.7970 # SOURCE3 5 0.0082
- bond_coeff @bond:ce-sy harmonic 248.9 1.7820 # SOURCE3 5 0.0114
- bond_coeff @bond:c-f harmonic 387.9 1.3250 # SOURCE2 6 0.0147
- bond_coeff @bond:cf-cf harmonic 390.5 1.4510 # SOURCE1 66 0.0060
- bond_coeff @bond:cf-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000
- bond_coeff @bond:cf-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000
- bond_coeff @bond:cf-h4 harmonic 337.4 1.0919 # CORR 144
- bond_coeff @bond:cf-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056
- bond_coeff @bond:cf-n1 harmonic 536.1 1.3113 # CORR 13
- bond_coeff @bond:cf-n2 harmonic 599.8 1.2790 # SOURCE1 75 same_as_ce-n2
- bond_coeff @bond:cf-n harmonic 368.9 1.4249 # CORR 136
- bond_coeff @bond:cf-ne harmonic 574.0 1.2916 # CORR 42
- bond_coeff @bond:cf-nf harmonic 381.8 1.4140 # SOURCE3 7 same_as_ce-ne
- bond_coeff @bond:cf-nh harmonic 412.3 1.3901 # CORR 168
- bond_coeff @bond:cf-oh harmonic 402.9 1.3493 # CORR 37
- bond_coeff @bond:cf-os harmonic 372.8 1.3727 # CORR 45
- bond_coeff @bond:cf-p2 harmonic 259.1 1.8140 # SOUECE3 1 same_as_ce-p2
- bond_coeff @bond:cf-pf harmonic 256.5 1.8180 # SOURCE3 8 same_as_ce-pe
- bond_coeff @bond:cf-px harmonic 254.6 1.8210 # SOURCE3 6 same_as_ce-px
- bond_coeff @bond:cf-py harmonic 272.3 1.7940 # SOURCE3 5 same_as_ce-py
- bond_coeff @bond:cf-s harmonic 324.5 1.6800 # SOUECE3 1 same_as_ce-s
- bond_coeff @bond:cf-sx harmonic 239.7 1.7970 # SOURCE3 5 same_as_ce-sx
- bond_coeff @bond:cf-sy harmonic 248.9 1.7820 # SOURCE3 5 same_as_ce-sy
- bond_coeff @bond:cg-cg harmonic 494.2 1.3770 # SOURCE1 42 0.0000
- bond_coeff @bond:cg-ch harmonic 949.5 1.1910 # SOURCE1 80 0.0015
- bond_coeff @bond:cg-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018
- bond_coeff @bond:cg-ne harmonic 509.5 1.3262 # SOURCE4 17 0.0009
- bond_coeff @bond:cg-pe harmonic 429.8 1.6210 # SOURCE3 11 0.2008
- bond_coeff @bond:c-h4 harmonic 310.5 1.1123 # SOURCE4 125 0.0023
- bond_coeff @bond:c-h5 harmonic 319.4 1.1053 # SOURCE4 42 0.0028
- bond_coeff @bond:c-ha harmonic 325.1 1.1010 # SOURCE3 53 0.0102
- bond_coeff @bond:ch-ch harmonic 494.2 1.3770 # SOURCE1 42 0.0000
- bond_coeff @bond:ch-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018
- bond_coeff @bond:ch-nf harmonic 509.5 1.3262 # SOURCE4 17 same_as_cg-ne
- bond_coeff @bond:ch-pf harmonic 429.8 1.6210 # SOURCE3 11 same_as_cg-pe
- bond_coeff @bond:c-i harmonic 198.9 2.2090 # SOURCE3 4 0.0365
- bond_coeff @bond:cl-cl harmonic 143.3 2.2670 # SOURCE1 2 0.0395
- bond_coeff @bond:cl-cx harmonic 301.8 1.7550 # SOURCE1 64 0.0000
- bond_coeff @bond:cl-cy harmonic 292.0 1.7680 # SOURCE2 2 0.0070
- bond_coeff @bond:cl-f harmonic 298.6 1.6480 # SOURCE2 2 0.0500
- bond_coeff @bond:cl-i harmonic 163.5 2.5500 # SOURCE1 6 0.0893
- bond_coeff @bond:cl-n1 harmonic 431.6 1.6300 # SOUECE3 1
- bond_coeff @bond:cl-n2 harmonic 263.4 1.8190 # SOURCE3 6 0.1020
- bond_coeff @bond:cl-n3 harmonic 290.4 1.7800 # SOURCE4 5 0.0021
- bond_coeff @bond:cl-n harmonic 344.2 1.7140 # SOURCE4 5 0.0005
- bond_coeff @bond:cl-n4 harmonic 311.1 1.7530 # SOURCE3 4 0.0098
- bond_coeff @bond:cl-na harmonic 253.2 1.8350 # SOURCE3 7 0.2083
- bond_coeff @bond:cl-nh harmonic 303.2 1.7630 # SOURCE3 1 0.0000
- bond_coeff @bond:cl-no harmonic 250.1 1.8400 # SOURCE2 1 0.0000
- bond_coeff @bond:cl-o harmonic 557.6 1.4830 # SOURCE3 4 0.0000
- bond_coeff @bond:cl-oh harmonic 309.7 1.6900 # SOURCE2 1 0.0000
- bond_coeff @bond:cl-os harmonic 278.8 1.7300 # SOURCE3 4 0.0000
- bond_coeff @bond:cl-p2 harmonic 217.5 2.0700 # SOURCE3 6 0.0108
- bond_coeff @bond:cl-p3 harmonic 249.4 2.0080 # SOURCE1 111 0.0000
- bond_coeff @bond:cl-p4 harmonic 249.4 2.0080 # SOURCE1 111 0.0000
- bond_coeff @bond:cl-p5 harmonic 249.4 2.0080 # SOURCE1 111 0.0000
- bond_coeff @bond:cl-pb harmonic 255.6 1.9970 # SOURCE1 46 0.0000
- bond_coeff @bond:cl-s harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:cl-s2 harmonic 172.7 2.1610 # SOURCE2 1 0.0000
- bond_coeff @bond:cl-s4 harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:cl-s6 harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:cl-sh harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:cl-ss harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:cl-sx harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:cl-sy harmonic 208.7 2.0720 # SOURCE1 6 0.0000
- bond_coeff @bond:c-n2 harmonic 374.6 1.4200 # SOUECE3 1
- bond_coeff @bond:c-n4 harmonic 255.5 1.5460 # SOURCE3 4 0.0388
- bond_coeff @bond:c-n harmonic 478.2 1.3450 # SOURCE1 1235 0.0215
- bond_coeff @bond:c-nc harmonic 412.1 1.3906 # CORR 124
- bond_coeff @bond:c-nd harmonic 412.1 1.3906 # CORR 124
- bond_coeff @bond:c-ne harmonic 408.2 1.3932 # CORR 52
- bond_coeff @bond:c-nf harmonic 408.2 1.3932 # CORR 52
- bond_coeff @bond:c-no harmonic 260.1 1.5400 # SOUECE3 1
- bond_coeff @bond:c-o harmonic 648.0 1.2140 # SOURCE1 3682 0.0165
- bond_coeff @bond:c-oh harmonic 466.4 1.3060 # SOURCE1 271 0.0041
- bond_coeff @bond:c-os harmonic 411.3 1.3430 # SOURCE1 1044 0.0171
- bond_coeff @bond:c-p2 harmonic 210.3 1.9000 # SOUECE3 1
- bond_coeff @bond:c-p3 harmonic 219.0 1.8830 # SOURCE3 6 0.0129
- bond_coeff @bond:c-p4 harmonic 220.6 1.8800 # SOUECE3 1
- bond_coeff @bond:c-p5 harmonic 219.8 1.8815 # SOURCE4 11 0.0078
- bond_coeff @bond:cp-cp harmonic 346.5 1.4900 # SOURCE1 242 0.0010
- bond_coeff @bond:cp-cq harmonic 419.3 1.4282 # SOURCE4 7 0.0034
- bond_coeff @bond:c-pe harmonic 204.9 1.9110 # SOURCE3 3 0.0025
- bond_coeff @bond:c-pf harmonic 204.9 1.9110 # SOURCE3 3 same_as_c-pe
- bond_coeff @bond:cp-na harmonic 420.5 1.3840 # SOURCE4 7 0.0181
- bond_coeff @bond:cp-nb harmonic 486.7 1.3398 # SOURCE4 70 0.0062
- bond_coeff @bond:c-px harmonic 208.3 1.9040 # SOURCE3 1 0.0000
- bond_coeff @bond:c-py harmonic 227.6 1.8670 # SOURCE3 6 0.0199
- bond_coeff @bond:cq-cq harmonic 346.5 1.4900 # SOURCE1 242 0.0010
- bond_coeff @bond:c-s harmonic 328.9 1.6750 # SOURCE1 401 0.0128
- bond_coeff @bond:c-s4 harmonic 200.4 1.8700 # SOUECE3 1
- bond_coeff @bond:c-s6 harmonic 200.4 1.8700 # SOUECE3 1
- bond_coeff @bond:c-sh harmonic 249.6 1.7810 # SOURCE3 6 0.0171
- bond_coeff @bond:c-ss harmonic 261.9 1.7620 # SOURCE1 20 0.0000
- bond_coeff @bond:c-sx harmonic 193.3 1.8850 # SOURCE3 5 0.0088
- bond_coeff @bond:c-sy harmonic 202.8 1.8650 # SOURCE3 5 0.0085
- bond_coeff @bond:cu-cu harmonic 653.7 1.2940 # SOURCE1 10 0.0000
- bond_coeff @bond:cu-cx harmonic 327.3 1.5090 # SOURCE1 20 0.0000
- bond_coeff @bond:cu-ha harmonic 353.0 1.0810 # SOURCE2 3 0.0111
- bond_coeff @bond:cv-cv harmonic 568.1 1.3350 # SOURCE1 25 0.0000
- bond_coeff @bond:cv-cy harmonic 323.5 1.5130 # SOURCE1 50 0.0000
- bond_coeff @bond:cv-ha harmonic 344.3 1.0870 # SOURCE3 2 0.0000
- bond_coeff @bond:cx-cv harmonic 328.3 1.5080 # SOURCE1 2536 as
- bond_coeff @bond:cx-cx harmonic 337.3 1.4990 # SOURCE1 1204 0.0183
- bond_coeff @bond:cx-cy harmonic 321.5 1.5150 # SOURCE3 2 0.0000
- bond_coeff @bond:cx-f harmonic 347.2 1.3580 # SOURCE2 3 0.0050
- bond_coeff @bond:cx-h1 harmonic 344.3 1.0870 # SOURCE3 10 0.0017
- bond_coeff @bond:cx-h2 harmonic 350.1 1.0830 # SOURCE3 2 0.0000
- bond_coeff @bond:cx-hc harmonic 345.8 1.0860 # SOURCE3 44 0.0011
- bond_coeff @bond:cx-hx harmonic 347.2 1.0850 # SOURCE4 5 0.0002
- bond_coeff @bond:cx-n2 harmonic 309.1 1.4820 # SOURCE3 2 0.0000
- bond_coeff @bond:cx-n3 harmonic 318.7 1.4720 # SOURCE1 134 0.0000
- bond_coeff @bond:cx-n harmonic 350.6 1.4411 # SOURCE4 11 0.0092
- bond_coeff @bond:cx-na harmonic 329.0 1.4616 # SOURCE4 11 0.0016
- bond_coeff @bond:cx-nh harmonic 336.7 1.4541 # SOURCE4 83 0.0076
- bond_coeff @bond:cx-oh harmonic 387.4 1.3610 # SOURCE3 3 0.0018
- bond_coeff @bond:cx-os harmonic 320.1 1.4200 # SOURCE3 7 0.0222
- bond_coeff @bond:cx-p3 harmonic 227.6 1.8670 # SOURCE2 1 0.0000
- bond_coeff @bond:cx-s4 harmonic 225.3 1.8220 # SOURCE2 1 0.0000
- bond_coeff @bond:cx-s6 harmonic 283.7 1.7310 # SOURCE2 1 0.0000
- bond_coeff @bond:cx-ss harmonic 229.2 1.8150 # SOURCE2 1 0.0000
- bond_coeff @bond:cy-cy harmonic 286.8 1.5540 # SOURCE1 742 0.0041
- bond_coeff @bond:cy-f harmonic 355.5 1.3509 # SOURCE4 8 0.0047
- bond_coeff @bond:cy-h1 harmonic 330.4 1.0970 # SOURCE3 17 0.0058
- bond_coeff @bond:cy-h2 harmonic 335.8 1.0931 # SOURCE4 80 0.0019
- bond_coeff @bond:cy-hc harmonic 334.5 1.0940 # SOURCE3 63 0.0014
- bond_coeff @bond:cy-n harmonic 321.3 1.4693 # SOURCE4 250 0.0102
- bond_coeff @bond:cy-n3 harmonic 307.2 1.4840 # SOURCE1 21 0.0000
- bond_coeff @bond:cy-oh harmonic 325.2 1.4150 # SOURCE3 2 0.0000
- bond_coeff @bond:cy-os harmonic 308.6 1.4316 # SOURCE4 23 0.0136
- bond_coeff @bond:cy-s6 harmonic 209.6 1.8514 # SOURCE4 9 0.0166
- bond_coeff @bond:cy-ss harmonic 211.3 1.8481 # SOURCE4 78 0.0080
- bond_coeff @bond:cz-nh harmonic 487.8 1.3391 # SOURCE4 32 0.0045
- bond_coeff @bond:f-n1 harmonic 375.7 1.4100 # SOUECE3 1
- bond_coeff @bond:f-n2 harmonic 337.5 1.4440 # SOURCE3 5 0.0377
- bond_coeff @bond:f-n3 harmonic 380.6 1.4060 # SOURCE1 9 0.0000
- bond_coeff @bond:f-n harmonic 391.7 1.3970 # SOURCE3 3 0.0112
- bond_coeff @bond:f-n4 harmonic 526.8 1.3080 # SOURCE3 2 0.0000
- bond_coeff @bond:f-na harmonic 374.5 1.4110 # SOURCE3 7 0.0611
- bond_coeff @bond:f-nh harmonic 357.1 1.4260 # SOURCE3 3 0.0085
- bond_coeff @bond:f-no harmonic 314.4 1.4670 # SOURCE2 1 0.0000
- bond_coeff @bond:f-o harmonic 442.2 1.3300 # SOUECE3 1
- bond_coeff @bond:f-oh harmonic 305.4 1.4440 # SOURCE3 1 0.0000
- bond_coeff @bond:f-os harmonic 326.2 1.4230 # SOURCE3 2 0.0000
- bond_coeff @bond:f-p2 harmonic 287.3 1.5360 # SOURCE3 7 0.2054
- bond_coeff @bond:f-p3 harmonic 254.5 1.5780 # SOURCE2 8 0.0103
- bond_coeff @bond:f-p4 harmonic 246.0 1.5900 # SOUECE3 1
- bond_coeff @bond:f-p5 harmonic 253.8 1.5790 # SOURCE1 72 0.0000
- bond_coeff @bond:f-s2 harmonic 244.4 1.6430 # SOURCE2 1 0.0000
- bond_coeff @bond:f-s harmonic 233.3 1.6600 # SOUECE3 1
- bond_coeff @bond:f-s4 harmonic 282.4 1.5910 # SOURCE2 4 0.0065
- bond_coeff @bond:f-s6 harmonic 312.1 1.5560 # SOURCE2 5 0.0220
- bond_coeff @bond:f-sh harmonic 240.4 1.6490 # SOURCE3 1 0.0000
- bond_coeff @bond:f-ss harmonic 250.5 1.6340 # SOURCE3 3 0.0156
- bond_coeff @bond:hn-n1 harmonic 455.1 0.9860 # SOURCE2 1 0.0000
- bond_coeff @bond:hn-n2 harmonic 375.5 1.0290 # SOURCE3 108 0.0096
- bond_coeff @bond:hn-n3 harmonic 394.1 1.0180 # SOURCE3 157 0.0086
- bond_coeff @bond:hn-n harmonic 410.2 1.0090 # SOURCE3 149 0.0098
- bond_coeff @bond:hn-n4 harmonic 369.0 1.0330 # SOURCE3 264 0.0082
- bond_coeff @bond:hn-na harmonic 406.6 1.0110 # SOURCE3 46 0.0107
- bond_coeff @bond:hn-nh harmonic 401.2 1.0140 # SOURCE3 209 0.0091
- bond_coeff @bond:hn-no harmonic 385.6 1.0230 # SOURCE3 1 0.0000
- bond_coeff @bond:ho-o harmonic 357.9 0.9810 # SOURCE3 1 0.0000
- bond_coeff @bond:ho-oh harmonic 369.6 0.9740 # SOURCE3 367 0.0105
- bond_coeff @bond:hp-p2 harmonic 385.1 1.3360 # SOURCE3 87 0.1706
- bond_coeff @bond:hp-p3 harmonic 303.1 1.4090 # SOURCE3 101 0.0617
- bond_coeff @bond:hp-p4 harmonic 368.7 1.3490 # SOURCE3 17 0.1577
- bond_coeff @bond:hp-p5 harmonic 305.0 1.4070 # SOURCE3 7 0.0062
- bond_coeff @bond:hs-s harmonic 286.4 1.3530 # SOURCE3 1 0.0000
- bond_coeff @bond:hs-s4 harmonic 266.4 1.3750 # SOURCE3 5 0.0004
- bond_coeff @bond:hs-s6 harmonic 280.8 1.3590 # SOURCE3 5 0.0015
- bond_coeff @bond:hs-sh harmonic 302.2 1.3370 # SOURCE3 98 0.0486
- bond_coeff @bond:i-i harmonic 109.2 2.9170 # SOURCE1 1 0.0000
- bond_coeff @bond:i-n1 harmonic 302.1 2.0600 # SOUECE3 1
- bond_coeff @bond:i-n2 harmonic 182.6 2.3040 # SOURCE3 6 0.1186
- bond_coeff @bond:i-n harmonic 278.3 2.0980 # SOURCE3 5 0.0156
- bond_coeff @bond:i-n3 harmonic 231.8 2.1850 # SOURCE3 3 0.0437
- bond_coeff @bond:i-n4 harmonic 246.6 2.1550 # SOURCE3 3 0.0168
- bond_coeff @bond:i-na harmonic 260.5 2.1290 # SOURCE3 8 0.1276
- bond_coeff @bond:i-nh harmonic 249.2 2.1500 # SOURCE3 1 0.0000
- bond_coeff @bond:i-no harmonic 211.0 2.2310 # SOURCE3 1 0.0000
- bond_coeff @bond:i-o harmonic 323.8 1.9800 # SOUECE3 1
- bond_coeff @bond:i-oh harmonic 247.9 2.1010 # SOURCE3 2 0.0000
- bond_coeff @bond:i-os harmonic 233.6 2.1290 # SOURCE3 3 0.0146
- bond_coeff @bond:i-p2 harmonic 108.2 2.6430 # SOURCE3 6 0.0297
- bond_coeff @bond:i-p3 harmonic 123.6 2.5660 # SOURCE3 3 0.0016
- bond_coeff @bond:i-p4 harmonic 183.0 2.3520 # SOURCE3 4 0.2600
- bond_coeff @bond:i-p5 harmonic 117.3 2.5960 # SOURCE3 3 0.0143
- bond_coeff @bond:i-s harmonic 175.1 2.4300 # SOUECE3 1
- bond_coeff @bond:i-s4 harmonic 82.8 2.8700 # SOUECE3 1
- bond_coeff @bond:i-s6 harmonic 82.8 2.8700 # SOURCE3 1 0.0000
- bond_coeff @bond:i-sh harmonic 138.5 2.5600 # SOUECE3 1
- bond_coeff @bond:i-ss harmonic 135.9 2.5710 # SOURCE3 3 0.0065
- bond_coeff @bond:n1-n1 harmonic 1221.7 1.1240 # SOURCE1 19 0.0000
- bond_coeff @bond:n1-n2 harmonic 857.4 1.2160 # SOURCE1 19 0.0000
- bond_coeff @bond:n1-n3 harmonic 535.7 1.3500 # SOUECE3 1
- bond_coeff @bond:n1-n4 harmonic 518.2 1.3600 # SOUECE3 1
- bond_coeff @bond:n1-na harmonic 535.7 1.3500 # SOUECE3 1
- bond_coeff @bond:n1-nc harmonic 857.4 1.2160 # SOURCE1 38 0.0000
- bond_coeff @bond:n1-nd harmonic 857.4 1.2160 # SOURCE1 38 0.0000
- bond_coeff @bond:n1-ne harmonic 751.9 1.2520 # SOURCE2 1 0.0000
- bond_coeff @bond:n1-nf harmonic 751.9 1.2520 # SOURCE2 1 same_as_n1-ne
- bond_coeff @bond:n1-nh harmonic 553.9 1.3400 # SOUECE3 1
- bond_coeff @bond:n1-no harmonic 454.8 1.4000 # SOUECE3 1
- bond_coeff @bond:n1-o harmonic 617.5 1.2770 # SOURCE3 5 0.0438
- bond_coeff @bond:n1-oh harmonic 569.8 1.3000 # SOUECE3 1
- bond_coeff @bond:n1-os harmonic 550.5 1.3100 # SOUECE3 1
- bond_coeff @bond:n1-p2 harmonic 358.8 1.6780 # SOURCE3 2 0.0282
- bond_coeff @bond:n1-p3 harmonic 376.7 1.6600 # SOUECE3 1
- bond_coeff @bond:n1-p4 harmonic 353.0 1.6800 # SOURCE3 0
- bond_coeff @bond:n1-p5 harmonic 482.7 1.5710 # SOURCE1 132 0.0000
- bond_coeff @bond:n1-s2 harmonic 604.3 1.4490 # SOURCE2 2 0.0010
- bond_coeff @bond:n1-s harmonic 328.7 1.6590 # SOURCE3 6 0.0789
- bond_coeff @bond:n1-s4 harmonic 336.8 1.6500 # SOUECE3 1
- bond_coeff @bond:n1-s6 harmonic 670.3 1.4160 # SOURCE2 2 0.0000
- bond_coeff @bond:n1-sh harmonic 376.1 1.6100 # SOUECE3 1
- bond_coeff @bond:n1-ss harmonic 376.1 1.6100 # SOUECE3 1
- bond_coeff @bond:n2-n2 harmonic 702.7 1.2710 # SOURCE3 27 0.0347
- bond_coeff @bond:n2-n3 harmonic 574.8 1.3290 # SOURCE2 1 0.0000
- bond_coeff @bond:n2-n4 harmonic 200.8 1.6790 # SOURCE3 7 0.3138
- bond_coeff @bond:n2-na harmonic 503.9 1.3685 # SOURCE4 18 0.0066
- bond_coeff @bond:n2-nc harmonic 743.9 1.2550 # SOURCE1 13 0.0000
- bond_coeff @bond:n2-nd harmonic 743.9 1.2550 # SOURCE1 13 same_as_n2_nc
- bond_coeff @bond:n2-ne harmonic 685.5 1.2780 # SOURCE3 30 0.0302
- bond_coeff @bond:n2-nf harmonic 685.5 1.2780 # SOURCE3 30 same_as_n2-ne
- bond_coeff @bond:n2-nh harmonic 525.1 1.3560 # SOURCE3 22 0.0300
- bond_coeff @bond:n2-no harmonic 231.9 1.6260 # SOURCE3 4 0.1933
- bond_coeff @bond:n2-o harmonic 789.9 1.2090 # SOURCE3 20 0.0344
- bond_coeff @bond:n2-oh harmonic 416.2 1.3940 # SOURCE1 67 0.0000
- bond_coeff @bond:n2-os harmonic 400.5 1.4060 # SOURCE3 10 0.0147
- bond_coeff @bond:n2-p2 harmonic 438.3 1.6050 # SOURCE3 35 0.0737
- bond_coeff @bond:n2-p3 harmonic 286.5 1.7640 # SOURCE3 7 0.0374
- bond_coeff @bond:n2-p4 harmonic 317.7 1.7240 # SOUECE3 1
- bond_coeff @bond:n2-p5 harmonic 445.8 1.5990 # SOURCE1 7 0.0000
- bond_coeff @bond:n2-pe harmonic 527.9 1.5400 # SOURCE3 20 0.1392
- bond_coeff @bond:n2-pf harmonic 527.9 1.5400 # SOURCE3 20 same_as_n2-pe
- bond_coeff @bond:n2-s2 harmonic 499.0 1.5120 # SOURCE2 1 0.0000
- bond_coeff @bond:n2-s4 harmonic 376.1 1.6100 # SOUECE3 1
- bond_coeff @bond:n2-s harmonic 458.1 1.5410 # SOURCE1 37 0.0000
- bond_coeff @bond:n2-s6 harmonic 444.6 1.5513 # SOURCE4 5 0.0011
- bond_coeff @bond:n2-sh harmonic 266.6 1.7380 # SOURCE3 5 0.0511
- bond_coeff @bond:n2-ss harmonic 331.4 1.6560 # SOURCE1 36 0.0000
- bond_coeff @bond:n3-n3 harmonic 383.6 1.4540 # SOURCE1 44 0.0000
- bond_coeff @bond:n3-n4 harmonic 434.9 1.4140 # SOURCE1 13 0.0000
- bond_coeff @bond:n3-na harmonic 426.7 1.4200 # SOURCE1 68 0.0000
- bond_coeff @bond:n3-nh harmonic 426.7 1.4200 # SOURCE1 68 0.0000
- bond_coeff @bond:n3-no harmonic 394.5 1.4450 # SOURCE3 3 0.0208
- bond_coeff @bond:n3-o harmonic 564.0 1.3030 # SOURCE3 4 0.1217
- bond_coeff @bond:n3-oh harmonic 413.5 1.3960 # SOURCE1 28 0.0000
- bond_coeff @bond:n3-os harmonic 359.6 1.4400 # SOURCE1 34 0.0315
- bond_coeff @bond:n3-p2 harmonic 366.6 1.6700 # SOUECE3 1
- bond_coeff @bond:n3-p3 harmonic 312.8 1.7300 # SOURCE1 40 0.0000
- bond_coeff @bond:n3-p4 harmonic 341.1 1.6970 # SOURCE1 88 0.0000
- bond_coeff @bond:n3-p5 harmonic 373.6 1.6630 # SOURCE1 501 0.0086
- bond_coeff @bond:n3-py harmonic 338.1 1.7003 # SOURCE4 6 0.0044
- bond_coeff @bond:n3-s harmonic 232.3 1.7920 # SOURCE3 3 0.0178
- bond_coeff @bond:n3-s4 harmonic 251.3 1.7610 # SOURCE3 6 0.0766
- bond_coeff @bond:n3-s6 harmonic 353.8 1.6320 # SOURCE1 99 0.0136
- bond_coeff @bond:n3-sh harmonic 265.9 1.7390 # SOURCE3 3 0.0154
- bond_coeff @bond:n3-ss harmonic 277.9 1.7220 # SOURCE3 5 0.0207
- bond_coeff @bond:n3-sy harmonic 297.3 1.6964 # SOURCE4 226 0.0081
- bond_coeff @bond:n4-n4 harmonic 349.9 1.4840 # SOURCE3 4 0.0089
- bond_coeff @bond:n4-na harmonic 407.0 1.4350 # SOURCE3 9 0.0390
- bond_coeff @bond:n4-nh harmonic 369.7 1.4660 # SOURCE3 5 0.0108
- bond_coeff @bond:n4-no harmonic 354.2 1.4800 # SOUECE3 1
- bond_coeff @bond:n4-o harmonic 463.6 1.3610 # SOURCE3 3 0.0041
- bond_coeff @bond:n4-oh harmonic 408.2 1.4000 # SOURCE3 3 0.0115
- bond_coeff @bond:n4-os harmonic 381.8 1.4210 # SOURCE3 5 0.0249
- bond_coeff @bond:n4-p2 harmonic 185.9 1.9420 # SOURCE3 10 0.0643
- bond_coeff @bond:n4-p3 harmonic 215.1 1.8800 # SOURCE3 5 0.0146
- bond_coeff @bond:n4-p4 harmonic 187.6 1.9380 # SOURCE3 1 0.0000
- bond_coeff @bond:n4-p5 harmonic 242.9 1.8300 # SOURCE3 5 0.0087
- bond_coeff @bond:n4-py harmonic 204.2 1.9020 # SOURCE3 4 0.0000
- bond_coeff @bond:n4-s harmonic 210.3 1.8320 # SOURCE3 3 0.0004
- bond_coeff @bond:n4-s4 harmonic 151.0 1.9720 # SOURCE3 3 0.0198
- bond_coeff @bond:n4-s6 harmonic 172.7 1.9140 # SOURCE3 5 0.0432
- bond_coeff @bond:n4-sh harmonic 221.5 1.8110 # SOURCE3 3 0.0027
- bond_coeff @bond:n4-ss harmonic 221.0 1.8120 # SOURCE3 5 0.0064
- bond_coeff @bond:na-na harmonic 453.3 1.4010 # SOURCE1 40 0.0000
- bond_coeff @bond:na-nb harmonic 546.5 1.3440 # SOURCE4 5 0.0070
- bond_coeff @bond:na-nc harmonic 535.7 1.3500 # SOURCE3 152 0.0180
- bond_coeff @bond:na-nd harmonic 535.7 1.3500 # SOURCE3 152 0.0180
- bond_coeff @bond:na-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000
- bond_coeff @bond:na-no harmonic 401.9 1.4390 # SOURCE3 9 0.0289
- bond_coeff @bond:na-o harmonic 644.3 1.2650 # SOURCE1 25 0.0347
- bond_coeff @bond:na-oh harmonic 412.2 1.3970 # SOURCE3 9 0.0217
- bond_coeff @bond:na-os harmonic 355.2 1.4440 # SOURCE3 45 0.0423
- bond_coeff @bond:na-p2 harmonic 297.8 1.7490 # SOURCE3 11 0.0192
- bond_coeff @bond:na-p3 harmonic 288.0 1.7620 # SOURCE3 8 0.0113
- bond_coeff @bond:na-p4 harmonic 492.4 1.5640 # SOURCE3 5 0.2161
- bond_coeff @bond:na-p5 harmonic 325.3 1.7150 # SOURCE3 11 0.0238
- bond_coeff @bond:na-pc harmonic 311.1 1.7320 # SOURCE3 81 0.0207
- bond_coeff @bond:na-pd harmonic 311.1 1.7320 # SOURCE3 81 same_as_na-pc
- bond_coeff @bond:na-py harmonic 327.8 1.7120 # SOURCE3 2 0.0000
- bond_coeff @bond:na-s harmonic 248.7 1.7650 # SOURCE3 8 0.0095
- bond_coeff @bond:na-s4 harmonic 231.7 1.7930 # SOURCE3 10 0.0421
- bond_coeff @bond:na-s6 harmonic 274.3 1.7270 # SOURCE3 10 0.0201
- bond_coeff @bond:na-sh harmonic 278.6 1.7210 # SOURCE3 9 0.0113
- bond_coeff @bond:na-ss harmonic 270.1 1.7330 # SOURCE3 38 0.0412
- bond_coeff @bond:na-sy harmonic 274.3 1.7270 # SOURCE3 1
- bond_coeff @bond:nb-nb harmonic 550.2 1.3420 # SOURCE1 15 0.0314
- bond_coeff @bond:nb-pb harmonic 461.1 1.5870 # SOURCE1 162 0.0091
- bond_coeff @bond:nc-nc harmonic 486.8 1.3790 # SOURCE3 9 0.0164
- bond_coeff @bond:nc-nd harmonic 602.9 1.3150 # SOURCE3 9 0.0221
- bond_coeff @bond:nc-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188
- bond_coeff @bond:nc-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000
- bond_coeff @bond:nc-sy harmonic 439.8 1.5550 # SOURCE3 2
- bond_coeff @bond:nd-nd harmonic 486.8 1.3790 # SOURCE3 9 0.0164
- bond_coeff @bond:nd-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188
- bond_coeff @bond:nd-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000
- bond_coeff @bond:nd-sy harmonic 439.8 1.5550 # SOURCE3 2
- bond_coeff @bond:ne-ne harmonic 355.3 1.4790 # SOURCE3 19 0.1705
- bond_coeff @bond:ne-nf harmonic 721.6 1.2635 # SOURCE4 25 0.0034
- bond_coeff @bond:ne-o harmonic 736.4 1.2280 # SOURCE3 40 0.0255
- bond_coeff @bond:ne-p2 harmonic 493.9 1.5630 # SOURCE3 14 0.1325
- bond_coeff @bond:ne-pe harmonic 327.8 1.7120 # SOURCE3 28 0.1076
- bond_coeff @bond:ne-px harmonic 336.6 1.7020 # SOURCE3 11 0.0883
- bond_coeff @bond:ne-py harmonic 425.4 1.6157 # SOURCE4 10 0.0094
- bond_coeff @bond:ne-s harmonic 463.5 1.5370 # SOURCE3 22 0.1708
- bond_coeff @bond:ne-sx harmonic 207.3 1.8380 # SOURCE3 7 0.1060
- bond_coeff @bond:ne-sy harmonic 257.1 1.7520 # SOURCE3 7 0.0814
- bond_coeff @bond:nf-nf harmonic 355.3 1.4790 # SOURCE3 19 same_as_ne-ne
- bond_coeff @bond:nf-o harmonic 736.4 1.2280 # SOURCE3 40 same_as_ne-o
- bond_coeff @bond:nf-p2 harmonic 493.9 1.5630 # SOURCE3 14 same_as_ne-p2
- bond_coeff @bond:nf-pf harmonic 327.8 1.7120 # SOURCE3 28 same_as_ne-pe
- bond_coeff @bond:nf-px harmonic 336.6 1.7020 # SOURCE3 11 same_as_ne-px
- bond_coeff @bond:nf-py harmonic 425.4 1.6157 # SOURCE4 10 same_as_ne-py
- bond_coeff @bond:nf-s harmonic 463.5 1.5370 # SOURCE3 22 same_as_ne-s
- bond_coeff @bond:nf-sx harmonic 207.3 1.8380 # SOURCE3 7 same_as_ne-sx
- bond_coeff @bond:nf-sy harmonic 257.1 1.7520 # SOURCE3 7 same_as_ne-sy
- bond_coeff @bond:nh-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000
- bond_coeff @bond:nh-no harmonic 477.4 1.3850 # SOURCE4 7 0.0036
- bond_coeff @bond:nh-o harmonic 596.2 1.2870 # SOURCE3 3 0.0450
- bond_coeff @bond:nh-oh harmonic 389.9 1.4144 # SOURCE4 19 0.0064
- bond_coeff @bond:nh-os harmonic 387.8 1.4161 # SOURCE4 6 0.0039
- bond_coeff @bond:nh-p2 harmonic 357.8 1.6790 # SOURCE3 17 0.0872
- bond_coeff @bond:nh-p3 harmonic 312.8 1.7300 # SOURCE3 3 0.0016
- bond_coeff @bond:nh-p4 harmonic 333.1 1.7060 # SOURCE3 3 0.0008
- bond_coeff @bond:nh-p5 harmonic 365.6 1.6710 # SOURCE3 3 0.0007
- bond_coeff @bond:nh-s harmonic 237.0 1.7840 # SOURCE3 3 0.0076
- bond_coeff @bond:nh-s4 harmonic 259.1 1.7490 # SOURCE3 3 0.0203
- bond_coeff @bond:nh-s6 harmonic 297.2 1.6965 # SOURCE4 33 0.0062
- bond_coeff @bond:nh-sh harmonic 288.3 1.7080 # SOURCE3 1 0.0000
- bond_coeff @bond:nh-ss harmonic 288.3 1.7080 # SOURCE1 52 0.0015
- bond_coeff @bond:nh-sy harmonic 283.5 1.7144 # SOURCE4 80 0.0066
- bond_coeff @bond:n-n1 harmonic 553.9 1.3400 # SOUECE3 1
- bond_coeff @bond:n-n2 harmonic 499.7 1.3710 # SOURCE3 9 0.0200
- bond_coeff @bond:n-n3 harmonic 443.3 1.4080 # SOURCE3 5 0.0087
- bond_coeff @bond:n-n4 harmonic 410.8 1.4320 # SOURCE3 5 0.0098
- bond_coeff @bond:n-n harmonic 469.7 1.3900 # SOURCE3 5 0.0038
- bond_coeff @bond:n-na harmonic 486.8 1.3790 # SOURCE3 11 0.0071
- bond_coeff @bond:n-nc harmonic 523.7 1.3568 # CORR 76
- bond_coeff @bond:n-nd harmonic 523.7 1.3568 # CORR 76
- bond_coeff @bond:n-nh harmonic 451.2 1.4025 # SOURCE4 20 0.0074
- bond_coeff @bond:n-no harmonic 381.2 1.4560 # SOURCE3 4 0.0327
- bond_coeff @bond:n-o harmonic 646.6 1.2640 # SOURCE3 9 0.0381
- bond_coeff @bond:n-oh harmonic 395.4 1.4100 # SOURCE3 6 0.0106
- bond_coeff @bond:no-no harmonic 138.3 1.8240 # SOURCE3 1 0.0000
- bond_coeff @bond:no-o harmonic 761.2 1.2190 # SOURCE1 1838 0.0049
- bond_coeff @bond:no-oh harmonic 400.5 1.4060 # SOURCE2 1 0.0000
- bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076
- bond_coeff @bond:no-p2 harmonic 306.3 1.7380 # SOURCE3 10 0.2231
- bond_coeff @bond:no-p3 harmonic 234.7 1.8440 # SOURCE3 3 0.0005
- bond_coeff @bond:no-p4 harmonic 220.4 1.8700 # SOURCE3 3 0.0006
- bond_coeff @bond:no-p5 harmonic 240.5 1.8340 # SOURCE3 4 0.0020
- bond_coeff @bond:no-s harmonic 263.8 1.7420 # SOURCE3 2 0.0000
- bond_coeff @bond:n-os harmonic 395.0 1.4103 # SOURCE4 30 0.0112
- bond_coeff @bond:no-s4 harmonic 143.0 1.9960 # SOURCE3 3 0.0313
- bond_coeff @bond:no-s6 harmonic 149.6 1.9760 # SOURCE3 3 0.0520
- bond_coeff @bond:no-sh harmonic 225.4 1.8040 # SOURCE3 1 0.0000
- bond_coeff @bond:no-ss harmonic 212.4 1.8280 # SOURCE3 3 0.0244
- bond_coeff @bond:n-p2 harmonic 310.3 1.7330 # SOURCE3 8 0.0217
- bond_coeff @bond:n-p3 harmonic 282.2 1.7700 # SOURCE3 9 0.0118
- bond_coeff @bond:n-p4 harmonic 309.5 1.7340 # SOURCE3 1 0.0000
- bond_coeff @bond:n-p5 harmonic 331.3 1.7080 # SOURCE4 6 0.0022
- bond_coeff @bond:n-pc harmonic 304.8 1.7400 # SOURCE3 3 0.0010
- bond_coeff @bond:n-pd harmonic 304.8 1.7400 # SOURCE3 3 same_as_n-pc
- bond_coeff @bond:n-s harmonic 247.5 1.7670 # SOURCE3 3 0.0011
- bond_coeff @bond:n-s4 harmonic 238.2 1.7820 # SOURCE3 4 0.0214
- bond_coeff @bond:n-s6 harmonic 283.0 1.7151 # SOURCE4 13 0.0138
- bond_coeff @bond:n-sh harmonic 273.6 1.7280 # SOURCE3 4 0.0128
- bond_coeff @bond:n-ss harmonic 281.6 1.7170 # SOURCE3 7 0.0133
- bond_coeff @bond:n-sy harmonic 282.9 1.7152 # SOURCE4 51 0.0079
- bond_coeff @bond:oh-oh harmonic 340.5 1.4690 # SOURCE3 1 0.0000
- bond_coeff @bond:oh-os harmonic 355.8 1.4547 # SOURCE4 19 0.0050
- bond_coeff @bond:oh-p2 harmonic 316.8 1.6300 # SOURCE3 8 0.0916
- bond_coeff @bond:oh-p3 harmonic 278.8 1.6770 # SOURCE3 3 0.0148
- bond_coeff @bond:oh-p4 harmonic 307.4 1.6410 # SOURCE3 4 0.0092
- bond_coeff @bond:oh-p5 harmonic 321.2 1.6250 # SOURCE3 92 0.0451
- bond_coeff @bond:oh-py harmonic 332.1 1.6130 # SOURCE3 79 0.0138
- bond_coeff @bond:oh-s harmonic 190.0 1.8120 # SOURCE3 2 0.0000
- bond_coeff @bond:oh-s4 harmonic 256.3 1.6954 # SOURCE4 10 0.0091
- bond_coeff @bond:oh-s6 harmonic 344.1 1.5880 # SOURCE3 13 0.0091
- bond_coeff @bond:oh-sh harmonic 258.6 1.6920 # SOURCE3 2 0.0003
- bond_coeff @bond:oh-ss harmonic 265.6 1.6820 # SOURCE3 4 0.0131
- bond_coeff @bond:oh-sy harmonic 290.4 1.6490 # SOURCE4 33 0.0044
- bond_coeff @bond:o-o harmonic 384.3 1.4300 # SOURCE3 2 0.0500
- bond_coeff @bond:o-oh harmonic 294.6 1.5170 # SOURCE3 2 0.0000
- bond_coeff @bond:o-os harmonic 306.3 1.5040 # SOURCE3 3 0.0117
- bond_coeff @bond:o-p2 harmonic 449.7 1.5080 # SOURCE3 17 0.0306
- bond_coeff @bond:o-p3 harmonic 440.4 1.5150 # SOURCE3 35 0.0297
- bond_coeff @bond:o-p4 harmonic 456.4 1.5030 # SOURCE3 42 0.0749
- bond_coeff @bond:o-p5 harmonic 487.7 1.4810 # SOURCE1 263 0.0205
- bond_coeff @bond:o-pe harmonic 432.6 1.5210 # SOURCE3 20 0.0171
- bond_coeff @bond:o-pf harmonic 432.6 1.5210 # SOURCE3 20 same_as_o-pe
- bond_coeff @bond:o-px harmonic 459.2 1.5010 # SOURCE3 37 0.0160
- bond_coeff @bond:o-py harmonic 477.5 1.4880 # SOURCE3 63 0.0091
- bond_coeff @bond:o-s harmonic 194.8 1.8020 # SOURCE3 2 0.0000
- bond_coeff @bond:o-s2 harmonic 333.6 1.5990 # SOURCE3 3 0.0707
- bond_coeff @bond:o-s4 harmonic 448.7 1.4970 # SOURCE1 90 0.0000
- bond_coeff @bond:o-s6 harmonic 541.1 1.4360 # SOURCE1 1038 0.0128
- bond_coeff @bond:o-sh harmonic 328.0 1.6050 # SOURCE3 2 0.0000
- bond_coeff @bond:os-os harmonic 343.6 1.4660 # SOURCE1 20 0.0067
- bond_coeff @bond:os-p2 harmonic 371.9 1.5730 # SOURCE1 16 0.0000
- bond_coeff @bond:os-p3 harmonic 272.2 1.6860 # SOURCE3 6 0.0201
- bond_coeff @bond:os-p4 harmonic 311.6 1.6360 # SOURCE3 4 0.0057
- bond_coeff @bond:os-p5 harmonic 342.5 1.6020 # SOURCE1 248 0.0400
- bond_coeff @bond:os-py harmonic 328.5 1.6170 # SOURCE3 17 0.0139
- bond_coeff @bond:os-s harmonic 195.8 1.8000 # SOURCE3 3 0.0052
- bond_coeff @bond:o-ss harmonic 398.5 1.5370 # SOURCE3 3 0.0501
- bond_coeff @bond:os-s4 harmonic 253.9 1.6990 # SOURCE3 8 0.0223
- bond_coeff @bond:os-s6 harmonic 355.0 1.5770 # SOURCE1 75 0.0030
- bond_coeff @bond:os-sh harmonic 273.6 1.6710 # SOURCE3 3 0.0106
- bond_coeff @bond:os-ss harmonic 250.5 1.7040 # SOURCE3 9 0.0277
- bond_coeff @bond:os-sy harmonic 253.9 1.6990 # SOURCE3 1 0.0000
- bond_coeff @bond:o-sx harmonic 434.2 1.5080 # SOURCE3 40 0.0130
- bond_coeff @bond:o-sy harmonic 493.0 1.4660 # SOURCE3 92 0.0114
- bond_coeff @bond:p2-p2 harmonic 490.3 1.7860 # SOURCE3 25 0.3488
- bond_coeff @bond:p2-p3 harmonic 211.9 2.1520 # SOURCE3 9 0.1777
- bond_coeff @bond:p2-p4 harmonic 200.4 2.1790 # SOUECE3 1
- bond_coeff @bond:p2-p5 harmonic 199.9 2.1800 # SOUECE3 1
- bond_coeff @bond:p2-pe harmonic 401.6 1.8670 # SOURCE3 16 0.3571
- bond_coeff @bond:p2-pf harmonic 401.6 1.8670 # SOURCE3 16 same_as_p2-pe
- bond_coeff @bond:p2-s harmonic 361.6 1.7720 # SOURCE3 26 0.3014
- bond_coeff @bond:p2-s4 harmonic 139.4 2.1900 # SOUECE3 1
- bond_coeff @bond:p2-s6 harmonic 142.3 2.1800 # SOUECE3 1
- bond_coeff @bond:p2-sh harmonic 224.0 1.9710 # SOURCE3 10 0.2829
- bond_coeff @bond:p2-ss harmonic 226.6 1.9660 # SOURCE3 10 0.2739
- bond_coeff @bond:p3-p3 harmonic 186.5 2.2140 # SOURCE1 41 0.0000
- bond_coeff @bond:p3-p4 harmonic 185.7 2.2160 # SOURCE3 3 0.0011
- bond_coeff @bond:p3-p5 harmonic 186.9 2.2130 # SOURCE3 9 0.0265
- bond_coeff @bond:p3-s harmonic 179.7 2.0700 # SOUECE3 1
- bond_coeff @bond:p3-s4 harmonic 173.2 2.0870 # SOURCE3 8 0.2235
- bond_coeff @bond:p3-s6 harmonic 176.9 2.0770 # SOURCE3 11 0.1420
- bond_coeff @bond:p3-sh harmonic 157.3 2.1320 # SOURCE3 3 0.0078
- bond_coeff @bond:p3-ss harmonic 161.0 2.1210 # SOURCE3 3 0.0059
- bond_coeff @bond:p4-p4 harmonic 273.1 2.0340 # SOURCE1 1 0.0000
- bond_coeff @bond:p4-p5 harmonic 178.0 2.2370 # SOUECE3 1
- bond_coeff @bond:p4-s harmonic 152.7 2.1460 # SOURCE3 5 0.0601
- bond_coeff @bond:p4-s4 harmonic 123.2 2.2510 # SOUECE3 1
- bond_coeff @bond:p4-s6 harmonic 118.9 2.2690 # SOUECE3 1
- bond_coeff @bond:p4-sh harmonic 163.1 2.1150 # SOURCE3 4 0.0008
- bond_coeff @bond:p4-ss harmonic 167.0 2.1040 # SOURCE3 4 0.0044
- bond_coeff @bond:p5-p5 harmonic 261.4 2.0540 # SOURCE1 1 0.0000
- bond_coeff @bond:p5-s harmonic 250.8 1.9220 # SOURCE1 89 0.0140
- bond_coeff @bond:p5-s4 harmonic 191.9 2.0400 # SOUECE3 1
- bond_coeff @bond:p5-s6 harmonic 191.9 2.0400 # SOUECE3 1
- bond_coeff @bond:p5-sh harmonic 175.0 2.0820 # SOURCE3 3 0.0035
- bond_coeff @bond:p5-ss harmonic 163.1 2.1149 # SOURCE4 24 0.0106
- bond_coeff @bond:pe-pe harmonic 240.7 2.0920 # SOURCE3 7 0.1369
- bond_coeff @bond:pe-pf harmonic 260.8 2.0550 # SOURCE3 1 0.0000
- bond_coeff @bond:pe-px harmonic 291.4 2.0050 # SOURCE3 12 0.2609
- bond_coeff @bond:pe-py harmonic 278.6 2.0250 # SOURCE3 12 0.2617
- bond_coeff @bond:pe-s harmonic 374.7 1.7580 # SOURCE3 31 0.3197
- bond_coeff @bond:pe-sx harmonic 145.9 2.1680 # SOURCE3 9 0.1743
- bond_coeff @bond:pe-sy harmonic 133.0 2.2130 # SOURCE3 6 0.0127
- bond_coeff @bond:pf-pf harmonic 240.7 2.0920 # SOURCE3 7 same_as_pe-pe
- bond_coeff @bond:pf-px harmonic 291.4 2.0050 # SOURCE3 12 same_as_pe-px
- bond_coeff @bond:pf-py harmonic 278.6 2.0250 # SOURCE3 12 same_as_pe-py
- bond_coeff @bond:pf-s harmonic 374.7 1.7580 # SOURCE3 31 same_as_pe-s
- bond_coeff @bond:pf-sx harmonic 145.9 2.1680 # SOURCE3 9 same_as_pe-sx
- bond_coeff @bond:pf-sy harmonic 133.0 2.2130 # SOURCE3 6 same_as_pe-sy
- bond_coeff @bond:px-py harmonic 192.3 2.1990 # SOURCE3 5 0.0238
- bond_coeff @bond:px-sx harmonic 125.4 2.2420 # SOURCE3 3 0.0119
- bond_coeff @bond:px-sy harmonic 123.7 2.2490 # SOURCE3 3 0.0272
- bond_coeff @bond:py-py harmonic 197.5 2.1860 # SOURCE3 8 0.0132
- bond_coeff @bond:py-sx harmonic 121.2 2.2590 # SOURCE3 7 0.0603
- bond_coeff @bond:py-sy harmonic 141.7 2.1820 # SOURCE3 5 0.0047
- bond_coeff @bond:s4-s4 harmonic 151.5 2.0800 # SOUECE3 1
- bond_coeff @bond:s4-s6 harmonic 151.5 2.0800 # SOUECE3 1
- bond_coeff @bond:s4-sh harmonic 125.7 2.1680 # SOURCE3 3 0.0227
- bond_coeff @bond:s4-ss harmonic 126.2 2.1660 # SOURCE3 5 0.0247
- bond_coeff @bond:s6-s6 harmonic 151.5 2.0800 # SOUECE3 1
- bond_coeff @bond:s6-sh harmonic 142.6 2.1080 # SOURCE3 3 0.0144
- bond_coeff @bond:s6-ss harmonic 139.6 2.1180 # SOURCE3 5 0.0209
- bond_coeff @bond:sh-sh harmonic 158.9 2.0580 # SOURCE2 1 0.0000
- bond_coeff @bond:sh-ss harmonic 155.8 2.0670 # SOURCE3 3 0.0029
- bond_coeff @bond:s-s harmonic 169.0 2.0300 # SOURCE3 1 0.0000
- bond_coeff @bond:s-s2 harmonic 229.2 1.8970 # SOURCE1 5 0.0000
- bond_coeff @bond:s-s4 harmonic 152.8 2.0760 # SOURCE3 4 0.0345
- bond_coeff @bond:s-s6 harmonic 166.0 2.0380 # SOURCE3 3 0.0311
- bond_coeff @bond:s-sh harmonic 142.0 2.1100 # SOURCE3 2 0.0000
- bond_coeff @bond:s-ss harmonic 148.5 2.0890 # SOURCE3 1 0.0000
- bond_coeff @bond:ss-ss harmonic 161.7 2.0500 # SOURCE1 225 0.0015
- bond_coeff @bond:sx-sx harmonic 80.9 2.3910 # SOURCE3 3 0.0185
- bond_coeff @bond:sx-sy harmonic 105.3 2.2550 # SOURCE3 5 0.0737
- bond_coeff @bond:sy-sy harmonic 106.4 2.2500 # SOURCE3 3 0.0289
- bond_coeff @bond:br-cd harmonic 277.6 1.8847 # NEW 39
- bond_coeff @bond:c1-cf harmonic 607.4 1.3153 # NEW 6
- bond_coeff @bond:cd-f harmonic 368.6 1.3401 # NEW 24
- bond_coeff @bond:cd-n4 harmonic 299.0 1.4930 # NEW 7
- bond_coeff @bond:cd-nf harmonic 427.4 1.3790 # NEW 30
- bond_coeff @bond:cd-no harmonic 367.4 1.4262 # NEW 133
- bond_coeff @bond:cd-sh harmonic 257.9 1.7681 # NEW 8
- bond_coeff @bond:cd-sx harmonic 231.3 1.8113 # NEW 16
- bond_coeff @bond:cc-cy harmonic 330.9 1.5054 # NEW 10
- bond_coeff @bond:cf-cl harmonic 292.6 1.7671 # NEW 24
- bond_coeff @bond:cf-cx harmonic 337.0 1.4993 # NEW 5
- bond_coeff @bond:cf-cy harmonic 323.0 1.5135 # NEW 17
- bond_coeff @bond:cf-na harmonic 373.8 1.4207 # NEW 5
- bond_coeff @bond:cf-ss harmonic 243.6 1.7906 # NEW 10
- bond_coeff @bond:cq-na harmonic 420.5 1.3840 # NEW 7
- bond_coeff @bond:cq-nb harmonic 486.7 1.3398 # NEW 70
- } # (end of bond_coeffs)
-
- write_once("Data Bonds By Type") {
- @bond:ow-hw @atom:ow @atom:hw
- @bond:hw-hw @atom:hw @atom:hw
- @bond:br-br @atom:br @atom:br
- @bond:br-c1 @atom:br @atom:c1
- @bond:br-c2 @atom:br @atom:c2
- @bond:br-c @atom:br @atom:c
- @bond:br-c3 @atom:br @atom:c3
- @bond:br-ca @atom:br @atom:ca
- @bond:br-cc @atom:br @atom:cc
- @bond:br-cx @atom:br @atom:cx
- @bond:br-i @atom:br @atom:i
- @bond:br-n1 @atom:br @atom:n1
- @bond:br-n2 @atom:br @atom:n2
- @bond:br-n @atom:br @atom:n
- @bond:br-n3 @atom:br @atom:n3
- @bond:br-n4 @atom:br @atom:n4
- @bond:br-na @atom:br @atom:na
- @bond:br-nh @atom:br @atom:nh
- @bond:br-no @atom:br @atom:no
- @bond:br-o @atom:br @atom:o
- @bond:br-oh @atom:br @atom:oh
- @bond:br-os @atom:br @atom:os
- @bond:br-p2 @atom:br @atom:p2
- @bond:br-p3 @atom:br @atom:p3
- @bond:br-p4 @atom:br @atom:p4
- @bond:br-p5 @atom:br @atom:p5
- @bond:br-s @atom:br @atom:s
- @bond:br-s4 @atom:br @atom:s4
- @bond:br-s6 @atom:br @atom:s6
- @bond:br-sh @atom:br @atom:sh
- @bond:br-ss @atom:br @atom:ss
- @bond:c1-c1 @atom:c1 @atom:c1
- @bond:c1-c2 @atom:c1 @atom:c2
- @bond:c1-c3 @atom:c1 @atom:c3
- @bond:c1-ca @atom:c1 @atom:ca
- @bond:c1-ce @atom:c1 @atom:ce
- @bond:c1-cg @atom:c1 @atom:cg
- @bond:c1-ch @atom:c1 @atom:ch
- @bond:c1-cl @atom:c1 @atom:cl
- @bond:c1-cx @atom:c1 @atom:cx
- @bond:c1-f @atom:c1 @atom:f
- @bond:c1-ha @atom:c1 @atom:ha
- @bond:c1-hc @atom:c1 @atom:hc
- @bond:c1-i @atom:c1 @atom:i
- @bond:c1-n1 @atom:c1 @atom:n1
- @bond:c1-n2 @atom:c1 @atom:n2
- @bond:c1-n3 @atom:c1 @atom:n3
- @bond:c1-n4 @atom:c1 @atom:n4
- @bond:c1-n @atom:c1 @atom:n
- @bond:c1-na @atom:c1 @atom:na
- @bond:c1-ne @atom:c1 @atom:ne
- @bond:c1-nf @atom:c1 @atom:nf
- @bond:c1-nh @atom:c1 @atom:nh
- @bond:c1-no @atom:c1 @atom:no
- @bond:c1-o @atom:c1 @atom:o
- @bond:c1-oh @atom:c1 @atom:oh
- @bond:c1-os @atom:c1 @atom:os
- @bond:c1-p2 @atom:c1 @atom:p2
- @bond:c1-p3 @atom:c1 @atom:p3
- @bond:c1-p4 @atom:c1 @atom:p4
- @bond:c1-p5 @atom:c1 @atom:p5
- @bond:c1-s2 @atom:c1 @atom:s2
- @bond:c1-s @atom:c1 @atom:s
- @bond:c1-s4 @atom:c1 @atom:s4
- @bond:c1-s6 @atom:c1 @atom:s6
- @bond:c1-sh @atom:c1 @atom:sh
- @bond:c1-ss @atom:c1 @atom:ss
- @bond:c2-c2 @atom:c2 @atom:c2
- @bond:c2-c3 @atom:c2 @atom:c3
- @bond:c2-ca @atom:c2 @atom:ca
- @bond:c2-cc @atom:c2 @atom:cc
- @bond:c2-cd @atom:c2 @atom:cd
- @bond:c2-ce @atom:c2 @atom:ce
- @bond:c2-cf @atom:c2 @atom:cf
- @bond:c2-cl @atom:c2 @atom:cl
- @bond:c2-cu @atom:c2 @atom:cu
- @bond:c2-cx @atom:c2 @atom:cx
- @bond:c2-cy @atom:c2 @atom:cy
- @bond:c2-f @atom:c2 @atom:f
- @bond:c2-h4 @atom:c2 @atom:h4
- @bond:c2-h5 @atom:c2 @atom:h5
- @bond:c2-ha @atom:c2 @atom:ha
- @bond:c2-hc @atom:c2 @atom:hc
- @bond:c2-hx @atom:c2 @atom:hx
- @bond:c2-i @atom:c2 @atom:i
- @bond:c2-n1 @atom:c2 @atom:n1
- @bond:c2-n2 @atom:c2 @atom:n2
- @bond:c2-n3 @atom:c2 @atom:n3
- @bond:c2-n @atom:c2 @atom:n
- @bond:c2-n4 @atom:c2 @atom:n4
- @bond:c2-na @atom:c2 @atom:na
- @bond:c2-nc @atom:c2 @atom:nc
- @bond:c2-nd @atom:c2 @atom:nd
- @bond:c2-ne @atom:c2 @atom:ne
- @bond:c2-nf @atom:c2 @atom:nf
- @bond:c2-nh @atom:c2 @atom:nh
- @bond:c2-no @atom:c2 @atom:no
- @bond:c2-o @atom:c2 @atom:o
- @bond:c2-oh @atom:c2 @atom:oh
- @bond:c2-os @atom:c2 @atom:os
- @bond:c2-p2 @atom:c2 @atom:p2
- @bond:c2-p3 @atom:c2 @atom:p3
- @bond:c2-p4 @atom:c2 @atom:p4
- @bond:c2-p5 @atom:c2 @atom:p5
- @bond:c2-pe @atom:c2 @atom:pe
- @bond:c2-pf @atom:c2 @atom:pf
- @bond:c2-s2 @atom:c2 @atom:s2
- @bond:c2-s @atom:c2 @atom:s
- @bond:c2-s4 @atom:c2 @atom:s4
- @bond:c2-s6 @atom:c2 @atom:s6
- @bond:c2-sh @atom:c2 @atom:sh
- @bond:c2-ss @atom:c2 @atom:ss
- @bond:c3-c3 @atom:c3 @atom:c3
- @bond:c3-ca @atom:c3 @atom:ca
- @bond:c3-cc @atom:c3 @atom:cc
- @bond:c3-cd @atom:c3 @atom:cd
- @bond:c3-ce @atom:c3 @atom:ce
- @bond:c3-cf @atom:c3 @atom:cf
- @bond:c3-cl @atom:c3 @atom:cl
- @bond:c3-cu @atom:c3 @atom:cu
- @bond:c3-cv @atom:c3 @atom:cv
- @bond:c3-cx @atom:c3 @atom:cx
- @bond:c3-cy @atom:c3 @atom:cy
- @bond:c3-f @atom:c3 @atom:f
- @bond:c3-h1 @atom:c3 @atom:h1
- @bond:c3-h2 @atom:c3 @atom:h2
- @bond:c3-h3 @atom:c3 @atom:h3
- @bond:c3-hc @atom:c3 @atom:hc
- @bond:c3-hx @atom:c3 @atom:hx
- @bond:c3-i @atom:c3 @atom:i
- @bond:c3-n1 @atom:c3 @atom:n1
- @bond:c3-n2 @atom:c3 @atom:n2
- @bond:c3-n @atom:c3 @atom:n
- @bond:c3-n3 @atom:c3 @atom:n3
- @bond:c3-n4 @atom:c3 @atom:n4
- @bond:c3-na @atom:c3 @atom:na
- @bond:c3-nc @atom:c3 @atom:nc
- @bond:c3-nd @atom:c3 @atom:nd
- @bond:c3-nh @atom:c3 @atom:nh
- @bond:c3-no @atom:c3 @atom:no
- @bond:c3-o @atom:c3 @atom:o
- @bond:c3-oh @atom:c3 @atom:oh
- @bond:c3-os @atom:c3 @atom:os
- @bond:c3-p2 @atom:c3 @atom:p2
- @bond:c3-p3 @atom:c3 @atom:p3
- @bond:c3-p4 @atom:c3 @atom:p4
- @bond:c3-p5 @atom:c3 @atom:p5
- @bond:c3-px @atom:c3 @atom:px
- @bond:c3-py @atom:c3 @atom:py
- @bond:c3-s @atom:c3 @atom:s
- @bond:c3-s4 @atom:c3 @atom:s4
- @bond:c3-s6 @atom:c3 @atom:s6
- @bond:c3-sh @atom:c3 @atom:sh
- @bond:c3-ss @atom:c3 @atom:ss
- @bond:c3-sx @atom:c3 @atom:sx
- @bond:c3-sy @atom:c3 @atom:sy
- @bond:ca-ca @atom:ca @atom:ca
- @bond:ca-cc @atom:ca @atom:cc
- @bond:ca-cd @atom:ca @atom:cd
- @bond:ca-ce @atom:ca @atom:ce
- @bond:ca-cf @atom:ca @atom:cf
- @bond:ca-cg @atom:ca @atom:cg
- @bond:ca-ch @atom:ca @atom:ch
- @bond:ca-cl @atom:ca @atom:cl
- @bond:ca-cp @atom:ca @atom:cp
- @bond:ca-cq @atom:ca @atom:cq
- @bond:ca-cx @atom:ca @atom:cx
- @bond:ca-cy @atom:ca @atom:cy
- @bond:ca-f @atom:ca @atom:f
- @bond:ca-h4 @atom:ca @atom:h4
- @bond:ca-h5 @atom:ca @atom:h5
- @bond:ca-ha @atom:ca @atom:ha
- @bond:ca-i @atom:ca @atom:i
- @bond:ca-n1 @atom:ca @atom:n1
- @bond:ca-n2 @atom:ca @atom:n2
- @bond:ca-n @atom:ca @atom:n
- @bond:ca-n4 @atom:ca @atom:n4
- @bond:ca-na @atom:ca @atom:na
- @bond:ca-nb @atom:ca @atom:nb
- @bond:ca-nc @atom:ca @atom:nc
- @bond:ca-nd @atom:ca @atom:nd
- @bond:ca-ne @atom:ca @atom:ne
- @bond:ca-nf @atom:ca @atom:nf
- @bond:ca-nh @atom:ca @atom:nh
- @bond:ca-no @atom:ca @atom:no
- @bond:ca-o @atom:ca @atom:o
- @bond:ca-oh @atom:ca @atom:oh
- @bond:ca-os @atom:ca @atom:os
- @bond:ca-p2 @atom:ca @atom:p2
- @bond:ca-p3 @atom:ca @atom:p3
- @bond:ca-p4 @atom:ca @atom:p4
- @bond:ca-p5 @atom:ca @atom:p5
- @bond:ca-pe @atom:ca @atom:pe
- @bond:ca-pf @atom:ca @atom:pf
- @bond:ca-px @atom:ca @atom:px
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- @bond:n-nc @atom:n @atom:nc
- @bond:n-nd @atom:n @atom:nd
- @bond:n-nh @atom:n @atom:nh
- @bond:n-no @atom:n @atom:no
- @bond:n-o @atom:n @atom:o
- @bond:n-oh @atom:n @atom:oh
- @bond:no-no @atom:no @atom:no
- @bond:no-o @atom:no @atom:o
- @bond:no-oh @atom:no @atom:oh
- @bond:no-os @atom:no @atom:os
- @bond:no-p2 @atom:no @atom:p2
- @bond:no-p3 @atom:no @atom:p3
- @bond:no-p4 @atom:no @atom:p4
- @bond:no-p5 @atom:no @atom:p5
- @bond:no-s @atom:no @atom:s
- @bond:n-os @atom:n @atom:os
- @bond:no-s4 @atom:no @atom:s4
- @bond:no-s6 @atom:no @atom:s6
- @bond:no-sh @atom:no @atom:sh
- @bond:no-ss @atom:no @atom:ss
- @bond:n-p2 @atom:n @atom:p2
- @bond:n-p3 @atom:n @atom:p3
- @bond:n-p4 @atom:n @atom:p4
- @bond:n-p5 @atom:n @atom:p5
- @bond:n-pc @atom:n @atom:pc
- @bond:n-pd @atom:n @atom:pd
- @bond:n-s @atom:n @atom:s
- @bond:n-s4 @atom:n @atom:s4
- @bond:n-s6 @atom:n @atom:s6
- @bond:n-sh @atom:n @atom:sh
- @bond:n-ss @atom:n @atom:ss
- @bond:n-sy @atom:n @atom:sy
- @bond:oh-oh @atom:oh @atom:oh
- @bond:oh-os @atom:oh @atom:os
- @bond:oh-p2 @atom:oh @atom:p2
- @bond:oh-p3 @atom:oh @atom:p3
- @bond:oh-p4 @atom:oh @atom:p4
- @bond:oh-p5 @atom:oh @atom:p5
- @bond:oh-py @atom:oh @atom:py
- @bond:oh-s @atom:oh @atom:s
- @bond:oh-s4 @atom:oh @atom:s4
- @bond:oh-s6 @atom:oh @atom:s6
- @bond:oh-sh @atom:oh @atom:sh
- @bond:oh-ss @atom:oh @atom:ss
- @bond:oh-sy @atom:oh @atom:sy
- @bond:o-o @atom:o @atom:o
- @bond:o-oh @atom:o @atom:oh
- @bond:o-os @atom:o @atom:os
- @bond:o-p2 @atom:o @atom:p2
- @bond:o-p3 @atom:o @atom:p3
- @bond:o-p4 @atom:o @atom:p4
- @bond:o-p5 @atom:o @atom:p5
- @bond:o-pe @atom:o @atom:pe
- @bond:o-pf @atom:o @atom:pf
- @bond:o-px @atom:o @atom:px
- @bond:o-py @atom:o @atom:py
- @bond:o-s @atom:o @atom:s
- @bond:o-s2 @atom:o @atom:s2
- @bond:o-s4 @atom:o @atom:s4
- @bond:o-s6 @atom:o @atom:s6
- @bond:o-sh @atom:o @atom:sh
- @bond:os-os @atom:os @atom:os
- @bond:os-p2 @atom:os @atom:p2
- @bond:os-p3 @atom:os @atom:p3
- @bond:os-p4 @atom:os @atom:p4
- @bond:os-p5 @atom:os @atom:p5
- @bond:os-py @atom:os @atom:py
- @bond:os-s @atom:os @atom:s
- @bond:o-ss @atom:o @atom:ss
- @bond:os-s4 @atom:os @atom:s4
- @bond:os-s6 @atom:os @atom:s6
- @bond:os-sh @atom:os @atom:sh
- @bond:os-ss @atom:os @atom:ss
- @bond:os-sy @atom:os @atom:sy
- @bond:o-sx @atom:o @atom:sx
- @bond:o-sy @atom:o @atom:sy
- @bond:p2-p2 @atom:p2 @atom:p2
- @bond:p2-p3 @atom:p2 @atom:p3
- @bond:p2-p4 @atom:p2 @atom:p4
- @bond:p2-p5 @atom:p2 @atom:p5
- @bond:p2-pe @atom:p2 @atom:pe
- @bond:p2-pf @atom:p2 @atom:pf
- @bond:p2-s @atom:p2 @atom:s
- @bond:p2-s4 @atom:p2 @atom:s4
- @bond:p2-s6 @atom:p2 @atom:s6
- @bond:p2-sh @atom:p2 @atom:sh
- @bond:p2-ss @atom:p2 @atom:ss
- @bond:p3-p3 @atom:p3 @atom:p3
- @bond:p3-p4 @atom:p3 @atom:p4
- @bond:p3-p5 @atom:p3 @atom:p5
- @bond:p3-s @atom:p3 @atom:s
- @bond:p3-s4 @atom:p3 @atom:s4
- @bond:p3-s6 @atom:p3 @atom:s6
- @bond:p3-sh @atom:p3 @atom:sh
- @bond:p3-ss @atom:p3 @atom:ss
- @bond:p4-p4 @atom:p4 @atom:p4
- @bond:p4-p5 @atom:p4 @atom:p5
- @bond:p4-s @atom:p4 @atom:s
- @bond:p4-s4 @atom:p4 @atom:s4
- @bond:p4-s6 @atom:p4 @atom:s6
- @bond:p4-sh @atom:p4 @atom:sh
- @bond:p4-ss @atom:p4 @atom:ss
- @bond:p5-p5 @atom:p5 @atom:p5
- @bond:p5-s @atom:p5 @atom:s
- @bond:p5-s4 @atom:p5 @atom:s4
- @bond:p5-s6 @atom:p5 @atom:s6
- @bond:p5-sh @atom:p5 @atom:sh
- @bond:p5-ss @atom:p5 @atom:ss
- @bond:pe-pe @atom:pe @atom:pe
- @bond:pe-pf @atom:pe @atom:pf
- @bond:pe-px @atom:pe @atom:px
- @bond:pe-py @atom:pe @atom:py
- @bond:pe-s @atom:pe @atom:s
- @bond:pe-sx @atom:pe @atom:sx
- @bond:pe-sy @atom:pe @atom:sy
- @bond:pf-pf @atom:pf @atom:pf
- @bond:pf-px @atom:pf @atom:px
- @bond:pf-py @atom:pf @atom:py
- @bond:pf-s @atom:pf @atom:s
- @bond:pf-sx @atom:pf @atom:sx
- @bond:pf-sy @atom:pf @atom:sy
- @bond:px-py @atom:px @atom:py
- @bond:px-sx @atom:px @atom:sx
- @bond:px-sy @atom:px @atom:sy
- @bond:py-py @atom:py @atom:py
- @bond:py-sx @atom:py @atom:sx
- @bond:py-sy @atom:py @atom:sy
- @bond:s4-s4 @atom:s4 @atom:s4
- @bond:s4-s6 @atom:s4 @atom:s6
- @bond:s4-sh @atom:s4 @atom:sh
- @bond:s4-ss @atom:s4 @atom:ss
- @bond:s6-s6 @atom:s6 @atom:s6
- @bond:s6-sh @atom:s6 @atom:sh
- @bond:s6-ss @atom:s6 @atom:ss
- @bond:sh-sh @atom:sh @atom:sh
- @bond:sh-ss @atom:sh @atom:ss
- @bond:s-s @atom:s @atom:s
- @bond:s-s2 @atom:s @atom:s2
- @bond:s-s4 @atom:s @atom:s4
- @bond:s-s6 @atom:s @atom:s6
- @bond:s-sh @atom:s @atom:sh
- @bond:s-ss @atom:s @atom:ss
- @bond:ss-ss @atom:ss @atom:ss
- @bond:sx-sx @atom:sx @atom:sx
- @bond:sx-sy @atom:sx @atom:sy
- @bond:sy-sy @atom:sy @atom:sy
- @bond:br-cd @atom:br @atom:cd
- @bond:c1-cf @atom:c1 @atom:cf
- @bond:cd-f @atom:cd @atom:f
- @bond:cd-n4 @atom:cd @atom:n4
- @bond:cd-nf @atom:cd @atom:nf
- @bond:cd-no @atom:cd @atom:no
- @bond:cd-sh @atom:cd @atom:sh
- @bond:cd-sx @atom:cd @atom:sx
- @bond:cc-cy @atom:cc @atom:cy
- @bond:cf-cl @atom:cf @atom:cl
- @bond:cf-cx @atom:cf @atom:cx
- @bond:cf-cy @atom:cf @atom:cy
- @bond:cf-na @atom:cf @atom:na
- @bond:cf-ss @atom:cf @atom:ss
- @bond:cq-na @atom:cq @atom:na
- @bond:cq-nb @atom:cq @atom:nb
- } # (end of Bonds By Type)
-
- write_once("In Settings") {
- angle_coeff @angle:hw-ow-hw harmonic 100.00 104.52 # AMBER 1 TIP3P_water
- angle_coeff @angle:hw-hw-ow harmonic 0.00 127.74 # AMBER 1 (found_in_crystallographic_water_with_3_bonds)
- angle_coeff @angle:br-c1-br harmonic 57.76 180.00 # Guess 0
- angle_coeff @angle:br-c1-c1 harmonic 54.93 180.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-c1 harmonic 64.41 180.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-c2 harmonic 60.84 180.00 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-c1-c3 harmonic 56.28 178.46 # SOURCE4 188 0.6631
- angle_coeff @angle:c1-c1-ca harmonic 56.92 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-cl harmonic 51.40 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-f harmonic 61.02 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-ha harmonic 44.84 178.38 # SOURCE3 41 2.0683
- angle_coeff @angle:c1-c1-hc harmonic 44.73 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-i harmonic 49.80 180.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-n1 harmonic 67.17 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-n2 harmonic 65.17 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-n3 harmonic 59.77 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-n4 harmonic 59.09 179.56 # SOURCE3 3 0.3096
- angle_coeff @angle:c1-c1-n harmonic 62.13 177.18 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-na harmonic 61.23 176.75 # SOURCE3 8 2.9328
- angle_coeff @angle:c1-c1-nh harmonic 61.44 179.27 # SOURCE3 3 0.2357
- angle_coeff @angle:c1-c1-no harmonic 59.38 180.00 # SOURCE3 3 0.0000
- angle_coeff @angle:c1-c1-o harmonic 66.79 180.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-oh harmonic 62.70 176.65 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-os harmonic 62.77 176.42 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-c1-p2 harmonic 65.19 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-p3 harmonic 66.41 169.63 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-c1-p4 harmonic 64.47 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-p5 harmonic 66.52 176.17 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-c1-s4 harmonic 54.12 167.47 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-c1-s6 harmonic 53.74 174.38 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-c1-s harmonic 55.65 179.97 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c1-sh harmonic 54.14 180.00 # SOURCE3 1
- angle_coeff @angle:c1-c1-ss harmonic 55.22 173.22 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-c1-c2 harmonic 58.20 180.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-c1-ce harmonic 58.18 179.01 # SOURCE4 6 0.4656
- angle_coeff @angle:c2-c1-n1 harmonic 63.14 180.00 # HF/6-31G* 1
- angle_coeff @angle:c2-c1-o harmonic 63.07 179.50 # SOURCE2 1 0.0000
- angle_coeff @angle:c2-c1-s2 harmonic 56.73 172.98 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-c1-c3 harmonic 51.75 180.00 # Guess 0
- angle_coeff @angle:c3-c1-cg harmonic 55.79 178.52 # SOURCE4 39 0.5063
- angle_coeff @angle:c3-c1-n1 harmonic 58.10 178.50 # SOURCE4 77 0.5443
- angle_coeff @angle:ca-c1-ca harmonic 52.83 180.00 # Guess 0
- angle_coeff @angle:c-c1-c1 harmonic 56.33 180.00 # SOURCE3 1
- angle_coeff @angle:cg-c1-ha harmonic 43.98 177.41 # SOURCE3 22 2.4947
- angle_coeff @angle:ch-c1-ha harmonic 43.98 177.41 # SOURCE3 22 same_as_cg-c1-ha
- angle_coeff @angle:cl-c1-cl harmonic 46.64 180.00 # Guess 0
- angle_coeff @angle:f-c1-f harmonic 58.19 180.00 # Guess 0
- angle_coeff @angle:i-c1-i harmonic 53.41 180.00 # Guess 0
- angle_coeff @angle:n1-c1-n1 harmonic 93.20 102.01 # SOURCE3 1
- angle_coeff @angle:n1-c1-n3 harmonic 63.71 169.70 # SOURCE2 1 0.0000
- angle_coeff @angle:n1-c1-nh harmonic 64.02 177.43 # SOURCE4 7 0.7877
- angle_coeff @angle:n1-c1-os harmonic 64.72 178.59 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-c1-p3 harmonic 67.69 171.20 # SOURCE2 1 0.0000
- angle_coeff @angle:n1-c1-ss harmonic 55.82 178.68 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-c1-n2 harmonic 65.99 180.00 # Guess 0
- angle_coeff @angle:n2-c1-o harmonic 69.15 171.79 # SOURCE3 2 0.3594
- angle_coeff @angle:n2-c1-s harmonic 57.48 176.01 # SOURCE4 9 0.1123
- angle_coeff @angle:n3-c1-n3 harmonic 57.36 180.00 # Guess 0
- angle_coeff @angle:n4-c1-n4 harmonic 56.35 180.00 # Guess 0
- angle_coeff @angle:na-c1-na harmonic 58.62 180.00 # Guess 0
- angle_coeff @angle:ne-c1-o harmonic 69.39 172.33 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-c1-s harmonic 57.59 175.81 # SOURCE4 8 0.2356
- angle_coeff @angle:nf-c1-o harmonic 69.39 172.33 # SOURCE3 1 same_as_ne-c1-o
- angle_coeff @angle:nh-c1-nh harmonic 59.55 180.00 # Guess 0
- angle_coeff @angle:n-c1-n harmonic 60.03 180.00 # Guess 0
- angle_coeff @angle:no-c1-no harmonic 56.83 180.00 # Guess 0
- angle_coeff @angle:oh-c1-oh harmonic 60.91 180.00 # Guess 0
- angle_coeff @angle:o-c1-o harmonic 69.27 180.00 # Guess 0
- angle_coeff @angle:os-c1-os harmonic 60.96 180.00 # Guess 0
- angle_coeff @angle:p2-c1-p2 harmonic 80.59 180.00 # Guess 0
- angle_coeff @angle:p3-c1-p3 harmonic 79.69 180.00 # Guess 0
- angle_coeff @angle:p4-c1-p4 harmonic 79.69 180.00 # Guess 0
- angle_coeff @angle:p5-c1-p5 harmonic 81.37 180.00 # Guess 0
- angle_coeff @angle:s2-c1-s2 harmonic 55.83 180.00 # Guess 0
- angle_coeff @angle:s4-c1-s4 harmonic 51.00 180.00 # Guess 0
- angle_coeff @angle:s6-c1-s6 harmonic 51.72 180.00 # Guess 0
- angle_coeff @angle:sh-c1-sh harmonic 53.01 180.00 # Guess 0
- angle_coeff @angle:s-c1-s harmonic 54.63 180.00 # Guess 0
- angle_coeff @angle:ss-c1-ss harmonic 53.04 180.00 # Guess 0
- angle_coeff @angle:br-c2-br harmonic 68.56 115.06 # SOURCE3 1 0.0000
- angle_coeff @angle:br-c2-c2 harmonic 63.97 118.96 # SOURCE4 6 0.4902
- angle_coeff @angle:br-c2-c3 harmonic 63.71 115.33 # SOURCE4 6 0.5872
- angle_coeff @angle:br-c2-ce harmonic 63.21 121.59 # SOURCE4 7 0.7078
- angle_coeff @angle:br-c2-h4 harmonic 43.04 113.94 # SOURCE4 6 0.4017
- angle_coeff @angle:br-c2-ha harmonic 43.18 113.28 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-c2-c1 harmonic 72.26 116.77 # SOURCE3 1
- angle_coeff @angle:c1-c2-c2 harmonic 70.34 121.62 # SOURCE3 1
- angle_coeff @angle:c1-c2-c3 harmonic 64.22 124.92 # SOURCE4 17 0.7576
- angle_coeff @angle:c1-c2-f harmonic 67.99 124.90 # SOURCE2 1 0.0000
- angle_coeff @angle:c1-c2-ha harmonic 50.43 121.37 # SOURCE3 8 0.0055
- angle_coeff @angle:c2-c2-c2 harmonic 69.84 121.81 # SOURCE3 10 0.3843
- angle_coeff @angle:c2-c2-c3 harmonic 64.33 123.42 # SOURCE3 41 2.6057
- angle_coeff @angle:c2-c2-ca harmonic 66.88 117.00 # SOURCE3 1
- angle_coeff @angle:c2-c2-cc harmonic 70.22 117.21 # SOURCE3 2 0.3418
- angle_coeff @angle:c2-c2-cd harmonic 70.22 117.21 # SOURCE3 2 same_as_c2-c2-cc
- angle_coeff @angle:c2-c2-cl harmonic 58.43 122.85 # SOURCE4 23 0.6711
- angle_coeff @angle:c2-c2-cx harmonic 64.50 125.40 # SOURCE4 12 1.8494
- angle_coeff @angle:c2-c2-cy harmonic 70.42 103.30 # SOURCE2 1 0.0000
- angle_coeff @angle:c2-c2-f harmonic 68.11 122.92 # SOURCE4 12 0.5301
- angle_coeff @angle:c2-c2-h4 harmonic 49.75 122.54 # SOURCE4 69 1.1900
- angle_coeff @angle:c2-c2-ha harmonic 50.04 120.94 # SOURCE3 254 1.3150
- angle_coeff @angle:c2-c2-hc harmonic 50.30 119.70 # SOURCE3 1
- angle_coeff @angle:c2-c2-hx harmonic 48.98 126.45 # SOURCE3 3 0.0219
- angle_coeff @angle:c2-c2-i harmonic 56.28 121.03 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-c2-n1 harmonic 71.69 122.98 # HF/6-31G* 1
- angle_coeff @angle:c2-c2-n2 harmonic 71.29 126.01 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-c2-n3 harmonic 70.33 124.55 # SOURCE3 1
- angle_coeff @angle:c2-c2-n4 harmonic 67.18 121.52 # SOURCE3 5 1.2656
- angle_coeff @angle:c2-c2-n harmonic 68.86 123.20 # SOURCE4 15 1.8657
- angle_coeff @angle:c2-c2-na harmonic 69.83 121.38 # SOURCE3 26 6.9463
- angle_coeff @angle:c2-c2-nh harmonic 69.80 124.99 # SOURCE3 7 0.9929
- angle_coeff @angle:c2-c2-no harmonic 67.52 124.09 # SOURCE4 6 1.2772
- angle_coeff @angle:c2-c2-o harmonic 71.92 130.89 # SOURCE3 2 0.0201
- angle_coeff @angle:c2-c2-oh harmonic 71.64 122.07 # SOURCE4 6 1.0883
- angle_coeff @angle:c2-c2-os harmonic 71.04 121.89 # SOURCE4 33 1.3457
- angle_coeff @angle:c2-c2-p2 harmonic 84.73 115.10 # SOURCE3 1
- angle_coeff @angle:c2-c2-p3 harmonic 75.19 124.83 # SOURCE3 5 2.1222
- angle_coeff @angle:c2-c2-p4 harmonic 77.22 119.76 # SOURCE3 1
- angle_coeff @angle:c2-c2-p5 harmonic 73.70 125.97 # SOURCE3 1
- angle_coeff @angle:c2-c2-s4 harmonic 62.85 119.84 # SOURCE3 1
- angle_coeff @angle:c2-c2-s6 harmonic 62.81 120.01 # SOURCE3 1
- angle_coeff @angle:c2-c2-s harmonic 61.25 129.37 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-c2-sh harmonic 60.87 125.70 # SOURCE3 3 1.3390
- angle_coeff @angle:c2-c2-ss harmonic 62.79 122.86 # SOURCE4 13 1.7467
- angle_coeff @angle:c3-c2-c3 harmonic 62.70 116.52 # SOURCE3 15 3.1001
- angle_coeff @angle:c3-c2-cc harmonic 63.22 125.39 # CORR 27
- angle_coeff @angle:c3-c2-cd harmonic 63.22 125.39 # CORR 27
- angle_coeff @angle:c3-c2-ce harmonic 64.17 123.08 # CORR 1288
- angle_coeff @angle:c3-c2-cf harmonic 64.17 123.08 # CORR 1288
- angle_coeff @angle:c3-c2-h4 harmonic 45.30 119.25 # SOURCE4 22 2.1707
- angle_coeff @angle:c3-c2-ha harmonic 45.66 117.30 # SOURCE3 33 1.7453
- angle_coeff @angle:c3-c2-hc harmonic 45.15 120.00 # SOURCE3 1
- angle_coeff @angle:c3-c2-n2 harmonic 66.47 123.52 # SOURCE4 141 2.2935
- angle_coeff @angle:c3-c2-n harmonic 66.79 114.80 # SOURCE4 12 1.8112
- angle_coeff @angle:c3-c2-na harmonic 64.95 122.54 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-c2-ne harmonic 66.96 122.15 # SOURCE3 4 0.2197
- angle_coeff @angle:c3-c2-nf harmonic 66.96 122.15 # SOURCE3 4 same_as_c3-c2-ne
- angle_coeff @angle:c3-c2-nh harmonic 66.69 118.59 # SOURCE3 6 2.2622
- angle_coeff @angle:c3-c2-o harmonic 67.88 123.18 # SOURCE4 5 0.9226
- angle_coeff @angle:c3-c2-oh harmonic 68.50 115.04 # SOURCE4 36 2.0110
- angle_coeff @angle:c3-c2-os harmonic 68.77 112.69 # SOURCE4 50 2.4254
- angle_coeff @angle:c3-c2-p2 harmonic 78.98 122.74 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-c2-s harmonic 62.79 115.44 # SOURCE3 2 0.0115
- angle_coeff @angle:c3-c2-ss harmonic 61.62 119.66 # SOURCE4 45 1.9732
- angle_coeff @angle:ca-c2-ca harmonic 63.51 117.88 # SOURCE3 1
- angle_coeff @angle:ca-c2-hc harmonic 45.28 123.30 # SOURCE3 1
- angle_coeff @angle:c-c2-c2 harmonic 67.93 120.70 # SOURCE3 1
- angle_coeff @angle:c-c2-c3 harmonic 63.87 119.70 # SOURCE3 1
- angle_coeff @angle:c-c2-c harmonic 66.57 118.88 # SOURCE3 1
- angle_coeff @angle:cc-c2-h4 harmonic 49.19 120.33 # SOURCE4 7 0.0865
- angle_coeff @angle:cc-c2-ha harmonic 49.07 120.76 # SOURCE3 11 1.4155
- angle_coeff @angle:cc-c2-nh harmonic 69.46 122.96 # SOURCE4 10 0.7347
- angle_coeff @angle:cc-c2-o harmonic 72.80 123.59 # SOURCE4 6 0.0560
- angle_coeff @angle:cd-c2-ha harmonic 49.07 120.76 # SOURCE3 11 1.4155
- angle_coeff @angle:ce-c2-cl harmonic 58.06 123.90 # SOURCE4 11 0.3570
- angle_coeff @angle:ce-c2-h4 harmonic 49.38 122.29 # SOURCE4 75 1.4008
- angle_coeff @angle:ce-c2-ha harmonic 49.57 121.19 # SOURCE3 122 0.5318
- angle_coeff @angle:ce-c2-na harmonic 68.82 123.71 # SOURCE4 6 2.0109
- angle_coeff @angle:ce-c2-nh harmonic 70.64 120.72 # SOURCE4 93 2.2537
- angle_coeff @angle:ce-c2-no harmonic 68.45 119.65 # SOURCE4 5 0.9817
- angle_coeff @angle:ce-c2-o harmonic 73.66 123.08 # SOURCE4 5 0.2391
- angle_coeff @angle:ce-c2-oh harmonic 70.90 123.27 # SOURCE4 42 1.8111
- angle_coeff @angle:ce-c2-os harmonic 70.47 122.52 # SOURCE4 51 2.4680
- angle_coeff @angle:cf-c2-ha harmonic 49.57 121.19 # SOURCE3 122 same_as_ce-c2-ha
- angle_coeff @angle:c-c2-ha harmonic 47.67 121.33 # SOURCE3 4 0.2462
- angle_coeff @angle:c-c2-hc harmonic 48.00 119.70 # SOURCE3 1
- angle_coeff @angle:cl-c2-cl harmonic 55.44 114.27 # SOURCE4 10 0.5850
- angle_coeff @angle:cl-c2-h4 harmonic 40.76 113.77 # SOURCE4 9 0.6228
- angle_coeff @angle:cl-c2-ha harmonic 40.86 113.20 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-c2-ha harmonic 46.61 115.89 # SOURCE4 15 0.3682
- angle_coeff @angle:f-c2-f harmonic 70.67 109.60 # SOURCE2 2 0.6000
- angle_coeff @angle:f-c2-ha harmonic 51.25 110.00 # SOURCE2 1 0.0000
- angle_coeff @angle:h4-c2-n2 harmonic 52.40 120.69 # SOURCE4 13 1.3105
- angle_coeff @angle:h4-c2-n harmonic 50.48 113.57 # SOURCE4 26 1.0283
- angle_coeff @angle:h4-c2-na harmonic 51.03 113.22 # SOURCE4 9 0.6345
- angle_coeff @angle:h4-c2-ne harmonic 52.87 119.63 # SOURCE4 10 1.6786
- angle_coeff @angle:h4-c2-nh harmonic 51.55 115.64 # SOURCE4 31 1.0081
- angle_coeff @angle:h4-c2-no harmonic 49.39 113.38 # SOURCE4 6 0.1240
- angle_coeff @angle:h4-c2-os harmonic 52.23 113.70 # SOURCE3 13 2.0464
- angle_coeff @angle:h4-c2-ss harmonic 42.85 118.47 # SOURCE3 9 2.5335
- angle_coeff @angle:h5-c2-n2 harmonic 52.41 120.16 # SOURCE4 27 1.8999
- angle_coeff @angle:h5-c2-na harmonic 48.23 126.39 # SOURCE3 4 0.3299
- angle_coeff @angle:h5-c2-ne harmonic 52.76 119.62 # SOURCE4 17 1.3235
- angle_coeff @angle:h5-c2-nh harmonic 51.85 113.93 # SOURCE4 50 0.8394
- angle_coeff @angle:ha-c2-ha harmonic 38.02 117.65 # SOURCE3 349 1.3426
- angle_coeff @angle:ha-c2-n1 harmonic 51.83 120.76 # SOURCE3 8 0.6632
- angle_coeff @angle:ha-c2-n2 harmonic 52.39 120.54 # SOURCE3 92 1.4571
- angle_coeff @angle:ha-c2-n3 harmonic 52.44 113.54 # SOURCE3 1
- angle_coeff @angle:ha-c2-n harmonic 50.49 113.40 # SOURCE3 4 1.2182
- angle_coeff @angle:ha-c2-na harmonic 51.18 112.42 # SOURCE3 8 0.6507
- angle_coeff @angle:ha-c2-ne harmonic 52.48 121.18 # SOURCE3 68 0.6824
- angle_coeff @angle:ha-c2-nf harmonic 52.48 121.18 # SOURCE3 68 same_as_ha-c2-ne
- angle_coeff @angle:ha-c2-nh harmonic 51.29 116.68 # SOURCE3 13 2.5734
- angle_coeff @angle:ha-c2-no harmonic 49.64 112.14 # SOURCE3 2 0.0264
- angle_coeff @angle:ha-c2-o harmonic 55.30 117.23 # SOURCE3 2 0.0201
- angle_coeff @angle:ha-c2-oh harmonic 52.34 116.18 # SOURCE3 2 0.0000
- angle_coeff @angle:ha-c2-os harmonic 52.43 112.69 # SOURCE3 13 2.5851
- angle_coeff @angle:ha-c2-p2 harmonic 55.74 121.48 # SOURCE3 122 0.4329
- angle_coeff @angle:ha-c2-p3 harmonic 52.04 114.31 # SOURCE3 3 0.0000
- angle_coeff @angle:ha-c2-p4 harmonic 51.62 117.86 # SOURCE3 1
- angle_coeff @angle:ha-c2-p5 harmonic 49.81 120.10 # SOURCE3 2 0.0000
- angle_coeff @angle:ha-c2-pe harmonic 55.05 121.46 # SOURCE3 104 0.7821
- angle_coeff @angle:ha-c2-pf harmonic 55.05 121.46 # SOURCE3 104 same_as_ha-c2-pe
- angle_coeff @angle:ha-c2-s2 harmonic 46.19 118.74 # SOURCE3 2 0.0000
- angle_coeff @angle:ha-c2-s4 harmonic 42.81 115.30 # SOURCE3 2 0.0000
- angle_coeff @angle:ha-c2-s harmonic 43.42 115.70 # SOURCE3 2 0.0000
- angle_coeff @angle:ha-c2-s6 harmonic 42.58 116.60 # SOURCE3 2 0.0000
- angle_coeff @angle:ha-c2-sh harmonic 43.04 111.74 # SOURCE3 1 0.0000
- angle_coeff @angle:ha-c2-ss harmonic 43.18 116.72 # SOURCE3 7 2.7543
- angle_coeff @angle:hc-c2-hc harmonic 37.81 118.92 # SOURCE3 1
- angle_coeff @angle:hc-c2-n2 harmonic 52.42 120.40 # SOURCE3 1
- angle_coeff @angle:hc-c2-n harmonic 50.35 114.04 # SOURCE3 1
- angle_coeff @angle:hc-c2-na harmonic 49.73 119.10 # SOURCE3 1
- angle_coeff @angle:hc-c2-nh harmonic 52.03 113.36 # SOURCE3 1
- angle_coeff @angle:hc-c2-no harmonic 49.64 112.12 # SOURCE3 1
- angle_coeff @angle:hc-c2-oh harmonic 52.33 116.22 # SOURCE3 1
- angle_coeff @angle:hc-c2-os harmonic 51.65 116.11 # SOURCE3 1
- angle_coeff @angle:hc-c2-p3 harmonic 51.40 117.19 # SOURCE3 1
- angle_coeff @angle:hc-c2-p5 harmonic 49.92 119.58 # SOURCE3 1
- angle_coeff @angle:hc-c2-s4 harmonic 42.66 116.12 # SOURCE3 1
- angle_coeff @angle:hc-c2-s6 harmonic 42.79 115.45 # SOURCE3 1
- angle_coeff @angle:hc-c2-sh harmonic 42.31 115.63 # SOURCE3 1
- angle_coeff @angle:hc-c2-ss harmonic 43.38 115.62 # SOURCE3 1
- angle_coeff @angle:hx-c2-n4 harmonic 48.42 113.03 # SOURCE3 3 0.3873
- angle_coeff @angle:i-c2-i harmonic 60.96 117.94 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-c2-n1 harmonic 73.61 124.15 # HF/6-31G* 1
- angle_coeff @angle:n2-c2-n2 harmonic 77.96 113.82 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-c2-n4 harmonic 72.03 113.05 # SOURCE4 6 0.3318
- angle_coeff @angle:n2-c2-na harmonic 71.71 123.62 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-c2-nh harmonic 72.62 124.27 # SOURCE3 12 2.4114
- angle_coeff @angle:n2-c2-oh harmonic 74.36 122.08 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-c2-os harmonic 74.32 119.82 # SOURCE4 20 1.2664
- angle_coeff @angle:n2-c2-ss harmonic 62.86 129.77 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-c2-n3 harmonic 73.45 118.47 # SOURCE3 1
- angle_coeff @angle:n4-c2-n4 harmonic 67.72 113.93 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-c2-ss harmonic 64.40 116.26 # SOURCE4 7 2.4226
- angle_coeff @angle:na-c2-na harmonic 73.65 109.33 # SOURCE3 3 3.0187
- angle_coeff @angle:ne-c2-nh harmonic 73.03 123.56 # CORR 128
- angle_coeff @angle:ne-c2-os harmonic 74.86 118.76 # SOURCE4 5 0.3382
- angle_coeff @angle:ne-c2-ss harmonic 65.41 120.06 # SOURCE4 9 1.3423
- angle_coeff @angle:nf-c2-nh harmonic 73.03 123.56 # CORR 128
- angle_coeff @angle:nh-c2-nh harmonic 74.46 112.72 # SOURCE4 257 1.8176
- angle_coeff @angle:nh-c2-oh harmonic 74.05 117.16 # SOURCE4 7 0.8698
- angle_coeff @angle:nh-c2-os harmonic 74.32 114.29 # SOURCE4 18 1.0900
- angle_coeff @angle:nh-c2-ss harmonic 67.23 111.55 # SOURCE4 37 1.1778
- angle_coeff @angle:n-c2-n2 harmonic 70.56 125.95 # SOURCE3 2 5.0202
- angle_coeff @angle:n-c2-n harmonic 71.55 113.23 # SOURCE3 1 0.0000
- angle_coeff @angle:n-c2-na harmonic 74.57 105.42 # SOURCE3 1 0.0000
- angle_coeff @angle:n-c2-ne harmonic 70.89 125.38 # SOURCE4 10 1.6819
- angle_coeff @angle:n-c2-nh harmonic 74.20 109.14 # SOURCE4 22 1.5634
- angle_coeff @angle:no-c2-no harmonic 69.43 113.90 # SOURCE3 1 0.0000
- angle_coeff @angle:n-c2-ss harmonic 66.83 111.06 # SOURCE4 9 0.5522
- angle_coeff @angle:oh-c2-oh harmonic 76.03 114.33 # SOURCE3 1 0.0000
- angle_coeff @angle:o-c2-o harmonic 80.23 121.69 # SOURCE3 1
- angle_coeff @angle:o-c2-oh harmonic 76.69 121.23 # SOURCE4 6 0.0958
- angle_coeff @angle:o-c2-s harmonic 64.15 127.68 # SOURCE3 2 0.0547
- angle_coeff @angle:os-c2-os harmonic 74.21 115.80 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-c2-p2 harmonic 100.59 129.80 # SOURCE3 1
- angle_coeff @angle:p3-c2-p3 harmonic 97.08 115.54 # SOURCE3 1 0.0000
- angle_coeff @angle:p5-c2-p5 harmonic 92.92 121.85 # SOURCE3 1
- angle_coeff @angle:s4-c2-s4 harmonic 61.89 120.32 # SOURCE3 1
- angle_coeff @angle:s4-c2-s6 harmonic 61.98 119.95 # SOURCE3 1
- angle_coeff @angle:s6-c2-s6 harmonic 61.98 119.97 # SOURCE3 1
- angle_coeff @angle:sh-c2-sh harmonic 63.96 110.48 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-c2-ss harmonic 62.65 117.82 # SOURCE3 1
- angle_coeff @angle:s-c2-s harmonic 62.47 121.67 # SOURCE3 1
- angle_coeff @angle:ss-c2-ss harmonic 62.77 120.24 # SOURCE3 1 0.0000
- angle_coeff @angle:br-c3-br harmonic 67.46 109.03 # SOURCE4 6 0.5435
- angle_coeff @angle:br-c3-c1 harmonic 62.77 111.80 # SOURCE2 3 0.2160
- angle_coeff @angle:br-c3-c3 harmonic 63.03 109.25 # SOURCE3 10 0.5685
- angle_coeff @angle:br-c3-c harmonic 62.92 110.37 # SOURCE4 13 2.4747
- angle_coeff @angle:br-c3-h1 harmonic 43.12 103.04 # SOURCE3 5 0.3092
- angle_coeff @angle:br-c3-h2 harmonic 42.34 107.10 # SOURCE4 7 0.2378
- angle_coeff @angle:br-c3-hc harmonic 42.40 106.50 # SOURCE3 1
- angle_coeff @angle:c1-c3-c1 harmonic 66.50 109.00 # SOURCE2 1 0.0000
- angle_coeff @angle:c1-c3-c2 harmonic 65.00 111.11 # SOURCE4 12 0.7366
- angle_coeff @angle:c1-c3-c3 harmonic 64.29 111.42 # SOURCE4 197 1.2106
- angle_coeff @angle:c1-c3-ca harmonic 64.93 110.95 # SOURCE4 28 1.1203
- angle_coeff @angle:c1-c3-cc harmonic 64.32 114.20 # CORR 13
- angle_coeff @angle:c1-c3-cd harmonic 64.32 114.20 # CORR 13
- angle_coeff @angle:c1-c3-cl harmonic 58.49 110.63 # SOURCE2 3 1.2257
- angle_coeff @angle:c1-c3-h1 harmonic 48.35 109.29 # SOURCE4 133 0.5701
- angle_coeff @angle:c1-c3-hc harmonic 48.25 109.75 # SOURCE3 12 0.8436
- angle_coeff @angle:c1-c3-hx harmonic 47.76 112.05 # SOURCE4 17 0.2587
- angle_coeff @angle:c1-c3-n3 harmonic 67.03 112.59 # SOURCE4 28 0.9555
- angle_coeff @angle:c1-c3-n4 harmonic 66.53 112.04 # SOURCE4 11 0.5701
- angle_coeff @angle:c1-c3-n harmonic 67.41 112.08 # SOURCE4 18 0.9568
- angle_coeff @angle:c1-c3-nh harmonic 67.25 112.79 # SOURCE4 8 0.9453
- angle_coeff @angle:c1-c3-oh harmonic 69.49 109.14 # SOURCE4 39 0.6500
- angle_coeff @angle:c1-c3-os harmonic 69.27 108.88 # SOURCE4 31 0.9597
- angle_coeff @angle:c2-c3-c2 harmonic 63.93 112.08 # SOURCE4 153 0.7742
- angle_coeff @angle:c2-c3-c3 harmonic 63.53 111.44 # SOURCE4 2891 1.7167
- angle_coeff @angle:c2-c3-ca harmonic 63.71 112.45 # SOURCE4 141 1.6755
- angle_coeff @angle:c2-c3-cc harmonic 64.24 111.64 # CORR 32
- angle_coeff @angle:c2-c3-cd harmonic 64.24 111.64 # CORR 32
- angle_coeff @angle:c2-c3-ce harmonic 64.05 111.87 # CORR 38
- angle_coeff @angle:c2-c3-cf harmonic 64.05 111.87 # CORR 38
- angle_coeff @angle:c2-c3-cl harmonic 57.71 112.07 # SOURCE4 6 0.9936
- angle_coeff @angle:c2-c3-cx harmonic 63.65 112.62 # SOURCE4 17 1.3287
- angle_coeff @angle:c2-c3-cy harmonic 66.76 101.33 # SOURCE4 58 0.9262
- angle_coeff @angle:c2-c3-f harmonic 66.52 110.96 # SOURCE4 25 0.2829
- angle_coeff @angle:c2-c3-h1 harmonic 47.03 110.46 # SOURCE3 17 1.1525
- angle_coeff @angle:c2-c3-h2 harmonic 46.84 111.19 # SOURCE4 17 0.8311
- angle_coeff @angle:c2-c3-hc harmonic 47.03 110.49 # SOURCE3 159 0.7479
- angle_coeff @angle:c2-c3-hx harmonic 46.83 111.45 # SOURCE4 20 0.9004
- angle_coeff @angle:c2-c3-n2 harmonic 67.09 108.99 # SOURCE4 10 1.2025
- angle_coeff @angle:c2-c3-n3 harmonic 66.47 111.52 # SOURCE4 158 1.4012
- angle_coeff @angle:c2-c3-n harmonic 66.73 111.38 # SOURCE4 67 1.7559
- angle_coeff @angle:c2-c3-na harmonic 66.24 113.30 # SOURCE4 27 1.2945
- angle_coeff @angle:c2-c3-nh harmonic 67.10 110.27 # SOURCE4 56 1.8018
- angle_coeff @angle:c2-c3-oh harmonic 68.18 110.21 # SOURCE4 220 1.4197
- angle_coeff @angle:c2-c3-os harmonic 68.45 108.48 # SOURCE4 204 1.6082
- angle_coeff @angle:c2-c3-s4 harmonic 62.57 109.73 # SOURCE4 6 0.1722
- angle_coeff @angle:c2-c3-ss harmonic 63.62 104.97 # SOURCE3 2 2.2248
- angle_coeff @angle:c3-c3-c3 harmonic 63.21 110.63 # SOURCE3 507 2.7845
- angle_coeff @angle:c3-c3-ca harmonic 63.25 112.09 # SOURCE4 3859 1.5523
- angle_coeff @angle:c3-c3-cc harmonic 63.58 111.89 # CORR 700
- angle_coeff @angle:c3-c3-cd harmonic 63.58 111.89 # CORR 700
- angle_coeff @angle:c3-c3-ce harmonic 63.70 111.06 # CORR 490
- angle_coeff @angle:c3-c3-cf harmonic 63.70 111.06 # CORR 490
- angle_coeff @angle:c3-c3-cl harmonic 57.85 110.33 # SOURCE3 20 1.1495
- angle_coeff @angle:c3-c3-cx harmonic 63.30 111.82 # SOURCE4 179 2.4814
- angle_coeff @angle:c3-c3-cy harmonic 63.63 109.62 # SOURCE3 5 2.0747
- angle_coeff @angle:c3-c3-f harmonic 66.22 109.41 # SOURCE3 18 1.1878
- angle_coeff @angle:c3-c3-h1 harmonic 46.36 110.07 # SOURCE3 457 1.1542
- angle_coeff @angle:c3-c3-h2 harmonic 46.02 111.59 # SOURCE3 8 1.1217
- angle_coeff @angle:c3-c3-hc harmonic 46.37 110.05 # SOURCE3 2092 0.6991
- angle_coeff @angle:c3-c3-hx harmonic 46.02 111.74 # SOURCE3 15 1.2365
- angle_coeff @angle:c3-c3-i harmonic 58.48 110.96 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-c3-n1 harmonic 66.64 108.86 # SOURCE4 9 0.8093
- angle_coeff @angle:c3-c3-n2 harmonic 66.40 109.16 # SOURCE3 8 1.4079
- angle_coeff @angle:c3-c3-n3 harmonic 66.18 110.38 # SOURCE3 69 2.9054
- angle_coeff @angle:c3-c3-n4 harmonic 64.45 114.32 # SOURCE4 567 2.4412
- angle_coeff @angle:c3-c3-n harmonic 65.85 112.13 # SOURCE3 31 2.0700
- angle_coeff @angle:c3-c3-na harmonic 65.73 112.81 # SOURCE4 595 1.5050
- angle_coeff @angle:c3-c3-nh harmonic 66.39 110.45 # SOURCE4 1514 1.3881
- angle_coeff @angle:c3-c3-no harmonic 65.21 109.27 # SOURCE4 25 1.1817
- angle_coeff @angle:c3-c3-o harmonic 68.59 112.97 # SOURCE4 14 1.0277
- angle_coeff @angle:c3-c3-oh harmonic 67.72 109.43 # SOURCE3 48 1.5023
- angle_coeff @angle:c3-c3-os harmonic 67.78 108.42 # SOURCE3 122 1.6759
- angle_coeff @angle:c3-c3-p3 harmonic 76.46 113.19 # SOURCE4 15 0.2974
- angle_coeff @angle:c3-c3-p5 harmonic 77.70 112.32 # SOURCE4 106 1.1753
- angle_coeff @angle:c3-c3-s4 harmonic 62.16 110.07 # SOURCE4 38 0.8510
- angle_coeff @angle:c3-c3-s6 harmonic 62.98 110.00 # SOURCE4 152 1.4278
- angle_coeff @angle:c3-c3-sh harmonic 60.98 113.02 # SOURCE4 80 1.3442
- angle_coeff @angle:c3-c3-ss harmonic 61.10 112.69 # SOURCE3 24 2.1842
- angle_coeff @angle:c3-c3-sy harmonic 62.81 109.91 # SOURCE4 22 0.9248
- angle_coeff @angle:ca-c3-ca harmonic 63.66 112.26 # SOURCE4 385 1.7047
- angle_coeff @angle:ca-c3-cc harmonic 63.92 112.38 # CORR 69
- angle_coeff @angle:ca-c3-cd harmonic 63.92 112.38 # CORR 69
- angle_coeff @angle:ca-c3-ce harmonic 63.81 112.33 # SOURCE4 51 1.1929
- angle_coeff @angle:ca-c3-cl harmonic 57.85 111.31 # SOURCE4 16 0.8077
- angle_coeff @angle:ca-c3-cx harmonic 63.69 112.10 # SOURCE4 5 2.1117
- angle_coeff @angle:ca-c3-f harmonic 66.14 111.76 # SOURCE4 449 0.3492
- angle_coeff @angle:ca-c3-h1 harmonic 46.78 110.95 # SOURCE3 12 1.1170
- angle_coeff @angle:ca-c3-h2 harmonic 47.03 109.66 # SOURCE4 29 1.2184
- angle_coeff @angle:ca-c3-hc harmonic 46.96 110.15 # SOURCE3 47 1.2602
- angle_coeff @angle:ca-c3-hx harmonic 46.69 111.44 # SOURCE4 33 0.4691
- angle_coeff @angle:ca-c3-n2 harmonic 65.92 112.49 # SOURCE4 22 1.1043
- angle_coeff @angle:ca-c3-n3 harmonic 66.18 112.13 # SOURCE4 387 1.2309
- angle_coeff @angle:ca-c3-n4 harmonic 64.87 114.54 # SOURCE4 22 2.3986
- angle_coeff @angle:ca-c3-n harmonic 66.29 112.43 # SOURCE4 201 1.5133
- angle_coeff @angle:ca-c3-na harmonic 66.27 112.81 # SOURCE4 104 1.5807
- angle_coeff @angle:ca-c3-nc harmonic 68.20 106.51 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-c3-nd harmonic 68.20 106.51 # SOURCE3 1 same_as_ca-c3-nc
- angle_coeff @angle:ca-c3-nh harmonic 66.64 111.41 # SOURCE4 147 1.0074
- angle_coeff @angle:ca-c3-oh harmonic 67.94 110.55 # SOURCE4 348 1.2310
- angle_coeff @angle:ca-c3-os harmonic 68.19 108.89 # SOURCE4 411 1.0102
- angle_coeff @angle:ca-c3-p5 harmonic 77.64 113.41 # SOURCE4 19 1.4444
- angle_coeff @angle:ca-c3-s6 harmonic 62.87 111.36 # SOURCE4 15 1.4775
- angle_coeff @angle:ca-c3-ss harmonic 61.90 110.66 # SOURCE4 78 1.4797
- angle_coeff @angle:ca-c3-sx harmonic 62.16 110.80 # SOURCE4 16 0.5396
- angle_coeff @angle:c-c3-c1 harmonic 64.56 112.64 # SOURCE4 11 1.0678
- angle_coeff @angle:c-c3-c2 harmonic 64.14 111.32 # SOURCE4 92 1.8522
- angle_coeff @angle:c-c3-c3 harmonic 63.79 110.53 # SOURCE3 62 1.9636
- angle_coeff @angle:c-c3-c harmonic 64.06 111.61 # SOURCE4 151 2.1872
- angle_coeff @angle:c-c3-ca harmonic 64.13 110.99 # SOURCE4 481 1.7257
- angle_coeff @angle:c-c3-cc harmonic 63.89 112.89 # CORR 104
- angle_coeff @angle:cc-c3-cc harmonic 64.61 111.05 # CORR 19
- angle_coeff @angle:cc-c3-cd harmonic 67.30 102.35 # SOURCE3 1 0.0000
- angle_coeff @angle:cc-c3-cx harmonic 63.85 112.55 # SOURCE4 5 1.4317
- angle_coeff @angle:c-c3-cd harmonic 63.89 112.89 # CORR 104
- angle_coeff @angle:c-c3-ce harmonic 64.02 111.98 # SOURCE4 16 2.1388
- angle_coeff @angle:cc-c3-f harmonic 66.70 111.22 # CORR 69
- angle_coeff @angle:cc-c3-h1 harmonic 47.03 111.62 # SOURCE3 20 1.0215
- angle_coeff @angle:cc-c3-hc harmonic 47.20 110.86 # SOURCE3 85 1.0276
- angle_coeff @angle:cc-c3-hx harmonic 47.17 111.02 # SOURCE4 9 0.7503
- angle_coeff @angle:c-c3-cl harmonic 57.94 111.16 # SOURCE4 41 1.2257
- angle_coeff @angle:cc-c3-n2 harmonic 66.85 110.47 # SOURCE4 11 0.5153
- angle_coeff @angle:cc-c3-n3 harmonic 66.79 111.17 # CORR 111
- angle_coeff @angle:cc-c3-n4 harmonic 64.88 115.58 # SOURCE4 6 1.1723
- angle_coeff @angle:cc-c3-n harmonic 66.84 111.71 # CORR 32
- angle_coeff @angle:cc-c3-na harmonic 66.43 113.39 # SOURCE4 8 0.8010
- angle_coeff @angle:cc-c3-nc harmonic 68.37 107.04 # SOURCE3 2 0.0000
- angle_coeff @angle:cc-c3-nh harmonic 66.68 112.38 # CORR 21
- angle_coeff @angle:cc-c3-oh harmonic 68.13 111.10 # CORR 116
- angle_coeff @angle:cc-c3-os harmonic 68.51 109.01 # CORR 91
- angle_coeff @angle:cc-c3-p5 harmonic 76.89 116.23 # SOURCE4 6 0.7766
- angle_coeff @angle:cc-c3-sh harmonic 61.11 114.02 # SOURCE3 1 same_as_cd-c3-sh
- angle_coeff @angle:cc-c3-ss harmonic 61.95 111.06 # CORR 43
- angle_coeff @angle:c-c3-cx harmonic 64.08 111.09 # SOURCE4 9 1.2357
- angle_coeff @angle:cd-c3-cd harmonic 64.61 111.05 # CORR 19
- angle_coeff @angle:cd-c3-f harmonic 66.70 111.22 # CORR 69
- angle_coeff @angle:cd-c3-h1 harmonic 47.03 111.62 # SOURCE3 20 1.0215
- angle_coeff @angle:cd-c3-hc harmonic 47.20 110.86 # SOURCE3 85 1.0276
- angle_coeff @angle:cd-c3-n3 harmonic 66.79 111.17 # CORR 111
- angle_coeff @angle:cd-c3-n harmonic 66.84 111.71 # CORR 32
- angle_coeff @angle:cd-c3-nd harmonic 68.37 107.04 # SOURCE3 2 same_as_cc-c3-nc
- angle_coeff @angle:cd-c3-nh harmonic 66.68 112.38 # CORR 21
- angle_coeff @angle:cd-c3-oh harmonic 68.13 111.10 # CORR 116
- angle_coeff @angle:cd-c3-os harmonic 68.51 109.01 # CORR 91
- angle_coeff @angle:cd-c3-sh harmonic 61.11 114.02 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-c3-ss harmonic 61.95 111.06 # CORR 43
- angle_coeff @angle:ce-c3-ce harmonic 64.24 111.44 # SOURCE4 18 0.3695
- angle_coeff @angle:ce-c3-cy harmonic 66.33 102.85 # CORR 55
- angle_coeff @angle:ce-c3-h1 harmonic 47.30 109.59 # CORR 119
- angle_coeff @angle:ce-c3-hc harmonic 47.00 110.98 # SOURCE3 27 0.1559
- angle_coeff @angle:ce-c3-n3 harmonic 66.45 111.83 # CORR 28
- angle_coeff @angle:ce-c3-n harmonic 67.09 110.41 # SOURCE4 6 1.1405
- angle_coeff @angle:ce-c3-oh harmonic 68.00 111.05 # SOURCE4 17 1.5159
- angle_coeff @angle:ce-c3-os harmonic 68.64 108.10 # SOURCE4 16 1.9583
- angle_coeff @angle:ce-c3-ss harmonic 61.87 111.10 # SOURCE4 7 2.0156
- angle_coeff @angle:c-c3-f harmonic 66.82 109.98 # SOURCE4 38 0.9895
- angle_coeff @angle:cf-c3-cy harmonic 66.33 102.85 # CORR 55
- angle_coeff @angle:cf-c3-h1 harmonic 47.30 109.59 # CORR 119
- angle_coeff @angle:cf-c3-hc harmonic 47.00 110.98 # SOURCE3 27 same_as_ce-c3-hc
- angle_coeff @angle:cf-c3-n3 harmonic 66.45 111.83 # CORR 28
- angle_coeff @angle:c-c3-h1 harmonic 47.63 107.66 # SOURCE3 66 1.4015
- angle_coeff @angle:c-c3-h2 harmonic 47.16 109.69 # SOURCE4 38 1.0614
- angle_coeff @angle:c-c3-hc harmonic 47.20 109.68 # SOURCE3 614 0.6426
- angle_coeff @angle:c-c3-hx harmonic 47.23 109.54 # SOURCE4 47 0.6627
- angle_coeff @angle:cl-c3-cl harmonic 54.23 111.03 # SOURCE2 6 1.1324
- angle_coeff @angle:cl-c3-f harmonic 59.15 109.02 # SOURCE4 15 0.3609
- angle_coeff @angle:cl-c3-h1 harmonic 40.66 105.93 # SOURCE3 19 1.1883
- angle_coeff @angle:cl-c3-h2 harmonic 40.44 107.14 # SOURCE4 50 0.5973
- angle_coeff @angle:cl-c3-hc harmonic 40.33 107.65 # SOURCE2 2 2.2500
- angle_coeff @angle:cl-c3-os harmonic 60.38 111.40 # SOURCE4 8 0.8275
- angle_coeff @angle:cl-c3-ss harmonic 57.60 112.94 # SOURCE4 10 1.4625
- angle_coeff @angle:c-c3-n2 harmonic 66.92 109.55 # SOURCE4 55 1.4579
- angle_coeff @angle:c-c3-n3 harmonic 66.59 111.14 # SOURCE4 629 1.6673
- angle_coeff @angle:c-c3-n4 harmonic 65.07 114.21 # SOURCE4 27 1.5388
- angle_coeff @angle:c-c3-n harmonic 66.67 111.56 # SOURCE3 28 1.7981
- angle_coeff @angle:c-c3-na harmonic 66.81 111.37 # SOURCE4 31 1.6229
- angle_coeff @angle:c-c3-nh harmonic 67.36 109.43 # SOURCE4 42 1.7022
- angle_coeff @angle:c-c3-oh harmonic 68.65 108.70 # SOURCE4 299 1.3415
- angle_coeff @angle:c-c3-os harmonic 68.03 109.82 # SOURCE3 10 2.0612
- angle_coeff @angle:c-c3-p5 harmonic 78.76 110.41 # SOURCE4 15 2.2683
- angle_coeff @angle:c-c3-s6 harmonic 63.26 110.22 # SOURCE4 5 2.0076
- angle_coeff @angle:c-c3-sh harmonic 62.46 108.82 # SOURCE4 12 0.8354
- angle_coeff @angle:c-c3-ss harmonic 61.70 111.58 # SOURCE3 5 1.9506
- angle_coeff @angle:cx-c3-cx harmonic 63.53 112.58 # SOURCE4 7 1.2211
- angle_coeff @angle:cx-c3-h1 harmonic 47.04 109.64 # SOURCE4 175 0.8822
- angle_coeff @angle:cx-c3-hc harmonic 46.92 110.20 # SOURCE4 356 0.8798
- angle_coeff @angle:cx-c3-hx harmonic 46.38 112.81 # SOURCE4 12 0.0977
- angle_coeff @angle:cx-c3-n3 harmonic 65.83 113.22 # SOURCE4 33 1.3978
- angle_coeff @angle:cx-c3-n4 harmonic 68.88 101.51 # SOURCE4 12 0.0760
- angle_coeff @angle:cx-c3-n harmonic 66.22 112.59 # SOURCE4 22 0.8034
- angle_coeff @angle:cx-c3-oh harmonic 68.10 109.97 # SOURCE4 25 1.3176
- angle_coeff @angle:cx-c3-os harmonic 68.40 108.16 # SOURCE4 26 1.0162
- angle_coeff @angle:cy-c3-h1 harmonic 47.00 107.88 # SOURCE4 162 0.9624
- angle_coeff @angle:cy-c3-hc harmonic 46.51 110.17 # SOURCE3 16 0.5693
- angle_coeff @angle:cy-c3-n3 harmonic 65.63 112.72 # SOURCE4 7 1.0639
- angle_coeff @angle:cy-c3-oh harmonic 67.22 111.56 # SOURCE4 138 0.5051
- angle_coeff @angle:cy-c3-os harmonic 68.45 106.79 # SOURCE4 5 1.0955
- angle_coeff @angle:f-c3-f harmonic 71.26 107.16 # SOURCE2 10 1.1324
- angle_coeff @angle:f-c3-h1 harmonic 51.57 107.85 # SOURCE3 14 0.9537
- angle_coeff @angle:f-c3-h2 harmonic 51.36 108.41 # SOURCE3 6 0.5081
- angle_coeff @angle:f-c3-h3 harmonic 51.05 110.01 # SOURCE4 19 0.6811
- angle_coeff @angle:f-c3-hc harmonic 51.33 108.92 # SOURCE2 5 3.0534
- angle_coeff @angle:f-c3-n2 harmonic 69.23 110.40 # SOURCE2 3 2.6470
- angle_coeff @angle:f-c3-os harmonic 70.66 110.61 # SOURCE4 45 1.1755
- angle_coeff @angle:f-c3-p5 harmonic 80.63 107.25 # SOURCE4 11 1.1735
- angle_coeff @angle:f-c3-s6 harmonic 64.18 109.67 # SOURCE4 24 0.4116
- angle_coeff @angle:f-c3-ss harmonic 62.13 111.89 # SOURCE4 11 0.9479
- angle_coeff @angle:h1-c3-h1 harmonic 39.18 109.55 # SOURCE3 1888 1.1205
- angle_coeff @angle:h1-c3-n1 harmonic 49.99 107.31 # HF/6-31G* 1
- angle_coeff @angle:h1-c3-n2 harmonic 49.26 109.61 # SOURCE3 63 1.0452
- angle_coeff @angle:h1-c3-n3 harmonic 49.39 109.92 # SOURCE3 313 1.1810
- angle_coeff @angle:h1-c3-n harmonic 49.82 109.32 # SOURCE3 91 1.0325
- angle_coeff @angle:h1-c3-na harmonic 49.90 109.45 # SOURCE3 53 0.9555
- angle_coeff @angle:h1-c3-nc harmonic 50.11 108.57 # SOURCE3 6 0.0764
- angle_coeff @angle:h1-c3-nd harmonic 50.11 108.57 # SOURCE3 6 same_as_h1-c3-nc
- angle_coeff @angle:h1-c3-nh harmonic 49.73 109.96 # SOURCE3 70 0.7000
- angle_coeff @angle:h1-c3-no harmonic 48.66 105.15 # SOURCE4 16 0.4950
- angle_coeff @angle:h1-c3-o harmonic 52.53 117.19 # SOURCE3 6 0.0003
- angle_coeff @angle:h1-c3-oh harmonic 50.97 109.88 # SOURCE3 63 1.3172
- angle_coeff @angle:h1-c3-os harmonic 50.84 108.82 # SOURCE3 541 0.8042
- angle_coeff @angle:h1-c3-p5 harmonic 54.25 107.99 # SOURCE4 72 1.1862
- angle_coeff @angle:h1-c3-s4 harmonic 42.89 108.66 # SOURCE3 201 0.3834
- angle_coeff @angle:h1-c3-s harmonic 41.18 112.60 # SOURCE3 6 0.0026
- angle_coeff @angle:h1-c3-s6 harmonic 43.86 108.11 # SOURCE3 160 0.5518
- angle_coeff @angle:h1-c3-sh harmonic 42.40 109.21 # SOURCE3 22 1.2028
- angle_coeff @angle:h1-c3-ss harmonic 42.40 109.34 # SOURCE3 356 0.6573
- angle_coeff @angle:h1-c3-sx harmonic 42.83 108.69 # SOURCE3 90 0.2749
- angle_coeff @angle:h1-c3-sy harmonic 43.65 108.09 # SOURCE3 93 0.2556
- angle_coeff @angle:h2-c3-h2 harmonic 39.00 109.19 # SOURCE3 29 3.1352
- angle_coeff @angle:h2-c3-i harmonic 38.69 104.99 # SOURCE3 2 0.0000
- angle_coeff @angle:h2-c3-n2 harmonic 49.08 110.22 # SOURCE3 6 0.2133
- angle_coeff @angle:h2-c3-n3 harmonic 49.37 109.80 # SOURCE4 189 1.2893
- angle_coeff @angle:h2-c3-n harmonic 50.22 107.38 # SOURCE4 258 1.3140
- angle_coeff @angle:h2-c3-na harmonic 50.27 107.66 # SOURCE3 6 1.4096
- angle_coeff @angle:h2-c3-nc harmonic 49.85 109.47 # SOURCE3 10 0.3133
- angle_coeff @angle:h2-c3-nd harmonic 49.85 109.47 # SOURCE3 10 same_as_h2-c3-nc
- angle_coeff @angle:h2-c3-nh harmonic 49.60 110.33 # SOURCE4 102 1.0596
- angle_coeff @angle:h2-c3-no harmonic 47.83 108.69 # SOURCE3 4 0.0000
- angle_coeff @angle:h2-c3-o harmonic 54.38 108.97 # SOURCE3 4 0.0000
- angle_coeff @angle:h2-c3-oh harmonic 51.29 108.30 # SOURCE3 6 0.5715
- angle_coeff @angle:h2-c3-os harmonic 50.84 108.58 # SOURCE3 44 1.2773
- angle_coeff @angle:h2-c3-s4 harmonic 42.93 108.58 # SOURCE3 8 0.2408
- angle_coeff @angle:h2-c3-s harmonic 42.32 106.75 # SOURCE3 4 0.0000
- angle_coeff @angle:h2-c3-s6 harmonic 44.20 106.54 # SOURCE4 27 0.9934
- angle_coeff @angle:h2-c3-sh harmonic 42.68 107.87 # SOURCE3 6 0.4376
- angle_coeff @angle:h2-c3-ss harmonic 42.34 109.75 # SOURCE3 10 0.3442
- angle_coeff @angle:h3-c3-n3 harmonic 49.73 108.39 # SOURCE4 12 1.7932
- angle_coeff @angle:h3-c3-nc harmonic 49.91 109.37 # SOURCE3 1 0.0000
- angle_coeff @angle:h3-c3-nd harmonic 49.91 109.37 # SOURCE3 1 same_as_h3-c3-nc
- angle_coeff @angle:h3-c3-nh harmonic 49.53 110.78 # SOURCE4 5 1.5993
- angle_coeff @angle:h3-c3-os harmonic 50.09 112.03 # SOURCE4 17 1.0957
- angle_coeff @angle:h3-c3-ss harmonic 42.42 109.27 # SOURCE4 8 0.8367
- angle_coeff @angle:hc-c3-hc harmonic 39.43 108.35 # SOURCE3 2380 0.9006
- angle_coeff @angle:hc-c3-i harmonic 38.62 104.99 # SOURCE3 1
- angle_coeff @angle:hc-c3-n2 harmonic 49.29 109.50 # SOURCE3 1
- angle_coeff @angle:hc-c3-n3 harmonic 49.42 109.80 # SOURCE2 5 2.0070
- angle_coeff @angle:hc-c3-n4 harmonic 49.01 107.90 # SOURCE3 1
- angle_coeff @angle:hc-c3-n harmonic 49.78 109.50 # SOURCE3 1
- angle_coeff @angle:hc-c3-na harmonic 49.90 109.50 # SOURCE3 1
- angle_coeff @angle:hc-c3-nh harmonic 49.38 111.54 # SOURCE3 1
- angle_coeff @angle:hc-c3-no harmonic 48.19 107.20 # SOURCE2 1 0.0000
- angle_coeff @angle:hc-c3-oh harmonic 51.07 109.50 # SOURCE3 1
- angle_coeff @angle:hc-c3-os harmonic 50.87 108.70 # SOURCE2 13 2.3739
- angle_coeff @angle:hc-c3-p2 harmonic 52.37 110.18 # SOURCE3 25 0.4057
- angle_coeff @angle:hc-c3-p3 harmonic 52.73 110.14 # SOURCE3 325 0.5126
- angle_coeff @angle:hc-c3-p4 harmonic 53.21 109.59 # SOURCE3 87 0.3196
- angle_coeff @angle:hc-c3-p5 harmonic 53.84 109.64 # SOURCE3 69 0.8112
- angle_coeff @angle:hc-c3-px harmonic 53.46 109.74 # SOURCE3 84 0.3474
- angle_coeff @angle:hc-c3-py harmonic 53.86 109.54 # SOURCE3 39 0.1999
- angle_coeff @angle:hc-c3-s4 harmonic 43.12 107.50 # SOURCE2 1 0.0000
- angle_coeff @angle:hc-c3-s6 harmonic 43.84 108.20 # SOURCE3 1
- angle_coeff @angle:hc-c3-sh harmonic 42.66 107.87 # SOURCE2 3 2.0981
- angle_coeff @angle:hc-c3-ss harmonic 42.51 108.76 # SOURCE2 3 1.6891
- angle_coeff @angle:hx-c3-hx harmonic 39.04 110.74 # SOURCE3 137 0.5531
- angle_coeff @angle:hx-c3-n4 harmonic 49.02 107.91 # SOURCE3 148 0.5899
- angle_coeff @angle:i-c3-i harmonic 61.98 113.12 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-c3-n1 harmonic 71.09 105.07 # HF/6-31G* 1
- angle_coeff @angle:n2-c3-n2 harmonic 69.89 107.70 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-c3-nh harmonic 69.26 111.06 # SOURCE4 5 0.7868
- angle_coeff @angle:n2-c3-oh harmonic 70.15 111.82 # SOURCE4 10 0.3451
- angle_coeff @angle:n2-c3-os harmonic 70.04 111.23 # SOURCE4 6 1.0463
- angle_coeff @angle:n3-c3-n3 harmonic 69.61 109.59 # SOURCE4 27 1.8125
- angle_coeff @angle:n3-c3-nc harmonic 68.79 113.29 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-c3-nd harmonic 68.79 113.29 # SOURCE3 1 same_as_n3-c3-nc
- angle_coeff @angle:n3-c3-nh harmonic 69.74 110.08 # SOURCE4 21 1.0686
- angle_coeff @angle:n3-c3-oh harmonic 70.71 110.63 # SOURCE4 20 1.0177
- angle_coeff @angle:n3-c3-os harmonic 71.15 108.33 # SOURCE4 17 1.9545
- angle_coeff @angle:n3-c3-p5 harmonic 81.55 109.51 # SOURCE4 10 1.5002
- angle_coeff @angle:n3-c3-ss harmonic 64.75 107.73 # SOURCE4 18 1.7621
- angle_coeff @angle:n4-c3-n4 harmonic 67.13 113.32 # SOURCE3 1 0.0000
- angle_coeff @angle:na-c3-na harmonic 69.06 113.49 # SOURCE3 1 0.0000
- angle_coeff @angle:na-c3-os harmonic 71.27 109.06 # SOURCE4 170 0.5450
- angle_coeff @angle:nc-c3-nc harmonic 69.96 110.61 # SOURCE3 1 0.0000
- angle_coeff @angle:nc-c3-nh harmonic 69.34 112.43 # SOURCE3 1 0.0000
- angle_coeff @angle:nc-c3-os harmonic 69.28 115.41 # SOURCE3 3 1.0288
- angle_coeff @angle:nd-c3-nd harmonic 69.96 110.61 # SOURCE3 1 same_as_nc-c3-nc
- angle_coeff @angle:nd-c3-nh harmonic 69.34 112.43 # SOURCE3 1 same_as_nc-c3-nh
- angle_coeff @angle:nd-c3-os harmonic 69.28 115.41 # SOURCE3 3 same_as_nc-c3-os
- angle_coeff @angle:nh-c3-nh harmonic 71.41 105.87 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-c3-oh harmonic 70.47 112.36 # SOURCE4 12 0.7775
- angle_coeff @angle:nh-c3-os harmonic 71.26 108.93 # SOURCE4 17 1.3775
- angle_coeff @angle:nh-c3-p5 harmonic 80.62 112.50 # SOURCE4 5 1.7371
- angle_coeff @angle:nh-c3-ss harmonic 64.53 108.88 # SOURCE4 8 2.1521
- angle_coeff @angle:n-c3-n2 harmonic 68.82 112.34 # SOURCE4 5 1.1443
- angle_coeff @angle:n-c3-n3 harmonic 69.39 111.03 # SOURCE4 15 1.8216
- angle_coeff @angle:n-c3-n harmonic 68.78 113.81 # SOURCE3 1 0.0000
- angle_coeff @angle:n-c3-nh harmonic 70.54 108.34 # SOURCE4 11 2.1727
- angle_coeff @angle:n-c3-oh harmonic 70.36 112.54 # SOURCE4 31 1.1295
- angle_coeff @angle:no-c3-no harmonic 68.37 104.47 # SOURCE4 5 0.9726
- angle_coeff @angle:n-c3-os harmonic 71.14 109.16 # SOURCE4 153 0.8778
- angle_coeff @angle:n-c3-p5 harmonic 81.48 110.05 # SOURCE4 5 1.2965
- angle_coeff @angle:oh-c3-oh harmonic 72.71 109.23 # SOURCE4 8 1.4978
- angle_coeff @angle:oh-c3-os harmonic 72.38 109.21 # SOURCE4 85 1.1964
- angle_coeff @angle:oh-c3-p5 harmonic 82.83 108.86 # SOURCE4 33 1.2025
- angle_coeff @angle:oh-c3-sh harmonic 63.30 115.46 # SOURCE3 1 0.0000
- angle_coeff @angle:o-c3-o harmonic 74.43 122.30 # SOURCE3 1 0.0000
- angle_coeff @angle:os-c3-os harmonic 71.72 110.24 # SOURCE3 17 2.1340
- angle_coeff @angle:os-c3-p5 harmonic 82.86 108.36 # SOURCE4 22 2.1937
- angle_coeff @angle:os-c3-ss harmonic 65.36 107.98 # SOURCE4 20 1.7464
- angle_coeff @angle:p2-c3-p2 harmonic 98.16 110.48 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-c3-p3 harmonic 98.88 110.16 # SOURCE3 1 0.0000
- angle_coeff @angle:p5-c3-p5 harmonic 100.59 110.13 # SOURCE4 33 2.4116
- angle_coeff @angle:p5-c3-ss harmonic 78.88 111.30 # SOURCE4 5 2.0560
- angle_coeff @angle:s4-c3-s4 harmonic 62.40 112.29 # SOURCE3 2 1.2724
- angle_coeff @angle:s4-c3-s6 harmonic 62.62 113.52 # SOURCE3 1
- angle_coeff @angle:s6-c3-s6 harmonic 63.71 111.75 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-c3-sh harmonic 60.82 116.26 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-c3-ss harmonic 62.33 110.73 # SOURCE3 1
- angle_coeff @angle:s-c3-s harmonic 58.31 123.35 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-c3-ss harmonic 62.40 110.57 # SOURCE4 15 1.4311
- angle_coeff @angle:br-ca-br harmonic 67.31 117.60 # SOURCE3 1
- angle_coeff @angle:br-ca-ca harmonic 63.48 118.13 # SOURCE3 8 0.6041
- angle_coeff @angle:c1-ca-c1 harmonic 64.70 120.00 # SOURCE3 1
- angle_coeff @angle:c1-ca-ca harmonic 65.86 120.00 # SOURCE3 1
- angle_coeff @angle:c2-ca-c2 harmonic 62.95 120.00 # SOURCE3 1
- angle_coeff @angle:c2-ca-ca harmonic 64.69 120.60 # SOURCE3 1
- angle_coeff @angle:c3-ca-c2 harmonic 62.24 120.00 # SOURCE3 1
- angle_coeff @angle:c3-ca-c3 harmonic 62.41 116.80 # SOURCE3 1
- angle_coeff @angle:c3-ca-ca harmonic 63.84 120.63 # SOURCE3 60 0.7175
- angle_coeff @angle:c3-ca-cp harmonic 63.64 120.63 # CORR 120
- angle_coeff @angle:c3-ca-cq harmonic 63.64 120.63 # CORR 120
- angle_coeff @angle:c3-ca-na harmonic 66.59 118.78 # SOURCE4 59 1.1184
- angle_coeff @angle:c3-ca-nb harmonic 67.33 116.66 # SOURCE4 408 0.9380
- angle_coeff @angle:ca-ca-ca harmonic 67.18 119.97 # SOURCE3 1969 0.3480
- angle_coeff @angle:ca-ca-cc harmonic 65.99 120.10 # SOURCE3 103 0.3451
- angle_coeff @angle:ca-ca-cd harmonic 65.99 120.10 # SOURCE3 103 0.3451
- angle_coeff @angle:ca-ca-ce harmonic 64.88 120.66 # SOURCE3 14 0.1564
- angle_coeff @angle:ca-ca-cf harmonic 64.88 120.66 # SOURCE3 14 same_as_ca-ca-ce
- angle_coeff @angle:ca-ca-cg harmonic 65.90 120.05 # SOURCE3 6 0.2397
- angle_coeff @angle:ca-ca-ch harmonic 65.90 120.05 # SOURCE3 6 same_as_ca-ca-cg
- angle_coeff @angle:ca-ca-cl harmonic 58.52 119.40 # SOURCE4 2459 0.5283
- angle_coeff @angle:ca-ca-cp harmonic 67.16 119.07 # CORR 28
- angle_coeff @angle:ca-ca-cq harmonic 67.16 119.07 # CORR 28
- angle_coeff @angle:ca-ca-cx harmonic 64.48 120.83 # SOURCE4 71 1.3062
- angle_coeff @angle:ca-ca-cy harmonic 63.77 120.86 # SOURCE4 17 2.0287
- angle_coeff @angle:ca-ca-f harmonic 67.51 118.95 # SOURCE4 967 0.3369
- angle_coeff @angle:ca-ca-h4 harmonic 48.24 121.09 # SOURCE3 57 1.4696
- angle_coeff @angle:ca-ca-ha harmonic 48.46 120.01 # SOURCE3 2980 0.2511
- angle_coeff @angle:ca-ca-i harmonic 58.59 118.47 # SOURCE3 10 0.6181
- angle_coeff @angle:ca-ca-n1 harmonic 68.92 118.50 # HF/6-31G* 1
- angle_coeff @angle:ca-ca-n2 harmonic 70.95 119.57 # SOURCE3 1
- angle_coeff @angle:ca-ca-n4 harmonic 67.28 118.41 # SOURCE3 6 0.1691
- angle_coeff @angle:ca-ca-n harmonic 67.97 119.89 # SOURCE3 18 0.2095
- angle_coeff @angle:ca-ca-na harmonic 70.21 118.34 # SOURCE3 54 3.6168
- angle_coeff @angle:ca-ca-nb harmonic 69.16 122.63 # SOURCE3 83 1.1249
- angle_coeff @angle:ca-ca-nc harmonic 70.14 119.72 # SOURCE3 22 3.3994
- angle_coeff @angle:ca-ca-nd harmonic 70.14 119.72 # SOURCE3 22 3.3994
- angle_coeff @angle:ca-ca-ne harmonic 67.74 119.88 # SOURCE3 24 0.3637
- angle_coeff @angle:ca-ca-nf harmonic 67.74 119.88 # SOURCE3 24 0.3637
- angle_coeff @angle:ca-ca-nh harmonic 69.34 120.13 # SOURCE3 193 0.6341
- angle_coeff @angle:ca-ca-no harmonic 66.88 119.54 # SOURCE3 10 1.3187
- angle_coeff @angle:ca-ca-o harmonic 71.85 123.29 # SOURCE4 11 1.2526
- angle_coeff @angle:ca-ca-oh harmonic 69.85 119.94 # SOURCE3 14 0.1627
- angle_coeff @angle:ca-ca-os harmonic 69.79 119.20 # SOURCE3 52 0.5240
- angle_coeff @angle:ca-ca-p2 harmonic 77.87 114.36 # SOURCE3 1
- angle_coeff @angle:ca-ca-p3 harmonic 76.34 120.73 # SOURCE3 6 0.1273
- angle_coeff @angle:ca-ca-p4 harmonic 77.11 120.30 # SOURCE3 1
- angle_coeff @angle:ca-ca-p5 harmonic 77.50 120.28 # SOURCE4 5 0.0177
- angle_coeff @angle:ca-ca-pe harmonic 76.26 120.45 # SOURCE3 20 0.2719
- angle_coeff @angle:ca-ca-pf harmonic 76.26 120.45 # SOURCE3 20 0.2719
- angle_coeff @angle:ca-ca-px harmonic 76.37 120.53 # SOURCE3 10 0.4509
- angle_coeff @angle:ca-ca-py harmonic 77.43 119.98 # SOURCE3 6 0.0670
- angle_coeff @angle:ca-ca-s4 harmonic 61.72 119.15 # SOURCE3 1
- angle_coeff @angle:ca-ca-s6 harmonic 62.18 120.54 # SOURCE4 36 1.2154
- angle_coeff @angle:ca-ca-s harmonic 62.22 122.55 # SOURCE3 4 0.0000
- angle_coeff @angle:ca-ca-sh harmonic 61.32 121.78 # SOURCE4 17 1.2849
- angle_coeff @angle:ca-ca-ss harmonic 62.03 119.93 # SOURCE3 16 0.3901
- angle_coeff @angle:ca-ca-sx harmonic 60.68 119.18 # SOURCE3 6 0.0434
- angle_coeff @angle:ca-ca-sy harmonic 61.64 119.89 # SOURCE3 24 1.8813
- angle_coeff @angle:c-ca-c3 harmonic 62.61 118.06 # SOURCE3 1
- angle_coeff @angle:c-ca-c harmonic 62.65 120.00 # SOURCE3 1
- angle_coeff @angle:c-ca-ca harmonic 64.64 120.14 # SOURCE3 40 0.4788
- angle_coeff @angle:cc-ca-cp harmonic 64.63 124.30 # SOURCE4 10 0.6423
- angle_coeff @angle:cc-ca-nb harmonic 69.19 118.02 # CORR 64
- angle_coeff @angle:cd-ca-nb harmonic 69.19 118.02 # CORR 64
- angle_coeff @angle:ce-ca-na harmonic 67.44 119.85 # SOURCE4 9 0.7001
- angle_coeff @angle:ce-ca-nb harmonic 68.24 117.59 # CORR 44
- angle_coeff @angle:cf-ca-nb harmonic 68.24 117.59 # CORR 44
- angle_coeff @angle:cg-ca-cp harmonic 65.26 121.53 # SOURCE4 12 0.1831
- angle_coeff @angle:c-ca-ha harmonic 46.51 115.90 # SOURCE3 1
- angle_coeff @angle:cl-ca-cl harmonic 54.17 118.72 # SOURCE3 1
- angle_coeff @angle:cl-ca-cp harmonic 58.19 120.31 # SOURCE4 18 0.5607
- angle_coeff @angle:cl-ca-nb harmonic 61.21 116.15 # SOURCE4 50 0.6047
- angle_coeff @angle:c-ca-nb harmonic 67.71 117.94 # SOURCE4 91 1.0536
- angle_coeff @angle:c-ca-nc harmonic 64.40 130.80 # SOURCE3 1
- angle_coeff @angle:c-ca-nd harmonic 64.40 130.80 # SOURCE3 1 same_as_c-ca-nc
- angle_coeff @angle:cp-ca-f harmonic 67.10 119.39 # SOURCE4 16 0.1724
- angle_coeff @angle:cp-ca-h4 harmonic 48.15 120.03 # SOURCE4 27 0.4431
- angle_coeff @angle:cp-ca-ha harmonic 47.94 121.08 # CORR 24
- angle_coeff @angle:cp-ca-na harmonic 72.91 108.79 # SOURCE4 165 0.5166
- angle_coeff @angle:cp-ca-nb harmonic 68.56 123.72 # SOURCE4 50 0.8176
- angle_coeff @angle:cp-ca-nh harmonic 68.66 121.52 # SOURCE4 11 0.5438
- angle_coeff @angle:cp-ca-oh harmonic 69.26 120.96 # SOURCE4 12 1.1400
- angle_coeff @angle:cp-ca-ss harmonic 63.87 112.75 # SOURCE4 8 0.6216
- angle_coeff @angle:cp-ca-sy harmonic 63.91 111.18 # CORR 4
- angle_coeff @angle:cq-ca-ha harmonic 47.94 121.08 # CORR 24
- angle_coeff @angle:cq-ca-sy harmonic 63.91 111.18 # CORR 4
- angle_coeff @angle:f-ca-f harmonic 68.05 117.50 # SOURCE3 1
- angle_coeff @angle:f-ca-nb harmonic 71.69 114.58 # SOURCE4 19 0.2987
- angle_coeff @angle:h4-ca-n harmonic 49.48 116.02 # SOURCE3 1
- angle_coeff @angle:h4-ca-na harmonic 51.88 114.65 # SOURCE3 5 1.5484
- angle_coeff @angle:h4-ca-nb harmonic 51.82 115.94 # SOURCE3 52 0.7370
- angle_coeff @angle:h4-ca-nc harmonic 51.46 118.36 # SOURCE3 1
- angle_coeff @angle:h4-ca-nd harmonic 51.46 118.36 # SOURCE3 1 same_as_h4-ca-nc
- angle_coeff @angle:h4-ca-os harmonic 52.30 111.15 # SOURCE3 1
- angle_coeff @angle:h4-ca-ss harmonic 42.40 116.19 # SOURCE3 1
- angle_coeff @angle:h5-ca-nb harmonic 51.76 116.35 # SOURCE3 30 0.5545
- angle_coeff @angle:h5-ca-nc harmonic 50.70 122.11 # SOURCE3 1
- angle_coeff @angle:h5-ca-nd harmonic 50.70 122.11 # SOURCE3 1 same_as_h5-ca-nc
- angle_coeff @angle:ha-ca-n2 harmonic 52.97 116.00 # SOURCE2 1 0.0000
- angle_coeff @angle:ha-ca-p2 harmonic 50.08 122.56 # SOURCE3 1
- angle_coeff @angle:i-ca-i harmonic 62.29 119.28 # SOURCE3 1
- angle_coeff @angle:n1-ca-n1 harmonic 70.73 117.03 # HF/6-31G* 1
- angle_coeff @angle:n2-ca-n2 harmonic 75.05 120.00 # SOURCE3 1
- angle_coeff @angle:n2-ca-na harmonic 73.80 119.60 # SOURCE3 1
- angle_coeff @angle:n4-ca-n4 harmonic 67.65 116.82 # SOURCE3 1
- angle_coeff @angle:na-ca-na harmonic 76.48 107.65 # SOURCE4 5 0.8751
- angle_coeff @angle:na-ca-nb harmonic 70.60 127.07 # SOURCE4 237 1.9392
- angle_coeff @angle:na-ca-nh harmonic 72.48 118.62 # SOURCE4 29 0.9759
- angle_coeff @angle:nb-ca-nb harmonic 70.78 127.19 # SOURCE4 585 1.1793
- angle_coeff @angle:nb-ca-nc harmonic 71.12 126.53 # CORR 22
- angle_coeff @angle:nb-ca-nd harmonic 71.12 126.53 # CORR 22
- angle_coeff @angle:nb-ca-nh harmonic 73.20 116.95 # SOURCE4 765 0.8040
- angle_coeff @angle:nb-ca-oh harmonic 73.57 117.30 # SOURCE4 64 0.9290
- angle_coeff @angle:nb-ca-os harmonic 72.54 119.66 # SOURCE4 76 0.6493
- angle_coeff @angle:nb-ca-sh harmonic 64.31 117.59 # SOURCE4 15 1.4616
- angle_coeff @angle:nb-ca-ss harmonic 64.10 119.30 # SOURCE4 41 1.3420
- angle_coeff @angle:nc-ca-nc harmonic 70.67 128.74 # SOURCE3 1
- angle_coeff @angle:nc-ca-nh harmonic 72.77 118.86 # SOURCE3 1
- angle_coeff @angle:nd-ca-nd harmonic 70.67 128.74 # SOURCE3 1 same_as_nc-ca-nc
- angle_coeff @angle:nd-ca-nh harmonic 72.77 118.86 # SOURCE3 1 same_as_nc-ca-nh
- angle_coeff @angle:nh-ca-nh harmonic 71.40 120.98 # SOURCE3 1
- angle_coeff @angle:n-ca-nc harmonic 69.66 123.86 # SOURCE3 1
- angle_coeff @angle:n-ca-nd harmonic 69.66 123.86 # SOURCE3 1 same_as_n-ca-nc
- angle_coeff @angle:n-ca-nh harmonic 71.29 116.16 # SOURCE3 1
- angle_coeff @angle:no-ca-no harmonic 67.42 117.14 # SOURCE3 1
- angle_coeff @angle:oh-ca-oh harmonic 72.63 120.00 # SOURCE3 1
- angle_coeff @angle:o-ca-o harmonic 78.21 126.82 # SOURCE3 1
- angle_coeff @angle:os-ca-os harmonic 74.01 113.73 # SOURCE3 1
- angle_coeff @angle:p2-ca-p2 harmonic 94.48 121.20 # SOURCE3 1
- angle_coeff @angle:p3-ca-p3 harmonic 95.21 121.46 # SOURCE3 1
- angle_coeff @angle:p5-ca-p5 harmonic 97.33 120.00 # SOURCE3 1
- angle_coeff @angle:s4-ca-s4 harmonic 64.96 105.81 # SOURCE3 1
- angle_coeff @angle:s6-ca-s6 harmonic 66.03 105.81 # SOURCE3 1
- angle_coeff @angle:sh-ca-sh harmonic 61.27 120.24 # SOURCE3 1
- angle_coeff @angle:s-ca-s harmonic 61.42 125.14 # SOURCE3 1
- angle_coeff @angle:ss-ca-ss harmonic 62.91 115.15 # SOURCE3 1
- angle_coeff @angle:br-c-br harmonic 66.91 113.10 # SOURCE3 1
- angle_coeff @angle:br-c-c3 harmonic 63.34 110.74 # SOURCE3 1 0.0000
- angle_coeff @angle:br-c-o harmonic 63.19 121.46 # SOURCE3 5 1.6264
- angle_coeff @angle:c1-c-c1 harmonic 65.09 115.32 # SOURCE3 1
- angle_coeff @angle:c1-c-o harmonic 69.92 122.34 # SOURCE3 1
- angle_coeff @angle:c2-c-c2 harmonic 67.17 116.78 # SOURCE3 1
- angle_coeff @angle:c2-c-ha harmonic 48.65 115.95 # SOURCE3 1
- angle_coeff @angle:c2-c-o harmonic 72.77 119.12 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-c-s harmonic 64.67 119.16 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-c-c3 harmonic 62.82 116.05 # SOURCE3 11 1.0986
- angle_coeff @angle:c3-c-ca harmonic 62.59 118.54 # SOURCE4 240 1.3614
- angle_coeff @angle:c3-c-cc harmonic 63.38 117.47 # CORR 46
- angle_coeff @angle:c3-c-cd harmonic 63.38 117.47 # CORR 46
- angle_coeff @angle:c3-c-ce harmonic 63.44 116.37 # CORR 233
- angle_coeff @angle:c3-c-cf harmonic 63.44 116.37 # CORR 233
- angle_coeff @angle:c3-c-cg harmonic 64.26 115.00 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-c-ch harmonic 64.26 115.00 # SOURCE2 1 same_as_c3-c-cg
- angle_coeff @angle:c3-c-cl harmonic 58.18 111.99 # SOURCE3 2 0.0125
- angle_coeff @angle:c3-c-f harmonic 66.93 110.70 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-c-h4 harmonic 46.11 114.40 # SOURCE4 57 0.4032
- angle_coeff @angle:c3-c-ha harmonic 46.01 115.22 # SOURCE3 15 0.3181
- angle_coeff @angle:c3-c-i harmonic 56.87 112.94 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-c-n2 harmonic 66.62 114.53 # SOURCE3 1
- angle_coeff @angle:c3-c-n4 harmonic 64.61 112.26 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-c-n harmonic 67.86 115.15 # SOURCE3 153 2.7443
- angle_coeff @angle:c3-c-ne harmonic 68.03 111.56 # CORR 12
- angle_coeff @angle:c3-c-nf harmonic 68.03 111.56 # CORR 12
- angle_coeff @angle:c3-c-o harmonic 68.03 123.11 # SOURCE3 267 3.0977
- angle_coeff @angle:c3-c-oh harmonic 69.84 112.20 # SOURCE3 14 1.8324
- angle_coeff @angle:c3-c-os harmonic 69.26 111.96 # SOURCE3 15 2.3072
- angle_coeff @angle:c3-c-p3 harmonic 74.55 116.42 # SOURCE3 3 0.1291
- angle_coeff @angle:c3-c-p5 harmonic 73.81 118.90 # SOURCE3 1
- angle_coeff @angle:c3-c-pe harmonic 74.19 114.85 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-c-pf harmonic 74.19 114.85 # SOURCE3 1 same_as_c3-c-pe
- angle_coeff @angle:c3-c-px harmonic 74.17 115.60 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-c-py harmonic 74.48 118.16 # SOURCE3 3 1.0735
- angle_coeff @angle:c3-c-s4 harmonic 59.64 114.79 # SOURCE3 1
- angle_coeff @angle:c3-c-s6 harmonic 59.65 114.72 # SOURCE3 1
- angle_coeff @angle:c3-c-s harmonic 62.03 123.73 # SOURCE3 9 1.4528
- angle_coeff @angle:c3-c-sh harmonic 61.97 114.21 # SOURCE3 3 2.3916
- angle_coeff @angle:c3-c-ss harmonic 62.41 114.32 # SOURCE3 5 2.7478
- angle_coeff @angle:c3-c-sx harmonic 59.48 113.97 # SOURCE3 3 0.0610
- angle_coeff @angle:c3-c-sy harmonic 59.89 114.28 # SOURCE3 3 0.7341
- angle_coeff @angle:ca-c-ca harmonic 63.03 118.58 # SOURCE4 144 2.1146
- angle_coeff @angle:ca-c-cc harmonic 64.24 116.07 # CORR 257
- angle_coeff @angle:ca-c-cd harmonic 64.24 116.07 # CORR 257
- angle_coeff @angle:ca-c-ce harmonic 63.21 118.92 # CORR 36
- angle_coeff @angle:ca-c-cf harmonic 63.21 118.92 # CORR 36
- angle_coeff @angle:ca-c-h4 harmonic 46.52 115.14 # SOURCE4 30 0.7320
- angle_coeff @angle:ca-c-ha harmonic 46.80 114.12 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-c-n harmonic 68.47 115.14 # SOURCE4 571 1.4648
- angle_coeff @angle:ca-c-ne harmonic 67.74 114.39 # SOURCE4 5 0.2958
- angle_coeff @angle:ca-c-o harmonic 68.67 123.44 # SOURCE3 18 2.5574
- angle_coeff @angle:ca-c-oh harmonic 70.11 113.44 # SOURCE4 222 0.8421
- angle_coeff @angle:ca-c-os harmonic 68.78 115.54 # SOURCE3 5 2.6708
- angle_coeff @angle:ca-c-s harmonic 62.52 123.04 # SOURCE4 12 0.7935
- angle_coeff @angle:ca-c-sh harmonic 61.05 118.63 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-c-ss harmonic 62.45 115.13 # SOURCE4 12 1.0069
- angle_coeff @angle:br-cc-c harmonic 63.98 115.68 # SOURCE4 8 0.4970
- angle_coeff @angle:br-cc-cc harmonic 61.82 124.89 # SOURCE4 8 1.9479
- angle_coeff @angle:br-cc-cd harmonic 62.26 124.56 # SOURCE4 32 2.4696
- angle_coeff @angle:br-cc-na harmonic 64.60 121.42 # SOURCE4 6 0.5507
- angle_coeff @angle:c2-cc-c3 harmonic 63.27 126.11 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-cc-ca harmonic 65.34 124.66 # CORR 16
- angle_coeff @angle:c2-cc-cc harmonic 66.24 121.77 # CORR 32
- angle_coeff @angle:c2-cc-cd harmonic 69.09 117.02 # SOURCE3 2 0.0703
- angle_coeff @angle:c2-cc-ha harmonic 48.69 122.72 # SOURCE3 2 0.0092
- angle_coeff @angle:c2-cc-n harmonic 67.74 126.90 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-cc-os harmonic 70.10 120.79 # CORR 13
- angle_coeff @angle:c-c-c3 harmonic 61.72 116.86 # SOURCE3 5 0.1653
- angle_coeff @angle:c3-cc-ca harmonic 61.96 125.89 # CORR 127
- angle_coeff @angle:c3-cc-cc harmonic 64.66 115.97 # SOURCE3 4 3.0507
- angle_coeff @angle:c3-cc-cd harmonic 64.81 119.45 # SOURCE3 35 8.2040
- angle_coeff @angle:c3-cc-cf harmonic 65.34 117.84 # CORR 2
- angle_coeff @angle:c3-cc-ha harmonic 45.11 121.52 # SOURCE3 32 3.2091
- angle_coeff @angle:c3-cc-n2 harmonic 65.80 126.87 # CORR 9
- angle_coeff @angle:c3-cc-n harmonic 66.33 119.11 # CORR 68
- angle_coeff @angle:c3-cc-na harmonic 65.50 122.78 # CORR 632
- angle_coeff @angle:c3-cc-nc harmonic 65.90 120.94 # CORR 309
- angle_coeff @angle:c3-cc-nd harmonic 66.32 122.13 # CORR 475
- angle_coeff @angle:c3-cc-os harmonic 67.54 116.88 # CORR 203
- angle_coeff @angle:c3-cc-ss harmonic 61.21 121.66 # CORR 171
- angle_coeff @angle:c-c-c harmonic 62.30 111.68 # SOURCE3 2 6.1226
- angle_coeff @angle:c-c-ca harmonic 61.73 118.34 # SOURCE4 26 1.0692
- angle_coeff @angle:ca-cc-cc harmonic 67.66 111.04 # SOURCE3 9 7.9455
- angle_coeff @angle:ca-cc-cd harmonic 68.23 113.51 # SOURCE3 26 7.4229
- angle_coeff @angle:ca-cc-ce harmonic 62.51 127.87 # SOURCE4 11 1.7579
- angle_coeff @angle:ca-cc-h4 harmonic 45.57 128.66 # SOURCE3 10 3.1167
- angle_coeff @angle:ca-cc-ha harmonic 46.40 124.04 # SOURCE3 34 3.6691
- angle_coeff @angle:ca-cc-n harmonic 68.46 117.67 # CORR 18
- angle_coeff @angle:ca-cc-nc harmonic 67.69 120.67 # CORR 162
- angle_coeff @angle:ca-cc-nd harmonic 67.92 123.02 # CORR 188
- angle_coeff @angle:ca-cc-nh harmonic 67.46 122.45 # SOURCE4 9 1.4092
- angle_coeff @angle:ca-cc-oh harmonic 69.61 117.71 # CORR 21
- angle_coeff @angle:ca-cc-os harmonic 69.82 115.16 # CORR 134
- angle_coeff @angle:ca-cc-ss harmonic 62.30 120.51 # CORR 43
- angle_coeff @angle:c-cc-c2 harmonic 65.60 120.92 # CORR 22
- angle_coeff @angle:c-cc-c3 harmonic 63.60 117.42 # CORR 126
- angle_coeff @angle:c-cc-c harmonic 63.42 121.17 # CORR 64
- angle_coeff @angle:c-c-cc harmonic 64.02 111.67 # SOURCE3 4 5.5146
- angle_coeff @angle:c-cc-ca harmonic 63.55 122.95 # SOURCE3 1 0.0000
- angle_coeff @angle:c-cc-cc harmonic 63.72 122.69 # SOURCE3 2 0.0000
- angle_coeff @angle:cc-c-cc harmonic 64.80 116.04 # CORR 56
- angle_coeff @angle:cc-cc-cc harmonic 67.88 110.70 # SOURCE3 54 3.4091
- angle_coeff @angle:cc-cc-cd harmonic 68.16 114.19 # SOURCE3 517 6.5960
- angle_coeff @angle:cc-cc-ce harmonic 62.78 127.20 # CORR 42
- angle_coeff @angle:cc-cc-cf harmonic 65.88 122.59 # CORR 39
- angle_coeff @angle:cc-cc-cg harmonic 63.63 126.15 # CORR 27
- angle_coeff @angle:c-cc-cd harmonic 65.25 121.42 # CORR 1708
- angle_coeff @angle:cc-c-cd harmonic 65.73 112.79 # SOURCE3 1 0.0000
- angle_coeff @angle:c-cc-ce harmonic 63.20 122.73 # CORR 10
- angle_coeff @angle:cc-c-ce harmonic 64.64 115.68 # SOURCE4 6 1.2033
- angle_coeff @angle:cc-cc-f harmonic 66.35 119.41 # SOURCE4 7 0.4917
- angle_coeff @angle:c-cc-cg harmonic 64.98 118.14 # SOURCE4 7 0.7745
- angle_coeff @angle:cc-cc-h4 harmonic 45.56 129.47 # SOURCE3 171 2.2734
- angle_coeff @angle:cc-cc-ha harmonic 47.14 120.86 # CORR 1751
- angle_coeff @angle:c-cc-cl harmonic 58.39 116.05 # CORR 24
- angle_coeff @angle:cc-cc-n2 harmonic 69.48 121.15 # CORR 12
- angle_coeff @angle:cc-cc-n harmonic 67.95 119.89 # SOURCE3 36 0.2095
- angle_coeff @angle:cc-cc-na harmonic 72.21 106.80 # SOURCE3 33 0.6297
- angle_coeff @angle:cc-cc-nc harmonic 67.53 121.69 # CORR 105
- angle_coeff @angle:cc-cc-nd harmonic 71.15 112.56 # SOURCE3 141 4.2871
- angle_coeff @angle:cc-cc-nh harmonic 68.41 119.51 # CORR 228
- angle_coeff @angle:cc-cc-oh harmonic 68.53 121.96 # CORR 27
- angle_coeff @angle:cc-cc-os harmonic 69.34 117.23 # CORR 211
- angle_coeff @angle:cc-cc-pd harmonic 80.79 115.36 # SOURCE3 84 same_as_cd-cd-pc
- angle_coeff @angle:cc-cc-ss harmonic 62.45 120.12 # CORR 31
- angle_coeff @angle:cc-cc-sy harmonic 59.22 128.36 # SOURCE4 8 0.9813
- angle_coeff @angle:c-c-cd harmonic 64.02 111.67 # SOURCE3 4 5.5146
- angle_coeff @angle:cd-cc-cd harmonic 67.89 120.23 # CORR 133
- angle_coeff @angle:cd-cc-ce harmonic 63.67 128.41 # CORR 210
- angle_coeff @angle:cd-cc-cl harmonic 57.46 123.70 # CORR 62
- angle_coeff @angle:cd-cc-f harmonic 67.42 121.08 # SOURCE4 28 0.8788
- angle_coeff @angle:cd-cc-h4 harmonic 47.19 129.11 # SOURCE3 418 3.1355
- angle_coeff @angle:cd-cc-ha harmonic 48.35 122.89 # SOURCE3 584 2.9334
- angle_coeff @angle:cd-cc-n harmonic 70.72 115.52 # SOURCE3 52 1.3322
- angle_coeff @angle:cd-cc-na harmonic 72.91 109.42 # SOURCE3 265 2.6051
- angle_coeff @angle:cd-cc-nc harmonic 72.01 111.75 # CORR 1101
- angle_coeff @angle:cd-cc-nh harmonic 68.69 123.89 # CORR 106
- angle_coeff @angle:cd-cc-no harmonic 65.78 128.95 # SOURCE4 117 1.4740
- angle_coeff @angle:cd-cc-oh harmonic 69.56 123.89 # CORR 106
- angle_coeff @angle:cd-cc-os harmonic 69.96 120.30 # SOURCE3 64 5.4354
- angle_coeff @angle:cd-cc-ss harmonic 65.44 111.55 # CORR 884
- angle_coeff @angle:cd-cc-sy harmonic 60.54 124.91 # CORR 41
- angle_coeff @angle:ce-cc-na harmonic 66.32 124.22 # CORR 48
- angle_coeff @angle:ce-cc-nc harmonic 67.01 121.29 # CORR 37
- angle_coeff @angle:ce-cc-nd harmonic 67.80 121.51 # CORR 37
- angle_coeff @angle:ce-cc-os harmonic 68.17 119.03 # CORR 66
- angle_coeff @angle:ce-cc-ss harmonic 61.83 121.44 # CORR 38
- angle_coeff @angle:c-cc-f harmonic 66.16 116.87 # SOURCE4 16 0.5322
- angle_coeff @angle:cg-cc-na harmonic 67.51 122.35 # SOURCE4 5 0.8112
- angle_coeff @angle:cg-cc-ss harmonic 62.33 120.70 # SOURCE4 12 0.9090
- angle_coeff @angle:cc-c-h4 harmonic 47.13 115.45 # SOURCE4 5 0.8021
- angle_coeff @angle:c-cc-ha harmonic 46.99 117.02 # SOURCE3 56 1.9713
- angle_coeff @angle:cl-cc-na harmonic 59.37 121.61 # SOURCE4 12 0.3436
- angle_coeff @angle:cl-cc-nd harmonic 59.35 122.97 # CORR 6
- angle_coeff @angle:cl-cc-ss harmonic 58.09 119.85 # SOURCE4 11 1.0626
- angle_coeff @angle:c-cc-n2 harmonic 68.54 120.89 # CORR 2
- angle_coeff @angle:c-cc-n harmonic 68.11 116.32 # CORR 21
- angle_coeff @angle:cc-c-n harmonic 70.19 111.86 # SOURCE3 36 2.3407
- angle_coeff @angle:c-cc-nc harmonic 66.19 123.47 # CORR 24
- angle_coeff @angle:cc-c-nd harmonic 67.92 116.21 # CORR 33
- angle_coeff @angle:c-cc-nd harmonic 67.50 121.67 # CORR 47
- angle_coeff @angle:c-cc-ne harmonic 67.11 119.88 # SOURCE4 6 0.3139
- angle_coeff @angle:cc-c-o harmonic 68.91 125.71 # SOURCE3 66 2.4784
- angle_coeff @angle:c-cc-oh harmonic 70.04 113.64 # CORR 53
- angle_coeff @angle:cc-c-oh harmonic 71.00 113.10 # CORR 85
- angle_coeff @angle:c-cc-os harmonic 67.83 119.39 # CORR 78
- angle_coeff @angle:cc-c-os harmonic 70.50 112.30 # SOURCE3 6 2.7842
- angle_coeff @angle:cc-c-s harmonic 61.67 127.94 # SOURCE4 12 0.9342
- angle_coeff @angle:cc-c-ss harmonic 63.47 112.52 # SOURCE4 10 0.6933
- angle_coeff @angle:cx-cc-nd harmonic 65.61 127.75 # SOURCE4 12 1.7156
- angle_coeff @angle:cx-cc-os harmonic 67.94 118.08 # SOURCE4 10 0.0955
- angle_coeff @angle:cd-c-cd harmonic 64.80 116.04 # CORR 56
- angle_coeff @angle:cd-c-cx harmonic 63.88 117.46 # SOURCE4 13 0.1625
- angle_coeff @angle:cd-c-n harmonic 70.19 111.86 # SOURCE3 36 2.3407
- angle_coeff @angle:cd-c-nc harmonic 67.92 116.21 # CORR 33
- angle_coeff @angle:cd-c-nd harmonic 68.65 113.75 # SOURCE4 14 0.0860
- angle_coeff @angle:cd-c-o harmonic 68.91 125.71 # SOURCE3 66 2.4784
- angle_coeff @angle:cd-c-oh harmonic 71.00 113.10 # CORR 85
- angle_coeff @angle:cd-c-os harmonic 70.50 112.30 # SOURCE3 6 2.7842
- angle_coeff @angle:ce-c-ce harmonic 64.34 115.80 # CORR 74
- angle_coeff @angle:ce-c-cf harmonic 64.04 116.89 # SOURCE4 11 1.6021
- angle_coeff @angle:ce-c-cx harmonic 63.95 116.25 # SOURCE4 6 0.6351
- angle_coeff @angle:ce-c-h4 harmonic 46.93 114.88 # SOURCE4 19 0.3355
- angle_coeff @angle:ce-c-ha harmonic 46.93 115.22 # SOURCE3 7 2.4188
- angle_coeff @angle:ce-c-n harmonic 68.80 115.27 # CORR 32
- angle_coeff @angle:ce-c-o harmonic 69.27 122.92 # SOURCE3 17 3.5085
- angle_coeff @angle:ce-c-oh harmonic 70.32 114.09 # CORR 128
- angle_coeff @angle:ce-c-os harmonic 70.16 112.28 # CORR 149
- angle_coeff @angle:ce-c-s harmonic 64.09 117.80 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-c-ss harmonic 63.94 110.39 # SOURCE4 5 0.6050
- angle_coeff @angle:cf-c-cf harmonic 64.34 115.80 # CORR 74
- angle_coeff @angle:cf-c-ha harmonic 46.93 115.22 # SOURCE3 7 same_as_ce-c-ha
- angle_coeff @angle:cf-c-n harmonic 68.80 115.27 # CORR 32
- angle_coeff @angle:cf-c-o harmonic 69.27 122.92 # SOURCE3 17 3.5085
- angle_coeff @angle:cf-c-oh harmonic 70.32 114.09 # CORR 128
- angle_coeff @angle:cf-c-os harmonic 70.16 112.28 # CORR 149
- angle_coeff @angle:cf-c-s harmonic 64.09 117.80 # SOURCE3 1 same_as_ce-c-s
- angle_coeff @angle:cg-c-cg harmonic 65.44 115.38 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-c-ha harmonic 47.80 113.90 # SOURCE2 1 0.0000
- angle_coeff @angle:cg-c-o harmonic 70.21 122.31 # SOURCE3 2 0.0000
- angle_coeff @angle:c-c-h4 harmonic 44.62 116.36 # SOURCE4 5 0.5586
- angle_coeff @angle:h4-cc-n harmonic 50.39 117.62 # SOURCE3 53 0.9721
- angle_coeff @angle:h4-cc-na harmonic 50.22 119.66 # SOURCE3 294 2.4702
- angle_coeff @angle:h4-cc-nc harmonic 50.00 120.03 # SOURCE3 16 2.3863
- angle_coeff @angle:h4-cc-nd harmonic 51.39 119.11 # SOURCE3 135 1.6946
- angle_coeff @angle:h4-cc-os harmonic 52.27 111.89 # SOURCE3 61 2.3500
- angle_coeff @angle:h4-cc-ss harmonic 42.95 117.75 # SOURCE3 40 3.1156
- angle_coeff @angle:h5-cc-n harmonic 50.84 115.72 # CORR 20
- angle_coeff @angle:h5-cc-na harmonic 49.76 122.10 # SOURCE3 16 1.4626
- angle_coeff @angle:h5-cc-nc harmonic 49.29 123.70 # SOURCE3 6 0.3547
- angle_coeff @angle:h5-cc-nd harmonic 50.13 125.38 # SOURCE3 40 2.2157
- angle_coeff @angle:h5-cc-os harmonic 51.30 116.33 # SOURCE3 12 3.2919
- angle_coeff @angle:h5-cc-ss harmonic 42.19 122.00 # SOURCE3 6 0.7237
- angle_coeff @angle:c-c-ha harmonic 44.85 115.43 # SOURCE2 3 0.6549
- angle_coeff @angle:ha-cc-na harmonic 49.82 121.50 # SOURCE2 1 0.0000
- angle_coeff @angle:ha-cc-nc harmonic 50.73 116.54 # SOURCE3 5 1.4482
- angle_coeff @angle:ha-cc-nd harmonic 51.41 118.88 # SOURCE3 20 2.8923
- angle_coeff @angle:ha-cc-os harmonic 52.49 110.86 # SOURCE3 7 1.3846
- angle_coeff @angle:ha-cc-pd harmonic 53.59 121.76 # SOURCE3 84 same_as_ha-cd-pc
- angle_coeff @angle:ha-cc-ss harmonic 42.26 121.64 # SOURCE2 5 1.3276
- angle_coeff @angle:ch-c-ch harmonic 65.44 115.38 # SOURCE3 1 same_as_cg-c-cg
- angle_coeff @angle:ch-c-ha harmonic 47.80 113.90 # SOURCE2 1 same_as_cg-c-ha
- angle_coeff @angle:ch-c-o harmonic 70.21 122.31 # SOURCE3 2 same_as_cg-c-o
- angle_coeff @angle:cl-c-cl harmonic 54.78 111.30 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-c-f harmonic 59.05 112.00 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-c-ha harmonic 40.42 109.90 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-c-o harmonic 59.78 121.51 # SOURCE3 6 1.6987
- angle_coeff @angle:cl-c-s harmonic 56.74 127.60 # SOURCE2 1 0.0000
- angle_coeff @angle:c-c-n harmonic 67.53 112.14 # SOURCE4 53 2.1247
- angle_coeff @angle:na-cc-nc harmonic 70.72 121.62 # CORR 231
- angle_coeff @angle:na-cc-nd harmonic 74.78 112.02 # SOURCE3 17 2.2434
- angle_coeff @angle:na-cc-no harmonic 68.48 124.90 # SOURCE4 48 0.7933
- angle_coeff @angle:na-cc-oh harmonic 73.25 117.26 # SOURCE4 16 0.9090
- angle_coeff @angle:na-cc-sx harmonic 63.25 117.04 # SOURCE4 13 0.4187
- angle_coeff @angle:na-cc-sy harmonic 63.13 120.55 # SOURCE4 7 1.7547
- angle_coeff @angle:nc-cc-nd harmonic 73.35 115.96 # CORR 222
- angle_coeff @angle:nc-cc-nh harmonic 72.33 116.85 # CORR 35
- angle_coeff @angle:nc-cc-no harmonic 69.31 121.54 # SOURCE4 7 0.9221
- angle_coeff @angle:nc-cc-ss harmonic 64.63 119.86 # SOURCE3 2 0.0000
- angle_coeff @angle:nd-cc-nd harmonic 70.88 128.17 # SOURCE4 7 0.0269
- angle_coeff @angle:nd-cc-ne harmonic 69.29 129.66 # SOURCE4 7 0.4306
- angle_coeff @angle:nd-cc-nh harmonic 72.41 120.11 # SOURCE3 5 0.9313
- angle_coeff @angle:nd-cc-no harmonic 69.90 122.68 # SOURCE4 16 0.3393
- angle_coeff @angle:nd-cc-oh harmonic 72.93 121.54 # CORR 22
- angle_coeff @angle:nd-cc-os harmonic 73.85 116.29 # CORR 209
- angle_coeff @angle:nd-cc-sh harmonic 62.75 124.92 # SOURCE4 5 0.9563
- angle_coeff @angle:nd-cc-ss harmonic 66.51 114.51 # SOURCE3 8 0.3449
- angle_coeff @angle:nd-cc-sx harmonic 60.81 127.60 # SOURCE4 14 1.1650
- angle_coeff @angle:nd-cc-sy harmonic 62.75 123.08 # SOURCE4 13 1.0531
- angle_coeff @angle:ne-cc-ss harmonic 65.39 116.99 # SOURCE4 7 0.1657
- angle_coeff @angle:nh-cc-nh harmonic 72.93 115.96 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-cc-os harmonic 72.96 116.69 # CORR 25
- angle_coeff @angle:nh-cc-ss harmonic 64.19 121.94 # CORR 91
- angle_coeff @angle:n-cc-n2 harmonic 74.78 114.48 # SOURCE4 15 2.3208
- angle_coeff @angle:n-cc-na harmonic 70.47 122.14 # CORR 59
- angle_coeff @angle:n-cc-nc harmonic 69.35 125.66 # CORR 64
- angle_coeff @angle:n-cc-nd harmonic 71.12 122.98 # CORR 229
- angle_coeff @angle:n-cc-nh harmonic 72.22 116.87 # CORR 79
- angle_coeff @angle:no-cc-os harmonic 71.01 117.59 # SOURCE4 62 0.2199
- angle_coeff @angle:no-cc-ss harmonic 63.76 121.10 # SOURCE4 10 0.0957
- angle_coeff @angle:n-cc-ss harmonic 63.75 123.03 # CORR 45
- angle_coeff @angle:c-c-o harmonic 67.16 120.99 # SOURCE4 233 2.0333
- angle_coeff @angle:c-c-oh harmonic 68.20 113.23 # SOURCE3 5 0.5615
- angle_coeff @angle:c-c-os harmonic 68.18 111.39 # SOURCE4 14 0.4038
- angle_coeff @angle:os-cc-ss harmonic 61.99 132.01 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-cc-ss harmonic 62.44 121.37 # CORR 22
- angle_coeff @angle:ss-cc-sy harmonic 61.51 121.70 # CORR 39
- angle_coeff @angle:cx-c-cx harmonic 85.45 64.60 # SOURCE2 1 0.0000
- angle_coeff @angle:cx-c-n harmonic 68.69 114.49 # SOURCE4 23 1.4914
- angle_coeff @angle:cx-c-o harmonic 68.88 122.82 # SOURCE4 97 2.2075
- angle_coeff @angle:cx-c-oh harmonic 70.49 112.32 # SOURCE4 10 0.6413
- angle_coeff @angle:cx-c-os harmonic 70.06 111.48 # SOURCE4 16 1.3998
- angle_coeff @angle:cy-c-cy harmonic 70.14 90.55 # SOURCE2 2 2.4500
- angle_coeff @angle:cy-c-n harmonic 75.43 91.54 # SOURCE4 249 0.5104
- angle_coeff @angle:cy-c-o harmonic 64.27 135.04 # SOURCE4 253 1.3450
- angle_coeff @angle:cy-c-oh harmonic 69.09 112.48 # SOURCE4 5 1.0793
- angle_coeff @angle:cy-c-os harmonic 74.55 94.89 # SOURCE4 8 0.6016
- angle_coeff @angle:c2-cd-c3 harmonic 63.27 126.11 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-cd-ca harmonic 65.34 124.66 # CORR 16
- angle_coeff @angle:c2-cd-cc harmonic 69.09 117.02 # SOURCE3 2 same_as_c2-cc-cd
- angle_coeff @angle:c2-cd-cd harmonic 66.24 121.77 # CORR 32
- angle_coeff @angle:c2-cd-ha harmonic 48.69 122.72 # SOURCE3 2 same_as_c2-cc-ha
- angle_coeff @angle:c2-cd-n harmonic 67.74 126.90 # SOURCE3 1 same_as_c2-cc-n
- angle_coeff @angle:c2-cd-os harmonic 70.10 120.79 # CORR 13
- angle_coeff @angle:c3-cd-ca harmonic 61.96 125.89 # CORR 127
- angle_coeff @angle:c3-cd-cc harmonic 64.81 119.45 # SOURCE3 35 8.2040
- angle_coeff @angle:c3-cd-cd harmonic 64.66 115.97 # SOURCE3 4 3.0507
- angle_coeff @angle:c3-cd-ce harmonic 65.34 117.84 # CORR 2
- angle_coeff @angle:c3-cd-ha harmonic 45.11 121.52 # SOURCE3 32 3.2091
- angle_coeff @angle:c3-cd-n2 harmonic 65.80 126.87 # CORR 9
- angle_coeff @angle:c3-cd-n harmonic 66.33 119.11 # CORR 68
- angle_coeff @angle:c3-cd-na harmonic 65.50 122.78 # CORR 632
- angle_coeff @angle:c3-cd-nc harmonic 66.32 122.13 # CORR 475
- angle_coeff @angle:c3-cd-nd harmonic 65.90 120.94 # CORR 309
- angle_coeff @angle:c3-cd-os harmonic 67.54 116.88 # CORR 203
- angle_coeff @angle:c3-cd-ss harmonic 61.21 121.66 # CORR 171
- angle_coeff @angle:ca-cd-cc harmonic 68.23 113.51 # SOURCE3 26 7.4229
- angle_coeff @angle:ca-cd-cd harmonic 67.66 111.04 # SOURCE3 9 7.9455
- angle_coeff @angle:ca-cd-ce harmonic 65.09 125.10 # SOURCE4 9 1.9265
- angle_coeff @angle:ca-cd-h4 harmonic 45.57 128.66 # SOURCE3 10 3.1167
- angle_coeff @angle:ca-cd-ha harmonic 46.40 124.04 # SOURCE3 34 3.6691
- angle_coeff @angle:ca-cd-n harmonic 68.46 117.67 # CORR 18
- angle_coeff @angle:ca-cd-na harmonic 67.03 123.45 # SOURCE4 39 1.9138
- angle_coeff @angle:ca-cd-nc harmonic 67.92 123.02 # CORR 188
- angle_coeff @angle:ca-cd-nd harmonic 67.69 120.67 # CORR 162
- angle_coeff @angle:ca-cd-oh harmonic 69.61 117.71 # CORR 21
- angle_coeff @angle:ca-cd-os harmonic 69.82 115.16 # CORR 134
- angle_coeff @angle:ca-cd-ss harmonic 62.30 120.51 # CORR 43
- angle_coeff @angle:c-cd-c2 harmonic 65.60 120.92 # CORR 22
- angle_coeff @angle:c-cd-c3 harmonic 63.60 117.42 # CORR 126
- angle_coeff @angle:c-cd-c harmonic 63.42 121.17 # CORR 64
- angle_coeff @angle:c-cd-ca harmonic 63.55 122.95 # SOURCE3 1 same_as_c-cc-ca
- angle_coeff @angle:c-cd-cc harmonic 65.25 121.42 # CORR 1708
- angle_coeff @angle:cc-cd-cc harmonic 67.89 120.23 # CORR 133
- angle_coeff @angle:cc-cd-cd harmonic 68.16 114.19 # SOURCE3 517 6.5960
- angle_coeff @angle:cc-cd-cf harmonic 63.67 128.41 # CORR 210
- angle_coeff @angle:cc-cd-ch harmonic 64.92 126.05 # SOURCE4 30 1.4695
- angle_coeff @angle:cc-cd-cl harmonic 57.46 123.70 # CORR 62
- angle_coeff @angle:cc-cd-cy harmonic 63.93 122.13 # SOURCE4 10 0.8509
- angle_coeff @angle:c-cd-cd harmonic 63.72 122.69 # SOURCE3 2 0.0000
- angle_coeff @angle:c-cd-cf harmonic 63.20 122.73 # CORR 10
- angle_coeff @angle:cc-cd-h4 harmonic 47.19 129.11 # SOURCE3 418 3.1355
- angle_coeff @angle:cc-cd-ha harmonic 48.35 122.89 # SOURCE3 584 2.9334
- angle_coeff @angle:c-cd-cl harmonic 58.39 116.05 # CORR 24
- angle_coeff @angle:cc-cd-n harmonic 70.72 115.52 # SOURCE3 52 1.3322
- angle_coeff @angle:cc-cd-na harmonic 72.91 109.42 # SOURCE3 265 2.6051
- angle_coeff @angle:cc-cd-nc harmonic 69.42 123.82 # SOURCE4 14 0.3678
- angle_coeff @angle:cc-cd-nd harmonic 72.01 111.75 # CORR 1101
- angle_coeff @angle:cc-cd-nh harmonic 68.69 123.89 # CORR 106
- angle_coeff @angle:cc-cd-oh harmonic 69.56 123.89 # CORR 106
- angle_coeff @angle:cc-cd-os harmonic 69.96 120.30 # SOURCE3 64 5.4354
- angle_coeff @angle:cc-cd-ss harmonic 65.44 111.55 # CORR 884
- angle_coeff @angle:cc-cd-sy harmonic 60.54 124.91 # CORR 41
- angle_coeff @angle:cd-cd-cd harmonic 67.88 110.70 # SOURCE3 54 3.4091
- angle_coeff @angle:cd-cd-ce harmonic 65.88 122.59 # CORR 39
- angle_coeff @angle:cd-cd-cf harmonic 62.78 127.20 # CORR 42
- angle_coeff @angle:cd-cd-ch harmonic 63.63 126.15 # CORR 27
- angle_coeff @angle:cd-cd-cy harmonic 63.17 120.93 # SOURCE4 6 1.2205
- angle_coeff @angle:cd-cd-h4 harmonic 45.56 129.47 # SOURCE3 171 2.2734
- angle_coeff @angle:cd-cd-ha harmonic 47.14 120.86 # CORR 1751
- angle_coeff @angle:cd-cd-n2 harmonic 69.48 121.15 # CORR 12
- angle_coeff @angle:cd-cd-n harmonic 67.95 119.89 # SOURCE3 36 0.2095
- angle_coeff @angle:cd-cd-na harmonic 72.21 106.80 # SOURCE3 33 same_as_cc-cc-na
- angle_coeff @angle:cd-cd-nc harmonic 71.15 112.56 # SOURCE3 141 4.2871
- angle_coeff @angle:cd-cd-nd harmonic 67.53 121.69 # CORR 105
- angle_coeff @angle:cd-cd-nh harmonic 68.41 119.51 # CORR 228
- angle_coeff @angle:cd-cd-oh harmonic 68.53 121.96 # CORR 27
- angle_coeff @angle:cd-cd-os harmonic 69.34 117.23 # CORR 211
- angle_coeff @angle:cd-cd-pc harmonic 80.79 115.36 # SOURCE3 84 3.2889
- angle_coeff @angle:cd-cd-ss harmonic 62.45 120.12 # CORR 31
- angle_coeff @angle:ce-cd-nd harmonic 68.22 124.90 # SOURCE4 5 2.3975
- angle_coeff @angle:cf-cd-na harmonic 66.32 124.22 # CORR 48
- angle_coeff @angle:cf-cd-nc harmonic 67.80 121.51 # CORR 37
- angle_coeff @angle:cf-cd-nd harmonic 67.01 121.29 # CORR 37
- angle_coeff @angle:cf-cd-os harmonic 68.17 119.03 # CORR 66
- angle_coeff @angle:cf-cd-ss harmonic 61.83 121.44 # CORR 38
- angle_coeff @angle:c-cd-h4 harmonic 46.77 118.19 # SOURCE4 8 0.2226
- angle_coeff @angle:c-cd-ha harmonic 46.99 117.02 # SOURCE3 56 1.9713
- angle_coeff @angle:cl-cd-nc harmonic 59.35 122.97 # CORR 6
- angle_coeff @angle:c-cd-n2 harmonic 68.54 120.89 # CORR 2
- angle_coeff @angle:c-cd-n harmonic 68.11 116.32 # CORR 21
- angle_coeff @angle:c-cd-nc harmonic 67.50 121.67 # CORR 47
- angle_coeff @angle:c-cd-nd harmonic 66.19 123.47 # CORR 24
- angle_coeff @angle:c-cd-oh harmonic 70.04 113.64 # CORR 53
- angle_coeff @angle:c-cd-os harmonic 67.83 119.39 # CORR 78
- angle_coeff @angle:h4-cd-n harmonic 50.39 117.62 # SOURCE3 53 0.9721
- angle_coeff @angle:h4-cd-na harmonic 50.22 119.66 # SOURCE3 294 2.4702
- angle_coeff @angle:h4-cd-nc harmonic 51.39 119.11 # SOURCE3 135 1.6946
- angle_coeff @angle:h4-cd-nd harmonic 50.00 120.03 # SOURCE3 16 2.3863
- angle_coeff @angle:h4-cd-os harmonic 52.27 111.89 # SOURCE3 61 2.3500
- angle_coeff @angle:h4-cd-ss harmonic 42.95 117.75 # SOURCE3 40 3.1156
- angle_coeff @angle:h5-cd-n harmonic 50.84 115.72 # CORR 20
- angle_coeff @angle:h5-cd-na harmonic 49.76 122.10 # SOURCE3 16 1.4626
- angle_coeff @angle:h5-cd-nc harmonic 50.13 125.38 # SOURCE3 40 2.2157
- angle_coeff @angle:h5-cd-nd harmonic 49.29 123.70 # SOURCE3 6 0.3547
- angle_coeff @angle:h5-cd-os harmonic 51.30 116.33 # SOURCE3 12 3.2919
- angle_coeff @angle:h5-cd-ss harmonic 42.19 122.00 # SOURCE3 6 0.7237
- angle_coeff @angle:ha-cd-na harmonic 49.82 121.50 # SOURCE2 1 same_as_ha-cc-na
- angle_coeff @angle:ha-cd-nc harmonic 51.41 118.88 # SOURCE3 20 2.8923
- angle_coeff @angle:ha-cd-nd harmonic 50.73 116.54 # SOURCE3 5 1.4482
- angle_coeff @angle:ha-cd-os harmonic 52.49 110.86 # SOURCE3 7 1.3846
- angle_coeff @angle:ha-cd-pc harmonic 53.59 121.76 # SOURCE3 84 2.2216
- angle_coeff @angle:ha-cd-ss harmonic 42.26 121.64 # SOURCE2 5 same_as_ha-cc-ss
- angle_coeff @angle:na-cd-nc harmonic 74.78 112.02 # SOURCE3 17 2.2434
- angle_coeff @angle:na-cd-nd harmonic 70.72 121.62 # CORR 231
- angle_coeff @angle:na-cd-nh harmonic 72.43 116.98 # SOURCE4 46 1.4937
- angle_coeff @angle:na-cd-ss harmonic 67.07 111.46 # SOURCE4 20 0.8600
- angle_coeff @angle:nc-cd-nd harmonic 73.35 115.96 # CORR 222
- angle_coeff @angle:nc-cd-nh harmonic 72.41 120.11 # SOURCE3 5 0.9313
- angle_coeff @angle:nc-cd-oh harmonic 72.93 121.54 # CORR 22
- angle_coeff @angle:nc-cd-os harmonic 73.85 116.29 # CORR 209
- angle_coeff @angle:nc-cd-ss harmonic 66.51 114.51 # SOURCE3 8 0.3449
- angle_coeff @angle:nd-cd-nd harmonic 69.47 125.58 # SOURCE4 13 0.4672
- angle_coeff @angle:nd-cd-nh harmonic 72.33 116.85 # CORR 35
- angle_coeff @angle:nd-cd-ss harmonic 64.63 119.86 # SOURCE3 2 same_as_nc-cc-ss
- angle_coeff @angle:nh-cd-nh harmonic 72.93 115.96 # SOURCE3 1 same_as_nh-cc-nh
- angle_coeff @angle:nh-cd-os harmonic 72.96 116.69 # CORR 25
- angle_coeff @angle:nh-cd-ss harmonic 64.19 121.94 # CORR 91
- angle_coeff @angle:n-cd-na harmonic 70.47 122.14 # CORR 59
- angle_coeff @angle:n-cd-nc harmonic 71.12 122.98 # CORR 229
- angle_coeff @angle:n-cd-nd harmonic 69.35 125.66 # CORR 64
- angle_coeff @angle:n-cd-nh harmonic 72.22 116.87 # CORR 79
- angle_coeff @angle:n-cd-ss harmonic 63.75 123.03 # CORR 45
- angle_coeff @angle:oh-cd-os harmonic 75.54 111.61 # SOURCE4 6 1.1909
- angle_coeff @angle:os-cd-ss harmonic 61.99 132.01 # SOURCE3 1 same_as_os-cc-ss
- angle_coeff @angle:ss-cd-ss harmonic 62.44 121.37 # CORR 22
- angle_coeff @angle:ss-cd-sy harmonic 61.51 121.70 # CORR 39
- angle_coeff @angle:c2-ce-c3 harmonic 64.30 122.89 # SOURCE3 7 1.0449
- angle_coeff @angle:c2-ce-ca harmonic 65.16 123.08 # SOURCE3 6 2.1589
- angle_coeff @angle:c2-ce-cc harmonic 65.62 123.27 # CORR 72
- angle_coeff @angle:c2-ce-ce harmonic 65.73 123.08 # SOURCE3 12 0.6518
- angle_coeff @angle:c2-ce-cg harmonic 66.66 121.67 # CORR 21
- angle_coeff @angle:c2-ce-cl harmonic 57.87 119.51 # SOURCE4 24 1.4963
- angle_coeff @angle:c2-ce-h4 harmonic 48.64 125.58 # SOURCE4 11 0.9381
- angle_coeff @angle:c2-ce-ha harmonic 49.56 121.10 # SOURCE3 46 2.4054
- angle_coeff @angle:c2-ce-n1 harmonic 72.67 117.85 # SOURCE4 7 0.3180
- angle_coeff @angle:c2-ce-n2 harmonic 70.34 128.70 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-ce-na harmonic 69.29 119.19 # SOURCE4 5 0.8452
- angle_coeff @angle:c2-ce-ne harmonic 69.73 118.32 # SOURCE3 7 1.0468
- angle_coeff @angle:c2-ce-oh harmonic 70.32 123.78 # SOURCE4 10 1.8182
- angle_coeff @angle:c2-ce-p2 harmonic 77.91 118.24 # SOURCE3 1
- angle_coeff @angle:c2-ce-pe harmonic 77.59 118.76 # SOURCE3 8 2.3984
- angle_coeff @angle:c2-ce-px harmonic 77.17 119.72 # SOURCE3 6 0.5213
- angle_coeff @angle:c2-ce-py harmonic 77.39 122.13 # SOURCE3 5 3.1367
- angle_coeff @angle:c2-ce-sx harmonic 61.64 119.87 # SOURCE3 5 0.8557
- angle_coeff @angle:c2-ce-sy harmonic 61.96 120.35 # SOURCE3 5 0.5401
- angle_coeff @angle:c3-ce-ca harmonic 62.76 119.28 # CORR 178
- angle_coeff @angle:c3-ce-cc harmonic 63.42 118.22 # CORR 39
- angle_coeff @angle:c3-ce-ce harmonic 63.80 116.99 # CORR 244
- angle_coeff @angle:c3-ce-cf harmonic 64.52 122.11 # CORR 221
- angle_coeff @angle:c3-ce-cg harmonic 63.79 118.48 # SOURCE4 8 1.4756
- angle_coeff @angle:c3-ce-n2 harmonic 66.92 122.70 # CORR 81
- angle_coeff @angle:c3-ce-nf harmonic 67.26 120.75 # SOURCE4 6 2.1938
- angle_coeff @angle:c3-ce-nh harmonic 65.76 119.90 # SOURCE4 5 0.9634
- angle_coeff @angle:ca-ce-ca harmonic 63.94 117.58 # CORR 112
- angle_coeff @angle:ca-ce-cc harmonic 64.21 118.06 # CORR 17
- angle_coeff @angle:ca-ce-ce harmonic 63.84 119.62 # SOURCE4 14 1.9171
- angle_coeff @angle:ca-ce-cf harmonic 64.07 127.39 # CORR 318
- angle_coeff @angle:ca-ce-cl harmonic 57.99 114.22 # SOURCE4 6 1.3164
- angle_coeff @angle:ca-ce-h4 harmonic 46.71 116.86 # SOURCE4 74 0.9179
- angle_coeff @angle:ca-ce-ha harmonic 47.07 115.16 # CORR 345
- angle_coeff @angle:ca-ce-n2 harmonic 68.51 120.72 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-ce-nf harmonic 67.74 122.66 # CORR 22
- angle_coeff @angle:ca-ce-nh harmonic 67.87 115.51 # SOURCE4 93 0.9284
- angle_coeff @angle:ca-ce-oh harmonic 68.85 116.37 # CORR 11
- angle_coeff @angle:ca-ce-os harmonic 68.60 115.58 # SOURCE4 8 1.0735
- angle_coeff @angle:ca-ce-ss harmonic 61.21 117.73 # SOURCE4 5 1.1596
- angle_coeff @angle:c-ce-c2 harmonic 65.82 120.42 # SOURCE3 13 1.8877
- angle_coeff @angle:c-ce-c3 harmonic 63.35 116.92 # CORR 188
- angle_coeff @angle:c-ce-c harmonic 62.59 122.38 # CORR 23
- angle_coeff @angle:c-ce-ca harmonic 63.79 117.98 # SOURCE4 8 1.5129
- angle_coeff @angle:cc-ce-cd harmonic 63.28 130.36 # SOURCE4 5 2.3402
- angle_coeff @angle:cc-ce-cf harmonic 64.87 126.20 # CORR 88
- angle_coeff @angle:c-ce-cd harmonic 63.81 126.07 # CORR 2
- angle_coeff @angle:c-ce-ce harmonic 63.46 120.89 # SOURCE4 16 1.8719
- angle_coeff @angle:c-ce-cf harmonic 64.26 126.41 # SOURCE3 2 5.7847
- angle_coeff @angle:c-ce-cg harmonic 64.57 118.32 # SOURCE4 15 1.0595
- angle_coeff @angle:cc-ce-h4 harmonic 47.52 115.40 # SOURCE4 29 0.8744
- angle_coeff @angle:cc-ce-ha harmonic 47.53 115.45 # CORR 113
- angle_coeff @angle:c-ce-cl harmonic 57.67 115.40 # SOURCE4 6 1.0958
- angle_coeff @angle:cc-ce-n2 harmonic 68.94 121.28 # CORR 69
- angle_coeff @angle:cc-ce-nh harmonic 67.31 119.17 # SOURCE4 8 2.1378
- angle_coeff @angle:c-ce-cy harmonic 72.72 88.22 # SOURCE4 19 0.3234
- angle_coeff @angle:cd-ce-ce harmonic 64.81 124.49 # CORR 12
- angle_coeff @angle:cd-ce-ha harmonic 49.97 115.48 # CORR 39
- angle_coeff @angle:ce-ce-ce harmonic 64.55 118.74 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-ce-cf harmonic 65.46 124.19 # CORR 341
- angle_coeff @angle:ce-ce-cl harmonic 57.29 117.93 # SOURCE4 12 0.2639
- angle_coeff @angle:ce-ce-h4 harmonic 47.06 117.97 # CORR 19
- angle_coeff @angle:ce-ce-ha harmonic 47.50 115.90 # SOURCE3 12 0.4670
- angle_coeff @angle:ce-ce-n1 harmonic 66.79 127.15 # CORR 4
- angle_coeff @angle:ce-ce-n2 harmonic 69.57 119.33 # CORR 13
- angle_coeff @angle:ce-ce-oh harmonic 69.29 116.89 # SOURCE4 11 2.0380
- angle_coeff @angle:cf-ce-cg harmonic 66.10 123.79 # CORR 41
- angle_coeff @angle:cf-ce-cy harmonic 60.53 137.74 # SOURCE4 13 0.3952
- angle_coeff @angle:cf-ce-h4 harmonic 49.02 123.76 # SOURCE4 5 1.0909
- angle_coeff @angle:cf-ce-ha harmonic 50.21 118.12 # CORR 655
- angle_coeff @angle:cf-ce-n1 harmonic 72.03 120.03 # SOURCE4 6 1.9451
- angle_coeff @angle:cf-ce-n harmonic 72.60 108.25 # CORR 64
- angle_coeff @angle:cf-ce-nh harmonic 69.48 121.52 # SOURCE4 12 2.0106
- angle_coeff @angle:cf-ce-oh harmonic 70.92 121.78 # CORR 24
- angle_coeff @angle:cg-ce-cg harmonic 65.58 118.26 # CORR 7
- angle_coeff @angle:cg-ce-ha harmonic 47.93 116.54 # CORR 18
- angle_coeff @angle:cg-ce-n1 harmonic 69.49 119.50 # CORR 2
- angle_coeff @angle:cg-ce-n2 harmonic 69.59 121.43 # SOURCE4 6 0.8382
- angle_coeff @angle:c-ce-ha harmonic 46.59 117.26 # SOURCE3 11 2.7158
- angle_coeff @angle:c-ce-n harmonic 66.20 118.62 # CORR 137
- angle_coeff @angle:c-ce-nh harmonic 67.79 115.62 # CORR 19
- angle_coeff @angle:c-ce-oh harmonic 68.34 117.92 # SOURCE4 5 1.4580
- angle_coeff @angle:c-ce-os harmonic 69.09 113.78 # SOURCE4 21 1.8258
- angle_coeff @angle:h4-ce-n1 harmonic 52.58 116.36 # SOURCE4 7 0.2182
- angle_coeff @angle:h4-ce-n2 harmonic 52.36 121.58 # CORR 116
- angle_coeff @angle:h4-ce-ne harmonic 49.72 115.81 # SOURCE4 7 1.9836
- angle_coeff @angle:ha-ce-n1 harmonic 52.70 115.96 # CORR 4
- angle_coeff @angle:ha-ce-n2 harmonic 52.85 119.51 # SOURCE3 2 0.4623
- angle_coeff @angle:ha-ce-ne harmonic 49.16 118.59 # SOURCE3 5 1.1113
- angle_coeff @angle:ha-ce-nh harmonic 50.62 114.99 # CORR 2
- angle_coeff @angle:ha-ce-p2 harmonic 51.40 120.11 # SOURCE3 1
- angle_coeff @angle:ha-ce-pe harmonic 51.44 119.33 # SOURCE3 6 0.8966
- angle_coeff @angle:ha-ce-px harmonic 51.66 117.90 # SOURCE3 6 0.1809
- angle_coeff @angle:ha-ce-py harmonic 52.32 118.72 # SOURCE3 3 0.3064
- angle_coeff @angle:ha-ce-sx harmonic 41.85 115.45 # SOURCE3 3 0.6640
- angle_coeff @angle:ha-ce-sy harmonic 42.34 114.86 # SOURCE3 3 0.4717
- angle_coeff @angle:n2-ce-nh harmonic 71.56 124.96 # CORR 92
- angle_coeff @angle:n2-ce-os harmonic 74.58 118.13 # SOURCE4 6 0.1367
- angle_coeff @angle:n2-ce-ss harmonic 64.40 117.23 # SOURCE4 6 2.0518
- angle_coeff @angle:ne-ce-ne harmonic 68.07 123.87 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-ce-nh harmonic 71.89 112.91 # SOURCE4 12 1.1263
- angle_coeff @angle:nf-ce-nh harmonic 73.31 118.13 # SOURCE4 6 0.5842
- angle_coeff @angle:pe-ce-pe harmonic 92.40 129.79 # SOURCE3 1 0.0000
- angle_coeff @angle:py-ce-py harmonic 102.62 108.06 # SOURCE3 1 0.0000
- angle_coeff @angle:sx-ce-sx harmonic 60.61 120.32 # SOURCE3 1 0.0000
- angle_coeff @angle:sy-ce-sy harmonic 61.21 119.97 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-cf-c3 harmonic 64.30 122.89 # SOURCE3 7 same_as_c2-ce-c3
- angle_coeff @angle:c2-cf-ca harmonic 65.16 123.08 # SOURCE3 6 same_as_c2-ce-ca
- angle_coeff @angle:c2-cf-cd harmonic 65.62 123.27 # CORR 72
- angle_coeff @angle:c2-cf-cf harmonic 65.73 123.08 # SOURCE3 12 same_as_c2-ce-ce
- angle_coeff @angle:c2-cf-ch harmonic 66.66 121.67 # CORR 21
- angle_coeff @angle:c2-cf-ha harmonic 49.56 121.10 # SOURCE3 46 same_as_c2-ce-ha
- angle_coeff @angle:c2-cf-n2 harmonic 70.34 128.70 # SOURCE3 1 same_as_c2-ce-n2
- angle_coeff @angle:c2-cf-nf harmonic 69.73 118.32 # SOURCE3 7 same_as_c2-ce-ne
- angle_coeff @angle:c2-cf-p2 harmonic 77.91 118.24 # SOURCE3 1 same_as_c2-ce-p2
- angle_coeff @angle:c2-cf-pf harmonic 77.59 118.76 # SOURCE3 8 same_as_c2-ce-pe
- angle_coeff @angle:c2-cf-px harmonic 77.17 119.72 # SOURCE3 6 same_as_c2-ce-px
- angle_coeff @angle:c2-cf-py harmonic 77.39 122.13 # SOURCE3 5 same_as_c2-ce-py
- angle_coeff @angle:c2-cf-sx harmonic 61.64 119.87 # SOURCE3 5 same_as_c2-ce-sx
- angle_coeff @angle:c2-cf-sy harmonic 61.96 120.35 # SOURCE3 5 same_as_c2-ce-sy
- angle_coeff @angle:c3-cf-ca harmonic 62.76 119.28 # CORR 178
- angle_coeff @angle:c3-cf-cd harmonic 63.42 118.22 # CORR 39
- angle_coeff @angle:c3-cf-ce harmonic 64.52 122.11 # CORR 221
- angle_coeff @angle:c3-cf-cf harmonic 63.80 116.99 # CORR 244
- angle_coeff @angle:c3-cf-n2 harmonic 66.92 122.70 # CORR 81
- angle_coeff @angle:ca-cf-ca harmonic 63.94 117.58 # CORR 112
- angle_coeff @angle:ca-cf-cc harmonic 62.70 130.80 # SOURCE4 12 1.2696
- angle_coeff @angle:ca-cf-cd harmonic 64.21 118.06 # CORR 17
- angle_coeff @angle:ca-cf-ce harmonic 64.07 127.39 # CORR 318
- angle_coeff @angle:ca-cf-ha harmonic 47.07 115.16 # CORR 345
- angle_coeff @angle:ca-cf-n2 harmonic 68.51 120.72 # SOURCE3 1 same_as_ca-ce-n2
- angle_coeff @angle:ca-cf-ne harmonic 67.74 122.66 # CORR 22
- angle_coeff @angle:ca-cf-oh harmonic 68.85 116.37 # CORR 11
- angle_coeff @angle:c-cf-c2 harmonic 65.82 120.42 # SOURCE3 13 same_as_c-ce-c2
- angle_coeff @angle:c-cf-c3 harmonic 63.35 116.92 # CORR 188
- angle_coeff @angle:c-cf-c harmonic 62.59 122.38 # CORR 23
- angle_coeff @angle:c-cf-cc harmonic 63.81 126.07 # CORR 2
- angle_coeff @angle:cc-cf-cf harmonic 64.81 124.49 # CORR 12
- angle_coeff @angle:c-cf-cd harmonic 64.25 117.76 # SOURCE4 10 1.2451
- angle_coeff @angle:c-cf-ce harmonic 64.26 126.41 # SOURCE3 2 same_as_c-ce-cf
- angle_coeff @angle:cc-cf-ha harmonic 49.97 115.48 # CORR 39
- angle_coeff @angle:cd-cf-ce harmonic 64.87 126.20 # CORR 88
- angle_coeff @angle:cd-cf-ha harmonic 47.53 115.45 # CORR 113
- angle_coeff @angle:cd-cf-n2 harmonic 68.94 121.28 # CORR 69
- angle_coeff @angle:ce-cf-cf harmonic 65.46 124.19 # CORR 341
- angle_coeff @angle:ce-cf-ch harmonic 66.10 123.79 # CORR 41
- angle_coeff @angle:ce-cf-ha harmonic 50.21 118.12 # CORR 655
- angle_coeff @angle:ce-cf-n harmonic 72.60 108.25 # CORR 64
- angle_coeff @angle:ce-cf-oh harmonic 70.92 121.78 # CORR 24
- angle_coeff @angle:cf-cf-cf harmonic 64.55 118.74 # SOURCE3 1 same_as_ce-ce-ce
- angle_coeff @angle:cf-cf-h4 harmonic 47.06 117.97 # CORR 19
- angle_coeff @angle:cf-cf-ha harmonic 47.50 115.90 # SOURCE3 12 0.4670
- angle_coeff @angle:cf-cf-n1 harmonic 66.79 127.15 # CORR 4
- angle_coeff @angle:cf-cf-n2 harmonic 69.57 119.33 # CORR 13
- angle_coeff @angle:c-cf-ha harmonic 46.59 117.26 # SOURCE3 11 2.7158
- angle_coeff @angle:ch-cf-ch harmonic 65.58 118.26 # CORR 7
- angle_coeff @angle:ch-cf-ha harmonic 47.93 116.54 # CORR 18
- angle_coeff @angle:ch-cf-n1 harmonic 69.49 119.50 # CORR 2
- angle_coeff @angle:c-cf-n2 harmonic 70.16 114.88 # SOURCE4 5 1.3647
- angle_coeff @angle:c-cf-n harmonic 66.20 118.62 # CORR 137
- angle_coeff @angle:c-cf-nh harmonic 67.79 115.62 # CORR 19
- angle_coeff @angle:f-c-f harmonic 72.22 107.35 # SOURCE2 2 0.2500
- angle_coeff @angle:h4-cf-n2 harmonic 52.36 121.58 # CORR 116
- angle_coeff @angle:h4-cf-ne harmonic 52.29 120.21 # SOURCE4 6 0.8104
- angle_coeff @angle:ha-cf-n1 harmonic 52.70 115.96 # CORR 4
- angle_coeff @angle:ha-cf-n2 harmonic 52.85 119.51 # SOURCE3 2 same_as_ha-ce-n2
- angle_coeff @angle:ha-cf-nf harmonic 49.16 118.59 # SOURCE3 5 same_as_ha-ce-ne
- angle_coeff @angle:ha-cf-nh harmonic 50.62 114.99 # CORR 2
- angle_coeff @angle:ha-cf-p2 harmonic 51.40 120.11 # SOURCE3 1 same_as_ha-ce-p2
- angle_coeff @angle:ha-cf-pf harmonic 51.44 119.33 # SOURCE3 6 same_as_ha-ce-pe
- angle_coeff @angle:ha-cf-px harmonic 51.66 117.90 # SOURCE3 6 same_as_ha-ce-px
- angle_coeff @angle:ha-cf-py harmonic 52.32 118.72 # SOURCE3 3 same_as_ha-ce-py
- angle_coeff @angle:ha-cf-sx harmonic 41.85 115.45 # SOURCE3 3 same_as_ha-ce-sx
- angle_coeff @angle:ha-cf-sy harmonic 42.34 114.86 # SOURCE3 3 same_as_ha-ce-sy
- angle_coeff @angle:n2-cf-nh harmonic 71.56 124.96 # CORR 92
- angle_coeff @angle:nf-cf-nf harmonic 68.07 123.87 # SOURCE3 1 same_as_ne-ce-ne
- angle_coeff @angle:f-c-o harmonic 73.21 123.44 # SOURCE3 1
- angle_coeff @angle:pf-cf-pf harmonic 92.40 129.79 # SOURCE3 1 same_as_pe-ce-pe
- angle_coeff @angle:py-cf-py harmonic 102.62 108.06 # SOURCE3 1 same_as_py-ce-py
- angle_coeff @angle:f-c-s harmonic 63.41 124.00 # SOURCE2 1 0.0000
- angle_coeff @angle:sx-cf-sx harmonic 60.61 120.32 # SOURCE3 1 same_as_sx-ce-sx
- angle_coeff @angle:sy-cf-sy harmonic 61.21 119.97 # SOURCE3 1 same_as_sy-ce-sy
- angle_coeff @angle:c1-cg-ca harmonic 56.52 179.52 # CORR 19
- angle_coeff @angle:c1-cg-cc harmonic 56.97 178.60 # SOURCE4 6 0.3822
- angle_coeff @angle:c1-cg-ce harmonic 56.95 178.05 # CORR 7
- angle_coeff @angle:c1-cg-cg harmonic 58.17 179.70 # CORR 18
- angle_coeff @angle:c1-cg-ne harmonic 62.73 170.02 # SOURCE3 4 1.1724
- angle_coeff @angle:c1-cg-pe harmonic 71.80 173.29 # SOURCE3 11 4.9305
- angle_coeff @angle:ca-cg-ch harmonic 56.91 179.64 # CORR 13
- angle_coeff @angle:ca-cg-n1 harmonic 58.93 179.43 # CORR 103
- angle_coeff @angle:c-cg-c1 harmonic 56.19 179.14 # SOURCE3 2 0.0000
- angle_coeff @angle:cc-cg-n1 harmonic 59.43 178.54 # CORR 50
- angle_coeff @angle:ce-cg-ch harmonic 57.39 177.94 # CORR 17
- angle_coeff @angle:ce-cg-n1 harmonic 59.39 177.97 # CORR 67
- angle_coeff @angle:n1-cg-ne harmonic 64.98 174.44 # CORR 17
- angle_coeff @angle:h4-c-o harmonic 54.28 120.93 # SOURCE4 129 0.5769
- angle_coeff @angle:h5-c-n harmonic 52.39 112.19 # SOURCE4 33 0.4220
- angle_coeff @angle:h5-c-o harmonic 53.89 123.26 # SOURCE4 38 0.4806
- angle_coeff @angle:ha-c-ha harmonic 37.86 115.61 # SOURCE3 4 0.0458
- angle_coeff @angle:ha-c-i harmonic 36.71 110.58 # SOURCE3 1 0.0000
- angle_coeff @angle:ha-c-n harmonic 52.40 112.37 # SOURCE3 4 0.6424
- angle_coeff @angle:ha-c-o harmonic 54.27 121.94 # SOURCE3 51 2.3235
- angle_coeff @angle:ha-c-oh harmonic 53.97 111.82 # SOURCE3 4 1.9375
- angle_coeff @angle:ha-c-os harmonic 53.24 110.34 # SOURCE3 8 1.9344
- angle_coeff @angle:ha-c-s harmonic 44.27 119.56 # SOURCE3 3 0.7586
- angle_coeff @angle:c1-ch-ca harmonic 56.52 179.52 # CORR 19
- angle_coeff @angle:c1-ch-cf harmonic 56.95 178.05 # CORR 7
- angle_coeff @angle:c1-ch-ch harmonic 58.17 179.70 # CORR 18
- angle_coeff @angle:c1-ch-nf harmonic 62.73 170.02 # SOURCE3 4 same_as_c1-cg-ne
- angle_coeff @angle:c1-ch-pf harmonic 71.80 173.29 # SOURCE3 11 same_as_c1-cg-pe
- angle_coeff @angle:ca-ch-cg harmonic 56.91 179.64 # CORR 13
- angle_coeff @angle:ca-ch-n1 harmonic 58.93 179.43 # CORR 103
- angle_coeff @angle:c-ch-c1 harmonic 56.19 179.14 # SOURCE3 2 same_as_c-cg-c1
- angle_coeff @angle:cd-ch-n1 harmonic 59.43 178.54 # CORR 50
- angle_coeff @angle:cf-ch-cg harmonic 57.39 177.94 # CORR 17
- angle_coeff @angle:cf-ch-n1 harmonic 59.39 177.97 # CORR 67
- angle_coeff @angle:cg-ch-ch harmonic 58.68 179.67 # SOURCE4 7 0.1439
- angle_coeff @angle:n1-ch-nf harmonic 64.98 174.44 # CORR 17
- angle_coeff @angle:i-c-i harmonic 59.79 116.45 # SOURCE3 1 0.0000
- angle_coeff @angle:i-c-o harmonic 55.51 122.02 # SOURCE3 4 1.2961
- angle_coeff @angle:f-cl-f harmonic 0.00 87.50 # SOURCE2 1 estimated_force_constant
- angle_coeff @angle:n2-c-n2 harmonic 71.83 110.31 # SOURCE3 1
- angle_coeff @angle:n2-c-o harmonic 73.02 122.50 # SOURCE3 1
- angle_coeff @angle:n4-c-n4 harmonic 64.71 114.64 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-c-o harmonic 69.58 118.83 # SOURCE3 4 3.8516
- angle_coeff @angle:nc-c-o harmonic 73.92 122.97 # CORR 121
- angle_coeff @angle:nd-c-o harmonic 73.92 122.97 # CORR 121
- angle_coeff @angle:ne-c-ne harmonic 73.21 110.31 # CORR 2
- angle_coeff @angle:ne-c-o harmonic 72.96 125.91 # CORR 42
- angle_coeff @angle:nf-c-nf harmonic 73.21 110.31 # CORR 2
- angle_coeff @angle:nf-c-o harmonic 72.96 125.91 # CORR 42
- angle_coeff @angle:n-c-n harmonic 74.80 113.38 # SOURCE4 635 1.4358
- angle_coeff @angle:n-c-nc harmonic 72.35 117.05 # CORR 77
- angle_coeff @angle:n-c-nd harmonic 72.35 117.05 # CORR 77
- angle_coeff @angle:n-c-ne harmonic 74.43 110.37 # SOURCE4 10 1.7492
- angle_coeff @angle:n-c-o harmonic 75.83 122.03 # SOURCE3 221 2.3565
- angle_coeff @angle:n-c-oh harmonic 76.22 113.63 # SOURCE4 5 1.1209
- angle_coeff @angle:no-c-no harmonic 66.54 109.28 # SOURCE3 1
- angle_coeff @angle:no-c-o harmonic 67.95 125.36 # SOURCE3 1
- angle_coeff @angle:n-c-os harmonic 76.68 109.28 # SOURCE4 318 0.8749
- angle_coeff @angle:n-c-s harmonic 65.73 123.88 # SOURCE3 5 1.2935
- angle_coeff @angle:n-c-sh harmonic 65.61 112.61 # SOURCE4 8 1.2601
- angle_coeff @angle:n-c-ss harmonic 66.85 110.42 # SOURCE4 59 1.5507
- angle_coeff @angle:oh-c-oh harmonic 78.91 110.56 # SOURCE3 2 0.5498
- angle_coeff @angle:oh-c-s harmonic 66.64 123.44 # SOURCE3 1 0.0000
- angle_coeff @angle:o-c-o harmonic 78.17 130.38 # SOURCE4 429 1.0315
- angle_coeff @angle:o-c-oh harmonic 77.38 122.88 # SOURCE3 33 2.1896
- angle_coeff @angle:o-c-os harmonic 75.93 123.33 # SOURCE4 1708 1.0632
- angle_coeff @angle:o-c-p2 harmonic 75.65 123.10 # SOURCE3 1
- angle_coeff @angle:o-c-p3 harmonic 77.08 120.79 # SOURCE3 1
- angle_coeff @angle:o-c-p5 harmonic 77.01 121.20 # SOURCE4 8 1.2117
- angle_coeff @angle:o-c-pe harmonic 75.23 123.02 # SOURCE3 3 0.1404
- angle_coeff @angle:o-c-pf harmonic 75.23 123.02 # SOURCE3 3 same_as_o-c-pe
- angle_coeff @angle:o-c-px harmonic 76.75 119.10 # SOURCE3 1 0.0000
- angle_coeff @angle:o-c-py harmonic 77.45 121.71 # SOURCE4 5 0.3133
- angle_coeff @angle:o-c-s4 harmonic 61.24 121.15 # SOURCE3 1
- angle_coeff @angle:o-c-s6 harmonic 61.67 119.45 # SOURCE3 1
- angle_coeff @angle:o-c-s harmonic 68.21 120.44 # SOURCE3 2 0.0000
- angle_coeff @angle:o-c-sh harmonic 64.19 121.41 # SOURCE3 4 1.4052
- angle_coeff @angle:os-c-os harmonic 76.45 111.38 # SOURCE4 12 0.8309
- angle_coeff @angle:o-c-ss harmonic 64.62 122.29 # SOURCE3 7 1.9240
- angle_coeff @angle:os-c-s harmonic 65.82 125.03 # SOURCE4 18 0.9978
- angle_coeff @angle:os-c-ss harmonic 66.30 113.63 # SOURCE4 5 0.7367
- angle_coeff @angle:o-c-sx harmonic 60.75 121.15 # SOURCE3 5 3.6452
- angle_coeff @angle:o-c-sy harmonic 61.88 119.32 # SOURCE3 5 2.4495
- angle_coeff @angle:p2-c-p2 harmonic 94.44 113.75 # SOURCE3 1
- angle_coeff @angle:p3-c-p3 harmonic 93.55 118.04 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-c-py harmonic 107.54 90.08 # SOURCE3 1 0.0000
- angle_coeff @angle:p5-c-p5 harmonic 91.43 123.76 # SOURCE3 1
- angle_coeff @angle:ca-cp-ca harmonic 67.11 118.33 # CORR 526
- angle_coeff @angle:ca-cp-cp harmonic 64.09 121.13 # CORR 991
- angle_coeff @angle:ca-cp-na harmonic 68.78 119.43 # SOURCE4 21 0.6591
- angle_coeff @angle:ca-cp-nb harmonic 69.19 121.65 # SOURCE4 63 0.6564
- angle_coeff @angle:cp-cp-cp harmonic 72.20 90.00 # SOURCE3 4 0.0000
- angle_coeff @angle:cp-cp-cq harmonic 62.64 124.47 # CORR 10
- angle_coeff @angle:cp-cp-nb harmonic 68.05 116.60 # SOURCE4 88 1.1887
- angle_coeff @angle:pe-c-pe harmonic 93.89 113.77 # SOURCE3 1 0.0000
- angle_coeff @angle:pf-c-pf harmonic 93.89 113.77 # SOURCE3 1 same_as_pe-c-pe
- angle_coeff @angle:nb-cp-nb harmonic 71.31 125.72 # SOURCE4 5 0.6674
- angle_coeff @angle:py-c-py harmonic 92.13 123.80 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-cq-ca harmonic 67.11 118.33 # CORR 526
- angle_coeff @angle:ca-cq-cq harmonic 64.09 121.13 # CORR 991
- angle_coeff @angle:ca-cq-nb harmonic 69.19 121.65 # SOURCE4 63 same as ca-cp-nb
- angle_coeff @angle:cp-cq-cq harmonic 62.64 124.47 # CORR 10
- angle_coeff @angle:cq-cq-cq harmonic 72.20 90.00 # SOURCE3 4 0.0000
- angle_coeff @angle:cq-cq-nb harmonic 68.05 116.60 # SOURCE4 88 same as cp-cp-nb
- angle_coeff @angle:s4-c-s4 harmonic 61.25 108.81 # SOURCE3 1
- angle_coeff @angle:s6-c-s6 harmonic 59.39 115.75 # SOURCE3 1
- angle_coeff @angle:sh-c-sh harmonic 62.47 115.33 # SOURCE3 1 0.0000
- angle_coeff @angle:s-c-s harmonic 65.01 120.40 # SOURCE3 2 1.2766
- angle_coeff @angle:s-c-sh harmonic 62.29 122.76 # SOURCE4 11 1.5734
- angle_coeff @angle:s-c-ss harmonic 61.88 125.90 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-c-ss harmonic 63.79 113.00 # SOURCE3 1 0.0000
- angle_coeff @angle:sx-c-sx harmonic 60.77 108.80 # SOURCE3 1 0.0000
- angle_coeff @angle:sy-c-sy harmonic 59.54 115.78 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-cu-cx harmonic 58.56 148.21 # SOURCE4 6 1.8305
- angle_coeff @angle:c-cu-cu harmonic 94.97 62.60 # SOURCE2 1 0.0000
- angle_coeff @angle:cu-cu-cx harmonic 100.97 50.80 # SOURCE2 1 0.0000
- angle_coeff @angle:cu-cu-ha harmonic 46.11 147.73 # SOURCE2 3 2.0950
- angle_coeff @angle:cv-cv-cy harmonic 73.28 94.17 # SOURCE3 2 0.0000
- angle_coeff @angle:cv-cv-ha harmonic 47.30 133.70 # SOURCE3 2 0.0000
- angle_coeff @angle:cx-cv-cx harmonic 84.66 63.90 # SOURCE2 1 0.0000
- angle_coeff @angle:cy-cv-ha harmonic 42.89 132.14 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-cx-cx harmonic 63.10 120.66 # SOURCE4 9 0.9067
- angle_coeff @angle:c2-cx-cx harmonic 62.33 120.54 # SOURCE4 51 2.2377
- angle_coeff @angle:c2-cx-h1 harmonic 46.63 115.78 # SOURCE4 8 0.2332
- angle_coeff @angle:c2-cx-hc harmonic 46.77 115.10 # SOURCE4 12 0.7463
- angle_coeff @angle:c2-cx-os harmonic 67.14 116.17 # SOURCE4 14 1.2782
- angle_coeff @angle:c3-cx-c3 harmonic 63.00 114.48 # SOURCE4 46 1.9627
- angle_coeff @angle:c3-cx-cx harmonic 61.82 120.06 # SOURCE4 448 2.1467
- angle_coeff @angle:c3-cx-h1 harmonic 45.87 115.42 # SOURCE4 89 1.1096
- angle_coeff @angle:c3-cx-hc harmonic 46.12 114.16 # SOURCE4 85 1.1118
- angle_coeff @angle:c3-cx-n3 harmonic 64.31 118.50 # SOURCE4 17 2.4897
- angle_coeff @angle:c3-cx-os harmonic 66.57 115.50 # SOURCE4 161 1.3016
- angle_coeff @angle:ca-cx-cx harmonic 61.86 122.18 # SOURCE4 65 1.6898
- angle_coeff @angle:ca-cx-h1 harmonic 46.81 114.57 # SOURCE4 7 0.6498
- angle_coeff @angle:ca-cx-hc harmonic 47.05 113.41 # SOURCE4 18 0.7843
- angle_coeff @angle:ca-cx-oh harmonic 69.25 112.93 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-cx-os harmonic 66.42 118.50 # SOURCE4 6 0.7514
- angle_coeff @angle:c-cx-c3 harmonic 62.91 116.93 # SOURCE4 18 1.8253
- angle_coeff @angle:cc-cx-cx harmonic 62.90 119.31 # CORR 39
- angle_coeff @angle:cc-cx-hc harmonic 47.37 113.84 # SOURCE4 15 0.6682
- angle_coeff @angle:c-cx-cx harmonic 62.96 117.96 # SOURCE4 147 1.8483
- angle_coeff @angle:cd-cx-cx harmonic 62.90 119.31 # CORR 39
- angle_coeff @angle:c-cx-h1 harmonic 46.27 117.25 # SOURCE4 24 0.7935
- angle_coeff @angle:c-cx-hc harmonic 46.42 116.53 # SOURCE4 36 1.2830
- angle_coeff @angle:cl-cx-cl harmonic 54.42 114.20 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-cx-cx harmonic 56.53 120.10 # SOURCE4 15 0.5917
- angle_coeff @angle:cl-cx-h1 harmonic 40.37 111.43 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-cx-hc harmonic 39.60 115.80 # SOURCE2 1 0.0000
- angle_coeff @angle:c-cx-os harmonic 67.25 115.59 # SOURCE4 36 0.8227
- angle_coeff @angle:cu-cx-cu harmonic 91.53 54.60 # SOURCE2 1 0.0000
- angle_coeff @angle:cu-cx-cx harmonic 88.72 58.50 # SOURCE4 7 0.1333
- angle_coeff @angle:cu-cx-hc harmonic 45.49 118.09 # SOURCE4 7 1.0126
- angle_coeff @angle:cx-cx-cx harmonic 87.90 60.00 # SOURCE4 681 0.6259
- angle_coeff @angle:cx-cx-cy harmonic 67.54 100.53 # SOURCE3 4 0.0000
- angle_coeff @angle:cx-cx-f harmonic 64.53 117.93 # SOURCE4 7 1.1613
- angle_coeff @angle:cx-cx-h1 harmonic 45.45 119.66 # SOURCE3 12 0.4529
- angle_coeff @angle:cx-cx-hc harmonic 45.79 117.92 # SOURCE3 92 1.1927
- angle_coeff @angle:cx-cx-hx harmonic 45.47 119.62 # SOURCE4 9 0.1118
- angle_coeff @angle:cx-cx-n3 harmonic 91.17 59.59 # SOURCE4 154 0.3104
- angle_coeff @angle:cx-cx-na harmonic 62.94 125.85 # SOURCE4 16 2.0385
- angle_coeff @angle:cx-cx-nh harmonic 92.03 59.15 # SOURCE4 116 0.6758
- angle_coeff @angle:cx-cx-os harmonic 93.61 59.07 # SOURCE4 306 0.5253
- angle_coeff @angle:cy-cx-hc harmonic 43.98 125.43 # SOURCE3 2 0.0000
- angle_coeff @angle:f-cx-f harmonic 70.61 106.90 # SOURCE2 2 1.4000
- angle_coeff @angle:f-cx-h1 harmonic 50.35 111.68 # SOURCE3 1 0.0000
- angle_coeff @angle:f-cx-hc harmonic 50.22 112.30 # SOURCE2 1 0.0000
- angle_coeff @angle:h1-cx-h1 harmonic 38.38 115.45 # SOURCE4 230 0.3302
- angle_coeff @angle:h1-cx-n3 harmonic 47.97 116.43 # SOURCE4 173 1.4531
- angle_coeff @angle:h1-cx-n harmonic 49.06 115.42 # SOURCE4 12 1.0443
- angle_coeff @angle:h1-cx-na harmonic 49.96 108.67 # SOURCE4 8 1.6134
- angle_coeff @angle:h1-cx-nh harmonic 48.50 116.32 # SOURCE4 151 1.0310
- angle_coeff @angle:h1-cx-os harmonic 50.01 115.17 # SOURCE3 8 0.0226
- angle_coeff @angle:h2-cx-h2 harmonic 37.87 119.43 # SOURCE3 1 0.0000
- angle_coeff @angle:h2-cx-n2 harmonic 47.55 117.18 # SOURCE3 4 0.0000
- angle_coeff @angle:hc-cx-hc harmonic 38.58 114.47 # SOURCE3 19 0.3295
- angle_coeff @angle:hc-cx-os harmonic 50.25 114.10 # SOURCE2 1 0.0000
- angle_coeff @angle:hx-cx-n4 harmonic 49.89 114.47 # SOURCE4 8 0.1059
- angle_coeff @angle:n2-cx-n2 harmonic 102.06 50.16 # SOURCE3 1 0.0000
- angle_coeff @angle:n-cx-oh harmonic 70.16 119.75 # SOURCE3 2 0.0000
- angle_coeff @angle:n-cx-os harmonic 92.71 65.98 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-cx-oh harmonic 76.67 107.85 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-cx-os harmonic 71.64 118.12 # SOURCE3 4 1.3581
- angle_coeff @angle:os-cx-os harmonic 70.90 115.84 # SOURCE4 7 2.0760
- angle_coeff @angle:c2-cy-cy harmonic 66.57 100.40 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-cy-c3 harmonic 63.19 111.58 # SOURCE4 15 1.0060
- angle_coeff @angle:c3-cy-cy harmonic 60.76 118.70 # SOURCE4 293 1.8510
- angle_coeff @angle:c3-cy-h1 harmonic 46.16 111.77 # SOURCE4 119 0.4412
- angle_coeff @angle:c3-cy-hc harmonic 46.21 111.55 # SOURCE3 5 0.6276
- angle_coeff @angle:c3-cy-n3 harmonic 65.28 112.92 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-cy-n harmonic 68.32 104.05 # SOURCE4 122 0.5745
- angle_coeff @angle:c3-cy-os harmonic 66.99 111.96 # SOURCE4 11 1.0668
- angle_coeff @angle:c-cy-c3 harmonic 61.78 116.72 # SOURCE4 129 0.5236
- angle_coeff @angle:cc-cy-cy harmonic 60.58 121.17 # CORR 19
- angle_coeff @angle:c-cy-cy harmonic 71.81 84.99 # SOURCE4 263 0.6952
- angle_coeff @angle:cd-cy-cy harmonic 60.58 121.17 # CORR 19
- angle_coeff @angle:ce-cy-h2 harmonic 45.50 117.25 # SOURCE4 17 0.5351
- angle_coeff @angle:ce-cy-n harmonic 74.69 88.02 # SOURCE4 14 0.1416
- angle_coeff @angle:ce-cy-ss harmonic 58.47 121.33 # SOURCE4 13 0.1599
- angle_coeff @angle:c-cy-h1 harmonic 45.89 113.10 # SOURCE4 71 0.7655
- angle_coeff @angle:c-cy-hc harmonic 45.75 113.85 # SOURCE3 8 0.2067
- angle_coeff @angle:cl-cy-cy harmonic 57.58 112.00 # SOURCE3 2 0.0000
- angle_coeff @angle:cl-cy-h1 harmonic 40.98 106.59 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-cy-hc harmonic 39.62 114.00 # SOURCE2 1 0.0000
- angle_coeff @angle:c-cy-n harmonic 64.32 117.39 # SOURCE4 70 1.0742
- angle_coeff @angle:c-cy-os harmonic 66.27 114.42 # SOURCE4 6 1.2052
- angle_coeff @angle:cv-cy-cy harmonic 71.46 86.67 # SOURCE4 6 1.1600
- angle_coeff @angle:cv-cy-hc harmonic 46.06 114.47 # SOURCE4 7 0.4307
- angle_coeff @angle:cx-cy-cy harmonic 66.08 101.23 # SOURCE3 4 0.0000
- angle_coeff @angle:cx-cy-hc harmonic 45.25 118.30 # SOURCE2 3 5.7799
- angle_coeff @angle:cy-cy-cy harmonic 70.16 87.61 # SOURCE3 32 1.5407
- angle_coeff @angle:cy-cy-f harmonic 64.55 112.87 # SOURCE4 13 1.6772
- angle_coeff @angle:cy-cy-h1 harmonic 44.87 114.84 # SOURCE3 20 2.5651
- angle_coeff @angle:cy-cy-h2 harmonic 44.51 116.77 # SOURCE4 83 0.8683
- angle_coeff @angle:cy-cy-hc harmonic 44.82 115.14 # SOURCE3 114 0.8364
- angle_coeff @angle:cy-cy-n3 harmonic 73.47 87.58 # SOURCE3 4 0.6135
- angle_coeff @angle:cy-cy-n harmonic 65.22 112.13 # SOURCE3 31 2.0700
- angle_coeff @angle:cy-cy-na harmonic 63.12 119.70 # SOURCE4 9 0.3333
- angle_coeff @angle:cy-cy-oh harmonic 66.00 114.19 # SOURCE3 4 0.0000
- angle_coeff @angle:cy-cy-os harmonic 66.41 111.77 # SOURCE4 18 2.1334
- angle_coeff @angle:cy-cy-s6 harmonic 58.93 117.46 # SOURCE4 7 1.2423
- angle_coeff @angle:cy-cy-ss harmonic 58.83 118.18 # SOURCE4 55 0.9860
- angle_coeff @angle:h1-cy-h1 harmonic 39.01 109.72 # SOURCE3 6 0.8087
- angle_coeff @angle:h1-cy-n3 harmonic 48.21 113.36 # SOURCE3 6 1.4509
- angle_coeff @angle:h1-cy-n harmonic 49.10 111.18 # SOURCE4 141 0.5848
- angle_coeff @angle:h1-cy-oh harmonic 50.89 111.49 # SOURCE3 2 0.0000
- angle_coeff @angle:h1-cy-os harmonic 50.53 110.94 # SOURCE3 8 0.6522
- angle_coeff @angle:h1-cy-s6 harmonic 41.05 112.57 # SOURCE4 5 1.2943
- angle_coeff @angle:h2-cy-n harmonic 48.42 114.44 # SOURCE4 88 0.7114
- angle_coeff @angle:h2-cy-os harmonic 50.97 109.19 # SOURCE4 6 0.4162
- angle_coeff @angle:h2-cy-s6 harmonic 42.11 106.85 # SOURCE4 6 0.3975
- angle_coeff @angle:h2-cy-ss harmonic 41.64 109.73 # SOURCE4 92 0.7424
- angle_coeff @angle:hc-cy-hc harmonic 39.24 109.04 # SOURCE3 28 0.5962
- angle_coeff @angle:n-cy-os harmonic 71.62 107.50 # SOURCE4 9 2.3773
- angle_coeff @angle:n-cy-s6 harmonic 65.24 103.45 # SOURCE4 6 0.7197
- angle_coeff @angle:n-cy-ss harmonic 64.81 105.12 # SOURCE4 69 0.3987
- angle_coeff @angle:nh-cz-nh harmonic 72.97 120.17 # SOURCE4 26 0.3964
- angle_coeff @angle:br-n1-c1 harmonic 51.10 180.00 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-c1 harmonic 64.91 179.92 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-c2 harmonic 60.25 177.73 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-c3 harmonic 54.83 180.00 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-ca harmonic 56.97 179.99 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-cl harmonic 50.10 179.95 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-f harmonic 55.86 179.96 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-hn harmonic 45.62 179.98 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-i harmonic 46.23 179.95 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-n1 harmonic 66.89 180.00 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-n2 harmonic 65.70 171.56 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-n3 harmonic 60.69 175.59 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-n4 harmonic 59.68 179.69 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-na harmonic 59.95 180.00 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-nh harmonic 60.88 176.35 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-o harmonic 62.62 179.95 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-oh harmonic 62.88 174.31 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-os harmonic 62.15 176.61 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-p2 harmonic 68.11 172.83 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-p3 harmonic 68.68 173.51 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-p4 harmonic 67.87 173.64 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-p5 harmonic 71.49 177.28 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-s2 harmonic 60.33 178.11 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-s4 harmonic 55.20 169.60 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-s harmonic 53.31 179.99 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-s6 harmonic 61.81 175.92 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-sh harmonic 55.72 174.25 # HF/6-31G* 1
- angle_coeff @angle:c1-n1-ss harmonic 55.44 176.06 # HF/6-31G* 1
- angle_coeff @angle:c2-n1-n1 harmonic 61.58 180.00 # HF/6-31G* 1
- angle_coeff @angle:c2-n1-o harmonic 73.09 116.94 # SOURCE3 2 0.0060
- angle_coeff @angle:c2-n1-s harmonic 64.71 118.00 # SOURCE3 2 0.0121
- angle_coeff @angle:c3-n1-n1 harmonic 56.30 180.00 # HF/6-31G* 1
- angle_coeff @angle:ca-n1-n1 harmonic 58.54 180.00 # HF/6-31G* 1
- angle_coeff @angle:ce-n1-o harmonic 71.28 122.40 # CORR 2
- angle_coeff @angle:ce-n1-s harmonic 64.84 117.34 # CORR 2
- angle_coeff @angle:cf-n1-o harmonic 71.28 122.40 # CORR 2
- angle_coeff @angle:cf-n1-s harmonic 64.84 117.34 # CORR 2
- angle_coeff @angle:cl-n1-n1 harmonic 51.37 179.94 # HF/6-31G* 1
- angle_coeff @angle:f-n1-n1 harmonic 57.39 179.93 # HF/6-31G* 1
- angle_coeff @angle:hn-n1-n1 harmonic 47.14 179.91 # HF/6-31G* 1
- angle_coeff @angle:i-n1-n1 harmonic 47.26 179.94 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-n1 harmonic 68.97 179.97 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-n2 harmonic 67.65 171.57 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-n3 harmonic 62.49 175.09 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-n4 harmonic 61.31 179.91 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-na harmonic 61.63 179.97 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-nh harmonic 62.66 176.00 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-o harmonic 64.43 179.94 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-oh harmonic 64.78 173.77 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-os harmonic 64.01 176.12 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-p2 harmonic 69.42 174.71 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-p3 harmonic 70.24 174.27 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-s harmonic 54.64 180.00 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-n1-sh harmonic 57.01 175.07 # HF/6-31G* 1
- angle_coeff @angle:n1-n1-ss harmonic 56.92 175.61 # HF/6-31G* 1
- angle_coeff @angle:o-n1-p2 harmonic 84.67 116.05 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n1-s harmonic 80.34 119.93 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n2-br harmonic 63.89 106.60 # SOURCE3 1
- angle_coeff @angle:br-n2-c2 harmonic 59.13 112.40 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n2-n2 harmonic 61.08 110.42 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n2-o harmonic 60.10 114.47 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n2-p2 harmonic 80.05 111.03 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n2-s harmonic 62.40 115.78 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-n2-c1 harmonic 74.41 121.10 # SOURCE3 1
- angle_coeff @angle:c1-n2-c3 harmonic 58.67 151.88 # SOURCE3 4 15.8282
- angle_coeff @angle:c1-n2-cl harmonic 55.36 118.80 # SOURCE2 1 0.0000
- angle_coeff @angle:c1-n2-hn harmonic 51.47 126.50 # SOURCE2 3 7.6267
- angle_coeff @angle:c1-n2-n2 harmonic 76.75 113.40 # SOURCE3 1
- angle_coeff @angle:c1-n2-o harmonic 79.20 113.59 # SOURCE3 1
- angle_coeff @angle:c1-n2-p2 harmonic 84.76 119.57 # SOURCE3 1
- angle_coeff @angle:c1-n2-s harmonic 69.80 117.67 # SOURCE3 1
- angle_coeff @angle:c2-n2-c2 harmonic 70.76 118.18 # SOURCE3 1
- angle_coeff @angle:c2-n2-c3 harmonic 66.13 115.30 # SOURCE3 8 4.2940
- angle_coeff @angle:c2-n2-ca harmonic 69.83 119.94 # SOURCE3 1
- angle_coeff @angle:c2-n2-cl harmonic 56.69 112.64 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n2-f harmonic 68.30 108.14 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n2-hn harmonic 52.63 110.33 # SOURCE3 9 0.6498
- angle_coeff @angle:c2-n2-i harmonic 51.86 114.74 # SOURCE3 2 0.0139
- angle_coeff @angle:c2-n2-n1 harmonic 75.45 115.09 # HF/6-31G* 1
- angle_coeff @angle:c2-n2-n2 harmonic 77.94 103.59 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-n2-n3 harmonic 71.34 118.14 # SOURCE3 1
- angle_coeff @angle:c2-n2-n4 harmonic 62.39 112.22 # SOURCE3 3 0.0406
- angle_coeff @angle:c2-n2-n harmonic 70.16 117.98 # SOURCE4 11 0.9019
- angle_coeff @angle:c2-n2-na harmonic 70.35 117.58 # SOURCE3 8 1.6671
- angle_coeff @angle:c2-n2-nh harmonic 70.71 117.61 # SOURCE3 6 3.2642
- angle_coeff @angle:c2-n2-no harmonic 64.22 111.54 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n2-o harmonic 75.47 116.94 # SOURCE3 1
- angle_coeff @angle:c2-n2-oh harmonic 72.08 110.89 # SOURCE4 22 1.2709
- angle_coeff @angle:c2-n2-os harmonic 71.83 110.51 # SOURCE4 13 0.7888
- angle_coeff @angle:c2-n2-p2 harmonic 85.03 116.00 # SOURCE3 1
- angle_coeff @angle:c2-n2-p3 harmonic 77.54 119.30 # SOURCE3 3 2.8489
- angle_coeff @angle:c2-n2-p4 harmonic 79.28 118.77 # SOURCE3 1
- angle_coeff @angle:c2-n2-s4 harmonic 68.12 112.29 # SOURCE3 1
- angle_coeff @angle:c2-n2-s6 harmonic 68.85 116.24 # SOURCE3 1
- angle_coeff @angle:c2-n2-s harmonic 68.67 118.00 # SOURCE3 1
- angle_coeff @angle:c2-n2-sh harmonic 63.09 115.48 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n2-ss harmonic 64.97 118.04 # SOURCE3 4 2.2804
- angle_coeff @angle:c3-n2-c3 harmonic 63.76 110.70 # SOURCE3 1
- angle_coeff @angle:c3-n2-ca harmonic 65.97 114.95 # SOURCE4 5 0.9744
- angle_coeff @angle:c3-n2-ce harmonic 65.37 118.53 # CORR 123
- angle_coeff @angle:c3-n2-cf harmonic 65.37 118.53 # CORR 123
- angle_coeff @angle:c3-n2-hn harmonic 45.18 118.40 # SOURCE3 1
- angle_coeff @angle:c3-n2-n1 harmonic 68.64 116.20 # SOURCE4 12 0.5407
- angle_coeff @angle:c3-n2-n2 harmonic 69.29 111.18 # SOURCE3 7 0.4349
- angle_coeff @angle:c3-n2-nh harmonic 68.08 109.99 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n2-o harmonic 70.29 112.40 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-n2-p2 harmonic 82.11 114.21 # SOURCE3 2 2.2772
- angle_coeff @angle:c3-n2-s6 harmonic 66.28 113.84 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n2-s harmonic 65.70 116.72 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-n2-ca harmonic 71.79 112.20 # SOURCE3 1
- angle_coeff @angle:ca-n2-hn harmonic 50.01 120.00 # SOURCE3 1
- angle_coeff @angle:ca-n2-n2 harmonic 74.00 113.53 # SOURCE3 1
- angle_coeff @angle:ca-n2-o harmonic 75.26 116.00 # SOURCE2 1 0.0000
- angle_coeff @angle:ca-n2-p2 harmonic 84.03 118.11 # SOURCE3 1
- angle_coeff @angle:ca-n2-s harmonic 67.84 120.11 # SOURCE3 1
- angle_coeff @angle:c-n2-c2 harmonic 66.22 120.97 # SOURCE3 1
- angle_coeff @angle:c-n2-c harmonic 62.71 123.80 # SOURCE3 1
- angle_coeff @angle:c-n2-ca harmonic 66.05 120.50 # SOURCE3 1
- angle_coeff @angle:cc-n2-cl harmonic 55.90 115.79 # CORR 2
- angle_coeff @angle:cc-n2-hn harmonic 52.42 110.72 # CORR 20
- angle_coeff @angle:cc-n2-na harmonic 73.01 108.92 # SOURCE4 9 1.6245
- angle_coeff @angle:cc-n2-nh harmonic 70.37 118.47 # SOURCE4 6 1.7995
- angle_coeff @angle:cd-n2-cl harmonic 55.90 115.79 # CORR 2
- angle_coeff @angle:cd-n2-hn harmonic 52.42 110.72 # CORR 20
- angle_coeff @angle:ce-n2-hn harmonic 52.74 111.05 # CORR 69
- angle_coeff @angle:ce-n2-n harmonic 70.35 118.04 # CORR 101
- angle_coeff @angle:ce-n2-nh harmonic 70.64 118.57 # CORR 54
- angle_coeff @angle:ce-n2-o harmonic 77.37 112.16 # SOURCE3 1
- angle_coeff @angle:ce-n2-oh harmonic 71.48 113.38 # CORR 37
- angle_coeff @angle:ce-n2-os harmonic 71.23 112.97 # CORR 40
- angle_coeff @angle:ce-n2-s harmonic 69.30 116.28 # SOURCE3 1
- angle_coeff @angle:cf-n2-hn harmonic 52.74 111.05 # CORR 69
- angle_coeff @angle:cf-n2-n harmonic 70.35 118.04 # CORR 101
- angle_coeff @angle:cf-n2-nh harmonic 70.64 118.57 # CORR 54
- angle_coeff @angle:cf-n2-o harmonic 77.37 112.16 # SOURCE3 1 same_as_ce-n2-o
- angle_coeff @angle:cf-n2-oh harmonic 71.48 113.38 # CORR 37
- angle_coeff @angle:cf-n2-os harmonic 71.23 112.97 # CORR 40
- angle_coeff @angle:cf-n2-s harmonic 69.30 116.28 # SOURCE3 1 same_as_ce-n2-s
- angle_coeff @angle:cl-n2-n1 harmonic 59.29 108.70 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-n2-n2 harmonic 58.70 110.47 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-n2-o harmonic 58.23 114.03 # SOURCE3 1
- angle_coeff @angle:cl-n2-p2 harmonic 73.98 112.98 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-n2-s harmonic 58.50 115.77 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-n2-n2 harmonic 90.46 64.92 # SOURCE3 2 0.0000
- angle_coeff @angle:f-n2-n2 harmonic 68.29 114.60 # SOURCE2 1 0.0000
- angle_coeff @angle:f-n2-o harmonic 71.17 110.10 # SOURCE2 1 0.0000
- angle_coeff @angle:f-n2-p2 harmonic 84.30 107.10 # SOURCE3 1 0.0000
- angle_coeff @angle:f-n2-s harmonic 67.14 110.73 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n2-hn harmonic 38.61 120.00 # SOURCE3 1
- angle_coeff @angle:hn-n2-n1 harmonic 55.33 114.10 # SOURCE2 1 0.0000
- angle_coeff @angle:hn-n2-n2 harmonic 55.84 105.01 # SOURCE3 19 1.5183
- angle_coeff @angle:hn-n2-ne harmonic 54.69 108.56 # SOURCE3 29 5.5708
- angle_coeff @angle:hn-n2-nf harmonic 54.69 108.56 # SOURCE3 29 same_as_hn-n2-ne
- angle_coeff @angle:hn-n2-o harmonic 57.61 107.37 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n2-p2 harmonic 58.61 112.09 # SOURCE3 18 4.0663
- angle_coeff @angle:hn-n2-p4 harmonic 54.50 111.33 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n2-p5 harmonic 56.32 122.34 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n2-pe harmonic 61.28 111.41 # SOURCE3 20 4.9895
- angle_coeff @angle:hn-n2-pf harmonic 61.28 111.41 # SOURCE3 20 same_as_hn-n2-pe
- angle_coeff @angle:hn-n2-s2 harmonic 48.34 115.80 # SOURCE2 1 0.0000
- angle_coeff @angle:hn-n2-s4 harmonic 46.34 111.21 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n2-s harmonic 49.11 108.17 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n2-s6 harmonic 47.82 112.59 # SOURCE3 2 0.0000
- angle_coeff @angle:i-n2-n2 harmonic 53.71 111.79 # SOURCE3 1 0.0000
- angle_coeff @angle:i-n2-o harmonic 52.33 116.82 # SOURCE3 1 0.0000
- angle_coeff @angle:i-n2-p2 harmonic 72.31 113.26 # SOURCE3 1 0.0000
- angle_coeff @angle:i-n2-s harmonic 56.35 116.85 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-n2-n1 harmonic 80.82 112.00 # HF/6-31G* 1
- angle_coeff @angle:n2-n2-n1 harmonic 62.28 180.00 # dac_for_azides 0
- angle_coeff @angle:n2-n2-n2 harmonic 78.20 109.49 # SOURCE3 2 0.0000
- angle_coeff @angle:n2-n2-n3 harmonic 76.59 108.88 # SOURCE3 1
- angle_coeff @angle:n2-n2-n4 harmonic 65.78 106.45 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n2-na harmonic 74.18 112.23 # SOURCE3 1
- angle_coeff @angle:n2-n2-nh harmonic 74.76 111.70 # SOURCE3 5 0.3475
- angle_coeff @angle:n2-n2-no harmonic 67.68 105.97 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n2-o harmonic 80.17 110.43 # SOURCE3 1
- angle_coeff @angle:n2-n2-oh harmonic 74.02 111.51 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n2-os harmonic 74.69 108.38 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n2-p2 harmonic 90.07 109.15 # SOURCE3 1
- angle_coeff @angle:n2-n2-p3 harmonic 81.73 113.05 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n2-p4 harmonic 81.37 118.77 # SOURCE3 1
- angle_coeff @angle:n2-n2-p5 harmonic 89.80 110.46 # SOURCE3 1
- angle_coeff @angle:n2-n2-s4 harmonic 71.60 107.30 # SOURCE3 1
- angle_coeff @angle:n2-n2-s6 harmonic 72.35 111.25 # SOURCE3 1
- angle_coeff @angle:n2-n2-s harmonic 71.24 115.91 # SOURCE3 1
- angle_coeff @angle:n2-n2-sh harmonic 66.00 111.10 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n2-ss harmonic 68.46 112.14 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-n2-n3 harmonic 72.95 115.07 # SOURCE3 1
- angle_coeff @angle:n3-n2-o harmonic 76.86 114.00 # SOURCE2 1 0.0000
- angle_coeff @angle:n3-n2-p2 harmonic 86.69 115.34 # SOURCE3 1
- angle_coeff @angle:n3-n2-s harmonic 69.96 117.13 # SOURCE3 1
- angle_coeff @angle:n4-n2-n4 harmonic 59.97 106.70 # SOURCE3 1
- angle_coeff @angle:n4-n2-o harmonic 64.86 112.20 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-n2-p2 harmonic 79.54 113.07 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-n2-s harmonic 62.44 118.50 # SOURCE3 1 0.0000
- angle_coeff @angle:na-n2-na harmonic 73.47 107.00 # SOURCE3 1
- angle_coeff @angle:na-n2-o harmonic 75.74 113.09 # SOURCE3 1 0.0000
- angle_coeff @angle:na-n2-p2 harmonic 84.58 119.16 # SOURCE3 1 0.0000
- angle_coeff @angle:na-n2-s harmonic 68.94 118.26 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-n2-nh harmonic 74.13 113.09 # CORR 12
- angle_coeff @angle:ne-n2-o harmonic 79.97 110.31 # SOURCE3 1
- angle_coeff @angle:ne-n2-s harmonic 71.04 116.22 # SOURCE3 1
- angle_coeff @angle:nf-n2-nh harmonic 74.13 113.09 # CORR 12
- angle_coeff @angle:nf-n2-o harmonic 79.97 110.31 # SOURCE3 1 same_as_ne-n2-o
- angle_coeff @angle:nf-n2-s harmonic 71.04 116.22 # SOURCE3 1 same_as_ne-n2-s
- angle_coeff @angle:nh-n2-nh harmonic 69.67 121.20 # SOURCE3 1
- angle_coeff @angle:nh-n2-o harmonic 76.02 113.60 # SOURCE4 13 1.0945
- angle_coeff @angle:nh-n2-p2 harmonic 84.93 118.83 # SOURCE3 2 0.1024
- angle_coeff @angle:nh-n2-s harmonic 69.56 116.90 # SOURCE3 2 0.2276
- angle_coeff @angle:n-n2-n2 harmonic 75.48 108.18 # SOURCE4 8 0.3496
- angle_coeff @angle:n-n2-o harmonic 74.99 115.10 # SOURCE4 31 0.2796
- angle_coeff @angle:no-n2-no harmonic 62.81 103.70 # SOURCE3 1
- angle_coeff @angle:no-n2-o harmonic 70.40 100.76 # SOURCE3 1 0.0000
- angle_coeff @angle:no-n2-p2 harmonic 81.32 111.95 # SOURCE3 1 0.0000
- angle_coeff @angle:n-n2-p2 harmonic 85.20 117.30 # SOURCE3 1 0.0000
- angle_coeff @angle:n-n2-s harmonic 69.64 115.74 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-n2-oh harmonic 74.84 101.70 # SOURCE3 1
- angle_coeff @angle:oh-n2-p2 harmonic 86.05 115.11 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-n2-s harmonic 69.52 116.08 # SOURCE3 1 0.0000
- angle_coeff @angle:o-n2-o harmonic 81.02 115.37 # SOURCE3 1
- angle_coeff @angle:o-n2-oh harmonic 75.56 112.15 # SOURCE2 2 1.4500
- angle_coeff @angle:o-n2-os harmonic 75.73 110.35 # SOURCE3 2 0.0042
- angle_coeff @angle:o-n2-p2 harmonic 88.65 116.08 # SOURCE3 1
- angle_coeff @angle:o-n2-p3 harmonic 82.37 113.43 # SOURCE3 1 0.0000
- angle_coeff @angle:o-n2-p4 harmonic 85.23 110.61 # SOURCE3 1
- angle_coeff @angle:o-n2-p5 harmonic 91.73 109.11 # SOURCE3 1
- angle_coeff @angle:o-n2-pe harmonic 85.18 134.56 # SOURCE3 1
- angle_coeff @angle:o-n2-pf harmonic 85.18 134.56 # SOURCE3 1 same_as_o-n2-pe
- angle_coeff @angle:o-n2-s4 harmonic 72.12 108.91 # SOURCE3 1
- angle_coeff @angle:o-n2-s6 harmonic 73.56 111.34 # SOURCE3 1
- angle_coeff @angle:o-n2-s harmonic 72.09 117.18 # SOURCE3 1
- angle_coeff @angle:o-n2-sh harmonic 65.55 114.98 # SOURCE3 1 0.0000
- angle_coeff @angle:os-n2-os harmonic 71.25 110.29 # SOURCE3 1
- angle_coeff @angle:os-n2-p2 harmonic 87.70 110.20 # SOURCE3 1 0.0000
- angle_coeff @angle:o-n2-ss harmonic 68.39 115.34 # SOURCE3 1 0.0000
- angle_coeff @angle:os-n2-s harmonic 70.47 112.23 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n2-p2 harmonic 107.12 116.80 # SOURCE3 1
- angle_coeff @angle:p2-n2-p3 harmonic 98.43 124.48 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n2-p4 harmonic 98.27 128.37 # SOURCE3 1
- angle_coeff @angle:p2-n2-p5 harmonic 104.38 123.47 # SOURCE3 1
- angle_coeff @angle:p2-n2-s4 harmonic 86.26 112.10 # SOURCE3 1
- angle_coeff @angle:p2-n2-s6 harmonic 86.44 115.70 # SOURCE3 1
- angle_coeff @angle:p2-n2-s harmonic 85.91 117.84 # SOURCE3 1
- angle_coeff @angle:p2-n2-sh harmonic 80.45 118.45 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n2-ss harmonic 82.01 120.43 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-n2-p3 harmonic 96.00 120.40 # SOURCE3 1
- angle_coeff @angle:p3-n2-s harmonic 80.08 120.86 # SOURCE3 1 0.0000
- angle_coeff @angle:p4-n2-s harmonic 77.83 131.84 # SOURCE3 1
- angle_coeff @angle:p5-n2-p5 harmonic 105.81 120.60 # SOURCE3 1
- angle_coeff @angle:p5-n2-s harmonic 85.34 119.89 # SOURCE3 1
- angle_coeff @angle:pe-n2-s harmonic 88.59 115.73 # SOURCE3 1
- angle_coeff @angle:pf-n2-s harmonic 88.59 115.73 # SOURCE3 1 same_as_pe-n2-s
- angle_coeff @angle:s4-n2-s4 harmonic 66.00 119.18 # SOURCE3 1
- angle_coeff @angle:s4-n2-s6 harmonic 67.18 119.18 # SOURCE3 1
- angle_coeff @angle:s6-n2-s6 harmonic 68.49 119.18 # SOURCE3 1
- angle_coeff @angle:sh-n2-sh harmonic 59.95 123.93 # SOURCE3 1
- angle_coeff @angle:sh-n2-ss harmonic 61.33 123.93 # SOURCE3 1
- angle_coeff @angle:s-n2-s harmonic 68.47 120.88 # SOURCE3 1
- angle_coeff @angle:s-n2-s4 harmonic 69.20 113.00 # SOURCE3 1
- angle_coeff @angle:s-n2-s6 harmonic 68.60 119.61 # SOURCE3 1
- angle_coeff @angle:s-n2-sh harmonic 63.58 122.05 # SOURCE3 1 0.0000
- angle_coeff @angle:s-n2-ss harmonic 66.58 118.19 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-n2-ss harmonic 62.92 123.93 # SOURCE3 1
- angle_coeff @angle:br-n3-br harmonic 66.54 107.15 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n3-c3 harmonic 62.70 106.93 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-n3-c1 harmonic 64.09 123.34 # SOURCE3 1
- angle_coeff @angle:c1-n3-f harmonic 68.22 104.70 # SOURCE2 1 0.0000
- angle_coeff @angle:c1-n3-hn harmonic 47.74 118.31 # SOURCE3 1
- angle_coeff @angle:c1-n3-o harmonic 70.01 116.63 # SOURCE3 1
- angle_coeff @angle:c2-n3-c2 harmonic 66.22 124.68 # SOURCE3 1
- angle_coeff @angle:c2-n3-hn harmonic 49.11 119.38 # SOURCE3 1
- angle_coeff @angle:c3-n3-c3 harmonic 64.01 110.90 # SOURCE3 40 2.3048
- angle_coeff @angle:c3-n3-cl harmonic 57.82 107.23 # SOURCE3 3 0.3673
- angle_coeff @angle:c3-n3-cx harmonic 62.45 116.32 # SOURCE4 24 0.5119
- angle_coeff @angle:c3-n3-cy harmonic 61.69 118.26 # SOURCE4 14 0.8788
- angle_coeff @angle:c3-n3-f harmonic 66.81 103.13 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-n3-hn harmonic 47.13 109.92 # SOURCE3 120 2.2590
- angle_coeff @angle:c3-n3-i harmonic 56.98 108.48 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-n3-n2 harmonic 66.23 118.75 # SOURCE2 2 2.6500
- angle_coeff @angle:c3-n3-n3 harmonic 66.76 108.15 # SOURCE3 15 1.3999
- angle_coeff @angle:c3-n3-n4 harmonic 67.18 109.65 # SOURCE3 3 0.1146
- angle_coeff @angle:c3-n3-n harmonic 66.67 111.75 # SOURCE4 50 1.6777
- angle_coeff @angle:c3-n3-nh harmonic 66.37 111.89 # SOURCE4 21 1.3006
- angle_coeff @angle:c3-n3-no harmonic 66.02 111.27 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n3-o harmonic 68.68 113.31 # SOURCE3 5 8.9081
- angle_coeff @angle:c3-n3-oh harmonic 69.07 106.14 # SOURCE4 14 1.1040
- angle_coeff @angle:c3-n3-os harmonic 68.48 104.95 # SOURCE4 9 0.9687
- angle_coeff @angle:c3-n3-p3 harmonic 75.79 121.93 # SOURCE3 3 5.6009
- angle_coeff @angle:c3-n3-p5 harmonic 78.53 119.81 # SOURCE4 58 1.8367
- angle_coeff @angle:c3-n3-s4 harmonic 61.45 112.91 # SOURCE3 3 0.8983
- angle_coeff @angle:c3-n3-s6 harmonic 63.67 116.57 # SOURCE4 73 1.8772
- angle_coeff @angle:c3-n3-s harmonic 61.46 110.02 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n3-sh harmonic 62.06 112.70 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n3-ss harmonic 61.59 116.01 # SOURCE3 3 1.1944
- angle_coeff @angle:c3-n3-sy harmonic 62.43 115.27 # SOURCE4 108 1.7647
- angle_coeff @angle:cl-n3-cl harmonic 53.49 108.28 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-n3-hn harmonic 39.61 104.39 # SOURCE3 2 0.0000
- angle_coeff @angle:cl-n3-n3 harmonic 59.29 107.65 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-n3-cx harmonic 86.39 60.71 # SOURCE4 57 0.2359
- angle_coeff @angle:cx-n3-hn harmonic 47.15 109.57 # SOURCE4 26 0.7439
- angle_coeff @angle:cx-n3-p5 harmonic 78.66 119.32 # SOURCE4 71 1.1948
- angle_coeff @angle:cx-n3-py harmonic 76.73 121.75 # SOURCE4 10 1.0295
- angle_coeff @angle:cy-n3-cy harmonic 70.04 90.87 # SOURCE4 10 0.5777
- angle_coeff @angle:cy-n3-hn harmonic 46.25 112.12 # SOURCE4 9 1.9058
- angle_coeff @angle:f-n3-f harmonic 67.71 102.22 # SOURCE2 4 0.7562
- angle_coeff @angle:f-n3-hn harmonic 50.78 99.80 # SOURCE2 1 0.0000
- angle_coeff @angle:hn-n3-hn harmonic 41.30 107.13 # SOURCE3 44 1.9687
- angle_coeff @angle:hn-n3-i harmonic 35.43 109.98 # SOURCE3 2 0.0000
- angle_coeff @angle:hn-n3-n1 harmonic 52.05 110.17 # HF/6-31G* 1
- angle_coeff @angle:hn-n3-n2 harmonic 51.40 115.94 # SOURCE3 1
- angle_coeff @angle:hn-n3-n3 harmonic 50.16 103.98 # SOURCE3 18 1.8593
- angle_coeff @angle:hn-n3-n4 harmonic 50.87 106.40 # SOURCE3 5 0.5863
- angle_coeff @angle:hn-n3-n harmonic 51.02 106.57 # SOURCE3 6 1.0767
- angle_coeff @angle:hn-n3-na harmonic 50.32 107.89 # SOURCE3 1
- angle_coeff @angle:hn-n3-nh harmonic 50.44 107.39 # SOURCE3 11 1.6294
- angle_coeff @angle:hn-n3-no harmonic 50.25 104.78 # SOURCE3 3 1.1126
- angle_coeff @angle:hn-n3-o harmonic 53.14 113.32 # SOURCE3 3 4.3945
- angle_coeff @angle:hn-n3-oh harmonic 53.08 101.11 # SOURCE3 4 0.9921
- angle_coeff @angle:hn-n3-os harmonic 51.67 100.92 # SOURCE3 6 0.7295
- angle_coeff @angle:hn-n3-p2 harmonic 54.24 120.26 # SOURCE3 1
- angle_coeff @angle:hn-n3-p3 harmonic 52.93 116.89 # SOURCE3 9 3.8816
- angle_coeff @angle:hn-n3-p4 harmonic 54.97 113.05 # SOURCE3 2 0.0000
- angle_coeff @angle:hn-n3-p5 harmonic 56.04 113.68 # SOURCE3 6 2.1781
- angle_coeff @angle:hn-n3-s4 harmonic 42.47 108.93 # SOURCE3 7 1.7819
- angle_coeff @angle:hn-n3-s harmonic 41.53 109.47 # SOURCE3 1
- angle_coeff @angle:hn-n3-s6 harmonic 46.06 109.33 # SOURCE4 86 0.9610
- angle_coeff @angle:hn-n3-sh harmonic 43.12 108.67 # SOURCE3 3 2.5025
- angle_coeff @angle:hn-n3-ss harmonic 43.36 109.85 # SOURCE3 5 2.3215
- angle_coeff @angle:hn-n3-sy harmonic 44.15 109.49 # SOURCE4 278 0.7897
- angle_coeff @angle:i-n3-i harmonic 60.04 111.27 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-n3-n1 harmonic 72.40 113.21 # HF/6-31G* 1
- angle_coeff @angle:n2-n3-n2 harmonic 71.82 118.73 # SOURCE3 1
- angle_coeff @angle:n2-n3-o harmonic 74.13 114.91 # SOURCE3 1
- angle_coeff @angle:n3-n3-n3 harmonic 69.57 105.71 # SOURCE3 3 0.3561
- angle_coeff @angle:n4-n3-n4 harmonic 69.04 113.48 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-n3-nh harmonic 70.91 107.14 # SOURCE3 1
- angle_coeff @angle:na-n3-na harmonic 69.21 112.00 # SOURCE3 1
- angle_coeff @angle:nh-n3-nh harmonic 70.75 107.15 # SOURCE3 1 0.0000
- angle_coeff @angle:n-n3-n harmonic 70.25 110.55 # SOURCE3 1 0.0000
- angle_coeff @angle:no-n3-no harmonic 67.04 115.26 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-n3-oh harmonic 72.79 107.18 # SOURCE3 1 0.0000
- angle_coeff @angle:o-n3-o harmonic 71.89 126.14 # SOURCE3 1
- angle_coeff @angle:o-n3-p2 harmonic 84.34 117.02 # SOURCE3 1
- angle_coeff @angle:o-n3-p4 harmonic 83.38 116.65 # SOURCE3 1
- angle_coeff @angle:o-n3-s4 harmonic 64.56 114.09 # SOURCE3 1
- angle_coeff @angle:o-n3-s6 harmonic 68.82 113.80 # SOURCE3 1
- angle_coeff @angle:o-n3-s harmonic 62.04 119.81 # SOURCE3 1
- angle_coeff @angle:os-n3-os harmonic 70.79 106.52 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n3-p2 harmonic 97.53 130.13 # SOURCE3 1
- angle_coeff @angle:p3-n3-p3 harmonic 98.56 118.74 # SOURCE3 3 3.3755
- angle_coeff @angle:p4-n3-p4 harmonic 101.51 116.35 # SOURCE3 1
- angle_coeff @angle:p5-n3-p5 harmonic 102.24 119.42 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-n3-s4 harmonic 60.13 120.02 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-n3-s6 harmonic 61.99 120.95 # SOURCE3 1
- angle_coeff @angle:s6-n3-s6 harmonic 63.29 126.13 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-n3-sh harmonic 61.24 118.63 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-n3-ss harmonic 61.27 119.67 # SOURCE3 1
- angle_coeff @angle:s-n3-s harmonic 56.48 131.36 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-n3-ss harmonic 61.60 119.57 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n4-br harmonic 65.14 114.82 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n4-hn harmonic 41.38 108.44 # SOURCE3 7 0.5630
- angle_coeff @angle:c1-n4-c1 harmonic 65.53 113.87 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-n4-hn harmonic 48.62 110.19 # SOURCE3 7 1.0847
- angle_coeff @angle:c2-n4-c2 harmonic 63.01 112.58 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n4-c3 harmonic 63.10 110.96 # SOURCE4 13 2.4632
- angle_coeff @angle:c2-n4-hn harmonic 46.43 111.36 # SOURCE3 13 1.2672
- angle_coeff @angle:c3-n4-c3 harmonic 62.84 110.64 # SOURCE3 13 1.3060
- angle_coeff @angle:c3-n4-ca harmonic 63.61 110.40 # SOURCE4 46 1.4643
- angle_coeff @angle:c3-n4-cc harmonic 62.84 111.09 # SOURCE4 7 0.7065
- angle_coeff @angle:c3-n4-cl harmonic 57.92 108.04 # SOURCE3 3 0.0000
- angle_coeff @angle:c3-n4-hn harmonic 46.19 110.11 # SOURCE3 100 1.3136
- angle_coeff @angle:c3-n4-n3 harmonic 66.73 108.72 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-n4-n4 harmonic 63.72 114.07 # SOURCE3 4 0.0000
- angle_coeff @angle:c3-n4-n harmonic 66.20 109.26 # SOURCE4 7 1.9859
- angle_coeff @angle:c3-n4-nh harmonic 64.76 111.73 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-no harmonic 65.25 109.08 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-o harmonic 67.25 111.66 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-oh harmonic 65.90 113.73 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-os harmonic 67.38 107.42 # SOURCE3 3 3.5920
- angle_coeff @angle:c3-n4-p2 harmonic 71.92 112.52 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-p3 harmonic 74.40 110.73 # SOURCE3 3 2.1084
- angle_coeff @angle:c3-n4-p5 harmonic 75.11 113.22 # SOURCE3 3 0.4021
- angle_coeff @angle:c3-n4-s4 harmonic 57.21 108.23 # SOURCE3 3 0.4195
- angle_coeff @angle:c3-n4-s6 harmonic 57.75 111.56 # SOURCE3 3 1.8851
- angle_coeff @angle:c3-n4-s harmonic 59.21 113.55 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-sh harmonic 59.13 115.81 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-n4-ss harmonic 59.66 113.68 # SOURCE3 3 1.1405
- angle_coeff @angle:ca-n4-ca harmonic 63.21 114.48 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-n4-hn harmonic 47.54 108.52 # SOURCE3 5 1.1693
- angle_coeff @angle:c-n4-c harmonic 61.50 108.61 # SOURCE3 1 0.0000
- angle_coeff @angle:c-n4-hn harmonic 44.68 110.86 # SOURCE3 10 1.0073
- angle_coeff @angle:cl-n4-cl harmonic 52.73 114.91 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-n4-hn harmonic 39.53 108.87 # SOURCE3 7 0.7719
- angle_coeff @angle:f-n4-f harmonic 70.47 109.05 # SOURCE3 1 0.0000
- angle_coeff @angle:f-n4-hn harmonic 51.67 108.39 # SOURCE3 4 0.0000
- angle_coeff @angle:hn-n4-hn harmonic 40.52 108.11 # SOURCE3 208 1.4126
- angle_coeff @angle:hn-n4-i harmonic 36.44 108.72 # SOURCE3 7 1.2717
- angle_coeff @angle:hn-n4-n1 harmonic 51.79 109.39 # HF/6-31G* 1
- angle_coeff @angle:hn-n4-n2 harmonic 42.29 109.68 # SOURCE3 19 0.6266
- angle_coeff @angle:hn-n4-n3 harmonic 49.85 110.40 # SOURCE3 11 0.7307
- angle_coeff @angle:hn-n4-n4 harmonic 48.09 108.66 # SOURCE3 18 1.2967
- angle_coeff @angle:hn-n4-n harmonic 49.59 109.08 # SOURCE3 13 1.6047
- angle_coeff @angle:hn-n4-na harmonic 49.43 109.38 # SOURCE3 25 1.0758
- angle_coeff @angle:hn-n4-nh harmonic 48.36 109.92 # SOURCE3 12 0.7304
- angle_coeff @angle:hn-n4-no harmonic 49.19 104.38 # SOURCE3 2 0.0000
- angle_coeff @angle:hn-n4-o harmonic 52.09 109.26 # SOURCE3 6 2.1203
- angle_coeff @angle:hn-n4-oh harmonic 51.12 108.09 # SOURCE3 6 1.6728
- angle_coeff @angle:hn-n4-os harmonic 50.15 109.39 # SOURCE3 10 1.4403
- angle_coeff @angle:hn-n4-p2 harmonic 47.71 110.50 # SOURCE3 25 1.0664
- angle_coeff @angle:hn-n4-p3 harmonic 49.73 109.89 # SOURCE3 10 2.3870
- angle_coeff @angle:hn-n4-p4 harmonic 47.65 111.33 # SOURCE3 3 0.0000
- angle_coeff @angle:hn-n4-p5 harmonic 51.29 110.00 # SOURCE3 10 1.0282
- angle_coeff @angle:hn-n4-py harmonic 47.36 117.89 # SOURCE3 8 0.0000
- angle_coeff @angle:hn-n4-s4 harmonic 37.07 110.10 # SOURCE3 6 0.8471
- angle_coeff @angle:hn-n4-s harmonic 41.06 106.89 # SOURCE3 6 1.0775
- angle_coeff @angle:hn-n4-s6 harmonic 38.64 108.94 # SOURCE3 10 0.5715
- angle_coeff @angle:hn-n4-sh harmonic 41.29 108.56 # SOURCE3 6 0.8535
- angle_coeff @angle:hn-n4-ss harmonic 41.15 109.17 # SOURCE3 10 0.8455
- angle_coeff @angle:i-n4-i harmonic 58.99 118.49 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-n4-n1 harmonic 72.69 110.67 # HF/6-31G* 1
- angle_coeff @angle:n2-n4-n2 harmonic 59.43 108.64 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-n4-n3 harmonic 69.79 111.07 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-n4-n4 harmonic 65.21 115.49 # SOURCE3 1 0.0000
- angle_coeff @angle:na-n4-na harmonic 66.27 119.60 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-n4-nh harmonic 67.83 109.38 # SOURCE3 1 0.0000
- angle_coeff @angle:n-n4-n harmonic 66.68 118.62 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-n4-oh harmonic 72.25 108.19 # SOURCE3 1 0.0000
- angle_coeff @angle:o-n4-o harmonic 70.28 120.97 # SOURCE3 1 0.0000
- angle_coeff @angle:os-n4-os harmonic 72.46 104.40 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n4-p2 harmonic 89.65 113.91 # SOURCE3 2 0.0000
- angle_coeff @angle:p3-n4-p3 harmonic 89.71 121.38 # SOURCE3 1 0.0000
- angle_coeff @angle:p5-n4-p5 harmonic 98.15 107.02 # SOURCE3 1 0.0000
- angle_coeff @angle:py-n4-py harmonic 116.94 69.79 # SOURCE3 2 0.0000
- angle_coeff @angle:s4-n4-s4 harmonic 54.75 115.43 # SOURCE3 1
- angle_coeff @angle:s6-n4-s6 harmonic 57.91 109.51 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-n4-sh harmonic 60.37 112.59 # SOURCE3 1 0.0000
- angle_coeff @angle:s-n4-s harmonic 56.74 124.55 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-n4-ss harmonic 61.26 109.20 # SOURCE3 1 0.0000
- angle_coeff @angle:br-na-br harmonic 60.55 123.00 # SOURCE3 1
- angle_coeff @angle:br-na-c2 harmonic 63.61 100.48 # SOURCE3 2 1.0536
- angle_coeff @angle:br-na-ca harmonic 57.15 124.81 # SOURCE3 1
- angle_coeff @angle:br-na-cc harmonic 57.16 124.62 # SOURCE3 3 0.5348
- angle_coeff @angle:br-na-cd harmonic 57.16 124.62 # SOURCE3 3 same_as_br-na-cc
- angle_coeff @angle:br-na-nc harmonic 59.86 119.42 # SOURCE3 4 1.6703
- angle_coeff @angle:br-na-nd harmonic 59.86 119.42 # SOURCE3 4 same_as_br-na-nc
- angle_coeff @angle:br-na-os harmonic 63.92 104.99 # SOURCE3 1 0.0000
- angle_coeff @angle:br-na-p2 harmonic 75.91 121.01 # SOURCE3 1
- angle_coeff @angle:br-na-pc harmonic 76.39 120.26 # SOURCE3 3 2.1456
- angle_coeff @angle:br-na-pd harmonic 76.39 120.26 # SOURCE3 3 same_as_br-na-pc
- angle_coeff @angle:br-na-ss harmonic 62.46 112.28 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-na-c1 harmonic 67.20 117.20 # SOURCE3 1
- angle_coeff @angle:c1-na-c2 harmonic 64.32 125.20 # SOURCE3 1
- angle_coeff @angle:c1-na-ca harmonic 66.54 120.57 # SOURCE3 1
- angle_coeff @angle:c1-na-cc harmonic 65.82 121.35 # SOURCE3 6 0.6517
- angle_coeff @angle:c1-na-cd harmonic 65.82 121.35 # SOURCE3 6 0.6517
- angle_coeff @angle:c1-na-nc harmonic 68.27 120.24 # SOURCE3 4 1.6849
- angle_coeff @angle:c1-na-nd harmonic 68.27 120.24 # SOURCE3 4 same_as_c1-na-nc
- angle_coeff @angle:c1-na-os harmonic 70.24 106.96 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-na-p2 harmonic 76.49 122.25 # SOURCE3 1
- angle_coeff @angle:c1-na-pc harmonic 77.33 121.48 # SOURCE3 3 2.1681
- angle_coeff @angle:c1-na-pd harmonic 77.33 121.48 # SOURCE3 3 same_as_c1-na-pc
- angle_coeff @angle:c1-na-ss harmonic 61.89 118.30 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-na-c2 harmonic 67.80 110.37 # SOURCE3 6 0.5121
- angle_coeff @angle:c2-na-c3 harmonic 64.23 117.20 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-na-ca harmonic 64.55 125.33 # SOURCE4 7 0.5648
- angle_coeff @angle:c2-na-cc harmonic 63.98 125.75 # SOURCE3 10 1.5856
- angle_coeff @angle:c2-na-cd harmonic 63.98 125.75 # SOURCE3 10 1.5856
- angle_coeff @angle:c2-na-cl harmonic 58.85 101.01 # SOURCE3 2 1.5799
- angle_coeff @angle:c2-na-f harmonic 68.64 103.11 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-na-hn harmonic 47.62 119.28 # SOURCE3 14 6.6027
- angle_coeff @angle:c2-na-i harmonic 58.98 106.74 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-na-n1 harmonic 66.27 124.81 # HF/6-31G* 1
- angle_coeff @angle:c2-na-n2 harmonic 65.80 125.00 # SOURCE3 1
- angle_coeff @angle:c2-na-n3 harmonic 64.64 124.80 # SOURCE3 1
- angle_coeff @angle:c2-na-n4 harmonic 65.19 121.32 # SOURCE3 1
- angle_coeff @angle:c2-na-n harmonic 65.63 124.70 # SOURCE3 1
- angle_coeff @angle:c2-na-na harmonic 65.14 124.60 # SOURCE3 1
- angle_coeff @angle:c2-na-nc harmonic 67.42 120.61 # CORR 9
- angle_coeff @angle:c2-na-nd harmonic 67.42 120.61 # CORR 9
- angle_coeff @angle:c2-na-nh harmonic 65.04 124.98 # SOURCE3 1
- angle_coeff @angle:c2-na-no harmonic 64.34 124.20 # SOURCE3 1
- angle_coeff @angle:c2-na-o harmonic 68.21 125.90 # SOURCE3 1
- angle_coeff @angle:c2-na-oh harmonic 65.80 123.90 # SOURCE3 1
- angle_coeff @angle:c2-na-os harmonic 68.53 110.33 # SOURCE3 4 3.2172
- angle_coeff @angle:c2-na-p2 harmonic 76.19 122.14 # SOURCE3 1
- angle_coeff @angle:c2-na-p3 harmonic 74.55 126.10 # SOURCE3 1
- angle_coeff @angle:c2-na-p4 harmonic 81.58 125.00 # SOURCE3 1
- angle_coeff @angle:c2-na-p5 harmonic 76.43 125.10 # SOURCE3 1
- angle_coeff @angle:c2-na-pc harmonic 76.96 121.56 # SOURCE3 3 1.6252
- angle_coeff @angle:c2-na-pd harmonic 76.96 121.56 # SOURCE3 3 same_as_c2-na-pc
- angle_coeff @angle:c2-na-s4 harmonic 58.37 124.90 # SOURCE3 1
- angle_coeff @angle:c2-na-s6 harmonic 60.24 124.40 # SOURCE3 1
- angle_coeff @angle:c2-na-s harmonic 58.90 125.80 # SOURCE3 1
- angle_coeff @angle:c2-na-sh harmonic 60.23 125.10 # SOURCE3 1
- angle_coeff @angle:c2-na-ss harmonic 62.34 115.53 # SOURCE3 5 1.4036
- angle_coeff @angle:c3-na-c3 harmonic 60.72 125.59 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-na-ca harmonic 63.15 124.36 # SOURCE3 5 4.2557
- angle_coeff @angle:c3-na-cc harmonic 62.56 125.09 # SOURCE3 18 1.2138
- angle_coeff @angle:c3-na-cd harmonic 62.56 125.09 # SOURCE3 18 1.2138
- angle_coeff @angle:c3-na-cp harmonic 63.76 119.46 # SOURCE4 7 0.4108
- angle_coeff @angle:c3-na-n2 harmonic 65.48 120.05 # SOURCE4 5 0.8795
- angle_coeff @angle:c3-na-n harmonic 67.37 112.68 # SOURCE4 12 0.5122
- angle_coeff @angle:c3-na-nc harmonic 65.74 120.46 # SOURCE3 8 2.1625
- angle_coeff @angle:c3-na-nd harmonic 65.74 120.46 # SOURCE3 8 2.1625
- angle_coeff @angle:c3-na-os harmonic 68.91 104.39 # SOURCE3 3 1.2017
- angle_coeff @angle:c3-na-p2 harmonic 75.04 123.12 # SOURCE3 1
- angle_coeff @angle:c3-na-pc harmonic 75.89 122.11 # SOURCE3 3 2.8504
- angle_coeff @angle:c3-na-pd harmonic 75.89 122.11 # SOURCE3 3 same_as_c3-na-pc
- angle_coeff @angle:c3-na-sh harmonic 63.38 110.28 # SOURCE3 1
- angle_coeff @angle:c3-na-ss harmonic 62.90 110.87 # SOURCE3 3 0.8260
- angle_coeff @angle:ca-na-ca harmonic 66.98 120.09 # SOURCE4 321 1.7366
- angle_coeff @angle:ca-na-cc harmonic 68.46 113.15 # SOURCE3 18 9.8644
- angle_coeff @angle:ca-na-cd harmonic 68.46 113.15 # SOURCE3 18 9.8644
- angle_coeff @angle:ca-na-cl harmonic 53.17 124.79 # SOURCE3 1
- angle_coeff @angle:ca-na-cp harmonic 65.88 120.96 # SOURCE4 20 1.2820
- angle_coeff @angle:ca-na-cx harmonic 63.07 124.09 # SOURCE4 12 1.8167
- angle_coeff @angle:ca-na-f harmonic 65.51 116.40 # SOURCE3 1
- angle_coeff @angle:ca-na-hn harmonic 47.63 125.59 # SOURCE4 437 1.1893
- angle_coeff @angle:ca-na-i harmonic 55.21 121.62 # SOURCE3 1
- angle_coeff @angle:ca-na-n2 harmonic 68.21 119.85 # SOURCE4 6 1.2043
- angle_coeff @angle:ca-na-n4 harmonic 66.37 120.19 # SOURCE3 1
- angle_coeff @angle:ca-na-n harmonic 67.34 122.00 # SOURCE3 1
- angle_coeff @angle:ca-na-na harmonic 66.29 123.76 # SOURCE3 1
- angle_coeff @angle:ca-na-nb harmonic 68.18 122.16 # SOURCE4 7 0.8543
- angle_coeff @angle:ca-na-nc harmonic 69.27 117.85 # SOURCE3 6 3.6536
- angle_coeff @angle:ca-na-nd harmonic 69.27 117.85 # SOURCE3 6 same_as_ca-na-nc
- angle_coeff @angle:ca-na-nh harmonic 66.14 124.33 # SOURCE4 7 1.3855
- angle_coeff @angle:ca-na-o harmonic 71.14 119.99 # SOURCE4 51 1.2671
- angle_coeff @angle:ca-na-oh harmonic 66.69 124.08 # SOURCE3 1
- angle_coeff @angle:ca-na-os harmonic 69.70 109.46 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-na-p2 harmonic 75.51 125.85 # SOURCE3 1
- angle_coeff @angle:ca-na-p3 harmonic 75.50 124.38 # SOURCE3 1
- angle_coeff @angle:ca-na-p4 harmonic 82.41 124.97 # SOURCE3 1
- angle_coeff @angle:ca-na-p5 harmonic 77.51 123.30 # SOURCE3 1
- angle_coeff @angle:ca-na-pc harmonic 77.26 122.13 # SOURCE3 3 2.2393
- angle_coeff @angle:ca-na-pd harmonic 77.26 122.13 # SOURCE3 3 same_as_ca-na-pc
- angle_coeff @angle:ca-na-py harmonic 72.61 140.88 # SOURCE3 2 0.0000
- angle_coeff @angle:ca-na-s4 harmonic 60.55 117.23 # SOURCE3 1
- angle_coeff @angle:ca-na-s6 harmonic 61.55 120.69 # SOURCE3 1
- angle_coeff @angle:ca-na-s harmonic 59.27 125.64 # SOURCE3 1
- angle_coeff @angle:ca-na-sh harmonic 60.55 125.44 # SOURCE3 1
- angle_coeff @angle:ca-na-ss harmonic 59.16 129.91 # SOURCE4 8 0.1449
- angle_coeff @angle:cc-na-cc harmonic 68.94 109.90 # SOURCE3 109 1.5547
- angle_coeff @angle:cc-na-cd harmonic 63.88 128.01 # SOURCE3 1 0.0000
- angle_coeff @angle:cc-na-ce harmonic 63.05 126.61 # SOURCE4 8 0.5158
- angle_coeff @angle:cc-na-cl harmonic 53.10 124.61 # SOURCE3 3 0.5208
- angle_coeff @angle:cc-na-f harmonic 64.60 118.03 # SOURCE3 4 0.3081
- angle_coeff @angle:cc-na-hn harmonic 47.02 125.50 # CORR 861
- angle_coeff @angle:cc-na-i harmonic 54.34 125.70 # SOURCE3 6 0.7821
- angle_coeff @angle:cc-na-n2 harmonic 66.83 122.96 # SOURCE3 15 0.9350
- angle_coeff @angle:cc-na-n4 harmonic 65.90 120.31 # SOURCE3 10 3.4394
- angle_coeff @angle:cc-na-n harmonic 66.52 123.19 # SOURCE3 13 0.3010
- angle_coeff @angle:cc-na-na harmonic 65.91 123.43 # SOURCE3 23 0.2088
- angle_coeff @angle:cc-na-nc harmonic 70.18 113.02 # SOURCE3 38 2.2867
- angle_coeff @angle:cc-na-nd harmonic 66.41 126.22 # CORR 124
- angle_coeff @angle:cc-na-nh harmonic 66.23 122.25 # SOURCE3 19 0.2010
- angle_coeff @angle:cc-na-no harmonic 65.40 121.78 # SOURCE3 9 0.3521
- angle_coeff @angle:cc-na-o harmonic 69.01 125.21 # SOURCE3 10 0.0124
- angle_coeff @angle:cc-na-oh harmonic 66.67 122.38 # SOURCE3 10 0.1570
- angle_coeff @angle:cc-na-os harmonic 67.01 116.86 # CORR 48
- angle_coeff @angle:cc-na-p2 harmonic 75.29 125.86 # SOURCE3 14 2.2993
- angle_coeff @angle:cc-na-p3 harmonic 75.02 125.25 # SOURCE3 8 0.1998
- angle_coeff @angle:cc-na-p4 harmonic 81.11 127.73 # SOURCE3 7 3.6077
- angle_coeff @angle:cc-na-p5 harmonic 76.81 124.70 # SOURCE3 13 1.4225
- angle_coeff @angle:cc-na-s4 harmonic 59.45 121.03 # SOURCE3 10 0.5589
- angle_coeff @angle:cc-na-s6 harmonic 60.98 122.19 # SOURCE3 10 0.9634
- angle_coeff @angle:cc-na-s harmonic 59.10 125.66 # SOURCE3 8 0.1880
- angle_coeff @angle:cc-na-sh harmonic 60.71 123.96 # SOURCE3 10 0.3424
- angle_coeff @angle:cc-na-ss harmonic 61.34 120.10 # CORR 44
- angle_coeff @angle:cd-na-cd harmonic 68.94 109.90 # SOURCE3 109 1.5547
- angle_coeff @angle:cd-na-cl harmonic 53.10 124.61 # SOURCE3 3 same_as_cc-na-cl
- angle_coeff @angle:cd-na-f harmonic 64.60 118.03 # SOURCE3 4 0.3081
- angle_coeff @angle:cd-na-hn harmonic 47.02 125.50 # CORR 861
- angle_coeff @angle:cd-na-i harmonic 54.34 125.70 # SOURCE3 6 0.7821
- angle_coeff @angle:cd-na-n2 harmonic 66.83 122.96 # SOURCE3 15 0.9350
- angle_coeff @angle:cd-na-n4 harmonic 65.90 120.31 # SOURCE3 10 3.4394
- angle_coeff @angle:cd-na-n harmonic 66.52 123.19 # SOURCE3 13 0.3010
- angle_coeff @angle:cd-na-na harmonic 65.91 123.43 # SOURCE3 23 0.2088
- angle_coeff @angle:cd-na-nc harmonic 66.41 126.22 # CORR 124
- angle_coeff @angle:cd-na-nd harmonic 70.18 113.02 # SOURCE3 38 2.2867
- angle_coeff @angle:cd-na-nh harmonic 66.23 122.25 # SOURCE3 19 0.2010
- angle_coeff @angle:cd-na-no harmonic 65.40 121.78 # SOURCE3 9 0.3521
- angle_coeff @angle:cd-na-o harmonic 69.01 125.21 # SOURCE3 10 0.0124
- angle_coeff @angle:cd-na-oh harmonic 66.67 122.38 # SOURCE3 10 0.1570
- angle_coeff @angle:cd-na-os harmonic 67.01 116.86 # CORR 48
- angle_coeff @angle:cd-na-p2 harmonic 75.29 125.86 # SOURCE3 14 2.2993
- angle_coeff @angle:cd-na-p3 harmonic 75.02 125.25 # SOURCE3 8 0.1998
- angle_coeff @angle:cd-na-p4 harmonic 81.11 127.73 # SOURCE3 7 same_as_cc-na-p4
- angle_coeff @angle:cd-na-p5 harmonic 76.81 124.70 # SOURCE3 13 1.4225
- angle_coeff @angle:cd-na-s4 harmonic 59.45 121.03 # SOURCE3 10 0.5589
- angle_coeff @angle:cd-na-s6 harmonic 60.98 122.19 # SOURCE3 10 0.9634
- angle_coeff @angle:cd-na-s harmonic 59.10 125.66 # SOURCE3 8 0.1880
- angle_coeff @angle:cd-na-sh harmonic 60.71 123.96 # SOURCE3 10 0.3424
- angle_coeff @angle:cd-na-ss harmonic 61.34 120.10 # CORR 44
- angle_coeff @angle:cl-na-cl harmonic 48.73 122.80 # SOURCE3 1
- angle_coeff @angle:cl-na-nc harmonic 55.70 119.36 # SOURCE3 4 1.7128
- angle_coeff @angle:cl-na-nd harmonic 55.70 119.36 # SOURCE3 4 same_as_cl-na-nc
- angle_coeff @angle:cl-na-os harmonic 58.63 106.58 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-na-p2 harmonic 68.67 121.29 # SOURCE3 1
- angle_coeff @angle:cl-na-pc harmonic 69.19 120.51 # SOURCE3 3 2.1985
- angle_coeff @angle:cl-na-pd harmonic 69.19 120.51 # SOURCE3 3 same_as_cl-na-pc
- angle_coeff @angle:cl-na-ss harmonic 56.71 111.91 # SOURCE3 1 0.0000
- angle_coeff @angle:f-na-f harmonic 62.22 120.20 # SOURCE3 1
- angle_coeff @angle:f-na-nc harmonic 66.64 118.05 # SOURCE3 4 1.7931
- angle_coeff @angle:f-na-nd harmonic 66.64 118.05 # SOURCE3 4 same_as_f-na-nc
- angle_coeff @angle:f-na-os harmonic 69.15 103.86 # SOURCE3 1 0.0000
- angle_coeff @angle:f-na-p2 harmonic 75.54 119.95 # SOURCE3 1
- angle_coeff @angle:f-na-pc harmonic 76.37 119.10 # SOURCE3 3 2.3967
- angle_coeff @angle:f-na-pd harmonic 76.37 119.10 # SOURCE3 3 same_as_f-na-pc
- angle_coeff @angle:f-na-ss harmonic 63.34 108.01 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-na-hn harmonic 39.83 116.80 # SOURCE3 1
- angle_coeff @angle:hn-na-n harmonic 50.90 111.26 # SOURCE4 5 1.1280
- angle_coeff @angle:hn-na-nc harmonic 50.00 119.61 # SOURCE3 16 1.8079
- angle_coeff @angle:hn-na-nd harmonic 50.00 119.61 # SOURCE3 16 1.8079
- angle_coeff @angle:hn-na-os harmonic 51.44 101.41 # SOURCE3 7 3.0814
- angle_coeff @angle:hn-na-p2 harmonic 51.02 122.52 # SOURCE3 1
- angle_coeff @angle:hn-na-pc harmonic 51.81 121.48 # SOURCE3 3 2.9355
- angle_coeff @angle:hn-na-pd harmonic 51.81 121.48 # SOURCE3 3 same_as_hn-na-pc
- angle_coeff @angle:hn-na-ss harmonic 42.24 113.95 # SOURCE3 1 0.0000
- angle_coeff @angle:i-na-i harmonic 58.32 124.20 # SOURCE3 1
- angle_coeff @angle:i-na-nc harmonic 56.94 120.03 # SOURCE3 4 2.0032
- angle_coeff @angle:i-na-nd harmonic 56.94 120.03 # SOURCE3 4 same_as_i-na-nc
- angle_coeff @angle:i-na-os harmonic 59.85 109.91 # SOURCE3 1 0.0000
- angle_coeff @angle:i-na-p2 harmonic 73.36 122.28 # SOURCE3 1
- angle_coeff @angle:i-na-pc harmonic 73.81 121.40 # SOURCE3 3 2.4763
- angle_coeff @angle:i-na-pd harmonic 73.81 121.40 # SOURCE3 3 same_as_i-na-pc
- angle_coeff @angle:i-na-ss harmonic 59.04 118.40 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-na-n2 harmonic 70.35 116.71 # SOURCE3 1
- angle_coeff @angle:n2-na-nc harmonic 69.85 119.96 # SOURCE3 4 4.5041
- angle_coeff @angle:n2-na-nd harmonic 69.85 119.96 # SOURCE3 4 same_as_n2-na-nc
- angle_coeff @angle:n2-na-os harmonic 70.33 111.53 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-na-p2 harmonic 77.46 124.88 # SOURCE3 1
- angle_coeff @angle:n2-na-pc harmonic 78.60 123.18 # SOURCE3 3 4.7947
- angle_coeff @angle:n2-na-pd harmonic 78.60 123.18 # SOURCE3 3 same_as_n2-na-pc
- angle_coeff @angle:n2-na-ss harmonic 61.71 124.64 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-na-n3 harmonic 65.77 124.00 # SOURCE3 1
- angle_coeff @angle:n4-na-n4 harmonic 68.57 111.70 # SOURCE3 1
- angle_coeff @angle:n4-na-nc harmonic 69.09 116.44 # SOURCE3 4 3.6604
- angle_coeff @angle:n4-na-nd harmonic 69.09 116.44 # SOURCE3 4 same_as_n4-na-nc
- angle_coeff @angle:n4-na-os harmonic 71.61 102.97 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-na-p2 harmonic 77.04 123.56 # SOURCE3 1
- angle_coeff @angle:n4-na-pc harmonic 78.10 121.98 # SOURCE3 3 4.4884
- angle_coeff @angle:n4-na-pd harmonic 78.10 121.98 # SOURCE3 3 same_as_n4-na-pc
- angle_coeff @angle:na-na-na harmonic 66.77 123.60 # SOURCE3 1
- angle_coeff @angle:na-na-nc harmonic 69.08 119.64 # SOURCE3 4 1.6920
- angle_coeff @angle:na-na-nd harmonic 69.08 119.64 # SOURCE3 4 same_as_na-na-nc
- angle_coeff @angle:na-na-os harmonic 70.25 109.47 # SOURCE3 1 0.0000
- angle_coeff @angle:na-na-p2 harmonic 78.07 121.72 # SOURCE3 1
- angle_coeff @angle:na-na-pc harmonic 78.92 120.91 # SOURCE3 3 2.3033
- angle_coeff @angle:na-na-pd harmonic 78.92 120.91 # SOURCE3 3 same_as_na-na-pc
- angle_coeff @angle:na-na-ss harmonic 63.50 116.50 # SOURCE3 1 0.0000
- angle_coeff @angle:nc-na-nc harmonic 71.20 117.08 # SOURCE3 31 1.8121
- angle_coeff @angle:nc-na-nd harmonic 69.53 122.77 # SOURCE4 5 0.1352
- angle_coeff @angle:nc-na-nh harmonic 68.82 120.55 # SOURCE3 8 1.1436
- angle_coeff @angle:nc-na-no harmonic 68.19 119.15 # SOURCE3 4 1.6049
- angle_coeff @angle:nc-na-o harmonic 72.04 122.79 # SOURCE3 6 1.3154
- angle_coeff @angle:nc-na-oh harmonic 69.71 119.22 # SOURCE3 4 1.7201
- angle_coeff @angle:nc-na-os harmonic 68.30 119.65 # SOURCE3 4 1.5019
- angle_coeff @angle:nc-na-p2 harmonic 79.23 119.99 # SOURCE3 4 3.6009
- angle_coeff @angle:nc-na-p3 harmonic 78.72 120.07 # SOURCE3 4 3.7188
- angle_coeff @angle:nc-na-p4 harmonic 86.25 119.77 # SOURCE3 3 0.3747
- angle_coeff @angle:nc-na-p5 harmonic 80.84 118.95 # SOURCE3 4 3.1194
- angle_coeff @angle:nc-na-pc harmonic 80.31 118.66 # SOURCE3 27 1.5082
- angle_coeff @angle:nc-na-s4 harmonic 61.52 119.20 # SOURCE3 4 2.3841
- angle_coeff @angle:nc-na-s6 harmonic 63.45 119.24 # SOURCE3 4 2.2262
- angle_coeff @angle:nc-na-s harmonic 61.55 122.26 # SOURCE3 4 0.9173
- angle_coeff @angle:nc-na-sh harmonic 63.29 120.50 # SOURCE3 4 1.5016
- angle_coeff @angle:nc-na-ss harmonic 62.94 120.50 # SOURCE3 4 1.5615
- angle_coeff @angle:nd-na-nd harmonic 71.20 117.08 # SOURCE3 31 1.8121
- angle_coeff @angle:nd-na-nh harmonic 68.82 120.55 # SOURCE3 8 same_as_nc-na-nh
- angle_coeff @angle:nd-na-no harmonic 68.19 119.15 # SOURCE3 4 same_as_nc-na-no
- angle_coeff @angle:nd-na-o harmonic 72.04 122.79 # SOURCE3 6 same_as_nc-na-o
- angle_coeff @angle:nd-na-oh harmonic 69.71 119.22 # SOURCE3 4 same_as_nc-na-oh
- angle_coeff @angle:nd-na-os harmonic 68.30 119.65 # SOURCE3 4 same_as_nc-na-os
- angle_coeff @angle:nd-na-p2 harmonic 79.23 119.99 # SOURCE3 4 same_as_nc-na-p2
- angle_coeff @angle:nd-na-p3 harmonic 78.72 120.07 # SOURCE3 4 same_as_nc-na-p3
- angle_coeff @angle:nd-na-p4 harmonic 86.25 119.77 # SOURCE3 3 same_as_nc-na-p4
- angle_coeff @angle:nd-na-p5 harmonic 80.84 118.95 # SOURCE3 4 same_as_nc-na-p5
- angle_coeff @angle:nd-na-pd harmonic 80.31 118.66 # SOURCE3 27 same_as_nc-na-pc
- angle_coeff @angle:nd-na-s4 harmonic 61.52 119.20 # SOURCE3 4 same_as_nc-na-s4
- angle_coeff @angle:nd-na-s6 harmonic 63.45 119.24 # SOURCE3 4 same_as_nc-na-s6
- angle_coeff @angle:nd-na-s harmonic 61.55 122.26 # SOURCE3 4 same_as_nc-na-s
- angle_coeff @angle:nd-na-sh harmonic 63.29 120.50 # SOURCE3 4 same_as_nc-na-sh
- angle_coeff @angle:nd-na-ss harmonic 62.94 120.50 # SOURCE3 4 same_as_nc-na-ss
- angle_coeff @angle:nh-na-nh harmonic 66.77 123.60 # SOURCE3 1
- angle_coeff @angle:nh-na-os harmonic 69.65 111.37 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-na-p2 harmonic 78.35 120.86 # SOURCE3 1
- angle_coeff @angle:nh-na-pc harmonic 79.10 120.38 # SOURCE3 6 1.3513
- angle_coeff @angle:nh-na-pd harmonic 79.10 120.38 # SOURCE3 6 same_as_nh-na-pc
- angle_coeff @angle:nh-na-ss harmonic 64.66 112.35 # SOURCE3 2 5.2951
- angle_coeff @angle:n-na-n harmonic 67.78 123.80 # SOURCE3 1
- angle_coeff @angle:n-na-nc harmonic 69.61 119.85 # SOURCE3 4 1.6156
- angle_coeff @angle:n-na-nd harmonic 69.61 119.85 # SOURCE3 4 same_as_n-na-nc
- angle_coeff @angle:no-na-no harmonic 65.22 122.80 # SOURCE3 1
- angle_coeff @angle:no-na-os harmonic 70.30 106.55 # SOURCE3 1 0.0000
- angle_coeff @angle:no-na-pc harmonic 78.65 120.11 # SOURCE3 3 2.0821
- angle_coeff @angle:no-na-pd harmonic 78.65 120.11 # SOURCE3 3 same_as_no-na-pc
- angle_coeff @angle:n-na-os harmonic 72.34 104.71 # SOURCE3 1 0.0000
- angle_coeff @angle:no-na-ss harmonic 63.49 114.95 # SOURCE3 1 0.0000
- angle_coeff @angle:n-na-p2 harmonic 78.46 121.35 # SOURCE3 1
- angle_coeff @angle:n-na-pc harmonic 79.30 120.64 # SOURCE3 3 2.0168
- angle_coeff @angle:n-na-pd harmonic 79.30 120.64 # SOURCE3 3 same_as_n-na-pc
- angle_coeff @angle:n-na-ss harmonic 63.84 116.10 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-na-oh harmonic 68.13 122.20 # SOURCE3 1
- angle_coeff @angle:oh-na-p2 harmonic 78.88 120.76 # SOURCE3 1
- angle_coeff @angle:oh-na-pc harmonic 79.74 119.99 # SOURCE3 3 2.1734
- angle_coeff @angle:oh-na-pd harmonic 79.74 119.99 # SOURCE3 3 same_as_oh-na-pc
- angle_coeff @angle:oh-na-ss harmonic 64.88 113.04 # SOURCE3 1 0.0000
- angle_coeff @angle:o-na-o harmonic 74.03 126.20 # SOURCE3 1
- angle_coeff @angle:o-na-os harmonic 70.76 118.39 # SOURCE3 1 0.0000
- angle_coeff @angle:o-na-p2 harmonic 79.51 122.80 # SOURCE3 1
- angle_coeff @angle:o-na-pc harmonic 80.36 122.34 # SOURCE3 3 1.2908
- angle_coeff @angle:o-na-pd harmonic 80.36 122.34 # SOURCE3 3 same_as_o-na-pc
- angle_coeff @angle:os-na-os harmonic 71.29 104.45 # SOURCE3 2 0.0983
- angle_coeff @angle:os-na-p2 harmonic 79.21 117.86 # SOURCE3 1 0.0000
- angle_coeff @angle:os-na-p3 harmonic 83.58 104.70 # SOURCE3 1 0.0000
- angle_coeff @angle:os-na-p5 harmonic 82.64 111.41 # SOURCE3 1 0.0000
- angle_coeff @angle:os-na-pc harmonic 79.09 119.91 # SOURCE3 3 1.9002
- angle_coeff @angle:os-na-pd harmonic 79.09 119.91 # SOURCE3 3 same_as_os-na-pc
- angle_coeff @angle:os-na-s4 harmonic 64.81 105.88 # SOURCE3 2 0.0000
- angle_coeff @angle:os-na-s6 harmonic 64.80 112.00 # SOURCE3 2 0.0000
- angle_coeff @angle:os-na-ss harmonic 65.33 109.64 # SOURCE3 3 4.1395
- angle_coeff @angle:p2-na-p2 harmonic 96.62 120.91 # SOURCE3 1
- angle_coeff @angle:p2-na-p3 harmonic 94.74 124.80 # SOURCE3 1
- angle_coeff @angle:p2-na-p5 harmonic 96.33 123.99 # SOURCE3 1
- angle_coeff @angle:p2-na-pc harmonic 97.16 120.72 # SOURCE3 3 0.2407
- angle_coeff @angle:p2-na-pd harmonic 97.16 120.72 # SOURCE3 3 same_as_p2-na-pc
- angle_coeff @angle:p2-na-s4 harmonic 74.88 122.47 # SOURCE3 1
- angle_coeff @angle:p2-na-s6 harmonic 76.31 122.50 # SOURCE3 1
- angle_coeff @angle:p2-na-s harmonic 75.69 121.85 # SOURCE3 1
- angle_coeff @angle:p2-na-sh harmonic 76.68 121.75 # SOURCE3 1
- angle_coeff @angle:p2-na-ss harmonic 76.38 121.88 # SOURCE3 1
- angle_coeff @angle:p3-na-p3 harmonic 93.72 126.60 # SOURCE3 1
- angle_coeff @angle:p3-na-pc harmonic 95.76 123.32 # SOURCE3 3 4.1781
- angle_coeff @angle:p3-na-pd harmonic 95.76 123.32 # SOURCE3 3 same_as_p3-na-pc
- angle_coeff @angle:p5-na-p5 harmonic 97.06 124.60 # SOURCE3 1
- angle_coeff @angle:p5-na-pc harmonic 97.33 122.69 # SOURCE3 3 3.6738
- angle_coeff @angle:p5-na-pd harmonic 97.33 122.69 # SOURCE3 3 same_as_p5-na-pc
- angle_coeff @angle:p5-na-ss harmonic 78.22 118.52 # SOURCE3 1 0.0000
- angle_coeff @angle:pc-na-pc harmonic 97.62 120.78 # SOURCE3 27 1.6457
- angle_coeff @angle:pc-na-s4 harmonic 75.52 121.51 # SOURCE3 3 2.7242
- angle_coeff @angle:pc-na-s6 harmonic 76.99 121.55 # SOURCE3 3 2.7065
- angle_coeff @angle:pc-na-s harmonic 76.17 121.47 # SOURCE3 3 1.0668
- angle_coeff @angle:pc-na-sh harmonic 77.28 121.08 # SOURCE3 3 1.8942
- angle_coeff @angle:pc-na-ss harmonic 76.97 121.20 # SOURCE3 3 1.9295
- angle_coeff @angle:pd-na-pd harmonic 97.62 120.78 # SOURCE3 27 same_as_pc-na-pc
- angle_coeff @angle:pd-na-s4 harmonic 75.52 121.51 # SOURCE3 3 same_as_pc-na-s4
- angle_coeff @angle:pd-na-s6 harmonic 76.99 121.55 # SOURCE3 3 same_as_pc-na-s6
- angle_coeff @angle:pd-na-s harmonic 76.17 121.47 # SOURCE3 3 same_as_pc-na-s
- angle_coeff @angle:pd-na-sh harmonic 77.28 121.08 # SOURCE3 3 same_as_pc-na-sh
- angle_coeff @angle:pd-na-ss harmonic 76.97 121.20 # SOURCE3 3 same_as_pc-na-ss
- angle_coeff @angle:py-na-py harmonic 122.69 78.25 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-na-s4 harmonic 58.05 124.20 # SOURCE3 1
- angle_coeff @angle:s4-na-s6 harmonic 62.00 112.86 # SOURCE3 1
- angle_coeff @angle:s4-na-ss harmonic 62.16 111.92 # SOURCE3 1 0.0000
- angle_coeff @angle:s6-na-s6 harmonic 60.51 123.20 # SOURCE3 1
- angle_coeff @angle:s6-na-ss harmonic 61.44 119.10 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-na-sh harmonic 60.38 124.60 # SOURCE3 1
- angle_coeff @angle:sh-na-ss harmonic 61.63 118.79 # SOURCE3 1 0.0000
- angle_coeff @angle:s-na-s harmonic 58.55 126.00 # SOURCE3 1
- angle_coeff @angle:s-na-ss harmonic 62.52 112.49 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-na-ss harmonic 62.90 113.24 # SOURCE3 2 6.6084
- angle_coeff @angle:sy-na-sy harmonic 60.51 123.20 # SOURCE3 1
- angle_coeff @angle:ca-nb-ca harmonic 68.59 115.86 # SOURCE3 46 1.1645
- angle_coeff @angle:ca-nb-cp harmonic 68.01 118.04 # SOURCE4 58 0.7819
- angle_coeff @angle:ca-nb-cq harmonic 68.01 118.04 # SOURCE4 58 same as ca-nb-cp
- angle_coeff @angle:ca-nb-nb harmonic 69.37 118.89 # SOURCE3 10 0.6031
- angle_coeff @angle:cp-nb-nb harmonic 68.79 121.11 # SOURCE4 12 0.4315
- angle_coeff @angle:nb-nb-nb harmonic 70.44 121.04 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n-br harmonic 66.59 116.20 # SOURCE3 1 0.0000
- angle_coeff @angle:br-n-c harmonic 61.85 120.77 # SOURCE3 5 2.6390
- angle_coeff @angle:br-n-ca harmonic 62.07 118.19 # SOURCE3 1
- angle_coeff @angle:br-n-cc harmonic 62.34 118.19 # SOURCE3 1 same_as_br-n-cd
- angle_coeff @angle:br-n-cd harmonic 62.34 118.19 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-n-c1 harmonic 73.52 102.69 # SOURCE3 1
- angle_coeff @angle:c1-n-ca harmonic 65.90 118.88 # SOURCE3 1
- angle_coeff @angle:c1-n-cc harmonic 67.02 118.88 # SOURCE3 1 same_as_c1-n-cd
- angle_coeff @angle:c1-n-cd harmonic 67.02 118.88 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n-c2 harmonic 65.18 116.75 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n-c3 harmonic 63.06 119.98 # SOURCE4 23 2.3373
- angle_coeff @angle:c2-n-ca harmonic 64.88 116.54 # SOURCE3 1
- angle_coeff @angle:c2-n-cc harmonic 65.85 116.54 # SOURCE3 1 same_as_c2-n-cd
- angle_coeff @angle:c2-n-cd harmonic 65.85 116.54 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-n-hn harmonic 47.33 118.36 # SOURCE4 40 1.8005
- angle_coeff @angle:c3-n-c3 harmonic 63.13 115.56 # SOURCE4 392 2.0191
- angle_coeff @angle:c3-n-ca harmonic 62.76 119.96 # SOURCE4 165 2.0808
- angle_coeff @angle:c3-n-cc harmonic 63.33 121.00 # CORR 267
- angle_coeff @angle:c3-n-cd harmonic 63.33 121.00 # CORR 267
- angle_coeff @angle:c3-n-cy harmonic 62.51 117.11 # SOURCE4 49 1.0344
- angle_coeff @angle:c3-n-hn harmonic 46.04 116.78 # SOURCE3 39 2.1985
- angle_coeff @angle:c3-n-n2 harmonic 64.89 121.68 # SOURCE4 52 1.3175
- angle_coeff @angle:c3-n-n harmonic 66.40 114.82 # SOURCE4 9 0.7008
- angle_coeff @angle:c3-n-nc harmonic 66.97 115.21 # CORR 48
- angle_coeff @angle:c3-n-nd harmonic 66.97 115.21 # CORR 48
- angle_coeff @angle:c3-n-oh harmonic 66.88 113.05 # SOURCE4 31 0.8144
- angle_coeff @angle:c3-n-os harmonic 66.99 112.65 # SOURCE4 16 1.5399
- angle_coeff @angle:c3-n-sy harmonic 60.53 121.27 # SOURCE4 5 1.1298
- angle_coeff @angle:ca-n-ca harmonic 64.31 117.39 # SOURCE4 39 1.6465
- angle_coeff @angle:ca-n-cc harmonic 66.19 114.06 # CORR 34
- angle_coeff @angle:ca-n-cd harmonic 66.19 114.06 # CORR 34
- angle_coeff @angle:ca-n-cl harmonic 57.24 117.72 # SOURCE3 1
- angle_coeff @angle:ca-n-f harmonic 64.62 114.92 # SOURCE3 1
- angle_coeff @angle:ca-n-hn harmonic 47.36 115.94 # SOURCE4 537 1.8890
- angle_coeff @angle:ca-n-i harmonic 56.58 119.30 # SOURCE3 1
- angle_coeff @angle:ca-n-n2 harmonic 65.72 122.17 # SOURCE4 5 0.2545
- angle_coeff @angle:ca-n-n4 harmonic 64.15 122.98 # SOURCE3 1
- angle_coeff @angle:ca-n-n harmonic 66.30 118.54 # SOURCE4 21 0.3399
- angle_coeff @angle:ca-n-na harmonic 66.33 119.31 # SOURCE4 16 0.3168
- angle_coeff @angle:ca-n-nc harmonic 68.25 114.36 # CORR 6
- angle_coeff @angle:ca-n-nd harmonic 68.25 114.36 # CORR 6
- angle_coeff @angle:ca-n-nh harmonic 66.60 116.45 # SOURCE3 1
- angle_coeff @angle:ca-n-p2 harmonic 79.60 112.32 # SOURCE3 1
- angle_coeff @angle:ca-n-p3 harmonic 74.22 125.11 # SOURCE3 1
- angle_coeff @angle:ca-n-s4 harmonic 59.97 118.40 # SOURCE3 1
- angle_coeff @angle:ca-n-s6 harmonic 62.01 117.32 # SOURCE3 1
- angle_coeff @angle:ca-n-ss harmonic 62.15 116.60 # SOURCE3 1
- angle_coeff @angle:c-n-c1 harmonic 68.47 117.04 # SOURCE3 1 0.0000
- angle_coeff @angle:c-n-c2 harmonic 65.09 122.15 # SOURCE3 9 5.1016
- angle_coeff @angle:c-n-c3 harmonic 63.92 121.35 # SOURCE3 54 2.3808
- angle_coeff @angle:c3-nc-cd harmonic 67.60 109.51 # SOURCE3 9 5.4142
- angle_coeff @angle:c-n-c harmonic 65.33 127.14 # SOURCE4 514 2.0111
- angle_coeff @angle:c-n-ca harmonic 64.29 123.71 # SOURCE3 10 3.8159
- angle_coeff @angle:ca-nc-ca harmonic 70.73 109.95 # SOURCE3 1
- angle_coeff @angle:ca-nc-cd harmonic 72.43 104.94 # CORR 437
- angle_coeff @angle:ca-nc-n harmonic 73.68 104.69 # CORR 2
- angle_coeff @angle:ca-nc-na harmonic 74.57 102.74 # CORR 14
- angle_coeff @angle:ca-nc-os harmonic 73.08 104.48 # CORR 10
- angle_coeff @angle:ca-nc-ss harmonic 67.84 116.29 # SOURCE3 1
- angle_coeff @angle:c-n-cc harmonic 65.24 124.19 # SOURCE3 57 2.2262
- angle_coeff @angle:c-nc-ca harmonic 66.11 120.66 # CORR 2
- angle_coeff @angle:cc-n-cc harmonic 68.80 108.92 # SOURCE3 11 0.3167
- angle_coeff @angle:cc-nc-cc harmonic 70.50 104.34 # CORR 6
- angle_coeff @angle:cc-nc-cd harmonic 71.08 105.67 # CORR 1240
- angle_coeff @angle:c-nc-cd harmonic 66.18 120.48 # CORR 138
- angle_coeff @angle:cc-n-cl harmonic 57.67 117.72 # SOURCE3 1 same_as_cd-n-cl
- angle_coeff @angle:cc-nc-na harmonic 73.38 102.97 # SOURCE3 1 0.0000
- angle_coeff @angle:cc-nc-nd harmonic 72.54 107.94 # SOURCE3 6 1.4052
- angle_coeff @angle:c-n-cd harmonic 65.24 124.19 # SOURCE3 57 2.2262
- angle_coeff @angle:cd-nc-cd harmonic 68.53 117.28 # CORR 17
- angle_coeff @angle:cd-nc-n harmonic 69.66 117.19 # CORR 64
- angle_coeff @angle:cd-nc-na harmonic 74.24 103.73 # SOURCE3 122 2.3292
- angle_coeff @angle:cd-nc-nc harmonic 71.99 107.88 # CORR 355
- angle_coeff @angle:cd-nc-os harmonic 73.04 104.66 # CORR 116
- angle_coeff @angle:cd-nc-ss harmonic 70.36 108.15 # CORR 45
- angle_coeff @angle:c-n-ce harmonic 62.21 131.83 # SOURCE4 146 1.3048
- angle_coeff @angle:cc-n-f harmonic 65.61 114.92 # SOURCE3 1 same_as_cd-n-f
- angle_coeff @angle:cc-n-hn harmonic 47.99 119.14 # CORR 276
- angle_coeff @angle:cc-n-i harmonic 56.61 119.30 # SOURCE3 1 same_as_cd-n-i
- angle_coeff @angle:c-n-cl harmonic 58.34 116.35 # SOURCE4 11 0.6829
- angle_coeff @angle:cc-n-n2 harmonic 70.09 110.87 # SOURCE3 1 same_as_cd-n-n2
- angle_coeff @angle:cc-n-n harmonic 66.53 121.37 # SOURCE3 1 same_as_cd-n-n
- angle_coeff @angle:cc-n-na harmonic 67.87 117.57 # SOURCE3 1 same_as_cd-n-na
- angle_coeff @angle:cc-n-nc harmonic 70.08 112.03 # CORR 14
- angle_coeff @angle:cc-n-nh harmonic 67.30 117.52 # SOURCE3 1 same_as_cd-n-nh
- angle_coeff @angle:cc-n-no harmonic 66.40 115.92 # SOURCE3 1 same_as_cd-n-no
- angle_coeff @angle:cc-n-o harmonic 70.07 120.54 # SOURCE3 1 same_as_cd-n-o
- angle_coeff @angle:cc-n-oh harmonic 67.32 118.15 # SOURCE3 1 same_as_cd-n-oh
- angle_coeff @angle:cc-n-os harmonic 68.06 115.56 # SOURCE3 1 same_as_cd-n-os
- angle_coeff @angle:cc-n-p2 harmonic 80.17 112.32 # SOURCE3 1 same_as_cd-n-p2
- angle_coeff @angle:cc-n-p3 harmonic 74.70 125.11 # SOURCE3 1 same_as_cd-n-p3
- angle_coeff @angle:cc-n-p5 harmonic 78.11 121.00 # SOURCE3 1 same_as_cd-n-p5
- angle_coeff @angle:cc-n-s4 harmonic 60.34 118.40 # SOURCE3 1 same_as_cd-n-s4
- angle_coeff @angle:cc-n-s6 harmonic 62.48 117.32 # SOURCE3 1 same_as_cd-n-s6
- angle_coeff @angle:cc-n-s harmonic 60.78 118.29 # SOURCE3 1 same_as_cd-n-s
- angle_coeff @angle:cc-n-sh harmonic 61.64 119.13 # SOURCE3 1 same_as_cd-n-sh
- angle_coeff @angle:cc-n-ss harmonic 62.62 116.60 # SOURCE3 2 same_as_cd-n-ss
- angle_coeff @angle:c-n-cx harmonic 64.22 122.07 # SOURCE4 11 1.9478
- angle_coeff @angle:c-n-cy harmonic 72.26 94.23 # SOURCE4 270 1.3777
- angle_coeff @angle:cd-n-cd harmonic 68.80 108.92 # SOURCE3 11 same_as_cc-n-cc
- angle_coeff @angle:cd-n-cl harmonic 57.67 117.72 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-f harmonic 65.61 114.92 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-hn harmonic 47.99 119.14 # CORR 276
- angle_coeff @angle:cd-n-i harmonic 56.61 119.30 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-n2 harmonic 70.09 110.87 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-n harmonic 66.53 121.37 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-na harmonic 67.87 117.57 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-nd harmonic 70.08 112.03 # CORR 14
- angle_coeff @angle:cd-n-nh harmonic 67.30 117.52 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-no harmonic 66.40 115.92 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-o harmonic 70.07 120.54 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-oh harmonic 67.32 118.15 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-os harmonic 68.06 115.56 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-p2 harmonic 80.17 112.32 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-p3 harmonic 74.70 125.11 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-p5 harmonic 78.11 121.00 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-s4 harmonic 60.34 118.40 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-s6 harmonic 62.48 117.32 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-s harmonic 60.78 118.29 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-sh harmonic 61.64 119.13 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-n-ss harmonic 62.62 116.60 # SOURCE3 2 1.8318
- angle_coeff @angle:ce-n-cy harmonic 64.70 111.89 # CORR 152
- angle_coeff @angle:c-n-f harmonic 68.30 108.63 # SOURCE3 3 4.6785
- angle_coeff @angle:cf-n-cy harmonic 64.70 111.89 # CORR 152
- angle_coeff @angle:c-n-hn harmonic 49.21 118.46 # SOURCE3 157 2.4094
- angle_coeff @angle:c-n-i harmonic 56.34 120.38 # SOURCE3 5 2.1600
- angle_coeff @angle:cl-n-cl harmonic 54.70 111.69 # SOURCE3 1 0.0000
- angle_coeff @angle:c-n-n2 harmonic 68.06 120.59 # SOURCE3 9 3.2410
- angle_coeff @angle:c-n-n3 harmonic 67.13 120.43 # SOURCE3 5 0.9481
- angle_coeff @angle:c-n-n4 harmonic 68.85 112.32 # SOURCE3 5 1.2622
- angle_coeff @angle:c-n-n harmonic 68.18 118.42 # SOURCE3 10 2.8922
- angle_coeff @angle:c-n-na harmonic 68.25 119.20 # SOURCE3 11 2.3032
- angle_coeff @angle:na-nc-nd harmonic 75.97 105.47 # SOURCE3 6 0.6349
- angle_coeff @angle:c-n-nc harmonic 67.16 125.19 # CORR 84
- angle_coeff @angle:nc-nc-nd harmonic 73.11 111.29 # CORR 61
- angle_coeff @angle:c-n-nd harmonic 67.16 125.19 # CORR 84
- angle_coeff @angle:nd-nc-os harmonic 74.42 107.22 # SOURCE3 3 0.4707
- angle_coeff @angle:c-n-nh harmonic 68.02 117.81 # SOURCE4 21 1.5935
- angle_coeff @angle:c-n-no harmonic 66.47 118.16 # SOURCE3 4 5.4870
- angle_coeff @angle:c-n-o harmonic 71.64 118.90 # SOURCE3 9 5.4085
- angle_coeff @angle:c-n-oh harmonic 69.53 113.39 # SOURCE3 6 1.3345
- angle_coeff @angle:c-n-os harmonic 69.60 113.14 # SOURCE3 7 3.0839
- angle_coeff @angle:c-n-p2 harmonic 76.53 124.56 # SOURCE3 8 3.6907
- angle_coeff @angle:c-n-p3 harmonic 75.82 122.54 # SOURCE3 9 4.4802
- angle_coeff @angle:c-n-p4 harmonic 76.84 123.44 # SOURCE3 1 0.0000
- angle_coeff @angle:c-n-p5 harmonic 76.23 128.50 # SOURCE4 6 0.5353
- angle_coeff @angle:c-n-pc harmonic 77.00 122.23 # SOURCE3 3 2.8787
- angle_coeff @angle:c-n-pd harmonic 77.00 122.23 # SOURCE3 3 same_as_c-n-pc
- angle_coeff @angle:c-n-s4 harmonic 60.09 120.41 # SOURCE3 4 3.1760
- angle_coeff @angle:c-n-s6 harmonic 60.86 125.01 # SOURCE4 13 1.6314
- angle_coeff @angle:c-n-s harmonic 59.04 126.55 # SOURCE3 3 4.3365
- angle_coeff @angle:c-n-sh harmonic 61.87 119.54 # SOURCE3 4 1.7681
- angle_coeff @angle:c-n-ss harmonic 61.97 120.37 # SOURCE3 7 1.4450
- angle_coeff @angle:c-n-sy harmonic 60.91 124.81 # SOURCE4 51 1.0517
- angle_coeff @angle:cx-n-hn harmonic 46.26 118.58 # SOURCE4 5 0.3288
- angle_coeff @angle:cx-n-os harmonic 97.40 54.04 # SOURCE3 1 0.0000
- angle_coeff @angle:cy-n-hn harmonic 45.34 119.00 # SOURCE4 65 1.3840
- angle_coeff @angle:c3-nd-cc harmonic 67.60 109.51 # SOURCE3 9 same_as_c3-nc-cd
- angle_coeff @angle:ca-nd-ca harmonic 70.73 109.95 # SOURCE3 1 same_as_ca-nc-ca
- angle_coeff @angle:ca-nd-cc harmonic 72.43 104.94 # CORR 437
- angle_coeff @angle:ca-nd-n harmonic 73.68 104.69 # CORR 2
- angle_coeff @angle:ca-nd-na harmonic 74.57 102.74 # CORR 14
- angle_coeff @angle:ca-nd-nc harmonic 73.55 108.41 # SOURCE4 9 0.1575
- angle_coeff @angle:ca-nd-os harmonic 73.08 104.48 # CORR 10
- angle_coeff @angle:ca-nd-ss harmonic 67.84 116.29 # SOURCE3 1 same_as_ca-nc-ss
- angle_coeff @angle:c-nd-ca harmonic 66.11 120.66 # CORR 2
- angle_coeff @angle:c-nd-cc harmonic 66.18 120.48 # CORR 138
- angle_coeff @angle:cc-nd-cc harmonic 68.53 117.28 # CORR 17
- angle_coeff @angle:cc-nd-cd harmonic 71.08 105.67 # CORR 1240
- angle_coeff @angle:cc-nd-n harmonic 69.66 117.19 # CORR 64
- angle_coeff @angle:cc-nd-na harmonic 74.24 103.73 # SOURCE3 122 2.3292
- angle_coeff @angle:cc-nd-nd harmonic 71.99 107.88 # CORR 355
- angle_coeff @angle:cc-nd-os harmonic 73.04 104.66 # CORR 116
- angle_coeff @angle:cc-nd-ss harmonic 70.36 108.15 # CORR 45
- angle_coeff @angle:cd-nd-cd harmonic 70.50 104.34 # CORR 6
- angle_coeff @angle:cd-nd-na harmonic 73.38 102.97 # SOURCE3 1 same_as_cc-nc-na
- angle_coeff @angle:cd-nd-nc harmonic 72.54 107.94 # SOURCE3 6 1.4052
- angle_coeff @angle:na-nd-nc harmonic 75.97 105.47 # SOURCE3 6 0.6349
- angle_coeff @angle:nc-nd-nd harmonic 73.11 111.29 # CORR 61
- angle_coeff @angle:nc-nd-os harmonic 74.42 107.22 # SOURCE3 3 same_as_nd-nc-os
- angle_coeff @angle:c1-ne-ca harmonic 60.41 150.84 # CORR 9
- angle_coeff @angle:c1-ne-cg harmonic 66.00 140.00 # SOURCE2 1 0.0000
- angle_coeff @angle:c2-ne-ca harmonic 66.09 120.84 # CORR 55
- angle_coeff @angle:c2-ne-ce harmonic 67.33 118.17 # SOURCE3 3 1.2374
- angle_coeff @angle:c2-ne-cg harmonic 68.36 123.58 # SOURCE4 12 0.8560
- angle_coeff @angle:c2-ne-n2 harmonic 74.56 113.31 # SOURCE3 1
- angle_coeff @angle:c2-ne-ne harmonic 69.17 110.86 # SOURCE3 7 4.5874
- angle_coeff @angle:c2-ne-p2 harmonic 80.83 134.03 # SOURCE3 1
- angle_coeff @angle:c2-ne-pe harmonic 79.24 120.52 # SOURCE3 8 8.1381
- angle_coeff @angle:c2-ne-px harmonic 80.57 117.75 # SOURCE3 5 0.8581
- angle_coeff @angle:c2-ne-py harmonic 84.33 117.04 # SOURCE3 3 1.4398
- angle_coeff @angle:c2-ne-sx harmonic 60.95 111.98 # SOURCE3 3 0.4090
- angle_coeff @angle:c2-ne-sy harmonic 61.78 118.92 # CORR 9
- angle_coeff @angle:ca-ne-cf harmonic 65.56 121.98 # CORR 15
- angle_coeff @angle:ca-ne-n2 harmonic 69.73 114.06 # CORR 11
- angle_coeff @angle:ca-ne-nf harmonic 69.69 115.12 # CORR 44
- angle_coeff @angle:ca-ne-o harmonic 71.10 113.96 # SOURCE3 3 1.1253
- angle_coeff @angle:ca-ne-p2 harmonic 83.08 118.09 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-ne-s harmonic 65.75 120.11 # SOURCE3 1 0.0000
- angle_coeff @angle:c-ne-c2 harmonic 67.85 118.53 # CORR 6
- angle_coeff @angle:ce-ne-n2 harmonic 71.16 111.19 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-ne-o harmonic 72.26 112.16 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-ne-p2 harmonic 83.85 117.02 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-ne-s harmonic 67.15 116.28 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-ne-n1 harmonic 71.71 120.20 # SOURCE2 1 0.0000
- angle_coeff @angle:cg-ne-n2 harmonic 73.16 113.39 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-ne-o harmonic 74.43 114.70 # SOURCE2 1 0.0000
- angle_coeff @angle:cg-ne-p2 harmonic 84.75 119.57 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-ne-s harmonic 68.28 117.70 # SOURCE3 1 0.0000
- angle_coeff @angle:c-ne-sy harmonic 61.66 116.05 # SOURCE4 6 1.2661
- angle_coeff @angle:n2-ne-n2 harmonic 78.59 107.22 # SOURCE3 1
- angle_coeff @angle:n2-ne-ne harmonic 70.94 110.72 # SOURCE3 9 6.1488
- angle_coeff @angle:n2-ne-o harmonic 78.09 114.10 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-ne-p2 harmonic 91.59 109.66 # SOURCE3 1
- angle_coeff @angle:n2-ne-pe harmonic 84.18 112.15 # SOURCE3 7 6.5273
- angle_coeff @angle:n2-ne-px harmonic 83.20 115.97 # SOURCE3 3 1.9854
- angle_coeff @angle:n2-ne-py harmonic 87.34 114.60 # SOURCE3 3 2.9261
- angle_coeff @angle:n2-ne-s harmonic 71.27 115.90 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-ne-sx harmonic 63.80 107.29 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-ne-sy harmonic 65.46 111.21 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-ne-o harmonic 72.28 110.45 # SOURCE3 10 1.8535
- angle_coeff @angle:ne-ne-p2 harmonic 85.32 114.39 # SOURCE3 6 4.0528
- angle_coeff @angle:ne-ne-s harmonic 67.59 115.95 # SOURCE3 6 3.4604
- angle_coeff @angle:o-ne-o harmonic 76.91 124.09 # SOURCE3 2 8.7534
- angle_coeff @angle:o-ne-pe harmonic 78.32 132.32 # SOURCE3 11 23.9559
- angle_coeff @angle:o-ne-px harmonic 86.11 110.62 # SOURCE3 1 0.0000
- angle_coeff @angle:o-ne-py harmonic 90.01 110.79 # SOURCE3 4 1.6818
- angle_coeff @angle:o-ne-s harmonic 71.99 117.19 # SOURCE3 2 0.0225
- angle_coeff @angle:o-ne-sx harmonic 63.79 108.92 # SOURCE3 1 0.0000
- angle_coeff @angle:o-ne-sy harmonic 66.05 111.34 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-ne-pe harmonic 104.56 116.81 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-ne-px harmonic 100.10 128.35 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-ne-py harmonic 105.15 123.47 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-ne-sx harmonic 80.48 112.12 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-ne-sy harmonic 81.80 115.73 # SOURCE3 1 0.0000
- angle_coeff @angle:pe-ne-s harmonic 83.52 115.73 # SOURCE3 1 0.0000
- angle_coeff @angle:px-ne-s harmonic 78.54 131.84 # SOURCE3 1 0.0000
- angle_coeff @angle:py-ne-s harmonic 86.30 116.18 # SOURCE3 4 3.7135
- angle_coeff @angle:s-ne-s harmonic 68.65 120.87 # SOURCE3 1 0.0000
- angle_coeff @angle:s-ne-sx harmonic 63.66 112.96 # SOURCE3 1 0.0000
- angle_coeff @angle:s-ne-sy harmonic 63.94 119.63 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-nf-ca harmonic 60.41 150.84 # CORR 9
- angle_coeff @angle:c1-nf-ch harmonic 66.00 140.00 # SOURCE2 1 same_as_c1-ne-cg
- angle_coeff @angle:c2-nf-ca harmonic 66.09 120.84 # CORR 55
- angle_coeff @angle:c2-nf-cf harmonic 67.33 118.17 # SOURCE3 3 same_as_c2-ne-ce
- angle_coeff @angle:c2-nf-n2 harmonic 74.56 113.31 # SOURCE3 1 same_as_c2-ne-n2
- angle_coeff @angle:c2-nf-nf harmonic 69.17 110.86 # SOURCE3 7 same_as_c2-ne-ne
- angle_coeff @angle:c2-nf-p2 harmonic 80.83 134.03 # SOURCE3 1 same_as_c2-ne-p2
- angle_coeff @angle:c2-nf-pf harmonic 79.24 120.52 # SOURCE3 8 same_as_c2-ne-pe
- angle_coeff @angle:c2-nf-px harmonic 80.57 117.75 # SOURCE3 5 same_as_c2-ne-px
- angle_coeff @angle:c2-nf-py harmonic 84.33 117.04 # SOURCE3 3 same_as_c2-ne-py
- angle_coeff @angle:c2-nf-sx harmonic 60.95 111.98 # SOURCE3 3 same_as_c2-ne-sx
- angle_coeff @angle:c2-nf-sy harmonic 61.78 118.92 # CORR 9
- angle_coeff @angle:ca-nf-ce harmonic 65.56 121.98 # CORR 15
- angle_coeff @angle:ca-nf-n2 harmonic 69.73 114.06 # CORR 11
- angle_coeff @angle:ca-nf-ne harmonic 69.69 115.12 # CORR 44
- angle_coeff @angle:ca-nf-o harmonic 71.10 113.96 # SOURCE3 3 same_as_ca-ne-o
- angle_coeff @angle:ca-nf-p2 harmonic 83.08 118.09 # SOURCE3 1 same_as_ca-ne-p2
- angle_coeff @angle:ca-nf-s harmonic 65.75 120.11 # SOURCE3 1 same_as_ca-ne-s
- angle_coeff @angle:c-nf-c2 harmonic 67.85 118.53 # CORR 6
- angle_coeff @angle:cf-nf-n2 harmonic 71.16 111.19 # SOURCE3 1 same_as_ce-ne-n2
- angle_coeff @angle:cf-nf-o harmonic 72.26 112.16 # SOURCE3 1 same_as_ce-ne-o
- angle_coeff @angle:cf-nf-p2 harmonic 83.85 117.02 # SOURCE3 1 same_as_ce-ne-p2
- angle_coeff @angle:cf-nf-s harmonic 67.15 116.28 # SOURCE3 1 same_as_ce-ne-s
- angle_coeff @angle:ch-nf-n1 harmonic 71.71 120.20 # SOURCE2 1 same_as_cg-ne-n1
- angle_coeff @angle:ch-nf-n2 harmonic 73.16 113.39 # SOURCE3 1 same_as_cg-ne-n2
- angle_coeff @angle:ch-nf-o harmonic 74.43 114.70 # SOURCE2 1 same_as_cg-ne-o
- angle_coeff @angle:ch-nf-p2 harmonic 84.75 119.57 # SOURCE3 1 same_as_cg-ne-p2
- angle_coeff @angle:ch-nf-s harmonic 68.28 117.70 # SOURCE3 1 same_as_cg-ne-s
- angle_coeff @angle:f-n-f harmonic 67.90 102.98 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-nf-n2 harmonic 78.59 107.22 # SOURCE3 1 same_as_n2-ne-n2
- angle_coeff @angle:n2-nf-nf harmonic 70.94 110.72 # SOURCE3 9 same_as_n2-ne-ne
- angle_coeff @angle:n2-nf-o harmonic 78.09 114.10 # SOURCE3 1 same_as_n2-ne-o
- angle_coeff @angle:n2-nf-p2 harmonic 91.59 109.66 # SOURCE3 1 same_as_n2-ne-p2
- angle_coeff @angle:n2-nf-pf harmonic 84.18 112.15 # SOURCE3 7 same_as_n2-ne-pe
- angle_coeff @angle:n2-nf-px harmonic 83.20 115.97 # SOURCE3 3 same_as_n2-ne-px
- angle_coeff @angle:n2-nf-py harmonic 87.34 114.60 # SOURCE3 3 same_as_n2-ne-py
- angle_coeff @angle:n2-nf-s harmonic 71.27 115.90 # SOURCE3 1 same_as_n2-ne-s
- angle_coeff @angle:n2-nf-sx harmonic 63.80 107.29 # SOURCE3 1 same_as_n2-ne-sx
- angle_coeff @angle:n2-nf-sy harmonic 65.46 111.21 # SOURCE3 1 same_as_n2-ne-sy
- angle_coeff @angle:nf-nf-o harmonic 72.28 110.45 # SOURCE3 10 same_as_ne-ne-o
- angle_coeff @angle:nf-nf-p2 harmonic 85.32 114.39 # SOURCE3 6 same_as_ne-ne-p2
- angle_coeff @angle:nf-nf-s harmonic 67.59 115.95 # SOURCE3 6 same_as_ne-ne-s
- angle_coeff @angle:o-nf-o harmonic 76.91 124.09 # SOURCE3 2 same_as_o-ne-o
- angle_coeff @angle:o-nf-pf harmonic 78.32 132.32 # SOURCE3 11 same_as_o-ne-pe
- angle_coeff @angle:o-nf-px harmonic 86.11 110.62 # SOURCE3 1 same_as_o-ne-px
- angle_coeff @angle:o-nf-py harmonic 90.01 110.79 # SOURCE3 4 same_as_o-ne-py
- angle_coeff @angle:o-nf-s harmonic 71.99 117.19 # SOURCE3 2 same_as_o-ne-s
- angle_coeff @angle:o-nf-sx harmonic 63.79 108.92 # SOURCE3 1 same_as_o-ne-sx
- angle_coeff @angle:o-nf-sy harmonic 66.05 111.34 # SOURCE3 1 same_as_o-ne-sy
- angle_coeff @angle:p2-nf-pf harmonic 104.56 116.81 # SOURCE3 1 same_as_p2-ne-pe
- angle_coeff @angle:p2-nf-px harmonic 100.10 128.35 # SOURCE3 1 same_as_p2-ne-px
- angle_coeff @angle:p2-nf-py harmonic 105.15 123.47 # SOURCE3 1 same_as_p2-ne-py
- angle_coeff @angle:p2-nf-sx harmonic 80.48 112.12 # SOURCE3 1 same_as_p2-ne-sx
- angle_coeff @angle:p2-nf-sy harmonic 81.80 115.73 # SOURCE3 1 same_as_p2-ne-sy
- angle_coeff @angle:pf-nf-s harmonic 83.52 115.73 # SOURCE3 1 same_as_pe-ne-s
- angle_coeff @angle:px-nf-s harmonic 78.54 131.84 # SOURCE3 1 same_as_px-ne-s
- angle_coeff @angle:py-nf-s harmonic 86.30 116.18 # SOURCE3 4 same_as_py-ne-s
- angle_coeff @angle:s-nf-s harmonic 68.65 120.87 # SOURCE3 1 same_as_s-ne-s
- angle_coeff @angle:s-nf-sx harmonic 63.66 112.96 # SOURCE3 1 same_as_s-ne-sx
- angle_coeff @angle:s-nf-sy harmonic 63.94 119.63 # SOURCE3 1 same_as_s-ne-sy
- angle_coeff @angle:br-nh-br harmonic 67.09 106.27 # SOURCE3 1
- angle_coeff @angle:br-nh-ca harmonic 62.04 111.88 # SOURCE3 1 0.0000
- angle_coeff @angle:br-nh-hn harmonic 42.11 101.56 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-nh-c1 harmonic 68.33 116.98 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-nh-c2 harmonic 66.36 122.71 # SOURCE4 5 1.0077
- angle_coeff @angle:c1-nh-ca harmonic 66.22 122.36 # SOURCE3 3 1.2016
- angle_coeff @angle:c1-nh-hn harmonic 49.55 117.30 # SOURCE4 8 0.7120
- angle_coeff @angle:c2-nh-c2 harmonic 65.54 124.50 # SOURCE4 43 1.7515
- angle_coeff @angle:c2-nh-c3 harmonic 63.17 123.71 # SOURCE3 8 3.5348
- angle_coeff @angle:c2-nh-ca harmonic 64.59 127.34 # SOURCE4 97 2.4321
- angle_coeff @angle:c2-nh-cc harmonic 64.92 126.03 # CORR 11
- angle_coeff @angle:c2-nh-cd harmonic 64.92 126.03 # CORR 11
- angle_coeff @angle:c2-nh-cx harmonic 63.08 124.44 # SOURCE4 10 1.6817
- angle_coeff @angle:c2-nh-hn harmonic 49.62 114.89 # SOURCE4 1000 1.4571
- angle_coeff @angle:c2-nh-n2 harmonic 68.36 120.00 # SOURCE4 33 1.1823
- angle_coeff @angle:c2-nh-n3 harmonic 67.57 116.98 # SOURCE4 14 1.4183
- angle_coeff @angle:c2-nh-no harmonic 66.09 125.63 # SOURCE4 7 0.7554
- angle_coeff @angle:c2-nh-oh harmonic 69.45 112.51 # SOURCE4 12 1.1687
- angle_coeff @angle:c2-nh-os harmonic 69.27 112.93 # SOURCE4 6 0.3945
- angle_coeff @angle:c2-nh-sy harmonic 61.76 121.13 # SOURCE4 10 0.5133
- angle_coeff @angle:c3-nh-c3 harmonic 63.53 114.44 # SOURCE4 523 2.1428
- angle_coeff @angle:c3-nh-ca harmonic 64.56 117.77 # SOURCE3 8 1.7521
- angle_coeff @angle:c3-nh-cc harmonic 64.17 119.23 # CORR 163
- angle_coeff @angle:c3-nh-cd harmonic 64.17 119.23 # CORR 163
- angle_coeff @angle:c3-nh-cf harmonic 63.47 119.92 # SOURCE4 20 1.8571
- angle_coeff @angle:c3-nh-cz harmonic 63.01 125.51 # SOURCE4 12 0.5177
- angle_coeff @angle:c3-nh-hn harmonic 46.46 114.95 # SOURCE3 19 2.4787
- angle_coeff @angle:c3-nh-n2 harmonic 67.89 112.35 # SOURCE3 9 4.0058
- angle_coeff @angle:c3-nh-n harmonic 67.10 111.71 # SOURCE4 6 2.4251
- angle_coeff @angle:c3-nh-na harmonic 66.92 112.43 # SOURCE4 8 1.4219
- angle_coeff @angle:c3-nh-p2 harmonic 77.12 123.35 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-nh-sy harmonic 61.91 116.12 # SOURCE4 13 1.2830
- angle_coeff @angle:ca-nh-ca harmonic 64.34 127.46 # SOURCE3 2 0.0002
- angle_coeff @angle:ca-nh-cc harmonic 63.77 129.77 # CORR 38
- angle_coeff @angle:ca-nh-cd harmonic 63.77 129.77 # CORR 38
- angle_coeff @angle:ca-nh-cl harmonic 57.67 113.15 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-nh-cx harmonic 63.11 123.63 # SOURCE4 36 0.5899
- angle_coeff @angle:ca-nh-f harmonic 67.90 106.09 # SOURCE3 3 1.0660
- angle_coeff @angle:ca-nh-hn harmonic 49.08 116.13 # SOURCE4 1780 1.2853
- angle_coeff @angle:ca-nh-i harmonic 55.55 117.83 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-nh-n1 harmonic 69.37 117.13 # HF/6-31G* 1
- angle_coeff @angle:ca-nh-n2 harmonic 67.82 121.11 # SOURCE4 19 0.9700
- angle_coeff @angle:ca-nh-n3 harmonic 68.18 114.21 # SOURCE3 6 2.2412
- angle_coeff @angle:ca-nh-n4 harmonic 68.56 108.94 # SOURCE3 5 0.6562
- angle_coeff @angle:ca-nh-n harmonic 68.07 116.15 # SOURCE4 12 0.8135
- angle_coeff @angle:ca-nh-na harmonic 68.58 114.54 # SOURCE3 8 0.7807
- angle_coeff @angle:ca-nh-nh harmonic 68.49 114.87 # SOURCE3 6 2.1432
- angle_coeff @angle:ca-nh-no harmonic 69.19 113.92 # SOURCE3 4 2.9561
- angle_coeff @angle:ca-nh-o harmonic 69.64 121.92 # SOURCE3 2 3.9630
- angle_coeff @angle:ca-nh-oh harmonic 69.15 112.80 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-nh-os harmonic 69.93 110.17 # SOURCE3 3 0.6448
- angle_coeff @angle:ca-nh-p2 harmonic 77.99 125.27 # SOURCE3 8 5.1798
- angle_coeff @angle:ca-nh-p3 harmonic 76.07 125.70 # SOURCE3 3 5.7796
- angle_coeff @angle:ca-nh-p4 harmonic 77.43 124.01 # SOURCE3 3 2.5810
- angle_coeff @angle:ca-nh-p5 harmonic 78.16 125.61 # SOURCE3 3 0.5287
- angle_coeff @angle:ca-nh-s4 harmonic 62.13 115.62 # SOURCE3 3 0.3434
- angle_coeff @angle:ca-nh-s6 harmonic 61.56 123.53 # SOURCE4 33 2.0385
- angle_coeff @angle:ca-nh-s harmonic 59.38 122.54 # SOURCE3 3 2.7001
- angle_coeff @angle:ca-nh-sh harmonic 61.78 121.41 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-nh-ss harmonic 61.75 121.50 # SOURCE3 3 2.6255
- angle_coeff @angle:ca-nh-sy harmonic 60.64 125.26 # SOURCE4 41 1.7517
- angle_coeff @angle:cc-nh-cx harmonic 63.09 123.72 # CORR 58
- angle_coeff @angle:cc-nh-hn harmonic 48.86 117.16 # SOURCE3 11 2.6137
- angle_coeff @angle:cc-nh-n2 harmonic 68.23 119.66 # SOURCE4 5 1.3903
- angle_coeff @angle:cc-nh-sy harmonic 61.22 122.91 # SOURCE4 23 1.2029
- angle_coeff @angle:cd-nh-cx harmonic 63.09 123.72 # CORR 58
- angle_coeff @angle:cd-nh-hn harmonic 48.86 117.16 # SOURCE3 11 2.6137
- angle_coeff @angle:ce-nh-hn harmonic 48.38 115.62 # CORR 203
- angle_coeff @angle:ce-nh-o harmonic 66.85 129.43 # CORR 2
- angle_coeff @angle:ce-nh-sy harmonic 63.58 112.97 # SOURCE4 7 1.0636
- angle_coeff @angle:cf-nh-hn harmonic 48.38 115.62 # CORR 203
- angle_coeff @angle:cf-nh-o harmonic 66.85 129.43 # CORR 2
- angle_coeff @angle:cl-nh-cl harmonic 54.43 106.60 # SOURCE3 1
- angle_coeff @angle:cl-nh-hn harmonic 40.07 104.14 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-nh-cx harmonic 86.53 62.02 # SOURCE4 45 0.6189
- angle_coeff @angle:cx-nh-hn harmonic 45.79 118.89 # SOURCE4 8 0.1391
- angle_coeff @angle:cz-nh-hn harmonic 48.79 121.24 # SOURCE4 40 0.5682
- angle_coeff @angle:f-nh-f harmonic 66.93 101.70 # SOURCE3 1 0.0000
- angle_coeff @angle:f-nh-hn harmonic 49.80 101.23 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-nh-hn harmonic 40.05 114.85 # SOURCE4 1108 2.0811
- angle_coeff @angle:hn-nh-i harmonic 36.55 107.57 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-nh-n1 harmonic 52.31 110.57 # HF/6-31G* 1
- angle_coeff @angle:hn-nh-n2 harmonic 50.08 118.22 # SOURCE4 75 2.3319
- angle_coeff @angle:hn-nh-n3 harmonic 50.05 109.12 # SOURCE3 5 2.3680
- angle_coeff @angle:hn-nh-n4 harmonic 49.69 104.40 # SOURCE3 3 0.5056
- angle_coeff @angle:hn-nh-n harmonic 50.89 107.96 # SOURCE4 16 1.2025
- angle_coeff @angle:hn-nh-na harmonic 50.95 107.91 # SOURCE3 26 1.5528
- angle_coeff @angle:hn-nh-nh harmonic 50.32 110.64 # SOURCE4 8 1.3390
- angle_coeff @angle:hn-nh-no harmonic 50.99 109.93 # SOURCE4 7 0.2027
- angle_coeff @angle:hn-nh-o harmonic 52.99 116.45 # SOURCE3 2 0.6063
- angle_coeff @angle:hn-nh-oh harmonic 51.13 106.55 # SOURCE4 8 0.4590
- angle_coeff @angle:hn-nh-os harmonic 51.51 104.76 # SOURCE3 3 0.4883
- angle_coeff @angle:hn-nh-p2 harmonic 54.38 118.18 # SOURCE3 21 3.6927
- angle_coeff @angle:hn-nh-p3 harmonic 53.06 116.19 # SOURCE3 3 3.0539
- angle_coeff @angle:hn-nh-p4 harmonic 54.74 112.60 # SOURCE3 3 0.8237
- angle_coeff @angle:hn-nh-p5 harmonic 55.35 115.26 # SOURCE3 3 0.9168
- angle_coeff @angle:hn-nh-s4 harmonic 43.06 107.48 # SOURCE3 3 1.3960
- angle_coeff @angle:hn-nh-s harmonic 40.81 114.37 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-nh-s6 harmonic 44.04 109.98 # SOURCE4 29 0.7478
- angle_coeff @angle:hn-nh-sh harmonic 43.27 112.25 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-nh-ss harmonic 42.95 113.89 # SOURCE3 3 1.4030
- angle_coeff @angle:hn-nh-sy harmonic 43.28 111.23 # SOURCE4 62 1.1413
- angle_coeff @angle:i-nh-i harmonic 59.80 115.82 # SOURCE3 1
- angle_coeff @angle:n1-nh-n1 harmonic 75.13 106.71 # HF/6-31G* 1
- angle_coeff @angle:n2-nh-n2 harmonic 70.76 117.50 # SOURCE3 2 1.1907
- angle_coeff @angle:n2-nh-n3 harmonic 69.63 115.54 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-nh-o harmonic 70.40 126.06 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-nh-n3 harmonic 69.52 110.98 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-nh-n4 harmonic 68.15 108.36 # SOURCE3 1 0.0000
- angle_coeff @angle:na-nh-na harmonic 70.14 112.01 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-hn harmonic 39.73 117.85 # SOURCE3 15 2.3694
- angle_coeff @angle:nh-nh-nh harmonic 70.07 112.23 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-i harmonic 36.08 117.24 # SOURCE3 2 0.4435
- angle_coeff @angle:hn-n-n2 harmonic 49.62 118.33 # SOURCE3 5 2.2377
- angle_coeff @angle:hn-n-n3 harmonic 48.69 117.22 # SOURCE4 37 1.3737
- angle_coeff @angle:hn-n-n4 harmonic 48.90 112.68 # SOURCE3 3 1.9746
- angle_coeff @angle:hn-n-n harmonic 50.14 113.12 # SOURCE3 7 3.2954
- angle_coeff @angle:hn-n-na harmonic 50.40 113.55 # SOURCE3 8 1.9324
- angle_coeff @angle:hn-n-nc harmonic 50.74 115.24 # SOURCE4 10 0.4966
- angle_coeff @angle:hn-n-nh harmonic 49.74 113.13 # SOURCE4 12 1.2125
- angle_coeff @angle:hn-n-no harmonic 48.71 110.11 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-o harmonic 53.83 116.32 # SOURCE3 2 0.0175
- angle_coeff @angle:n-nh-o harmonic 72.07 115.63 # SOURCE3 1
- angle_coeff @angle:hn-n-oh harmonic 50.33 110.71 # SOURCE4 46 1.1278
- angle_coeff @angle:no-nh-no harmonic 72.07 108.55 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-os harmonic 50.52 109.82 # SOURCE4 12 0.6996
- angle_coeff @angle:hn-n-p2 harmonic 52.51 118.05 # SOURCE3 7 3.0564
- angle_coeff @angle:hn-n-p3 harmonic 50.93 119.63 # SOURCE3 2 0.0000
- angle_coeff @angle:hn-n-p4 harmonic 53.00 115.71 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-p5 harmonic 54.50 113.20 # SOURCE4 6 1.0341
- angle_coeff @angle:hn-n-s4 harmonic 41.18 112.46 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-s harmonic 41.14 114.92 # SOURCE3 2 0.0260
- angle_coeff @angle:hn-n-s6 harmonic 43.06 112.18 # SOURCE4 6 0.6101
- angle_coeff @angle:hn-n-sh harmonic 42.19 114.91 # SOURCE3 1 0.0000
- angle_coeff @angle:hn-n-ss harmonic 42.36 115.60 # SOURCE3 3 0.6414
- angle_coeff @angle:hn-n-sy harmonic 43.02 112.34 # SOURCE4 38 0.6039
- angle_coeff @angle:oh-nh-oh harmonic 72.15 106.27 # SOURCE3 1
- angle_coeff @angle:o-nh-o harmonic 72.24 128.06 # SOURCE3 1
- angle_coeff @angle:os-nh-os harmonic 72.41 105.27 # SOURCE3 1
- angle_coeff @angle:p2-nh-p2 harmonic 98.07 127.33 # SOURCE3 2 2.7857
- angle_coeff @angle:p3-nh-p3 harmonic 96.03 125.08 # SOURCE3 1
- angle_coeff @angle:p5-nh-p5 harmonic 104.72 112.76 # SOURCE3 1
- angle_coeff @angle:s4-nh-s4 harmonic 62.56 112.39 # SOURCE3 1
- angle_coeff @angle:s6-nh-s6 harmonic 62.35 120.27 # SOURCE3 1
- angle_coeff @angle:sh-nh-sh harmonic 62.26 119.00 # SOURCE3 1
- angle_coeff @angle:s-nh-s harmonic 59.67 118.73 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-nh-ss harmonic 62.19 119.25 # SOURCE3 1
- angle_coeff @angle:i-n-i harmonic 60.66 118.20 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-n-n2 harmonic 70.16 116.89 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-n-n3 harmonic 68.02 117.94 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-n-n4 harmonic 68.42 112.69 # SOURCE3 1 0.0000
- angle_coeff @angle:na-n-na harmonic 69.61 117.38 # SOURCE3 1 0.0000
- angle_coeff @angle:nc-n-nc harmonic 71.04 116.41 # CORR 2
- angle_coeff @angle:nc-n-p2 harmonic 80.69 117.21 # CORR 2
- angle_coeff @angle:nc-n-pc harmonic 80.42 117.21 # CORR 2
- angle_coeff @angle:nd-n-nd harmonic 71.04 116.41 # CORR 2
- angle_coeff @angle:nd-n-p2 harmonic 80.69 117.21 # CORR 2
- angle_coeff @angle:nd-n-pd harmonic 80.42 117.21 # CORR 2
- angle_coeff @angle:nh-n-nh harmonic 69.10 115.18 # SOURCE3 1 0.0000
- angle_coeff @angle:n-n-n harmonic 69.89 114.62 # SOURCE3 1 0.0000
- angle_coeff @angle:no-n-no harmonic 68.52 108.66 # SOURCE3 1 0.0000
- angle_coeff @angle:br-no-o harmonic 58.48 113.19 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-no-o harmonic 71.34 116.63 # SOURCE3 6 0.0000
- angle_coeff @angle:c2-no-o harmonic 69.87 116.87 # SOURCE3 8 0.4200
- angle_coeff @angle:c3-no-o harmonic 66.96 116.56 # SOURCE3 6 0.3959
- angle_coeff @angle:ca-no-o harmonic 68.74 118.10 # SOURCE3 10 1.1524
- angle_coeff @angle:cc-no-o harmonic 70.34 117.52 # SOURCE4 198 0.6255
- angle_coeff @angle:cl-no-o harmonic 57.30 115.08 # SOURCE3 2 0.0000
- angle_coeff @angle:c-no-o harmonic 67.10 115.26 # SOURCE3 1
- angle_coeff @angle:hn-no-o harmonic 55.31 115.49 # SOURCE3 2 0.0000
- angle_coeff @angle:oh-n-oh harmonic 72.05 107.26 # SOURCE3 1 0.0000
- angle_coeff @angle:i-no-o harmonic 54.60 116.31 # SOURCE3 2 0.0000
- angle_coeff @angle:n1-no-o harmonic 73.78 115.00 # HF/6-31G* 1
- angle_coeff @angle:n2-no-o harmonic 65.79 115.10 # SOURCE2 2 2.4000
- angle_coeff @angle:n3-no-o harmonic 72.01 115.56 # SOURCE3 6 0.6427
- angle_coeff @angle:n4-no-o harmonic 72.87 109.00 # SOURCE3 2 0.0000
- angle_coeff @angle:na-no-o harmonic 72.24 115.49 # SOURCE3 18 0.5640
- angle_coeff @angle:nh-no-o harmonic 74.08 115.71 # SOURCE3 8 0.4811
- angle_coeff @angle:n-no-o harmonic 71.67 115.41 # SOURCE3 8 0.3748
- angle_coeff @angle:no-no-o harmonic 59.92 112.38 # SOURCE3 4 0.0000
- angle_coeff @angle:o-n-o harmonic 73.39 128.61 # SOURCE3 3 1.0626
- angle_coeff @angle:o-no-o harmonic 77.15 125.13 # SOURCE4 461 0.7605
- angle_coeff @angle:o-no-oh harmonic 74.09 114.70 # SOURCE3 2 0.0000
- angle_coeff @angle:o-no-os harmonic 73.71 114.01 # SOURCE3 8 0.9778
- angle_coeff @angle:o-no-p2 harmonic 82.07 117.38 # SOURCE3 20 0.8083
- angle_coeff @angle:o-no-p3 harmonic 77.73 116.78 # SOURCE3 6 0.4929
- angle_coeff @angle:o-no-p4 harmonic 76.69 116.64 # SOURCE3 6 0.0089
- angle_coeff @angle:o-no-p5 harmonic 78.18 116.69 # SOURCE3 8 0.4507
- angle_coeff @angle:o-no-s4 harmonic 57.15 114.49 # SOURCE3 6 0.5674
- angle_coeff @angle:o-no-s6 harmonic 57.79 114.39 # SOURCE3 6 0.8311
- angle_coeff @angle:o-no-s harmonic 64.05 119.81 # SOURCE3 4 0.0042
- angle_coeff @angle:o-no-sh harmonic 62.94 116.10 # SOURCE3 2 0.0000
- angle_coeff @angle:o-no-ss harmonic 62.27 115.58 # SOURCE3 6 0.5860
- angle_coeff @angle:os-n-os harmonic 72.28 106.53 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-n-p2 harmonic 98.03 119.62 # SOURCE3 1
- angle_coeff @angle:p3-n-p3 harmonic 100.67 108.73 # SOURCE3 3 0.2591
- angle_coeff @angle:p4-n-p4 harmonic 102.85 108.55 # SOURCE3 1
- angle_coeff @angle:p5-n-p5 harmonic 108.79 99.99 # SOURCE3 1
- angle_coeff @angle:pc-n-pc harmonic 97.64 119.62 # SOURCE3 1 0.0000
- angle_coeff @angle:pd-n-pd harmonic 97.64 119.62 # SOURCE3 1 same_as_pc-n-pc
- angle_coeff @angle:s4-n-s4 harmonic 61.03 113.75 # SOURCE3 1 0.0000
- angle_coeff @angle:s6-n-s6 harmonic 61.82 119.68 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-n-sh harmonic 61.53 119.03 # SOURCE3 1 0.0000
- angle_coeff @angle:s-n-s harmonic 58.48 126.00 # SOURCE3 1
- angle_coeff @angle:ss-n-ss harmonic 62.06 118.49 # SOURCE3 1 0.0000
- angle_coeff @angle:br-oh-ho harmonic 42.15 101.60 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-oh-ho harmonic 50.20 108.76 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-oh-ho harmonic 49.91 108.98 # SOURCE3 6 2.2379
- angle_coeff @angle:c3-oh-ho harmonic 47.09 108.16 # SOURCE3 42 1.3034
- angle_coeff @angle:ca-oh-ho harmonic 48.85 109.47 # SOURCE3 7 1.0405
- angle_coeff @angle:cc-oh-ho harmonic 49.96 107.06 # CORR 117
- angle_coeff @angle:cd-oh-ho harmonic 49.96 107.06 # CORR 117
- angle_coeff @angle:ce-oh-ho harmonic 49.85 106.95 # CORR 34
- angle_coeff @angle:cf-oh-ho harmonic 49.85 106.95 # CORR 34
- angle_coeff @angle:c-oh-ho harmonic 51.19 107.37 # SOURCE3 34 1.6830
- angle_coeff @angle:cl-oh-ho harmonic 40.51 102.40 # SOURCE2 1 0.0000
- angle_coeff @angle:cx-oh-ho harmonic 49.64 106.17 # SOURCE3 3 0.0644
- angle_coeff @angle:cy-oh-ho harmonic 47.62 107.32 # SOURCE4 5 0.4955
- angle_coeff @angle:f-oh-ho harmonic 48.47 96.80 # SOURCE2 1 0.0000
- angle_coeff @angle:ho-oh-ho harmonic 41.93 104.80 # SOURCE2 1 0.0000
- angle_coeff @angle:ho-oh-i harmonic 35.67 107.98 # SOURCE3 2 0.0000
- angle_coeff @angle:ho-oh-n1 harmonic 52.55 107.81 # HF/6-31G* 1
- angle_coeff @angle:ho-oh-n2 harmonic 50.57 102.74 # SOURCE3 9 2.1286
- angle_coeff @angle:ho-oh-n3 harmonic 50.61 102.33 # SOURCE3 5 1.2591
- angle_coeff @angle:ho-oh-n4 harmonic 49.44 106.63 # SOURCE3 3 0.2770
- angle_coeff @angle:ho-oh-n harmonic 50.46 101.03 # SOURCE3 6 1.4086
- angle_coeff @angle:ho-oh-na harmonic 50.24 103.71 # SOURCE3 9 1.2590
- angle_coeff @angle:ho-oh-nh harmonic 49.97 102.42 # SOURCE4 15 0.6819
- angle_coeff @angle:ho-oh-no harmonic 50.31 102.17 # SOURCE3 1 0.0000
- angle_coeff @angle:ho-oh-o harmonic 47.26 100.87 # SOURCE3 1
- angle_coeff @angle:ho-oh-oh harmonic 49.34 98.72 # SOURCE3 2 0.0000
- angle_coeff @angle:ho-oh-os harmonic 49.58 99.69 # SOURCE4 18 0.3384
- angle_coeff @angle:ho-oh-p2 harmonic 55.87 109.45 # SOURCE3 8 3.3491
- angle_coeff @angle:ho-oh-p3 harmonic 53.84 110.64 # SOURCE3 3 0.5191
- angle_coeff @angle:ho-oh-p4 harmonic 55.27 110.19 # SOURCE3 4 0.2372
- angle_coeff @angle:ho-oh-p5 harmonic 55.88 110.14 # SOURCE3 92 3.8033
- angle_coeff @angle:ho-oh-py harmonic 56.18 110.73 # SOURCE3 79 1.7835
- angle_coeff @angle:ho-oh-s4 harmonic 42.77 106.76 # SOURCE4 9 0.4035
- angle_coeff @angle:ho-oh-s harmonic 40.86 100.15 # SOURCE3 2 0.0000
- angle_coeff @angle:ho-oh-s6 harmonic 45.46 109.20 # SOURCE3 13 0.1856
- angle_coeff @angle:ho-oh-sh harmonic 42.97 106.24 # SOURCE3 2 0.0661
- angle_coeff @angle:ho-oh-ss harmonic 43.10 107.06 # SOURCE3 4 0.9967
- angle_coeff @angle:ho-oh-sy harmonic 44.20 106.41 # SOURCE4 33 0.3729
- angle_coeff @angle:br-os-br harmonic 65.08 110.63 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-os-c1 harmonic 66.99 115.02 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-os-c3 harmonic 64.47 113.39 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-os-c2 harmonic 65.95 113.14 # SOURCE3 6 2.1932
- angle_coeff @angle:c2-os-c3 harmonic 64.21 112.09 # SOURCE3 7 4.1809
- angle_coeff @angle:c2-os-ca harmonic 65.43 113.59 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-os-n2 harmonic 64.91 118.13 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-os-na harmonic 68.21 103.85 # SOURCE3 4 0.6297
- angle_coeff @angle:c2-os-os harmonic 68.35 102.77 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-os-p5 harmonic 77.31 126.37 # SOURCE4 7 1.7939
- angle_coeff @angle:c2-os-ss harmonic 63.08 108.13 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-os-c3 harmonic 62.39 112.45 # SOURCE4 1293 1.6468
- angle_coeff @angle:c3-os-ca harmonic 62.27 117.97 # SOURCE4 2495 1.4576
- angle_coeff @angle:c3-os-cc harmonic 62.50 117.33 # CORR 248
- angle_coeff @angle:c3-os-cd harmonic 62.50 117.33 # CORR 248
- angle_coeff @angle:c3-os-ce harmonic 62.79 116.05 # CORR 37
- angle_coeff @angle:c3-os-cf harmonic 62.79 116.05 # CORR 37
- angle_coeff @angle:c3-os-cl harmonic 56.20 110.50 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-os-cy harmonic 61.67 115.65 # SOURCE4 5 0.2390
- angle_coeff @angle:c3-os-i harmonic 54.88 113.70 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-os-n1 harmonic 66.31 113.50 # HF/6-31G* 1
- angle_coeff @angle:c3-os-n2 harmonic 65.92 108.12 # SOURCE3 7 0.3048
- angle_coeff @angle:c3-os-n3 harmonic 64.52 110.28 # SOURCE4 14 1.9026
- angle_coeff @angle:c3-os-n4 harmonic 64.88 110.50 # SOURCE3 3 0.5426
- angle_coeff @angle:c3-os-n harmonic 65.40 109.52 # SOURCE4 14 0.6827
- angle_coeff @angle:c3-os-na harmonic 64.54 109.91 # SOURCE3 9 1.8268
- angle_coeff @angle:c3-os-nc harmonic 64.80 112.73 # SOURCE3 2 1.0358
- angle_coeff @angle:c3-os-nd harmonic 64.80 112.73 # SOURCE3 2 same_as_c3-os-nc
- angle_coeff @angle:c3-os-nh harmonic 65.22 109.69 # SOURCE4 8 0.1662
- angle_coeff @angle:c3-os-no harmonic 63.89 113.80 # SOURCE4 42 0.2726
- angle_coeff @angle:c3-os-o harmonic 65.62 103.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-os-oh harmonic 65.24 107.97 # SOURCE4 11 0.4333
- angle_coeff @angle:c3-os-os harmonic 65.89 105.01 # SOURCE3 7 0.6328
- angle_coeff @angle:c3-os-p2 harmonic 80.24 115.47 # SOURCE3 8 2.6374
- angle_coeff @angle:c3-os-p3 harmonic 76.51 115.97 # SOURCE3 3 0.3597
- angle_coeff @angle:c3-os-p4 harmonic 77.59 117.48 # SOURCE3 4 0.3850
- angle_coeff @angle:c3-os-p5 harmonic 78.48 118.00 # SOURCE3 31 1.2882
- angle_coeff @angle:c3-os-py harmonic 78.07 117.80 # SOURCE3 16 0.9654
- angle_coeff @angle:c3-os-s4 harmonic 61.32 111.50 # SOURCE3 6 1.4240
- angle_coeff @angle:c3-os-s6 harmonic 63.21 115.79 # SOURCE4 60 1.2588
- angle_coeff @angle:c3-os-s harmonic 59.28 109.55 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-os-sh harmonic 61.67 112.82 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-os-ss harmonic 60.74 113.19 # SOURCE3 3 0.2455
- angle_coeff @angle:ca-os-ca harmonic 63.31 119.95 # SOURCE4 107 1.6535
- angle_coeff @angle:ca-os-cc harmonic 67.21 106.65 # CORR 62
- angle_coeff @angle:ca-os-cd harmonic 67.21 106.65 # CORR 62
- angle_coeff @angle:ca-os-n3 harmonic 65.39 112.19 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-os-na harmonic 66.47 108.24 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-os-nc harmonic 66.09 113.68 # SOURCE3 2
- angle_coeff @angle:ca-os-nd harmonic 66.09 113.68 # SOURCE3 2
- angle_coeff @angle:ca-os-p5 harmonic 77.96 123.42 # SOURCE4 54 1.1358
- angle_coeff @angle:ca-os-s6 harmonic 63.95 116.97 # SOURCE4 15 0.9514
- angle_coeff @angle:c-os-c2 harmonic 64.91 118.02 # SOURCE4 7 0.3666
- angle_coeff @angle:c-os-c3 harmonic 63.63 115.14 # SOURCE3 17 1.8967
- angle_coeff @angle:c-os-c harmonic 64.54 120.64 # SOURCE4 7 1.5114
- angle_coeff @angle:c-os-ca harmonic 63.75 120.87 # SOURCE4 257 1.7209
- angle_coeff @angle:c-os-cc harmonic 64.15 119.62 # SOURCE3 5 6.0675
- angle_coeff @angle:cc-os-cc harmonic 67.27 106.69 # CORR 252
- angle_coeff @angle:cc-os-cd harmonic 63.80 118.62 # SOURCE4 14 1.9764
- angle_coeff @angle:c-os-cd harmonic 64.15 119.62 # SOURCE3 5 6.0675
- angle_coeff @angle:cc-os-na harmonic 65.51 111.66 # SOURCE3 28 4.1343
- angle_coeff @angle:cc-os-nc harmonic 68.12 107.23 # SOURCE3 6 2.7507
- angle_coeff @angle:cc-os-os harmonic 66.27 108.47 # SOURCE3 2 0.0000
- angle_coeff @angle:cc-os-ss harmonic 59.85 119.59 # SOURCE3 1 0.0000
- angle_coeff @angle:c-os-cy harmonic 71.75 91.10 # SOURCE3 2 0.0155
- angle_coeff @angle:cd-os-cd harmonic 67.27 106.69 # CORR 252
- angle_coeff @angle:cd-os-na harmonic 65.51 111.66 # SOURCE3 28 4.1343
- angle_coeff @angle:cd-os-nd harmonic 68.12 107.23 # SOURCE3 6 2.7507
- angle_coeff @angle:cd-os-os harmonic 66.27 108.47 # SOURCE3 2 same_as_cc-os-os
- angle_coeff @angle:cd-os-ss harmonic 59.85 119.59 # SOURCE3 1 same_as_cc-os-ss
- angle_coeff @angle:cl-os-cl harmonic 52.29 110.76 # SOURCE3 2 0.0000
- angle_coeff @angle:c-os-n2 harmonic 66.95 112.08 # SOURCE4 6 0.1154
- angle_coeff @angle:c-os-n harmonic 66.83 112.10 # SOURCE4 6 0.6163
- angle_coeff @angle:c-os-oh harmonic 66.50 110.50 # SOURCE3 1 0.0000
- angle_coeff @angle:c-os-os harmonic 66.25 110.28 # SOURCE4 10 1.3612
- angle_coeff @angle:c-os-p5 harmonic 78.89 122.10 # SOURCE4 5 0.5870
- angle_coeff @angle:c-os-sy harmonic 61.85 113.49 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-os-cx harmonic 85.27 61.82 # SOURCE4 107 0.1793
- angle_coeff @angle:cx-os-n harmonic 88.98 59.99 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-os-os harmonic 90.38 56.52 # SOURCE3 2 0.0000
- angle_coeff @angle:cy-os-cy harmonic 68.81 93.40 # SOURCE2 2 1.4000
- angle_coeff @angle:f-os-f harmonic 63.94 103.30 # SOURCE2 1 0.0000
- angle_coeff @angle:f-os-os harmonic 63.94 109.50 # SOURCE2 1 0.0000
- angle_coeff @angle:i-os-i harmonic 58.06 115.67 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-os-n1 harmonic 70.28 117.79 # HF/6-31G* 1
- angle_coeff @angle:n2-os-n2 harmonic 68.76 106.83 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-os-s6 harmonic 66.63 111.30 # SOURCE4 7 0.5651
- angle_coeff @angle:n3-os-n3 harmonic 67.76 104.88 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-os-n4 harmonic 65.66 114.68 # SOURCE3 1 0.0000
- angle_coeff @angle:na-os-na harmonic 66.10 109.59 # SOURCE3 1 0.0000
- angle_coeff @angle:na-os-ss harmonic 64.75 104.34 # SOURCE3 1 0.0000
- angle_coeff @angle:nc-os-nc harmonic 68.17 110.40 # SOURCE2 1 0.0000
- angle_coeff @angle:nc-os-ss harmonic 63.38 110.97 # SOURCE3 1 0.0000
- angle_coeff @angle:nd-os-nd harmonic 68.17 110.40 # SOURCE2 1 same_as_nc-os-nc
- angle_coeff @angle:nd-os-ss harmonic 63.38 110.97 # SOURCE3 1 same_as_nc-os-ss
- angle_coeff @angle:nh-os-nh harmonic 67.81 108.29 # SOURCE3 1 0.0000
- angle_coeff @angle:n-os-n harmonic 68.08 108.31 # SOURCE3 1 0.0000
- angle_coeff @angle:no-os-no harmonic 66.40 111.86 # SOURCE3 1 0.0000
- angle_coeff @angle:n-os-s6 harmonic 65.87 113.62 # SOURCE4 5 0.0928
- angle_coeff @angle:o-os-o harmonic 62.76 114.68 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-os-p2 harmonic 103.59 120.02 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-os-p5 harmonic 108.26 107.86 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-os-p3 harmonic 96.17 121.22 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-os-py harmonic 105.11 105.58 # SOURCE3 1 0.0000
- angle_coeff @angle:p5-os-p5 harmonic 99.18 126.25 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-os-s4 harmonic 62.09 111.63 # SOURCE3 1 0.0000
- angle_coeff @angle:s6-os-s6 harmonic 64.77 119.07 # SOURCE3 2 0.4318
- angle_coeff @angle:sh-os-sh harmonic 61.15 118.95 # SOURCE3 1 0.0000
- angle_coeff @angle:s-os-s harmonic 56.98 118.08 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-os-ss harmonic 60.82 115.64 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p2-br harmonic 40.68 108.60 # SOURCE3 1
- angle_coeff @angle:br-p2-c2 harmonic 39.43 102.32 # SOURCE3 2 0.0146
- angle_coeff @angle:br-p2-n2 harmonic 40.42 103.33 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p2-o harmonic 39.43 110.87 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p2-p2 harmonic 50.16 115.46 # SOURCE3 4 7.8622
- angle_coeff @angle:br-p2-s harmonic 40.59 110.52 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-p2-c1 harmonic 39.20 99.04 # SOURCE3 1
- angle_coeff @angle:c1-p2-c2 harmonic 39.82 101.29 # SOURCE3 1
- angle_coeff @angle:c1-p2-n2 harmonic 41.36 101.79 # SOURCE3 1
- angle_coeff @angle:c1-p2-o harmonic 41.32 107.62 # SOURCE3 1
- angle_coeff @angle:c1-p2-p2 harmonic 53.31 99.54 # SOURCE3 1
- angle_coeff @angle:c1-p2-s harmonic 41.00 105.90 # SOURCE3 1
- angle_coeff @angle:c2-p2-c2 harmonic 40.45 104.50 # SOURCE3 1
- angle_coeff @angle:c2-p2-c3 harmonic 38.60 101.90 # SOURCE3 4 0.1132
- angle_coeff @angle:c2-p2-ca harmonic 38.79 101.95 # SOURCE3 1
- angle_coeff @angle:c2-p2-cl harmonic 35.61 102.72 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-p2-f harmonic 41.60 103.47 # SOURCE3 2 0.0136
- angle_coeff @angle:c2-p2-hp harmonic 30.13 97.19 # SOURCE3 3 0.0216
- angle_coeff @angle:c2-p2-i harmonic 33.85 101.94 # SOURCE3 2 0.0368
- angle_coeff @angle:c2-p2-n2 harmonic 43.20 99.88 # SOURCE3 1
- angle_coeff @angle:c2-p2-n3 harmonic 41.99 101.80 # SOURCE3 1
- angle_coeff @angle:c2-p2-n4 harmonic 39.07 98.26 # SOURCE3 6 0.1522
- angle_coeff @angle:c2-p2-n harmonic 40.89 103.28 # SOURCE3 4 3.3113
- angle_coeff @angle:c2-p2-na harmonic 40.54 103.99 # SOURCE3 8 1.6834
- angle_coeff @angle:c2-p2-nh harmonic 41.20 105.17 # SOURCE3 8 0.8263
- angle_coeff @angle:c2-p2-no harmonic 41.91 97.97 # SOURCE3 3 0.4175
- angle_coeff @angle:c2-p2-o harmonic 41.51 115.16 # SOURCE3 1
- angle_coeff @angle:c2-p2-oh harmonic 42.50 102.89 # SOURCE3 3 0.8191
- angle_coeff @angle:c2-p2-os harmonic 43.35 102.12 # SOURCE3 4 0.8783
- angle_coeff @angle:c2-p2-p2 harmonic 54.72 99.56 # SOURCE3 1
- angle_coeff @angle:c2-p2-p3 harmonic 48.11 99.27 # SOURCE3 4 1.1590
- angle_coeff @angle:c2-p2-p4 harmonic 48.19 96.94 # SOURCE3 1
- angle_coeff @angle:c2-p2-p5 harmonic 48.01 97.61 # SOURCE3 1
- angle_coeff @angle:c2-p2-s4 harmonic 38.27 95.15 # SOURCE3 1
- angle_coeff @angle:c2-p2-s6 harmonic 38.35 95.51 # SOURCE3 1
- angle_coeff @angle:c2-p2-s harmonic 42.19 105.53 # SOURCE3 1
- angle_coeff @angle:c2-p2-sh harmonic 40.19 101.49 # SOURCE3 3 0.0057
- angle_coeff @angle:c2-p2-ss harmonic 40.19 101.81 # SOURCE3 4 0.5883
- angle_coeff @angle:c3-p2-c3 harmonic 37.36 99.30 # SOURCE3 1
- angle_coeff @angle:c3-p2-n2 harmonic 40.30 100.82 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p2-o harmonic 40.10 106.72 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p2-os harmonic 40.68 101.34 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p2-p2 harmonic 51.78 100.48 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p2-s harmonic 40.04 105.68 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-p2-ca harmonic 37.59 99.70 # SOURCE3 1
- angle_coeff @angle:ca-p2-n2 harmonic 40.53 100.82 # SOURCE3 1
- angle_coeff @angle:ca-p2-n harmonic 41.68 89.97 # SOURCE3 1
- angle_coeff @angle:ca-p2-na harmonic 41.69 89.21 # SOURCE3 1
- angle_coeff @angle:ca-p2-o harmonic 40.31 106.88 # SOURCE3 1
- angle_coeff @angle:ca-p2-s harmonic 39.79 107.93 # SOURCE3 1
- angle_coeff @angle:c-p2-c2 harmonic 38.89 97.30 # SOURCE3 1
- angle_coeff @angle:c-p2-c harmonic 38.29 90.10 # SOURCE3 1
- angle_coeff @angle:ce-p2-o harmonic 40.63 107.44 # SOURCE3 1
- angle_coeff @angle:ce-p2-s harmonic 40.55 105.54 # SOURCE3 1
- angle_coeff @angle:cf-p2-o harmonic 40.63 107.44 # SOURCE3 1 same_as_ce-p2-o
- angle_coeff @angle:cf-p2-s harmonic 40.55 105.54 # SOURCE3 1 same_as_ce-p2-s
- angle_coeff @angle:cl-p2-cl harmonic 32.00 108.70 # SOURCE3 1
- angle_coeff @angle:cl-p2-n2 harmonic 36.67 103.38 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-p2-o harmonic 36.00 110.57 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-p2-p2 harmonic 47.78 103.11 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-p2-s harmonic 36.62 110.11 # SOURCE3 1 0.0000
- angle_coeff @angle:f-p2-f harmonic 42.20 107.10 # SOURCE3 1
- angle_coeff @angle:f-p2-n2 harmonic 43.59 103.57 # SOURCE3 1 0.0000
- angle_coeff @angle:f-p2-o harmonic 43.81 110.61 # SOURCE3 1 0.0000
- angle_coeff @angle:f-p2-p2 harmonic 54.54 103.48 # SOURCE3 1 0.0000
- angle_coeff @angle:f-p2-s harmonic 41.15 114.71 # SOURCE3 2 5.2794
- angle_coeff @angle:hp-p2-hp harmonic 22.84 98.76 # SOURCE3 1
- angle_coeff @angle:hp-p2-n1 harmonic 31.08 95.18 # SOURCE3 2 1.5708
- angle_coeff @angle:hp-p2-n2 harmonic 32.08 95.54 # SOURCE3 19 4.7352
- angle_coeff @angle:hp-p2-ne harmonic 31.94 100.10 # SOURCE3 14 6.1290
- angle_coeff @angle:hp-p2-nf harmonic 31.94 100.10 # SOURCE3 14 same_as_hp-p2-ne
- angle_coeff @angle:hp-p2-o harmonic 32.04 105.58 # SOURCE3 1 0.0000
- angle_coeff @angle:hp-p2-p2 harmonic 38.16 101.88 # SOURCE3 27 12.9535
- angle_coeff @angle:hp-p2-p4 harmonic 32.69 94.51 # SOURCE3 1 0.0000
- angle_coeff @angle:hp-p2-p5 harmonic 33.66 89.07 # SOURCE3 1 0.0000
- angle_coeff @angle:hp-p2-pe harmonic 37.56 97.25 # SOURCE3 16 8.8916
- angle_coeff @angle:hp-p2-pf harmonic 37.56 97.25 # SOURCE3 16 same_as_hp-p2-pe
- angle_coeff @angle:hp-p2-s4 harmonic 26.33 89.99 # SOURCE3 1 0.0000
- angle_coeff @angle:hp-p2-s harmonic 30.26 102.52 # SOURCE3 1 0.0000
- angle_coeff @angle:hp-p2-s6 harmonic 26.74 88.13 # SOURCE3 1 0.0000
- angle_coeff @angle:i-p2-i harmonic 35.75 104.16 # SOURCE3 1
- angle_coeff @angle:i-p2-n2 harmonic 34.63 101.77 # SOURCE3 1 0.0000
- angle_coeff @angle:i-p2-o harmonic 33.34 109.51 # SOURCE3 1 0.0000
- angle_coeff @angle:i-p2-p2 harmonic 46.22 102.63 # SOURCE3 1 0.0000
- angle_coeff @angle:i-p2-s harmonic 35.18 110.60 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-p2-n1 harmonic 46.52 86.22 # HF/6-31G* 1
- angle_coeff @angle:n2-p2-n2 harmonic 45.62 98.00 # SOURCE3 1
- angle_coeff @angle:n2-p2-n3 harmonic 44.14 100.42 # SOURCE3 1
- angle_coeff @angle:n2-p2-n4 harmonic 41.53 93.42 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-na harmonic 42.63 102.03 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-nh harmonic 43.69 101.87 # SOURCE3 2 0.8491
- angle_coeff @angle:n2-p2-no harmonic 43.64 98.12 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-o harmonic 43.53 115.34 # SOURCE3 1
- angle_coeff @angle:n2-p2-oh harmonic 43.02 109.72 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-os harmonic 45.35 102.29 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-p3 harmonic 49.55 99.51 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-p4 harmonic 48.48 101.73 # SOURCE3 1
- angle_coeff @angle:n2-p2-p5 harmonic 50.50 93.68 # SOURCE3 1
- angle_coeff @angle:n2-p2-s4 harmonic 38.89 97.83 # SOURCE3 1
- angle_coeff @angle:n2-p2-s6 harmonic 38.99 98.14 # SOURCE3 1
- angle_coeff @angle:n2-p2-s harmonic 42.45 112.94 # SOURCE3 1
- angle_coeff @angle:n2-p2-sh harmonic 41.75 100.82 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-p2-ss harmonic 41.64 101.76 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-p2-n3 harmonic 42.10 106.30 # SOURCE3 1
- angle_coeff @angle:n3-p2-o harmonic 44.16 106.83 # SOURCE3 1
- angle_coeff @angle:n3-p2-p2 harmonic 55.78 100.58 # SOURCE3 1
- angle_coeff @angle:n3-p2-s harmonic 43.18 105.75 # SOURCE3 1
- angle_coeff @angle:n4-p2-n4 harmonic 39.61 88.80 # SOURCE3 1
- angle_coeff @angle:n4-p2-o harmonic 40.67 101.36 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-p2-p2 harmonic 52.72 96.53 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-p2-s harmonic 40.06 104.98 # SOURCE3 1 0.0000
- angle_coeff @angle:na-p2-na harmonic 40.23 106.10 # SOURCE3 1
- angle_coeff @angle:na-p2-o harmonic 42.71 107.46 # SOURCE3 1 0.0000
- angle_coeff @angle:na-p2-s harmonic 41.81 108.15 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-p2-o harmonic 45.72 107.71 # SOURCE3 1
- angle_coeff @angle:ne-p2-s harmonic 44.34 105.50 # SOURCE3 1
- angle_coeff @angle:nf-p2-o harmonic 45.72 107.71 # SOURCE3 1 same_as_ne-p2-o
- angle_coeff @angle:nf-p2-s harmonic 44.34 105.50 # SOURCE3 1 same_as_ne-p2-s
- angle_coeff @angle:nh-p2-nh harmonic 42.33 104.00 # SOURCE3 1
- angle_coeff @angle:nh-p2-o harmonic 43.75 108.11 # SOURCE3 2 0.6773
- angle_coeff @angle:nh-p2-p2 harmonic 53.77 107.73 # SOURCE3 3 3.1678
- angle_coeff @angle:nh-p2-s harmonic 42.31 109.62 # SOURCE3 2 1.7725
- angle_coeff @angle:n-p2-n2 harmonic 43.55 98.85 # SOURCE3 1 0.0000
- angle_coeff @angle:n-p2-o harmonic 43.46 105.08 # SOURCE3 1 0.0000
- angle_coeff @angle:no-p2-no harmonic 42.08 98.20 # SOURCE3 1
- angle_coeff @angle:no-p2-o harmonic 43.42 104.87 # SOURCE3 1 0.0000
- angle_coeff @angle:no-p2-p2 harmonic 52.75 108.57 # SOURCE3 3 8.2121
- angle_coeff @angle:no-p2-s harmonic 41.76 109.06 # SOURCE3 2 5.4074
- angle_coeff @angle:n-p2-p2 harmonic 54.46 102.12 # SOURCE3 1 0.0000
- angle_coeff @angle:n-p2-s harmonic 41.20 112.34 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-p2-oh harmonic 44.96 100.10 # SOURCE3 1
- angle_coeff @angle:oh-p2-p2 harmonic 54.71 107.82 # SOURCE3 2 2.6708
- angle_coeff @angle:oh-p2-s harmonic 43.05 109.75 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p2-o harmonic 44.39 119.96 # SOURCE3 1
- angle_coeff @angle:o-p2-oh harmonic 44.33 110.46 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p2-os harmonic 45.59 108.81 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p2-p2 harmonic 54.57 114.23 # SOURCE3 1
- angle_coeff @angle:o-p2-p3 harmonic 48.45 106.69 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p2-p4 harmonic 48.42 104.37 # SOURCE3 1
- angle_coeff @angle:o-p2-p5 harmonic 48.37 104.49 # SOURCE3 1
- angle_coeff @angle:o-p2-pe harmonic 46.73 145.96 # SOURCE3 1
- angle_coeff @angle:o-p2-pf harmonic 46.73 145.96 # SOURCE3 1 same_as_o-p2-pe
- angle_coeff @angle:o-p2-s4 harmonic 37.68 106.59 # SOURCE3 1
- angle_coeff @angle:o-p2-s6 harmonic 38.12 105.04 # SOURCE3 1
- angle_coeff @angle:o-p2-s harmonic 42.77 117.42 # SOURCE3 1
- angle_coeff @angle:o-p2-sh harmonic 40.81 109.60 # SOURCE3 1 0.0000
- angle_coeff @angle:os-p2-os harmonic 47.01 98.30 # SOURCE3 1
- angle_coeff @angle:os-p2-p2 harmonic 57.14 101.46 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p2-ss harmonic 40.89 109.60 # SOURCE3 1 0.0000
- angle_coeff @angle:os-p2-s harmonic 43.89 108.47 # SOURCE3 3 1.7065
- angle_coeff @angle:p2-p2-n2 harmonic 57.57 97.40 # SOURCE3 1
- angle_coeff @angle:p2-p2-p3 harmonic 64.09 101.73 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-p2-p4 harmonic 63.42 101.98 # SOURCE3 1
- angle_coeff @angle:p2-p2-p5 harmonic 64.24 99.33 # SOURCE3 1
- angle_coeff @angle:p2-p2-s4 harmonic 51.53 95.73 # SOURCE3 1
- angle_coeff @angle:p2-p2-s6 harmonic 51.64 95.95 # SOURCE3 1
- angle_coeff @angle:p2-p2-s harmonic 54.52 111.28 # SOURCE3 1
- angle_coeff @angle:p2-p2-sh harmonic 50.78 113.94 # SOURCE3 3 8.5009
- angle_coeff @angle:p3-p2-p3 harmonic 59.88 101.00 # SOURCE3 1
- angle_coeff @angle:p3-p2-s harmonic 48.09 113.28 # SOURCE3 2 6.7035
- angle_coeff @angle:p4-p2-s harmonic 49.75 103.89 # SOURCE3 1
- angle_coeff @angle:p5-p2-p5 harmonic 62.82 89.40 # SOURCE3 1
- angle_coeff @angle:p5-p2-s harmonic 50.38 101.21 # SOURCE3 1
- angle_coeff @angle:pe-p2-s harmonic 54.45 106.35 # SOURCE3 1
- angle_coeff @angle:pf-p2-s harmonic 54.45 106.35 # SOURCE3 1 same_as_pe-p2-s
- angle_coeff @angle:s4-p2-s4 harmonic 39.97 85.30 # SOURCE3 1
- angle_coeff @angle:s6-p2-s6 harmonic 37.42 98.20 # SOURCE3 1
- angle_coeff @angle:sh-p2-sh harmonic 41.33 98.50 # SOURCE3 1
- angle_coeff @angle:s-p2-s harmonic 44.19 106.60 # SOURCE3 1
- angle_coeff @angle:s-p2-s4 harmonic 38.90 105.29 # SOURCE3 1
- angle_coeff @angle:s-p2-s6 harmonic 38.73 106.93 # SOURCE3 1
- angle_coeff @angle:s-p2-sh harmonic 40.82 110.73 # SOURCE3 2 0.0232
- angle_coeff @angle:s-p2-ss harmonic 40.27 114.14 # SOURCE3 4 5.9223
- angle_coeff @angle:ss-p2-ss harmonic 41.56 97.90 # SOURCE3 1
- angle_coeff @angle:br-p3-br harmonic 41.27 103.54 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p3-hp harmonic 26.94 96.36 # SOURCE3 4 0.6701
- angle_coeff @angle:c1-p3-c1 harmonic 38.48 100.50 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-p3-f harmonic 40.73 96.90 # SOURCE2 1 0.0000
- angle_coeff @angle:c1-p3-hp harmonic 28.14 97.67 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-p3-c2 harmonic 37.32 101.77 # SOURCE3 3 0.0000
- angle_coeff @angle:c2-p3-hp harmonic 27.57 97.85 # SOURCE3 4 0.0000
- angle_coeff @angle:c3-p3-c3 harmonic 37.51 99.66 # SOURCE3 40 0.9854
- angle_coeff @angle:c3-p3-ca harmonic 37.29 101.94 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-p3-cl harmonic 35.74 99.89 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p3-f harmonic 39.74 97.80 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-p3-hp harmonic 27.47 97.66 # SOURCE3 9 0.4096
- angle_coeff @angle:c3-p3-n2 harmonic 39.87 96.55 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-p3-n3 harmonic 39.28 101.18 # SOURCE3 10 2.2338
- angle_coeff @angle:c3-p3-n4 harmonic 38.58 96.94 # SOURCE3 6 0.4815
- angle_coeff @angle:c3-p3-n harmonic 38.78 101.77 # SOURCE3 12 2.4449
- angle_coeff @angle:c3-p3-na harmonic 39.16 100.17 # SOURCE3 4 0.0554
- angle_coeff @angle:c3-p3-nh harmonic 38.65 104.50 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-p3-no harmonic 38.96 96.98 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-p3-o harmonic 39.33 111.67 # SOURCE3 28 5.3387
- angle_coeff @angle:c3-p3-oh harmonic 40.60 98.21 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-p3-os harmonic 40.25 99.53 # SOURCE3 3 1.7678
- angle_coeff @angle:c3-p3-p3 harmonic 45.77 100.31 # SOURCE3 18 2.1836
- angle_coeff @angle:c3-p3-p5 harmonic 45.65 100.90 # SOURCE3 10 2.7070
- angle_coeff @angle:c3-p3-s4 harmonic 37.94 98.88 # SOURCE3 8 6.2235
- angle_coeff @angle:c3-p3-s6 harmonic 37.62 101.18 # SOURCE3 12 6.4536
- angle_coeff @angle:c3-p3-sh harmonic 37.43 98.71 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-p3-ss harmonic 37.44 99.37 # SOURCE3 2 0.0000
- angle_coeff @angle:ca-p3-ca harmonic 37.89 99.86 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-p3-hp harmonic 27.74 97.50 # SOURCE3 2 0.0000
- angle_coeff @angle:c-p3-c3 harmonic 37.60 97.06 # SOURCE3 3 1.1490
- angle_coeff @angle:c-p3-c harmonic 36.51 100.90 # SOURCE3 1 0.0000
- angle_coeff @angle:c-p3-hp harmonic 27.15 96.55 # SOURCE3 6 0.5223
- angle_coeff @angle:cl-p3-cl harmonic 33.91 102.82 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-p3-f harmonic 37.03 99.20 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-p3-hp harmonic 25.67 96.30 # SOURCE3 3 0.6203
- angle_coeff @angle:c-p3-os harmonic 43.95 81.32 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-p3-hp harmonic 27.54 95.20 # SOURCE2 1 0.0000
- angle_coeff @angle:f-p3-f harmonic 43.08 97.40 # SOURCE2 8 1.6636
- angle_coeff @angle:f-p3-hp harmonic 30.56 96.41 # SOURCE3 2 0.0000
- angle_coeff @angle:f-p3-n3 harmonic 41.86 100.60 # SOURCE2 1 0.0000
- angle_coeff @angle:f-p3-os harmonic 42.42 102.20 # SOURCE2 1 0.0000
- angle_coeff @angle:f-p3-p3 harmonic 47.13 97.20 # SOURCE2 1 0.0000
- angle_coeff @angle:hp-p3-hp harmonic 22.02 95.52 # SOURCE3 44 2.4200
- angle_coeff @angle:hp-p3-i harmonic 23.42 96.19 # SOURCE3 4 0.6454
- angle_coeff @angle:hp-p3-n1 harmonic 31.27 92.98 # HF/6-31G* 1
- angle_coeff @angle:hp-p3-n2 harmonic 29.07 98.28 # SOURCE3 10 1.8860
- angle_coeff @angle:hp-p3-n3 harmonic 30.10 94.46 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-n4 harmonic 28.34 93.21 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-n harmonic 29.47 95.15 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-na harmonic 29.25 97.27 # SOURCE3 12 0.9318
- angle_coeff @angle:hp-p3-nh harmonic 30.16 94.10 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-no harmonic 28.83 93.06 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-o harmonic 32.01 101.02 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-oh harmonic 30.73 95.95 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-os harmonic 30.39 97.35 # SOURCE3 6 2.8326
- angle_coeff @angle:hp-p3-p2 harmonic 32.41 99.11 # SOURCE3 16 4.3022
- angle_coeff @angle:hp-p3-p3 harmonic 32.07 95.52 # SOURCE3 4 0.0844
- angle_coeff @angle:hp-p3-p4 harmonic 31.97 95.95 # SOURCE3 6 0.0489
- angle_coeff @angle:hp-p3-p5 harmonic 32.08 95.54 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-s4 harmonic 26.89 95.49 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-s6 harmonic 27.38 92.95 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-sh harmonic 26.51 94.21 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p3-ss harmonic 26.59 94.61 # SOURCE3 2 0.0000
- angle_coeff @angle:i-p3-i harmonic 36.63 105.25 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-p3-n1 harmonic 45.91 90.44 # HF/6-31G* 1
- angle_coeff @angle:n2-p3-n2 harmonic 40.40 103.46 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-p3-n3 harmonic 39.27 113.80 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-p3-o harmonic 43.04 107.10 # SOURCE3 4 0.0000
- angle_coeff @angle:n3-p3-oh harmonic 43.13 98.36 # SOURCE3 1
- angle_coeff @angle:n4-p3-n4 harmonic 38.45 100.53 # SOURCE3 1 0.0000
- angle_coeff @angle:na-p3-na harmonic 39.91 106.22 # SOURCE3 1
- angle_coeff @angle:nh-p3-nh harmonic 40.11 109.11 # SOURCE3 1 0.0000
- angle_coeff @angle:n-p3-n harmonic 40.04 104.58 # SOURCE3 1
- angle_coeff @angle:n-p3-o harmonic 42.80 104.99 # SOURCE3 4 0.0000
- angle_coeff @angle:no-p3-no harmonic 39.64 98.33 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-p3-oh harmonic 42.77 104.48 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p3-o harmonic 43.78 122.18 # SOURCE3 2 7.8556
- angle_coeff @angle:o-p3-p3 harmonic 45.09 116.74 # SOURCE3 14 0.7525
- angle_coeff @angle:o-p3-p5 harmonic 46.98 107.62 # SOURCE3 4 0.0000
- angle_coeff @angle:o-p3-s4 harmonic 38.63 110.70 # SOURCE3 4 0.7259
- angle_coeff @angle:o-p3-s6 harmonic 39.52 106.66 # SOURCE3 6 3.4017
- angle_coeff @angle:os-p3-os harmonic 42.11 106.65 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-p3-p2 harmonic 59.12 103.58 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-p3-p3 harmonic 57.00 105.31 # SOURCE3 4 3.5864
- angle_coeff @angle:p4-p3-p4 harmonic 58.70 99.09 # SOURCE3 1
- angle_coeff @angle:p5-p3-p5 harmonic 58.78 99.10 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-p3-s4 harmonic 39.08 98.26 # SOURCE3 1 0.0000
- angle_coeff @angle:s6-p3-s6 harmonic 39.36 97.78 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-p3-sh harmonic 36.56 107.58 # SOURCE3 1 0.0000
- angle_coeff @angle:s-p3-s harmonic 34.08 131.32 # SOURCE3 1
- angle_coeff @angle:ss-p3-ss harmonic 36.47 109.24 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p4-br harmonic 41.07 110.41 # SOURCE3 1
- angle_coeff @angle:br-p4-o harmonic 37.80 124.80 # SOURCE3 1
- angle_coeff @angle:c2-p4-c2 harmonic 37.13 104.21 # SOURCE3 1
- angle_coeff @angle:c2-p4-hp harmonic 27.68 99.50 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-p4-o harmonic 39.43 113.59 # SOURCE3 1
- angle_coeff @angle:c3-p4-c3 harmonic 37.20 102.55 # SOURCE3 4 0.0192
- angle_coeff @angle:c3-p4-n2 harmonic 39.09 103.17 # SOURCE3 1
- angle_coeff @angle:c3-p4-n3 harmonic 39.50 102.37 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p4-n4 harmonic 37.54 99.57 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p4-n harmonic 38.98 103.26 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p4-na harmonic 37.92 117.67 # SOURCE3 5 19.0404
- angle_coeff @angle:c3-p4-nh harmonic 39.33 102.79 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p4-no harmonic 38.24 99.80 # SOURCE3 3 0.2151
- angle_coeff @angle:c3-p4-o harmonic 38.77 116.44 # SOURCE3 25 2.6494
- angle_coeff @angle:c3-p4-oh harmonic 41.01 98.56 # SOURCE3 2 0.4558
- angle_coeff @angle:c3-p4-os harmonic 41.17 98.01 # SOURCE3 2 0.0931
- angle_coeff @angle:c3-p4-p2 harmonic 44.43 109.27 # SOURCE3 1
- angle_coeff @angle:c3-p4-p3 harmonic 45.09 103.53 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p4-p4 harmonic 48.14 102.12 # SOURCE3 1
- angle_coeff @angle:c3-p4-p5 harmonic 44.64 104.15 # SOURCE3 1
- angle_coeff @angle:c3-p4-sh harmonic 37.43 100.17 # SOURCE3 2 0.0815
- angle_coeff @angle:c3-p4-ss harmonic 37.38 101.19 # SOURCE3 1
- angle_coeff @angle:ca-p4-ca harmonic 36.83 107.77 # SOURCE3 1
- angle_coeff @angle:ca-p4-o harmonic 40.03 111.64 # SOURCE3 1
- angle_coeff @angle:cl-p4-cl harmonic 33.80 103.51 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-p4-o harmonic 36.03 116.53 # SOURCE3 2 0.0000
- angle_coeff @angle:hp-p4-hp harmonic 22.57 99.21 # SOURCE3 4 6.4572
- angle_coeff @angle:hp-p4-n1 harmonic 30.24 99.91 # HF/6-31G* 1
- angle_coeff @angle:hp-p4-o harmonic 31.44 109.35 # SOURCE3 6 10.8284
- angle_coeff @angle:hp-p4-p3 harmonic 31.40 98.96 # SOURCE3 4 0.0000
- angle_coeff @angle:hp-p4-s harmonic 24.32 110.24 # SOURCE3 4 4.1081
- angle_coeff @angle:i-p4-i harmonic 38.53 113.22 # SOURCE3 2 6.7916
- angle_coeff @angle:i-p4-o harmonic 37.71 110.22 # SOURCE3 4 9.7726
- angle_coeff @angle:n1-p4-n1 harmonic 43.01 100.61 # HF/6-31G* 1
- angle_coeff @angle:n1-p4-o harmonic 42.53 114.59 # HF/6-31G* 1
- angle_coeff @angle:n2-p4-n2 harmonic 41.52 102.54 # SOURCE3 1
- angle_coeff @angle:n2-p4-o harmonic 40.81 120.28 # SOURCE3 1
- angle_coeff @angle:n3-p4-o harmonic 42.50 113.27 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-p4-o harmonic 39.56 107.61 # SOURCE3 1 0.0000
- angle_coeff @angle:na-p4-o harmonic 45.17 110.60 # SOURCE3 5 1.3133
- angle_coeff @angle:nh-p4-nh harmonic 43.52 95.30 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-p4-o harmonic 41.87 115.86 # SOURCE3 3 3.2712
- angle_coeff @angle:n-p4-o harmonic 41.05 117.99 # SOURCE3 1 0.0000
- angle_coeff @angle:no-p4-o harmonic 39.42 114.69 # SOURCE3 3 0.1070
- angle_coeff @angle:oh-p4-oh harmonic 45.67 95.71 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p4-o harmonic 45.06 117.22 # SOURCE3 6 2.7792
- angle_coeff @angle:o-p4-oh harmonic 42.88 117.39 # SOURCE3 4 1.0083
- angle_coeff @angle:o-p4-os harmonic 43.10 116.67 # SOURCE3 4 0.6923
- angle_coeff @angle:o-p4-p2 harmonic 44.91 121.35 # SOURCE3 1
- angle_coeff @angle:o-p4-p3 harmonic 45.60 114.00 # SOURCE3 3 0.6663
- angle_coeff @angle:o-p4-p4 harmonic 48.81 116.43 # SOURCE3 1
- angle_coeff @angle:o-p4-p5 harmonic 46.05 109.76 # SOURCE3 1
- angle_coeff @angle:o-p4-s4 harmonic 35.77 112.19 # SOURCE3 1
- angle_coeff @angle:o-p4-s6 harmonic 35.22 113.89 # SOURCE3 1
- angle_coeff @angle:o-p4-s harmonic 37.34 112.78 # SOURCE3 2 0.0000
- angle_coeff @angle:o-p4-sh harmonic 36.99 118.09 # SOURCE3 1
- angle_coeff @angle:os-p4-os harmonic 44.74 100.34 # SOURCE3 1 0.0000
- angle_coeff @angle:o-p4-ss harmonic 37.47 116.14 # SOURCE3 4 1.0636
- angle_coeff @angle:p2-p4-p2 harmonic 56.48 110.71 # SOURCE3 1
- angle_coeff @angle:p3-p4-p3 harmonic 54.50 114.98 # SOURCE3 1 0.0000
- angle_coeff @angle:p4-p4-p4 harmonic 61.44 107.38 # SOURCE3 1
- angle_coeff @angle:p5-p4-p5 harmonic 55.76 107.78 # SOURCE3 1
- angle_coeff @angle:s4-p4-s4 harmonic 36.61 96.24 # SOURCE3 1
- angle_coeff @angle:s6-p4-s6 harmonic 35.22 102.36 # SOURCE3 1
- angle_coeff @angle:sh-p4-sh harmonic 38.45 98.81 # SOURCE3 1 0.0000
- angle_coeff @angle:s-p4-s harmonic 36.54 106.30 # SOURCE3 2 25.0119
- angle_coeff @angle:ss-p4-ss harmonic 37.60 104.41 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p5-br harmonic 41.96 103.38 # SOURCE3 1 0.0000
- angle_coeff @angle:br-p5-o harmonic 39.04 114.65 # SOURCE3 3 1.0910
- angle_coeff @angle:br-p5-oh harmonic 40.90 102.92 # SOURCE3 4 0.5468
- angle_coeff @angle:c1-p5-c1 harmonic 38.83 102.89 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-p5-o harmonic 40.32 115.77 # SOURCE3 2 0.0000
- angle_coeff @angle:c1-p5-oh harmonic 41.43 102.79 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-p5-c2 harmonic 35.85 106.56 # SOURCE3 1
- angle_coeff @angle:c2-p5-o harmonic 39.62 109.24 # SOURCE4 7 2.2628
- angle_coeff @angle:c2-p5-oh harmonic 40.04 101.69 # SOURCE3 1
- angle_coeff @angle:c2-p5-os harmonic 39.90 103.34 # SOURCE3 1
- angle_coeff @angle:c3-p5-c3 harmonic 36.95 106.23 # SOURCE3 14 2.6389
- angle_coeff @angle:c3-p5-hp harmonic 27.05 103.62 # SOURCE4 7 1.1616
- angle_coeff @angle:c3-p5-n3 harmonic 40.01 102.76 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-p5-o harmonic 39.91 112.50 # SOURCE3 23 4.4203
- angle_coeff @angle:c3-p5-oh harmonic 40.83 101.56 # SOURCE3 17 2.1803
- angle_coeff @angle:c3-p5-os harmonic 41.20 100.77 # SOURCE4 51 2.0928
- angle_coeff @angle:c3-p5-p4 harmonic 44.32 106.27 # SOURCE3 1
- angle_coeff @angle:c3-p5-s harmonic 37.51 113.40 # SOURCE3 4 2.0067
- angle_coeff @angle:c3-p5-ss harmonic 36.91 103.76 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-p5-ca harmonic 37.10 107.53 # SOURCE3 1
- angle_coeff @angle:ca-p5-o harmonic 39.95 113.98 # SOURCE3 1
- angle_coeff @angle:ca-p5-oh harmonic 41.04 101.77 # SOURCE3 1
- angle_coeff @angle:ca-p5-os harmonic 40.86 103.75 # SOURCE3 1
- angle_coeff @angle:c-p5-c harmonic 35.96 104.16 # SOURCE3 1
- angle_coeff @angle:cl-p5-cl harmonic 33.77 103.70 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-p5-o harmonic 36.29 115.32 # SOURCE3 2 0.0000
- angle_coeff @angle:cl-p5-oh harmonic 37.85 102.44 # SOURCE3 2 0.0000
- angle_coeff @angle:c-p5-o harmonic 39.74 107.19 # SOURCE4 16 0.5711
- angle_coeff @angle:c-p5-oh harmonic 39.73 102.12 # SOURCE3 1
- angle_coeff @angle:f-p5-f harmonic 42.49 99.96 # SOURCE2 4 0.9197
- angle_coeff @angle:f-p5-o harmonic 43.22 112.03 # SOURCE4 7 0.5178
- angle_coeff @angle:f-p5-oh harmonic 43.33 101.98 # SOURCE3 2 0.0000
- angle_coeff @angle:f-p5-os harmonic 43.51 102.70 # SOURCE4 5 0.1524
- angle_coeff @angle:f-p5-s harmonic 38.09 117.40 # SOURCE2 1 0.0000
- angle_coeff @angle:hp-p5-hp harmonic 21.44 101.09 # SOURCE3 4 1.3036
- angle_coeff @angle:hp-p5-n1 harmonic 31.09 101.32 # HF/6-31G* 1
- angle_coeff @angle:hp-p5-o harmonic 30.21 116.58 # SOURCE3 7 1.3282
- angle_coeff @angle:hp-p5-oh harmonic 30.57 101.45 # SOURCE3 5 0.9084
- angle_coeff @angle:hp-p5-s harmonic 25.97 119.20 # SOURCE2 1 0.0000
- angle_coeff @angle:i-p5-i harmonic 35.88 107.17 # SOURCE3 1 0.0000
- angle_coeff @angle:i-p5-o harmonic 32.99 115.93 # SOURCE3 3 0.0415
- angle_coeff @angle:i-p5-oh harmonic 35.44 102.26 # SOURCE3 4 1.9577
- angle_coeff @angle:n1-p5-n1 harmonic 45.78 101.55 # HF/6-31G* 1
- angle_coeff @angle:n1-p5-o harmonic 44.71 113.78 # HF/6-31G* 1
- angle_coeff @angle:n2-p5-n2 harmonic 43.96 106.34 # SOURCE3 1
- angle_coeff @angle:n2-p5-o harmonic 44.30 113.53 # SOURCE3 1
- angle_coeff @angle:n2-p5-oh harmonic 44.68 102.40 # SOURCE3 1
- angle_coeff @angle:n3-p5-n3 harmonic 42.87 103.37 # SOURCE4 47 2.1009
- angle_coeff @angle:n3-p5-nh harmonic 42.63 104.02 # SOURCE4 5 1.8740
- angle_coeff @angle:n3-p5-o harmonic 43.02 114.64 # SOURCE4 76 2.2728
- angle_coeff @angle:n3-p5-oh harmonic 43.43 104.18 # SOURCE3 6 0.4373
- angle_coeff @angle:n3-p5-os harmonic 44.20 101.94 # SOURCE4 34 2.3553
- angle_coeff @angle:n3-p5-s harmonic 39.05 117.12 # SOURCE4 7 0.7109
- angle_coeff @angle:n4-p5-n4 harmonic 39.18 102.20 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-p5-o harmonic 41.10 109.78 # SOURCE3 5 2.7519
- angle_coeff @angle:n4-p5-oh harmonic 42.23 98.48 # SOURCE3 6 0.4104
- angle_coeff @angle:n4-p5-os harmonic 43.31 94.55 # SOURCE3 2 0.0000
- angle_coeff @angle:na-p5-na harmonic 40.56 108.57 # SOURCE3 1 0.0000
- angle_coeff @angle:na-p5-o harmonic 42.38 113.43 # SOURCE3 11 0.8968
- angle_coeff @angle:na-p5-oh harmonic 43.14 102.07 # SOURCE3 16 1.4144
- angle_coeff @angle:na-p5-os harmonic 43.20 103.06 # SOURCE3 4 0.7463
- angle_coeff @angle:nh-p5-nh harmonic 43.48 99.51 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-p5-o harmonic 42.11 118.91 # SOURCE3 3 1.3237
- angle_coeff @angle:nh-p5-oh harmonic 43.40 103.81 # SOURCE3 2 0.0000
- angle_coeff @angle:nh-p5-os harmonic 44.39 100.51 # SOURCE3 2 0.0000
- angle_coeff @angle:n-p5-n3 harmonic 42.13 104.11 # SOURCE4 11 1.4088
- angle_coeff @angle:n-p5-n harmonic 41.80 103.09 # SOURCE3 1 0.0000
- angle_coeff @angle:n-p5-o harmonic 43.40 108.73 # SOURCE4 5 0.2571
- angle_coeff @angle:n-p5-oh harmonic 43.17 102.44 # SOURCE3 4 0.0999
- angle_coeff @angle:no-p5-no harmonic 40.40 95.68 # SOURCE3 1 0.0000
- angle_coeff @angle:no-p5-o harmonic 40.49 112.75 # SOURCE3 4 3.3684
- angle_coeff @angle:no-p5-oh harmonic 41.56 101.35 # SOURCE3 2 0.0000
- angle_coeff @angle:no-p5-os harmonic 41.69 101.70 # SOURCE3 4 0.0565
- angle_coeff @angle:n-p5-os harmonic 43.85 100.48 # SOURCE3 2 0.0000
- angle_coeff @angle:oh-p5-oh harmonic 44.58 102.45 # SOURCE3 39 2.4223
- angle_coeff @angle:oh-p5-os harmonic 44.91 102.37 # SOURCE3 8 1.5063
- angle_coeff @angle:oh-p5-p2 harmonic 48.24 103.53 # SOURCE3 1
- angle_coeff @angle:oh-p5-p3 harmonic 47.55 103.83 # SOURCE3 13 0.4303
- angle_coeff @angle:oh-p5-p4 harmonic 47.57 101.79 # SOURCE3 1
- angle_coeff @angle:oh-p5-p5 harmonic 51.43 100.45 # SOURCE3 1
- angle_coeff @angle:oh-p5-s4 harmonic 40.30 103.24 # SOURCE3 1
- angle_coeff @angle:oh-p5-s6 harmonic 40.65 101.48 # SOURCE3 1
- angle_coeff @angle:oh-p5-s harmonic 42.20 102.88 # SOURCE3 3 1.6044
- angle_coeff @angle:oh-p5-sh harmonic 40.01 101.41 # SOURCE3 2 0.0000
- angle_coeff @angle:oh-p5-ss harmonic 38.95 104.33 # SOURCE3 6 2.0112
- angle_coeff @angle:o-p5-o harmonic 46.01 115.80 # SOURCE3 17 5.7902
- angle_coeff @angle:o-p5-oh harmonic 43.79 115.26 # SOURCE4 740 1.3004
- angle_coeff @angle:o-p5-os harmonic 44.01 116.09 # SOURCE3 35 3.2062
- angle_coeff @angle:o-p5-p2 harmonic 46.23 114.60 # SOURCE3 1
- angle_coeff @angle:o-p5-p3 harmonic 45.38 115.48 # SOURCE3 9 2.1084
- angle_coeff @angle:o-p5-p4 harmonic 45.07 114.66 # SOURCE3 1
- angle_coeff @angle:o-p5-p5 harmonic 49.11 113.44 # SOURCE3 1
- angle_coeff @angle:o-p5-s4 harmonic 39.61 110.23 # SOURCE3 1
- angle_coeff @angle:o-p5-s6 harmonic 39.34 111.75 # SOURCE3 1
- angle_coeff @angle:o-p5-s harmonic 40.46 116.94 # SOURCE3 3 2.9506
- angle_coeff @angle:o-p5-sh harmonic 38.14 114.56 # SOURCE3 3 1.7645
- angle_coeff @angle:os-p5-os harmonic 45.37 101.77 # SOURCE4 243 2.0816
- angle_coeff @angle:os-p5-p3 harmonic 47.66 103.67 # SOURCE3 2 0.0000
- angle_coeff @angle:os-p5-p5 harmonic 50.58 104.48 # SOURCE3 1
- angle_coeff @angle:os-p5-s4 harmonic 40.57 102.52 # SOURCE3 1
- angle_coeff @angle:os-p5-s6 harmonic 40.69 101.89 # SOURCE3 1
- angle_coeff @angle:o-p5-ss harmonic 37.95 112.46 # SOURCE3 6 2.7392
- angle_coeff @angle:os-p5-s harmonic 39.69 117.28 # SOURCE4 74 0.7542
- angle_coeff @angle:os-p5-sh harmonic 39.51 104.59 # SOURCE3 2 0.0000
- angle_coeff @angle:os-p5-ss harmonic 39.36 102.65 # SOURCE4 25 1.8093
- angle_coeff @angle:p2-p5-p2 harmonic 57.39 107.14 # SOURCE3 1
- angle_coeff @angle:p3-p5-p3 harmonic 57.04 105.23 # SOURCE3 3 5.1024
- angle_coeff @angle:p4-p5-p4 harmonic 57.42 101.62 # SOURCE3 1
- angle_coeff @angle:p5-p5-p5 harmonic 59.38 112.72 # SOURCE3 1
- angle_coeff @angle:s6-p5-s6 harmonic 38.64 105.18 # SOURCE3 1
- angle_coeff @angle:sh-p5-sh harmonic 37.97 104.56 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-p5-ss harmonic 37.22 107.13 # SOURCE3 1
- angle_coeff @angle:s-p5-s harmonic 39.37 114.13 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-p5-ss harmonic 36.51 109.61 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-pc-n harmonic 42.75 90.80 # SOURCE3 3 2.3423
- angle_coeff @angle:cd-pc-na harmonic 43.00 90.18 # SOURCE3 81 2.7619
- angle_coeff @angle:cc-pd-n harmonic 42.75 90.80 # SOURCE3 3 same_as_cd-pc-n
- angle_coeff @angle:cc-pd-na harmonic 43.00 90.18 # SOURCE3 81 same_as_cd-pc-na
- angle_coeff @angle:c2-pe-ca harmonic 38.84 101.44 # SOURCE3 3 0.7177
- angle_coeff @angle:c2-pe-ce harmonic 38.68 103.01 # SOURCE3 4 1.4470
- angle_coeff @angle:c2-pe-cg harmonic 40.85 104.03 # SOURCE3 3 3.8740
- angle_coeff @angle:c2-pe-n2 harmonic 44.94 94.14 # SOURCE3 1
- angle_coeff @angle:c2-pe-ne harmonic 41.85 98.70 # SOURCE3 12 5.3383
- angle_coeff @angle:c2-pe-o harmonic 41.06 115.16 # SOURCE3 2 0.0149
- angle_coeff @angle:c2-pe-p2 harmonic 50.94 107.82 # SOURCE3 1
- angle_coeff @angle:c2-pe-pe harmonic 48.17 102.99 # SOURCE3 9 8.2860
- angle_coeff @angle:c2-pe-px harmonic 51.11 97.37 # SOURCE3 4 0.6655
- angle_coeff @angle:c2-pe-py harmonic 50.92 96.71 # SOURCE3 4 1.2755
- angle_coeff @angle:c2-pe-s harmonic 41.06 111.16 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-pe-sx harmonic 38.51 95.11 # SOURCE3 4 0.2676
- angle_coeff @angle:c2-pe-sy harmonic 37.78 95.56 # SOURCE3 2 0.0462
- angle_coeff @angle:ca-pe-n2 harmonic 40.97 102.03 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-pe-o harmonic 40.40 106.88 # SOURCE3 2 0.0018
- angle_coeff @angle:ca-pe-p2 harmonic 50.96 100.79 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-pe-pf harmonic 48.44 99.70 # SOURCE3 2 0.0000
- angle_coeff @angle:ca-pe-s harmonic 40.07 107.93 # SOURCE3 1 0.0000
- angle_coeff @angle:c-pe-c2 harmonic 38.58 97.30 # SOURCE3 3 0.0335
- angle_coeff @angle:ce-pe-n2 harmonic 41.45 100.55 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-pe-o harmonic 40.47 107.44 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-pe-p2 harmonic 51.42 99.56 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-pe-s harmonic 40.65 105.54 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-pe-n2 harmonic 44.31 101.79 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-pe-o harmonic 43.57 107.62 # SOURCE3 1 0.0000
- angle_coeff @angle:cg-pe-p2 harmonic 52.47 104.68 # SOURCE3 2 5.1435
- angle_coeff @angle:cg-pe-s harmonic 42.30 108.60 # SOURCE3 4 2.6981
- angle_coeff @angle:n2-pe-n2 harmonic 45.26 108.14 # SOURCE3 1
- angle_coeff @angle:n2-pe-ne harmonic 42.89 106.80 # SOURCE3 6 4.5981
- angle_coeff @angle:n2-pe-o harmonic 44.34 115.39 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-pe-p2 harmonic 52.85 111.60 # SOURCE3 1
- angle_coeff @angle:n2-pe-pe harmonic 48.70 109.40 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-pe-px harmonic 50.28 110.30 # SOURCE3 3 6.0548
- angle_coeff @angle:n2-pe-py harmonic 54.11 93.68 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-pe-s harmonic 42.94 114.84 # SOURCE3 3 3.6512
- angle_coeff @angle:n2-pe-sx harmonic 39.42 97.83 # SOURCE3 1 0.0000
- angle_coeff @angle:n2-pe-sy harmonic 38.61 98.14 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-pe-o harmonic 42.65 110.24 # SOURCE3 3 3.8478
- angle_coeff @angle:ne-pe-p2 harmonic 52.77 104.48 # SOURCE3 2 7.1207
- angle_coeff @angle:ne-pe-s harmonic 42.21 109.19 # SOURCE3 5 3.6708
- angle_coeff @angle:o-pe-o harmonic 44.01 119.96 # SOURCE3 1 0.0000
- angle_coeff @angle:o-pe-p2 harmonic 52.71 114.23 # SOURCE3 1 0.0000
- angle_coeff @angle:o-pe-pe harmonic 42.47 145.96 # SOURCE3 1 0.0000
- angle_coeff @angle:o-pe-px harmonic 52.10 104.37 # SOURCE3 1 0.0000
- angle_coeff @angle:o-pe-py harmonic 51.64 104.49 # SOURCE3 1 0.0000
- angle_coeff @angle:o-pe-s harmonic 42.89 117.42 # SOURCE3 2 0.0426
- angle_coeff @angle:o-pe-sx harmonic 38.02 106.59 # SOURCE3 1 0.0000
- angle_coeff @angle:o-pe-sy harmonic 37.56 105.04 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-pe-pe harmonic 65.58 98.24 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-pe-px harmonic 64.12 108.28 # SOURCE3 2 6.2959
- angle_coeff @angle:p2-pe-py harmonic 62.99 110.87 # SOURCE3 3 8.1645
- angle_coeff @angle:p2-pe-s harmonic 53.42 111.28 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-pe-sx harmonic 51.26 95.73 # SOURCE3 1 0.0000
- angle_coeff @angle:p2-pe-sy harmonic 50.47 95.95 # SOURCE3 1 0.0000
- angle_coeff @angle:pe-pe-s harmonic 50.40 107.91 # SOURCE3 2 1.5577
- angle_coeff @angle:px-pe-s harmonic 51.97 107.62 # SOURCE3 2 3.7266
- angle_coeff @angle:py-pe-s harmonic 51.36 108.73 # SOURCE3 3 5.3201
- angle_coeff @angle:s-pe-s harmonic 34.43 178.44 # SOURCE3 1 0.0000
- angle_coeff @angle:s-pe-sx harmonic 38.72 108.32 # SOURCE3 2 3.0318
- angle_coeff @angle:s-pe-sy harmonic 38.35 106.93 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-pf-ca harmonic 38.84 101.44 # SOURCE3 3 same_as_c2-pe-ca
- angle_coeff @angle:c2-pf-cf harmonic 38.68 103.01 # SOURCE3 4 same_as_c2-pe-ce
- angle_coeff @angle:c2-pf-ch harmonic 40.85 104.03 # SOURCE3 3 same_as_c2-pe-cg
- angle_coeff @angle:c2-pf-n2 harmonic 44.94 94.14 # SOURCE3 1 same_as_c2-pe-n2
- angle_coeff @angle:c2-pf-nf harmonic 41.85 98.70 # SOURCE3 12 same_as_c2-pe-ne
- angle_coeff @angle:c2-pf-o harmonic 41.06 115.16 # SOURCE3 2 same_as_c2-pe-o
- angle_coeff @angle:c2-pf-p2 harmonic 50.94 107.82 # SOURCE3 1 same_as_c2-pe-p2
- angle_coeff @angle:c2-pf-pf harmonic 48.17 102.99 # SOURCE3 9 same_as_c2-pe-pe
- angle_coeff @angle:c2-pf-px harmonic 51.11 97.37 # SOURCE3 4 same_as_c2-pe-px
- angle_coeff @angle:c2-pf-py harmonic 50.92 96.71 # SOURCE3 4 same_as_c2-pe-py
- angle_coeff @angle:c2-pf-s harmonic 41.06 111.16 # SOURCE3 2 same_as_c2-pe-s
- angle_coeff @angle:c2-pf-sx harmonic 38.51 95.11 # SOURCE3 4 same_as_c2-pe-sx
- angle_coeff @angle:c2-pf-sy harmonic 37.78 95.56 # SOURCE3 2 same_as_c2-pe-sy
- angle_coeff @angle:ca-pf-n2 harmonic 40.97 102.03 # SOURCE3 1 same_as_ca-pe-n2
- angle_coeff @angle:ca-pf-o harmonic 40.40 106.88 # SOURCE3 2 same_as_ca-pe-o
- angle_coeff @angle:ca-pf-p2 harmonic 50.96 100.79 # SOURCE3 1 same_as_ca-pe-p2
- angle_coeff @angle:ca-pf-pe harmonic 48.44 99.70 # SOURCE3 2 0.0000
- angle_coeff @angle:ca-pf-s harmonic 40.07 107.93 # SOURCE3 1 same_as_ca-pe-s
- angle_coeff @angle:c-pf-c2 harmonic 38.58 97.30 # SOURCE3 3 same_as_c-pe-c2
- angle_coeff @angle:cf-pf-n2 harmonic 41.45 100.55 # SOURCE3 1 same_as_ce-pe-n2
- angle_coeff @angle:cf-pf-o harmonic 40.47 107.44 # SOURCE3 1 same_as_ce-pe-o
- angle_coeff @angle:cf-pf-p2 harmonic 51.42 99.56 # SOURCE3 1 same_as_ce-pe-p2
- angle_coeff @angle:cf-pf-s harmonic 40.65 105.54 # SOURCE3 1 same_as_ce-pe-s
- angle_coeff @angle:ch-pf-n2 harmonic 44.31 101.79 # SOURCE3 1 same_as_cg-pe-n2
- angle_coeff @angle:ch-pf-o harmonic 43.57 107.62 # SOURCE3 1 same_as_cg-pe-o
- angle_coeff @angle:ch-pf-p2 harmonic 52.47 104.68 # SOURCE3 2 same_as_cg-pe-p2
- angle_coeff @angle:ch-pf-s harmonic 42.30 108.60 # SOURCE3 4 same_as_cg-pe-s
- angle_coeff @angle:n2-pf-n2 harmonic 45.26 108.14 # SOURCE3 1 same_as_n2-pe-n2
- angle_coeff @angle:n2-pf-nf harmonic 42.89 106.80 # SOURCE3 6 same_as_n2-pe-ne
- angle_coeff @angle:n2-pf-o harmonic 44.34 115.39 # SOURCE3 1 same_as_n2-pe-o
- angle_coeff @angle:n2-pf-p2 harmonic 52.85 111.60 # SOURCE3 1 same_as_n2-pe-p2
- angle_coeff @angle:n2-pf-pf harmonic 48.70 109.40 # SOURCE3 1 same_as_n2-pe-pe
- angle_coeff @angle:n2-pf-px harmonic 50.28 110.30 # SOURCE3 3 same_as_n2-pe-px
- angle_coeff @angle:n2-pf-py harmonic 54.11 93.68 # SOURCE3 1 same_as_n2-pe-py
- angle_coeff @angle:n2-pf-s harmonic 42.94 114.84 # SOURCE3 3 same_as_n2-pe-s
- angle_coeff @angle:n2-pf-sx harmonic 39.42 97.83 # SOURCE3 1 same_as_n2-pe-sx
- angle_coeff @angle:n2-pf-sy harmonic 38.61 98.14 # SOURCE3 1 same_as_n2-pe-sy
- angle_coeff @angle:nf-pf-o harmonic 42.65 110.24 # SOURCE3 3 same_as_ne-pe-o
- angle_coeff @angle:nf-pf-p2 harmonic 52.77 104.48 # SOURCE3 2 same_as_ne-pe-p2
- angle_coeff @angle:nf-pf-s harmonic 42.21 109.19 # SOURCE3 5 same_as_ne-pe-s
- angle_coeff @angle:o-pf-o harmonic 44.01 119.96 # SOURCE3 1 same_as_o-pe-o
- angle_coeff @angle:o-pf-p2 harmonic 52.71 114.23 # SOURCE3 1 same_as_o-pe-p2
- angle_coeff @angle:o-pf-pf harmonic 42.47 145.96 # SOURCE3 1 same_as_o-pe-pe
- angle_coeff @angle:o-pf-px harmonic 52.10 104.37 # SOURCE3 1 same_as_o-pe-px
- angle_coeff @angle:o-pf-py harmonic 51.64 104.49 # SOURCE3 1 same_as_o-pe-py
- angle_coeff @angle:o-pf-s harmonic 42.89 117.42 # SOURCE3 2 same_as_o-pe-s
- angle_coeff @angle:o-pf-sx harmonic 38.02 106.59 # SOURCE3 1 same_as_o-pe-sx
- angle_coeff @angle:o-pf-sy harmonic 37.56 105.04 # SOURCE3 1 same_as_o-pe-sy
- angle_coeff @angle:p2-pf-pf harmonic 65.58 98.24 # SOURCE3 1 same_as_p2-pe-pe
- angle_coeff @angle:p2-pf-px harmonic 64.12 108.28 # SOURCE3 2 same_as_p2-pe-px
- angle_coeff @angle:p2-pf-py harmonic 62.99 110.87 # SOURCE3 3 same_as_p2-pe-py
- angle_coeff @angle:p2-pf-s harmonic 53.42 111.28 # SOURCE3 1 same_as_p2-pe-s
- angle_coeff @angle:p2-pf-sx harmonic 51.26 95.73 # SOURCE3 1 same_as_p2-pe-sx
- angle_coeff @angle:p2-pf-sy harmonic 50.47 95.95 # SOURCE3 1 same_as_p2-pe-sy
- angle_coeff @angle:pf-pf-s harmonic 50.40 107.91 # SOURCE3 2 same_as_pe-pe-s
- angle_coeff @angle:px-pf-s harmonic 51.97 107.62 # SOURCE3 2 same_as_px-pe-s
- angle_coeff @angle:py-pf-s harmonic 51.36 108.73 # SOURCE3 3 same_as_py-pe-s
- angle_coeff @angle:s-pf-s harmonic 34.43 178.44 # SOURCE3 1 same_as_s-pe-s
- angle_coeff @angle:s-pf-sx harmonic 38.72 108.32 # SOURCE3 2 same_as_s-pe-sx
- angle_coeff @angle:s-pf-sy harmonic 38.35 106.93 # SOURCE3 1 same_as_s-pe-sy
- angle_coeff @angle:c3-px-ca harmonic 36.97 104.79 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-px-ce harmonic 37.00 104.86 # SOURCE3 4 0.6354
- angle_coeff @angle:c3-px-cf harmonic 37.00 104.86 # SOURCE3 4 same_as_c3-px-ce
- angle_coeff @angle:c3-px-ne harmonic 39.55 102.46 # SOURCE3 7 1.8685
- angle_coeff @angle:c3-px-nf harmonic 39.55 102.46 # SOURCE3 7 same_as_c3-px-ne
- angle_coeff @angle:c3-px-o harmonic 39.39 113.68 # SOURCE3 28 4.8990
- angle_coeff @angle:c3-px-pe harmonic 47.82 105.73 # SOURCE3 10 4.4059
- angle_coeff @angle:c3-px-pf harmonic 47.82 105.73 # SOURCE3 10 same_as_c3-px-pe
- angle_coeff @angle:c3-px-py harmonic 45.50 103.11 # SOURCE3 3 0.8680
- angle_coeff @angle:c3-px-sx harmonic 36.06 99.55 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-px-sy harmonic 35.30 103.41 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-px-ca harmonic 37.08 104.15 # SOURCE3 2 3.6168
- angle_coeff @angle:ca-px-o harmonic 40.49 107.50 # SOURCE3 5 5.7355
- angle_coeff @angle:c-px-c3 harmonic 36.70 101.72 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-px-ce harmonic 37.15 104.21 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-px-o harmonic 39.42 113.79 # SOURCE3 6 0.3877
- angle_coeff @angle:cf-px-cf harmonic 37.15 104.21 # SOURCE3 1 same_as_ce-px-ce
- angle_coeff @angle:cf-px-o harmonic 39.42 113.79 # SOURCE3 6 same_as_ce-px-o
- angle_coeff @angle:c-px-o harmonic 37.98 114.47 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-px-ne harmonic 41.92 103.22 # SOURCE3 2 0.6807
- angle_coeff @angle:ne-px-o harmonic 42.27 114.13 # SOURCE3 11 8.9737
- angle_coeff @angle:nf-px-nf harmonic 41.92 103.22 # SOURCE3 2 same_as_ne-px-ne
- angle_coeff @angle:nf-px-o harmonic 42.27 114.13 # SOURCE3 11 same_as_ne-px-o
- angle_coeff @angle:o-px-pe harmonic 49.41 116.50 # SOURCE3 12 8.2925
- angle_coeff @angle:o-px-pf harmonic 49.41 116.50 # SOURCE3 12 same_as_o-px-pe
- angle_coeff @angle:o-px-py harmonic 45.90 114.20 # SOURCE3 5 1.7165
- angle_coeff @angle:o-px-sx harmonic 35.81 112.81 # SOURCE3 3 0.8799
- angle_coeff @angle:o-px-sy harmonic 35.59 113.54 # SOURCE3 3 0.5010
- angle_coeff @angle:pe-px-pe harmonic 61.38 110.71 # SOURCE3 1 0.0000
- angle_coeff @angle:pf-px-pf harmonic 61.38 110.71 # SOURCE3 1 same_as_pe-px-pe
- angle_coeff @angle:py-px-py harmonic 56.72 107.78 # SOURCE3 1 0.0000
- angle_coeff @angle:sx-px-sx harmonic 36.76 96.24 # SOURCE3 1 0.0000
- angle_coeff @angle:sy-px-sy harmonic 35.53 102.36 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-py-n4 harmonic 37.34 103.83 # SOURCE3 4 0.0000
- angle_coeff @angle:c3-py-na harmonic 38.76 106.89 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-py-o harmonic 38.95 117.87 # SOURCE3 13 2.3554
- angle_coeff @angle:c3-py-oh harmonic 41.22 100.16 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-py-os harmonic 40.15 105.39 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-py-px harmonic 44.89 106.27 # SOURCE3 2 0.0000
- angle_coeff @angle:c3-py-py harmonic 43.54 113.97 # SOURCE3 10 1.6346
- angle_coeff @angle:c3-py-sx harmonic 34.74 106.36 # SOURCE3 4 0.0000
- angle_coeff @angle:ca-py-ca harmonic 36.99 107.55 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-py-o harmonic 39.82 113.98 # SOURCE3 3 0.5309
- angle_coeff @angle:ca-py-oh harmonic 40.90 102.68 # SOURCE4 5 1.2945
- angle_coeff @angle:ca-py-os harmonic 40.66 103.75 # SOURCE3 2 0.0000
- angle_coeff @angle:c-py-c3 harmonic 35.71 110.36 # SOURCE3 1 0.0000
- angle_coeff @angle:c-py-c harmonic 36.23 104.20 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-py-ce harmonic 37.29 106.54 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-py-o harmonic 40.24 112.16 # SOURCE3 5 3.2594
- angle_coeff @angle:ce-py-oh harmonic 40.58 104.77 # SOURCE3 6 2.1852
- angle_coeff @angle:ce-py-os harmonic 40.82 103.34 # SOURCE3 2 0.0000
- angle_coeff @angle:cf-py-cf harmonic 37.29 106.54 # SOURCE3 1 same_as_ce-py-ce
- angle_coeff @angle:cf-py-o harmonic 40.24 112.16 # SOURCE3 5 same_as_ce-py-o
- angle_coeff @angle:cf-py-oh harmonic 40.58 104.77 # SOURCE3 6 same_as_ce-py-oh
- angle_coeff @angle:cf-py-os harmonic 40.82 103.34 # SOURCE3 2 same_as_ce-py-os
- angle_coeff @angle:c-py-o harmonic 38.52 115.25 # SOURCE3 6 2.6519
- angle_coeff @angle:c-py-oh harmonic 40.03 102.14 # SOURCE3 6 1.0654
- angle_coeff @angle:c-py-os harmonic 41.32 95.74 # SOURCE3 3 9.0999
- angle_coeff @angle:n3-py-ne harmonic 41.93 108.44 # SOURCE4 12 0.9498
- angle_coeff @angle:n4-py-o harmonic 38.83 115.58 # SOURCE3 4 0.0000
- angle_coeff @angle:n4-py-py harmonic 63.24 55.10 # SOURCE3 4 0.0000
- angle_coeff @angle:na-py-o harmonic 40.78 122.40 # SOURCE3 2 0.0000
- angle_coeff @angle:na-py-py harmonic 67.66 50.88 # SOURCE3 2 0.0000
- angle_coeff @angle:ne-py-ne harmonic 43.51 106.29 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-py-o harmonic 44.00 113.21 # SOURCE3 15 3.8894
- angle_coeff @angle:ne-py-oh harmonic 44.13 104.70 # SOURCE3 26 2.7513
- angle_coeff @angle:ne-py-os harmonic 44.80 101.33 # SOURCE3 2 0.0000
- angle_coeff @angle:nf-py-nf harmonic 43.51 106.29 # SOURCE3 1 same_as_ne-py-ne
- angle_coeff @angle:nf-py-o harmonic 44.00 113.21 # SOURCE3 15 same_as_ne-py-o
- angle_coeff @angle:nf-py-oh harmonic 44.13 104.70 # SOURCE3 26 same_as_ne-py-oh
- angle_coeff @angle:nf-py-os harmonic 44.80 101.33 # SOURCE3 2 same_as_ne-py-os
- angle_coeff @angle:oh-py-oh harmonic 45.06 101.78 # SOURCE3 35 2.2937
- angle_coeff @angle:oh-py-pe harmonic 50.99 104.84 # SOURCE3 22 2.0337
- angle_coeff @angle:oh-py-pf harmonic 50.99 104.84 # SOURCE3 22 same_as_oh-py-pe
- angle_coeff @angle:oh-py-px harmonic 47.75 104.30 # SOURCE3 8 1.2772
- angle_coeff @angle:oh-py-py harmonic 48.91 100.45 # SOURCE3 6 0.0000
- angle_coeff @angle:oh-py-sx harmonic 37.44 100.94 # SOURCE3 4 0.0000
- angle_coeff @angle:oh-py-sy harmonic 38.51 101.47 # SOURCE3 6 0.2490
- angle_coeff @angle:o-py-oh harmonic 43.74 116.14 # SOURCE3 79 2.1455
- angle_coeff @angle:o-py-os harmonic 43.55 116.79 # SOURCE3 17 1.3534
- angle_coeff @angle:o-py-pe harmonic 49.46 114.56 # SOURCE3 12 3.6114
- angle_coeff @angle:o-py-pf harmonic 49.46 114.56 # SOURCE3 12 same_as_o-py-pe
- angle_coeff @angle:o-py-px harmonic 46.50 111.37 # SOURCE3 5 0.3803
- angle_coeff @angle:o-py-py harmonic 44.97 120.43 # SOURCE3 16 6.0629
- angle_coeff @angle:os-py-os harmonic 45.06 101.25 # SOURCE3 8 2.0860
- angle_coeff @angle:os-py-py harmonic 47.94 104.48 # SOURCE3 4 0.0000
- angle_coeff @angle:os-py-sx harmonic 36.90 103.86 # SOURCE3 2 0.0000
- angle_coeff @angle:os-py-sy harmonic 38.37 102.12 # SOURCE3 2 0.0000
- angle_coeff @angle:o-py-sx harmonic 34.68 118.56 # SOURCE3 7 6.2976
- angle_coeff @angle:o-py-sy harmonic 36.96 111.71 # SOURCE3 5 1.1937
- angle_coeff @angle:pe-py-pe harmonic 61.78 107.14 # SOURCE3 1 0.0000
- angle_coeff @angle:pf-py-pf harmonic 61.78 107.14 # SOURCE3 1 same_as_pe-py-pe
- angle_coeff @angle:py-py-py harmonic 55.80 112.70 # SOURCE3 1 0.0000
- angle_coeff @angle:py-py-sx harmonic 58.65 61.54 # SOURCE3 4 0.0000
- angle_coeff @angle:sy-py-sy harmonic 36.13 105.17 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-s2-o harmonic 65.76 117.25 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-s2-n2 harmonic 68.67 110.84 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-s2-o harmonic 66.18 114.70 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-s2-n1 harmonic 53.42 117.70 # SOURCE2 1 0.0000
- angle_coeff @angle:f-s2-n1 harmonic 66.15 116.90 # SOURCE2 1 0.0000
- angle_coeff @angle:n1-s2-o harmonic 73.05 108.46 # HF/6-31G* 1
- angle_coeff @angle:n2-s2-o harmonic 67.93 121.20 # SOURCE2 2 0.8000
- angle_coeff @angle:o-s2-o harmonic 67.99 116.17 # SOURCE3 1 0.0000
- angle_coeff @angle:o-s2-s harmonic 63.79 118.30 # SOURCE2 1 0.0000
- angle_coeff @angle:s-s2-s harmonic 63.50 115.04 # SOURCE3 1 0.0000
- angle_coeff @angle:br-s4-br harmonic 64.61 98.02 # SOURCE3 1
- angle_coeff @angle:br-s4-c3 harmonic 62.19 92.98 # SOURCE3 1 0.0000
- angle_coeff @angle:br-s4-o harmonic 59.20 112.07 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-s4-c1 harmonic 65.35 93.55 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-s4-o harmonic 65.98 110.36 # SOURCE3 2 0.0000
- angle_coeff @angle:c2-s4-c2 harmonic 62.00 102.29 # SOURCE3 1
- angle_coeff @angle:c2-s4-c3 harmonic 63.48 94.95 # SOURCE3 1
- angle_coeff @angle:c2-s4-o harmonic 66.61 107.09 # SOURCE3 1
- angle_coeff @angle:c3-s4-c3 harmonic 62.07 96.82 # SOURCE3 11 1.5580
- angle_coeff @angle:c3-s4-ca harmonic 62.99 95.00 # SOURCE3 1
- angle_coeff @angle:c3-s4-f harmonic 66.32 91.70 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-hs harmonic 46.55 90.60 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-i harmonic 52.86 90.53 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-n2 harmonic 69.07 90.59 # SOURCE3 1
- angle_coeff @angle:c3-s4-n3 harmonic 65.18 94.49 # SOURCE3 4 1.5570
- angle_coeff @angle:c3-s4-n harmonic 64.28 96.07 # SOURCE3 4 1.0354
- angle_coeff @angle:c3-s4-n4 harmonic 61.99 92.47 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-na harmonic 65.11 93.07 # SOURCE3 10 1.8813
- angle_coeff @angle:c3-s4-nh harmonic 64.51 97.08 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-no harmonic 62.53 89.53 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-o harmonic 65.63 106.21 # SOURCE3 60 2.0426
- angle_coeff @angle:c3-s4-oh harmonic 68.22 90.25 # SOURCE4 8 0.3023
- angle_coeff @angle:c3-s4-os harmonic 68.23 90.06 # SOURCE3 4 0.4484
- angle_coeff @angle:c3-s4-p2 harmonic 76.43 94.37 # SOURCE3 1
- angle_coeff @angle:c3-s4-p3 harmonic 78.19 96.54 # SOURCE3 4 1.3634
- angle_coeff @angle:c3-s4-p4 harmonic 73.69 97.40 # SOURCE3 1
- angle_coeff @angle:c3-s4-p5 harmonic 78.32 99.18 # SOURCE3 1
- angle_coeff @angle:c3-s4-s4 harmonic 64.31 89.50 # SOURCE3 1
- angle_coeff @angle:c3-s4-s harmonic 61.31 98.72 # SOURCE3 2 0.0185
- angle_coeff @angle:c3-s4-s6 harmonic 61.62 97.48 # SOURCE3 1
- angle_coeff @angle:c3-s4-sh harmonic 60.74 94.66 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s4-ss harmonic 60.58 95.31 # SOURCE3 3 1.4101
- angle_coeff @angle:ca-s4-ca harmonic 63.26 95.21 # SOURCE3 1
- angle_coeff @angle:ca-s4-o harmonic 66.01 106.63 # SOURCE3 1
- angle_coeff @angle:c-s4-c3 harmonic 61.53 95.07 # SOURCE3 1
- angle_coeff @angle:c-s4-c harmonic 63.34 86.83 # SOURCE3 1
- angle_coeff @angle:cl-s4-cl harmonic 53.89 97.68 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-s4-o harmonic 58.13 108.34 # SOURCE3 2 0.0000
- angle_coeff @angle:c-s4-o harmonic 63.97 106.17 # SOURCE3 1
- angle_coeff @angle:cx-s4-cx harmonic 86.71 48.80 # SOURCE2 1 0.0000
- angle_coeff @angle:cx-s4-o harmonic 64.10 110.00 # SOURCE2 1 0.0000
- angle_coeff @angle:f-s4-f harmonic 69.99 92.71 # SOURCE2 3 0.1490
- angle_coeff @angle:f-s4-o harmonic 70.11 106.81 # SOURCE2 2 0.0100
- angle_coeff @angle:f-s4-s harmonic 59.78 107.50 # SOURCE2 1 0.0000
- angle_coeff @angle:hs-s4-hs harmonic 37.79 87.00 # SOURCE3 2 0.0202
- angle_coeff @angle:hs-s4-n1 harmonic 51.22 90.51 # HF/6-31G* 1
- angle_coeff @angle:hs-s4-o harmonic 49.80 110.27 # SOURCE3 5 0.1908
- angle_coeff @angle:i-s4-i harmonic 54.45 97.29 # SOURCE3 1
- angle_coeff @angle:i-s4-o harmonic 47.32 113.91 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-s4-n1 harmonic 72.41 94.02 # HF/6-31G* 1
- angle_coeff @angle:n1-s4-o harmonic 70.24 110.09 # HF/6-31G* 1
- angle_coeff @angle:n2-s4-n2 harmonic 75.77 90.17 # SOURCE3 1
- angle_coeff @angle:n2-s4-o harmonic 72.12 107.57 # SOURCE3 1
- angle_coeff @angle:n3-s4-n3 harmonic 68.89 91.19 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-s4-o harmonic 67.59 109.07 # SOURCE3 6 2.3605
- angle_coeff @angle:n4-s4-n4 harmonic 60.39 94.61 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-s4-o harmonic 63.17 104.91 # SOURCE3 3 0.4370
- angle_coeff @angle:na-s4-na harmonic 63.63 103.10 # SOURCE3 1
- angle_coeff @angle:na-s4-o harmonic 66.52 109.75 # SOURCE3 10 2.6919
- angle_coeff @angle:nh-s4-nh harmonic 68.96 92.24 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-s4-o harmonic 68.40 107.54 # SOURCE3 3 0.0401
- angle_coeff @angle:n-s4-n harmonic 68.03 91.30 # SOURCE3 1
- angle_coeff @angle:n-s4-o harmonic 68.09 105.70 # SOURCE3 4 1.6857
- angle_coeff @angle:no-s4-no harmonic 63.55 83.40 # SOURCE3 1 0.0000
- angle_coeff @angle:no-s4-o harmonic 62.93 103.58 # SOURCE3 3 1.5109
- angle_coeff @angle:oh-s4-oh harmonic 69.00 100.34 # SOURCE3 1
- angle_coeff @angle:o-s4-o harmonic 74.43 110.61 # SOURCE3 5 3.6413
- angle_coeff @angle:o-s4-oh harmonic 69.42 110.13 # SOURCE4 10 0.5760
- angle_coeff @angle:o-s4-os harmonic 69.67 109.02 # SOURCE3 8 1.5005
- angle_coeff @angle:o-s4-p2 harmonic 76.18 106.77 # SOURCE3 1
- angle_coeff @angle:o-s4-p3 harmonic 79.76 106.51 # SOURCE3 8 4.0943
- angle_coeff @angle:o-s4-p4 harmonic 75.38 103.36 # SOURCE3 1
- angle_coeff @angle:o-s4-p5 harmonic 85.32 96.95 # SOURCE3 1
- angle_coeff @angle:o-s4-s4 harmonic 63.80 104.55 # SOURCE3 1
- angle_coeff @angle:o-s4-s harmonic 61.69 112.22 # SOURCE3 4 2.8682
- angle_coeff @angle:o-s4-s6 harmonic 64.33 102.84 # SOURCE3 1
- angle_coeff @angle:o-s4-sh harmonic 60.56 107.51 # SOURCE3 3 0.7511
- angle_coeff @angle:os-s4-os harmonic 71.26 93.68 # SOURCE3 2 2.4166
- angle_coeff @angle:o-s4-ss harmonic 60.06 109.49 # SOURCE3 5 1.8509
- angle_coeff @angle:p2-s4-p2 harmonic 98.20 92.62 # SOURCE3 1
- angle_coeff @angle:p3-s4-p3 harmonic 101.37 95.71 # SOURCE3 2 1.2239
- angle_coeff @angle:p5-s4-p5 harmonic 104.72 93.86 # SOURCE3 1
- angle_coeff @angle:s4-s4-s4 harmonic 65.42 90.17 # SOURCE3 1
- angle_coeff @angle:s4-s4-s6 harmonic 65.42 90.17 # SOURCE3 1
- angle_coeff @angle:s6-s4-s6 harmonic 64.23 93.52 # SOURCE3 1
- angle_coeff @angle:sh-s4-sh harmonic 58.79 102.76 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-s4-ss harmonic 58.85 102.64 # SOURCE3 1
- angle_coeff @angle:s-s4-s harmonic 59.87 108.08 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-s4-ss harmonic 61.05 95.47 # SOURCE3 1 0.0000
- angle_coeff @angle:br-s6-br harmonic 67.11 101.57 # SOURCE3 1 0.0000
- angle_coeff @angle:br-s6-c3 harmonic 63.24 98.99 # SOURCE3 1 0.0000
- angle_coeff @angle:br-s6-f harmonic 63.06 100.60 # SOURCE2 1 0.0000
- angle_coeff @angle:br-s6-o harmonic 63.90 107.58 # SOURCE3 6 0.3000
- angle_coeff @angle:c1-s6-c1 harmonic 64.09 99.99 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-s6-o harmonic 68.10 108.23 # SOURCE3 4 0.0000
- angle_coeff @angle:c2-s6-c2 harmonic 61.86 102.75 # SOURCE3 1
- angle_coeff @angle:c2-s6-c3 harmonic 61.23 104.05 # SOURCE3 1
- angle_coeff @angle:c2-s6-o harmonic 67.53 106.58 # SOURCE3 1
- angle_coeff @angle:c3-s6-c3 harmonic 61.35 102.83 # SOURCE3 7 1.2531
- angle_coeff @angle:c3-s6-ca harmonic 61.51 103.17 # SOURCE3 1
- angle_coeff @angle:c3-s6-cy harmonic 62.55 94.57 # SOURCE4 8 0.4183
- angle_coeff @angle:c3-s6-f harmonic 65.73 97.11 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s6-hs harmonic 44.94 100.62 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s6-i harmonic 50.82 97.74 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s6-n2 harmonic 63.42 112.95 # SOURCE4 11 0.7920
- angle_coeff @angle:c3-s6-n3 harmonic 65.71 101.38 # SOURCE4 60 0.9507
- angle_coeff @angle:c3-s6-n harmonic 63.84 102.97 # SOURCE3 4 0.8785
- angle_coeff @angle:c3-s6-n4 harmonic 61.33 99.40 # SOURCE3 3 0.4695
- angle_coeff @angle:c3-s6-na harmonic 63.68 102.81 # SOURCE3 10 3.1256
- angle_coeff @angle:c3-s6-nh harmonic 63.74 104.31 # SOURCE4 34 1.5848
- angle_coeff @angle:c3-s6-no harmonic 60.08 99.57 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s6-o harmonic 66.59 108.32 # SOURCE3 112 1.8014
- angle_coeff @angle:c3-s6-oh harmonic 67.71 98.60 # SOURCE4 42 0.8366
- angle_coeff @angle:c3-s6-os harmonic 68.68 96.32 # SOURCE4 30 0.4539
- angle_coeff @angle:c3-s6-p2 harmonic 72.54 106.47 # SOURCE3 1
- angle_coeff @angle:c3-s6-p3 harmonic 76.24 103.40 # SOURCE3 3 0.8516
- angle_coeff @angle:c3-s6-p4 harmonic 71.10 104.12 # SOURCE3 1
- angle_coeff @angle:c3-s6-p5 harmonic 77.16 103.46 # SOURCE3 1
- angle_coeff @angle:c3-s6-s4 harmonic 61.78 98.10 # SOURCE3 1
- angle_coeff @angle:c3-s6-s harmonic 60.70 104.50 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s6-s6 harmonic 60.60 101.95 # SOURCE3 1
- angle_coeff @angle:c3-s6-sh harmonic 60.07 101.84 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-s6-ss harmonic 59.68 102.47 # SOURCE3 3 1.7451
- angle_coeff @angle:ca-s6-ca harmonic 61.80 103.08 # SOURCE3 1
- angle_coeff @angle:ca-s6-o harmonic 68.37 104.07 # SOURCE4 59 0.5636
- angle_coeff @angle:c-s6-c3 harmonic 60.12 101.24 # SOURCE3 1
- angle_coeff @angle:c-s6-c harmonic 59.07 99.82 # SOURCE3 1
- angle_coeff @angle:cc-s6-o harmonic 65.29 103.63 # SOURCE4 9 0.5934
- angle_coeff @angle:cl-s6-cl harmonic 52.93 101.25 # SOURCE3 1 0.0000
- angle_coeff @angle:cl-s6-f harmonic 57.88 99.00 # SOURCE2 1 0.0000
- angle_coeff @angle:cl-s6-o harmonic 58.51 107.66 # SOURCE3 4 0.0000
- angle_coeff @angle:c-s6-o harmonic 63.97 107.97 # SOURCE3 1
- angle_coeff @angle:c-s6-os harmonic 64.36 102.12 # SOURCE3 1
- angle_coeff @angle:cx-s6-cx harmonic 86.21 54.70 # SOURCE2 1 0.0000
- angle_coeff @angle:cy-s6-o harmonic 63.83 110.22 # SOURCE4 20 1.1009
- angle_coeff @angle:f-s6-f harmonic 70.81 94.70 # SOURCE2 3 0.9899
- angle_coeff @angle:f-s6-o harmonic 72.38 106.48 # SOURCE3 2 0.0000
- angle_coeff @angle:hs-s6-hs harmonic 35.84 99.02 # SOURCE3 2 0.0595
- angle_coeff @angle:hs-s6-n1 harmonic 54.71 97.27 # HF/6-31G* 1
- angle_coeff @angle:hs-s6-o harmonic 51.91 107.60 # SOURCE3 10 0.0343
- angle_coeff @angle:i-s6-i harmonic 53.90 99.25 # SOURCE3 1
- angle_coeff @angle:i-s6-o harmonic 47.73 109.74 # SOURCE3 2 0.0000
- angle_coeff @angle:n1-s6-n1 harmonic 83.71 95.52 # HF/6-31G* 1
- angle_coeff @angle:n1-s6-o harmonic 78.79 107.52 # HF/6-31G* 1
- angle_coeff @angle:n2-s6-n2 harmonic 75.20 98.61 # SOURCE3 1
- angle_coeff @angle:n2-s6-o harmonic 72.08 116.41 # SOURCE3 3 5.0830
- angle_coeff @angle:n2-s6-oh harmonic 71.75 106.96 # SOURCE3 2 0.0000
- angle_coeff @angle:n2-s6-os harmonic 73.30 103.25 # SOURCE3 1
- angle_coeff @angle:n3-s6-n3 harmonic 71.49 98.57 # SOURCE4 7 0.2690
- angle_coeff @angle:n3-s6-o harmonic 72.90 106.80 # SOURCE3 14 1.7908
- angle_coeff @angle:n3-s6-os harmonic 72.84 99.26 # SOURCE4 8 0.5141
- angle_coeff @angle:n4-s6-n4 harmonic 59.97 101.85 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-s6-o harmonic 65.83 102.92 # SOURCE3 10 1.5434
- angle_coeff @angle:na-s6-na harmonic 67.74 98.04 # SOURCE3 1
- angle_coeff @angle:na-s6-o harmonic 70.46 105.67 # SOURCE3 20 0.8019
- angle_coeff @angle:nh-s6-nh harmonic 70.22 94.56 # SOURCE3 1 0.0000
- angle_coeff @angle:nh-s6-o harmonic 70.23 109.12 # SOURCE3 6 0.9556
- angle_coeff @angle:n-s6-n harmonic 66.18 104.16 # SOURCE3 1
- angle_coeff @angle:n-s6-o harmonic 70.74 105.91 # SOURCE3 8 0.2953
- angle_coeff @angle:no-s6-no harmonic 61.24 91.63 # SOURCE3 1 0.0000
- angle_coeff @angle:no-s6-o harmonic 62.67 107.43 # SOURCE3 6 1.5494
- angle_coeff @angle:n-s6-os harmonic 70.81 99.23 # SOURCE4 5 0.9794
- angle_coeff @angle:oh-s6-oh harmonic 73.67 100.34 # SOURCE3 6 0.0076
- angle_coeff @angle:oh-s6-os harmonic 75.33 96.62 # SOURCE4 26 0.6688
- angle_coeff @angle:oh-s6-p2 harmonic 75.13 109.67 # SOURCE3 2 0.0000
- angle_coeff @angle:o-s6-o harmonic 74.58 119.73 # SOURCE4 324 2.0530
- angle_coeff @angle:o-s6-oh harmonic 74.13 108.21 # SOURCE3 18 0.7437
- angle_coeff @angle:o-s6-os harmonic 74.58 107.84 # SOURCE3 12 0.7025
- angle_coeff @angle:o-s6-p2 harmonic 76.65 106.61 # SOURCE3 1
- angle_coeff @angle:o-s6-p3 harmonic 80.16 107.07 # SOURCE3 22 1.0550
- angle_coeff @angle:o-s6-p4 harmonic 73.92 105.67 # SOURCE3 1
- angle_coeff @angle:o-s6-p5 harmonic 81.69 106.64 # SOURCE3 1
- angle_coeff @angle:o-s6-s4 harmonic 63.02 107.85 # SOURCE3 1
- angle_coeff @angle:o-s6-s harmonic 63.52 110.29 # SOURCE3 6 2.2405
- angle_coeff @angle:o-s6-s6 harmonic 63.55 106.07 # SOURCE3 1
- angle_coeff @angle:o-s6-sh harmonic 62.53 106.81 # SOURCE3 6 0.6292
- angle_coeff @angle:os-s6-os harmonic 74.80 98.70 # SOURCE3 1 0.0000
- angle_coeff @angle:o-s6-ss harmonic 62.06 107.43 # SOURCE3 10 1.1423
- angle_coeff @angle:p3-s6-p3 harmonic 94.93 110.17 # SOURCE3 4 5.3678
- angle_coeff @angle:p5-s6-p5 harmonic 99.25 104.49 # SOURCE3 1
- angle_coeff @angle:s4-s6-s4 harmonic 61.51 101.99 # SOURCE3 1
- angle_coeff @angle:s4-s6-s6 harmonic 65.42 90.17 # SOURCE3 1
- angle_coeff @angle:s6-s6-s6 harmonic 61.12 103.29 # SOURCE3 1
- angle_coeff @angle:sh-s6-sh harmonic 59.41 106.43 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-s6-ss harmonic 60.36 102.64 # SOURCE3 1
- angle_coeff @angle:s-s6-s harmonic 60.63 109.34 # SOURCE3 1 0.0000
- angle_coeff @angle:ss-s6-ss harmonic 60.46 101.82 # SOURCE3 1 0.0000
- angle_coeff @angle:br-sh-hs harmonic 43.54 95.64 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-sh-hs harmonic 48.23 95.99 # calculated_based_on_C#C-SH 0
- angle_coeff @angle:c2-sh-hs harmonic 45.81 97.08 # SOURCE4 5 0.3132
- angle_coeff @angle:c3-sh-hs harmonic 44.94 96.60 # SOURCE3 12 0.8009
- angle_coeff @angle:ca-sh-hs harmonic 46.32 94.84 # SOURCE4 13 0.4130
- angle_coeff @angle:cc-sh-hs harmonic 46.41 95.38 # SOURCE4 8 1.1410
- angle_coeff @angle:c-sh-hs harmonic 45.96 96.07 # SOURCE3 6 1.1164
- angle_coeff @angle:f-sh-hs harmonic 48.09 96.50 # SOURCE3 1 0.0000
- angle_coeff @angle:hs-sh-hs harmonic 37.45 93.72 # SOURCE3 3 0.4777
- angle_coeff @angle:hs-sh-i harmonic 37.09 96.44 # SOURCE3 1 0.0000
- angle_coeff @angle:hs-sh-n1 harmonic 51.69 93.51 # HF/6-31G* 1
- angle_coeff @angle:hs-sh-n2 harmonic 48.12 95.82 # SOURCE3 5 3.1495
- angle_coeff @angle:hs-sh-n harmonic 48.41 95.59 # SOURCE3 4 3.9065
- angle_coeff @angle:hs-sh-n3 harmonic 48.06 95.98 # SOURCE3 3 1.1735
- angle_coeff @angle:hs-sh-n4 harmonic 47.15 93.13 # SOURCE3 3 0.1675
- angle_coeff @angle:hs-sh-na harmonic 48.12 97.38 # SOURCE3 9 1.0223
- angle_coeff @angle:hs-sh-nh harmonic 47.52 101.11 # SOURCE3 1 0.0000
- angle_coeff @angle:hs-sh-no harmonic 47.35 92.93 # SOURCE3 1 0.0000
- angle_coeff @angle:hs-sh-o harmonic 48.22 109.23 # SOURCE3 2 0.0068
- angle_coeff @angle:hs-sh-oh harmonic 48.75 98.64 # SOURCE3 2 0.0605
- angle_coeff @angle:hs-sh-os harmonic 49.35 98.15 # SOURCE3 3 0.1661
- angle_coeff @angle:hs-sh-p2 harmonic 56.52 99.12 # SOURCE3 10 5.4110
- angle_coeff @angle:hs-sh-p3 harmonic 53.11 95.81 # SOURCE3 3 0.4396
- angle_coeff @angle:hs-sh-p4 harmonic 54.01 94.22 # SOURCE3 4 0.7605
- angle_coeff @angle:hs-sh-p5 harmonic 54.80 94.52 # SOURCE3 3 0.5589
- angle_coeff @angle:hs-sh-s harmonic 40.94 102.87 # SOURCE3 2 0.0000
- angle_coeff @angle:hs-sh-s4 harmonic 42.04 92.16 # SOURCE3 3 1.6519
- angle_coeff @angle:hs-sh-s6 harmonic 42.91 93.83 # SOURCE3 3 1.2561
- angle_coeff @angle:hs-sh-sh harmonic 42.80 99.07 # SOURCE3 2 0.0000
- angle_coeff @angle:hs-sh-ss harmonic 42.59 99.17 # SOURCE3 3 0.2457
- angle_coeff @angle:br-ss-br harmonic 67.00 102.92 # SOURCE3 1 0.0000
- angle_coeff @angle:br-ss-c3 harmonic 63.06 99.03 # SOURCE3 1 0.0000
- angle_coeff @angle:c1-ss-c1 harmonic 66.30 98.30 # SOURCE2 1 0.0000
- angle_coeff @angle:c1-ss-c3 harmonic 62.89 99.90 # SOURCE2 1 0.0000
- angle_coeff @angle:c2-ss-c2 harmonic 63.71 99.56 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-ss-c3 harmonic 61.87 100.37 # SOURCE4 100 2.3280
- angle_coeff @angle:c2-ss-cy harmonic 65.30 88.61 # SOURCE4 27 0.4481
- angle_coeff @angle:c2-ss-n2 harmonic 64.45 106.76 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-ss-na harmonic 65.02 100.51 # SOURCE3 6 6.9702
- angle_coeff @angle:c2-ss-os harmonic 69.78 89.76 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-ss-ss harmonic 64.78 92.26 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-c3 harmonic 60.63 99.92 # SOURCE3 14 2.0723
- angle_coeff @angle:c3-ss-ca harmonic 60.80 102.12 # SOURCE4 161 1.3084
- angle_coeff @angle:c3-ss-cc harmonic 61.74 100.75 # CORR 87
- angle_coeff @angle:c3-ss-cd harmonic 61.74 100.75 # CORR 87
- angle_coeff @angle:c3-ss-cl harmonic 56.40 99.40 # SOURCE2 1 0.0000
- angle_coeff @angle:c3-ss-cy harmonic 61.94 94.32 # SOURCE4 62 0.3646
- angle_coeff @angle:c3-ss-f harmonic 63.40 97.49 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-i harmonic 56.03 100.00 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-n1 harmonic 65.93 98.44 # HF/6-31G* 1
- angle_coeff @angle:c3-ss-n2 harmonic 65.94 96.42 # SOURCE3 5 1.3604
- angle_coeff @angle:c3-ss-n3 harmonic 64.10 98.83 # SOURCE3 3 0.2909
- angle_coeff @angle:c3-ss-n harmonic 63.71 100.30 # SOURCE3 4 0.6579
- angle_coeff @angle:c3-ss-n4 harmonic 62.94 97.79 # SOURCE3 3 0.2002
- angle_coeff @angle:c3-ss-na harmonic 63.51 100.14 # SOURCE3 12 1.7415
- angle_coeff @angle:c3-ss-nh harmonic 63.75 100.63 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-no harmonic 62.40 98.62 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-o harmonic 64.67 106.60 # SOURCE3 2 1.6714
- angle_coeff @angle:c3-ss-oh harmonic 65.29 98.28 # SOURCE3 2 1.4326
- angle_coeff @angle:c3-ss-os harmonic 64.97 98.21 # SOURCE3 4 1.7097
- angle_coeff @angle:c3-ss-p2 harmonic 80.22 98.41 # SOURCE3 8 0.9454
- angle_coeff @angle:c3-ss-p3 harmonic 76.29 98.70 # SOURCE3 3 0.0356
- angle_coeff @angle:c3-ss-p4 harmonic 76.93 98.16 # SOURCE3 4 0.1361
- angle_coeff @angle:c3-ss-p5 harmonic 75.86 100.22 # SOURCE4 23 1.1410
- angle_coeff @angle:c3-ss-s4 harmonic 60.11 96.37 # SOURCE3 3 0.0202
- angle_coeff @angle:c3-ss-s harmonic 59.94 101.90 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-s6 harmonic 60.94 96.76 # SOURCE3 3 1.5680
- angle_coeff @angle:c3-ss-sh harmonic 60.36 101.93 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-ss-ss harmonic 60.34 103.10 # SOURCE4 70 1.3377
- angle_coeff @angle:ca-ss-ca harmonic 62.76 98.71 # SOURCE4 97 1.2321
- angle_coeff @angle:ca-ss-cc harmonic 66.53 89.47 # CORR 134
- angle_coeff @angle:ca-ss-cd harmonic 66.53 89.47 # CORR 134
- angle_coeff @angle:ca-ss-cl harmonic 56.45 101.05 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-ss-n harmonic 65.76 97.16 # SOURCE3 1
- angle_coeff @angle:ca-ss-na harmonic 64.76 99.32 # SOURCE3 1
- angle_coeff @angle:ca-ss-nc harmonic 69.21 94.76 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-ss-nd harmonic 69.21 94.76 # SOURCE3 1 same_as_ca-ss-nc
- angle_coeff @angle:ca-ss-ss harmonic 60.39 104.90 # SOURCE4 19 0.8743
- angle_coeff @angle:c-ss-c2 harmonic 65.63 92.43 # SOURCE3 1 0.0000
- angle_coeff @angle:c-ss-c3 harmonic 61.48 100.29 # SOURCE3 5 2.2127
- angle_coeff @angle:c-ss-c harmonic 62.20 101.40 # SOURCE3 1 0.0000
- angle_coeff @angle:c-ss-cc harmonic 65.61 92.43 # SOURCE4 14 2.3600
- angle_coeff @angle:cc-ss-cc harmonic 67.01 89.91 # SOURCE3 11 2.2164
- angle_coeff @angle:cc-ss-cd harmonic 67.07 89.74 # SOURCE4 49 0.7509
- angle_coeff @angle:cc-ss-n harmonic 66.42 97.16 # SOURCE3 1 same_as_cd-ss-n
- angle_coeff @angle:cc-ss-na harmonic 65.39 99.33 # SOURCE3 18 same_as_cd-ss-na
- angle_coeff @angle:cc-ss-nc harmonic 70.31 94.08 # CORR 13
- angle_coeff @angle:cc-ss-os harmonic 66.48 98.81 # SOURCE3 2 2.1583
- angle_coeff @angle:cc-ss-ss harmonic 63.91 94.76 # CORR 13
- angle_coeff @angle:cd-ss-cd harmonic 67.01 89.91 # SOURCE3 11 2.2164
- angle_coeff @angle:cd-ss-n harmonic 66.42 97.16 # SOURCE3 1 0.0000
- angle_coeff @angle:cd-ss-na harmonic 65.39 99.33 # SOURCE3 18 2.5847
- angle_coeff @angle:cd-ss-nd harmonic 70.31 94.08 # CORR 13
- angle_coeff @angle:cd-ss-os harmonic 66.48 98.81 # SOURCE3 2 same_as_cc-ss-os
- angle_coeff @angle:cd-ss-ss harmonic 63.91 94.76 # CORR 13
- angle_coeff @angle:cl-ss-cl harmonic 52.39 103.37 # SOURCE3 1 0.0000
- angle_coeff @angle:cx-ss-cx harmonic 87.49 48.30 # SOURCE2 1 0.0000
- angle_coeff @angle:f-ss-f harmonic 66.18 98.30 # SOURCE2 1 0.0000
- angle_coeff @angle:f-ss-ss harmonic 59.85 108.30 # SOURCE2 1 0.0000
- angle_coeff @angle:i-ss-i harmonic 58.15 106.29 # SOURCE3 1 0.0000
- angle_coeff @angle:n1-ss-n1 harmonic 73.07 96.96 # HF/6-31G* 1
- angle_coeff @angle:n2-ss-n2 harmonic 71.12 96.75 # SOURCE3 1 0.0000
- angle_coeff @angle:n3-ss-n3 harmonic 66.50 102.34 # SOURCE3 1 0.0000
- angle_coeff @angle:n4-ss-n4 harmonic 63.55 101.19 # SOURCE3 1 0.0000
- angle_coeff @angle:na-ss-na harmonic 65.92 102.81 # SOURCE3 1 0.0000
- angle_coeff @angle:nc-ss-nc harmonic 75.03 97.94 # CORR 9
- angle_coeff @angle:nd-ss-nd harmonic 75.03 97.94 # CORR 9
- angle_coeff @angle:nh-ss-nh harmonic 65.30 107.89 # SOURCE3 1 0.0000
- angle_coeff @angle:n-ss-n harmonic 66.45 103.10 # SOURCE3 1 0.0000
- angle_coeff @angle:no-ss-no harmonic 61.43 106.43 # SOURCE3 1 0.0000
- angle_coeff @angle:oh-ss-oh harmonic 68.23 104.25 # SOURCE3 1 0.0000
- angle_coeff @angle:o-ss-o harmonic 69.80 119.30 # SOURCE2 1 0.0000
- angle_coeff @angle:o-ss-p5 harmonic 78.64 106.41 # SOURCE3 1 0.0000
- angle_coeff @angle:o-ss-s6 harmonic 62.35 105.39 # SOURCE3 1
- angle_coeff @angle:os-ss-os harmonic 67.76 102.99 # SOURCE3 1 0.0000
- angle_coeff @angle:o-ss-ss harmonic 62.04 112.70 # SOURCE2 1 0.0000
- angle_coeff @angle:p2-ss-p2 harmonic 105.52 99.52 # SOURCE3 1 0.0000
- angle_coeff @angle:p3-ss-p3 harmonic 96.77 101.67 # SOURCE3 1
- angle_coeff @angle:p5-ss-p5 harmonic 103.25 89.83 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-ss-s4 harmonic 60.86 96.08 # SOURCE3 1 0.0000
- angle_coeff @angle:s4-ss-s6 harmonic 59.93 101.26 # SOURCE3 1
- angle_coeff @angle:s6-ss-s6 harmonic 60.46 101.81 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-ss-sh harmonic 60.28 107.54 # SOURCE3 1 0.0000
- angle_coeff @angle:sh-ss-ss harmonic 60.81 106.53 # SOURCE3 1
- angle_coeff @angle:s-ss-s harmonic 57.67 115.04 # SOURCE3 1
- angle_coeff @angle:ss-ss-ss harmonic 60.44 108.76 # SOURCE4 8 0.2385
- angle_coeff @angle:c3-sx-ca harmonic 61.85 96.41 # SOURCE4 13 0.3130
- angle_coeff @angle:c3-sx-cc harmonic 62.52 95.11 # SOURCE4 17 0.6557
- angle_coeff @angle:c3-sx-ce harmonic 62.82 94.95 # SOURCE3 3 0.0007
- angle_coeff @angle:c3-sx-cf harmonic 62.82 94.95 # SOURCE3 3 same_as_c3-sx-ce
- angle_coeff @angle:c3-sx-ne harmonic 65.33 90.06 # SOURCE3 5 1.9627
- angle_coeff @angle:c3-sx-nf harmonic 65.33 90.06 # SOURCE3 5 same_as_c3-sx-ne
- angle_coeff @angle:c3-sx-o harmonic 64.94 107.88 # SOURCE3 30 0.8721
- angle_coeff @angle:c3-sx-pe harmonic 76.99 94.32 # SOURCE3 7 0.5547
- angle_coeff @angle:c3-sx-pf harmonic 76.99 94.32 # SOURCE3 7 same_as_c3-sx-pe
- angle_coeff @angle:c3-sx-px harmonic 74.26 96.46 # SOURCE3 3 1.3351
- angle_coeff @angle:c3-sx-py harmonic 74.13 95.67 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-sx-sx harmonic 57.22 91.47 # SOURCE3 4 1.9919
- angle_coeff @angle:c3-sx-sy harmonic 58.71 95.47 # SOURCE3 3 2.8422
- angle_coeff @angle:ca-sx-ca harmonic 61.97 95.21 # SOURCE3 1 0.0000
- angle_coeff @angle:ca-sx-o harmonic 64.82 106.89 # SOURCE4 25 0.5562
- angle_coeff @angle:c-sx-c3 harmonic 62.01 92.71 # SOURCE3 3 0.3095
- angle_coeff @angle:c-sx-c harmonic 62.83 86.85 # SOURCE3 1 0.0000
- angle_coeff @angle:cc-sx-o harmonic 65.92 104.49 # SOURCE4 17 1.7759
- angle_coeff @angle:ce-sx-ce harmonic 63.02 94.96 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-sx-o harmonic 65.38 107.47 # SOURCE3 5 0.3128
- angle_coeff @angle:cf-sx-cf harmonic 63.02 94.96 # SOURCE3 1 same_as_ce-sx-ce
- angle_coeff @angle:cf-sx-o harmonic 65.38 107.47 # SOURCE3 5 same_as_ce-sx-o
- angle_coeff @angle:c-sx-o harmonic 63.47 106.17 # SOURCE3 5 0.9477
- angle_coeff @angle:ne-sx-ne harmonic 66.37 90.17 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-sx-o harmonic 65.36 109.20 # SOURCE3 7 1.4542
- angle_coeff @angle:nf-sx-nf harmonic 66.37 90.17 # SOURCE3 1 same_as_ne-sx-ne
- angle_coeff @angle:nf-sx-o harmonic 65.36 109.20 # SOURCE3 7 same_as_ne-sx-o
- angle_coeff @angle:o-sx-pe harmonic 77.00 106.43 # SOURCE3 9 2.8345
- angle_coeff @angle:o-sx-pf harmonic 77.00 106.43 # SOURCE3 9 same_as_o-sx-pe
- angle_coeff @angle:o-sx-px harmonic 75.16 104.77 # SOURCE3 3 1.9810
- angle_coeff @angle:o-sx-py harmonic 73.10 109.13 # SOURCE3 7 5.6840
- angle_coeff @angle:o-sx-sx harmonic 55.68 104.65 # SOURCE3 6 3.0524
- angle_coeff @angle:o-sx-sy harmonic 59.44 103.41 # SOURCE3 5 0.9618
- angle_coeff @angle:pe-sx-pe harmonic 99.19 92.62 # SOURCE3 1 0.0000
- angle_coeff @angle:pf-sx-pf harmonic 99.19 92.62 # SOURCE3 1 same_as_pe-sx-pe
- angle_coeff @angle:py-sx-py harmonic 110.11 69.23 # SOURCE3 3 17.4143
- angle_coeff @angle:sx-sx-sx harmonic 58.65 84.90 # SOURCE3 1 0.0000
- angle_coeff @angle:sy-sx-sy harmonic 59.25 93.52 # SOURCE3 1 0.0000
- angle_coeff @angle:c3-sy-ca harmonic 60.74 103.86 # SOURCE4 54 0.3180
- angle_coeff @angle:c3-sy-cc harmonic 61.24 102.19 # SOURCE4 12 1.5324
- angle_coeff @angle:c3-sy-ce harmonic 60.79 103.81 # SOURCE3 3 0.3368
- angle_coeff @angle:c3-sy-cf harmonic 60.79 103.81 # SOURCE3 3 same_as_c3-sy-ce
- angle_coeff @angle:c3-sy-ne harmonic 63.01 103.12 # SOURCE3 5 4.1882
- angle_coeff @angle:c3-sy-nf harmonic 63.01 103.12 # SOURCE3 5 same_as_c3-sy-ne
- angle_coeff @angle:c3-sy-o harmonic 65.97 108.48 # SOURCE3 62 0.8576
- angle_coeff @angle:c3-sy-pe harmonic 71.79 106.03 # SOURCE3 6 2.6117
- angle_coeff @angle:c3-sy-pf harmonic 71.79 106.03 # SOURCE3 6 same_as_c3-sy-pe
- angle_coeff @angle:c3-sy-px harmonic 71.71 103.62 # SOURCE3 3 0.7078
- angle_coeff @angle:c3-sy-py harmonic 73.48 103.39 # SOURCE3 3 0.4563
- angle_coeff @angle:c3-sy-sx harmonic 56.27 104.64 # SOURCE3 3 4.6276
- angle_coeff @angle:c3-sy-sy harmonic 57.43 100.78 # SOURCE3 4 1.1633
- angle_coeff @angle:ca-sy-ca harmonic 60.65 104.04 # SOURCE4 25 2.0762
- angle_coeff @angle:ca-sy-cc harmonic 60.36 105.09 # SOURCE4 5 0.3628
- angle_coeff @angle:ca-sy-n3 harmonic 64.10 102.48 # SOURCE4 180 1.0802
- angle_coeff @angle:ca-sy-n harmonic 62.89 105.45 # SOURCE4 51 1.1497
- angle_coeff @angle:ca-sy-ne harmonic 62.86 103.47 # SOURCE4 11 1.6071
- angle_coeff @angle:ca-sy-nh harmonic 62.86 105.59 # SOURCE4 78 1.5805
- angle_coeff @angle:ca-sy-o harmonic 65.84 108.73 # SOURCE3 26 1.2638
- angle_coeff @angle:ca-sy-oh harmonic 65.64 101.25 # SOURCE4 23 0.9100
- angle_coeff @angle:ca-sy-os harmonic 67.64 92.98 # SOURCE3 1 0.0000
- angle_coeff @angle:c-sy-c3 harmonic 60.09 101.25 # SOURCE3 3 1.1850
- angle_coeff @angle:c-sy-c harmonic 59.23 99.81 # SOURCE3 1 0.0000
- angle_coeff @angle:cc-sy-n3 harmonic 64.10 102.54 # CORR 30
- angle_coeff @angle:cc-sy-o harmonic 66.17 107.71 # CORR 100
- angle_coeff @angle:cd-sy-n3 harmonic 64.10 102.54 # CORR 30
- angle_coeff @angle:cd-sy-nh harmonic 65.53 97.20 # SOURCE4 6 0.2429
- angle_coeff @angle:cd-sy-o harmonic 66.17 107.71 # CORR 100
- angle_coeff @angle:ce-sy-ce harmonic 61.09 102.78 # SOURCE3 1 0.0000
- angle_coeff @angle:ce-sy-o harmonic 66.35 107.25 # SOURCE3 10 0.5477
- angle_coeff @angle:cf-sy-cf harmonic 61.09 102.78 # SOURCE3 1 same_as_ce-sy-ce
- angle_coeff @angle:cf-sy-o harmonic 66.35 107.25 # SOURCE3 10 same_as_ce-sy-o
- angle_coeff @angle:c-sy-o harmonic 64.07 107.23 # SOURCE3 10 0.8425
- angle_coeff @angle:f-sy-o harmonic 63.64 105.60 # SOURCE4 7 0.2000
- angle_coeff @angle:n2-sy-o harmonic 61.16 123.53 # SOURCE4 6 1.2388
- angle_coeff @angle:n3-sy-ne harmonic 66.36 102.40 # SOURCE4 5 1.3390
- angle_coeff @angle:n3-sy-o harmonic 70.45 107.11 # SOURCE4 375 1.1257
- angle_coeff @angle:na-sy-na harmonic 67.74 98.04 # SOURCE3 1
- angle_coeff @angle:nc-sy-nc harmonic 75.24 98.04 # SOURCE3 2
- angle_coeff @angle:nd-sy-nd harmonic 75.24 98.04 # SOURCE3 2
- angle_coeff @angle:ne-sy-ne harmonic 66.58 98.62 # SOURCE3 1 0.0000
- angle_coeff @angle:ne-sy-o harmonic 68.89 107.06 # SOURCE3 14 2.2705
- angle_coeff @angle:nf-sy-nf harmonic 66.58 98.62 # SOURCE3 1 same_as_ne-sy-ne
- angle_coeff @angle:nf-sy-o harmonic 68.89 107.06 # SOURCE3 14 same_as_ne-sy-o
- angle_coeff @angle:nh-sy-o harmonic 70.18 106.38 # SOURCE4 123 1.6517
- angle_coeff @angle:n-sy-o harmonic 69.79 107.50 # SOURCE4 61 1.8720
- angle_coeff @angle:o-sy-o harmonic 72.40 121.88 # SOURCE3 46 0.9495
- angle_coeff @angle:o-sy-oh harmonic 72.26 106.93 # SOURCE3 8 0.7424
- angle_coeff @angle:o-sy-os harmonic 70.39 108.31 # SOURCE4 7 0.1222
- angle_coeff @angle:o-sy-pe harmonic 75.40 106.90 # SOURCE3 12 1.4524
- angle_coeff @angle:o-sy-pf harmonic 75.40 106.90 # SOURCE3 12 same_as_o-sy-pe
- angle_coeff @angle:o-sy-px harmonic 74.45 106.17 # SOURCE3 6 0.7059
- angle_coeff @angle:o-sy-py harmonic 76.54 106.67 # SOURCE3 10 0.6478
- angle_coeff @angle:o-sy-sx harmonic 58.62 106.33 # SOURCE3 10 2.0456
- angle_coeff @angle:o-sy-sy harmonic 58.79 106.19 # SOURCE3 12 0.1754
- angle_coeff @angle:py-sy-py harmonic 92.79 104.49 # SOURCE3 1 0.0000
- angle_coeff @angle:sx-sy-sx harmonic 56.74 101.99 # SOURCE3 1 0.0000
- angle_coeff @angle:sy-sy-sy harmonic 56.50 103.29 # SOURCE3 1 0.0000
- angle_coeff @angle:c2-c1-cf harmonic 58.18 179.01 # NEW 6
- angle_coeff @angle:c3-c1-ch harmonic 55.79 178.52 # NEW 39
- angle_coeff @angle:nf-c1-s harmonic 57.59 175.81 # NEW 8
- angle_coeff @angle:br-c2-cf harmonic 63.21 121.59 # NEW 7
- angle_coeff @angle:cd-c2-h4 harmonic 49.19 120.33 # NEW 7
- angle_coeff @angle:cd-c2-nh harmonic 69.46 122.96 # NEW 10
- angle_coeff @angle:cd-c2-o harmonic 72.80 123.59 # NEW 6
- angle_coeff @angle:cf-c2-cl harmonic 58.06 123.90 # NEW 11
- angle_coeff @angle:cf-c2-h4 harmonic 49.38 122.29 # NEW 75
- angle_coeff @angle:cf-c2-na harmonic 68.82 123.71 # NEW 6
- angle_coeff @angle:cf-c2-nh harmonic 70.64 120.72 # NEW 93
- angle_coeff @angle:cf-c2-no harmonic 68.45 119.65 # NEW 5
- angle_coeff @angle:cf-c2-o harmonic 73.66 123.08 # NEW 5
- angle_coeff @angle:cf-c2-oh harmonic 70.90 123.27 # NEW 42
- angle_coeff @angle:cf-c2-os harmonic 70.47 122.52 # NEW 51
- angle_coeff @angle:h4-c2-nf harmonic 52.87 119.63 # NEW 10
- angle_coeff @angle:h5-c2-nf harmonic 52.76 119.62 # NEW 17
- angle_coeff @angle:nf-c2-os harmonic 74.86 118.76 # NEW 5
- angle_coeff @angle:nf-c2-ss harmonic 65.41 120.06 # NEW 9
- angle_coeff @angle:n-c2-nf harmonic 70.89 125.38 # NEW 10
- angle_coeff @angle:ca-c3-cf harmonic 63.81 112.33 # NEW 51
- angle_coeff @angle:cd-c3-cx harmonic 63.85 112.55 # NEW 5
- angle_coeff @angle:c-c3-cf harmonic 64.02 111.98 # NEW 16
- angle_coeff @angle:cd-c3-hx harmonic 47.17 111.02 # NEW 9
- angle_coeff @angle:cd-c3-n2 harmonic 66.85 110.47 # NEW 11
- angle_coeff @angle:cd-c3-n4 harmonic 64.88 115.58 # NEW 6
- angle_coeff @angle:cd-c3-na harmonic 66.43 113.39 # NEW 8
- angle_coeff @angle:cd-c3-p5 harmonic 76.89 116.23 # NEW 6
- angle_coeff @angle:cf-c3-cf harmonic 64.24 111.44 # NEW 18
- angle_coeff @angle:cf-c3-n harmonic 67.09 110.41 # NEW 6
- angle_coeff @angle:cf-c3-oh harmonic 68.00 111.05 # NEW 17
- angle_coeff @angle:cf-c3-os harmonic 68.64 108.10 # NEW 16
- angle_coeff @angle:cf-c3-ss harmonic 61.87 111.10 # NEW 7
- angle_coeff @angle:cd-ca-cq harmonic 64.63 124.30 # NEW 10
- angle_coeff @angle:cf-ca-na harmonic 67.44 119.85 # NEW 9
- angle_coeff @angle:ch-ca-cq harmonic 65.26 121.53 # NEW 12
- angle_coeff @angle:cl-ca-cq harmonic 58.19 120.31 # NEW 18
- angle_coeff @angle:cq-ca-f harmonic 67.10 119.39 # NEW 16
- angle_coeff @angle:cq-ca-h4 harmonic 48.15 120.03 # NEW 27
- angle_coeff @angle:cq-ca-na harmonic 72.91 108.79 # NEW 165
- angle_coeff @angle:cq-ca-nb harmonic 68.56 123.72 # NEW 50
- angle_coeff @angle:cq-ca-nh harmonic 68.66 121.52 # NEW 11
- angle_coeff @angle:cq-ca-oh harmonic 69.26 120.96 # NEW 12
- angle_coeff @angle:cq-ca-ss harmonic 63.87 112.75 # NEW 8
- angle_coeff @angle:ca-c-nf harmonic 67.74 114.39 # NEW 5
- angle_coeff @angle:br-cd-c harmonic 63.98 115.68 # NEW 8
- angle_coeff @angle:br-cd-cd harmonic 61.82 124.89 # NEW 8
- angle_coeff @angle:br-cd-cc harmonic 62.26 124.56 # NEW 32
- angle_coeff @angle:br-cd-na harmonic 64.60 121.42 # NEW 6
- angle_coeff @angle:ca-cd-cf harmonic 62.51 127.87 # NEW 11
- angle_coeff @angle:ca-cd-nh harmonic 67.46 122.45 # NEW 9
- angle_coeff @angle:cd-c-cf harmonic 64.64 115.68 # NEW 6
- angle_coeff @angle:cd-cd-f harmonic 66.35 119.41 # NEW 7
- angle_coeff @angle:c-cd-ch harmonic 64.98 118.14 # NEW 7
- angle_coeff @angle:cd-cd-sy harmonic 59.22 128.36 # NEW 8
- angle_coeff @angle:cc-cd-f harmonic 67.42 121.08 # NEW 28
- angle_coeff @angle:cc-cd-no harmonic 65.78 128.95 # NEW 117
- angle_coeff @angle:c-cd-f harmonic 66.16 116.87 # NEW 16
- angle_coeff @angle:ch-cd-na harmonic 67.51 122.35 # NEW 5
- angle_coeff @angle:ch-cd-ss harmonic 62.33 120.70 # NEW 12
- angle_coeff @angle:cd-c-h4 harmonic 47.13 115.45 # NEW 5
- angle_coeff @angle:cl-cd-na harmonic 59.37 121.61 # NEW 12
- angle_coeff @angle:cl-cd-ss harmonic 58.09 119.85 # NEW 11
- angle_coeff @angle:c-cd-nf harmonic 67.11 119.88 # NEW 6
- angle_coeff @angle:cd-c-s harmonic 61.67 127.94 # NEW 12
- angle_coeff @angle:cd-c-ss harmonic 63.47 112.52 # NEW 10
- angle_coeff @angle:cx-cd-nc harmonic 65.61 127.75 # NEW 12
- angle_coeff @angle:cx-cd-os harmonic 67.94 118.08 # NEW 10
- angle_coeff @angle:cc-c-cx harmonic 63.88 117.46 # NEW 13
- angle_coeff @angle:cc-c-nc harmonic 68.65 113.75 # NEW 14
- angle_coeff @angle:cf-c-cx harmonic 63.95 116.25 # NEW 6
- angle_coeff @angle:cf-c-h4 harmonic 46.93 114.88 # NEW 19
- angle_coeff @angle:cf-c-ss harmonic 63.94 110.39 # NEW 5
- angle_coeff @angle:na-cd-no harmonic 68.48 124.90 # NEW 48
- angle_coeff @angle:na-cd-oh harmonic 73.25 117.26 # NEW 16
- angle_coeff @angle:na-cd-sx harmonic 63.25 117.04 # NEW 13
- angle_coeff @angle:na-cd-sy harmonic 63.13 120.55 # NEW 7
- angle_coeff @angle:nd-cd-no harmonic 69.31 121.54 # NEW 7
- angle_coeff @angle:nc-cd-nc harmonic 70.88 128.17 # NEW 7
- angle_coeff @angle:nc-cd-nf harmonic 69.29 129.66 # NEW 7
- angle_coeff @angle:nc-cd-no harmonic 69.90 122.68 # NEW 16
- angle_coeff @angle:nc-cd-sh harmonic 62.75 124.92 # NEW 5
- angle_coeff @angle:nc-cd-sx harmonic 60.81 127.60 # NEW 14
- angle_coeff @angle:nc-cd-sy harmonic 62.75 123.08 # NEW 13
- angle_coeff @angle:nf-cd-ss harmonic 65.39 116.99 # NEW 7
- angle_coeff @angle:n-cd-n2 harmonic 74.78 114.48 # NEW 15
- angle_coeff @angle:no-cd-os harmonic 71.01 117.59 # NEW 62
- angle_coeff @angle:no-cd-ss harmonic 63.76 121.10 # NEW 10
- angle_coeff @angle:ca-cc-cf harmonic 65.09 125.10 # NEW 9
- angle_coeff @angle:ca-cc-na harmonic 67.03 123.45 # NEW 39
- angle_coeff @angle:cd-cc-cg harmonic 64.92 126.05 # NEW 30
- angle_coeff @angle:cd-cc-cy harmonic 63.93 122.13 # NEW 10
- angle_coeff @angle:cd-cc-nd harmonic 69.42 123.82 # NEW 14
- angle_coeff @angle:cc-cc-cy harmonic 63.17 120.93 # NEW 6
- angle_coeff @angle:cf-cc-nc harmonic 68.22 124.90 # NEW 5
- angle_coeff @angle:c-cc-h4 harmonic 46.77 118.19 # NEW 8
- angle_coeff @angle:na-cc-nh harmonic 72.43 116.98 # NEW 46
- angle_coeff @angle:na-cc-ss harmonic 67.07 111.46 # NEW 20
- angle_coeff @angle:nc-cc-nc harmonic 69.47 125.58 # NEW 13
- angle_coeff @angle:oh-cc-os harmonic 75.54 111.61 # NEW 6
- angle_coeff @angle:c2-cf-cl harmonic 57.87 119.51 # NEW 24
- angle_coeff @angle:c2-cf-h4 harmonic 48.64 125.58 # NEW 11
- angle_coeff @angle:c2-cf-n1 harmonic 72.67 117.85 # NEW 7
- angle_coeff @angle:c2-cf-na harmonic 69.29 119.19 # NEW 5
- angle_coeff @angle:c2-cf-oh harmonic 70.32 123.78 # NEW 10
- angle_coeff @angle:c3-cf-ch harmonic 63.79 118.48 # NEW 8
- angle_coeff @angle:c3-cf-ne harmonic 67.26 120.75 # NEW 6
- angle_coeff @angle:c3-cf-nh harmonic 65.76 119.90 # NEW 5
- angle_coeff @angle:ca-cf-cf harmonic 63.84 119.62 # NEW 14
- angle_coeff @angle:ca-cf-cl harmonic 57.99 114.22 # NEW 6
- angle_coeff @angle:ca-cf-h4 harmonic 46.71 116.86 # NEW 74
- angle_coeff @angle:ca-cf-nh harmonic 67.87 115.51 # NEW 93
- angle_coeff @angle:ca-cf-os harmonic 68.60 115.58 # NEW 8
- angle_coeff @angle:ca-cf-ss harmonic 61.21 117.73 # NEW 5
- angle_coeff @angle:c-cf-ca harmonic 63.79 117.98 # NEW 8
- angle_coeff @angle:cd-cf-cc harmonic 63.28 130.36 # NEW 5
- angle_coeff @angle:c-cf-cf harmonic 63.46 120.89 # NEW 16
- angle_coeff @angle:c-cf-ch harmonic 64.57 118.32 # NEW 15
- angle_coeff @angle:cd-cf-h4 harmonic 47.52 115.40 # NEW 29
- angle_coeff @angle:c-cf-cl harmonic 57.67 115.40 # NEW 6
- angle_coeff @angle:cd-cf-nh harmonic 67.31 119.17 # NEW 8
- angle_coeff @angle:c-cf-cy harmonic 72.72 88.22 # NEW 19
- angle_coeff @angle:cf-cf-cl harmonic 57.29 117.93 # NEW 12
- angle_coeff @angle:cf-cf-oh harmonic 69.29 116.89 # NEW 11
- angle_coeff @angle:ce-cf-cy harmonic 60.53 137.74 # NEW 13
- angle_coeff @angle:ce-cf-h4 harmonic 49.02 123.76 # NEW 5
- angle_coeff @angle:ce-cf-n1 harmonic 72.03 120.03 # NEW 6
- angle_coeff @angle:ce-cf-nh harmonic 69.48 121.52 # NEW 12
- angle_coeff @angle:ch-cf-n2 harmonic 69.59 121.43 # NEW 6
- angle_coeff @angle:c-cf-oh harmonic 68.34 117.92 # NEW 5
- angle_coeff @angle:c-cf-os harmonic 69.09 113.78 # NEW 21
- angle_coeff @angle:h4-cf-n1 harmonic 52.58 116.36 # NEW 7
- angle_coeff @angle:h4-cf-nf harmonic 49.72 115.81 # NEW 7
- angle_coeff @angle:n2-cf-os harmonic 74.58 118.13 # NEW 6
- angle_coeff @angle:n2-cf-ss harmonic 64.40 117.23 # NEW 6
- angle_coeff @angle:nf-cf-nh harmonic 71.89 112.91 # NEW 12
- angle_coeff @angle:ne-cf-nh harmonic 73.31 118.13 # NEW 6
- angle_coeff @angle:ca-ce-cd harmonic 62.70 130.80 # NEW 12
- angle_coeff @angle:c-ce-cc harmonic 64.25 117.76 # NEW 10
- angle_coeff @angle:c-ce-n2 harmonic 70.16 114.88 # NEW 5
- angle_coeff @angle:h4-ce-nf harmonic 52.29 120.21 # NEW 6
- angle_coeff @angle:c1-ch-cd harmonic 56.97 178.60 # NEW 6
- angle_coeff @angle:ch-cg-cg harmonic 58.68 179.67 # NEW 7
- angle_coeff @angle:n-c-nf harmonic 74.43 110.37 # NEW 10
- angle_coeff @angle:ca-cq-na harmonic 68.78 119.43 # NEW 21
- angle_coeff @angle:nb-cq-nb harmonic 71.31 125.72 # NEW 5
- angle_coeff @angle:cd-cx-hc harmonic 47.37 113.84 # NEW 15
- angle_coeff @angle:cf-cy-h2 harmonic 45.50 117.25 # NEW 17
- angle_coeff @angle:cf-cy-n harmonic 74.69 88.02 # NEW 14
- angle_coeff @angle:cf-cy-ss harmonic 58.47 121.33 # NEW 13
- angle_coeff @angle:cd-n2-na harmonic 73.01 108.92 # NEW 9
- angle_coeff @angle:cd-n2-nh harmonic 70.37 118.47 # NEW 6
- angle_coeff @angle:c3-n4-cd harmonic 62.84 111.09 # NEW 7
- angle_coeff @angle:c3-na-cq harmonic 63.76 119.46 # NEW 7
- angle_coeff @angle:ca-na-cq harmonic 65.88 120.96 # NEW 20
- angle_coeff @angle:cd-na-cf harmonic 63.05 126.61 # NEW 8
- angle_coeff @angle:cq-nb-nb harmonic 68.79 121.11 # NEW 12
- angle_coeff @angle:c-n-cf harmonic 62.21 131.83 # NEW 146
- angle_coeff @angle:ca-nc-nd harmonic 73.55 108.41 # NEW 9
- angle_coeff @angle:c2-nf-ch harmonic 68.36 123.58 # NEW 12
- angle_coeff @angle:c-nf-sy harmonic 61.66 116.05 # NEW 6
- angle_coeff @angle:c3-nh-ce harmonic 63.47 119.92 # NEW 20
- angle_coeff @angle:cd-nh-n2 harmonic 68.23 119.66 # NEW 5
- angle_coeff @angle:cd-nh-sy harmonic 61.22 122.91 # NEW 23
- angle_coeff @angle:cf-nh-sy harmonic 63.58 112.97 # NEW 7
- angle_coeff @angle:hn-n-nd harmonic 50.74 115.24 # NEW 10
- angle_coeff @angle:cd-no-o harmonic 70.34 117.52 # NEW 198
- angle_coeff @angle:n3-py-nf harmonic 41.93 108.44 # NEW 12
- angle_coeff @angle:cd-s6-o harmonic 70.23 103.63 # NEW 9
- angle_coeff @angle:cd-sh-hs harmonic 46.41 95.38 # NEW 8
- angle_coeff @angle:c-ss-cd harmonic 65.61 92.43 # NEW 14
- angle_coeff @angle:c3-sx-cd harmonic 62.52 95.11 # NEW 17
- angle_coeff @angle:cd-sx-o harmonic 65.92 104.49 # NEW 17
- angle_coeff @angle:c3-sy-cd harmonic 61.24 102.19 # NEW 12
- angle_coeff @angle:ca-sy-cd harmonic 60.36 105.09 # NEW 5
- angle_coeff @angle:ca-sy-nf harmonic 62.86 103.47 # NEW 11
- angle_coeff @angle:cc-sy-nh harmonic 65.53 97.20 # NEW 6
- angle_coeff @angle:n3-sy-nf harmonic 66.36 102.40 # NEW 5
- } # (end of angle_coeffs)
-
- write_once("Data Angles By Type") {
- @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw
- @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow
- @angle:br-c1-br @atom:br @atom:c1 @atom:br
- @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1
- @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1
- @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2
- @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3
- @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca
- @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl
- @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f
- @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha
- @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc
- @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i
- @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1
- @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2
- @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3
- @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4
- @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n
- @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na
- @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh
- @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no
- @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o
- @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh
- @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os
- @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2
- @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3
- @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4
- @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5
- @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4
- @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6
- @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s
- @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh
- @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss
- @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2
- @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce
- @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1
- @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o
- @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2
- @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3
- @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg
- @angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1
- @angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca
- @angle:c-c1-c1 @atom:c @atom:c1 @atom:c1
- @angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha
- @angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha
- @angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl
- @angle:f-c1-f @atom:f @atom:c1 @atom:f
- @angle:i-c1-i @atom:i @atom:c1 @atom:i
- @angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1
- @angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3
- @angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh
- @angle:n1-c1-os @atom:n1 @atom:c1 @atom:os
- @angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3
- @angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss
- @angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2
- @angle:n2-c1-o @atom:n2 @atom:c1 @atom:o
- @angle:n2-c1-s @atom:n2 @atom:c1 @atom:s
- @angle:n3-c1-n3 @atom:n3 @atom:c1 @atom:n3
- @angle:n4-c1-n4 @atom:n4 @atom:c1 @atom:n4
- @angle:na-c1-na @atom:na @atom:c1 @atom:na
- @angle:ne-c1-o @atom:ne @atom:c1 @atom:o
- @angle:ne-c1-s @atom:ne @atom:c1 @atom:s
- @angle:nf-c1-o @atom:nf @atom:c1 @atom:o
- @angle:nh-c1-nh @atom:nh @atom:c1 @atom:nh
- @angle:n-c1-n @atom:n @atom:c1 @atom:n
- @angle:no-c1-no @atom:no @atom:c1 @atom:no
- @angle:oh-c1-oh @atom:oh @atom:c1 @atom:oh
- @angle:o-c1-o @atom:o @atom:c1 @atom:o
- @angle:os-c1-os @atom:os @atom:c1 @atom:os
- @angle:p2-c1-p2 @atom:p2 @atom:c1 @atom:p2
- @angle:p3-c1-p3 @atom:p3 @atom:c1 @atom:p3
- @angle:p4-c1-p4 @atom:p4 @atom:c1 @atom:p4
- @angle:p5-c1-p5 @atom:p5 @atom:c1 @atom:p5
- @angle:s2-c1-s2 @atom:s2 @atom:c1 @atom:s2
- @angle:s4-c1-s4 @atom:s4 @atom:c1 @atom:s4
- @angle:s6-c1-s6 @atom:s6 @atom:c1 @atom:s6
- @angle:sh-c1-sh @atom:sh @atom:c1 @atom:sh
- @angle:s-c1-s @atom:s @atom:c1 @atom:s
- @angle:ss-c1-ss @atom:ss @atom:c1 @atom:ss
- @angle:br-c2-br @atom:br @atom:c2 @atom:br
- @angle:br-c2-c2 @atom:br @atom:c2 @atom:c2
- @angle:br-c2-c3 @atom:br @atom:c2 @atom:c3
- @angle:br-c2-ce @atom:br @atom:c2 @atom:ce
- @angle:br-c2-h4 @atom:br @atom:c2 @atom:h4
- @angle:br-c2-ha @atom:br @atom:c2 @atom:ha
- @angle:c1-c2-c1 @atom:c1 @atom:c2 @atom:c1
- @angle:c1-c2-c2 @atom:c1 @atom:c2 @atom:c2
- @angle:c1-c2-c3 @atom:c1 @atom:c2 @atom:c3
- @angle:c1-c2-f @atom:c1 @atom:c2 @atom:f
- @angle:c1-c2-ha @atom:c1 @atom:c2 @atom:ha
- @angle:c2-c2-c2 @atom:c2 @atom:c2 @atom:c2
- @angle:c2-c2-c3 @atom:c2 @atom:c2 @atom:c3
- @angle:c2-c2-ca @atom:c2 @atom:c2 @atom:ca
- @angle:c2-c2-cc @atom:c2 @atom:c2 @atom:cc
- @angle:c2-c2-cd @atom:c2 @atom:c2 @atom:cd
- @angle:c2-c2-cl @atom:c2 @atom:c2 @atom:cl
- @angle:c2-c2-cx @atom:c2 @atom:c2 @atom:cx
- @angle:c2-c2-cy @atom:c2 @atom:c2 @atom:cy
- @angle:c2-c2-f @atom:c2 @atom:c2 @atom:f
- @angle:c2-c2-h4 @atom:c2 @atom:c2 @atom:h4
- @angle:c2-c2-ha @atom:c2 @atom:c2 @atom:ha
- @angle:c2-c2-hc @atom:c2 @atom:c2 @atom:hc
- @angle:c2-c2-hx @atom:c2 @atom:c2 @atom:hx
- @angle:c2-c2-i @atom:c2 @atom:c2 @atom:i
- @angle:c2-c2-n1 @atom:c2 @atom:c2 @atom:n1
- @angle:c2-c2-n2 @atom:c2 @atom:c2 @atom:n2
- @angle:c2-c2-n3 @atom:c2 @atom:c2 @atom:n3
- @angle:c2-c2-n4 @atom:c2 @atom:c2 @atom:n4
- @angle:c2-c2-n @atom:c2 @atom:c2 @atom:n
- @angle:c2-c2-na @atom:c2 @atom:c2 @atom:na
- @angle:c2-c2-nh @atom:c2 @atom:c2 @atom:nh
- @angle:c2-c2-no @atom:c2 @atom:c2 @atom:no
- @angle:c2-c2-o @atom:c2 @atom:c2 @atom:o
- @angle:c2-c2-oh @atom:c2 @atom:c2 @atom:oh
- @angle:c2-c2-os @atom:c2 @atom:c2 @atom:os
- @angle:c2-c2-p2 @atom:c2 @atom:c2 @atom:p2
- @angle:c2-c2-p3 @atom:c2 @atom:c2 @atom:p3
- @angle:c2-c2-p4 @atom:c2 @atom:c2 @atom:p4
- @angle:c2-c2-p5 @atom:c2 @atom:c2 @atom:p5
- @angle:c2-c2-s4 @atom:c2 @atom:c2 @atom:s4
- @angle:c2-c2-s6 @atom:c2 @atom:c2 @atom:s6
- @angle:c2-c2-s @atom:c2 @atom:c2 @atom:s
- @angle:c2-c2-sh @atom:c2 @atom:c2 @atom:sh
- @angle:c2-c2-ss @atom:c2 @atom:c2 @atom:ss
- @angle:c3-c2-c3 @atom:c3 @atom:c2 @atom:c3
- @angle:c3-c2-cc @atom:c3 @atom:c2 @atom:cc
- @angle:c3-c2-cd @atom:c3 @atom:c2 @atom:cd
- @angle:c3-c2-ce @atom:c3 @atom:c2 @atom:ce
- @angle:c3-c2-cf @atom:c3 @atom:c2 @atom:cf
- @angle:c3-c2-h4 @atom:c3 @atom:c2 @atom:h4
- @angle:c3-c2-ha @atom:c3 @atom:c2 @atom:ha
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- @angle:ca-sy-cc @atom:ca @atom:sy @atom:cc
- @angle:ca-sy-n3 @atom:ca @atom:sy @atom:n3
- @angle:ca-sy-n @atom:ca @atom:sy @atom:n
- @angle:ca-sy-ne @atom:ca @atom:sy @atom:ne
- @angle:ca-sy-nh @atom:ca @atom:sy @atom:nh
- @angle:ca-sy-o @atom:ca @atom:sy @atom:o
- @angle:ca-sy-oh @atom:ca @atom:sy @atom:oh
- @angle:ca-sy-os @atom:ca @atom:sy @atom:os
- @angle:c-sy-c3 @atom:c @atom:sy @atom:c3
- @angle:c-sy-c @atom:c @atom:sy @atom:c
- @angle:cc-sy-n3 @atom:cc @atom:sy @atom:n3
- @angle:cc-sy-o @atom:cc @atom:sy @atom:o
- @angle:cd-sy-n3 @atom:cd @atom:sy @atom:n3
- @angle:cd-sy-nh @atom:cd @atom:sy @atom:nh
- @angle:cd-sy-o @atom:cd @atom:sy @atom:o
- @angle:ce-sy-ce @atom:ce @atom:sy @atom:ce
- @angle:ce-sy-o @atom:ce @atom:sy @atom:o
- @angle:cf-sy-cf @atom:cf @atom:sy @atom:cf
- @angle:cf-sy-o @atom:cf @atom:sy @atom:o
- @angle:c-sy-o @atom:c @atom:sy @atom:o
- @angle:f-sy-o @atom:f @atom:sy @atom:o
- @angle:n2-sy-o @atom:n2 @atom:sy @atom:o
- @angle:n3-sy-ne @atom:n3 @atom:sy @atom:ne
- @angle:n3-sy-o @atom:n3 @atom:sy @atom:o
- @angle:na-sy-na @atom:na @atom:sy @atom:na
- @angle:nc-sy-nc @atom:nc @atom:sy @atom:nc
- @angle:nd-sy-nd @atom:nd @atom:sy @atom:nd
- @angle:ne-sy-ne @atom:ne @atom:sy @atom:ne
- @angle:ne-sy-o @atom:ne @atom:sy @atom:o
- @angle:nf-sy-nf @atom:nf @atom:sy @atom:nf
- @angle:nf-sy-o @atom:nf @atom:sy @atom:o
- @angle:nh-sy-o @atom:nh @atom:sy @atom:o
- @angle:n-sy-o @atom:n @atom:sy @atom:o
- @angle:o-sy-o @atom:o @atom:sy @atom:o
- @angle:o-sy-oh @atom:o @atom:sy @atom:oh
- @angle:o-sy-os @atom:o @atom:sy @atom:os
- @angle:o-sy-pe @atom:o @atom:sy @atom:pe
- @angle:o-sy-pf @atom:o @atom:sy @atom:pf
- @angle:o-sy-px @atom:o @atom:sy @atom:px
- @angle:o-sy-py @atom:o @atom:sy @atom:py
- @angle:o-sy-sx @atom:o @atom:sy @atom:sx
- @angle:o-sy-sy @atom:o @atom:sy @atom:sy
- @angle:py-sy-py @atom:py @atom:sy @atom:py
- @angle:sx-sy-sx @atom:sx @atom:sy @atom:sx
- @angle:sy-sy-sy @atom:sy @atom:sy @atom:sy
- @angle:c2-c1-cf @atom:c2 @atom:c1 @atom:cf
- @angle:c3-c1-ch @atom:c3 @atom:c1 @atom:ch
- @angle:nf-c1-s @atom:nf @atom:c1 @atom:s
- @angle:br-c2-cf @atom:br @atom:c2 @atom:cf
- @angle:cd-c2-h4 @atom:cd @atom:c2 @atom:h4
- @angle:cd-c2-nh @atom:cd @atom:c2 @atom:nh
- @angle:cd-c2-o @atom:cd @atom:c2 @atom:o
- @angle:cf-c2-cl @atom:cf @atom:c2 @atom:cl
- @angle:cf-c2-h4 @atom:cf @atom:c2 @atom:h4
- @angle:cf-c2-na @atom:cf @atom:c2 @atom:na
- @angle:cf-c2-nh @atom:cf @atom:c2 @atom:nh
- @angle:cf-c2-no @atom:cf @atom:c2 @atom:no
- @angle:cf-c2-o @atom:cf @atom:c2 @atom:o
- @angle:cf-c2-oh @atom:cf @atom:c2 @atom:oh
- @angle:cf-c2-os @atom:cf @atom:c2 @atom:os
- @angle:h4-c2-nf @atom:h4 @atom:c2 @atom:nf
- @angle:h5-c2-nf @atom:h5 @atom:c2 @atom:nf
- @angle:nf-c2-os @atom:nf @atom:c2 @atom:os
- @angle:nf-c2-ss @atom:nf @atom:c2 @atom:ss
- @angle:n-c2-nf @atom:n @atom:c2 @atom:nf
- @angle:ca-c3-cf @atom:ca @atom:c3 @atom:cf
- @angle:cd-c3-cx @atom:cd @atom:c3 @atom:cx
- @angle:c-c3-cf @atom:c @atom:c3 @atom:cf
- @angle:cd-c3-hx @atom:cd @atom:c3 @atom:hx
- @angle:cd-c3-n2 @atom:cd @atom:c3 @atom:n2
- @angle:cd-c3-n4 @atom:cd @atom:c3 @atom:n4
- @angle:cd-c3-na @atom:cd @atom:c3 @atom:na
- @angle:cd-c3-p5 @atom:cd @atom:c3 @atom:p5
- @angle:cf-c3-cf @atom:cf @atom:c3 @atom:cf
- @angle:cf-c3-n @atom:cf @atom:c3 @atom:n
- @angle:cf-c3-oh @atom:cf @atom:c3 @atom:oh
- @angle:cf-c3-os @atom:cf @atom:c3 @atom:os
- @angle:cf-c3-ss @atom:cf @atom:c3 @atom:ss
- @angle:cd-ca-cq @atom:cd @atom:ca @atom:cq
- @angle:cf-ca-na @atom:cf @atom:ca @atom:na
- @angle:ch-ca-cq @atom:ch @atom:ca @atom:cq
- @angle:cl-ca-cq @atom:cl @atom:ca @atom:cq
- @angle:cq-ca-f @atom:cq @atom:ca @atom:f
- @angle:cq-ca-h4 @atom:cq @atom:ca @atom:h4
- @angle:cq-ca-na @atom:cq @atom:ca @atom:na
- @angle:cq-ca-nb @atom:cq @atom:ca @atom:nb
- @angle:cq-ca-nh @atom:cq @atom:ca @atom:nh
- @angle:cq-ca-oh @atom:cq @atom:ca @atom:oh
- @angle:cq-ca-ss @atom:cq @atom:ca @atom:ss
- @angle:ca-c-nf @atom:ca @atom:c @atom:nf
- @angle:br-cd-c @atom:br @atom:cd @atom:c
- @angle:br-cd-cd @atom:br @atom:cd @atom:cd
- @angle:br-cd-cc @atom:br @atom:cd @atom:cc
- @angle:br-cd-na @atom:br @atom:cd @atom:na
- @angle:ca-cd-cf @atom:ca @atom:cd @atom:cf
- @angle:ca-cd-nh @atom:ca @atom:cd @atom:nh
- @angle:cd-c-cf @atom:cd @atom:c @atom:cf
- @angle:cd-cd-f @atom:cd @atom:cd @atom:f
- @angle:c-cd-ch @atom:c @atom:cd @atom:ch
- @angle:cd-cd-sy @atom:cd @atom:cd @atom:sy
- @angle:cc-cd-f @atom:cc @atom:cd @atom:f
- @angle:cc-cd-no @atom:cc @atom:cd @atom:no
- @angle:c-cd-f @atom:c @atom:cd @atom:f
- @angle:ch-cd-na @atom:ch @atom:cd @atom:na
- @angle:ch-cd-ss @atom:ch @atom:cd @atom:ss
- @angle:cd-c-h4 @atom:cd @atom:c @atom:h4
- @angle:cl-cd-na @atom:cl @atom:cd @atom:na
- @angle:cl-cd-ss @atom:cl @atom:cd @atom:ss
- @angle:c-cd-nf @atom:c @atom:cd @atom:nf
- @angle:cd-c-s @atom:cd @atom:c @atom:s
- @angle:cd-c-ss @atom:cd @atom:c @atom:ss
- @angle:cx-cd-nc @atom:cx @atom:cd @atom:nc
- @angle:cx-cd-os @atom:cx @atom:cd @atom:os
- @angle:cc-c-cx @atom:cc @atom:c @atom:cx
- @angle:cc-c-nc @atom:cc @atom:c @atom:nc
- @angle:cf-c-cx @atom:cf @atom:c @atom:cx
- @angle:cf-c-h4 @atom:cf @atom:c @atom:h4
- @angle:cf-c-ss @atom:cf @atom:c @atom:ss
- @angle:na-cd-no @atom:na @atom:cd @atom:no
- @angle:na-cd-oh @atom:na @atom:cd @atom:oh
- @angle:na-cd-sx @atom:na @atom:cd @atom:sx
- @angle:na-cd-sy @atom:na @atom:cd @atom:sy
- @angle:nd-cd-no @atom:nd @atom:cd @atom:no
- @angle:nc-cd-nc @atom:nc @atom:cd @atom:nc
- @angle:nc-cd-nf @atom:nc @atom:cd @atom:nf
- @angle:nc-cd-no @atom:nc @atom:cd @atom:no
- @angle:nc-cd-sh @atom:nc @atom:cd @atom:sh
- @angle:nc-cd-sx @atom:nc @atom:cd @atom:sx
- @angle:nc-cd-sy @atom:nc @atom:cd @atom:sy
- @angle:nf-cd-ss @atom:nf @atom:cd @atom:ss
- @angle:n-cd-n2 @atom:n @atom:cd @atom:n2
- @angle:no-cd-os @atom:no @atom:cd @atom:os
- @angle:no-cd-ss @atom:no @atom:cd @atom:ss
- @angle:ca-cc-cf @atom:ca @atom:cc @atom:cf
- @angle:ca-cc-na @atom:ca @atom:cc @atom:na
- @angle:cd-cc-cg @atom:cd @atom:cc @atom:cg
- @angle:cd-cc-cy @atom:cd @atom:cc @atom:cy
- @angle:cd-cc-nd @atom:cd @atom:cc @atom:nd
- @angle:cc-cc-cy @atom:cc @atom:cc @atom:cy
- @angle:cf-cc-nc @atom:cf @atom:cc @atom:nc
- @angle:c-cc-h4 @atom:c @atom:cc @atom:h4
- @angle:na-cc-nh @atom:na @atom:cc @atom:nh
- @angle:na-cc-ss @atom:na @atom:cc @atom:ss
- @angle:nc-cc-nc @atom:nc @atom:cc @atom:nc
- @angle:oh-cc-os @atom:oh @atom:cc @atom:os
- @angle:c2-cf-cl @atom:c2 @atom:cf @atom:cl
- @angle:c2-cf-h4 @atom:c2 @atom:cf @atom:h4
- @angle:c2-cf-n1 @atom:c2 @atom:cf @atom:n1
- @angle:c2-cf-na @atom:c2 @atom:cf @atom:na
- @angle:c2-cf-oh @atom:c2 @atom:cf @atom:oh
- @angle:c3-cf-ch @atom:c3 @atom:cf @atom:ch
- @angle:c3-cf-ne @atom:c3 @atom:cf @atom:ne
- @angle:c3-cf-nh @atom:c3 @atom:cf @atom:nh
- @angle:ca-cf-cf @atom:ca @atom:cf @atom:cf
- @angle:ca-cf-cl @atom:ca @atom:cf @atom:cl
- @angle:ca-cf-h4 @atom:ca @atom:cf @atom:h4
- @angle:ca-cf-nh @atom:ca @atom:cf @atom:nh
- @angle:ca-cf-os @atom:ca @atom:cf @atom:os
- @angle:ca-cf-ss @atom:ca @atom:cf @atom:ss
- @angle:c-cf-ca @atom:c @atom:cf @atom:ca
- @angle:cd-cf-cc @atom:cd @atom:cf @atom:cc
- @angle:c-cf-cf @atom:c @atom:cf @atom:cf
- @angle:c-cf-ch @atom:c @atom:cf @atom:ch
- @angle:cd-cf-h4 @atom:cd @atom:cf @atom:h4
- @angle:c-cf-cl @atom:c @atom:cf @atom:cl
- @angle:cd-cf-nh @atom:cd @atom:cf @atom:nh
- @angle:c-cf-cy @atom:c @atom:cf @atom:cy
- @angle:cf-cf-cl @atom:cf @atom:cf @atom:cl
- @angle:cf-cf-oh @atom:cf @atom:cf @atom:oh
- @angle:ce-cf-cy @atom:ce @atom:cf @atom:cy
- @angle:ce-cf-h4 @atom:ce @atom:cf @atom:h4
- @angle:ce-cf-n1 @atom:ce @atom:cf @atom:n1
- @angle:ce-cf-nh @atom:ce @atom:cf @atom:nh
- @angle:ch-cf-n2 @atom:ch @atom:cf @atom:n2
- @angle:c-cf-oh @atom:c @atom:cf @atom:oh
- @angle:c-cf-os @atom:c @atom:cf @atom:os
- @angle:h4-cf-n1 @atom:h4 @atom:cf @atom:n1
- @angle:h4-cf-nf @atom:h4 @atom:cf @atom:nf
- @angle:n2-cf-os @atom:n2 @atom:cf @atom:os
- @angle:n2-cf-ss @atom:n2 @atom:cf @atom:ss
- @angle:nf-cf-nh @atom:nf @atom:cf @atom:nh
- @angle:ne-cf-nh @atom:ne @atom:cf @atom:nh
- @angle:ca-ce-cd @atom:ca @atom:ce @atom:cd
- @angle:c-ce-cc @atom:c @atom:ce @atom:cc
- @angle:c-ce-n2 @atom:c @atom:ce @atom:n2
- @angle:h4-ce-nf @atom:h4 @atom:ce @atom:nf
- @angle:c1-ch-cd @atom:c1 @atom:ch @atom:cd
- @angle:ch-cg-cg @atom:ch @atom:cg @atom:cg
- @angle:n-c-nf @atom:n @atom:c @atom:nf
- @angle:ca-cq-na @atom:ca @atom:cq @atom:na
- @angle:nb-cq-nb @atom:nb @atom:cq @atom:nb
- @angle:cd-cx-hc @atom:cd @atom:cx @atom:hc
- @angle:cf-cy-h2 @atom:cf @atom:cy @atom:h2
- @angle:cf-cy-n @atom:cf @atom:cy @atom:n
- @angle:cf-cy-ss @atom:cf @atom:cy @atom:ss
- @angle:cd-n2-na @atom:cd @atom:n2 @atom:na
- @angle:cd-n2-nh @atom:cd @atom:n2 @atom:nh
- @angle:c3-n4-cd @atom:c3 @atom:n4 @atom:cd
- @angle:c3-na-cq @atom:c3 @atom:na @atom:cq
- @angle:ca-na-cq @atom:ca @atom:na @atom:cq
- @angle:cd-na-cf @atom:cd @atom:na @atom:cf
- @angle:cq-nb-nb @atom:cq @atom:nb @atom:nb
- @angle:c-n-cf @atom:c @atom:n @atom:cf
- @angle:ca-nc-nd @atom:ca @atom:nc @atom:nd
- @angle:c2-nf-ch @atom:c2 @atom:nf @atom:ch
- @angle:c-nf-sy @atom:c @atom:nf @atom:sy
- @angle:c3-nh-ce @atom:c3 @atom:nh @atom:ce
- @angle:cd-nh-n2 @atom:cd @atom:nh @atom:n2
- @angle:cd-nh-sy @atom:cd @atom:nh @atom:sy
- @angle:cf-nh-sy @atom:cf @atom:nh @atom:sy
- @angle:hn-n-nd @atom:hn @atom:n @atom:nd
- @angle:cd-no-o @atom:cd @atom:no @atom:o
- @angle:n3-py-nf @atom:n3 @atom:py @atom:nf
- @angle:cd-s6-o @atom:cd @atom:s6 @atom:o
- @angle:cd-sh-hs @atom:cd @atom:sh @atom:hs
- @angle:c-ss-cd @atom:c @atom:ss @atom:cd
- @angle:c3-sx-cd @atom:c3 @atom:sx @atom:cd
- @angle:cd-sx-o @atom:cd @atom:sx @atom:o
- @angle:c3-sy-cd @atom:c3 @atom:sy @atom:cd
- @angle:ca-sy-cd @atom:ca @atom:sy @atom:cd
- @angle:ca-sy-nf @atom:ca @atom:sy @atom:nf
- @angle:cc-sy-nh @atom:cc @atom:sy @atom:nh
- @angle:n3-sy-nf @atom:n3 @atom:sy @atom:nf
- } # (end of Angles By Type)
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 #
- dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X
- dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230
- dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230
- dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230
- dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013
- dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value
- dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value
- dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh)
- dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X
- dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X
- dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X
- dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond
- dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond
- dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 #
- dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 #
- dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X
- dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated
- dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated
- dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond
- dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond
- dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 #
- dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 #
- dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 #
- dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 #
- dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 #
- dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 #
- dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 #
- dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 #
- dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 #
- dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 #
- dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 #
- dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds
- dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds
- dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds
- dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds
- dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds
- dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds
- dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99
- dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99
- dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94
- dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94
- dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94
- dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013
- dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 #
- dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99
- dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99
- dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99
- dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond
- dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond
- dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94
- dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94
- dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol.
- dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol.
- dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 #
- dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 #
- dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 #
- dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99
- dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99
- dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond
- dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond
- dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond
- dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond
- dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond
- dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond
- dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated
- dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated
- dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated
- dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated
- dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated
- dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated
- dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 #
- dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!!
- dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!!
- dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!!
- dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 #
- dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 #
- dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 #
- dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!!
- dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!!
- dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!!
- dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 #
- dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 #
- dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 #
- dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 #
- dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 #
- dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!!
- dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!!
- dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!!
- dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 #
- dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 #
- dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 #
- dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!!
- dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!!
- dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!!
- dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 #
- dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 #
- dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 #
- dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X
- dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X
- dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X
- dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X
- dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 #
- dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 #
- dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 #
- dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 #
- dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 #
- dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 #
- dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 #
- dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 #
- dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 #
- dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 #
- dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 #
- dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 #
- dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X
- dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X
- dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6
- dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 #
- dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 #
- dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 #
- dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 #
- dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 #
- dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 #
- dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X
- dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X
- dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X
- dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 #
- dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X
- dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X
- dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 #
- dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99
- dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X
- dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 #
- dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X
- dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X
- dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol
- dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol
- dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 #
- dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X
- dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 #
- dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X
- dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 #
- dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 #
- dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X
- dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 #
- dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X
- dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94
- dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 #
- dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 #
- dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 #
- dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 #
- dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 #
- dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 #
- dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 #
- dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 #
- dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 #
- dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 #
- dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 #
- dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 #
- dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 #
- dihedral_coeff @dihedral:X-n-pf-X fourier 1 1.0 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n-pd-X fourier 1 4.8 2 180.0 #
- dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 #
- dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 #
- dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 #
- dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 #
- dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 #
- dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 #
- dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 #
- dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 #
- dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 #
- dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 #
- dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 #
- dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 #
- dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
- dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
- dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
- dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
- dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol
- dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol
- dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol
- dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol
- dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol
- dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X
- dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X
- dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 #
- dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 #
- dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 #
- dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 #
- dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 #
- dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 #
- dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 #
- dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 #
- dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 #
- dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 #
- dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 #
- dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 #
- dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 #
- dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 #
- dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 #
- dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 #
- dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 #
- dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 #
- dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 #
- dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 #
- dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 #
- dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond
- dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond
- dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 #
- dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 #
- dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 #
- dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 #
- dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 #
- dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 #
- dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 #
- dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 #
- dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 #
- dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 #
- dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 #
- dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 #
- dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 #
- dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 #
- dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 #
- dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 #
- dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 #
- dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 #
- dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 #
- dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 #
- dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 #
- dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 #
- dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 #
- dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 #
- dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 #
- dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 #
- dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 #
- dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 #
- dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 #
- dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 #
- dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 #
- dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 #
- dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 #
- dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 #
- dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 #
- dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 #
- dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 #
- dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 #
- dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 #
- dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 #
- dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 #
- dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 #
- dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 #
- dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 #
- dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 #
- dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 #
- dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 #
- dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 #
- dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 #
- dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 #
- dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 #
- dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 #
- dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 #
- dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 #
- dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 #
- dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 #
- dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 #
- dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 #
- dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 #
- dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 #
- dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 #
- dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 #
- dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 #
- dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 #
- dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 #
- dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 #
- dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 #
- dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 #
- dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 #
- dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 #
- dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 #
- dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 #
- dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 #
- dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 #
- dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 #
- dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 #
- dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 #
- dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 #
- dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 #
- dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 #
- dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 #
- dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 #
- dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 #
- dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 #
- dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 #
- dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 #
- dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 #
- dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 #
- dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 #
- dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 #
- dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 #
- dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 #
- dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 #
- dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 #
- dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 #
- dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 #
- dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 #
- dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 #
- dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 #
- dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 #
- dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 #
- dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 #
- dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 #
- dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 #
- dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 #
- dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 #
- dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 #
- dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 #
- dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 #
- dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 #
- dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 #
- dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 #
- dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 #
- dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 #
- dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 #
- dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 #
- dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 #
- dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 #
- dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 #
- dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 #
- dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 #
- dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 #
- dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 #
- dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 #
- dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 #
- dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 #
- dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 #
- dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 #
- dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 #
- dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 #
- dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 #
- dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 #
- dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond
- dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond
- dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol.
- dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 #
- dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 #
- dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 #
- dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 #
- dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 #
- dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 #
- dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 #
- dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 #
- dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 #
- dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 #
- dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 #
- dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 #
- dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 #
- dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 #
- dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 #
- dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 #
- dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 #
- dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 #
- dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 #
- dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 #
- dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 #
- dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 #
- dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 #
- dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 #
- dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 #
- dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 #
- dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 #
- dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 #
- dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 #
- dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 #
- dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 #
- dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 #
- dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 #
- dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 #
- dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 #
- dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 #
- dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 #
- dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 #
- dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 #
- dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 #
- dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 #
- dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 #
- dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 #
- dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 #
- dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 #
- dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 #
- dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 #
- dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 #
- dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 #
- dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 #
- dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 #
- dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
- dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 #
- dihedral_coeff @dihedral:X-cf-pe-X fourier 1 6.65 2 180.0 # NEW
- dihedral_coeff @dihedral:X-nd-os-X fourier 1 4.8 2 180.0 # NEW
- dihedral_coeff @dihedral:X-nd-ss-X fourier 1 4.8 2 180.0 # NEW
- dihedral_coeff @dihedral:X-nf-pe-X fourier 1 5.4 2 180.0 # NEW
- dihedral_coeff @dihedral:c3-c-sh-hs fourier 2 2.25 2 180.0 1.3 1 180.0 #
- dihedral_coeff @dihedral:c2-c2-ss-c3 fourier 2 1.1 2 180.0 0.7 3 180.0 #
- dihedral_coeff @dihedral:c2-c2-n-c fourier 2 0.65 2 180.0 1.2 1 180.0 #
- dihedral_coeff @dihedral:c-n-p2-c2 fourier 2 1.0 2 180.0 1.9 1 180.0 #
- dihedral_coeff @dihedral:n-c3-c-n fourier 2 1.7 1 180.0 2.0 2 180.0 #
- dihedral_coeff @dihedral:c-n-c3-c fourier 2 0.85 2 180.0 0.8 1 0.0 #
- dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.5 4 180.0 0.15 3 180.0 0.53 1 0.0 # phi,psi,parm94
- dihedral_coeff @dihedral:c3-c3-c-n fourier 2 0.1 4 0.0 0.07 2 0.0 # phi,psi,parm94
- dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
- dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
- dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
- dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
- dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
- dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
- dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.5 2 0.0 0.6 3 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:c3-n3-nh-ca fourier 2 1.9 2 0.0 1.9 3 0.0 #
- dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 #
- dihedral_coeff @dihedral:ca-nh-oh-ho fourier 2 1.2 1 0.0 1.5 2 0.0 #
- dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230
- dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.15 3 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.16 3 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.38 3 180.0 1.15 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 2 0.16 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 6.65 2 180.0 1.9 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c3-c3-n3-c3 fourier 2 0.3 3 0.0 0.48 2 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c3-c3-os-c3 fourier 2 0.383 3 0.0 0.1 2 180.0 #
- dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c3-os-c3-os fourier 3 0.1 3 0.0 0.85 2 180.0 1.35 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK
- dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK
- dihedral_coeff @dihedral:os-c3-c3-os fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK
- dihedral_coeff @dihedral:os-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK
- dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK
- dihedral_coeff @dihedral:f-c3-c3-f fourier 2 0.0 3 0.0 1.2 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.0 3 0.0 0.45 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.0 3 0.0 0.0 1 180.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
- dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999
- } # (end of dihedral_coeffs)
-
- write_once("Data Dihedrals By Type") {
- @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:*
- @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:*
- @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:*
- @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:*
- @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:*
- @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:*
- @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:*
- @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:*
- @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:*
- @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:*
- @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:*
- @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:*
- @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:*
- @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:*
- @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:*
- @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:*
- @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:*
- @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:*
- @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:*
- @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:*
- @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:*
- @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:*
- @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:*
- @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:*
- @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:*
- @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:*
- @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:*
- @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:*
- @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:*
- @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:*
- @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:*
- @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:*
- @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:*
- @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:*
- @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:*
- @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:*
- @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:*
- @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:*
- @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:*
- @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:*
- @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:*
- @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:*
- @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:*
- @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:*
- @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:*
- @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:*
- @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:*
- @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:*
- @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:*
- @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:*
- @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:*
- @dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:*
- @dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:*
- @dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:*
- @dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:*
- @dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:*
- @dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:*
- @dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:*
- @dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:*
- @dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:*
- @dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:*
- @dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:*
- @dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:*
- @dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:*
- @dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:*
- @dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:*
- @dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:*
- @dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:*
- @dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:*
- @dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:*
- @dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:*
- @dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:*
- @dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:*
- @dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:*
- @dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:*
- @dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:*
- @dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:*
- @dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:*
- @dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:*
- @dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:*
- @dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:*
- @dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:*
- @dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:*
- @dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:*
- @dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:*
- @dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:*
- @dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:*
- @dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:*
- @dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:*
- @dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:*
- @dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:*
- @dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:*
- @dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:*
- @dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:*
- @dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:*
- @dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:*
- @dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:*
- @dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:*
- @dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:*
- @dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:*
- @dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:*
- @dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:*
- @dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:*
- @dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:*
- @dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:*
- @dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:*
- @dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:*
- @dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:*
- @dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:*
- @dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:*
- @dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:*
- @dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:*
- @dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:*
- @dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:*
- @dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:*
- @dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:*
- @dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:*
- @dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:*
- @dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:*
- @dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:*
- @dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:*
- @dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:*
- @dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:*
- @dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:*
- @dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:*
- @dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:*
- @dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:*
- @dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:*
- @dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:*
- @dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:*
- @dihedral:X-c2-pd-X @atom:* @atom:c2 @atom:pd @atom:*
- @dihedral:X-cc-pc-X @atom:* @atom:cc @atom:pc @atom:*
- @dihedral:X-cc-pd-X @atom:* @atom:cc @atom:pd @atom:*
- @dihedral:X-cd-pc-X @atom:* @atom:cd @atom:pc @atom:*
- @dihedral:X-cd-pd-X @atom:* @atom:cd @atom:pd @atom:*
- @dihedral:X-c2-p3-X @atom:* @atom:c2 @atom:p3 @atom:*
- @dihedral:X-c2-p4-X @atom:* @atom:c2 @atom:p4 @atom:*
- @dihedral:X-ce-p4-X @atom:* @atom:ce @atom:p4 @atom:*
- @dihedral:X-cf-p4-X @atom:* @atom:cf @atom:p4 @atom:*
- @dihedral:X-c2-px-X @atom:* @atom:c2 @atom:px @atom:*
- @dihedral:X-ce-px-X @atom:* @atom:ce @atom:px @atom:*
- @dihedral:X-cf-px-X @atom:* @atom:cf @atom:px @atom:*
- @dihedral:X-c2-p5-X @atom:* @atom:c2 @atom:p5 @atom:*
- @dihedral:X-ce-p5-X @atom:* @atom:ce @atom:p5 @atom:*
- @dihedral:X-cf-p5-X @atom:* @atom:cf @atom:p5 @atom:*
- @dihedral:X-c2-py-X @atom:* @atom:c2 @atom:py @atom:*
- @dihedral:X-ce-py-X @atom:* @atom:ce @atom:py @atom:*
- @dihedral:X-cf-py-X @atom:* @atom:cf @atom:py @atom:*
- @dihedral:X-c2-sh-X @atom:* @atom:c2 @atom:sh @atom:*
- @dihedral:X-c2-ss-X @atom:* @atom:c2 @atom:ss @atom:*
- @dihedral:X-c2-s4-X @atom:* @atom:c2 @atom:s4 @atom:*
- @dihedral:X-ce-s4-X @atom:* @atom:ce @atom:s4 @atom:*
- @dihedral:X-cf-s4-X @atom:* @atom:cf @atom:s4 @atom:*
- @dihedral:X-c2-sx-X @atom:* @atom:c2 @atom:sx @atom:*
- @dihedral:X-ce-sx-X @atom:* @atom:ce @atom:sx @atom:*
- @dihedral:X-cf-sx-X @atom:* @atom:cf @atom:sx @atom:*
- @dihedral:X-c2-s6-X @atom:* @atom:c2 @atom:s6 @atom:*
- @dihedral:X-ce-s6-X @atom:* @atom:ce @atom:s6 @atom:*
- @dihedral:X-cf-s6-X @atom:* @atom:cf @atom:s6 @atom:*
- @dihedral:X-c2-sy-X @atom:* @atom:c2 @atom:sy @atom:*
- @dihedral:X-ce-sy-X @atom:* @atom:ce @atom:sy @atom:*
- @dihedral:X-cf-sy-X @atom:* @atom:cf @atom:sy @atom:*
- @dihedral:X-c3-c3-X @atom:* @atom:c3 @atom:c3 @atom:*
- @dihedral:X-cx-cx-X @atom:* @atom:cx @atom:cx @atom:*
- @dihedral:X-cy-cy-X @atom:* @atom:cy @atom:cy @atom:*
- @dihedral:X-c3-ca-X @atom:* @atom:c3 @atom:ca @atom:*
- @dihedral:X-c3-n-X @atom:* @atom:c3 @atom:n @atom:*
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- @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl
- @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br
- @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br
- @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os
- @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os
- @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh
- @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh
- @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f
- @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f
- @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl
- @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl
- @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br
- @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br
- } # (end of Dihedrals By Type)
-
- write_once("In Settings") {
- improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes
- improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230
- improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94
- improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94
- improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 #
- improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 #
- improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 #
- improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 #
- improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 #
- improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 #
- improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 #
- improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 #
- improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 #
- improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!)
- improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 #
- improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 #
- improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94
- improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999
- improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 #
- improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94
- improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94
- improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94
- } # (end of improper_coeffs)
-
- write_once("Data Impropers By Type (gaff_imp.py)") {
- @improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o
- @improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o
- @improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha
- @improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn
- @improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn
- @improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn
- @improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3
- @improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2
- @improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3
- @improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3
- @improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn
- @improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o
- @improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3
- @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3
- @improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc
- @improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc
- @improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o
- @improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh
- @improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2
- @improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na
- @improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2
- @improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na
- @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2
- @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3
- @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f
- @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl
- @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br
- @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i
- @improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh
- @improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3
- @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3
- @improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o
- @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2
- @improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh
- @improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os
- @improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2
- @improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2
- @improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2
- } # (end of Impropers By Type)
-
-
- write_once("In Init") {
- # Default styles and settings for AMBER based force-fields:
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid fourier
- improper_style hybrid cvff
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- kspace_style pppm 0.0001
-
- # NOTE: If you do not want to use long-range coulombic forces,
- # comment out the two lines above and uncomment this line:
- # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
-
- pair_modify mix arithmetic
- special_bonds amber
- }
-
-}
-
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/graphene.lt b/tools/moltemplate/src/moltemplate_force_fields/graphene.lt
deleted file mode 100644
index c54a380f6..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/graphene.lt
+++ /dev/null
@@ -1,55 +0,0 @@
-# The minimal unit cell for graphine contains only 2 atoms:
-# (which I arbitrarily named "C1" and "C2")
-
-Graphene {
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0000
- $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0000
- }
-
- # Now define the "C" atom type
- write_once("Data Masses") {
- @atom:C 12.0
- }
- write_once("In Settings") {
- # i j epsilon sigma
- pair_coeff @atom:C @atom:C lj/cut/coul/long 0.068443 3.407
-
- # These Lennard-Jones parameters come from
- # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
- # Chem Phys Lett, 348:187 (2001)
-
- # Define a group consisting of only carbon atoms in graphene molecules
- group Cgraphene type @atom:C
- }
- write_once("In Init") {
- # -- Default styles (used in this file for graphene carbon) --
- units real
- atom_style full #(full enables you to to add other molecules later)
- pair_style hybrid lj/cut/coul/long 10.0
- }
-} # Graphene
-
-
-
-
-# This is a 2-dimensional hexagonal unit cell. The unit vectors are:
-#
-# (2.4595121467478, 0, 0)
-# (1.2297560733739, 2.13, 0)
-#
-# You can create a sheet of single-layer graphene this way:
-#
-# small_crystal = new Graphene [3].move(2.45951214, 0, 0)
-# [3].move(1.229756, 2.13, 0)
-#
-# For thicker sheets, follow the instructions in the "graphite.lt" file.
-#
-# Note: The length of each carbon-carbon bond is currently 1.42 Angstroms.
-# To increase it to 1.422 Angstroms, uncomment the following line:
-#
-# Graphene.scale(1.0014084507042254) # 1.0014084507042254 = 1.422 / 1.42
-#
-# You will have to change the unit cell lattice vectors (see above) accordingly
diff --git a/tools/moltemplate/src/moltemplate_force_fields/graphite.lt b/tools/moltemplate/src/moltemplate_force_fields/graphite.lt
deleted file mode 100644
index 49fb49fb0..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/graphite.lt
+++ /dev/null
@@ -1,61 +0,0 @@
-import "graphene.lt" # defines "Graphene"
-
-
-# ------------ Graphite -----------
-#
-# Note: For graphite: sheets stacked in the Z direction are separated by a
-# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction
-# by a distance of d (1.42 Angstroms). To add additional graphene layers
-# you could use:
-# sheet2 = new Graphene [10].move(2.4595121467478,0,0)
-# [10].move(1.2297560733739,2.13,0)
-# sheet2[*][*].move(0, 1.42, 3.35)
-# sheet3 = new Graphene [10].move(2.4595121467478,0,0)
-# [10].move(1.2297560733739,2.13,0)
-# sheet3[*][*].move(0, -1.42, 6.70)
-# etc...
-#
-# This should work fine.
-# However, to build a thick sheet of graphite, it may be less trouble
-# to use a 4-atom unit cell which includes two graphene layers.
-# Here is one way to do that:
-
-Graphite inherits Graphene {
-
- # This allows us to access access the "@atom:C" carbon atom type
- # whose properties are defined in the "Graphene" object (see "graphene.lt").
- # That atom is NOT globally defined. It belongs to the "Graphene" object.
- # This is one way to access it. Alternately, you could redefine it here
-
- # atomID molID atomType charge x y z
- write("Data Atoms") {
- $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0
- $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0
- $atom:C3 $mol:... @atom:C 0.0 -0.61487803668695 1.065 3.35
- $atom:C4 $mol:... @atom:C 0.0 0.61487803668695 1.775 3.35
- }
-
- # Note: The first two lines in the "Data Atoms" section override the positions
- # of the $atom:C1 and $atom:C2 atoms previously defined in "Graphene"
- # (which this object inherits). This is okay.
-
-} # Graphite
-
-
-
-
-
-
-# This is a 3-dimensional hexagonal unit cell. The unit vectors are:
-#
-# (2.4595121467478, 0, 0 )
-# (1.2297560733739, 2.13, 0 )
-# ( 0, 0, 6.70)
-
-# Then you could create a thick sheet of graphite this way:
-#
-# graphite = new Graphite [10].move(2.4595121467478,0,0)
-# [10].move(1.2297560733739,2.13,0)
-# [5].move(0,0,6.70)
-#
-# (Your graphite slab will contain an even number of graphene sheets.)
diff --git a/tools/moltemplate/src/moltemplate_force_fields/images/graphene_unit_cell.jpg b/tools/moltemplate/src/moltemplate_force_fields/images/graphene_unit_cell.jpg
deleted file mode 100644
index 12dbf8fca..000000000
Binary files a/tools/moltemplate/src/moltemplate_force_fields/images/graphene_unit_cell.jpg and /dev/null differ
diff --git a/tools/moltemplate/src/moltemplate_force_fields/images/ice_rect8_unitcell.png b/tools/moltemplate/src/moltemplate_force_fields/images/ice_rect8_unitcell.png
deleted file mode 100644
index 5bd6057e1..000000000
Binary files a/tools/moltemplate/src/moltemplate_force_fields/images/ice_rect8_unitcell.png and /dev/null differ
diff --git a/tools/moltemplate/src/moltemplate_force_fields/images/spce_ball_and_stick.jpg b/tools/moltemplate/src/moltemplate_force_fields/images/spce_ball_and_stick.jpg
deleted file mode 100644
index 60aaf90b9..000000000
Binary files a/tools/moltemplate/src/moltemplate_force_fields/images/spce_ball_and_stick.jpg and /dev/null differ
diff --git a/tools/moltemplate/src/moltemplate_force_fields/loplsaa.lt b/tools/moltemplate/src/moltemplate_force_fields/loplsaa.lt
deleted file mode 100644
index 7901021e1..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/loplsaa.lt
+++ /dev/null
@@ -1,153 +0,0 @@
-###########################################################################
-## Extra OPLSAA parameters and atom types for long hydrocarbon chains ##
-## SOURCE: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 ##
-## CREDIT: Sebastian Echeverri (file format conversion) ##
-###########################################################################
-# This file was generated using:
-# tinkerparm2lt.py -name LOPLSAA -file loplsaa_ext.prm -dihedral-style opls
-# (and then edited manually to make sure the
-# bond, angle, and improper interactions for these atoms
-# remain unchanged)
-
-
-import "oplsaa.lt" # <-- Load the ordinary OPLS parameters
- # We will extend and override them below
-
-
-
-OPLSAA {
-
- # Additional atom types and parameters appended to the OPLSAA force-field:
-
- write_once("In Charges") {
- set type @atom:80L charge -0.222 # "Alkane CH3- (LOPLS CT_CH3)"
- set type @atom:81L charge -0.148 # "Alkane -CH2- (LOPLS CT_CH2)"
- set type @atom:85LCH3 charge 0.074 # "Alkane H-C CH3 (LOPLS HC_CH3)"
- set type @atom:85LCH2 charge 0.074 # "Alkane H-C CH2 (LOPLS HC_CH2)"
- set type @atom:87L charge -0.16 # "Alkene RH-C= (LOPLS CM_CH)"
- set type @atom:89L charge 0.16 # "Alkene H-C= (LOPLS HC_CH)"
- set type @atom:86L charge 0.0 # "Alkene R2-C= (LOPLS)"
- set type @atom:88L charge -0.23 # "Alkene H2-C= (LOPLS)"
- set type @atom:169L charge 0.005 # "Chloroalkene Cl-CH= (LOPLS)"
- set type @atom:266L charge -0.07 # "Uracil & Thymine C5 (LOPLS)"
- set type @atom:267L charge 0.08 # "Uracil & Thymine C6 (LOPLS)"
- set type @atom:280L charge -0.06 # "Cytosine C5 (LOPLS)"
- set type @atom:281L charge 0.1 # "Cytosine C6 (LOPLS)"
- set type @atom:324L charge -0.06 # "CytosineH+ C5 (LOPLS)"
- set type @atom:325L charge 0.1 # "CytosineH+ C6 (LOPLS)"
- set type @atom:340L charge 0.18 # "Trifluorothymine CF3- (LOPLS)"
- set type @atom:342L charge 0.12 # "Chloroalkene Cl2-C= (LOPLS)"
- set type @atom:458L charge -0.03 # "Vinyl Ether =CH-OR (LOPLS)"
- set type @atom:459L charge 0.085 # "Vinyl Ether =CR-OR (LOPLS)"
- set type @atom:649L charge -0.344 # "Cl..CH3..Cl- Sn2 TS (LOPLS)"
- set type @atom:900L charge -0.25 # "Allene/Ketene H2C=C=X (LOPLS)"
- set type @atom:901L charge -0.1 # "Allene/Ketene HRC=C=X (LOPLS)"
- set type @atom:902L charge 0.05 # "Allene/Ketene R2C=C=X (LOPLS)"
- } #(end of atom partial charges)
-
-
- write_once("Data Masses") {
- @atom:80L 12.011
- @atom:81L 12.011
- @atom:85LCH3 1.008
- @atom:85LCH2 1.008
- @atom:87L 12.011
- @atom:89L 1.008
- @atom:86L 12.011
- @atom:88L 12.011
- @atom:169L 12.011
- @atom:266L 12.011
- @atom:267L 12.011
- @atom:280L 12.011
- @atom:281L 12.011
- @atom:324L 12.011
- @atom:325L 12.011
- @atom:340L 12.011
- @atom:342L 12.011
- @atom:458L 12.011
- @atom:459L 12.011
- @atom:649L 12.011
- @atom:900L 12.011
- @atom:901L 12.011
- @atom:902L 12.011
- } #(end of atom masses)
-
-
- write_once("In Settings") {
- pair_coeff @atom:80L_b13_a13_d13L_i13 @atom:80L_b13_a13_d13L_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:81L_b13_a13_d13L_i13 @atom:81L_b13_a13_d13L_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:85LCH3_b46_a46_d46_i46 @atom:85LCH3_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:85LCH2_b46_a46_d46_i46 @atom:85LCH2_b46_a46_d46_i46 lj/cut/coul/long 0.026290630975 2.5
- pair_coeff @atom:87L_b47_a47_d47L_i47 @atom:87L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:89L_b46_a46_d46_i46 @atom:89L_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:86L_b47_a47_d47L_i47 @atom:86L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:88L_b47_a47_d47L_i47 @atom:88L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:169L_b47_a47_d47L_i47 @atom:169L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:266L_b47_a47_d47L_i47 @atom:266L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:267L_b47_a47_d47L_i47 @atom:267L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:280L_b47_a47_d47L_i47 @atom:280L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:281L_b47_a47_d47L_i47 @atom:281L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:324L_b47_a47_d47L_i47 @atom:324L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:325L_b47_a47_d47L_i47 @atom:325L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:340L_b47_a47_d47L_i47 @atom:340L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:342L_b47_a47_d47L_i47 @atom:342L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:458L_b47_a47_d47L_i47 @atom:458L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:459L_b47_a47_d47L_i47 @atom:459L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:649L_b47_a47_d47L_i47 @atom:649L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:900L_b47_a47_d47L_i47 @atom:900L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:901L_b47_a47_d47L_i47 @atom:901L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:902L_b47_a47_d47L_i47 @atom:902L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3
- } #(end of pair_coeffs)
-
-
- # ------- force-field-IDs for bonded interaction lookup -------
- # (First append the "force-field-ID" to the atom type name.
- # Later use these expanded names for force-field lookup.)
- replace{ @atom:80L @atom:80L_b13_a13_d13L_i13 }
- replace{ @atom:81L @atom:81L_b13_a13_d13L_i13 }
- replace{ @atom:85LCH3 @atom:85LCH3_b46_a46_d46_i46 }
- replace{ @atom:85LCH2 @atom:85LCH2_b46_a46_d46_i46 }
- replace{ @atom:87L @atom:87L_b47_a47_d47L_i47 }
- replace{ @atom:89L @atom:89L_b46_a46_d46_i46 }
- replace{ @atom:86L @atom:86L_b47_a47_d47L_i47 }
- replace{ @atom:88L @atom:88L_b47_a47_d47L_i47 }
- replace{ @atom:169L @atom:169L_b47_a47_d47L_i47 }
- replace{ @atom:266L @atom:266L_b47_a47_d47L_i47 }
- replace{ @atom:267L @atom:267L_b47_a47_d47L_i47 }
- replace{ @atom:280L @atom:280L_b47_a47_d47L_i47 }
- replace{ @atom:281L @atom:281L_b47_a47_d47L_i47 }
- replace{ @atom:324L @atom:324L_b47_a47_d47L_i47 }
- replace{ @atom:325L @atom:325L_b47_a47_d47L_i47 }
- replace{ @atom:340L @atom:340L_b47_a47_d47L_i47 }
- replace{ @atom:342L @atom:342L_b47_a47_d47L_i47 }
- replace{ @atom:458L @atom:458L_b47_a47_d47L_i47 }
- replace{ @atom:459L @atom:459L_b47_a47_d47L_i47 }
- replace{ @atom:649L @atom:649L_b47_a47_d47L_i47 }
- replace{ @atom:900L @atom:900L_b47_a47_d47L_i47 }
- replace{ @atom:901L @atom:901L_b47_a47_d47L_i47 }
- replace{ @atom:902L @atom:902L_b47_a47_d47L_i47 }
- #(end of force-field-IDs)
-
- # Bond parameters for these atoms are not modified
-
- # Angle parameters for these atoms are not modified
-
- # Improper parameters for these atoms are not modified
-
- # Dihedral parameters for some of these atoms are modified:
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:13L-13L-13L-13L opls 0.6446926386 -0.2143420172 0.1782194073 0.0
- dihedral_coeff @dihedral:X-47L-47L-X opls 0.0 12.2502629063 0.0 0.0
- dihedral_coeff @dihedral:47L-47L-13L-13L opls -0.8050121893 0.3218905354 -0.1032768881 0.0
- dihedral_coeff @dihedral:13L-13L-13L-47L opls 0.4821902486 0.1343683078 0.1777461759 0.0
- } #(end of dihedral_coeffs)
-
- write_once("Data Dihedrals By Type") {
- @dihedral:13L-13L-13L-13L @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i*
- @dihedral:X-47L-47L-X @atom:* @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d47L_i* @atom:*
- @dihedral:47L-47L-13L-13L @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i*
- @dihedral:13L-13L-13L-47L @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d47L_i*
- } #(end of dihedrals by type)
-
-} # end of additional parameters appended to the "OPLSAA" object
diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa.lt b/tools/moltemplate/src/moltemplate_force_fields/oplsaa.lt
deleted file mode 100644
index 48d6f9ec6..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa.lt
+++ /dev/null
@@ -1,8934 +0,0 @@
-# This file contains OPLSAA parameters and rules for creating
-# angle, dihedral, and improper interactions according to OPLSAA conventions.
-#
-# USAGE: You can create molecules using this force-field this way:
-#
-# MyMolecule inherits OPLSAA {
-# # atom-id mol-id atom-type charge X Y Z
-# write('Data Atoms') {
-# $atom:C1 $mol @atom:88 0.00 -0.6695 0.000000 0.000000
-# $atom:H11 $mol @atom:89 0.00 -1.234217 -0.854458 0.000000
-# : : : : : :
-# }
-# }
-#
-# Responsibility for choosing the atom types (eg "@atom:88", "@atom:89") falls
-# on the user. You must select the type of each atom in the molecule carefully
-# by looking at the description in the "In Charges" section of this file
-# (see below), and looking for a reasonable match. If your simulation is
-# non-neutral, or moltemplate complains that you have missing bond, angle, or
-# dihedral types, this means at least one of your atom types is incorrect.
-
-
-OPLSAA {
-
- write_once("In Charges") {
- set type @atom:1 charge -0.22 # "Fluoride -CH2-F (UA)"
- set type @atom:2 charge 0.22 # "Fluoride -CH2-F (UA)"
- set type @atom:3 charge 0.55 # "Acetic Acid -COOH (UA)"
- set type @atom:4 charge -0.5 # "Acetic Acid >C=O (UA)"
- set type @atom:5 charge -0.58 # "Acetic Acid -OH (UA)"
- set type @atom:6 charge 0.08 # "Acetic Acid CH3- (UA)"
- set type @atom:7 charge 0.45 # "Acetic Acid -OH (UA)"
- set type @atom:8 charge 0.0 # "Methane CH4 (UA)"
- set type @atom:9 charge 0.0 # "Ethane CH3- (UA)"
- set type @atom:10 charge 0.0 # "N-Alkane CH3- (UA)"
- set type @atom:11 charge 0.0 # "Isobutane CH3- (UA)"
- set type @atom:12 charge 0.0 # "Neopentane CH3- (UA)"
- set type @atom:13 charge 0.0 # "Alkanes -CH2- (UA)"
- set type @atom:14 charge 0.0 # "1-Alkene CH2= (UA)"
- set type @atom:15 charge 0.0 # "Isobutane CH (UA)"
- set type @atom:16 charge 0.0 # "2-Alkene -CH= (UA)"
- set type @atom:17 charge 0.0 # "Aromatic CH (UA)"
- set type @atom:18 charge 0.0 # "Neopentane C (UA)"
- set type @atom:19 charge 0.0 # "Isobutene >C= (UA)"
- set type @atom:20 charge -0.7 # "Alcohol OH (UA)"
- set type @atom:21 charge 0.435 # "Alcohol OH (UA)"
- set type @atom:22 charge 0.265 # "Methanol CH3- (UA)"
- set type @atom:23 charge 0.265 # "Ethanol -CH2OH (UA)"
- set type @atom:24 charge -0.47 # "Hydrogen Sulfide H2S"
- set type @atom:25 charge -0.45 # "Alkyl Sulfide RSH (UA)"
- set type @atom:26 charge -0.47 # "Thioether RSR (UA)"
- set type @atom:27 charge -0.3 # "Disulfide RSSR (UA)"
- set type @atom:28 charge 0.235 # "Hydrogen Sulfide H2S"
- set type @atom:29 charge 0.27 # "Alkyl Sulfide RSH (UA)"
- set type @atom:30 charge 0.18 # "Methyl Sulfide CH3 (UA)"
- set type @atom:31 charge 0.18 # "Alkyl Sulfide CH2 (UA)"
- set type @atom:32 charge 0.235 # "Thioether CH3 (UA)"
- set type @atom:33 charge 0.235 # "Thioether CH2 (UA)"
- set type @atom:34 charge 0.3 # "Disulfide CH3 (UA)"
- set type @atom:35 charge 0.3 # "Disulfide CH2 (UA)"
- set type @atom:36 charge -0.43 # "Acetonitrile -CN (UA)"
- set type @atom:37 charge 0.28 # "Acetonitrile -CN (UA)"
- set type @atom:38 charge 0.15 # "Acetonitrile CH3 (UA)"
- set type @atom:39 charge 0.265 # "Isopropanol >CHOH (UA)"
- set type @atom:40 charge 0.265 # "t-Butanol COH (UA)"
- set type @atom:41 charge -0.5 # "Ether ROR (UA)"
- set type @atom:42 charge 0.25 # "Ether CH3-OR (UA)"
- set type @atom:43 charge 0.25 # "Ether -CH2-OR (UA)"
- set type @atom:44 charge 0.5 # "Methylene Chloride (UA)"
- set type @atom:45 charge -0.25 # "Methylene Chloride (UA)"
- set type @atom:46 charge 0.42 # "Chloroform CHCl3 (UA)"
- set type @atom:47 charge -0.14 # "Chloroform CHCl3 (UA)"
- set type @atom:48 charge 0.248 # "Carbon Tetrachloride"
- set type @atom:49 charge -0.062 # "Carbon Tetrachloride"
- set type @atom:50 charge 0.139 # "DMSO >S=O (UA)"
- set type @atom:51 charge -0.459 # "DMSO >S=O (UA)"
- set type @atom:52 charge 0.16 # "DMSO CH3- (UA)"
- set type @atom:53 charge -0.5 # "DMF C=O (UA)"
- set type @atom:54 charge -0.57 # "DMF CON< (UA)"
- set type @atom:55 charge 0.5 # "DMF C=O (UA)"
- set type @atom:56 charge 0.285 # "DMF CH3- (UA)"
- set type @atom:57 charge 0.0 # "Dummy Atom"
- set type @atom:58 charge 0.0 # "Helium Atom"
- set type @atom:59 charge 0.0 # "Neon Atom"
- set type @atom:60 charge 0.0 # "Argon Atom"
- set type @atom:61 charge 0.0 # "Krypton Atom"
- set type @atom:62 charge 0.0 # "Xenon Atom"
- set type @atom:63 charge -0.834 # "TIP3P Water O"
- set type @atom:64 charge 0.417 # "TIP3P Water H"
- set type @atom:65 charge 0.0 # "TIP4P Water O"
- set type @atom:66 charge 0.52 # "TIP4P Water H"
- set type @atom:67 charge -1.04 # "TIP4P Water M"
- set type @atom:68 charge -0.822 # "TIP3F Water O"
- set type @atom:69 charge 0.411 # "TIP3F Water H"
- set type @atom:70 charge 0.0 # "TIP4F Water O"
- set type @atom:71 charge 0.511 # "TIP4F Water H"
- set type @atom:72 charge -1.022 # "TIP4F Water M"
- set type @atom:73 charge 0.0 # "TIP5P Water O"
- set type @atom:74 charge 0.241 # "TIP5P Water H"
- set type @atom:75 charge -0.241 # "TIP5P Water LP"
- set type @atom:76 charge -0.82 # "SPC Water O"
- set type @atom:77 charge 0.41 # "SPC Water H"
- set type @atom:78 charge -1.02 # "Ammonia NH3"
- set type @atom:79 charge 0.34 # "Ammonia NH3"
- set type @atom:80 charge -0.18 # "Alkane CH3-"
- set type @atom:81 charge -0.12 # "Alkane -CH2-"
- set type @atom:82 charge -0.06 # "Alkane >CH-"
- set type @atom:83 charge -0.24 # "Methane CH4"
- set type @atom:84 charge 0.0 # "Alkane >C<"
- set type @atom:85 charge 0.06 # "Alkane H-C"
- set type @atom:86 charge 0.0 # "Alkene R2-C="
- set type @atom:87 charge -0.115 # "Alkene RH-C="
- set type @atom:88 charge -0.23 # "Alkene H2-C="
- set type @atom:89 charge 0.115 # "Alkene H-C="
- set type @atom:90 charge -0.115 # "Aromatic C"
- set type @atom:91 charge 0.115 # "Aromatic H-C"
- set type @atom:92 charge 0.0 # "Naphthalene Fusion C"
- set type @atom:93 charge -0.065 # "Ethyl Benzene CH3-"
- set type @atom:94 charge -0.005 # "Ethyl Benzene -CH2-"
- set type @atom:95 charge -0.115 # "Diene =CH-CH="
- set type @atom:96 charge -0.683 # "Alcohol -OH"
- set type @atom:97 charge 0.418 # "Alcohol -OH"
- set type @atom:98 charge 0.04 # "Methanol CH3-"
- set type @atom:99 charge 0.145 # "Alcohol CH3OH & RCH2OH"
- set type @atom:100 charge 0.205 # "Alcohol R2CHOH"
- set type @atom:101 charge 0.265 # "Alcohol R3COH"
- set type @atom:102 charge 0.1263 # "Trifluoroethanol -CH2-"
- set type @atom:103 charge 0.5323 # "Trifluoroethanol CF3-"
- set type @atom:104 charge -0.6351 # "Trifluoroethanol -OH"
- set type @atom:105 charge 0.4286 # "Trifluoroethanol -OH"
- set type @atom:106 charge -0.2057 # "Trifluoroethanol F"
- set type @atom:107 charge 0.0825 # "Trifluoroethanol -CH2-"
- set type @atom:108 charge 0.15 # "Phenol C-OH"
- set type @atom:109 charge -0.585 # "Phenol -OH"
- set type @atom:110 charge 0.435 # "Phenol -OH"
- set type @atom:111 charge -0.7 # "Diol -OH"
- set type @atom:112 charge 0.435 # "Diol -OH"
- set type @atom:113 charge -0.73 # "Triol -OH"
- set type @atom:114 charge 0.465 # "Triol -OH"
- set type @atom:115 charge 0.145 # "Diol & Triol -CH2OH"
- set type @atom:116 charge 0.205 # "Diol & Triol -CHROH"
- set type @atom:117 charge 0.265 # "Diol & Triol -CR2OH"
- set type @atom:118 charge 0.06 # "Diol & Triol H-COH"
- set type @atom:119 charge -0.17 # "Diphenyl Ether"
- set type @atom:120 charge 0.0 # "Diene =CR-CR="
- set type @atom:121 charge -0.285 # "Anisole -OCH3"
- set type @atom:122 charge -0.4 # "Dialkyl Ether -O-"
- set type @atom:123 charge 0.11 # "Methyl Ether CH3OR"
- set type @atom:124 charge 0.14 # "Ethyl Ether -CH2OR"
- set type @atom:125 charge 0.17 # "Isopropyl Ether >CHOR"
- set type @atom:126 charge 0.2 # "t-Butyl Ether COR"
- set type @atom:127 charge 0.03 # "Alkyl Ether H-COR"
- set type @atom:128 charge -0.4 # "Acetal RO-CR2OX"
- set type @atom:129 charge -0.7 # "Hemiacetal -OH"
- set type @atom:130 charge 0.435 # "Hemiacetal -OH"
- set type @atom:131 charge 0.2 # "Acetal RO-CH2-OR"
- set type @atom:132 charge 0.1 # "Acetal RO-CH2-OR"
- set type @atom:133 charge 0.265 # "Hemiacetal RO-CH2-OH"
- set type @atom:134 charge 0.1 # "Hemiacetal RO-CH2-OH"
- set type @atom:135 charge 0.3 # "Acetal RO-CHR-OR"
- set type @atom:136 charge 0.1 # "Acetal RO-CHR-OR"
- set type @atom:137 charge 0.365 # "Hemiacetal RO-CHR-OH"
- set type @atom:138 charge 0.1 # "Hemiacetal RO-CHR-OH"
- set type @atom:139 charge 0.4 # "Acetal RO-CR2-OR"
- set type @atom:140 charge 0.465 # "Hemiacetal RO-CR2-OH"
- set type @atom:141 charge 0.085 # "Anisole C-OCH3"
- set type @atom:142 charge -0.335 # "Thiol -SH"
- set type @atom:143 charge -0.47 # "Hydrogen Sulfide H2S"
- set type @atom:144 charge -0.435 # "Sulfide -S-"
- set type @atom:145 charge -0.2175 # "Disulfide -S-S-"
- set type @atom:146 charge 0.155 # "Thiol -SH"
- set type @atom:147 charge 0.235 # "Hydrogen Sulfide H2S"
- set type @atom:148 charge 0.06 # "Thiol -CH2-SH"
- set type @atom:149 charge 0.12 # "Thiol >CH-SH"
- set type @atom:150 charge 0.18 # "Thiol C-SH"
- set type @atom:151 charge 0.0375 # "Methyl Sulfide CH3-SR"
- set type @atom:152 charge 0.0975 # "Sulfide RCH2-SR"
- set type @atom:153 charge 0.1575 # "Sulfide R2CH-SR"
- set type @atom:154 charge 0.2175 # "Sulfide R3C-SR"
- set type @atom:155 charge 0.0375 # "Disulfide CH3-S-SR"
- set type @atom:156 charge 0.0975 # "Disulfide RCH2-S-SR"
- set type @atom:157 charge 0.1575 # "Disulfide R2CH-S-SR"
- set type @atom:158 charge 0.2175 # "Disulfide R3C-S-SR"
- set type @atom:159 charge 0.0 # "Methanethiol CH3-SH"
- set type @atom:160 charge 0.2 # "Benzyl Alcohol -CH2OH"
- set type @atom:161 charge 0.26 # "Benzyl Alcohol -CHROH"
- set type @atom:162 charge 0.32 # "Benzyl Alcohol -CR2OH"
- set type @atom:163 charge -0.055 # "Benzyl Alcohol/Nitrile"
- set type @atom:164 charge -0.32 # "Thioanisole -SCH3"
- set type @atom:165 charge 0.08 # "RCH2-NH2 & GLY CA"
- set type @atom:166 charge 0.14 # "RCHR-NH2 & ALA CA"
- set type @atom:167 charge 0.2 # "R3C-NH2 & AIB CA"
- set type @atom:168 charge -0.12 # "Chloroalkene Cl-CH="
- set type @atom:169 charge 0.005 # "Chloroalkene Cl-CH="
- set type @atom:170 charge 0.1025 # "Thioanisole C-SCH3"
- set type @atom:171 charge 0.14 # "Amide -NH-CHR2"
- set type @atom:172 charge 0.2 # "Amide -NH-CR3"
- set type @atom:173 charge 0.7 # "Benzophenone C=O"
- set type @atom:174 charge 0.565 # "Benzaldehyde C=O"
- set type @atom:175 charge 0.585 # "Acetophenone C=O"
- set type @atom:176 charge 0.615 # "Benzamide C=O"
- set type @atom:177 charge 0.5 # "Amide C=O"
- set type @atom:178 charge -0.5 # "Amide C=O"
- set type @atom:179 charge -0.76 # "Amide -CO-NH2"
- set type @atom:180 charge -0.5 # "Amide -CO-NHR"
- set type @atom:181 charge -0.14 # "Amide -CO-NR2"
- set type @atom:182 charge 0.38 # "Amide -CO-NH2"
- set type @atom:183 charge 0.3 # "Amide -CO-NHR"
- set type @atom:184 charge 0.02 # "Amide -NH-CH3"
- set type @atom:185 charge -0.11 # "Amide -NR-CH3"
- set type @atom:186 charge 0.08 # "Amide -NH-CH2R"
- set type @atom:187 charge -0.05 # "Amide -NR-CH2R & PRO CD"
- set type @atom:188 charge 0.01 # "Amide -NR-CHR2 & PRO CA"
- set type @atom:189 charge 0.142 # "Urea C=O"
- set type @atom:190 charge -0.39 # "Urea C=O"
- set type @atom:191 charge -0.542 # "Urea -NH2"
- set type @atom:192 charge 0.333 # "Urea -NH2"
- set type @atom:193 charge -0.49 # "Imide -NH-"
- set type @atom:194 charge 0.42 # "Imide C=O"
- set type @atom:195 charge -0.42 # "Imide C=O"
- set type @atom:196 charge 0.37 # "Imide -NH-"
- set type @atom:197 charge 0.06 # "Formimide H-C=O"
- set type @atom:198 charge -0.12 # "Imide CH3-CONHCO-"
- set type @atom:199 charge -0.06 # "Imide -CH2-CONHCO-"
- set type @atom:200 charge 0.0 # "Imide >CH-CONHCO-"
- set type @atom:201 charge 0.06 # "Imide C-CONHCO-"
- set type @atom:202 charge 0.035 # "Benzonitrile C-CN"
- set type @atom:203 charge 0.395 # "Benzonitrile -CN"
- set type @atom:204 charge -0.43 # "Benzonitrile -CN"
- set type @atom:205 charge 0.18 # "Chlorobenzene C-Cl"
- set type @atom:206 charge -0.18 # "Chlorobenzene C-Cl"
- set type @atom:207 charge -0.385 # "N-Phenylacetamide N"
- set type @atom:208 charge 0.085 # "N-Phenylacetamide N-CA"
- set type @atom:209 charge 0.52 # "Carboxylic Acid -COOH"
- set type @atom:210 charge -0.44 # "Carboxylic Acid C=O"
- set type @atom:211 charge -0.53 # "Carboxylic Acid -OH"
- set type @atom:212 charge 0.45 # "Carboxylic Acid -COOH"
- set type @atom:213 charge 0.7 # "Carboxylate COO-"
- set type @atom:214 charge -0.8 # "Carboxylate COO-"
- set type @atom:215 charge -0.28 # "Carboxylate CH3-COO-"
- set type @atom:216 charge -0.22 # "Carboxylate RCH2-COO-"
- set type @atom:217 charge -0.16 # "Carboxylate R2CH-COO-"
- set type @atom:218 charge -0.1 # "Carboxylate R3C-COO-"
- set type @atom:219 charge 0.45 # "Aldehyde/Acyl Halide C=O"
- set type @atom:220 charge -0.45 # "Aldehyde/Acyl Halide C=O"
- set type @atom:221 charge 0.0 # "Aldehyde/Formamide H-C=O"
- set type @atom:222 charge 0.47 # "Ketone C=O"
- set type @atom:223 charge -0.47 # "Ketone C=O"
- set type @atom:224 charge 0.06 # "Acyl H-C-COX"
- set type @atom:225 charge 0.04 # "C-Terminal ALA CA"
- set type @atom:226 charge -0.02 # "C-Terminal GLY CA"
- set type @atom:227 charge 0.1 # "C-Terminal AIB CA"
- set type @atom:228 charge -0.09 # "C-Terminal PRO CA"
- set type @atom:229 charge -0.4 # "Ammonium NH4+"
- set type @atom:230 charge -0.3 # "Ammonium RNH3+"
- set type @atom:231 charge 0.0 # "Ammonium R4N+"
- set type @atom:232 charge 0.35 # "Ammonium NH4+"
- set type @atom:233 charge 0.33 # "Ammonium RNH3+"
- set type @atom:234 charge 0.13 # "Ammonium CH3-NH3+"
- set type @atom:235 charge 0.19 # "CH3NH3+/N-Term GLY CA"
- set type @atom:236 charge 0.25 # "RCH2NH3+/N-Term ALA CA"
- set type @atom:237 charge 0.31 # "R3C-NH3+/N-Term AIB CA"
- set type @atom:238 charge 0.23 # "N-Terminal PRO CA"
- set type @atom:239 charge 0.17 # "N-Terminal PRO CD"
- set type @atom:240 charge 0.11 # "Ammonium CH3-NH2R+"
- set type @atom:241 charge 0.09 # "GLY Zwitterion CA"
- set type @atom:242 charge 0.15 # "ALA Zwitterion CA"
- set type @atom:243 charge -0.8 # "Guanidinium -NH2"
- set type @atom:244 charge 0.46 # "Guanidinium -NH2"
- set type @atom:245 charge 0.64 # "Guanidinium C+"
- set type @atom:246 charge -0.7 # "Guanidinium -NHR"
- set type @atom:247 charge 0.44 # "Guanidinium -NHR"
- set type @atom:248 charge 0.2 # "Me Guanidinium CH3-"
- set type @atom:249 charge -0.11 # "Et Guanidinium CH3-"
- set type @atom:250 charge 0.19 # "Et Guan -CH2- & ARG CD"
- set type @atom:251 charge -0.05 # "Pr Guan -CH2- & ARG CG"
- set type @atom:252 charge -0.2 # "Ammonium R2NH2+"
- set type @atom:253 charge 0.31 # "Ammonium R2NH2+"
- set type @atom:254 charge -0.46 # "Diaminopyridine N1"
- set type @atom:255 charge 0.36 # "Diaminopyridine C2"
- set type @atom:256 charge -0.85 # "Diaminopyridine -NH2"
- set type @atom:257 charge 0.37 # "Diaminopyridine -NH2"
- set type @atom:258 charge -0.15 # "Diaminopyridine C3"
- set type @atom:259 charge 0.1 # "Diaminopyridine H3"
- set type @atom:260 charge -0.04 # "Diaminopyridine C4"
- set type @atom:261 charge 0.1 # "Diaminopyridine H4"
- set type @atom:262 charge -0.6 # "Uracil & Thymine N1"
- set type @atom:263 charge 0.5 # "Uracil & Thymine C2"
- set type @atom:264 charge -0.51 # "Uracil & Thymine N3"
- set type @atom:265 charge 0.45 # "Uracil & Thymine C4"
- set type @atom:266 charge -0.07 # "Uracil & Thymine C5"
- set type @atom:267 charge 0.08 # "Uracil & Thymine C6"
- set type @atom:268 charge 0.41 # "Uracil & Thymine HN1"
- set type @atom:269 charge -0.4 # "Uracil & Thymine O2"
- set type @atom:270 charge 0.36 # "Uracil & Thymine HN3"
- set type @atom:271 charge -0.42 # "Uracil & Thymine O4"
- set type @atom:272 charge 0.1 # "Uracil & Thymine HC5"
- set type @atom:273 charge 0.1 # "Uracil & Thymine HC6"
- set type @atom:274 charge -0.14 # "Thymine CH3-"
- set type @atom:275 charge 0.08 # "Thymine CH3-"
- set type @atom:276 charge -0.56 # "Cytosine N1"
- set type @atom:277 charge 0.55 # "Cytosine C2"
- set type @atom:278 charge -0.54 # "Cytosine N3"
- set type @atom:279 charge 0.46 # "Cytosine C4"
- set type @atom:280 charge -0.06 # "Cytosine C5"
- set type @atom:281 charge 0.1 # "Cytosine C6"
- set type @atom:282 charge 0.38 # "Cytosine HN1"
- set type @atom:283 charge -0.48 # "Cytosine O2"
- set type @atom:284 charge -0.79 # "Cytosine NH2-"
- set type @atom:285 charge 0.385 # "Cytosine NH2- (N3)"
- set type @atom:286 charge 0.355 # "Cytosine NH2- (C5)"
- set type @atom:287 charge 0.1 # "Cytosine HC5"
- set type @atom:288 charge 0.1 # "Cytosine HC6"
- set type @atom:289 charge -0.53 # "Adenine N1"
- set type @atom:290 charge 0.22 # "Adenine C2"
- set type @atom:291 charge -0.55 # "Adenine N3"
- set type @atom:292 charge 0.38 # "Adenine C4"
- set type @atom:293 charge 0.15 # "Adenine C5"
- set type @atom:294 charge 0.44 # "Adenine C6"
- set type @atom:295 charge -0.49 # "Adenine & Guanine N7"
- set type @atom:296 charge 0.2 # "Adenine & Guanine C8"
- set type @atom:297 charge -0.5 # "Adenine & Guanine N9"
- set type @atom:298 charge 0.2 # "Adenine HC2"
- set type @atom:299 charge -0.81 # "Adenine NH2-"
- set type @atom:300 charge 0.385 # "Adenine NH2- (N1)"
- set type @atom:301 charge 0.355 # "Adenine NH2- (C5)"
- set type @atom:302 charge 0.2 # "Adenine & Guanine HC8"
- set type @atom:303 charge 0.35 # "Adenine & Guanine HN9"
- set type @atom:304 charge -0.56 # "Guanine N1"
- set type @atom:305 charge 0.46 # "Guanine C2"
- set type @atom:306 charge -0.51 # "Guanine N3"
- set type @atom:307 charge 0.34 # "Guanine C4"
- set type @atom:308 charge 0.12 # "Guanine C5"
- set type @atom:309 charge 0.52 # "Guanine C6"
- set type @atom:310 charge 0.38 # "Guanine HN1"
- set type @atom:311 charge -0.8 # "Guanine NH2-"
- set type @atom:312 charge 0.4 # "Guanine NH2-"
- set type @atom:313 charge -0.51 # "Guanine O6"
- set type @atom:314 charge -0.01 # "9-Me A & 9-Me-G CH3-"
- set type @atom:315 charge 0.12 # "9-Me-A & 9-Me-G CH3-"
- set type @atom:316 charge -0.01 # "1-Me-U & 1-Me-T CH3-"
- set type @atom:317 charge 0.14 # "1-Me-U & 1-Me-T CH3-"
- set type @atom:318 charge -0.01 # "1-Me-Cytosine CH3-"
- set type @atom:319 charge 0.13 # "1-Me-Cytosine CH3-"
- set type @atom:320 charge -0.64 # "CytosineH+ N1"
- set type @atom:321 charge 0.65 # "CytosineH+ C2"
- set type @atom:322 charge -0.74 # "CytosineH+ N3"
- set type @atom:323 charge 0.66 # "CytosineH+ C4"
- set type @atom:324 charge -0.06 # "CytosineH+ C5"
- set type @atom:325 charge 0.1 # "CytosineH+ C6"
- set type @atom:326 charge 0.49 # "CytosineH+ HN1"
- set type @atom:327 charge -0.3 # "CytosineH+ O2"
- set type @atom:328 charge 0.48 # "CytosineH+ HN3"
- set type @atom:329 charge -0.81 # "CytosineH+ NH2-"
- set type @atom:330 charge 0.46 # "CytosineH+ NH2- (N3)"
- set type @atom:331 charge 0.43 # "CytosineH+ NH2- (C5)"
- set type @atom:332 charge 0.14 # "CytosineH+ HC5"
- set type @atom:333 charge 0.14 # "CytosineH+ HC6"
- set type @atom:334 charge 0.01 # "1-Me-CytosineH+ CH3-"
- set type @atom:335 charge 0.16 # "1-Me-CytosineH+ CH3-"
- set type @atom:336 charge 0.78 # "DiMePhosphate P (UA)"
- set type @atom:337 charge -0.66 # "DiMePhosphate O=P-O (UA)"
- set type @atom:338 charge -0.43 # "DiMePhosphate CH3-O (UA)"
- set type @atom:339 charge 0.2 # "DiMePhosphate CH3-O (UA)"
- set type @atom:340 charge 0.18 # "Trifluorothymine CF3-"
- set type @atom:341 charge -0.06 # "Chloroalkene Cl2-C="
- set type @atom:342 charge 0.12 # "Chloroalkene Cl2-C="
- set type @atom:343 charge -1.0 # "Fluoride Ion F-"
- set type @atom:344 charge -1.0 # "Chloride Ion Cl-"
- set type @atom:345 charge -1.0 # "Bromide Ion Br-"
- set type @atom:346 charge -1.0 # "Iodide Ion I-"
- set type @atom:347 charge 1.0 # "Ammonium Ion NH4+ (UA)"
- set type @atom:348 charge 1.0 # "Lithium Ion Li+"
- set type @atom:349 charge 1.0 # "Sodium Ion Na+"
- set type @atom:350 charge 1.0 # "Potassium Ion K+"
- set type @atom:351 charge 1.0 # "Rubidium Ion Rb+"
- set type @atom:352 charge 1.0 # "Cesium Ion Cs+"
- set type @atom:353 charge 2.0 # "Magnesium Ion Mg+2"
- set type @atom:354 charge 2.0 # "Calcium Ion Ca+2"
- set type @atom:355 charge 2.0 # "Strontium Ion Sr+2"
- set type @atom:356 charge 2.0 # "Barium Ion Ba+2"
- set type @atom:357 charge -0.4 # "Methyl Thiolate CH3S-"
- set type @atom:358 charge 0.1 # "Methyl Thiolate CH3S-"
- set type @atom:359 charge -0.9 # "Methyl Thiolate CH3S-"
- set type @atom:360 charge -0.2 # "Methoxide CH3O-"
- set type @atom:361 charge 0.06 # "Methoxide CH3O-"
- set type @atom:362 charge -0.98 # "Methoxide CH3O-"
- set type @atom:363 charge -1.07 # "Nitrile Anion CNCH2-"
- set type @atom:364 charge 0.19 # "Nitrile Anion CNCH2-"
- set type @atom:365 charge 0.51 # "Nitrile Anion CNCH2-"
- set type @atom:366 charge -0.82 # "Nitrile Anion CNCH2-"
- set type @atom:367 charge -0.3 # "Me Amine Anion CH3NH-"
- set type @atom:368 charge 0.07 # "Me Amine Anion CH3NH-"
- set type @atom:369 charge -1.31 # "Me Amine Anion CH3NH-"
- set type @atom:370 charge 0.4 # "Methyl Amine Anion"
- set type @atom:371 charge -0.4 # "Ethyl Anion CH3-CH2-"
- set type @atom:372 charge 0.08 # "Ethyl Anion CH3-CH2-"
- set type @atom:373 charge 0.0 # "Ethyl Anion CH3-CH2-"
- set type @atom:374 charge 0.07 # "Ethyl Anion CH3-CH2-"
- set type @atom:375 charge -0.98 # "Ethyl Anion CH3-CH2-"
- set type @atom:376 charge -1.3 # "Hydroxide Ion OH-"
- set type @atom:377 charge 0.3 # "Hydroxide Ion OH-"
- set type @atom:378 charge 2.5 # "Uranyl Ion UO2+"
- set type @atom:379 charge -0.25 # "Uranyl Ion UO2+"
- set type @atom:380 charge -0.865 # "GTP O-(POn)2"
- set type @atom:381 charge 1.62 # "DiMe Phosphate P"
- set type @atom:382 charge -0.92 # "DiMe Phosphate O=P-O"
- set type @atom:383 charge -0.6 # "DiMe Phosphate CH3-O"
- set type @atom:384 charge 0.3 # "DiMe Phosphate CH3-O"
- set type @atom:385 charge -0.03 # "DiMe Phosphate CH3-O"
- set type @atom:386 charge 1.92 # "Me Phosphate P"
- set type @atom:387 charge -1.12 # "Me Phosphate O=PO2"
- set type @atom:388 charge -0.7 # "Me Phosphate CH3-O"
- set type @atom:389 charge 0.44 # "Me Phosphate CH3-O"
- set type @atom:390 charge -0.1 # "Me Phosphate CH3-O"
- set type @atom:391 charge 1.62 # "Me MePhosphonate P"
- set type @atom:392 charge -0.97 # "Me MePhosphonate O=P-O"
- set type @atom:393 charge -0.63 # "Me MePhosphonate CH3-O"
- set type @atom:394 charge 0.28 # "Me MePhosphonate CH3-O"
- set type @atom:395 charge -0.02 # "Me MePhosphonate CH3-O"
- set type @atom:396 charge -0.51 # "Me MePhosphonate CH3-P"
- set type @atom:397 charge 0.08 # "Me MePhosphonate CH3-P"
- set type @atom:398 charge -0.14 # "Bz MePhosphonate Cipso"
- set type @atom:399 charge 0.32 # "Bz MePhosphonate CH3-O"
- set type @atom:400 charge 0.02 # "Bz MePhosphonate CH3-O"
- set type @atom:401 charge -0.04 # "Me BzPhosphonate Cipso"
- set type @atom:402 charge -0.47 # "Me BzPhosphonate CH3-P"
- set type @atom:403 charge 0.12 # "Me BzPhosphonate CH3-P"
- set type @atom:404 charge 0.14 # "Ph Phosphate Cipso"
- set type @atom:405 charge 0.24 # "Barbiturate C6(R2)"
- set type @atom:406 charge 0.51 # "Ester -COOR"
- set type @atom:407 charge -0.43 # "Ester C=O"
- set type @atom:408 charge -0.33 # "Ester CO-O-R"
- set type @atom:409 charge 0.16 # "Methyl Ester -OCH3"
- set type @atom:410 charge 0.03 # "Ester -OCH<"
- set type @atom:411 charge 0.635 # "Benzoic Acid -COOH"
- set type @atom:412 charge 0.625 # "Aryl Ester -COOR"
- set type @atom:413 charge 0.135 # "Phenyl Ester Cipso"
- set type @atom:414 charge -0.215 # "Phenyl Ester -OPh"
- set type @atom:415 charge 1.48 # "Sulfonamide -SO2N<"
- set type @atom:416 charge -0.68 # "Sulfonamide -SO2N<"
- set type @atom:417 charge -0.54 # "Sulfonamide CH3-S"
- set type @atom:418 charge 0.18 # "Sulfonamide CH3-S"
- set type @atom:419 charge -1.0 # "Sulfonamide -SO2NH2"
- set type @atom:420 charge 0.44 # "Sulfonamide -SO2NH2"
- set type @atom:421 charge -0.8 # "Sulfonamide -SO2NHR"
- set type @atom:422 charge 0.41 # "Sulfonamide -SO2NHR"
- set type @atom:423 charge 0.18 # "N-Me Sulfonamide CH3-"
- set type @atom:424 charge 0.03 # "N-Me Sulfonamide CH3-"
- set type @atom:425 charge 0.39 # "Sulfonamide N-CH2-R"
- set type @atom:426 charge -0.06 # "Sulfonamide N-CH2-R"
- set type @atom:427 charge -0.18 # "N-Et Sulfonamide CH3-"
- set type @atom:428 charge 0.06 # "N-Et Sulfonamide CH3-"
- set type @atom:429 charge 0.0 # "Aryl Sulfonamide C-SO2N"
- set type @atom:430 charge 0.03 # "Aryl Sulfoxide C-S=O"
- set type @atom:431 charge 0.19 # "Et Ester -OCH2R"
- set type @atom:432 charge 0.22 # "i-Pr Ester -OCHR2"
- set type @atom:433 charge 0.25 # "t-Bu Ester -OCR3"
- set type @atom:434 charge 1.374 # "Sulfone R-SO2-R"
- set type @atom:435 charge -0.687 # "Sulfone R-SO2-R"
- set type @atom:436 charge 0.245 # "Alkyl Aryl Sulfoxide"
- set type @atom:437 charge 0.13 # "Dialkyl Sulfoxide"
- set type @atom:438 charge -0.42 # "Sulfoxide R-SO-R"
- set type @atom:439 charge -0.035 # "Sulfoxide CH3-SO-R"
- set type @atom:440 charge 0.025 # "Sulfoxide -CH2-SO-R"
- set type @atom:441 charge 0.075 # "TRP CG"
- set type @atom:442 charge -0.055 # "TRP CD"
- set type @atom:443 charge 0.13 # "TRP CE"
- set type @atom:444 charge -0.57 # "TRP NE, HID ND & HIE NE"
- set type @atom:445 charge 0.42 # "TRP HNE & HID/HIE HN"
- set type @atom:446 charge -0.005 # "HIS CB"
- set type @atom:447 charge 0.295 # "HID & HIE CE1"
- set type @atom:448 charge -0.015 # "HID CD2 & HIE CG"
- set type @atom:449 charge 0.015 # "HID CG & HIE CD2"
- set type @atom:450 charge 0.385 # "HIP CE1"
- set type @atom:451 charge 0.215 # "HIP CG & CD2"
- set type @atom:452 charge -0.49 # "HID NE & HIE ND"
- set type @atom:453 charge -0.54 # "HIP ND & NE"
- set type @atom:454 charge 0.46 # "HIP HND & HNE"
- set type @atom:455 charge -0.115 # "TRP CD1"
- set type @atom:456 charge 0.055 # "i-Pr Benzene -CHMe2"
- set type @atom:457 charge 0.115 # "t-Bu Benzene -CMe3"
- set type @atom:458 charge -0.03 # "Vinyl Ether =CH-OR"
- set type @atom:459 charge 0.085 # "Vinyl Ether =CR-OR"
- set type @atom:460 charge 0.0 # "Biphenyl C1"
- set type @atom:461 charge -0.678 # "Pyridine N"
- set type @atom:462 charge 0.473 # "Pyridine C1"
- set type @atom:463 charge -0.447 # "Pyridine C2"
- set type @atom:464 charge 0.227 # "Pyridine C3"
- set type @atom:465 charge 0.012 # "Pyridine H1"
- set type @atom:466 charge 0.155 # "Pyridine H2"
- set type @atom:467 charge 0.065 # "Pyridine H3"
- set type @atom:468 charge -0.468 # "Pyrazine N"
- set type @atom:469 charge 0.192 # "Pyrazine CH"
- set type @atom:470 charge 0.042 # "Pyrazine CH"
- set type @atom:471 charge -0.839 # "Pyrimidine N"
- set type @atom:472 charge 0.874 # "Pyrimidine C2"
- set type @atom:473 charge 0.653 # "Pyrimidine C4"
- set type @atom:474 charge -0.689 # "Pyrimidine C5"
- set type @atom:475 charge -0.032 # "Pyrimidine HC2"
- set type @atom:476 charge 0.011 # "Pyrimidine HC4"
- set type @atom:477 charge 0.197 # "Pyrimidine HC5"
- set type @atom:478 charge -0.331 # "Pyridazine N"
- set type @atom:479 charge 0.378 # "Pyridazine C3"
- set type @atom:480 charge -0.16 # "Pyridazine C4"
- set type @atom:481 charge -0.009 # "Pyridazine HC3"
- set type @atom:482 charge 0.122 # "Pyridazine HC4"
- set type @atom:483 charge -0.239 # "Pyrrole N"
- set type @atom:484 charge -0.163 # "Pyrrole C2"
- set type @atom:485 charge -0.149 # "Pyrrole C3"
- set type @atom:486 charge 0.317 # "Pyrrole HN"
- set type @atom:487 charge 0.155 # "Pyrrole HC2"
- set type @atom:488 charge 0.118 # "Pyrrole HC3"
- set type @atom:489 charge -0.059 # "Pyrazole N1"
- set type @atom:490 charge -0.491 # "Pyrazole N2"
- set type @atom:491 charge 0.246 # "Pyrazole C3"
- set type @atom:492 charge -0.32 # "Pyrazole C4"
- set type @atom:493 charge -0.034 # "Pyrazole C5"
- set type @atom:494 charge 0.301 # "Pyrazole HN1"
- set type @atom:495 charge 0.072 # "Pyrazole HC3"
- set type @atom:496 charge 0.15 # "Pyrazole HC4"
- set type @atom:497 charge 0.135 # "Pyrazole HC5"
- set type @atom:498 charge -0.257 # "Imidazole N1"
- set type @atom:499 charge 0.275 # "Imidazole C2"
- set type @atom:500 charge -0.563 # "Imidazole N3"
- set type @atom:501 charge 0.185 # "Imidazole C4"
- set type @atom:502 charge -0.286 # "Imidazole C5"
- set type @atom:503 charge 0.306 # "Imidazole HN1"
- set type @atom:504 charge 0.078 # "Imidazole HC2"
- set type @atom:505 charge 0.075 # "Imidazole HC4"
- set type @atom:506 charge 0.187 # "Imidazole HC5"
- set type @atom:507 charge -0.19 # "Furan O"
- set type @atom:508 charge -0.019 # "Furan C2"
- set type @atom:509 charge -0.154 # "Furan C3"
- set type @atom:510 charge 0.142 # "Furan HC2"
- set type @atom:511 charge 0.126 # "Furan HC3"
- set type @atom:512 charge -0.257 # "Oxazole O"
- set type @atom:513 charge 0.511 # "Oxazole C2"
- set type @atom:514 charge -0.59 # "Oxazole N"
- set type @atom:515 charge 0.169 # "Oxazole C4"
- set type @atom:516 charge -0.148 # "Oxazole C5"
- set type @atom:517 charge 0.043 # "Oxazole HC2"
- set type @atom:518 charge 0.091 # "Oxazole HC4"
- set type @atom:519 charge 0.181 # "Oxazole HC5"
- set type @atom:520 charge -0.122 # "Isoxazole O"
- set type @atom:521 charge -0.413 # "Isoxazole N"
- set type @atom:522 charge 0.405 # "Isoxazole C3"
- set type @atom:523 charge -0.455 # "Isoxazole C4"
- set type @atom:524 charge 0.25 # "Isoxazole C5"
- set type @atom:525 charge 0.053 # "Isoxazole HC3"
- set type @atom:526 charge 0.184 # "Isoxazole HC4"
- set type @atom:527 charge 0.098 # "Isoxazole HC5"
- set type @atom:528 charge -0.5 # "Indole N1"
- set type @atom:529 charge 0.001 # "Indole C2"
- set type @atom:530 charge -0.39 # "Indole C3"
- set type @atom:531 charge -0.27 # "Indole C4"
- set type @atom:532 charge -0.127 # "Indole C5"
- set type @atom:533 charge -0.108 # "Indole C6"
- set type @atom:534 charge -0.258 # "Indole C7"
- set type @atom:535 charge 0.22 # "Indole C8"
- set type @atom:536 charge 0.225 # "Indole C9"
- set type @atom:537 charge 0.376 # "Indole HN1"
- set type @atom:538 charge 0.147 # "Indole HC2"
- set type @atom:539 charge 0.172 # "Indole HC3"
- set type @atom:540 charge 0.155 # "Indole HC4"
- set type @atom:541 charge 0.107 # "Indole HC5"
- set type @atom:542 charge 0.11 # "Indole HC6"
- set type @atom:543 charge 0.14 # "Indole HC7"
- set type @atom:544 charge -0.694 # "Quinoline N1"
- set type @atom:545 charge 0.425 # "Quinoline C2"
- set type @atom:546 charge -0.359 # "Quinoline C3"
- set type @atom:547 charge -0.008 # "Quinoline C4"
- set type @atom:548 charge -0.197 # "Quinoline C5"
- set type @atom:549 charge -0.112 # "Quinoline C6"
- set type @atom:550 charge -0.07 # "Quinoline C7"
- set type @atom:551 charge -0.307 # "Quinoline C8"
- set type @atom:552 charge 0.563 # "Quinoline C9"
- set type @atom:553 charge -0.051 # "Quinoline C10"
- set type @atom:554 charge 0.028 # "Quinoline HC2"
- set type @atom:555 charge 0.146 # "Quinoline HC3"
- set type @atom:556 charge 0.119 # "Quinoline HC4"
- set type @atom:557 charge 0.133 # "Quinoline HC5"
- set type @atom:558 charge 0.113 # "Quinoline HC6"
- set type @atom:559 charge 0.114 # "Quinoline HC7"
- set type @atom:560 charge 0.157 # "Quinoline HC8"
- set type @atom:561 charge -0.76 # "Purine N1"
- set type @atom:562 charge 0.679 # "Purine C2"
- set type @atom:563 charge -0.788 # "Purine N3"
- set type @atom:564 charge 0.736 # "Purine C4"
- set type @atom:565 charge 0.038 # "Purine C5"
- set type @atom:566 charge 0.343 # "Purine C6"
- set type @atom:567 charge -0.642 # "Purine N7"
- set type @atom:568 charge 0.452 # "Purine C8"
- set type @atom:569 charge -0.682 # "Purine N9"
- set type @atom:570 charge 0.024 # "Purine HC2"
- set type @atom:571 charge 0.101 # "Purine HC6"
- set type @atom:572 charge 0.086 # "Purine HC8"
- set type @atom:573 charge 0.413 # "Purine HN9"
- set type @atom:574 charge -0.03 # "Thiazole S"
- set type @atom:575 charge 0.242 # "Thiazole C2"
- set type @atom:576 charge -0.515 # "Thiazole N"
- set type @atom:577 charge 0.228 # "Thiazole C4"
- set type @atom:578 charge -0.299 # "Thiazole C5"
- set type @atom:579 charge 0.101 # "Thiazole HC2"
- set type @atom:580 charge 0.068 # "Thiazole HC4"
- set type @atom:581 charge 0.205 # "Thiazole HC5"
- set type @atom:582 charge -0.951 # "1,3,5-Triazine N"
- set type @atom:583 charge 0.965 # "1,3,5-Triazine CH"
- set type @atom:584 charge -0.014 # "1,3,5-Triazine CH"
- set type @atom:585 charge 0.13 # "Serotonin C5-OH"
- set type @atom:586 charge 0.052 # "Serotonin CH2 on C3"
- set type @atom:587 charge -0.599 # "1,10-Phenanthroline N"
- set type @atom:588 charge 0.392 # "1,10-Phenanthroline C2"
- set type @atom:589 charge -0.348 # "1,10-Phenanthroline C3"
- set type @atom:590 charge 0.02 # "1,10-Phenanthroline C4"
- set type @atom:591 charge -0.042 # "1,10-Phenanthroline C12"
- set type @atom:592 charge 0.347 # "1,10-Phenanthroline C11"
- set type @atom:593 charge -0.196 # "1,10-Phenanthroline C5"
- set type @atom:594 charge 0.032 # "1,10-Phenanthroline HC2"
- set type @atom:595 charge 0.146 # "1,10-Phenanthroline HC3"
- set type @atom:596 charge 0.108 # "1,10-Phenanthroline HC4"
- set type @atom:597 charge 0.14 # "1,10-Phenanthroline HC5"
- set type @atom:598 charge 0.122 # "1-Methylimidazole N1"
- set type @atom:599 charge 0.166 # "1-Methylimidazole C2"
- set type @atom:600 charge -0.58 # "1-Methylimidazole N3"
- set type @atom:601 charge 0.173 # "1-Methylimidazole C4"
- set type @atom:602 charge -0.395 # "1-Methylimidazole C5"
- set type @atom:603 charge -0.199 # "1-Methylimidazole CH3-"
- set type @atom:604 charge 0.118 # "1-Methylimidazole HC2"
- set type @atom:605 charge 0.093 # "1-Methylimidazole HC4"
- set type @atom:606 charge 0.208 # "1-Methylimidazole HC5"
- set type @atom:607 charge 0.098 # "1-Methylimidazole CH3-"
- set type @atom:608 charge -0.139 # "1-Et Imidazole RCH2-"
- set type @atom:609 charge -0.079 # "1-iPr Imidazole R2CH-"
- set type @atom:610 charge 0.099 # "1-MeO-Me-Imidazole CH2"
- set type @atom:611 charge -0.168 # "2-Me Pyridine CH3"
- set type @atom:612 charge -0.108 # "2-Et Pyridine CH2"
- set type @atom:613 charge -0.189 # "3-Me Pyridazine CH3"
- set type @atom:614 charge -0.129 # "3-Et Pyridazine CH2"
- set type @atom:615 charge -0.169 # "4-Me Pyrimidine CH3"
- set type @atom:616 charge -0.109 # "4-Et Pyrimidine CH2"
- set type @atom:617 charge -0.138 # "2-Me Pyrazine CH3"
- set type @atom:618 charge -0.078 # "2-Et Pyrazine CH2"
- set type @atom:619 charge -0.025 # "2-Me Pyrrole CH3"
- set type @atom:620 charge 0.035 # "2-Et Pyrrole CH2"
- set type @atom:621 charge -0.038 # "2-Me Furan CH3"
- set type @atom:622 charge 0.022 # "2-Et Furan CH2"
- set type @atom:623 charge -0.334 # "6-Mercaptopurine SH"
- set type @atom:624 charge 0.255 # "6-Mercaptopurine SH"
- set type @atom:625 charge 0.523 # "6-Mercaptopurine C6"
- set type @atom:626 charge 0.5 # "Beta-Lactam N-C=O"
- set type @atom:627 charge -0.14 # "Beta-Lactam N-C=O"
- set type @atom:628 charge 0.2275 # "Penicillin CH-N"
- set type @atom:629 charge 0.14 # "Penicillin CH-CO"
- set type @atom:630 charge -0.008 # "3-Me Indole CH3"
- set type @atom:631 charge 0.588 # "2-Phenyl Pyridine C2"
- set type @atom:632 charge -0.103 # "2-Phenyl Pyridine C2'"
- set type @atom:633 charge -0.332 # "2-Phenyl Pyridine C3"
- set type @atom:634 charge 0.04 # "2-Phenyl Pyridine C3'"
- set type @atom:635 charge 0.342 # "2-Phenyl Pyridine C4"
- set type @atom:636 charge -0.05 # "2-Phenyl Pyridine C4'"
- set type @atom:637 charge -0.205 # "Diphenyl Thioether S"
- set type @atom:638 charge 3.0 # "Actinium Ion Ac+3"
- set type @atom:639 charge 4.0 # "Thorium Ion Th+4"
- set type @atom:640 charge 3.0 # "Americium Ion Am+3"
- set type @atom:641 charge 0.619 # "t-Butyl Cation C+"
- set type @atom:642 charge -0.395 # "t-Butyl Cation CH3-"
- set type @atom:643 charge 0.174 # "t-Butyl Cation CH3-"
- set type @atom:644 charge 3.0 # "Lanthanum Ion La+3"
- set type @atom:645 charge 3.0 # "Neodymium Ion Nd+3"
- set type @atom:646 charge 3.0 # "Europium Ion Eu+3"
- set type @atom:647 charge 3.0 # "Gadolinium Ion Gd+3"
- set type @atom:648 charge 3.0 # "Ytterbium Ion Yb+3"
- set type @atom:649 charge -0.344 # "Cl..CH3..Cl- Sn2 TS"
- set type @atom:650 charge -0.628 # "Cl..CH3..Cl- Sn2 TS"
- set type @atom:651 charge 0.2 # "Cl..CH3..Cl- Sn2 TS"
- set type @atom:652 charge -0.12 # "Cyclopropane -CH2-"
- set type @atom:653 charge -0.06 # "Cyclopropane -CHR-"
- set type @atom:654 charge 0.0 # "Cyclopropane -CR2-"
- set type @atom:655 charge -0.23 # "Cyclopentadienyl Anion"
- set type @atom:656 charge 0.03 # "Cyclopentadienyl Anion"
- set type @atom:657 charge -0.099 # "Cyclopentadienyl Radical"
- set type @atom:658 charge 0.099 # "Cyclopentadienyl Radical"
- set type @atom:659 charge 0.22 # "Fluorobenzene CF"
- set type @atom:660 charge -0.22 # "Fluorobenzene CF"
- set type @atom:661 charge 0.13 # "Hexafluorobenzene CF"
- set type @atom:662 charge -0.13 # "Hexafluorobenzene CF"
- set type @atom:663 charge -0.22 # "Bromide -CH2-Br (UA)"
- set type @atom:664 charge 0.22 # "Bromide -CH2-Br (UA)"
- set type @atom:665 charge 0.15 # "TrifluoroMeBenzene C-CF3"
- set type @atom:666 charge 0.45 # "TrifluoroMeBenzene CF3-"
- set type @atom:667 charge -0.2 # "TrifluoroMeBenzene CF3-"
- set type @atom:668 charge 0.2 # "Difluorobenzene CF"
- set type @atom:669 charge -0.2 # "Difluorobenzene CF"
- set type @atom:670 charge 0.2 # "Bromobenzene CBr"
- set type @atom:671 charge -0.2 # "Bromobenzene CBr"
- set type @atom:672 charge 0.1 # "Iodobenzene CI"
- set type @atom:673 charge -0.1 # "Iodobenzene CI"
- set type @atom:674 charge 0.055 # "cProp/cBut Benzene C-Ar"
- set type @atom:675 charge -0.22 # "Thiophenol SH"
- set type @atom:676 charge 0.065 # "Thiophenol C-SH"
- set type @atom:677 charge 0.013 # "Benzamidine CG"
- set type @atom:678 charge -0.106 # "Benzamidine CD"
- set type @atom:679 charge -0.09 # "Benzamidine CE"
- set type @atom:680 charge -0.119 # "Benzamidine CZ"
- set type @atom:681 charge 0.141 # "Benzamidine HCD"
- set type @atom:682 charge 0.129 # "Benzamidine HCE"
- set type @atom:683 charge 0.827 # "Benzamidine C+"
- set type @atom:684 charge -0.885 # "Benzamidine -NH2"
- set type @atom:685 charge 0.426 # "Benzamidine H1-N"
- set type @atom:686 charge 0.465 # "Benzamidine H2-N"
- set type @atom:687 charge 0.119 # "Benzamidine HCG"
- set type @atom:688 charge -0.02 # "Neutral MeGdn CH3-"
- set type @atom:689 charge 0.04 # "Neutral ARG CD"
- set type @atom:690 charge -0.62 # "Neutral ARG NE"
- set type @atom:691 charge -0.785 # "Neutral ARG N1 (HN=C)"
- set type @atom:692 charge -0.785 # "Neutral ARG N2 (H2N-C)"
- set type @atom:693 charge 0.55 # "Neutral ARG CZ (>C=)"
- set type @atom:694 charge -0.56 # "Alkyl Nitrile -CN"
- set type @atom:695 charge 0.46 # "Alkyl Nitrile -CN"
- set type @atom:696 charge -0.08 # "Acetonitrile CH3-CN"
- set type @atom:697 charge -0.02 # "Alkyl Nitrile RCH2-CN"
- set type @atom:698 charge 0.04 # "Alkyl Nitrile R2CH-CN"
- set type @atom:699 charge 0.1 # "Alkyl Nitrile R3C-CN"
- set type @atom:700 charge 0.06 # "Alkyl Nitrile H-C-CN"
- set type @atom:701 charge 0.54 # "Nitroalkane -NO2"
- set type @atom:702 charge -0.37 # "Nitroalkane -NO2"
- set type @atom:703 charge 0.02 # "Nitromethane CH3-NO2"
- set type @atom:704 charge 0.06 # "Nitroalkane H-C-NO2"
- set type @atom:705 charge 0.08 # "Nitroalkane RCH2-NO2"
- set type @atom:706 charge 0.14 # "Nitroalkane R2CH-NO2"
- set type @atom:707 charge 0.2 # "Nitroalkane R3C-NO2"
- set type @atom:708 charge 0.65 # "Nitrobenzene -NO2"
- set type @atom:709 charge 0.09 # "Nitrobenzene C-NO2"
- set type @atom:710 charge 0.035 # "Benzonitrile -CH2-"
- set type @atom:711 charge -0.9 # "Neutral Benzamidine N"
- set type @atom:712 charge -0.5 # "Propylene Carbonate C=O"
- set type @atom:713 charge 0.86 # "Propylene Carbonate C=O"
- set type @atom:714 charge -0.45 # "Propylene Carbonate C-O"
- set type @atom:715 charge 0.21 # "Propylene Carbonate CH2"
- set type @atom:716 charge 0.16 # "Propylene Carbonate CH"
- set type @atom:717 charge -0.1 # "Propylene Carbonate CH3"
- set type @atom:718 charge 0.03 # "Propylene Carbonate CH2"
- set type @atom:719 charge 0.03 # "Propylene Carbonate CH"
- set type @atom:720 charge 0.06 # "Propylene Carbonate CH3"
- set type @atom:721 charge -0.78 # "GTP O-(POn)2"
- set type @atom:722 charge 0.9684 # "Phosphonium R4P+"
- set type @atom:723 charge -0.5081 # "Phosphonium CH3-PR3+"
- set type @atom:724 charge -0.008 # "Phosphonium RCH2-PR3+"
- set type @atom:725 charge 0.172 # "Phosphonium CH3-PR3+"
- set type @atom:726 charge 1.34 # "Hexafluorophosphate Ion"
- set type @atom:727 charge -0.39 # "Hexafluorophosphate Ion"
- set type @atom:728 charge 0.794 # "Nitrate Ion NO3-"
- set type @atom:729 charge -0.598 # "Nitrate Ion NO3-"
- set type @atom:730 charge -0.9 # "Amine RNH2"
- set type @atom:731 charge -0.78 # "Amine R2NH"
- set type @atom:732 charge -0.63 # "Amine R3N"
- set type @atom:733 charge 0.0 # "Amine CH3-NH2"
- set type @atom:734 charge 0.02 # "Amine CH3-NHR"
- set type @atom:735 charge 0.03 # "Amine CH3-NR2"
- set type @atom:736 charge 0.06 # "Amine RCH2-NH2"
- set type @atom:737 charge 0.08 # "Amine RCH2-NHR"
- set type @atom:738 charge 0.09 # "Amine RCH2-NR2"
- set type @atom:739 charge 0.36 # "Amine RNH2"
- set type @atom:740 charge 0.38 # "Amine R2NH"
- set type @atom:741 charge 0.06 # "Amine H-C-N"
- set type @atom:742 charge 0.12 # "Amine R2CH-NH2"
- set type @atom:743 charge 0.18 # "Amine R3C-NH2"
- set type @atom:744 charge 0.14 # "Amine R2CH-NHR"
- set type @atom:745 charge 0.15 # "Amine R2CH-NR2"
- set type @atom:746 charge 0.18 # "Aniline C-NH2"
- set type @atom:747 charge 0.2 # "N-Me Aniline C-NHR"
- set type @atom:748 charge 0.21 # "N-DiMe Aniline C-NR2"
- set type @atom:749 charge 0.115 # "Benzyl Amine -CH2NH2"
- set type @atom:750 charge 0.175 # "Benzyl Amine -CHRNH2"
- set type @atom:751 charge 0.235 # "Benzyl Amine -CR2NH2"
- set type @atom:752 charge 0.195 # "Benzyl Ether -CH2OR"
- set type @atom:753 charge 0.1525 # "Benzyl Sulfide -CH2SH"
- set type @atom:754 charge 0.135 # "Benzyl Amine -CH2NHR"
- set type @atom:755 charge -0.21 # "Alkyne HCC-"
- set type @atom:756 charge 0.2 # "Alkyne HCC-"
- set type @atom:757 charge 0.01 # "Alkyne RCCH R w/ 2/3 H"
- set type @atom:758 charge 0.01 # "Alkyne RCCH R w/ 1 H"
- set type @atom:759 charge 0.01 # "Alkyne RCCH R w/ O H/Ph"
- set type @atom:760 charge 0.06 # "Alkyne H-C-CC-"
- set type @atom:761 charge 0.45 # "A & G Sugar C1'"
- set type @atom:762 charge 0.48 # "C Sugar C1'"
- set type @atom:763 charge 0.51 # "U & T Sugar C1'"
- set type @atom:764 charge -0.655 # "Sugar O5'"
- set type @atom:765 charge 0.39 # "Sugar H3' (-OH)"
- set type @atom:766 charge -0.5 # "A & G Nucleoside N9"
- set type @atom:767 charge -0.56 # "C Nucleoside N1"
- set type @atom:768 charge -0.6 # "U & T Nucleoside N1"
- set type @atom:769 charge 0.0 # "Alkyne RCCR"
- set type @atom:770 charge -0.1 # "Ammonium R3NH+"
- set type @atom:771 charge 0.29 # "Ammonium R3NH+"
- set type @atom:772 charge 0.09 # "Ammonium CH3-NHR2+"
- set type @atom:773 charge 0.15 # "Ammonium RCH2-NHR2+"
- set type @atom:774 charge 0.21 # "Ammonium R2CH-NHR2+"
- set type @atom:775 charge 0.27 # "Ammonium R3C-NHR2+"
- set type @atom:776 charge 0.096 # "2-Phenyl Furan C2"
- set type @atom:777 charge -0.039 # "2-Phenyl Furan C3"
- set type @atom:778 charge 0.027 # "2-Phenyl Furan C2'"
- set type @atom:779 charge 0.011 # "2-Phenyl Furan C3'"
- set type @atom:780 charge 0.074 # "GLY Zwitterion HA"
- set type @atom:781 charge -0.029 # "GLY Zwitterion CA"
- set type @atom:782 charge 0.7 # "GLY Zwitterion C"
- set type @atom:783 charge -0.352 # "GLY Zwitterion N"
- set type @atom:784 charge -0.709 # "GLY Zwitterion O"
- set type @atom:785 charge 0.317 # "GLY Zwitterion HN"
- set type @atom:786 charge -0.22 # "Alkyl Fluoride C-F"
- set type @atom:787 charge 0.02 # "Alkyl Fluoride RCH2-F"
- set type @atom:788 charge 0.1 # "Alkyl Fluoride H-C-F"
- set type @atom:789 charge 0.12 # "Alkyl Fluoride R2CH-F"
- set type @atom:790 charge 0.22 # "Alkyl Fluoride R3C-F"
- set type @atom:791 charge 0.36 # "Perfluoroalkane CF3-"
- set type @atom:792 charge 0.24 # "Perfluoroalkane -CF2-"
- set type @atom:793 charge 0.12 # "Perfluoroalkane >CF-"
- set type @atom:794 charge 0.48 # "Tetrafluoromethane CF4"
- set type @atom:795 charge -0.12 # "Perfluoroalkane C-F"
- set type @atom:796 charge 0.25 # "DifluoroMeBenzene -CHF2"
- set type @atom:797 charge 0.15 # "DifluoroMeBenzene -CHF2"
- set type @atom:798 charge -0.08 # "Fluoroacetate FCH2-COO-"
- set type @atom:799 charge -0.106 # "Chloroacetate ClCH2-COO-"
- set type @atom:800 charge -0.2 # "Alkyl Chloride C-Cl"
- set type @atom:801 charge -0.006 # "Alkyl Chloride RCH2-Cl"
- set type @atom:802 charge 0.103 # "Alkyl Chloride H-C-Cl"
- set type @atom:803 charge 0.097 # "Alkyl Chloride R2CH-Cl"
- set type @atom:804 charge 0.2 # "Alkyl Chloride R3C-Cl"
- set type @atom:805 charge -0.2 # "Alkyl Bromide C-Br"
- set type @atom:806 charge -0.006 # "Alkyl Bromide RCH2-Br"
- set type @atom:807 charge 0.103 # "Alkyl Bromide H-C-Br"
- set type @atom:808 charge 0.097 # "Alkyl Bromide R2CH-Br"
- set type @atom:809 charge 0.2 # "Alkyl Bromide R3C-Br"
- set type @atom:810 charge -0.08 # "Acyl Fluoride F-C=O"
- set type @atom:811 charge -0.08 # "Acyl Chloride Cl-C=O"
- set type @atom:812 charge -0.08 # "Acyl Bromide Br-C=O"
- set type @atom:813 charge 0.1 # "Trifluoroanisole C-OCF3"
- set type @atom:814 charge -0.25 # "Trifluoroanisole -OCF3"
- set type @atom:815 charge 0.6 # "Trifluoroanisole -OCF3"
- set type @atom:816 charge -0.15 # "Trifluoroanisole -OCF3"
- set type @atom:817 charge -0.025 # "N-Me,N-PhAcetamide N"
- set type @atom:818 charge -0.045 # "N-Me,N-PhAcetamide Cipso"
- set type @atom:819 charge 0.145 # "Benzyl Amine -CH2NR2"
- set type @atom:820 charge 0.888 # "Alkyl Hydroxamic Acid C"
- set type @atom:821 charge 1.003 # "Aryl Hydroxamic Acid C"
- set type @atom:822 charge -0.658 # "Hydroxamic Acid C=O"
- set type @atom:823 charge -0.634 # "Hydroxamic Acid N"
- set type @atom:824 charge 0.411 # "Hydroxamic Acid HN"
- set type @atom:825 charge -0.442 # "Hydroxamic Acid OH"
- set type @atom:826 charge 0.435 # "Hydroxamic Acid OH"
- set type @atom:827 charge 0.225 # "Benzyl Ether -CHROR"
- set type @atom:828 charge 0.255 # "Benzyl Ether -CR2OR"
- set type @atom:829 charge -0.034 # "3-Phenyl Pyrrole C3"
- set type @atom:830 charge 0.003 # "3-Phenyl Pyrrole C3'"
- set type @atom:831 charge 0.3 # "4-Phenyl Imidazole C4"
- set type @atom:832 charge -0.04 # "4-Phenyl Imidazole C4'"
- set type @atom:833 charge -0.0575 # "Diphenylmethane Cipso"
- set type @atom:834 charge 2.0 # "Zinc Ion Zn+2"
- set type @atom:835 charge -0.07 # "Alkyl Iodide RCH2-I"
- set type @atom:836 charge 0.03 # "Alkyl Iodide R2CH-I"
- set type @atom:837 charge 0.13 # "Alkyl Iodide R3C-I"
- set type @atom:838 charge -0.13 # "Alkyl Iodide C-I"
- set type @atom:839 charge 0.1 # "Alkyl Iodide H-C-I"
- set type @atom:840 charge -0.685 # "N-Ph Sulfonamide -NHPh"
- set type @atom:841 charge 0.155 # "N-Ph Sulfonamide Cipso"
- set type @atom:842 charge -0.1 # "Benzoate C-COO-"
- set type @atom:843 charge -0.427 # "N-Phenyl Urea N"
- set type @atom:844 charge 0.218 # "N-Phenyl Urea Cipso"
- set type @atom:845 charge 0.6 # "Tertiary Amide -CO-NR2"
- set type @atom:846 charge -0.6 # "Tertiary Amide -CO-NR2"
- set type @atom:847 charge -0.36 # "Tertiary Amide -CO-NR2"
- set type @atom:848 charge 0.0 # "Tertiary Amide -NRCH3"
- set type @atom:849 charge 0.06 # "Tertiary Amide -NRCH2R"
- set type @atom:850 charge 0.12 # "Tertiary Amide -NRCHR2"
- set type @atom:851 charge 0.18 # "Tertiary Amide -NRCR3"
- set type @atom:852 charge 0.06 # "Tertiary Amide H-C-N"
- set type @atom:853 charge 0.57 # "Tertiary Formamide C=O"
- set type @atom:854 charge -0.57 # "Tertiary Formamide C=O"
- set type @atom:855 charge 0.0 # "Tertiary Formamide H-C=O"
- set type @atom:856 charge 0.02 # "B2-Peptide CA"
- set type @atom:857 charge -0.04 # "B3-Peptide CA Main/N-Ter"
- set type @atom:858 charge 0.0 # "B3-Pep CB GLY Main/C-Ter"
- set type @atom:859 charge 0.06 # "B3-Pep CB ALA Main/C-Ter"
- set type @atom:860 charge -0.07 # "B3-Pep CB PRO Main/C-Ter"
- set type @atom:861 charge -0.14 # "B3-Peptide CA C-Ter"
- set type @atom:862 charge 0.17 # "B3-Peptide CB ALA N-Ter"
- set type @atom:863 charge 0.11 # "B3-Peptide CB GLY N-Ter"
- set type @atom:864 charge 0.15 # "B3-Peptide CB PRO N-Ter"
- set type @atom:865 charge 0.17 # "B3-Peptide CE PRO N-Ter"
- set type @atom:866 charge 1.0 # "Alkyl Silane R4Si"
- set type @atom:867 charge 0.85 # "Alkyl Silane R3SiH"
- set type @atom:868 charge 0.7 # "Alkyl Silane R2SiH2"
- set type @atom:869 charge 0.55 # "Alkyl Silane RSiH3"
- set type @atom:870 charge -0.1 # "Alkyl Silane H-C-Si"
- set type @atom:871 charge -0.43 # "Methyl Silane CH3-Si"
- set type @atom:872 charge -0.37 # "Alkyl Silane RCH2-Si"
- set type @atom:873 charge -0.31 # "Alkyl Silane R2CH-Si"
- set type @atom:874 charge -0.25 # "Alkyl Silane R3C-Si"
- set type @atom:875 charge -1.0 # "Fluoride Ion (GBSA)"
- set type @atom:876 charge -1.0 # "Chloride Ion (GBSA)"
- set type @atom:877 charge -1.0 # "Bromide Ion (GBSA)"
- set type @atom:878 charge -1.0 # "Iodide Ion (GBSA)"
- set type @atom:879 charge 1.0 # "Lithium Ion (GBSA)"
- set type @atom:880 charge 1.0 # "Sodium Ion (GBSA)"
- set type @atom:881 charge 1.0 # "Potassium Ion (GBSA)"
- set type @atom:882 charge 1.0 # "Rubidium Ion (GBSA)"
- set type @atom:883 charge 1.0 # "Cesium Ion (GBSA)"
- set type @atom:884 charge 2.0 # "Magnesium Ion (GBSA)"
- set type @atom:885 charge 2.0 # "Calcium Ion (GBSA)"
- set type @atom:886 charge 2.0 # "Strontium Ion (GBSA)"
- set type @atom:887 charge 2.0 # "Barium Ion (GBSA)"
- set type @atom:888 charge -0.05 # "Ammonium CH3-NR3+"
- set type @atom:889 charge 0.05 # "Ammonium RCH2-NR3+"
- set type @atom:890 charge 0.15 # "Ammonium R2CH-NR3+"
- set type @atom:891 charge 0.25 # "Ammonium R3C-NR3+"
- set type @atom:892 charge 0.1 # "Ammonium CH3-NR3+"
- set type @atom:893 charge 0.115 # "Anilinium Ar-NR3+"
- set type @atom:894 charge 0.135 # "Anilinium C-NR3+"
- set type @atom:895 charge 0.015 # "Anilinium Ar-NHR2+"
- set type @atom:896 charge 0.155 # "Anilinium C-NHR2+"
- set type @atom:897 charge 0.0 # "Triene R2-C= (mid C=C)"
- set type @atom:898 charge -0.115 # "Triene RH-C= (mid C=C)"
- set type @atom:899 charge 0.15 # "Allene/Ketene H-C=C=X"
- set type @atom:900 charge -0.25 # "Allene/Ketene H2C=C=X"
- set type @atom:901 charge -0.1 # "Allene/Ketene HRC=C=X"
- set type @atom:902 charge 0.05 # "Allene/Ketene R2C=C=X"
- set type @atom:903 charge -0.1 # "Allene =C="
- set type @atom:904 charge 0.2 # "Ketene =C="
- set type @atom:905 charge -0.25 # "Ketene C=O"
- set type @atom:906 charge 0.088 # "N-Me-HIS CB"
- } #(end of atom partial charges)
-
-
- write_once("Data Masses") {
- @atom:1 18.998
- @atom:2 14.027
- @atom:3 12.011
- @atom:4 15.999
- @atom:5 15.999
- @atom:6 15.035
- @atom:7 1.008
- @atom:8 16.043
- @atom:9 15.035
- @atom:10 15.035
- @atom:11 15.035
- @atom:12 15.035
- @atom:13 14.027
- @atom:14 14.027
- @atom:15 13.019
- @atom:16 13.019
- @atom:17 13.019
- @atom:18 12.011
- @atom:19 12.011
- @atom:20 15.999
- @atom:21 1.008
- @atom:22 15.035
- @atom:23 14.027
- @atom:24 32.06
- @atom:25 32.06
- @atom:26 32.06
- @atom:27 32.06
- @atom:28 1.008
- @atom:29 1.008
- @atom:30 15.035
- @atom:31 14.027
- @atom:32 15.035
- @atom:33 14.027
- @atom:34 15.035
- @atom:35 14.027
- @atom:36 14.007
- @atom:37 12.011
- @atom:38 15.035
- @atom:39 13.019
- @atom:40 12.011
- @atom:41 15.999
- @atom:42 15.035
- @atom:43 14.027
- @atom:44 14.027
- @atom:45 35.453
- @atom:46 12.011
- @atom:47 35.453
- @atom:48 12.011
- @atom:49 35.453
- @atom:50 32.06
- @atom:51 15.999
- @atom:52 15.035
- @atom:53 15.999
- @atom:54 14.007
- @atom:55 12.011
- @atom:56 15.035
- @atom:57 1.0
- @atom:58 4.003
- @atom:59 20.179
- @atom:60 39.948
- @atom:61 83.8
- @atom:62 131.3
- @atom:63 15.999
- @atom:64 1.008
- @atom:65 15.999
- @atom:66 1.008
- @atom:67 1e-30
- @atom:68 15.999
- @atom:69 1.008
- @atom:70 15.999
- @atom:71 1.008
- @atom:72 1e-30
- @atom:73 15.999
- @atom:74 1.008
- @atom:75 1e-30
- @atom:76 15.999
- @atom:77 1.008
- @atom:78 14.007
- @atom:79 1.008
- @atom:80 12.011
- @atom:81 12.011
- @atom:82 12.011
- @atom:83 12.011
- @atom:84 12.011
- @atom:85 1.008
- @atom:86 12.011
- @atom:87 12.011
- @atom:88 12.011
- @atom:89 1.008
- @atom:90 12.011
- @atom:91 1.008
- @atom:92 12.011
- @atom:93 12.011
- @atom:94 12.011
- @atom:95 12.011
- @atom:96 15.999
- @atom:97 1.008
- @atom:98 1.008
- @atom:99 12.011
- @atom:100 12.011
- @atom:101 12.011
- @atom:102 12.011
- @atom:103 12.011
- @atom:104 15.999
- @atom:105 1.008
- @atom:106 18.998
- @atom:107 1.008
- @atom:108 12.011
- @atom:109 15.999
- @atom:110 1.008
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- } #(end of atom masses)
-
-
- write_once("In Settings") {
- pair_coeff @atom:1_b1_a1_d1_i1 @atom:1_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94
- pair_coeff @atom:2_b2_a2_d2_i2 @atom:2_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905
- pair_coeff @atom:3_b3_a3_d3_i3 @atom:3_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:4_b4_a4_d4_i4 @atom:4_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:5_b5_a5_d5_i5 @atom:5_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:6_b6_a6_d6_i6 @atom:6_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.91
- pair_coeff @atom:7_b7_a7_d7_i7 @atom:7_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:8_b8_a8_d8_i8 @atom:8_b8_a8_d8_i8 lj/cut/coul/long 0.294 3.73
- pair_coeff @atom:9_b6_a6_d6_i6 @atom:9_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775
- pair_coeff @atom:10_b6_a6_d6_i6 @atom:10_b6_a6_d6_i6 lj/cut/coul/long 0.175 3.905
- pair_coeff @atom:11_b6_a6_d6_i6 @atom:11_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.91
- pair_coeff @atom:12_b6_a6_d6_i6 @atom:12_b6_a6_d6_i6 lj/cut/coul/long 0.145 3.96
- pair_coeff @atom:13_b2_a2_d2_i2 @atom:13_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905
- pair_coeff @atom:14_b9_a9_d9_i9 @atom:14_b9_a9_d9_i9 lj/cut/coul/long 0.14 3.85
- pair_coeff @atom:15_b10_a10_d10_i10 @atom:15_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.85
- pair_coeff @atom:16_b11_a11_d11_i11 @atom:16_b11_a11_d11_i11 lj/cut/coul/long 0.115 3.8
- pair_coeff @atom:17_b12_a12_d12_i12 @atom:17_b12_a12_d12_i12 lj/cut/coul/long 0.11 3.75
- pair_coeff @atom:18_b13_a13_d13_i13 @atom:18_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8
- pair_coeff @atom:19_b14_a14_d14_i14 @atom:19_b14_a14_d14_i14 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:20_b5_a5_d5_i5 @atom:20_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07
- pair_coeff @atom:21_b7_a7_d7_i7 @atom:21_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:22_b6_a6_d6_i6 @atom:22_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775
- pair_coeff @atom:23_b2_a2_d2_i2 @atom:23_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905
- pair_coeff @atom:24_b15_a15_d15_i15 @atom:24_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.7
- pair_coeff @atom:25_b15_a15_d15_i15 @atom:25_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:26_b16_a16_d16_i16 @atom:26_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:27_b16_a16_d16_i16 @atom:27_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:28_b17_a17_d17_i17 @atom:28_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:29_b17_a17_d17_i17 @atom:29_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:30_b6_a6_d6_i6 @atom:30_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775
- pair_coeff @atom:31_b2_a2_d2_i2 @atom:31_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905
- pair_coeff @atom:32_b6_a6_d6_i6 @atom:32_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8
- pair_coeff @atom:33_b2_a2_d2_i2 @atom:33_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8
- pair_coeff @atom:34_b6_a6_d6_i6 @atom:34_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8
- pair_coeff @atom:35_b2_a2_d2_i2 @atom:35_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8
- pair_coeff @atom:36_b18_a18_d18_i18 @atom:36_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2
- pair_coeff @atom:37_b19_a19_d19_i19 @atom:37_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65
- pair_coeff @atom:38_b6_a6_d6_i6 @atom:38_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775
- pair_coeff @atom:39_b10_a10_d10_i10 @atom:39_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.85
- pair_coeff @atom:40_b13_a13_d13_i13 @atom:40_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8
- pair_coeff @atom:41_b20_a20_d20_i20 @atom:41_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:42_b6_a6_d6_i6 @atom:42_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8
- pair_coeff @atom:43_b2_a2_d2_i2 @atom:43_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8
- pair_coeff @atom:44_b2_a2_d2_i2 @atom:44_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8
- pair_coeff @atom:45_b21_a21_d21_i21 @atom:45_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:46_b10_a10_d10_i10 @atom:46_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.8
- pair_coeff @atom:47_b21_a21_d21_i21 @atom:47_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.47
- pair_coeff @atom:48_b13_a13_d13_i13 @atom:48_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8
- pair_coeff @atom:49_b21_a21_d21_i21 @atom:49_b21_a21_d21_i21 lj/cut/coul/long 0.266 3.47
- pair_coeff @atom:50_b22_a22_d22_i22 @atom:50_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56
- pair_coeff @atom:51_b23_a23_d23_i23 @atom:51_b23_a23_d23_i23 lj/cut/coul/long 0.28 2.93
- pair_coeff @atom:52_b6_a6_d6_i6 @atom:52_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.81
- pair_coeff @atom:53_b4_a4_d4_i4 @atom:53_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:54_b24_a24_d24_i24 @atom:54_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:55_b3_a3_d3_i3 @atom:55_b3_a3_d3_i3 lj/cut/coul/long 0.115 3.8
- pair_coeff @atom:56_b6_a6_d6_i6 @atom:56_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8
- pair_coeff @atom:57_b25_a25_d25_i25 @atom:57_b25_a25_d25_i25 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:58_b26_a26_d26_i26 @atom:58_b26_a26_d26_i26 lj/cut/coul/long 0.02 2.556
- pair_coeff @atom:59_b27_a27_d27_i27 @atom:59_b27_a27_d27_i27 lj/cut/coul/long 0.069 2.78
- pair_coeff @atom:60_b28_a28_d28_i28 @atom:60_b28_a28_d28_i28 lj/cut/coul/long 0.2339 3.401
- pair_coeff @atom:61_b29_a29_d29_i29 @atom:61_b29_a29_d29_i29 lj/cut/coul/long 0.317 3.624
- pair_coeff @atom:62_b30_a30_d30_i30 @atom:62_b30_a30_d30_i30 lj/cut/coul/long 0.433 3.935
- pair_coeff @atom:63_b31_a31_d31_i31 @atom:63_b31_a31_d31_i31 lj/cut/coul/long 0.1521 3.15061
- pair_coeff @atom:64_b32_a32_d32_i32 @atom:64_b32_a32_d32_i32 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:65_b31_a31_d31_i31 @atom:65_b31_a31_d31_i31 lj/cut/coul/long 0.155 3.15365
- pair_coeff @atom:66_b32_a32_d32_i32 @atom:66_b32_a32_d32_i32 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:67_b33_a33_d33_i33 @atom:67_b33_a33_d33_i33 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:68_b34_a34_d34_i34 @atom:68_b34_a34_d34_i34 lj/cut/coul/long 0.15 3.176
- pair_coeff @atom:69_b35_a35_d35_i35 @atom:69_b35_a35_d35_i35 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:70_b36_a36_d36_i36 @atom:70_b36_a36_d36_i36 lj/cut/coul/long 0.1 3.27
- pair_coeff @atom:71_b37_a37_d37_i37 @atom:71_b37_a37_d37_i37 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:72_b38_a38_d38_i38 @atom:72_b38_a38_d38_i38 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:73_b39_a39_d39_i39 @atom:73_b39_a39_d39_i39 lj/cut/coul/long 0.16 3.12
- pair_coeff @atom:74_b40_a40_d40_i40 @atom:74_b40_a40_d40_i40 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:75_b41_a41_d41_i41 @atom:75_b41_a41_d41_i41 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:76_b42_a42_d42_i42 @atom:76_b42_a42_d42_i42 lj/cut/coul/long 0.1554 3.16557
- pair_coeff @atom:77_b43_a43_d43_i43 @atom:77_b43_a43_d43_i43 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:78_b44_a44_d44_i44 @atom:78_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.42
- pair_coeff @atom:79_b45_a45_d45_i45 @atom:79_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:80_b13_a13_d13_i13 @atom:80_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:81_b13_a13_d13_i13 @atom:81_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:82_b13_a13_d13_i13 @atom:82_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:83_b13_a13_d13_i13 @atom:83_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:84_b13_a13_d13_i13 @atom:84_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:85_b46_a46_d46_i46 @atom:85_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:86_b47_a47_d47_i47 @atom:86_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:87_b47_a47_d47_i47 @atom:87_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:88_b47_a47_d47_i47 @atom:88_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:89_b46_a46_d46_i46 @atom:89_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:90_b48_a48_d48_i48 @atom:90_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:91_b49_a49_d49_i49 @atom:91_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:92_b48_a48_d48_i48 @atom:92_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:93_b13_a13_d13_i13 @atom:93_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:94_b13_a13_d13_i13 @atom:94_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:95_b50_a50_d50_i50 @atom:95_b50_a50_d50_i50 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:96_b5_a5_d5_i5 @atom:96_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12
- pair_coeff @atom:97_b7_a7_d7_i7 @atom:97_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:98_b46_a46_d46_i46 @atom:98_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:99_b13_a13_d13_i13 @atom:99_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:100_b13_a13_d13_i13 @atom:100_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:101_b13_a13_d13_i13 @atom:101_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:102_b13_a13_d13_i13 @atom:102_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:103_b13_a13_d13_i13 @atom:103_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25
- pair_coeff @atom:104_b5_a5_d5_i5 @atom:104_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07
- pair_coeff @atom:105_b7_a7_d7_i7 @atom:105_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:106_b1_a1_d1_i1 @atom:106_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94
- pair_coeff @atom:107_b46_a46_d46_i46 @atom:107_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:108_b48_a48_d48_i48 @atom:108_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:109_b5_a5_d5_i5 @atom:109_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07
- pair_coeff @atom:110_b7_a7_d7_i7 @atom:110_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:111_b5_a5_d5_i5 @atom:111_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07
- pair_coeff @atom:112_b7_a7_d7_i7 @atom:112_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:113_b5_a5_d5_i5 @atom:113_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07
- pair_coeff @atom:114_b7_a7_d7_i7 @atom:114_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:115_b13_a13_d13_i13 @atom:115_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:116_b13_a13_d13_i13 @atom:116_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:117_b13_a13_d13_i13 @atom:117_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:118_b46_a46_d46_i46 @atom:118_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:119_b20_a20_d20_i20 @atom:119_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:120_b50_a50_d50_i50 @atom:120_b50_a50_d50_i50 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:121_b20_a20_d20_i20 @atom:121_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:122_b20_a20_d20_i20 @atom:122_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:123_b13_a13_d13_i13 @atom:123_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:124_b13_a13_d13_i13 @atom:124_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:125_b13_a13_d13_i13 @atom:125_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:126_b13_a13_d13_i13 @atom:126_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:127_b46_a46_d46_i46 @atom:127_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:128_b20_a20_d20_i20 @atom:128_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:129_b5_a5_d5_i5 @atom:129_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07
- pair_coeff @atom:130_b7_a7_d7_i7 @atom:130_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:131_b51_a51_d51_i51 @atom:131_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:132_b46_a46_d46_i46 @atom:132_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:133_b51_a51_d51_i51 @atom:133_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:134_b46_a46_d46_i46 @atom:134_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:135_b51_a51_d51_i51 @atom:135_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:136_b46_a46_d46_i46 @atom:136_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:137_b51_a51_d51_i51 @atom:137_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:138_b46_a46_d46_i46 @atom:138_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:139_b51_a51_d51_i51 @atom:139_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:140_b51_a51_d51_i51 @atom:140_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:141_b48_a48_d48_i48 @atom:141_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:142_b15_a15_d15_i15 @atom:142_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:143_b15_a15_d15_i15 @atom:143_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.7
- pair_coeff @atom:144_b16_a16_d16_i16 @atom:144_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:145_b16_a16_d16_i16 @atom:145_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:146_b17_a17_d17_i17 @atom:146_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:147_b17_a17_d17_i17 @atom:147_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:148_b13_a13_d13_i13 @atom:148_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:149_b13_a13_d13_i13 @atom:149_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:150_b13_a13_d13_i13 @atom:150_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:151_b13_a13_d13_i13 @atom:151_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:152_b13_a13_d13_i13 @atom:152_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:153_b13_a13_d13_i13 @atom:153_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:154_b13_a13_d13_i13 @atom:154_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:155_b13_a13_d13_i13 @atom:155_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:156_b13_a13_d13_i13 @atom:156_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:157_b13_a13_d13_i13 @atom:157_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:158_b13_a13_d13_i13 @atom:158_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:159_b13_a13_d13_i13 @atom:159_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:160_b13_a13_d13_i13 @atom:160_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:161_b13_a13_d13_i13 @atom:161_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:162_b13_a13_d13_i13 @atom:162_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:163_b48_a48_d48_i48 @atom:163_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:164_b16_a16_d16_i16 @atom:164_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:165_b13_a13_d13_i13 @atom:165_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:166_b13_a13_d13_i13 @atom:166_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:167_b13_a13_d13_i13 @atom:167_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:168_b21_a21_d21_i21 @atom:168_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:169_b47_a47_d47_i47 @atom:169_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:170_b48_a48_d48_i48 @atom:170_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:171_b13_a13_d13_i13 @atom:171_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:172_b13_a13_d13_i13 @atom:172_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:173_b3_a3_d3_i3 @atom:173_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:174_b3_a3_d3_i3 @atom:174_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:175_b3_a3_d3_i3 @atom:175_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:176_b3_a3_d3_i3 @atom:176_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:177_b3_a3_d3_i3 @atom:177_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:178_b4_a4_d4_i4 @atom:178_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:179_b24_a24_d24_i24 @atom:179_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:180_b24_a24_d24_i24 @atom:180_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:181_b24_a24_d24_i24 @atom:181_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:182_b45_a45_d45_i45 @atom:182_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:183_b45_a45_d45_i45 @atom:183_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:184_b13_a13_d13_i13 @atom:184_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:185_b13_a13_d13_i13 @atom:185_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:186_b13_a13_d13_i13 @atom:186_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:187_b13_a13_d13_i13 @atom:187_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:188_b13_a13_d13_i13 @atom:188_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:189_b3_a3_d3_i3 @atom:189_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:190_b4_a4_d4_i4 @atom:190_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:191_b24_a24_d24_i24 @atom:191_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:192_b45_a45_d45_i45 @atom:192_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:193_b24_a24_d24_i24 @atom:193_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:194_b3_a3_d3_i3 @atom:194_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:195_b4_a4_d4_i4 @atom:195_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:196_b45_a45_d45_i45 @atom:196_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:197_b46_a46_d46_i46 @atom:197_b46_a46_d46_i46 lj/cut/coul/long 0.02 2.5
- pair_coeff @atom:198_b13_a13_d13_i13 @atom:198_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:199_b13_a13_d13_i13 @atom:199_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:200_b13_a13_d13_i13 @atom:200_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:201_b13_a13_d13_i13 @atom:201_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:202_b48_a48_d48_i48 @atom:202_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:203_b19_a19_d19_i19 @atom:203_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65
- pair_coeff @atom:204_b18_a18_d18_i18 @atom:204_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2
- pair_coeff @atom:205_b48_a48_d48_i48 @atom:205_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:206_b21_a21_d21_i21 @atom:206_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:207_b24_a24_d24_i24 @atom:207_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:208_b48_a48_d48_i48 @atom:208_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:209_b3_a3_d3_i3 @atom:209_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:210_b4_a4_d4_i4 @atom:210_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:211_b5_a5_d5_i5 @atom:211_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:212_b7_a7_d7_i7 @atom:212_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:213_b3_a3_d3_i3 @atom:213_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:214_b52_a52_d52_i52 @atom:214_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:215_b13_a13_d13_i13 @atom:215_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:216_b13_a13_d13_i13 @atom:216_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:217_b13_a13_d13_i13 @atom:217_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:218_b13_a13_d13_i13 @atom:218_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:219_b3_a3_d3_i3 @atom:219_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:220_b4_a4_d4_i4 @atom:220_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:221_b46_a46_d46_i46 @atom:221_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:222_b3_a3_d3_i3 @atom:222_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:223_b4_a4_d4_i4 @atom:223_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:224_b46_a46_d46_i46 @atom:224_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:225_b13_a13_d13_i13 @atom:225_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:226_b13_a13_d13_i13 @atom:226_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:227_b13_a13_d13_i13 @atom:227_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:228_b13_a13_d13_i13 @atom:228_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:229_b53_a53_d53_i53 @atom:229_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:230_b53_a53_d53_i53 @atom:230_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:231_b53_a53_d53_i53 @atom:231_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:232_b54_a54_d54_i54 @atom:232_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:233_b54_a54_d54_i54 @atom:233_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:234_b13_a13_d13_i13 @atom:234_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:235_b13_a13_d13_i13 @atom:235_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:236_b13_a13_d13_i13 @atom:236_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:237_b13_a13_d13_i13 @atom:237_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:238_b13_a13_d13_i13 @atom:238_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:239_b13_a13_d13_i13 @atom:239_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:240_b13_a13_d13_i13 @atom:240_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:241_b13_a13_d13_i13 @atom:241_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:242_b13_a13_d13_i13 @atom:242_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:243_b55_a55_d55_i55 @atom:243_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:244_b54_a54_d54_i54 @atom:244_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:245_b48_a48_d48_i48 @atom:245_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55
- pair_coeff @atom:246_b55_a55_d55_i55 @atom:246_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:247_b54_a54_d54_i54 @atom:247_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:248_b13_a13_d13_i13 @atom:248_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:249_b13_a13_d13_i13 @atom:249_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:250_b13_a13_d13_i13 @atom:250_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:251_b13_a13_d13_i13 @atom:251_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:252_b53_a53_d53_i53 @atom:252_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:253_b54_a54_d54_i54 @atom:253_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:254_b56_a56_d56_i56 @atom:254_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:255_b48_a48_d48_i48 @atom:255_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:256_b55_a55_d55_i55 @atom:256_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:257_b45_a45_d45_i45 @atom:257_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:258_b48_a48_d48_i48 @atom:258_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:259_b49_a49_d49_i49 @atom:259_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:260_b48_a48_d48_i48 @atom:260_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:261_b49_a49_d49_i49 @atom:261_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:262_b57_a57_d57_i57 @atom:262_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:263_b3_a3_d3_i3 @atom:263_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:264_b57_a57_d57_i57 @atom:264_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:265_b3_a3_d3_i3 @atom:265_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:266_b47_a47_d47_i47 @atom:266_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:267_b47_a47_d47_i47 @atom:267_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:268_b45_a45_d45_i45 @atom:268_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:269_b4_a4_d4_i4 @atom:269_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:270_b45_a45_d45_i45 @atom:270_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:271_b4_a4_d4_i4 @atom:271_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:272_b46_a46_d46_i46 @atom:272_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:273_b46_a46_d46_i46 @atom:273_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:274_b13_a13_d13_i13 @atom:274_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:275_b46_a46_d46_i46 @atom:275_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:276_b57_a57_d57_i57 @atom:276_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:277_b3_a3_d3_i3 @atom:277_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:278_b56_a56_d56_i56 @atom:278_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:279_b48_a48_d48_i48 @atom:279_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:280_b47_a47_d47_i47 @atom:280_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:281_b47_a47_d47_i47 @atom:281_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:282_b45_a45_d45_i45 @atom:282_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:283_b4_a4_d4_i4 @atom:283_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:284_b55_a55_d55_i55 @atom:284_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:285_b45_a45_d45_i45 @atom:285_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:286_b45_a45_d45_i45 @atom:286_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:287_b46_a46_d46_i46 @atom:287_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:288_b58_a58_d58_i58 @atom:288_b58_a58_d58_i58 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:289_b56_a56_d56_i56 @atom:289_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:290_b59_a59_d59_i59 @atom:290_b59_a59_d59_i59 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:291_b56_a56_d56_i56 @atom:291_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:292_b60_a60_d60_i60 @atom:292_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:293_b60_a60_d60_i60 @atom:293_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:294_b48_a48_d48_i48 @atom:294_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:295_b61_a61_d61_i61 @atom:295_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:296_b62_a62_d62_i62 @atom:296_b62_a62_d62_i62 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:297_b57_a57_d57_i57 @atom:297_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:298_b63_a63_d63_i63 @atom:298_b63_a63_d63_i63 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:299_b55_a55_d55_i55 @atom:299_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:300_b45_a45_d45_i45 @atom:300_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:301_b45_a45_d45_i45 @atom:301_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:302_b63_a63_d63_i63 @atom:302_b63_a63_d63_i63 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:303_b45_a45_d45_i45 @atom:303_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:304_b57_a57_d57_i57 @atom:304_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:305_b48_a48_d48_i48 @atom:305_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:306_b56_a56_d56_i56 @atom:306_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:307_b60_a60_d60_i60 @atom:307_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:308_b60_a60_d60_i60 @atom:308_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:309_b3_a3_d3_i3 @atom:309_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:310_b45_a45_d45_i45 @atom:310_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:311_b55_a55_d55_i55 @atom:311_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:312_b45_a45_d45_i45 @atom:312_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:313_b4_a4_d4_i4 @atom:313_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:314_b13_a13_d13_i13 @atom:314_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:315_b46_a46_d46_i46 @atom:315_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:316_b13_a13_d13_i13 @atom:316_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:317_b46_a46_d46_i46 @atom:317_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:318_b13_a13_d13_i13 @atom:318_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:319_b46_a46_d46_i46 @atom:319_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:320_b57_a57_d57_i57 @atom:320_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:321_b3_a3_d3_i3 @atom:321_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:322_b57_a57_d57_i57 @atom:322_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:323_b48_a48_d48_i48 @atom:323_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:324_b47_a47_d47_i47 @atom:324_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:325_b47_a47_d47_i47 @atom:325_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:326_b45_a45_d45_i45 @atom:326_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:327_b4_a4_d4_i4 @atom:327_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:328_b45_a45_d45_i45 @atom:328_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:329_b55_a55_d55_i55 @atom:329_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:330_b45_a45_d45_i45 @atom:330_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:331_b45_a45_d45_i45 @atom:331_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:332_b49_a49_d49_i49 @atom:332_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:333_b58_a58_d58_i58 @atom:333_b58_a58_d58_i58 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:334_b13_a13_d13_i13 @atom:334_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:335_b46_a46_d46_i46 @atom:335_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:336_b64_a64_d64_i64 @atom:336_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74
- pair_coeff @atom:337_b52_a52_d52_i52 @atom:337_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:338_b20_a20_d20_i20 @atom:338_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:339_b13_a13_d13_i13 @atom:339_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.55
- pair_coeff @atom:340_b47_a47_d47_i47 @atom:340_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5
- pair_coeff @atom:341_b21_a21_d21_i21 @atom:341_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:342_b47_a47_d47_i47 @atom:342_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:343_b1_a1_d1_i1 @atom:343_b1_a1_d1_i1 lj/cut/coul/long 0.71 3.05
- pair_coeff @atom:344_b21_a21_d21_i21 @atom:344_b21_a21_d21_i21 lj/cut/coul/long 0.71 4.02
- pair_coeff @atom:345_b65_a65_d65_i65 @atom:345_b65_a65_d65_i65 lj/cut/coul/long 0.71 4.28
- pair_coeff @atom:346_b66_a66_d66_i66 @atom:346_b66_a66_d66_i66 lj/cut/coul/long 0.71 4.81
- pair_coeff @atom:347_b67_a67_d67_i67 @atom:347_b67_a67_d67_i67 lj/cut/coul/long 0.0005 5.34
- pair_coeff @atom:348_b68_a68_d68_i68 @atom:348_b68_a68_d68_i68 lj/cut/coul/long 0.0005 2.87
- pair_coeff @atom:349_b69_a69_d69_i69 @atom:349_b69_a69_d69_i69 lj/cut/coul/long 0.0005 4.07
- pair_coeff @atom:350_b70_a70_d70_i70 @atom:350_b70_a70_d70_i70 lj/cut/coul/long 0.0005 5.17
- pair_coeff @atom:351_b71_a71_d71_i71 @atom:351_b71_a71_d71_i71 lj/cut/coul/long 0.0005 5.6
- pair_coeff @atom:352_b72_a72_d72_i72 @atom:352_b72_a72_d72_i72 lj/cut/coul/long 0.0005 6.2
- pair_coeff @atom:353_b73_a73_d73_i73 @atom:353_b73_a73_d73_i73 lj/cut/coul/long 0.875044 1.644471
- pair_coeff @atom:354_b74_a74_d74_i74 @atom:354_b74_a74_d74_i74 lj/cut/coul/long 0.449657 2.412031
- pair_coeff @atom:355_b75_a75_d75_i75 @atom:355_b75_a75_d75_i75 lj/cut/coul/long 0.118226 3.102688
- pair_coeff @atom:356_b76_a76_d76_i76 @atom:356_b76_a76_d76_i76 lj/cut/coul/long 0.047096 3.81661
- pair_coeff @atom:357_b6_a6_d6_i6 @atom:357_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2
- pair_coeff @atom:358_b46_a46_d46_i46 @atom:358_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:359_b15_a15_d15_i15 @atom:359_b15_a15_d15_i15 lj/cut/coul/long 0.5 4.25
- pair_coeff @atom:360_b6_a6_d6_i6 @atom:360_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2
- pair_coeff @atom:361_b46_a46_d46_i46 @atom:361_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:362_b5_a5_d5_i5 @atom:362_b5_a5_d5_i5 lj/cut/coul/long 0.25 3.15
- pair_coeff @atom:363_b13_a13_d13_i13 @atom:363_b13_a13_d13_i13 lj/cut/coul/long 0.3 4.2
- pair_coeff @atom:364_b46_a46_d46_i46 @atom:364_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:365_b19_a19_d19_i19 @atom:365_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65
- pair_coeff @atom:366_b18_a18_d18_i18 @atom:366_b18_a18_d18_i18 lj/cut/coul/long 0.25 3.4
- pair_coeff @atom:367_b6_a6_d6_i6 @atom:367_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2
- pair_coeff @atom:368_b46_a46_d46_i46 @atom:368_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:369_b53_a53_d53_i53 @atom:369_b53_a53_d53_i53 lj/cut/coul/long 0.25 3.4
- pair_coeff @atom:370_b45_a45_d45_i45 @atom:370_b45_a45_d45_i45 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:371_b6_a6_d6_i6 @atom:371_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2
- pair_coeff @atom:372_b46_a46_d46_i46 @atom:372_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:373_b13_a13_d13_i13 @atom:373_b13_a13_d13_i13 lj/cut/coul/long 0.3 4.2
- pair_coeff @atom:374_b46_a46_d46_i46 @atom:374_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5
- pair_coeff @atom:375_b33_a33_d33_i33 @atom:375_b33_a33_d33_i33 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:376_b5_a5_d5_i5 @atom:376_b5_a5_d5_i5 lj/cut/coul/long 0.25 3.2
- pair_coeff @atom:377_b7_a7_d7_i7 @atom:377_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:378_b77_a77_d77_i77 @atom:378_b77_a77_d77_i77 lj/cut/coul/long 0.4 2.81524
- pair_coeff @atom:379_b78_a78_d78_i78 @atom:379_b78_a78_d78_i78 lj/cut/coul/long 0.2 3.11815
- pair_coeff @atom:380_b20_a20_d20_i20 @atom:380_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:381_b64_a64_d64_i64 @atom:381_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74
- pair_coeff @atom:382_b52_a52_d52_i52 @atom:382_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15
- pair_coeff @atom:383_b20_a20_d20_i20 @atom:383_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:384_b13_a13_d13_i13 @atom:384_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:385_b46_a46_d46_i46 @atom:385_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:386_b64_a64_d64_i64 @atom:386_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74
- pair_coeff @atom:387_b52_a52_d52_i52 @atom:387_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15
- pair_coeff @atom:388_b20_a20_d20_i20 @atom:388_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:389_b13_a13_d13_i13 @atom:389_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:390_b46_a46_d46_i46 @atom:390_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:391_b64_a64_d64_i64 @atom:391_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74
- pair_coeff @atom:392_b52_a52_d52_i52 @atom:392_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15
- pair_coeff @atom:393_b20_a20_d20_i20 @atom:393_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:394_b13_a13_d13_i13 @atom:394_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:395_b46_a46_d46_i46 @atom:395_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:396_b13_a13_d13_i13 @atom:396_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:397_b46_a46_d46_i46 @atom:397_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:398_b48_a48_d48_i48 @atom:398_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:399_b13_a13_d13_i13 @atom:399_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:400_b46_a46_d46_i46 @atom:400_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:401_b48_a48_d48_i48 @atom:401_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:402_b13_a13_d13_i13 @atom:402_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:403_b46_a46_d46_i46 @atom:403_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:404_b48_a48_d48_i48 @atom:404_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:405_b13_a13_d13_i13 @atom:405_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:406_b3_a3_d3_i3 @atom:406_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:407_b4_a4_d4_i4 @atom:407_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:408_b20_a20_d20_i20 @atom:408_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:409_b13_a13_d13_i13 @atom:409_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:410_b46_a46_d46_i46 @atom:410_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:411_b3_a3_d3_i3 @atom:411_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:412_b3_a3_d3_i3 @atom:412_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:413_b48_a48_d48_i48 @atom:413_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:414_b20_a20_d20_i20 @atom:414_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:415_b79_a79_d79_i79 @atom:415_b79_a79_d79_i79 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:416_b23_a23_d23_i23 @atom:416_b23_a23_d23_i23 lj/cut/coul/long 0.17 2.96
- pair_coeff @atom:417_b13_a13_d13_i13 @atom:417_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:418_b46_a46_d46_i46 @atom:418_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:419_b24_a24_d24_i24 @atom:419_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:420_b45_a45_d45_i45 @atom:420_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:421_b24_a24_d24_i24 @atom:421_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:422_b45_a45_d45_i45 @atom:422_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:423_b13_a13_d13_i13 @atom:423_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:424_b46_a46_d46_i46 @atom:424_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:425_b13_a13_d13_i13 @atom:425_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:426_b46_a46_d46_i46 @atom:426_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:427_b13_a13_d13_i13 @atom:427_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:428_b46_a46_d46_i46 @atom:428_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:429_b48_a48_d48_i48 @atom:429_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:430_b48_a48_d48_i48 @atom:430_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:431_b13_a13_d13_i13 @atom:431_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:432_b13_a13_d13_i13 @atom:432_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:433_b13_a13_d13_i13 @atom:433_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:434_b79_a79_d79_i79 @atom:434_b79_a79_d79_i79 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:435_b23_a23_d23_i23 @atom:435_b23_a23_d23_i23 lj/cut/coul/long 0.17 2.96
- pair_coeff @atom:436_b22_a22_d22_i22 @atom:436_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56
- pair_coeff @atom:437_b22_a22_d22_i22 @atom:437_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56
- pair_coeff @atom:438_b23_a23_d23_i23 @atom:438_b23_a23_d23_i23 lj/cut/coul/long 0.28 2.93
- pair_coeff @atom:439_b13_a13_d13_i13 @atom:439_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:440_b13_a13_d13_i13 @atom:440_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:441_b80_a80_d80_i80 @atom:441_b80_a80_d80_i80 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:442_b60_a60_d60_i60 @atom:442_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:443_b81_a81_d81_i81 @atom:443_b81_a81_d81_i81 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:444_b57_a57_d57_i57 @atom:444_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:445_b45_a45_d45_i45 @atom:445_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:446_b13_a13_d13_i13 @atom:446_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:447_b82_a82_d82_i82 @atom:447_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:448_b83_a83_d83_i83 @atom:448_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:449_b84_a84_d84_i84 @atom:449_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:450_b82_a82_d82_i82 @atom:450_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:451_b85_a85_d85_i85 @atom:451_b85_a85_d85_i85 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:452_b61_a61_d61_i61 @atom:452_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:453_b57_a57_d57_i57 @atom:453_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:454_b45_a45_d45_i45 @atom:454_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:455_b84_a84_d84_i84 @atom:455_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:456_b13_a13_d13_i13 @atom:456_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:457_b13_a13_d13_i13 @atom:457_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:458_b47_a47_d47_i47 @atom:458_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:459_b47_a47_d47_i47 @atom:459_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:460_b86_a86_d86_i86 @atom:460_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:461_b56_a56_d56_i56 @atom:461_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:462_b48_a48_d48_i48 @atom:462_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:463_b48_a48_d48_i48 @atom:463_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:464_b48_a48_d48_i48 @atom:464_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:465_b49_a49_d49_i49 @atom:465_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:466_b49_a49_d49_i49 @atom:466_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:467_b49_a49_d49_i49 @atom:467_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:468_b56_a56_d56_i56 @atom:468_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:469_b48_a48_d48_i48 @atom:469_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:470_b49_a49_d49_i49 @atom:470_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:471_b56_a56_d56_i56 @atom:471_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:472_b59_a59_d59_i59 @atom:472_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:473_b48_a48_d48_i48 @atom:473_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:474_b48_a48_d48_i48 @atom:474_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:475_b49_a49_d49_i49 @atom:475_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:476_b49_a49_d49_i49 @atom:476_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:477_b49_a49_d49_i49 @atom:477_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:478_b56_a56_d56_i56 @atom:478_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:479_b48_a48_d48_i48 @atom:479_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:480_b48_a48_d48_i48 @atom:480_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:481_b49_a49_d49_i49 @atom:481_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:482_b49_a49_d49_i49 @atom:482_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:483_b57_a57_d57_i57 @atom:483_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:484_b84_a84_d84_i84 @atom:484_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:485_b87_a87_d87_i87 @atom:485_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:486_b45_a45_d45_i45 @atom:486_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:487_b49_a49_d49_i49 @atom:487_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:488_b49_a49_d49_i49 @atom:488_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:489_b57_a57_d57_i57 @atom:489_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:490_b61_a61_d61_i61 @atom:490_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:491_b88_a88_d88_i88 @atom:491_b88_a88_d88_i88 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:492_b87_a87_d87_i87 @atom:492_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:493_b84_a84_d84_i84 @atom:493_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:494_b45_a45_d45_i45 @atom:494_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:495_b49_a49_d49_i49 @atom:495_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:496_b49_a49_d49_i49 @atom:496_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:497_b49_a49_d49_i49 @atom:497_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:498_b57_a57_d57_i57 @atom:498_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:499_b82_a82_d82_i82 @atom:499_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:500_b61_a61_d61_i61 @atom:500_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:501_b83_a83_d83_i83 @atom:501_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:502_b84_a84_d84_i84 @atom:502_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:503_b45_a45_d45_i45 @atom:503_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:504_b49_a49_d49_i49 @atom:504_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:505_b49_a49_d49_i49 @atom:505_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:506_b49_a49_d49_i49 @atom:506_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:507_b20_a20_d20_i20 @atom:507_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:508_b84_a84_d84_i84 @atom:508_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:509_b87_a87_d87_i87 @atom:509_b87_a87_d87_i87 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:510_b49_a49_d49_i49 @atom:510_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:511_b49_a49_d49_i49 @atom:511_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:512_b20_a20_d20_i20 @atom:512_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:513_b82_a82_d82_i82 @atom:513_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:514_b61_a61_d61_i61 @atom:514_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:515_b83_a83_d83_i83 @atom:515_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:516_b84_a84_d84_i84 @atom:516_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:517_b49_a49_d49_i49 @atom:517_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:518_b49_a49_d49_i49 @atom:518_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:519_b49_a49_d49_i49 @atom:519_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:520_b20_a20_d20_i20 @atom:520_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:521_b61_a61_d61_i61 @atom:521_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:522_b88_a88_d88_i88 @atom:522_b88_a88_d88_i88 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:523_b87_a87_d87_i87 @atom:523_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:524_b84_a84_d84_i84 @atom:524_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:525_b49_a49_d49_i49 @atom:525_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:526_b49_a49_d49_i49 @atom:526_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:527_b49_a49_d49_i49 @atom:527_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:528_b57_a57_d57_i57 @atom:528_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:529_b84_a84_d84_i84 @atom:529_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:530_b87_a87_d87_i87 @atom:530_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:531_b48_a48_d48_i48 @atom:531_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:532_b48_a48_d48_i48 @atom:532_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:533_b48_a48_d48_i48 @atom:533_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:534_b48_a48_d48_i48 @atom:534_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:535_b81_a81_d81_i81 @atom:535_b81_a81_d81_i81 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:536_b60_a60_d60_i60 @atom:536_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:537_b45_a45_d45_i45 @atom:537_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:538_b49_a49_d49_i49 @atom:538_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:539_b49_a49_d49_i49 @atom:539_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:540_b49_a49_d49_i49 @atom:540_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:541_b49_a49_d49_i49 @atom:541_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:542_b49_a49_d49_i49 @atom:542_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:543_b49_a49_d49_i49 @atom:543_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:544_b56_a56_d56_i56 @atom:544_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:545_b48_a48_d48_i48 @atom:545_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:546_b48_a48_d48_i48 @atom:546_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:547_b48_a48_d48_i48 @atom:547_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:548_b48_a48_d48_i48 @atom:548_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:549_b48_a48_d48_i48 @atom:549_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:550_b48_a48_d48_i48 @atom:550_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:551_b48_a48_d48_i48 @atom:551_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:552_b48_a48_d48_i48 @atom:552_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:553_b48_a48_d48_i48 @atom:553_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:554_b49_a49_d49_i49 @atom:554_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:555_b49_a49_d49_i49 @atom:555_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:556_b49_a49_d49_i49 @atom:556_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:557_b49_a49_d49_i49 @atom:557_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:558_b49_a49_d49_i49 @atom:558_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:559_b49_a49_d49_i49 @atom:559_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:560_b49_a49_d49_i49 @atom:560_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:561_b56_a56_d56_i56 @atom:561_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:562_b59_a59_d59_i59 @atom:562_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:563_b56_a56_d56_i56 @atom:563_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:564_b60_a60_d60_i60 @atom:564_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:565_b60_a60_d60_i60 @atom:565_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:566_b48_a48_d48_i48 @atom:566_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:567_b61_a61_d61_i61 @atom:567_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:568_b62_a62_d62_i62 @atom:568_b62_a62_d62_i62 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:569_b57_a57_d57_i57 @atom:569_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:570_b49_a49_d49_i49 @atom:570_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:571_b49_a49_d49_i49 @atom:571_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:572_b49_a49_d49_i49 @atom:572_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:573_b45_a45_d45_i45 @atom:573_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:574_b16_a16_d16_i16 @atom:574_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:575_b82_a82_d82_i82 @atom:575_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:576_b61_a61_d61_i61 @atom:576_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:577_b83_a83_d83_i83 @atom:577_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:578_b84_a84_d84_i84 @atom:578_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:579_b49_a49_d49_i49 @atom:579_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:580_b49_a49_d49_i49 @atom:580_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:581_b49_a49_d49_i49 @atom:581_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:582_b56_a56_d56_i56 @atom:582_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:583_b59_a59_d59_i59 @atom:583_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:584_b49_a49_d49_i49 @atom:584_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:585_b48_a48_d48_i48 @atom:585_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:586_b13_a13_d13_i13 @atom:586_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:587_b56_a56_d56_i56 @atom:587_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:588_b48_a48_d48_i48 @atom:588_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:589_b48_a48_d48_i48 @atom:589_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:590_b48_a48_d48_i48 @atom:590_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:591_b48_a48_d48_i48 @atom:591_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:592_b48_a48_d48_i48 @atom:592_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:593_b48_a48_d48_i48 @atom:593_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:594_b49_a49_d49_i49 @atom:594_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:595_b49_a49_d49_i49 @atom:595_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:596_b49_a49_d49_i49 @atom:596_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:597_b49_a49_d49_i49 @atom:597_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:598_b57_a57_d57_i57 @atom:598_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:599_b82_a82_d82_i82 @atom:599_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:600_b61_a61_d61_i61 @atom:600_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:601_b83_a83_d83_i83 @atom:601_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:602_b84_a84_d84_i84 @atom:602_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:603_b13_a13_d13_i13 @atom:603_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:604_b49_a49_d49_i49 @atom:604_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:605_b49_a49_d49_i49 @atom:605_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:606_b49_a49_d49_i49 @atom:606_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:607_b46_a46_d46_i46 @atom:607_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:608_b13_a13_d13_i13 @atom:608_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:609_b13_a13_d13_i13 @atom:609_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:610_b13_a13_d13_i13 @atom:610_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:611_b13_a13_d13_i13 @atom:611_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:612_b13_a13_d13_i13 @atom:612_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:613_b13_a13_d13_i13 @atom:613_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:614_b13_a13_d13_i13 @atom:614_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:615_b13_a13_d13_i13 @atom:615_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:616_b13_a13_d13_i13 @atom:616_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:617_b13_a13_d13_i13 @atom:617_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:618_b13_a13_d13_i13 @atom:618_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:619_b13_a13_d13_i13 @atom:619_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:620_b13_a13_d13_i13 @atom:620_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:621_b13_a13_d13_i13 @atom:621_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:622_b13_a13_d13_i13 @atom:622_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:623_b15_a15_d15_i15 @atom:623_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:624_b17_a17_d17_i17 @atom:624_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:625_b48_a48_d48_i48 @atom:625_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:626_b89_a89_d89_i89 @atom:626_b89_a89_d89_i89 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:627_b90_a90_d90_i90 @atom:627_b90_a90_d90_i90 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:628_b91_a91_d91_i91 @atom:628_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:629_b91_a91_d91_i91 @atom:629_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:630_b13_a13_d13_i13 @atom:630_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:631_b86_a86_d86_i86 @atom:631_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:632_b86_a86_d86_i86 @atom:632_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:633_b86_a86_d86_i86 @atom:633_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:634_b86_a86_d86_i86 @atom:634_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:635_b86_a86_d86_i86 @atom:635_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:636_b86_a86_d86_i86 @atom:636_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:637_b16_a16_d16_i16 @atom:637_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:638_b92_a92_d92_i92 @atom:638_b92_a92_d92_i92 lj/cut/coul/long 0.054 3.473
- pair_coeff @atom:639_b93_a93_d93_i93 @atom:639_b93_a93_d93_i93 lj/cut/coul/long 0.05 3.3
- pair_coeff @atom:640_b94_a94_d94_i94 @atom:640_b94_a94_d94_i94 lj/cut/coul/long 0.05 3.3
- pair_coeff @atom:641_b95_a95_d95_i95 @atom:641_b95_a95_d95_i95 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:642_b13_a13_d13_i13 @atom:642_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:643_b46_a46_d46_i46 @atom:643_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:644_b96_a96_d96_i96 @atom:644_b96_a96_d96_i96 lj/cut/coul/long 0.06 3.75
- pair_coeff @atom:645_b97_a97_d97_i97 @atom:645_b97_a97_d97_i97 lj/cut/coul/long 0.054 3.473
- pair_coeff @atom:646_b98_a98_d98_i98 @atom:646_b98_a98_d98_i98 lj/cut/coul/long 0.05 3.3
- pair_coeff @atom:647_b99_a99_d99_i99 @atom:647_b99_a99_d99_i99 lj/cut/coul/long 0.05 3.3
- pair_coeff @atom:648_b100_a100_d100_i100 @atom:648_b100_a100_d100_i100 lj/cut/coul/long 0.04 2.95
- pair_coeff @atom:649_b47_a47_d47_i47 @atom:649_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:650_b21_a21_d21_i21 @atom:650_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:651_b46_a46_d46_i46 @atom:651_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:652_b91_a91_d91_i91 @atom:652_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:653_b91_a91_d91_i91 @atom:653_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:654_b91_a91_d91_i91 @atom:654_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:655_b48_a48_d48_i48 @atom:655_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:656_b49_a49_d49_i49 @atom:656_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:657_b48_a48_d48_i48 @atom:657_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:658_b49_a49_d49_i49 @atom:658_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:659_b48_a48_d48_i48 @atom:659_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:660_b1_a1_d1_i1 @atom:660_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85
- pair_coeff @atom:661_b48_a48_d48_i48 @atom:661_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:662_b1_a1_d1_i1 @atom:662_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85
- pair_coeff @atom:663_b65_a65_d65_i65 @atom:663_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47
- pair_coeff @atom:664_b2_a2_d2_i2 @atom:664_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905
- pair_coeff @atom:665_b48_a48_d48_i48 @atom:665_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:666_b13_a13_d13_i13 @atom:666_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25
- pair_coeff @atom:667_b1_a1_d1_i1 @atom:667_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94
- pair_coeff @atom:668_b48_a48_d48_i48 @atom:668_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:669_b1_a1_d1_i1 @atom:669_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85
- pair_coeff @atom:670_b48_a48_d48_i48 @atom:670_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:671_b65_a65_d65_i65 @atom:671_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47
- pair_coeff @atom:672_b48_a48_d48_i48 @atom:672_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:673_b66_a66_d66_i66 @atom:673_b66_a66_d66_i66 lj/cut/coul/long 0.6 3.75
- pair_coeff @atom:674_b91_a91_d91_i91 @atom:674_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:675_b15_a15_d15_i15 @atom:675_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55
- pair_coeff @atom:676_b48_a48_d48_i48 @atom:676_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:677_b48_a48_d48_i48 @atom:677_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:678_b48_a48_d48_i48 @atom:678_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:679_b48_a48_d48_i48 @atom:679_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:680_b48_a48_d48_i48 @atom:680_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:681_b49_a49_d49_i49 @atom:681_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:682_b49_a49_d49_i49 @atom:682_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:683_b48_a48_d48_i48 @atom:683_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55
- pair_coeff @atom:684_b55_a55_d55_i55 @atom:684_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:685_b45_a45_d45_i45 @atom:685_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:686_b45_a45_d45_i45 @atom:686_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:687_b49_a49_d49_i49 @atom:687_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:688_b13_a13_d13_i13 @atom:688_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:689_b13_a13_d13_i13 @atom:689_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:690_b101_a101_d101_i101 @atom:690_b101_a101_d101_i101 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:691_b56_a56_d56_i56 @atom:691_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:692_b101_a101_d101_i101 @atom:692_b101_a101_d101_i101 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:693_b48_a48_d48_i48 @atom:693_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55
- pair_coeff @atom:694_b18_a18_d18_i18 @atom:694_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2
- pair_coeff @atom:695_b19_a19_d19_i19 @atom:695_b19_a19_d19_i19 lj/cut/coul/long 0.066 3.3
- pair_coeff @atom:696_b13_a13_d13_i13 @atom:696_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3
- pair_coeff @atom:697_b13_a13_d13_i13 @atom:697_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3
- pair_coeff @atom:698_b13_a13_d13_i13 @atom:698_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3
- pair_coeff @atom:699_b13_a13_d13_i13 @atom:699_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3
- pair_coeff @atom:700_b46_a46_d46_i46 @atom:700_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5
- pair_coeff @atom:701_b102_a102_d102_i102 @atom:701_b102_a102_d102_i102 lj/cut/coul/long 0.12 3.25
- pair_coeff @atom:702_b103_a103_d103_i103 @atom:702_b103_a103_d103_i103 lj/cut/coul/long 0.17 2.96
- pair_coeff @atom:703_b13_a13_d13_i13 @atom:703_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:704_b46_a46_d46_i46 @atom:704_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5
- pair_coeff @atom:705_b13_a13_d13_i13 @atom:705_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:706_b13_a13_d13_i13 @atom:706_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:707_b13_a13_d13_i13 @atom:707_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:708_b102_a102_d102_i102 @atom:708_b102_a102_d102_i102 lj/cut/coul/long 0.12 3.25
- pair_coeff @atom:709_b48_a48_d48_i48 @atom:709_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:710_b13_a13_d13_i13 @atom:710_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3
- pair_coeff @atom:711_b56_a56_d56_i56 @atom:711_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:712_b4_a4_d4_i4 @atom:712_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:713_b3_a3_d3_i3 @atom:713_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:714_b20_a20_d20_i20 @atom:714_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0
- pair_coeff @atom:715_b13_a13_d13_i13 @atom:715_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:716_b13_a13_d13_i13 @atom:716_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:717_b13_a13_d13_i13 @atom:717_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:718_b46_a46_d46_i46 @atom:718_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:719_b46_a46_d46_i46 @atom:719_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:720_b46_a46_d46_i46 @atom:720_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:721_b20_a20_d20_i20 @atom:721_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:722_b104_a104_d104_i104 @atom:722_b104_a104_d104_i104 lj/cut/coul/long 0.2 3.74
- pair_coeff @atom:723_b13_a13_d13_i13 @atom:723_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:724_b13_a13_d13_i13 @atom:724_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:725_b46_a46_d46_i46 @atom:725_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:726_b64_a64_d64_i64 @atom:726_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74
- pair_coeff @atom:727_b1_a1_d1_i1 @atom:727_b1_a1_d1_i1 lj/cut/coul/long 0.061 3.1181
- pair_coeff @atom:728_b24_a24_d24_i24 @atom:728_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.15
- pair_coeff @atom:729_b4_a4_d4_i4 @atom:729_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.86
- pair_coeff @atom:730_b44_a44_d44_i44 @atom:730_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3
- pair_coeff @atom:731_b44_a44_d44_i44 @atom:731_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3
- pair_coeff @atom:732_b44_a44_d44_i44 @atom:732_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3
- pair_coeff @atom:733_b13_a13_d13_i13 @atom:733_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:734_b13_a13_d13_i13 @atom:734_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:735_b13_a13_d13_i13 @atom:735_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:736_b13_a13_d13_i13 @atom:736_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:737_b13_a13_d13_i13 @atom:737_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:738_b13_a13_d13_i13 @atom:738_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:739_b45_a45_d45_i45 @atom:739_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:740_b45_a45_d45_i45 @atom:740_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:741_b46_a46_d46_i46 @atom:741_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5
- pair_coeff @atom:742_b13_a13_d13_i13 @atom:742_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:743_b13_a13_d13_i13 @atom:743_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:744_b13_a13_d13_i13 @atom:744_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:745_b13_a13_d13_i13 @atom:745_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:746_b48_a48_d48_i48 @atom:746_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:747_b48_a48_d48_i48 @atom:747_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:748_b48_a48_d48_i48 @atom:748_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:749_b13_a13_d13_i13 @atom:749_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:750_b13_a13_d13_i13 @atom:750_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:751_b13_a13_d13_i13 @atom:751_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:752_b13_a13_d13_i13 @atom:752_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:753_b13_a13_d13_i13 @atom:753_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:754_b13_a13_d13_i13 @atom:754_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:755_b19_a19_d19_i19 @atom:755_b19_a19_d19_i19 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:756_b46_a46_d46_i46 @atom:756_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:757_b19_a19_d19_i19 @atom:757_b19_a19_d19_i19 lj/cut/coul/long 0.21 3.3
- pair_coeff @atom:758_b19_a19_d19_i19 @atom:758_b19_a19_d19_i19 lj/cut/coul/long 0.135 3.3
- pair_coeff @atom:759_b19_a19_d19_i19 @atom:759_b19_a19_d19_i19 lj/cut/coul/long 0.1 3.3
- pair_coeff @atom:760_b46_a46_d46_i46 @atom:760_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5
- pair_coeff @atom:761_b51_a51_d51_i51 @atom:761_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:762_b51_a51_d51_i51 @atom:762_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:763_b51_a51_d51_i51 @atom:763_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:764_b5_a5_d5_i5 @atom:764_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12
- pair_coeff @atom:765_b7_a7_d7_i7 @atom:765_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:766_b105_a105_d105_i105 @atom:766_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:767_b105_a105_d105_i105 @atom:767_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:768_b105_a105_d105_i105 @atom:768_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:769_b19_a19_d19_i19 @atom:769_b19_a19_d19_i19 lj/cut/coul/long 0.21 3.3
- pair_coeff @atom:770_b53_a53_d53_i53 @atom:770_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:771_b54_a54_d54_i54 @atom:771_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:772_b13_a13_d13_i13 @atom:772_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:773_b13_a13_d13_i13 @atom:773_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:774_b13_a13_d13_i13 @atom:774_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:775_b13_a13_d13_i13 @atom:775_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:776_b84_a84_d84_i84 @atom:776_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:777_b87_a87_d87_i87 @atom:777_b87_a87_d87_i87 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:778_b86_a86_d86_i86 @atom:778_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:779_b86_a86_d86_i86 @atom:779_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:780_b46_a46_d46_i46 @atom:780_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:781_b13_a13_d13_i13 @atom:781_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:782_b3_a3_d3_i3 @atom:782_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:783_b53_a53_d53_i53 @atom:783_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:784_b52_a52_d52_i52 @atom:784_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:785_b54_a54_d54_i54 @atom:785_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:786_b1_a1_d1_i1 @atom:786_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94
- pair_coeff @atom:787_b13_a13_d13_i13 @atom:787_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:788_b46_a46_d46_i46 @atom:788_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:789_b13_a13_d13_i13 @atom:789_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:790_b13_a13_d13_i13 @atom:790_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:791_b13_a13_d13_i13 @atom:791_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:792_b13_a13_d13_i13 @atom:792_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:793_b13_a13_d13_i13 @atom:793_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:794_b13_a13_d13_i13 @atom:794_b13_a13_d13_i13 lj/cut/coul/long 0.097 3.5
- pair_coeff @atom:795_b1_a1_d1_i1 @atom:795_b1_a1_d1_i1 lj/cut/coul/long 0.053 2.95
- pair_coeff @atom:796_b13_a13_d13_i13 @atom:796_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25
- pair_coeff @atom:797_b46_a46_d46_i46 @atom:797_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:798_b13_a13_d13_i13 @atom:798_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:799_b13_a13_d13_i13 @atom:799_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:800_b21_a21_d21_i21 @atom:800_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:801_b13_a13_d13_i13 @atom:801_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:802_b46_a46_d46_i46 @atom:802_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:803_b13_a13_d13_i13 @atom:803_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:804_b13_a13_d13_i13 @atom:804_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:805_b65_a65_d65_i65 @atom:805_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47
- pair_coeff @atom:806_b13_a13_d13_i13 @atom:806_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:807_b46_a46_d46_i46 @atom:807_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:808_b13_a13_d13_i13 @atom:808_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:809_b13_a13_d13_i13 @atom:809_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:810_b1_a1_d1_i1 @atom:810_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94
- pair_coeff @atom:811_b21_a21_d21_i21 @atom:811_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4
- pair_coeff @atom:812_b65_a65_d65_i65 @atom:812_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47
- pair_coeff @atom:813_b48_a48_d48_i48 @atom:813_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:814_b20_a20_d20_i20 @atom:814_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9
- pair_coeff @atom:815_b13_a13_d13_i13 @atom:815_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:816_b1_a1_d1_i1 @atom:816_b1_a1_d1_i1 lj/cut/coul/long 0.06 2.9
- pair_coeff @atom:817_b24_a24_d24_i24 @atom:817_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:818_b48_a48_d48_i48 @atom:818_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:819_b13_a13_d13_i13 @atom:819_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:820_b3_a3_d3_i3 @atom:820_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:821_b3_a3_d3_i3 @atom:821_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:822_b4_a4_d4_i4 @atom:822_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:823_b24_a24_d24_i24 @atom:823_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:824_b45_a45_d45_i45 @atom:824_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:825_b5_a5_d5_i5 @atom:825_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12
- pair_coeff @atom:826_b7_a7_d7_i7 @atom:826_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0
- pair_coeff @atom:827_b13_a13_d13_i13 @atom:827_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:828_b13_a13_d13_i13 @atom:828_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:829_b86_a86_d86_i86 @atom:829_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:830_b86_a86_d86_i86 @atom:830_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:831_b86_a86_d86_i86 @atom:831_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:832_b86_a86_d86_i86 @atom:832_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:833_b48_a48_d48_i48 @atom:833_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:834_b106_a106_d106_i106 @atom:834_b106_a106_d106_i106 lj/cut/coul/long 0.0125 1.96
- pair_coeff @atom:835_b13_a13_d13_i13 @atom:835_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:836_b13_a13_d13_i13 @atom:836_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:837_b13_a13_d13_i13 @atom:837_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:838_b66_a66_d66_i66 @atom:838_b66_a66_d66_i66 lj/cut/coul/long 0.6 3.75
- pair_coeff @atom:839_b46_a46_d46_i46 @atom:839_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:840_b24_a24_d24_i24 @atom:840_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:841_b48_a48_d48_i48 @atom:841_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:842_b48_a48_d48_i48 @atom:842_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:843_b24_a24_d24_i24 @atom:843_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:844_b48_a48_d48_i48 @atom:844_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:845_b3_a3_d3_i3 @atom:845_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:846_b4_a4_d4_i4 @atom:846_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:847_b107_a107_d107_i107 @atom:847_b107_a107_d107_i107 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:848_b13_a13_d13_i13 @atom:848_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:849_b13_a13_d13_i13 @atom:849_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:850_b13_a13_d13_i13 @atom:850_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:851_b13_a13_d13_i13 @atom:851_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:852_b46_a46_d46_i46 @atom:852_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:853_b3_a3_d3_i3 @atom:853_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75
- pair_coeff @atom:854_b4_a4_d4_i4 @atom:854_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:855_b46_a46_d46_i46 @atom:855_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42
- pair_coeff @atom:856_b13_a13_d13_i13 @atom:856_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:857_b13_a13_d13_i13 @atom:857_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:858_b13_a13_d13_i13 @atom:858_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:859_b13_a13_d13_i13 @atom:859_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:860_b13_a13_d13_i13 @atom:860_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:861_b13_a13_d13_i13 @atom:861_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:862_b13_a13_d13_i13 @atom:862_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:863_b13_a13_d13_i13 @atom:863_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:864_b13_a13_d13_i13 @atom:864_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:865_b13_a13_d13_i13 @atom:865_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:866_b108_a108_d108_i108 @atom:866_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0
- pair_coeff @atom:867_b108_a108_d108_i108 @atom:867_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0
- pair_coeff @atom:868_b108_a108_d108_i108 @atom:868_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0
- pair_coeff @atom:869_b108_a108_d108_i108 @atom:869_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0
- pair_coeff @atom:870_b45_a45_d45_i45 @atom:870_b45_a45_d45_i45 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:871_b13_a13_d13_i13 @atom:871_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:872_b13_a13_d13_i13 @atom:872_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:873_b13_a13_d13_i13 @atom:873_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:874_b13_a13_d13_i13 @atom:874_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:875_b1_a1_d1_i1 @atom:875_b1_a1_d1_i1 lj/cut/coul/long 0.72 3.08
- pair_coeff @atom:876_b21_a21_d21_i21 @atom:876_b21_a21_d21_i21 lj/cut/coul/long 0.11779 4.18
- pair_coeff @atom:877_b65_a65_d65_i65 @atom:877_b65_a65_d65_i65 lj/cut/coul/long 0.09 4.51
- pair_coeff @atom:878_b66_a66_d66_i66 @atom:878_b66_a66_d66_i66 lj/cut/coul/long 0.07 5.15
- pair_coeff @atom:879_b68_a68_d68_i68 @atom:879_b68_a68_d68_i68 lj/cut/coul/long 0.018279 2.7
- pair_coeff @atom:880_b69_a69_d69_i69 @atom:880_b69_a69_d69_i69 lj/cut/coul/long 0.002772 3.35
- pair_coeff @atom:881_b70_a70_d70_i70 @atom:881_b70_a70_d70_i70 lj/cut/coul/long 0.000328 4.06
- pair_coeff @atom:882_b71_a71_d71_i71 @atom:882_b71_a71_d71_i71 lj/cut/coul/long 0.000171 4.32
- pair_coeff @atom:883_b72_a72_d72_i72 @atom:883_b72_a72_d72_i72 lj/cut/coul/long 8.1e-05 4.82
- pair_coeff @atom:884_b73_a73_d73_i73 @atom:884_b73_a73_d73_i73 lj/cut/coul/long 0.875044 2.91
- pair_coeff @atom:885_b74_a74_d74_i74 @atom:885_b74_a74_d74_i74 lj/cut/coul/long 0.449657 3.47
- pair_coeff @atom:886_b75_a75_d75_i75 @atom:886_b75_a75_d75_i75 lj/cut/coul/long 0.118226 3.82
- pair_coeff @atom:887_b76_a76_d76_i76 @atom:887_b76_a76_d76_i76 lj/cut/coul/long 0.047096 4.18
- pair_coeff @atom:888_b13_a13_d13_i13 @atom:888_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:889_b13_a13_d13_i13 @atom:889_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:890_b13_a13_d13_i13 @atom:890_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:891_b13_a13_d13_i13 @atom:891_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- pair_coeff @atom:892_b46_a46_d46_i46 @atom:892_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5
- pair_coeff @atom:893_b53_a53_d53_i53 @atom:893_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:894_b48_a48_d48_i48 @atom:894_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:895_b53_a53_d53_i53 @atom:895_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25
- pair_coeff @atom:896_b48_a48_d48_i48 @atom:896_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55
- pair_coeff @atom:897_b109_a109_d109_i109 @atom:897_b109_a109_d109_i109 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:898_b109_a109_d109_i109 @atom:898_b109_a109_d109_i109 lj/cut/coul/long 0.076 3.55
- pair_coeff @atom:899_b46_a46_d46_i46 @atom:899_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42
- pair_coeff @atom:900_b47_a47_d47_i47 @atom:900_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:901_b47_a47_d47_i47 @atom:901_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:902_b47_a47_d47_i47 @atom:902_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:903_b110_a110_d110_i110 @atom:903_b110_a110_d110_i110 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:904_b110_a110_d110_i110 @atom:904_b110_a110_d110_i110 lj/cut/coul/long 0.086 3.3
- pair_coeff @atom:905_b4_a4_d4_i4 @atom:905_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96
- pair_coeff @atom:906_b13_a13_d13_i13 @atom:906_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5
- } #(end of pair_coeffs)
-
-
- # ------- force-field-IDs for bonded interaction lookup -------
- # (First append the "force-field-ID" to the atom type name.
- # Later use these expanded names for force-field lookup.)
- replace{ @atom:1 @atom:1_b1_a1_d1_i1 }
- replace{ @atom:2 @atom:2_b2_a2_d2_i2 }
- replace{ @atom:3 @atom:3_b3_a3_d3_i3 }
- replace{ @atom:4 @atom:4_b4_a4_d4_i4 }
- replace{ @atom:5 @atom:5_b5_a5_d5_i5 }
- replace{ @atom:6 @atom:6_b6_a6_d6_i6 }
- replace{ @atom:7 @atom:7_b7_a7_d7_i7 }
- replace{ @atom:8 @atom:8_b8_a8_d8_i8 }
- replace{ @atom:9 @atom:9_b6_a6_d6_i6 }
- replace{ @atom:10 @atom:10_b6_a6_d6_i6 }
- replace{ @atom:11 @atom:11_b6_a6_d6_i6 }
- replace{ @atom:12 @atom:12_b6_a6_d6_i6 }
- replace{ @atom:13 @atom:13_b2_a2_d2_i2 }
- replace{ @atom:14 @atom:14_b9_a9_d9_i9 }
- replace{ @atom:15 @atom:15_b10_a10_d10_i10 }
- replace{ @atom:16 @atom:16_b11_a11_d11_i11 }
- replace{ @atom:17 @atom:17_b12_a12_d12_i12 }
- replace{ @atom:18 @atom:18_b13_a13_d13_i13 }
- replace{ @atom:19 @atom:19_b14_a14_d14_i14 }
- replace{ @atom:20 @atom:20_b5_a5_d5_i5 }
- replace{ @atom:21 @atom:21_b7_a7_d7_i7 }
- replace{ @atom:22 @atom:22_b6_a6_d6_i6 }
- replace{ @atom:23 @atom:23_b2_a2_d2_i2 }
- replace{ @atom:24 @atom:24_b15_a15_d15_i15 }
- replace{ @atom:25 @atom:25_b15_a15_d15_i15 }
- replace{ @atom:26 @atom:26_b16_a16_d16_i16 }
- replace{ @atom:27 @atom:27_b16_a16_d16_i16 }
- replace{ @atom:28 @atom:28_b17_a17_d17_i17 }
- replace{ @atom:29 @atom:29_b17_a17_d17_i17 }
- replace{ @atom:30 @atom:30_b6_a6_d6_i6 }
- replace{ @atom:31 @atom:31_b2_a2_d2_i2 }
- replace{ @atom:32 @atom:32_b6_a6_d6_i6 }
- replace{ @atom:33 @atom:33_b2_a2_d2_i2 }
- replace{ @atom:34 @atom:34_b6_a6_d6_i6 }
- replace{ @atom:35 @atom:35_b2_a2_d2_i2 }
- replace{ @atom:36 @atom:36_b18_a18_d18_i18 }
- replace{ @atom:37 @atom:37_b19_a19_d19_i19 }
- replace{ @atom:38 @atom:38_b6_a6_d6_i6 }
- replace{ @atom:39 @atom:39_b10_a10_d10_i10 }
- replace{ @atom:40 @atom:40_b13_a13_d13_i13 }
- replace{ @atom:41 @atom:41_b20_a20_d20_i20 }
- replace{ @atom:42 @atom:42_b6_a6_d6_i6 }
- replace{ @atom:43 @atom:43_b2_a2_d2_i2 }
- replace{ @atom:44 @atom:44_b2_a2_d2_i2 }
- replace{ @atom:45 @atom:45_b21_a21_d21_i21 }
- replace{ @atom:46 @atom:46_b10_a10_d10_i10 }
- replace{ @atom:47 @atom:47_b21_a21_d21_i21 }
- replace{ @atom:48 @atom:48_b13_a13_d13_i13 }
- replace{ @atom:49 @atom:49_b21_a21_d21_i21 }
- replace{ @atom:50 @atom:50_b22_a22_d22_i22 }
- replace{ @atom:51 @atom:51_b23_a23_d23_i23 }
- replace{ @atom:52 @atom:52_b6_a6_d6_i6 }
- replace{ @atom:53 @atom:53_b4_a4_d4_i4 }
- replace{ @atom:54 @atom:54_b24_a24_d24_i24 }
- replace{ @atom:55 @atom:55_b3_a3_d3_i3 }
- replace{ @atom:56 @atom:56_b6_a6_d6_i6 }
- replace{ @atom:57 @atom:57_b25_a25_d25_i25 }
- replace{ @atom:58 @atom:58_b26_a26_d26_i26 }
- replace{ @atom:59 @atom:59_b27_a27_d27_i27 }
- replace{ @atom:60 @atom:60_b28_a28_d28_i28 }
- replace{ @atom:61 @atom:61_b29_a29_d29_i29 }
- replace{ @atom:62 @atom:62_b30_a30_d30_i30 }
- replace{ @atom:63 @atom:63_b31_a31_d31_i31 }
- replace{ @atom:64 @atom:64_b32_a32_d32_i32 }
- replace{ @atom:65 @atom:65_b31_a31_d31_i31 }
- replace{ @atom:66 @atom:66_b32_a32_d32_i32 }
- replace{ @atom:67 @atom:67_b33_a33_d33_i33 }
- replace{ @atom:68 @atom:68_b34_a34_d34_i34 }
- replace{ @atom:69 @atom:69_b35_a35_d35_i35 }
- replace{ @atom:70 @atom:70_b36_a36_d36_i36 }
- replace{ @atom:71 @atom:71_b37_a37_d37_i37 }
- replace{ @atom:72 @atom:72_b38_a38_d38_i38 }
- replace{ @atom:73 @atom:73_b39_a39_d39_i39 }
- replace{ @atom:74 @atom:74_b40_a40_d40_i40 }
- replace{ @atom:75 @atom:75_b41_a41_d41_i41 }
- replace{ @atom:76 @atom:76_b42_a42_d42_i42 }
- replace{ @atom:77 @atom:77_b43_a43_d43_i43 }
- replace{ @atom:78 @atom:78_b44_a44_d44_i44 }
- replace{ @atom:79 @atom:79_b45_a45_d45_i45 }
- replace{ @atom:80 @atom:80_b13_a13_d13_i13 }
- replace{ @atom:81 @atom:81_b13_a13_d13_i13 }
- replace{ @atom:82 @atom:82_b13_a13_d13_i13 }
- replace{ @atom:83 @atom:83_b13_a13_d13_i13 }
- replace{ @atom:84 @atom:84_b13_a13_d13_i13 }
- replace{ @atom:85 @atom:85_b46_a46_d46_i46 }
- replace{ @atom:86 @atom:86_b47_a47_d47_i47 }
- replace{ @atom:87 @atom:87_b47_a47_d47_i47 }
- replace{ @atom:88 @atom:88_b47_a47_d47_i47 }
- replace{ @atom:89 @atom:89_b46_a46_d46_i46 }
- replace{ @atom:90 @atom:90_b48_a48_d48_i48 }
- replace{ @atom:91 @atom:91_b49_a49_d49_i49 }
- replace{ @atom:92 @atom:92_b48_a48_d48_i48 }
- replace{ @atom:93 @atom:93_b13_a13_d13_i13 }
- replace{ @atom:94 @atom:94_b13_a13_d13_i13 }
- replace{ @atom:95 @atom:95_b50_a50_d50_i50 }
- replace{ @atom:96 @atom:96_b5_a5_d5_i5 }
- replace{ @atom:97 @atom:97_b7_a7_d7_i7 }
- replace{ @atom:98 @atom:98_b46_a46_d46_i46 }
- replace{ @atom:99 @atom:99_b13_a13_d13_i13 }
- replace{ @atom:100 @atom:100_b13_a13_d13_i13 }
- replace{ @atom:101 @atom:101_b13_a13_d13_i13 }
- replace{ @atom:102 @atom:102_b13_a13_d13_i13 }
- replace{ @atom:103 @atom:103_b13_a13_d13_i13 }
- replace{ @atom:104 @atom:104_b5_a5_d5_i5 }
- replace{ @atom:105 @atom:105_b7_a7_d7_i7 }
- replace{ @atom:106 @atom:106_b1_a1_d1_i1 }
- replace{ @atom:107 @atom:107_b46_a46_d46_i46 }
- replace{ @atom:108 @atom:108_b48_a48_d48_i48 }
- replace{ @atom:109 @atom:109_b5_a5_d5_i5 }
- replace{ @atom:110 @atom:110_b7_a7_d7_i7 }
- replace{ @atom:111 @atom:111_b5_a5_d5_i5 }
- replace{ @atom:112 @atom:112_b7_a7_d7_i7 }
- replace{ @atom:113 @atom:113_b5_a5_d5_i5 }
- replace{ @atom:114 @atom:114_b7_a7_d7_i7 }
- replace{ @atom:115 @atom:115_b13_a13_d13_i13 }
- replace{ @atom:116 @atom:116_b13_a13_d13_i13 }
- replace{ @atom:117 @atom:117_b13_a13_d13_i13 }
- replace{ @atom:118 @atom:118_b46_a46_d46_i46 }
- replace{ @atom:119 @atom:119_b20_a20_d20_i20 }
- replace{ @atom:120 @atom:120_b50_a50_d50_i50 }
- replace{ @atom:121 @atom:121_b20_a20_d20_i20 }
- replace{ @atom:122 @atom:122_b20_a20_d20_i20 }
- replace{ @atom:123 @atom:123_b13_a13_d13_i13 }
- replace{ @atom:124 @atom:124_b13_a13_d13_i13 }
- replace{ @atom:125 @atom:125_b13_a13_d13_i13 }
- replace{ @atom:126 @atom:126_b13_a13_d13_i13 }
- replace{ @atom:127 @atom:127_b46_a46_d46_i46 }
- replace{ @atom:128 @atom:128_b20_a20_d20_i20 }
- replace{ @atom:129 @atom:129_b5_a5_d5_i5 }
- replace{ @atom:130 @atom:130_b7_a7_d7_i7 }
- replace{ @atom:131 @atom:131_b51_a51_d51_i51 }
- replace{ @atom:132 @atom:132_b46_a46_d46_i46 }
- replace{ @atom:133 @atom:133_b51_a51_d51_i51 }
- replace{ @atom:134 @atom:134_b46_a46_d46_i46 }
- replace{ @atom:135 @atom:135_b51_a51_d51_i51 }
- replace{ @atom:136 @atom:136_b46_a46_d46_i46 }
- replace{ @atom:137 @atom:137_b51_a51_d51_i51 }
- replace{ @atom:138 @atom:138_b46_a46_d46_i46 }
- replace{ @atom:139 @atom:139_b51_a51_d51_i51 }
- replace{ @atom:140 @atom:140_b51_a51_d51_i51 }
- replace{ @atom:141 @atom:141_b48_a48_d48_i48 }
- replace{ @atom:142 @atom:142_b15_a15_d15_i15 }
- replace{ @atom:143 @atom:143_b15_a15_d15_i15 }
- replace{ @atom:144 @atom:144_b16_a16_d16_i16 }
- replace{ @atom:145 @atom:145_b16_a16_d16_i16 }
- replace{ @atom:146 @atom:146_b17_a17_d17_i17 }
- replace{ @atom:147 @atom:147_b17_a17_d17_i17 }
- replace{ @atom:148 @atom:148_b13_a13_d13_i13 }
- replace{ @atom:149 @atom:149_b13_a13_d13_i13 }
- replace{ @atom:150 @atom:150_b13_a13_d13_i13 }
- replace{ @atom:151 @atom:151_b13_a13_d13_i13 }
- replace{ @atom:152 @atom:152_b13_a13_d13_i13 }
- replace{ @atom:153 @atom:153_b13_a13_d13_i13 }
- replace{ @atom:154 @atom:154_b13_a13_d13_i13 }
- replace{ @atom:155 @atom:155_b13_a13_d13_i13 }
- replace{ @atom:156 @atom:156_b13_a13_d13_i13 }
- replace{ @atom:157 @atom:157_b13_a13_d13_i13 }
- replace{ @atom:158 @atom:158_b13_a13_d13_i13 }
- replace{ @atom:159 @atom:159_b13_a13_d13_i13 }
- replace{ @atom:160 @atom:160_b13_a13_d13_i13 }
- replace{ @atom:161 @atom:161_b13_a13_d13_i13 }
- replace{ @atom:162 @atom:162_b13_a13_d13_i13 }
- replace{ @atom:163 @atom:163_b48_a48_d48_i48 }
- replace{ @atom:164 @atom:164_b16_a16_d16_i16 }
- replace{ @atom:165 @atom:165_b13_a13_d13_i13 }
- replace{ @atom:166 @atom:166_b13_a13_d13_i13 }
- replace{ @atom:167 @atom:167_b13_a13_d13_i13 }
- replace{ @atom:168 @atom:168_b21_a21_d21_i21 }
- replace{ @atom:169 @atom:169_b47_a47_d47_i47 }
- replace{ @atom:170 @atom:170_b48_a48_d48_i48 }
- replace{ @atom:171 @atom:171_b13_a13_d13_i13 }
- replace{ @atom:172 @atom:172_b13_a13_d13_i13 }
- replace{ @atom:173 @atom:173_b3_a3_d3_i3 }
- replace{ @atom:174 @atom:174_b3_a3_d3_i3 }
- replace{ @atom:175 @atom:175_b3_a3_d3_i3 }
- replace{ @atom:176 @atom:176_b3_a3_d3_i3 }
- replace{ @atom:177 @atom:177_b3_a3_d3_i3 }
- replace{ @atom:178 @atom:178_b4_a4_d4_i4 }
- replace{ @atom:179 @atom:179_b24_a24_d24_i24 }
- replace{ @atom:180 @atom:180_b24_a24_d24_i24 }
- replace{ @atom:181 @atom:181_b24_a24_d24_i24 }
- replace{ @atom:182 @atom:182_b45_a45_d45_i45 }
- replace{ @atom:183 @atom:183_b45_a45_d45_i45 }
- replace{ @atom:184 @atom:184_b13_a13_d13_i13 }
- replace{ @atom:185 @atom:185_b13_a13_d13_i13 }
- replace{ @atom:186 @atom:186_b13_a13_d13_i13 }
- replace{ @atom:187 @atom:187_b13_a13_d13_i13 }
- replace{ @atom:188 @atom:188_b13_a13_d13_i13 }
- replace{ @atom:189 @atom:189_b3_a3_d3_i3 }
- replace{ @atom:190 @atom:190_b4_a4_d4_i4 }
- replace{ @atom:191 @atom:191_b24_a24_d24_i24 }
- replace{ @atom:192 @atom:192_b45_a45_d45_i45 }
- replace{ @atom:193 @atom:193_b24_a24_d24_i24 }
- replace{ @atom:194 @atom:194_b3_a3_d3_i3 }
- replace{ @atom:195 @atom:195_b4_a4_d4_i4 }
- replace{ @atom:196 @atom:196_b45_a45_d45_i45 }
- replace{ @atom:197 @atom:197_b46_a46_d46_i46 }
- replace{ @atom:198 @atom:198_b13_a13_d13_i13 }
- replace{ @atom:199 @atom:199_b13_a13_d13_i13 }
- replace{ @atom:200 @atom:200_b13_a13_d13_i13 }
- replace{ @atom:201 @atom:201_b13_a13_d13_i13 }
- replace{ @atom:202 @atom:202_b48_a48_d48_i48 }
- replace{ @atom:203 @atom:203_b19_a19_d19_i19 }
- replace{ @atom:204 @atom:204_b18_a18_d18_i18 }
- replace{ @atom:205 @atom:205_b48_a48_d48_i48 }
- replace{ @atom:206 @atom:206_b21_a21_d21_i21 }
- replace{ @atom:207 @atom:207_b24_a24_d24_i24 }
- replace{ @atom:208 @atom:208_b48_a48_d48_i48 }
- replace{ @atom:209 @atom:209_b3_a3_d3_i3 }
- replace{ @atom:210 @atom:210_b4_a4_d4_i4 }
- replace{ @atom:211 @atom:211_b5_a5_d5_i5 }
- replace{ @atom:212 @atom:212_b7_a7_d7_i7 }
- replace{ @atom:213 @atom:213_b3_a3_d3_i3 }
- replace{ @atom:214 @atom:214_b52_a52_d52_i52 }
- replace{ @atom:215 @atom:215_b13_a13_d13_i13 }
- replace{ @atom:216 @atom:216_b13_a13_d13_i13 }
- replace{ @atom:217 @atom:217_b13_a13_d13_i13 }
- replace{ @atom:218 @atom:218_b13_a13_d13_i13 }
- replace{ @atom:219 @atom:219_b3_a3_d3_i3 }
- replace{ @atom:220 @atom:220_b4_a4_d4_i4 }
- replace{ @atom:221 @atom:221_b46_a46_d46_i46 }
- replace{ @atom:222 @atom:222_b3_a3_d3_i3 }
- replace{ @atom:223 @atom:223_b4_a4_d4_i4 }
- replace{ @atom:224 @atom:224_b46_a46_d46_i46 }
- replace{ @atom:225 @atom:225_b13_a13_d13_i13 }
- replace{ @atom:226 @atom:226_b13_a13_d13_i13 }
- replace{ @atom:227 @atom:227_b13_a13_d13_i13 }
- replace{ @atom:228 @atom:228_b13_a13_d13_i13 }
- replace{ @atom:229 @atom:229_b53_a53_d53_i53 }
- replace{ @atom:230 @atom:230_b53_a53_d53_i53 }
- replace{ @atom:231 @atom:231_b53_a53_d53_i53 }
- replace{ @atom:232 @atom:232_b54_a54_d54_i54 }
- replace{ @atom:233 @atom:233_b54_a54_d54_i54 }
- replace{ @atom:234 @atom:234_b13_a13_d13_i13 }
- replace{ @atom:235 @atom:235_b13_a13_d13_i13 }
- replace{ @atom:236 @atom:236_b13_a13_d13_i13 }
- replace{ @atom:237 @atom:237_b13_a13_d13_i13 }
- replace{ @atom:238 @atom:238_b13_a13_d13_i13 }
- replace{ @atom:239 @atom:239_b13_a13_d13_i13 }
- replace{ @atom:240 @atom:240_b13_a13_d13_i13 }
- replace{ @atom:241 @atom:241_b13_a13_d13_i13 }
- replace{ @atom:242 @atom:242_b13_a13_d13_i13 }
- replace{ @atom:243 @atom:243_b55_a55_d55_i55 }
- replace{ @atom:244 @atom:244_b54_a54_d54_i54 }
- replace{ @atom:245 @atom:245_b48_a48_d48_i48 }
- replace{ @atom:246 @atom:246_b55_a55_d55_i55 }
- replace{ @atom:247 @atom:247_b54_a54_d54_i54 }
- replace{ @atom:248 @atom:248_b13_a13_d13_i13 }
- replace{ @atom:249 @atom:249_b13_a13_d13_i13 }
- replace{ @atom:250 @atom:250_b13_a13_d13_i13 }
- replace{ @atom:251 @atom:251_b13_a13_d13_i13 }
- replace{ @atom:252 @atom:252_b53_a53_d53_i53 }
- replace{ @atom:253 @atom:253_b54_a54_d54_i54 }
- replace{ @atom:254 @atom:254_b56_a56_d56_i56 }
- replace{ @atom:255 @atom:255_b48_a48_d48_i48 }
- replace{ @atom:256 @atom:256_b55_a55_d55_i55 }
- replace{ @atom:257 @atom:257_b45_a45_d45_i45 }
- replace{ @atom:258 @atom:258_b48_a48_d48_i48 }
- replace{ @atom:259 @atom:259_b49_a49_d49_i49 }
- replace{ @atom:260 @atom:260_b48_a48_d48_i48 }
- replace{ @atom:261 @atom:261_b49_a49_d49_i49 }
- replace{ @atom:262 @atom:262_b57_a57_d57_i57 }
- replace{ @atom:263 @atom:263_b3_a3_d3_i3 }
- replace{ @atom:264 @atom:264_b57_a57_d57_i57 }
- replace{ @atom:265 @atom:265_b3_a3_d3_i3 }
- replace{ @atom:266 @atom:266_b47_a47_d47_i47 }
- replace{ @atom:267 @atom:267_b47_a47_d47_i47 }
- replace{ @atom:268 @atom:268_b45_a45_d45_i45 }
- replace{ @atom:269 @atom:269_b4_a4_d4_i4 }
- replace{ @atom:270 @atom:270_b45_a45_d45_i45 }
- replace{ @atom:271 @atom:271_b4_a4_d4_i4 }
- replace{ @atom:272 @atom:272_b46_a46_d46_i46 }
- replace{ @atom:273 @atom:273_b46_a46_d46_i46 }
- replace{ @atom:274 @atom:274_b13_a13_d13_i13 }
- replace{ @atom:275 @atom:275_b46_a46_d46_i46 }
- replace{ @atom:276 @atom:276_b57_a57_d57_i57 }
- replace{ @atom:277 @atom:277_b3_a3_d3_i3 }
- replace{ @atom:278 @atom:278_b56_a56_d56_i56 }
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- replace{ @atom:899 @atom:899_b46_a46_d46_i46 }
- replace{ @atom:900 @atom:900_b47_a47_d47_i47 }
- replace{ @atom:901 @atom:901_b47_a47_d47_i47 }
- replace{ @atom:902 @atom:902_b47_a47_d47_i47 }
- replace{ @atom:903 @atom:903_b110_a110_d110_i110 }
- replace{ @atom:904 @atom:904_b110_a110_d110_i110 }
- replace{ @atom:905 @atom:905_b4_a4_d4_i4 }
- replace{ @atom:906 @atom:906_b13_a13_d13_i13 }
- #(end of force-field-IDs)
-
-
- write_once("In Settings") {
- bond_coeff @bond:1-2 harmonic 367.0 1.38
- bond_coeff @bond:1-3 harmonic 420.0 1.357
- bond_coeff @bond:1-13 harmonic 367.0 1.36
- bond_coeff @bond:1-19 harmonic 450.0 1.279
- bond_coeff @bond:1-25 harmonic 300.0 0.3
- bond_coeff @bond:1-47 harmonic 420.0 1.34
- bond_coeff @bond:1-48 harmonic 420.0 1.354
- bond_coeff @bond:1-82 harmonic 420.0 1.354
- bond_coeff @bond:1-83 harmonic 420.0 1.354
- bond_coeff @bond:1-84 harmonic 420.0 1.354
- bond_coeff @bond:1-87 harmonic 420.0 1.354
- bond_coeff @bond:1-88 harmonic 420.0 1.354
- bond_coeff @bond:1-108 harmonic 461.0 1.57
- bond_coeff @bond:2-2 harmonic 260.0 1.526
- bond_coeff @bond:2-3 harmonic 317.0 1.522
- bond_coeff @bond:2-5 harmonic 386.0 1.425
- bond_coeff @bond:2-6 harmonic 260.0 1.526
- bond_coeff @bond:2-10 harmonic 260.0 1.526
- bond_coeff @bond:2-11 harmonic 317.0 1.5
- bond_coeff @bond:2-12 harmonic 317.0 1.51
- bond_coeff @bond:2-13 harmonic 260.0 1.526
- bond_coeff @bond:2-14 harmonic 317.0 1.5
- bond_coeff @bond:2-15 harmonic 222.0 1.81
- bond_coeff @bond:2-16 harmonic 222.0 1.81
- bond_coeff @bond:2-20 harmonic 320.0 1.425
- bond_coeff @bond:2-24 harmonic 337.0 1.449
- bond_coeff @bond:2-44 harmonic 382.0 1.448
- bond_coeff @bond:2-48 harmonic 317.0 1.51
- bond_coeff @bond:2-51 harmonic 260.0 1.526
- bond_coeff @bond:2-53 harmonic 367.0 1.471
- bond_coeff @bond:2-55 harmonic 337.0 1.463
- bond_coeff @bond:2-80 harmonic 317.0 1.495
- bond_coeff @bond:3-3 harmonic 350.0 1.51
- bond_coeff @bond:3-4 harmonic 570.0 1.229
- bond_coeff @bond:3-5 harmonic 450.0 1.364
- bond_coeff @bond:3-6 harmonic 317.0 1.522
- bond_coeff @bond:3-10 harmonic 317.0 1.522
- bond_coeff @bond:3-12 harmonic 469.0 1.4
- bond_coeff @bond:3-13 harmonic 317.0 1.522
- bond_coeff @bond:3-19 harmonic 400.0 1.444
- bond_coeff @bond:3-20 harmonic 214.0 1.327
- bond_coeff @bond:3-21 harmonic 300.0 1.79
- bond_coeff @bond:3-24 harmonic 490.0 1.335
- bond_coeff @bond:3-44 harmonic 317.0 1.522
- bond_coeff @bond:3-46 harmonic 340.0 1.09
- bond_coeff @bond:3-47 harmonic 410.0 1.444
- bond_coeff @bond:3-48 harmonic 400.0 1.49
- bond_coeff @bond:3-50 harmonic 385.0 1.46
- bond_coeff @bond:3-52 harmonic 656.0 1.25
- bond_coeff @bond:3-56 harmonic 457.0 1.358
- bond_coeff @bond:3-57 harmonic 418.0 1.388
- bond_coeff @bond:3-60 harmonic 447.0 1.419
- bond_coeff @bond:3-65 harmonic 300.0 1.98
- bond_coeff @bond:3-84 harmonic 400.0 1.49
- bond_coeff @bond:3-86 harmonic 385.0 1.46
- bond_coeff @bond:3-105 harmonic 424.0 1.383
- bond_coeff @bond:3-107 harmonic 490.0 1.335
- bond_coeff @bond:4-25 harmonic 553.0 0.3
- bond_coeff @bond:4-64 harmonic 525.0 1.48
- bond_coeff @bond:4-89 harmonic 570.0 1.229
- bond_coeff @bond:4-110 harmonic 700.0 1.171
- bond_coeff @bond:5-6 harmonic 386.0 1.425
- bond_coeff @bond:5-7 harmonic 553.0 0.945
- bond_coeff @bond:5-10 harmonic 386.0 1.425
- bond_coeff @bond:5-13 harmonic 320.0 1.41
- bond_coeff @bond:5-20 harmonic 250.0 1.47
- bond_coeff @bond:5-24 harmonic 400.0 1.38
- bond_coeff @bond:5-25 harmonic 340.0 0.3
- bond_coeff @bond:5-44 harmonic 320.0 1.45
- bond_coeff @bond:5-47 harmonic 450.0 1.37
- bond_coeff @bond:5-48 harmonic 450.0 1.364
- bond_coeff @bond:5-51 harmonic 320.0 1.38
- bond_coeff @bond:5-64 harmonic 230.0 1.61
- bond_coeff @bond:5-79 harmonic 450.0 1.67
- bond_coeff @bond:5-106 harmonic 94.0 1.8
- bond_coeff @bond:5-108 harmonic 374.0 1.64
- bond_coeff @bond:6-6 harmonic 260.0 1.526
- bond_coeff @bond:6-10 harmonic 260.0 1.526
- bond_coeff @bond:6-11 harmonic 317.0 1.5
- bond_coeff @bond:6-13 harmonic 260.0 1.526
- bond_coeff @bond:6-14 harmonic 317.0 1.5
- bond_coeff @bond:6-15 harmonic 222.0 1.81
- bond_coeff @bond:6-16 harmonic 222.0 1.81
- bond_coeff @bond:6-20 harmonic 320.0 1.425
- bond_coeff @bond:6-24 harmonic 337.0 1.449
- bond_coeff @bond:6-44 harmonic 382.0 1.448
- bond_coeff @bond:6-47 harmonic 317.0 1.51
- bond_coeff @bond:6-51 harmonic 260.0 1.526
- bond_coeff @bond:6-53 harmonic 367.0 1.471
- bond_coeff @bond:6-55 harmonic 337.0 1.463
- bond_coeff @bond:6-79 harmonic 222.0 1.81
- bond_coeff @bond:6-105 harmonic 337.0 1.475
- bond_coeff @bond:7-20 harmonic 553.0 0.945
- bond_coeff @bond:7-25 harmonic 340.0 0.1
- bond_coeff @bond:9-9 harmonic 530.0 1.34
- bond_coeff @bond:9-11 harmonic 530.0 1.34
- bond_coeff @bond:9-14 harmonic 530.0 1.34
- bond_coeff @bond:10-10 harmonic 260.0 1.526
- bond_coeff @bond:10-11 harmonic 317.0 1.5
- bond_coeff @bond:10-14 harmonic 317.0 1.5
- bond_coeff @bond:10-20 harmonic 320.0 1.425
- bond_coeff @bond:10-24 harmonic 337.0 1.449
- bond_coeff @bond:10-44 harmonic 382.0 1.448
- bond_coeff @bond:10-105 harmonic 337.0 1.475
- bond_coeff @bond:11-11 harmonic 530.0 1.34
- bond_coeff @bond:11-13 harmonic 317.0 1.5
- bond_coeff @bond:11-14 harmonic 530.0 1.34
- bond_coeff @bond:11-79 harmonic 222.0 1.76
- bond_coeff @bond:12-12 harmonic 469.0 1.4
- bond_coeff @bond:12-48 harmonic 469.0 1.4
- bond_coeff @bond:12-60 harmonic 469.0 1.4
- bond_coeff @bond:12-81 harmonic 469.0 1.4
- bond_coeff @bond:13-13 harmonic 268.0 1.529
- bond_coeff @bond:13-14 harmonic 317.0 1.5
- bond_coeff @bond:13-15 harmonic 222.0 1.81
- bond_coeff @bond:13-16 harmonic 222.0 1.81
- bond_coeff @bond:13-18 harmonic 390.0 1.43
- bond_coeff @bond:13-19 harmonic 390.0 1.47
- bond_coeff @bond:13-20 harmonic 320.0 1.41
- bond_coeff @bond:13-21 harmonic 245.0 1.781
- bond_coeff @bond:13-22 harmonic 340.0 1.79
- bond_coeff @bond:13-24 harmonic 337.0 1.449
- bond_coeff @bond:13-25 harmonic 340.0 0.3
- bond_coeff @bond:13-44 harmonic 382.0 1.448
- bond_coeff @bond:13-46 harmonic 340.0 1.09
- bond_coeff @bond:13-47 harmonic 317.0 1.51
- bond_coeff @bond:13-48 harmonic 317.0 1.51
- bond_coeff @bond:13-50 harmonic 317.0 1.51
- bond_coeff @bond:13-51 harmonic 268.0 1.529
- bond_coeff @bond:13-53 harmonic 367.0 1.471
- bond_coeff @bond:13-55 harmonic 337.0 1.463
- bond_coeff @bond:13-56 harmonic 337.0 1.449
- bond_coeff @bond:13-57 harmonic 337.0 1.475
- bond_coeff @bond:13-60 harmonic 317.0 1.51
- bond_coeff @bond:13-64 harmonic 212.0 1.843
- bond_coeff @bond:13-65 harmonic 245.0 1.945
- bond_coeff @bond:13-66 harmonic 200.0 2.19
- bond_coeff @bond:13-79 harmonic 340.0 1.77
- bond_coeff @bond:13-80 harmonic 317.0 1.495
- bond_coeff @bond:13-83 harmonic 317.0 1.504
- bond_coeff @bond:13-84 harmonic 317.0 1.504
- bond_coeff @bond:13-85 harmonic 317.0 1.504
- bond_coeff @bond:13-87 harmonic 317.0 1.495
- bond_coeff @bond:13-90 harmonic 337.0 1.449
- bond_coeff @bond:13-91 harmonic 280.0 1.51
- bond_coeff @bond:13-95 harmonic 532.8 1.46
- bond_coeff @bond:13-101 harmonic 382.0 1.448
- bond_coeff @bond:13-102 harmonic 375.0 1.49
- bond_coeff @bond:13-104 harmonic 212.0 1.82
- bond_coeff @bond:13-105 harmonic 337.0 1.475
- bond_coeff @bond:13-107 harmonic 337.0 1.449
- bond_coeff @bond:13-108 harmonic 187.0 1.86
- bond_coeff @bond:13-109 harmonic 317.0 1.51
- bond_coeff @bond:14-14 harmonic 530.0 1.34
- bond_coeff @bond:15-17 harmonic 274.0 1.336
- bond_coeff @bond:15-48 harmonic 250.0 1.74
- bond_coeff @bond:16-16 harmonic 166.0 2.038
- bond_coeff @bond:16-19 harmonic 300.0 1.685
- bond_coeff @bond:16-24 harmonic 250.0 1.73
- bond_coeff @bond:16-25 harmonic 340.0 0.5
- bond_coeff @bond:16-47 harmonic 250.0 1.76
- bond_coeff @bond:16-48 harmonic 250.0 1.76
- bond_coeff @bond:16-61 harmonic 250.0 1.73
- bond_coeff @bond:16-82 harmonic 250.0 1.76
- bond_coeff @bond:16-84 harmonic 250.0 1.74
- bond_coeff @bond:16-91 harmonic 222.0 1.81
- bond_coeff @bond:16-108 harmonic 144.0 2.15
- bond_coeff @bond:17-25 harmonic 340.0 0.1
- bond_coeff @bond:18-18 harmonic 550.0 1.12
- bond_coeff @bond:18-19 harmonic 650.0 1.157
- bond_coeff @bond:18-48 harmonic 400.0 1.41
- bond_coeff @bond:18-56 harmonic 550.0 1.24
- bond_coeff @bond:19-19 harmonic 1150.0 1.21
- bond_coeff @bond:19-21 harmonic 330.0 1.637
- bond_coeff @bond:19-46 harmonic 420.0 1.08
- bond_coeff @bond:19-47 harmonic 400.0 1.426
- bond_coeff @bond:19-48 harmonic 400.0 1.451
- bond_coeff @bond:19-50 harmonic 400.0 1.426
- bond_coeff @bond:19-65 harmonic 330.0 1.784
- bond_coeff @bond:19-88 harmonic 400.0 1.451
- bond_coeff @bond:19-91 harmonic 400.0 1.451
- bond_coeff @bond:20-20 harmonic 250.0 1.47
- bond_coeff @bond:20-21 harmonic 200.0 1.69
- bond_coeff @bond:20-24 harmonic 320.0 1.45
- bond_coeff @bond:20-25 harmonic 340.0 0.3
- bond_coeff @bond:20-44 harmonic 320.0 1.45
- bond_coeff @bond:20-47 harmonic 450.0 1.37
- bond_coeff @bond:20-48 harmonic 450.0 1.364
- bond_coeff @bond:20-51 harmonic 320.0 1.38
- bond_coeff @bond:20-60 harmonic 340.0 1.36
- bond_coeff @bond:20-61 harmonic 462.0 1.399
- bond_coeff @bond:20-64 harmonic 230.0 1.61
- bond_coeff @bond:20-82 harmonic 462.0 1.357
- bond_coeff @bond:20-84 harmonic 340.0 1.36
- bond_coeff @bond:20-108 harmonic 374.0 1.64
- bond_coeff @bond:21-25 harmonic 300.0 0.3
- bond_coeff @bond:21-47 harmonic 300.0 1.725
- bond_coeff @bond:21-48 harmonic 300.0 1.725
- bond_coeff @bond:21-82 harmonic 300.0 1.725
- bond_coeff @bond:21-83 harmonic 300.0 1.725
- bond_coeff @bond:21-84 harmonic 300.0 1.725
- bond_coeff @bond:21-87 harmonic 300.0 1.725
- bond_coeff @bond:21-88 harmonic 300.0 1.725
- bond_coeff @bond:21-108 harmonic 223.0 2.02
- bond_coeff @bond:22-23 harmonic 700.0 1.53
- bond_coeff @bond:22-25 harmonic 340.0 0.5
- bond_coeff @bond:23-25 harmonic 340.0 0.3
- bond_coeff @bond:23-79 harmonic 700.0 1.44
- bond_coeff @bond:24-25 harmonic 367.0 0.3
- bond_coeff @bond:24-45 harmonic 434.0 1.01
- bond_coeff @bond:24-48 harmonic 427.0 1.381
- bond_coeff @bond:24-59 harmonic 427.0 1.381
- bond_coeff @bond:24-79 harmonic 434.0 1.67
- bond_coeff @bond:24-84 harmonic 427.0 1.381
- bond_coeff @bond:24-88 harmonic 427.0 1.381
- bond_coeff @bond:24-91 harmonic 337.0 1.449
- bond_coeff @bond:24-103 harmonic 500.0 1.27
- bond_coeff @bond:24-106 harmonic 40.0 2.05
- bond_coeff @bond:25-25 harmonic 340.0 0.3
- bond_coeff @bond:25-44 harmonic 340.0 0.3
- bond_coeff @bond:25-45 harmonic 340.0 0.1
- bond_coeff @bond:25-46 harmonic 340.0 0.3
- bond_coeff @bond:25-47 harmonic 340.0 0.3
- bond_coeff @bond:25-48 harmonic 367.0 0.3
- bond_coeff @bond:25-49 harmonic 340.0 0.3
- bond_coeff @bond:25-53 harmonic 340.0 0.3
- bond_coeff @bond:25-56 harmonic 367.0 0.3
- bond_coeff @bond:25-61 harmonic 367.0 0.3
- bond_coeff @bond:25-65 harmonic 300.0 0.3
- bond_coeff @bond:25-103 harmonic 340.0 0.1
- bond_coeff @bond:31-32 harmonic 600.0 0.9572
- bond_coeff @bond:31-33 harmonic 900.0 0.15
- bond_coeff @bond:31-106 harmonic 40.0 2.05
- bond_coeff @bond:34-35 harmonic 529.6 0.9572
- bond_coeff @bond:36-37 harmonic 600.0 0.9572
- bond_coeff @bond:36-38 harmonic 900.0 0.175
- bond_coeff @bond:39-40 harmonic 600.0 0.9572
- bond_coeff @bond:39-41 harmonic 900.0 0.7
- bond_coeff @bond:42-43 harmonic 600.0 1.0
- bond_coeff @bond:44-44 harmonic 350.0 1.445
- bond_coeff @bond:44-45 harmonic 434.0 1.01
- bond_coeff @bond:44-48 harmonic 481.0 1.34
- bond_coeff @bond:44-79 harmonic 340.0 1.77
- bond_coeff @bond:44-91 harmonic 382.0 1.448
- bond_coeff @bond:44-108 harmonic 266.0 1.74
- bond_coeff @bond:45-53 harmonic 434.0 1.01
- bond_coeff @bond:45-55 harmonic 434.0 1.01
- bond_coeff @bond:45-56 harmonic 434.0 1.01
- bond_coeff @bond:45-57 harmonic 434.0 1.01
- bond_coeff @bond:45-101 harmonic 434.0 1.01
- bond_coeff @bond:45-105 harmonic 434.0 1.01
- bond_coeff @bond:45-108 harmonic 166.0 1.48
- bond_coeff @bond:46-47 harmonic 340.0 1.08
- bond_coeff @bond:46-50 harmonic 340.0 1.08
- bond_coeff @bond:46-51 harmonic 340.0 1.09
- bond_coeff @bond:46-80 harmonic 340.0 1.08
- bond_coeff @bond:46-91 harmonic 340.0 1.088
- bond_coeff @bond:46-95 harmonic 532.8 1.084
- bond_coeff @bond:46-108 harmonic 166.0 1.48
- bond_coeff @bond:46-109 harmonic 340.0 1.08
- bond_coeff @bond:47-47 harmonic 549.0 1.34
- bond_coeff @bond:47-48 harmonic 427.0 1.433
- bond_coeff @bond:47-50 harmonic 549.0 1.34
- bond_coeff @bond:47-57 harmonic 448.0 1.365
- bond_coeff @bond:47-58 harmonic 367.0 1.08
- bond_coeff @bond:47-65 harmonic 300.0 1.9
- bond_coeff @bond:47-66 harmonic 250.0 2.08
- bond_coeff @bond:47-86 harmonic 385.0 1.46
- bond_coeff @bond:47-91 harmonic 317.0 1.51
- bond_coeff @bond:47-105 harmonic 448.0 1.365
- bond_coeff @bond:47-110 harmonic 700.0 1.305
- bond_coeff @bond:48-48 harmonic 469.0 1.4
- bond_coeff @bond:48-49 harmonic 367.0 1.08
- bond_coeff @bond:48-50 harmonic 427.0 1.433
- bond_coeff @bond:48-53 harmonic 400.0 1.45
- bond_coeff @bond:48-55 harmonic 481.0 1.34
- bond_coeff @bond:48-56 harmonic 483.0 1.339
- bond_coeff @bond:48-57 harmonic 427.0 1.381
- bond_coeff @bond:48-60 harmonic 469.0 1.404
- bond_coeff @bond:48-61 harmonic 414.0 1.391
- bond_coeff @bond:48-64 harmonic 220.0 1.78
- bond_coeff @bond:48-65 harmonic 300.0 1.87
- bond_coeff @bond:48-66 harmonic 250.0 2.08
- bond_coeff @bond:48-79 harmonic 340.0 1.77
- bond_coeff @bond:48-81 harmonic 469.0 1.4
- bond_coeff @bond:48-84 harmonic 546.0 1.367
- bond_coeff @bond:48-86 harmonic 469.0 1.4
- bond_coeff @bond:48-88 harmonic 469.0 1.421
- bond_coeff @bond:48-91 harmonic 317.0 1.49
- bond_coeff @bond:48-101 harmonic 382.0 1.385
- bond_coeff @bond:48-102 harmonic 400.0 1.46
- bond_coeff @bond:48-109 harmonic 427.0 1.433
- bond_coeff @bond:49-59 harmonic 367.0 1.08
- bond_coeff @bond:49-62 harmonic 340.0 1.08
- bond_coeff @bond:49-82 harmonic 367.0 1.08
- bond_coeff @bond:49-83 harmonic 367.0 1.08
- bond_coeff @bond:49-84 harmonic 367.0 1.08
- bond_coeff @bond:49-85 harmonic 367.0 1.08
- bond_coeff @bond:49-87 harmonic 367.0 1.08
- bond_coeff @bond:49-88 harmonic 367.0 1.08
- bond_coeff @bond:50-50 harmonic 385.0 1.46
- bond_coeff @bond:50-56 harmonic 457.0 1.29
- bond_coeff @bond:50-84 harmonic 549.0 1.365
- bond_coeff @bond:50-109 harmonic 385.0 1.46
- bond_coeff @bond:51-105 harmonic 337.0 1.475
- bond_coeff @bond:52-64 harmonic 525.0 1.48
- bond_coeff @bond:53-54 harmonic 434.0 1.01
- bond_coeff @bond:54-55 harmonic 434.0 1.01
- bond_coeff @bond:55-59 harmonic 481.0 1.34
- bond_coeff @bond:55-82 harmonic 481.0 1.34
- bond_coeff @bond:56-56 harmonic 500.0 1.32
- bond_coeff @bond:56-59 harmonic 502.0 1.324
- bond_coeff @bond:56-60 harmonic 461.0 1.354
- bond_coeff @bond:56-82 harmonic 461.0 1.354
- bond_coeff @bond:56-86 harmonic 483.0 1.339
- bond_coeff @bond:56-103 harmonic 550.0 1.21
- bond_coeff @bond:56-109 harmonic 457.0 1.29
- bond_coeff @bond:57-60 harmonic 436.0 1.374
- bond_coeff @bond:57-61 harmonic 400.0 1.349
- bond_coeff @bond:57-62 harmonic 440.0 1.371
- bond_coeff @bond:57-81 harmonic 428.0 1.38
- bond_coeff @bond:57-82 harmonic 477.0 1.343
- bond_coeff @bond:57-84 harmonic 427.0 1.381
- bond_coeff @bond:57-85 harmonic 427.0 1.381
- bond_coeff @bond:57-86 harmonic 385.0 1.44
- bond_coeff @bond:58-83 harmonic 367.0 1.08
- bond_coeff @bond:58-84 harmonic 367.0 1.08
- bond_coeff @bond:59-63 harmonic 367.0 1.08
- bond_coeff @bond:60-60 harmonic 520.0 1.37
- bond_coeff @bond:60-61 harmonic 414.0 1.391
- bond_coeff @bond:60-80 harmonic 388.0 1.459
- bond_coeff @bond:60-81 harmonic 447.0 1.419
- bond_coeff @bond:60-87 harmonic 469.0 1.424
- bond_coeff @bond:60-105 harmonic 436.0 1.374
- bond_coeff @bond:61-61 harmonic 400.0 1.28
- bond_coeff @bond:61-62 harmonic 529.0 1.304
- bond_coeff @bond:61-82 harmonic 488.0 1.335
- bond_coeff @bond:61-83 harmonic 410.0 1.394
- bond_coeff @bond:61-84 harmonic 410.0 1.394
- bond_coeff @bond:61-88 harmonic 410.0 1.32
- bond_coeff @bond:62-63 harmonic 367.0 1.08
- bond_coeff @bond:62-105 harmonic 440.0 1.371
- bond_coeff @bond:63-82 harmonic 367.0 1.08
- bond_coeff @bond:64-108 harmonic 108.0 2.25
- bond_coeff @bond:65-82 harmonic 300.0 1.87
- bond_coeff @bond:65-83 harmonic 300.0 1.87
- bond_coeff @bond:65-84 harmonic 300.0 1.87
- bond_coeff @bond:65-87 harmonic 300.0 1.87
- bond_coeff @bond:65-88 harmonic 300.0 1.87
- bond_coeff @bond:65-108 harmonic 151.0 2.19
- bond_coeff @bond:66-82 harmonic 250.0 2.08
- bond_coeff @bond:66-83 harmonic 250.0 2.08
- bond_coeff @bond:66-84 harmonic 250.0 2.08
- bond_coeff @bond:66-87 harmonic 250.0 2.08
- bond_coeff @bond:66-88 harmonic 250.0 2.08
- bond_coeff @bond:66-108 harmonic 108.0 2.44
- bond_coeff @bond:77-78 harmonic 500.0 1.8
- bond_coeff @bond:80-84 harmonic 546.0 1.352
- bond_coeff @bond:82-86 harmonic 385.0 1.46
- bond_coeff @bond:82-87 harmonic 520.0 1.37
- bond_coeff @bond:83-84 harmonic 520.0 1.37
- bond_coeff @bond:83-86 harmonic 385.0 1.46
- bond_coeff @bond:84-84 harmonic 512.0 1.375
- bond_coeff @bond:84-86 harmonic 385.0 1.46
- bond_coeff @bond:84-87 harmonic 546.0 1.367
- bond_coeff @bond:84-88 harmonic 520.0 1.37
- bond_coeff @bond:85-85 harmonic 520.0 1.37
- bond_coeff @bond:86-86 harmonic 385.0 1.46
- bond_coeff @bond:86-87 harmonic 385.0 1.46
- bond_coeff @bond:86-88 harmonic 385.0 1.46
- bond_coeff @bond:87-87 harmonic 469.0 1.424
- bond_coeff @bond:87-88 harmonic 469.0 1.424
- bond_coeff @bond:89-90 harmonic 490.0 1.335
- bond_coeff @bond:89-91 harmonic 317.0 1.522
- bond_coeff @bond:90-91 harmonic 337.0 1.449
- bond_coeff @bond:91-91 harmonic 260.0 1.52
- bond_coeff @bond:102-103 harmonic 550.0 1.225
- bond_coeff @bond:108-108 harmonic 94.0 2.32
- bond_coeff @bond:109-109 harmonic 549.0 1.345
- } #(end of bond_coeffs)
-
- write_once("Data Bonds By Type") {
- @bond:1-2 @atom:*_b1_a*_d*_i* @atom:*_b2_a*_d*_i*
- @bond:1-3 @atom:*_b1_a*_d*_i* @atom:*_b3_a*_d*_i*
- @bond:1-13 @atom:*_b1_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:1-19 @atom:*_b1_a*_d*_i* @atom:*_b19_a*_d*_i*
- @bond:1-25 @atom:*_b1_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:1-47 @atom:*_b1_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:1-48 @atom:*_b1_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:1-82 @atom:*_b1_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:1-83 @atom:*_b1_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:1-84 @atom:*_b1_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:1-87 @atom:*_b1_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:1-88 @atom:*_b1_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:1-108 @atom:*_b1_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:2-2 @atom:*_b2_a*_d*_i* @atom:*_b2_a*_d*_i*
- @bond:2-3 @atom:*_b2_a*_d*_i* @atom:*_b3_a*_d*_i*
- @bond:2-5 @atom:*_b2_a*_d*_i* @atom:*_b5_a*_d*_i*
- @bond:2-6 @atom:*_b2_a*_d*_i* @atom:*_b6_a*_d*_i*
- @bond:2-10 @atom:*_b2_a*_d*_i* @atom:*_b10_a*_d*_i*
- @bond:2-11 @atom:*_b2_a*_d*_i* @atom:*_b11_a*_d*_i*
- @bond:2-12 @atom:*_b2_a*_d*_i* @atom:*_b12_a*_d*_i*
- @bond:2-13 @atom:*_b2_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:2-14 @atom:*_b2_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:2-15 @atom:*_b2_a*_d*_i* @atom:*_b15_a*_d*_i*
- @bond:2-16 @atom:*_b2_a*_d*_i* @atom:*_b16_a*_d*_i*
- @bond:2-20 @atom:*_b2_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:2-24 @atom:*_b2_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:2-44 @atom:*_b2_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:2-48 @atom:*_b2_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:2-51 @atom:*_b2_a*_d*_i* @atom:*_b51_a*_d*_i*
- @bond:2-53 @atom:*_b2_a*_d*_i* @atom:*_b53_a*_d*_i*
- @bond:2-55 @atom:*_b2_a*_d*_i* @atom:*_b55_a*_d*_i*
- @bond:2-80 @atom:*_b2_a*_d*_i* @atom:*_b80_a*_d*_i*
- @bond:3-3 @atom:*_b3_a*_d*_i* @atom:*_b3_a*_d*_i*
- @bond:3-4 @atom:*_b3_a*_d*_i* @atom:*_b4_a*_d*_i*
- @bond:3-5 @atom:*_b3_a*_d*_i* @atom:*_b5_a*_d*_i*
- @bond:3-6 @atom:*_b3_a*_d*_i* @atom:*_b6_a*_d*_i*
- @bond:3-10 @atom:*_b3_a*_d*_i* @atom:*_b10_a*_d*_i*
- @bond:3-12 @atom:*_b3_a*_d*_i* @atom:*_b12_a*_d*_i*
- @bond:3-13 @atom:*_b3_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:3-19 @atom:*_b3_a*_d*_i* @atom:*_b19_a*_d*_i*
- @bond:3-20 @atom:*_b3_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:3-21 @atom:*_b3_a*_d*_i* @atom:*_b21_a*_d*_i*
- @bond:3-24 @atom:*_b3_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:3-44 @atom:*_b3_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:3-46 @atom:*_b3_a*_d*_i* @atom:*_b46_a*_d*_i*
- @bond:3-47 @atom:*_b3_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:3-48 @atom:*_b3_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:3-50 @atom:*_b3_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:3-52 @atom:*_b3_a*_d*_i* @atom:*_b52_a*_d*_i*
- @bond:3-56 @atom:*_b3_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:3-57 @atom:*_b3_a*_d*_i* @atom:*_b57_a*_d*_i*
- @bond:3-60 @atom:*_b3_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:3-65 @atom:*_b3_a*_d*_i* @atom:*_b65_a*_d*_i*
- @bond:3-84 @atom:*_b3_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:3-86 @atom:*_b3_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:3-105 @atom:*_b3_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:3-107 @atom:*_b3_a*_d*_i* @atom:*_b107_a*_d*_i*
- @bond:4-25 @atom:*_b4_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:4-64 @atom:*_b4_a*_d*_i* @atom:*_b64_a*_d*_i*
- @bond:4-89 @atom:*_b4_a*_d*_i* @atom:*_b89_a*_d*_i*
- @bond:4-110 @atom:*_b4_a*_d*_i* @atom:*_b110_a*_d*_i*
- @bond:5-6 @atom:*_b5_a*_d*_i* @atom:*_b6_a*_d*_i*
- @bond:5-7 @atom:*_b5_a*_d*_i* @atom:*_b7_a*_d*_i*
- @bond:5-10 @atom:*_b5_a*_d*_i* @atom:*_b10_a*_d*_i*
- @bond:5-13 @atom:*_b5_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:5-20 @atom:*_b5_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:5-24 @atom:*_b5_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:5-25 @atom:*_b5_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:5-44 @atom:*_b5_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:5-47 @atom:*_b5_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:5-48 @atom:*_b5_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:5-51 @atom:*_b5_a*_d*_i* @atom:*_b51_a*_d*_i*
- @bond:5-64 @atom:*_b5_a*_d*_i* @atom:*_b64_a*_d*_i*
- @bond:5-79 @atom:*_b5_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:5-106 @atom:*_b5_a*_d*_i* @atom:*_b106_a*_d*_i*
- @bond:5-108 @atom:*_b5_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:6-6 @atom:*_b6_a*_d*_i* @atom:*_b6_a*_d*_i*
- @bond:6-10 @atom:*_b6_a*_d*_i* @atom:*_b10_a*_d*_i*
- @bond:6-11 @atom:*_b6_a*_d*_i* @atom:*_b11_a*_d*_i*
- @bond:6-13 @atom:*_b6_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:6-14 @atom:*_b6_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:6-15 @atom:*_b6_a*_d*_i* @atom:*_b15_a*_d*_i*
- @bond:6-16 @atom:*_b6_a*_d*_i* @atom:*_b16_a*_d*_i*
- @bond:6-20 @atom:*_b6_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:6-24 @atom:*_b6_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:6-44 @atom:*_b6_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:6-47 @atom:*_b6_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:6-51 @atom:*_b6_a*_d*_i* @atom:*_b51_a*_d*_i*
- @bond:6-53 @atom:*_b6_a*_d*_i* @atom:*_b53_a*_d*_i*
- @bond:6-55 @atom:*_b6_a*_d*_i* @atom:*_b55_a*_d*_i*
- @bond:6-79 @atom:*_b6_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:6-105 @atom:*_b6_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:7-20 @atom:*_b7_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:7-25 @atom:*_b7_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:9-9 @atom:*_b9_a*_d*_i* @atom:*_b9_a*_d*_i*
- @bond:9-11 @atom:*_b9_a*_d*_i* @atom:*_b11_a*_d*_i*
- @bond:9-14 @atom:*_b9_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:10-10 @atom:*_b10_a*_d*_i* @atom:*_b10_a*_d*_i*
- @bond:10-11 @atom:*_b10_a*_d*_i* @atom:*_b11_a*_d*_i*
- @bond:10-14 @atom:*_b10_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:10-20 @atom:*_b10_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:10-24 @atom:*_b10_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:10-44 @atom:*_b10_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:10-105 @atom:*_b10_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:11-11 @atom:*_b11_a*_d*_i* @atom:*_b11_a*_d*_i*
- @bond:11-13 @atom:*_b11_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:11-14 @atom:*_b11_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:11-79 @atom:*_b11_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:12-12 @atom:*_b12_a*_d*_i* @atom:*_b12_a*_d*_i*
- @bond:12-48 @atom:*_b12_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:12-60 @atom:*_b12_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:12-81 @atom:*_b12_a*_d*_i* @atom:*_b81_a*_d*_i*
- @bond:13-13 @atom:*_b13_a*_d*_i* @atom:*_b13_a*_d*_i*
- @bond:13-14 @atom:*_b13_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:13-15 @atom:*_b13_a*_d*_i* @atom:*_b15_a*_d*_i*
- @bond:13-16 @atom:*_b13_a*_d*_i* @atom:*_b16_a*_d*_i*
- @bond:13-18 @atom:*_b13_a*_d*_i* @atom:*_b18_a*_d*_i*
- @bond:13-19 @atom:*_b13_a*_d*_i* @atom:*_b19_a*_d*_i*
- @bond:13-20 @atom:*_b13_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:13-21 @atom:*_b13_a*_d*_i* @atom:*_b21_a*_d*_i*
- @bond:13-22 @atom:*_b13_a*_d*_i* @atom:*_b22_a*_d*_i*
- @bond:13-24 @atom:*_b13_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:13-25 @atom:*_b13_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:13-44 @atom:*_b13_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:13-46 @atom:*_b13_a*_d*_i* @atom:*_b46_a*_d*_i*
- @bond:13-47 @atom:*_b13_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:13-48 @atom:*_b13_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:13-50 @atom:*_b13_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:13-51 @atom:*_b13_a*_d*_i* @atom:*_b51_a*_d*_i*
- @bond:13-53 @atom:*_b13_a*_d*_i* @atom:*_b53_a*_d*_i*
- @bond:13-55 @atom:*_b13_a*_d*_i* @atom:*_b55_a*_d*_i*
- @bond:13-56 @atom:*_b13_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:13-57 @atom:*_b13_a*_d*_i* @atom:*_b57_a*_d*_i*
- @bond:13-60 @atom:*_b13_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:13-64 @atom:*_b13_a*_d*_i* @atom:*_b64_a*_d*_i*
- @bond:13-65 @atom:*_b13_a*_d*_i* @atom:*_b65_a*_d*_i*
- @bond:13-66 @atom:*_b13_a*_d*_i* @atom:*_b66_a*_d*_i*
- @bond:13-79 @atom:*_b13_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:13-80 @atom:*_b13_a*_d*_i* @atom:*_b80_a*_d*_i*
- @bond:13-83 @atom:*_b13_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:13-84 @atom:*_b13_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:13-85 @atom:*_b13_a*_d*_i* @atom:*_b85_a*_d*_i*
- @bond:13-87 @atom:*_b13_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:13-90 @atom:*_b13_a*_d*_i* @atom:*_b90_a*_d*_i*
- @bond:13-91 @atom:*_b13_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:13-95 @atom:*_b13_a*_d*_i* @atom:*_b95_a*_d*_i*
- @bond:13-101 @atom:*_b13_a*_d*_i* @atom:*_b101_a*_d*_i*
- @bond:13-102 @atom:*_b13_a*_d*_i* @atom:*_b102_a*_d*_i*
- @bond:13-104 @atom:*_b13_a*_d*_i* @atom:*_b104_a*_d*_i*
- @bond:13-105 @atom:*_b13_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:13-107 @atom:*_b13_a*_d*_i* @atom:*_b107_a*_d*_i*
- @bond:13-108 @atom:*_b13_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:13-109 @atom:*_b13_a*_d*_i* @atom:*_b109_a*_d*_i*
- @bond:14-14 @atom:*_b14_a*_d*_i* @atom:*_b14_a*_d*_i*
- @bond:15-17 @atom:*_b15_a*_d*_i* @atom:*_b17_a*_d*_i*
- @bond:15-48 @atom:*_b15_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:16-16 @atom:*_b16_a*_d*_i* @atom:*_b16_a*_d*_i*
- @bond:16-19 @atom:*_b16_a*_d*_i* @atom:*_b19_a*_d*_i*
- @bond:16-24 @atom:*_b16_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:16-25 @atom:*_b16_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:16-47 @atom:*_b16_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:16-48 @atom:*_b16_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:16-61 @atom:*_b16_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:16-82 @atom:*_b16_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:16-84 @atom:*_b16_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:16-91 @atom:*_b16_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:16-108 @atom:*_b16_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:17-25 @atom:*_b17_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:18-18 @atom:*_b18_a*_d*_i* @atom:*_b18_a*_d*_i*
- @bond:18-19 @atom:*_b18_a*_d*_i* @atom:*_b19_a*_d*_i*
- @bond:18-48 @atom:*_b18_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:18-56 @atom:*_b18_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:19-19 @atom:*_b19_a*_d*_i* @atom:*_b19_a*_d*_i*
- @bond:19-21 @atom:*_b19_a*_d*_i* @atom:*_b21_a*_d*_i*
- @bond:19-46 @atom:*_b19_a*_d*_i* @atom:*_b46_a*_d*_i*
- @bond:19-47 @atom:*_b19_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:19-48 @atom:*_b19_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:19-50 @atom:*_b19_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:19-65 @atom:*_b19_a*_d*_i* @atom:*_b65_a*_d*_i*
- @bond:19-88 @atom:*_b19_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:19-91 @atom:*_b19_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:20-20 @atom:*_b20_a*_d*_i* @atom:*_b20_a*_d*_i*
- @bond:20-21 @atom:*_b20_a*_d*_i* @atom:*_b21_a*_d*_i*
- @bond:20-24 @atom:*_b20_a*_d*_i* @atom:*_b24_a*_d*_i*
- @bond:20-25 @atom:*_b20_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:20-44 @atom:*_b20_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:20-47 @atom:*_b20_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:20-48 @atom:*_b20_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:20-51 @atom:*_b20_a*_d*_i* @atom:*_b51_a*_d*_i*
- @bond:20-60 @atom:*_b20_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:20-61 @atom:*_b20_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:20-64 @atom:*_b20_a*_d*_i* @atom:*_b64_a*_d*_i*
- @bond:20-82 @atom:*_b20_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:20-84 @atom:*_b20_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:20-108 @atom:*_b20_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:21-25 @atom:*_b21_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:21-47 @atom:*_b21_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:21-48 @atom:*_b21_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:21-82 @atom:*_b21_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:21-83 @atom:*_b21_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:21-84 @atom:*_b21_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:21-87 @atom:*_b21_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:21-88 @atom:*_b21_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:21-108 @atom:*_b21_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:22-23 @atom:*_b22_a*_d*_i* @atom:*_b23_a*_d*_i*
- @bond:22-25 @atom:*_b22_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:23-25 @atom:*_b23_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:23-79 @atom:*_b23_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:24-25 @atom:*_b24_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:24-45 @atom:*_b24_a*_d*_i* @atom:*_b45_a*_d*_i*
- @bond:24-48 @atom:*_b24_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:24-59 @atom:*_b24_a*_d*_i* @atom:*_b59_a*_d*_i*
- @bond:24-79 @atom:*_b24_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:24-84 @atom:*_b24_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:24-88 @atom:*_b24_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:24-91 @atom:*_b24_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:24-103 @atom:*_b24_a*_d*_i* @atom:*_b103_a*_d*_i*
- @bond:24-106 @atom:*_b24_a*_d*_i* @atom:*_b106_a*_d*_i*
- @bond:25-25 @atom:*_b25_a*_d*_i* @atom:*_b25_a*_d*_i*
- @bond:25-44 @atom:*_b25_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:25-45 @atom:*_b25_a*_d*_i* @atom:*_b45_a*_d*_i*
- @bond:25-46 @atom:*_b25_a*_d*_i* @atom:*_b46_a*_d*_i*
- @bond:25-47 @atom:*_b25_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:25-48 @atom:*_b25_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:25-49 @atom:*_b25_a*_d*_i* @atom:*_b49_a*_d*_i*
- @bond:25-53 @atom:*_b25_a*_d*_i* @atom:*_b53_a*_d*_i*
- @bond:25-56 @atom:*_b25_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:25-61 @atom:*_b25_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:25-65 @atom:*_b25_a*_d*_i* @atom:*_b65_a*_d*_i*
- @bond:25-103 @atom:*_b25_a*_d*_i* @atom:*_b103_a*_d*_i*
- @bond:31-32 @atom:*_b31_a*_d*_i* @atom:*_b32_a*_d*_i*
- @bond:31-33 @atom:*_b31_a*_d*_i* @atom:*_b33_a*_d*_i*
- @bond:31-106 @atom:*_b31_a*_d*_i* @atom:*_b106_a*_d*_i*
- @bond:34-35 @atom:*_b34_a*_d*_i* @atom:*_b35_a*_d*_i*
- @bond:36-37 @atom:*_b36_a*_d*_i* @atom:*_b37_a*_d*_i*
- @bond:36-38 @atom:*_b36_a*_d*_i* @atom:*_b38_a*_d*_i*
- @bond:39-40 @atom:*_b39_a*_d*_i* @atom:*_b40_a*_d*_i*
- @bond:39-41 @atom:*_b39_a*_d*_i* @atom:*_b41_a*_d*_i*
- @bond:42-43 @atom:*_b42_a*_d*_i* @atom:*_b43_a*_d*_i*
- @bond:44-44 @atom:*_b44_a*_d*_i* @atom:*_b44_a*_d*_i*
- @bond:44-45 @atom:*_b44_a*_d*_i* @atom:*_b45_a*_d*_i*
- @bond:44-48 @atom:*_b44_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:44-79 @atom:*_b44_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:44-91 @atom:*_b44_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:44-108 @atom:*_b44_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:45-53 @atom:*_b45_a*_d*_i* @atom:*_b53_a*_d*_i*
- @bond:45-55 @atom:*_b45_a*_d*_i* @atom:*_b55_a*_d*_i*
- @bond:45-56 @atom:*_b45_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:45-57 @atom:*_b45_a*_d*_i* @atom:*_b57_a*_d*_i*
- @bond:45-101 @atom:*_b45_a*_d*_i* @atom:*_b101_a*_d*_i*
- @bond:45-105 @atom:*_b45_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:45-108 @atom:*_b45_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:46-47 @atom:*_b46_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:46-50 @atom:*_b46_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:46-51 @atom:*_b46_a*_d*_i* @atom:*_b51_a*_d*_i*
- @bond:46-80 @atom:*_b46_a*_d*_i* @atom:*_b80_a*_d*_i*
- @bond:46-91 @atom:*_b46_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:46-95 @atom:*_b46_a*_d*_i* @atom:*_b95_a*_d*_i*
- @bond:46-108 @atom:*_b46_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:46-109 @atom:*_b46_a*_d*_i* @atom:*_b109_a*_d*_i*
- @bond:47-47 @atom:*_b47_a*_d*_i* @atom:*_b47_a*_d*_i*
- @bond:47-48 @atom:*_b47_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:47-50 @atom:*_b47_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:47-57 @atom:*_b47_a*_d*_i* @atom:*_b57_a*_d*_i*
- @bond:47-58 @atom:*_b47_a*_d*_i* @atom:*_b58_a*_d*_i*
- @bond:47-65 @atom:*_b47_a*_d*_i* @atom:*_b65_a*_d*_i*
- @bond:47-66 @atom:*_b47_a*_d*_i* @atom:*_b66_a*_d*_i*
- @bond:47-86 @atom:*_b47_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:47-91 @atom:*_b47_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:47-105 @atom:*_b47_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:47-110 @atom:*_b47_a*_d*_i* @atom:*_b110_a*_d*_i*
- @bond:48-48 @atom:*_b48_a*_d*_i* @atom:*_b48_a*_d*_i*
- @bond:48-49 @atom:*_b48_a*_d*_i* @atom:*_b49_a*_d*_i*
- @bond:48-50 @atom:*_b48_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:48-53 @atom:*_b48_a*_d*_i* @atom:*_b53_a*_d*_i*
- @bond:48-55 @atom:*_b48_a*_d*_i* @atom:*_b55_a*_d*_i*
- @bond:48-56 @atom:*_b48_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:48-57 @atom:*_b48_a*_d*_i* @atom:*_b57_a*_d*_i*
- @bond:48-60 @atom:*_b48_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:48-61 @atom:*_b48_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:48-64 @atom:*_b48_a*_d*_i* @atom:*_b64_a*_d*_i*
- @bond:48-65 @atom:*_b48_a*_d*_i* @atom:*_b65_a*_d*_i*
- @bond:48-66 @atom:*_b48_a*_d*_i* @atom:*_b66_a*_d*_i*
- @bond:48-79 @atom:*_b48_a*_d*_i* @atom:*_b79_a*_d*_i*
- @bond:48-81 @atom:*_b48_a*_d*_i* @atom:*_b81_a*_d*_i*
- @bond:48-84 @atom:*_b48_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:48-86 @atom:*_b48_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:48-88 @atom:*_b48_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:48-91 @atom:*_b48_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:48-101 @atom:*_b48_a*_d*_i* @atom:*_b101_a*_d*_i*
- @bond:48-102 @atom:*_b48_a*_d*_i* @atom:*_b102_a*_d*_i*
- @bond:48-109 @atom:*_b48_a*_d*_i* @atom:*_b109_a*_d*_i*
- @bond:49-59 @atom:*_b49_a*_d*_i* @atom:*_b59_a*_d*_i*
- @bond:49-62 @atom:*_b49_a*_d*_i* @atom:*_b62_a*_d*_i*
- @bond:49-82 @atom:*_b49_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:49-83 @atom:*_b49_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:49-84 @atom:*_b49_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:49-85 @atom:*_b49_a*_d*_i* @atom:*_b85_a*_d*_i*
- @bond:49-87 @atom:*_b49_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:49-88 @atom:*_b49_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:50-50 @atom:*_b50_a*_d*_i* @atom:*_b50_a*_d*_i*
- @bond:50-56 @atom:*_b50_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:50-84 @atom:*_b50_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:50-109 @atom:*_b50_a*_d*_i* @atom:*_b109_a*_d*_i*
- @bond:51-105 @atom:*_b51_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:52-64 @atom:*_b52_a*_d*_i* @atom:*_b64_a*_d*_i*
- @bond:53-54 @atom:*_b53_a*_d*_i* @atom:*_b54_a*_d*_i*
- @bond:54-55 @atom:*_b54_a*_d*_i* @atom:*_b55_a*_d*_i*
- @bond:55-59 @atom:*_b55_a*_d*_i* @atom:*_b59_a*_d*_i*
- @bond:55-82 @atom:*_b55_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:56-56 @atom:*_b56_a*_d*_i* @atom:*_b56_a*_d*_i*
- @bond:56-59 @atom:*_b56_a*_d*_i* @atom:*_b59_a*_d*_i*
- @bond:56-60 @atom:*_b56_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:56-82 @atom:*_b56_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:56-86 @atom:*_b56_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:56-103 @atom:*_b56_a*_d*_i* @atom:*_b103_a*_d*_i*
- @bond:56-109 @atom:*_b56_a*_d*_i* @atom:*_b109_a*_d*_i*
- @bond:57-60 @atom:*_b57_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:57-61 @atom:*_b57_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:57-62 @atom:*_b57_a*_d*_i* @atom:*_b62_a*_d*_i*
- @bond:57-81 @atom:*_b57_a*_d*_i* @atom:*_b81_a*_d*_i*
- @bond:57-82 @atom:*_b57_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:57-84 @atom:*_b57_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:57-85 @atom:*_b57_a*_d*_i* @atom:*_b85_a*_d*_i*
- @bond:57-86 @atom:*_b57_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:58-83 @atom:*_b58_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:58-84 @atom:*_b58_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:59-63 @atom:*_b59_a*_d*_i* @atom:*_b63_a*_d*_i*
- @bond:60-60 @atom:*_b60_a*_d*_i* @atom:*_b60_a*_d*_i*
- @bond:60-61 @atom:*_b60_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:60-80 @atom:*_b60_a*_d*_i* @atom:*_b80_a*_d*_i*
- @bond:60-81 @atom:*_b60_a*_d*_i* @atom:*_b81_a*_d*_i*
- @bond:60-87 @atom:*_b60_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:60-105 @atom:*_b60_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:61-61 @atom:*_b61_a*_d*_i* @atom:*_b61_a*_d*_i*
- @bond:61-62 @atom:*_b61_a*_d*_i* @atom:*_b62_a*_d*_i*
- @bond:61-82 @atom:*_b61_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:61-83 @atom:*_b61_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:61-84 @atom:*_b61_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:61-88 @atom:*_b61_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:62-63 @atom:*_b62_a*_d*_i* @atom:*_b63_a*_d*_i*
- @bond:62-105 @atom:*_b62_a*_d*_i* @atom:*_b105_a*_d*_i*
- @bond:63-82 @atom:*_b63_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:64-108 @atom:*_b64_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:65-82 @atom:*_b65_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:65-83 @atom:*_b65_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:65-84 @atom:*_b65_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:65-87 @atom:*_b65_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:65-88 @atom:*_b65_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:65-108 @atom:*_b65_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:66-82 @atom:*_b66_a*_d*_i* @atom:*_b82_a*_d*_i*
- @bond:66-83 @atom:*_b66_a*_d*_i* @atom:*_b83_a*_d*_i*
- @bond:66-84 @atom:*_b66_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:66-87 @atom:*_b66_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:66-88 @atom:*_b66_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:66-108 @atom:*_b66_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:77-78 @atom:*_b77_a*_d*_i* @atom:*_b78_a*_d*_i*
- @bond:80-84 @atom:*_b80_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:82-86 @atom:*_b82_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:82-87 @atom:*_b82_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:83-84 @atom:*_b83_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:83-86 @atom:*_b83_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:84-84 @atom:*_b84_a*_d*_i* @atom:*_b84_a*_d*_i*
- @bond:84-86 @atom:*_b84_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:84-87 @atom:*_b84_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:84-88 @atom:*_b84_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:85-85 @atom:*_b85_a*_d*_i* @atom:*_b85_a*_d*_i*
- @bond:86-86 @atom:*_b86_a*_d*_i* @atom:*_b86_a*_d*_i*
- @bond:86-87 @atom:*_b86_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:86-88 @atom:*_b86_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:87-87 @atom:*_b87_a*_d*_i* @atom:*_b87_a*_d*_i*
- @bond:87-88 @atom:*_b87_a*_d*_i* @atom:*_b88_a*_d*_i*
- @bond:89-90 @atom:*_b89_a*_d*_i* @atom:*_b90_a*_d*_i*
- @bond:89-91 @atom:*_b89_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:90-91 @atom:*_b90_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:91-91 @atom:*_b91_a*_d*_i* @atom:*_b91_a*_d*_i*
- @bond:102-103 @atom:*_b102_a*_d*_i* @atom:*_b103_a*_d*_i*
- @bond:108-108 @atom:*_b108_a*_d*_i* @atom:*_b108_a*_d*_i*
- @bond:109-109 @atom:*_b109_a*_d*_i* @atom:*_b109_a*_d*_i*
- } #(end of bonds by type)
-
-
- write_once("In Settings") {
- angle_coeff @angle:25-1-25 harmonic 33.0 109.47
- angle_coeff @angle:1-2-2 harmonic 50.0 109.5
- angle_coeff @angle:2-2-2 harmonic 63.0 112.4
- angle_coeff @angle:2-2-3 harmonic 63.0 112.4
- angle_coeff @angle:2-2-5 harmonic 80.0 109.5
- angle_coeff @angle:2-2-6 harmonic 63.0 112.4
- angle_coeff @angle:6-2-6 harmonic 63.0 112.4
- angle_coeff @angle:5-2-6 harmonic 80.0 109.5
- angle_coeff @angle:2-2-10 harmonic 63.0 112.4
- angle_coeff @angle:3-2-10 harmonic 63.0 112.4
- angle_coeff @angle:6-2-10 harmonic 63.0 112.4
- angle_coeff @angle:10-2-10 harmonic 63.0 112.4
- angle_coeff @angle:5-2-10 harmonic 80.0 109.5
- angle_coeff @angle:10-2-12 harmonic 63.0 114.0
- angle_coeff @angle:6-2-13 harmonic 63.0 112.4
- angle_coeff @angle:10-2-15 harmonic 50.0 108.6
- angle_coeff @angle:2-2-16 harmonic 50.0 114.7
- angle_coeff @angle:10-2-16 harmonic 50.0 114.7
- angle_coeff @angle:2-2-20 harmonic 80.0 109.5
- angle_coeff @angle:6-2-20 harmonic 80.0 109.5
- angle_coeff @angle:10-2-20 harmonic 80.0 109.5
- angle_coeff @angle:3-2-24 harmonic 80.0 110.3
- angle_coeff @angle:2-2-24 harmonic 80.0 111.2
- angle_coeff @angle:2-2-44 harmonic 56.2 109.47
- angle_coeff @angle:6-2-44 harmonic 56.2 109.47
- angle_coeff @angle:10-2-44 harmonic 56.2 109.47
- angle_coeff @angle:13-2-44 harmonic 56.2 109.47
- angle_coeff @angle:3-2-44 harmonic 80.0 111.2
- angle_coeff @angle:2-2-48 harmonic 63.0 112.4
- angle_coeff @angle:10-2-48 harmonic 63.0 114.0
- angle_coeff @angle:2-2-51 harmonic 63.0 112.4
- angle_coeff @angle:6-2-51 harmonic 63.0 112.4
- angle_coeff @angle:2-2-53 harmonic 80.0 111.2
- angle_coeff @angle:2-2-55 harmonic 80.0 111.2
- angle_coeff @angle:10-2-80 harmonic 63.0 115.6
- angle_coeff @angle:2-3-4 harmonic 80.0 120.4
- angle_coeff @angle:1-3-4 harmonic 80.0 121.0
- angle_coeff @angle:3-3-4 harmonic 80.0 121.4
- angle_coeff @angle:4-3-4 harmonic 80.0 126.0
- angle_coeff @angle:4-3-5 harmonic 80.0 121.0
- angle_coeff @angle:4-3-6 harmonic 80.0 120.4
- angle_coeff @angle:5-3-10 harmonic 70.0 115.0
- angle_coeff @angle:4-3-10 harmonic 80.0 120.4
- angle_coeff @angle:5-3-12 harmonic 70.0 120.0
- angle_coeff @angle:12-3-12 harmonic 85.0 120.0
- angle_coeff @angle:5-3-13 harmonic 70.0 108.0
- angle_coeff @angle:13-3-13 harmonic 70.0 116.0
- angle_coeff @angle:1-3-13 harmonic 80.0 111.0
- angle_coeff @angle:3-3-13 harmonic 80.0 117.2
- angle_coeff @angle:4-3-13 harmonic 80.0 120.4
- angle_coeff @angle:10-3-20 harmonic 81.0 111.4
- angle_coeff @angle:13-3-20 harmonic 81.0 111.4
- angle_coeff @angle:4-3-20 harmonic 83.0 123.4
- angle_coeff @angle:13-3-21 harmonic 75.0 109.0
- angle_coeff @angle:4-3-21 harmonic 75.0 119.0
- angle_coeff @angle:24-3-24 harmonic 70.0 114.2
- angle_coeff @angle:2-3-24 harmonic 70.0 116.6
- angle_coeff @angle:3-3-24 harmonic 70.0 116.6
- angle_coeff @angle:6-3-24 harmonic 70.0 116.6
- angle_coeff @angle:10-3-24 harmonic 70.0 116.6
- angle_coeff @angle:13-3-24 harmonic 70.0 116.6
- angle_coeff @angle:4-3-24 harmonic 80.0 122.9
- angle_coeff @angle:20-3-24 harmonic 81.0 111.4
- angle_coeff @angle:13-3-44 harmonic 70.0 116.0
- angle_coeff @angle:4-3-44 harmonic 80.0 120.4
- angle_coeff @angle:13-3-46 harmonic 35.0 115.0
- angle_coeff @angle:46-3-46 harmonic 35.0 115.0
- angle_coeff @angle:4-3-46 harmonic 35.0 123.0
- angle_coeff @angle:24-3-46 harmonic 40.0 114.0
- angle_coeff @angle:5-3-46 harmonic 40.0 115.0
- angle_coeff @angle:20-3-46 harmonic 40.0 115.0
- angle_coeff @angle:24-3-47 harmonic 70.0 115.5
- angle_coeff @angle:4-3-47 harmonic 80.0 125.3
- angle_coeff @angle:46-3-48 harmonic 35.0 115.0
- angle_coeff @angle:24-3-48 harmonic 70.0 115.5
- angle_coeff @angle:13-3-48 harmonic 70.0 116.0
- angle_coeff @angle:5-3-48 harmonic 70.0 120.0
- angle_coeff @angle:4-3-48 harmonic 80.0 120.4
- angle_coeff @angle:20-3-48 harmonic 81.0 111.4
- angle_coeff @angle:48-3-48 harmonic 85.0 120.0
- angle_coeff @angle:13-3-50 harmonic 70.0 116.0
- angle_coeff @angle:46-3-50 harmonic 80.0 116.0
- angle_coeff @angle:4-3-50 harmonic 80.0 124.0
- angle_coeff @angle:10-3-52 harmonic 65.0 117.0
- angle_coeff @angle:2-3-52 harmonic 70.0 117.0
- angle_coeff @angle:6-3-52 harmonic 70.0 117.0
- angle_coeff @angle:13-3-52 harmonic 70.0 117.0
- angle_coeff @angle:48-3-52 harmonic 70.0 117.0
- angle_coeff @angle:4-3-52 harmonic 80.0 126.0
- angle_coeff @angle:52-3-52 harmonic 80.0 126.0
- angle_coeff @angle:46-3-56 harmonic 35.0 122.0
- angle_coeff @angle:4-3-56 harmonic 80.0 122.5
- angle_coeff @angle:47-3-57 harmonic 70.0 114.1
- angle_coeff @angle:56-3-57 harmonic 70.0 118.6
- angle_coeff @angle:57-3-57 harmonic 70.0 118.6
- angle_coeff @angle:4-3-57 harmonic 80.0 120.6
- angle_coeff @angle:24-3-60 harmonic 70.0 111.3
- angle_coeff @angle:57-3-60 harmonic 70.0 111.3
- angle_coeff @angle:4-3-60 harmonic 80.0 128.8
- angle_coeff @angle:13-3-65 harmonic 75.0 109.0
- angle_coeff @angle:4-3-65 harmonic 75.0 119.0
- angle_coeff @angle:44-3-84 harmonic 70.0 116.0
- angle_coeff @angle:4-3-84 harmonic 80.0 120.4
- angle_coeff @angle:4-3-87 harmonic 80.0 128.2
- angle_coeff @angle:57-3-105 harmonic 70.0 115.4
- angle_coeff @angle:56-3-105 harmonic 70.0 118.6
- angle_coeff @angle:4-3-105 harmonic 80.0 120.9
- angle_coeff @angle:13-3-107 harmonic 70.0 116.6
- angle_coeff @angle:4-3-107 harmonic 80.0 122.9
- angle_coeff @angle:25-4-25 harmonic 10.0 117.0
- angle_coeff @angle:3-4-25 harmonic 35.0 113.0
- angle_coeff @angle:3-5-7 harmonic 35.0 113.0
- angle_coeff @angle:2-5-7 harmonic 55.0 108.5
- angle_coeff @angle:6-5-7 harmonic 55.0 108.5
- angle_coeff @angle:7-5-10 harmonic 55.0 108.5
- angle_coeff @angle:7-5-13 harmonic 55.0 108.5
- angle_coeff @angle:7-5-24 harmonic 49.0 105.4
- angle_coeff @angle:25-5-25 harmonic 5.0 109.47
- angle_coeff @angle:7-5-25 harmonic 10.0 109.47
- angle_coeff @angle:13-5-25 harmonic 10.0 109.47
- angle_coeff @angle:7-5-47 harmonic 35.0 109.0
- angle_coeff @angle:25-5-48 harmonic 10.0 109.47
- angle_coeff @angle:7-5-48 harmonic 35.0 113.0
- angle_coeff @angle:7-5-51 harmonic 55.0 108.5
- angle_coeff @angle:7-5-64 harmonic 55.0 108.5
- angle_coeff @angle:13-5-64 harmonic 100.0 120.5
- angle_coeff @angle:7-5-79 harmonic 74.0 110.0
- angle_coeff @angle:7-5-106 harmonic 100.0 126.0
- angle_coeff @angle:5-7-25 harmonic 10.0 109.47
- angle_coeff @angle:25-7-25 harmonic 33.0 109.47
- angle_coeff @angle:2-10-2 harmonic 63.0 112.4
- angle_coeff @angle:2-10-3 harmonic 63.0 111.1
- angle_coeff @angle:2-10-5 harmonic 80.0 109.5
- angle_coeff @angle:3-10-6 harmonic 63.0 111.1
- angle_coeff @angle:6-10-6 harmonic 63.0 111.5
- angle_coeff @angle:2-10-6 harmonic 63.0 112.4
- angle_coeff @angle:5-10-6 harmonic 80.0 109.5
- angle_coeff @angle:3-10-10 harmonic 63.0 111.1
- angle_coeff @angle:2-10-10 harmonic 63.0 111.5
- angle_coeff @angle:6-10-10 harmonic 63.0 111.5
- angle_coeff @angle:10-10-10 harmonic 63.0 111.5
- angle_coeff @angle:5-10-10 harmonic 80.0 109.5
- angle_coeff @angle:2-10-20 harmonic 80.0 109.5
- angle_coeff @angle:6-10-20 harmonic 80.0 109.5
- angle_coeff @angle:10-10-20 harmonic 80.0 109.5
- angle_coeff @angle:3-10-24 harmonic 63.0 110.1
- angle_coeff @angle:6-10-24 harmonic 80.0 109.5
- angle_coeff @angle:2-10-24 harmonic 80.0 109.7
- angle_coeff @angle:10-10-24 harmonic 80.0 109.7
- angle_coeff @angle:2-10-44 harmonic 56.2 109.47
- angle_coeff @angle:6-10-44 harmonic 56.2 109.47
- angle_coeff @angle:10-10-44 harmonic 56.2 109.47
- angle_coeff @angle:13-10-44 harmonic 56.2 109.47
- angle_coeff @angle:3-10-44 harmonic 80.0 109.7
- angle_coeff @angle:2-10-48 harmonic 63.0 112.4
- angle_coeff @angle:20-10-48 harmonic 80.0 109.5
- angle_coeff @angle:2-10-105 harmonic 80.0 109.5
- angle_coeff @angle:10-10-105 harmonic 80.0 109.5
- angle_coeff @angle:20-10-105 harmonic 80.0 109.5
- angle_coeff @angle:2-11-2 harmonic 70.0 124.0
- angle_coeff @angle:2-11-6 harmonic 70.0 124.0
- angle_coeff @angle:6-11-6 harmonic 70.0 124.0
- angle_coeff @angle:2-11-9 harmonic 70.0 118.0
- angle_coeff @angle:6-11-9 harmonic 70.0 118.0
- angle_coeff @angle:9-11-10 harmonic 70.0 118.0
- angle_coeff @angle:2-11-10 harmonic 70.0 124.0
- angle_coeff @angle:6-11-10 harmonic 70.0 124.0
- angle_coeff @angle:10-11-10 harmonic 70.0 124.0
- angle_coeff @angle:2-11-11 harmonic 70.0 118.0
- angle_coeff @angle:6-11-11 harmonic 70.0 118.0
- angle_coeff @angle:9-11-11 harmonic 70.0 118.0
- angle_coeff @angle:10-11-11 harmonic 70.0 118.0
- angle_coeff @angle:11-11-11 harmonic 70.0 118.0
- angle_coeff @angle:9-11-13 harmonic 70.0 118.0
- angle_coeff @angle:11-11-13 harmonic 70.0 118.0
- angle_coeff @angle:2-11-13 harmonic 70.0 124.0
- angle_coeff @angle:6-11-13 harmonic 70.0 124.0
- angle_coeff @angle:10-11-13 harmonic 70.0 124.0
- angle_coeff @angle:13-11-13 harmonic 70.0 124.0
- angle_coeff @angle:9-11-14 harmonic 70.0 118.0
- angle_coeff @angle:11-11-14 harmonic 70.0 118.0
- angle_coeff @angle:9-11-79 harmonic 70.0 118.0
- angle_coeff @angle:2-12-12 harmonic 70.0 120.0
- angle_coeff @angle:3-12-12 harmonic 85.0 120.0
- angle_coeff @angle:12-12-12 harmonic 85.0 120.0
- angle_coeff @angle:12-12-48 harmonic 85.0 120.0
- angle_coeff @angle:12-12-60 harmonic 85.0 120.0
- angle_coeff @angle:12-12-81 harmonic 85.0 120.0
- angle_coeff @angle:1-13-1 harmonic 77.0 109.1
- angle_coeff @angle:2-13-2 harmonic 40.0 109.5
- angle_coeff @angle:1-13-3 harmonic 50.0 109.5
- angle_coeff @angle:2-13-3 harmonic 63.0 111.1
- angle_coeff @angle:3-13-3 harmonic 63.0 111.1
- angle_coeff @angle:2-13-6 harmonic 40.0 109.5
- angle_coeff @angle:6-13-6 harmonic 40.0 109.5
- angle_coeff @angle:3-13-6 harmonic 63.0 109.5
- angle_coeff @angle:1-13-13 harmonic 50.0 109.5
- angle_coeff @angle:5-13-13 harmonic 50.0 109.5
- angle_coeff @angle:13-13-13 harmonic 58.35 112.7
- angle_coeff @angle:3-13-13 harmonic 63.0 111.1
- angle_coeff @angle:13-13-15 harmonic 50.0 108.6
- angle_coeff @angle:13-13-16 harmonic 50.0 114.7
- angle_coeff @angle:13-13-19 harmonic 58.35 112.7
- angle_coeff @angle:3-13-20 harmonic 50.0 109.5
- angle_coeff @angle:13-13-20 harmonic 50.0 109.5
- angle_coeff @angle:3-13-21 harmonic 69.0 109.8
- angle_coeff @angle:13-13-21 harmonic 69.0 109.8
- angle_coeff @angle:21-13-21 harmonic 78.0 111.7
- angle_coeff @angle:13-13-22 harmonic 50.0 108.6
- angle_coeff @angle:20-13-24 harmonic 50.0 109.5
- angle_coeff @angle:3-13-24 harmonic 63.0 110.1
- angle_coeff @angle:2-13-24 harmonic 80.0 109.7
- angle_coeff @angle:13-13-24 harmonic 80.0 109.7
- angle_coeff @angle:16-13-44 harmonic 50.0 114.7
- angle_coeff @angle:2-13-44 harmonic 56.2 109.47
- angle_coeff @angle:6-13-44 harmonic 56.2 109.47
- angle_coeff @angle:10-13-44 harmonic 56.2 109.47
- angle_coeff @angle:13-13-44 harmonic 56.2 109.47
- angle_coeff @angle:3-13-44 harmonic 80.0 111.2
- angle_coeff @angle:46-13-46 harmonic 33.0 107.8
- angle_coeff @angle:18-13-46 harmonic 35.0 108.5
- angle_coeff @angle:19-13-46 harmonic 35.0 108.5
- angle_coeff @angle:2-13-46 harmonic 35.0 109.5
- angle_coeff @angle:3-13-46 harmonic 35.0 109.5
- angle_coeff @angle:5-13-46 harmonic 35.0 109.5
- angle_coeff @angle:15-13-46 harmonic 35.0 109.5
- angle_coeff @angle:16-13-46 harmonic 35.0 109.5
- angle_coeff @angle:20-13-46 harmonic 35.0 109.5
- angle_coeff @angle:22-13-46 harmonic 35.0 109.5
- angle_coeff @angle:24-13-46 harmonic 35.0 109.5
- angle_coeff @angle:44-13-46 harmonic 35.0 109.5
- angle_coeff @angle:13-13-46 harmonic 37.5 110.7
- angle_coeff @angle:1-13-46 harmonic 40.0 107.0
- angle_coeff @angle:21-13-46 harmonic 51.0 107.6
- angle_coeff @angle:46-13-47 harmonic 35.0 109.5
- angle_coeff @angle:1-13-47 harmonic 50.0 109.5
- angle_coeff @angle:13-13-47 harmonic 63.0 111.1
- angle_coeff @angle:47-13-47 harmonic 63.0 112.4
- angle_coeff @angle:46-13-48 harmonic 35.0 109.5
- angle_coeff @angle:47-13-48 harmonic 40.0 109.5
- angle_coeff @angle:48-13-48 harmonic 40.0 109.5
- angle_coeff @angle:1-13-48 harmonic 50.0 109.5
- angle_coeff @angle:5-13-48 harmonic 50.0 109.5
- angle_coeff @angle:20-13-48 harmonic 50.0 109.5
- angle_coeff @angle:16-13-48 harmonic 50.0 114.7
- angle_coeff @angle:3-13-48 harmonic 63.0 112.0
- angle_coeff @angle:2-13-48 harmonic 63.0 114.0
- angle_coeff @angle:13-13-48 harmonic 63.0 114.0
- angle_coeff @angle:44-13-48 harmonic 80.0 111.2
- angle_coeff @angle:46-13-50 harmonic 35.0 109.5
- angle_coeff @angle:46-13-51 harmonic 37.5 110.7
- angle_coeff @angle:5-13-51 harmonic 50.0 109.5
- angle_coeff @angle:13-13-51 harmonic 58.35 112.7
- angle_coeff @angle:46-13-53 harmonic 35.0 109.5
- angle_coeff @angle:3-13-53 harmonic 80.0 111.2
- angle_coeff @angle:13-13-53 harmonic 80.0 111.2
- angle_coeff @angle:46-13-55 harmonic 35.0 109.5
- angle_coeff @angle:13-13-55 harmonic 80.0 111.2
- angle_coeff @angle:46-13-56 harmonic 35.0 109.5
- angle_coeff @angle:3-13-56 harmonic 63.0 110.1
- angle_coeff @angle:13-13-56 harmonic 65.0 109.0
- angle_coeff @angle:46-13-57 harmonic 35.0 109.5
- angle_coeff @angle:48-13-57 harmonic 80.0 111.2
- angle_coeff @angle:46-13-60 harmonic 35.0 109.5
- angle_coeff @angle:13-13-60 harmonic 63.0 114.0
- angle_coeff @angle:46-13-64 harmonic 41.0 109.5
- angle_coeff @angle:13-13-64 harmonic 43.0 109.5
- angle_coeff @angle:48-13-64 harmonic 43.0 109.5
- angle_coeff @angle:46-13-65 harmonic 51.0 107.6
- angle_coeff @angle:3-13-65 harmonic 69.0 109.8
- angle_coeff @angle:13-13-65 harmonic 69.0 110.0
- angle_coeff @angle:48-13-65 harmonic 69.0 110.0
- angle_coeff @angle:65-13-65 harmonic 78.0 111.7
- angle_coeff @angle:46-13-66 harmonic 75.0 111.0
- angle_coeff @angle:13-13-66 harmonic 75.0 112.0
- angle_coeff @angle:46-13-79 harmonic 35.0 109.5
- angle_coeff @angle:13-13-79 harmonic 50.0 108.6
- angle_coeff @angle:1-13-79 harmonic 50.0 109.5
- angle_coeff @angle:46-13-80 harmonic 35.0 109.5
- angle_coeff @angle:13-13-80 harmonic 63.0 115.6
- angle_coeff @angle:46-13-83 harmonic 35.0 109.5
- angle_coeff @angle:13-13-83 harmonic 63.0 114.0
- angle_coeff @angle:46-13-84 harmonic 35.0 109.5
- angle_coeff @angle:16-13-84 harmonic 50.0 114.7
- angle_coeff @angle:13-13-84 harmonic 63.0 114.0
- angle_coeff @angle:46-13-85 harmonic 35.0 109.5
- angle_coeff @angle:13-13-85 harmonic 63.0 114.0
- angle_coeff @angle:46-13-87 harmonic 35.0 109.5
- angle_coeff @angle:13-13-87 harmonic 63.0 115.6
- angle_coeff @angle:46-13-90 harmonic 35.0 109.5
- angle_coeff @angle:13-13-90 harmonic 80.0 110.0
- angle_coeff @angle:3-13-90 harmonic 80.0 113.0
- angle_coeff @angle:46-13-91 harmonic 37.5 110.7
- angle_coeff @angle:46-13-95 harmonic 35.0 105.0
- angle_coeff @angle:13-13-95 harmonic 63.0 105.0
- angle_coeff @angle:46-13-101 harmonic 35.0 109.5
- angle_coeff @angle:13-13-101 harmonic 80.0 111.2
- angle_coeff @angle:46-13-102 harmonic 35.0 105.0
- angle_coeff @angle:13-13-102 harmonic 63.0 111.1
- angle_coeff @angle:46-13-104 harmonic 41.0 109.5
- angle_coeff @angle:13-13-104 harmonic 43.0 109.5
- angle_coeff @angle:46-13-105 harmonic 35.0 109.5
- angle_coeff @angle:13-13-105 harmonic 50.0 109.5
- angle_coeff @angle:20-13-105 harmonic 50.0 109.5
- angle_coeff @angle:46-13-107 harmonic 35.0 109.5
- angle_coeff @angle:13-13-107 harmonic 80.0 109.7
- angle_coeff @angle:46-13-108 harmonic 35.0 109.5
- angle_coeff @angle:13-13-108 harmonic 60.0 112.0
- angle_coeff @angle:2-14-2 harmonic 70.0 124.0
- angle_coeff @angle:2-14-6 harmonic 70.0 124.0
- angle_coeff @angle:6-14-6 harmonic 70.0 124.0
- angle_coeff @angle:2-14-9 harmonic 70.0 118.0
- angle_coeff @angle:6-14-9 harmonic 70.0 118.0
- angle_coeff @angle:9-14-10 harmonic 70.0 118.0
- angle_coeff @angle:2-14-10 harmonic 70.0 124.0
- angle_coeff @angle:6-14-10 harmonic 70.0 124.0
- angle_coeff @angle:10-14-10 harmonic 70.0 124.0
- angle_coeff @angle:2-14-11 harmonic 70.0 118.0
- angle_coeff @angle:6-14-11 harmonic 70.0 118.0
- angle_coeff @angle:9-14-11 harmonic 70.0 118.0
- angle_coeff @angle:10-14-11 harmonic 70.0 118.0
- angle_coeff @angle:11-14-11 harmonic 70.0 118.0
- angle_coeff @angle:9-14-13 harmonic 70.0 118.0
- angle_coeff @angle:11-14-13 harmonic 70.0 118.0
- angle_coeff @angle:2-14-13 harmonic 70.0 124.0
- angle_coeff @angle:6-14-13 harmonic 70.0 124.0
- angle_coeff @angle:10-14-13 harmonic 70.0 124.0
- angle_coeff @angle:13-14-13 harmonic 70.0 124.0
- angle_coeff @angle:2-14-14 harmonic 70.0 118.0
- angle_coeff @angle:6-14-14 harmonic 70.0 118.0
- angle_coeff @angle:9-14-14 harmonic 70.0 118.0
- angle_coeff @angle:10-14-14 harmonic 70.0 118.0
- angle_coeff @angle:11-14-14 harmonic 70.0 118.0
- angle_coeff @angle:13-14-14 harmonic 70.0 118.0
- angle_coeff @angle:14-14-14 harmonic 70.0 118.0
- angle_coeff @angle:17-15-17 harmonic 35.0 92.07
- angle_coeff @angle:2-15-17 harmonic 44.0 96.0
- angle_coeff @angle:6-15-17 harmonic 44.0 96.0
- angle_coeff @angle:13-15-17 harmonic 44.0 96.0
- angle_coeff @angle:25-15-25 harmonic 5.0 109.47
- angle_coeff @angle:13-15-25 harmonic 10.0 109.47
- angle_coeff @angle:33-15-33 harmonic 10.0 160.0
- angle_coeff @angle:2-15-33 harmonic 150.0 96.7
- angle_coeff @angle:6-15-33 harmonic 150.0 96.7
- angle_coeff @angle:13-15-33 harmonic 150.0 96.7
- angle_coeff @angle:17-15-33 harmonic 150.0 96.7
- angle_coeff @angle:17-15-48 harmonic 50.0 96.0
- angle_coeff @angle:2-16-6 harmonic 62.0 98.9
- angle_coeff @angle:13-16-13 harmonic 62.0 98.9
- angle_coeff @angle:2-16-16 harmonic 68.0 103.7
- angle_coeff @angle:6-16-16 harmonic 68.0 103.7
- angle_coeff @angle:13-16-16 harmonic 68.0 103.7
- angle_coeff @angle:13-16-19 harmonic 65.0 100.0
- angle_coeff @angle:25-16-25 harmonic 5.0 109.47
- angle_coeff @angle:13-16-25 harmonic 10.0 109.47
- angle_coeff @angle:33-16-33 harmonic 10.0 160.0
- angle_coeff @angle:2-16-33 harmonic 150.0 96.7
- angle_coeff @angle:6-16-33 harmonic 150.0 96.7
- angle_coeff @angle:13-16-33 harmonic 150.0 96.7
- angle_coeff @angle:16-16-33 harmonic 150.0 96.7
- angle_coeff @angle:13-16-48 harmonic 62.0 104.2
- angle_coeff @angle:47-16-48 harmonic 62.0 104.2
- angle_coeff @angle:24-16-60 harmonic 74.0 92.4
- angle_coeff @angle:25-16-61 harmonic 10.0 130.0
- angle_coeff @angle:25-16-82 harmonic 10.0 130.0
- angle_coeff @angle:60-16-82 harmonic 74.0 97.0
- angle_coeff @angle:25-16-84 harmonic 10.0 130.0
- angle_coeff @angle:82-16-84 harmonic 74.0 90.0
- angle_coeff @angle:60-16-84 harmonic 74.0 97.0
- angle_coeff @angle:84-16-84 harmonic 74.0 97.0
- angle_coeff @angle:13-16-91 harmonic 62.0 94.0
- angle_coeff @angle:15-17-25 harmonic 10.0 109.47
- angle_coeff @angle:25-17-25 harmonic 33.0 109.47
- angle_coeff @angle:13-18-19 harmonic 150.0 180.0
- angle_coeff @angle:19-18-48 harmonic 170.0 180.0
- angle_coeff @angle:18-18-56 harmonic 100.0 180.0
- angle_coeff @angle:13-19-18 harmonic 150.0 180.0
- angle_coeff @angle:16-19-19 harmonic 140.0 180.0
- angle_coeff @angle:13-19-19 harmonic 150.0 180.0
- angle_coeff @angle:18-19-25 harmonic 10.0 90.0
- angle_coeff @angle:19-19-46 harmonic 112.0 180.0
- angle_coeff @angle:18-19-47 harmonic 150.0 180.0
- angle_coeff @angle:19-19-47 harmonic 160.0 180.0
- angle_coeff @angle:18-19-48 harmonic 150.0 180.0
- angle_coeff @angle:19-19-48 harmonic 160.0 180.0
- angle_coeff @angle:19-19-50 harmonic 160.0 180.0
- angle_coeff @angle:18-19-55 harmonic 150.0 180.0
- angle_coeff @angle:18-19-88 harmonic 150.0 180.0
- angle_coeff @angle:2-20-2 harmonic 100.0 111.8
- angle_coeff @angle:2-20-3 harmonic 83.0 116.9
- angle_coeff @angle:3-20-6 harmonic 83.0 116.9
- angle_coeff @angle:2-20-6 harmonic 100.0 111.8
- angle_coeff @angle:2-20-7 harmonic 55.0 108.5
- angle_coeff @angle:7-20-10 harmonic 55.0 108.5
- angle_coeff @angle:3-20-10 harmonic 83.0 116.9
- angle_coeff @angle:10-20-10 harmonic 100.0 111.8
- angle_coeff @angle:13-20-13 harmonic 60.0 109.5
- angle_coeff @angle:3-20-13 harmonic 83.0 116.9
- angle_coeff @angle:25-20-25 harmonic 5.0 109.47
- angle_coeff @angle:13-20-25 harmonic 10.0 109.47
- angle_coeff @angle:13-20-47 harmonic 75.0 111.0
- angle_coeff @angle:25-20-48 harmonic 10.0 109.47
- angle_coeff @angle:13-20-48 harmonic 75.0 111.0
- angle_coeff @angle:47-20-48 harmonic 75.0 111.0
- angle_coeff @angle:48-20-48 harmonic 75.0 111.0
- angle_coeff @angle:3-20-48 harmonic 83.0 116.9
- angle_coeff @angle:2-20-48 harmonic 100.0 111.8
- angle_coeff @angle:13-20-51 harmonic 60.0 109.5
- angle_coeff @angle:2-20-51 harmonic 100.0 113.0
- angle_coeff @angle:6-20-51 harmonic 100.0 113.0
- angle_coeff @angle:10-20-51 harmonic 100.0 113.0
- angle_coeff @angle:24-20-60 harmonic 70.0 104.5
- angle_coeff @angle:25-20-61 harmonic 10.0 125.0
- angle_coeff @angle:2-20-64 harmonic 100.0 120.5
- angle_coeff @angle:6-20-64 harmonic 100.0 120.5
- angle_coeff @angle:10-20-64 harmonic 100.0 120.5
- angle_coeff @angle:13-20-64 harmonic 100.0 120.5
- angle_coeff @angle:48-20-64 harmonic 100.0 120.5
- angle_coeff @angle:64-20-64 harmonic 100.0 120.5
- angle_coeff @angle:25-20-82 harmonic 10.0 125.0
- angle_coeff @angle:60-20-82 harmonic 70.0 106.5
- angle_coeff @angle:82-20-82 harmonic 70.0 107.0
- angle_coeff @angle:25-20-84 harmonic 10.0 125.0
- angle_coeff @angle:82-20-84 harmonic 70.0 104.0
- angle_coeff @angle:60-20-84 harmonic 70.0 106.5
- angle_coeff @angle:84-20-84 harmonic 70.0 106.5
- angle_coeff @angle:61-20-84 harmonic 70.0 108.9
- angle_coeff @angle:108-20-108 harmonic 20.0 145.0
- angle_coeff @angle:13-20-108 harmonic 40.0 130.0
- angle_coeff @angle:25-21-25 harmonic 33.0 109.47
- angle_coeff @angle:13-22-13 harmonic 62.0 96.0
- angle_coeff @angle:13-22-23 harmonic 74.0 107.0
- angle_coeff @angle:23-22-25 harmonic 10.0 90.0
- angle_coeff @angle:2-24-3 harmonic 50.0 121.9
- angle_coeff @angle:3-24-3 harmonic 70.0 126.4
- angle_coeff @angle:3-24-5 harmonic 46.0 115.7
- angle_coeff @angle:2-24-6 harmonic 50.0 121.9
- angle_coeff @angle:3-24-6 harmonic 50.0 121.9
- angle_coeff @angle:2-24-10 harmonic 50.0 118.0
- angle_coeff @angle:3-24-10 harmonic 50.0 121.9
- angle_coeff @angle:13-24-13 harmonic 50.0 118.0
- angle_coeff @angle:3-24-13 harmonic 50.0 121.9
- angle_coeff @angle:3-24-16 harmonic 70.0 112.0
- angle_coeff @angle:3-24-20 harmonic 70.0 108.6
- angle_coeff @angle:3-24-25 harmonic 10.0 109.5
- angle_coeff @angle:25-24-45 harmonic 10.0 100.0
- angle_coeff @angle:5-24-45 harmonic 35.0 110.2
- angle_coeff @angle:3-24-45 harmonic 35.0 119.8
- angle_coeff @angle:45-24-45 harmonic 35.0 120.0
- angle_coeff @angle:2-24-45 harmonic 38.0 118.4
- angle_coeff @angle:6-24-45 harmonic 38.0 118.4
- angle_coeff @angle:10-24-45 harmonic 38.0 118.4
- angle_coeff @angle:13-24-45 harmonic 38.0 118.4
- angle_coeff @angle:45-24-48 harmonic 35.0 119.8
- angle_coeff @angle:13-24-48 harmonic 50.0 118.0
- angle_coeff @angle:3-24-48 harmonic 50.0 121.9
- angle_coeff @angle:48-24-48 harmonic 70.0 118.0
- angle_coeff @angle:54-24-54 harmonic 35.0 120.0
- angle_coeff @angle:45-24-59 harmonic 35.0 118.0
- angle_coeff @angle:3-24-59 harmonic 70.0 125.2
- angle_coeff @angle:13-24-79 harmonic 50.0 120.0
- angle_coeff @angle:45-24-79 harmonic 100.0 111.0
- angle_coeff @angle:45-24-84 harmonic 35.0 119.8
- angle_coeff @angle:48-24-84 harmonic 70.0 118.0
- angle_coeff @angle:16-24-86 harmonic 70.0 117.0
- angle_coeff @angle:45-24-87 harmonic 35.0 119.8
- angle_coeff @angle:48-24-87 harmonic 70.0 118.0
- angle_coeff @angle:45-24-88 harmonic 35.0 119.8
- angle_coeff @angle:48-24-88 harmonic 70.0 118.0
- angle_coeff @angle:45-24-91 harmonic 40.0 113.0
- angle_coeff @angle:3-24-91 harmonic 55.0 128.0
- angle_coeff @angle:48-24-103 harmonic 70.0 121.0
- angle_coeff @angle:3-24-106 harmonic 20.0 126.0
- angle_coeff @angle:25-25-25 harmonic 33.0 109.47
- angle_coeff @angle:32-31-32 harmonic 75.0 104.52
- angle_coeff @angle:32-31-33 harmonic 50.0 52.26
- angle_coeff @angle:35-34-35 harmonic 34.05 104.52
- angle_coeff @angle:37-36-37 harmonic 75.0 109.5
- angle_coeff @angle:37-36-38 harmonic 50.0 54.75
- angle_coeff @angle:40-39-40 harmonic 75.0 104.52
- angle_coeff @angle:41-39-41 harmonic 50.0 109.47
- angle_coeff @angle:40-39-41 harmonic 50.0 110.6948
- angle_coeff @angle:43-42-43 harmonic 75.0 109.47
- angle_coeff @angle:2-44-2 harmonic 51.8 107.2
- angle_coeff @angle:2-44-6 harmonic 51.8 107.2
- angle_coeff @angle:6-44-6 harmonic 51.8 107.2
- angle_coeff @angle:2-44-10 harmonic 51.8 107.2
- angle_coeff @angle:6-44-10 harmonic 51.8 107.2
- angle_coeff @angle:10-44-10 harmonic 51.8 107.2
- angle_coeff @angle:2-44-13 harmonic 51.8 107.2
- angle_coeff @angle:6-44-13 harmonic 51.8 107.2
- angle_coeff @angle:10-44-13 harmonic 51.8 107.2
- angle_coeff @angle:13-44-13 harmonic 51.8 107.2
- angle_coeff @angle:3-44-13 harmonic 63.0 111.1
- angle_coeff @angle:25-44-45 harmonic 10.0 100.0
- angle_coeff @angle:13-44-45 harmonic 35.0 109.5
- angle_coeff @angle:2-44-45 harmonic 43.2 108.1
- angle_coeff @angle:6-44-45 harmonic 43.2 108.1
- angle_coeff @angle:10-44-45 harmonic 43.2 108.1
- angle_coeff @angle:45-44-45 harmonic 43.6 106.4
- angle_coeff @angle:25-44-48 harmonic 10.0 109.5
- angle_coeff @angle:45-44-48 harmonic 35.0 116.0
- angle_coeff @angle:13-44-48 harmonic 50.0 116.0
- angle_coeff @angle:48-44-48 harmonic 50.0 116.0
- angle_coeff @angle:3-44-48 harmonic 63.0 112.0
- angle_coeff @angle:45-44-79 harmonic 35.0 115.0
- angle_coeff @angle:13-44-79 harmonic 50.0 108.6
- angle_coeff @angle:48-44-79 harmonic 50.0 108.6
- angle_coeff @angle:48-44-91 harmonic 50.0 109.5
- angle_coeff @angle:25-45-25 harmonic 33.0 109.47
- angle_coeff @angle:25-45-44 harmonic 10.0 109.5
- angle_coeff @angle:25-46-25 harmonic 33.0 109.47
- angle_coeff @angle:13-46-25 harmonic 37.5 109.47
- angle_coeff @angle:1-47-1 harmonic 80.0 108.0
- angle_coeff @angle:1-47-3 harmonic 80.0 121.5
- angle_coeff @angle:3-47-6 harmonic 85.0 119.7
- angle_coeff @angle:3-47-13 harmonic 70.0 119.7
- angle_coeff @angle:13-47-13 harmonic 70.0 130.0
- angle_coeff @angle:25-47-46 harmonic 10.0 90.0
- angle_coeff @angle:20-47-46 harmonic 35.0 114.5
- angle_coeff @angle:13-47-46 harmonic 35.0 117.0
- angle_coeff @angle:46-47-46 harmonic 35.0 117.0
- angle_coeff @angle:3-47-46 harmonic 35.0 119.7
- angle_coeff @angle:19-47-46 harmonic 35.0 120.0
- angle_coeff @angle:1-47-46 harmonic 50.0 112.0
- angle_coeff @angle:21-47-46 harmonic 60.0 114.0
- angle_coeff @angle:25-47-47 harmonic 2.0 90.0
- angle_coeff @angle:46-47-47 harmonic 35.0 120.0
- angle_coeff @angle:5-47-47 harmonic 70.0 123.0
- angle_coeff @angle:20-47-47 harmonic 70.0 123.0
- angle_coeff @angle:13-47-47 harmonic 70.0 124.0
- angle_coeff @angle:19-47-47 harmonic 70.0 124.0
- angle_coeff @angle:21-47-47 harmonic 75.0 121.5
- angle_coeff @angle:1-47-47 harmonic 80.0 121.5
- angle_coeff @angle:16-47-47 harmonic 85.0 119.4
- angle_coeff @angle:3-47-47 harmonic 85.0 120.7
- angle_coeff @angle:46-47-48 harmonic 35.0 123.3
- angle_coeff @angle:47-47-48 harmonic 85.0 117.0
- angle_coeff @angle:13-47-48 harmonic 85.0 119.7
- angle_coeff @angle:25-47-50 harmonic 2.0 90.0
- angle_coeff @angle:46-47-50 harmonic 35.0 120.0
- angle_coeff @angle:5-47-50 harmonic 70.0 123.0
- angle_coeff @angle:20-47-50 harmonic 70.0 123.0
- angle_coeff @angle:13-47-50 harmonic 70.0 124.0
- angle_coeff @angle:46-47-57 harmonic 35.0 119.1
- angle_coeff @angle:13-47-57 harmonic 70.0 120.0
- angle_coeff @angle:20-47-57 harmonic 70.0 120.0
- angle_coeff @angle:47-47-57 harmonic 70.0 121.2
- angle_coeff @angle:16-47-57 harmonic 85.0 119.4
- angle_coeff @angle:57-47-58 harmonic 35.0 119.1
- angle_coeff @angle:47-47-58 harmonic 35.0 119.7
- angle_coeff @angle:46-47-65 harmonic 60.0 114.0
- angle_coeff @angle:47-47-65 harmonic 75.0 120.0
- angle_coeff @angle:46-47-91 harmonic 35.0 135.0
- angle_coeff @angle:3-47-91 harmonic 70.0 119.7
- angle_coeff @angle:47-47-91 harmonic 70.0 124.0
- angle_coeff @angle:46-47-105 harmonic 35.0 119.1
- angle_coeff @angle:58-47-105 harmonic 35.0 119.1
- angle_coeff @angle:13-47-105 harmonic 70.0 120.0
- angle_coeff @angle:20-47-105 harmonic 70.0 120.0
- angle_coeff @angle:47-47-105 harmonic 70.0 121.2
- angle_coeff @angle:16-47-105 harmonic 85.0 119.4
- angle_coeff @angle:46-47-110 harmonic 40.0 121.0
- angle_coeff @angle:13-47-110 harmonic 80.0 122.0
- angle_coeff @angle:48-47-110 harmonic 80.0 122.0
- angle_coeff @angle:1-47-110 harmonic 80.0 125.0
- angle_coeff @angle:2-48-12 harmonic 70.0 120.0
- angle_coeff @angle:12-48-12 harmonic 85.0 120.0
- angle_coeff @angle:3-48-13 harmonic 70.0 119.7
- angle_coeff @angle:25-48-48 harmonic 10.0 90.0
- angle_coeff @angle:48-48-48 harmonic 63.0 120.0
- angle_coeff @angle:2-48-48 harmonic 70.0 120.0
- angle_coeff @angle:5-48-48 harmonic 70.0 120.0
- angle_coeff @angle:10-48-48 harmonic 70.0 120.0
- angle_coeff @angle:13-48-48 harmonic 70.0 120.0
- angle_coeff @angle:15-48-48 harmonic 70.0 120.0
- angle_coeff @angle:19-48-48 harmonic 70.0 120.0
- angle_coeff @angle:20-48-48 harmonic 70.0 120.0
- angle_coeff @angle:24-48-48 harmonic 70.0 120.0
- angle_coeff @angle:44-48-48 harmonic 70.0 120.0
- angle_coeff @angle:47-48-48 harmonic 70.0 124.0
- angle_coeff @angle:21-48-48 harmonic 75.0 120.0
- angle_coeff @angle:1-48-48 harmonic 80.0 120.0
- angle_coeff @angle:18-48-48 harmonic 80.0 120.0
- angle_coeff @angle:16-48-48 harmonic 85.0 119.4
- angle_coeff @angle:3-48-48 harmonic 85.0 120.0
- angle_coeff @angle:25-48-49 harmonic 2.0 90.0
- angle_coeff @angle:24-48-49 harmonic 35.0 119.1
- angle_coeff @angle:3-48-49 harmonic 35.0 120.0
- angle_coeff @angle:48-48-49 harmonic 35.0 120.0
- angle_coeff @angle:48-48-50 harmonic 70.0 124.0
- angle_coeff @angle:48-48-53 harmonic 70.0 120.0
- angle_coeff @angle:55-48-55 harmonic 70.0 120.0
- angle_coeff @angle:47-48-55 harmonic 70.0 120.1
- angle_coeff @angle:48-48-55 harmonic 70.0 120.1
- angle_coeff @angle:49-48-56 harmonic 35.0 116.0
- angle_coeff @angle:13-48-56 harmonic 70.0 116.0
- angle_coeff @angle:44-48-56 harmonic 70.0 116.0
- angle_coeff @angle:55-48-56 harmonic 70.0 119.3
- angle_coeff @angle:5-48-56 harmonic 70.0 120.0
- angle_coeff @angle:47-48-56 harmonic 70.0 121.5
- angle_coeff @angle:50-48-56 harmonic 70.0 121.5
- angle_coeff @angle:48-48-56 harmonic 70.0 124.0
- angle_coeff @angle:21-48-56 harmonic 75.0 120.0
- angle_coeff @angle:49-48-57 harmonic 35.0 120.0
- angle_coeff @angle:48-48-57 harmonic 70.0 108.7
- angle_coeff @angle:55-48-57 harmonic 70.0 116.0
- angle_coeff @angle:13-48-57 harmonic 70.0 120.0
- angle_coeff @angle:47-48-57 harmonic 70.0 121.5
- angle_coeff @angle:56-48-57 harmonic 70.0 123.3
- angle_coeff @angle:49-48-60 harmonic 35.0 120.0
- angle_coeff @angle:48-48-60 harmonic 63.0 120.0
- angle_coeff @angle:57-48-60 harmonic 70.0 108.7
- angle_coeff @angle:56-48-60 harmonic 70.0 117.3
- angle_coeff @angle:55-48-60 harmonic 70.0 123.5
- angle_coeff @angle:2-48-60 harmonic 70.0 128.6
- angle_coeff @angle:13-48-60 harmonic 70.0 128.6
- angle_coeff @angle:49-48-61 harmonic 35.0 119.1
- angle_coeff @angle:48-48-61 harmonic 70.0 108.7
- angle_coeff @angle:57-48-61 harmonic 70.0 123.3
- angle_coeff @angle:48-48-64 harmonic 85.0 119.4
- angle_coeff @angle:48-48-65 harmonic 75.0 120.0
- angle_coeff @angle:48-48-66 harmonic 75.0 120.0
- angle_coeff @angle:48-48-79 harmonic 85.0 119.4
- angle_coeff @angle:49-48-81 harmonic 35.0 120.0
- angle_coeff @angle:48-48-81 harmonic 85.0 120.0
- angle_coeff @angle:49-48-84 harmonic 35.0 126.9
- angle_coeff @angle:60-48-84 harmonic 63.0 106.4
- angle_coeff @angle:48-48-84 harmonic 70.0 107.4
- angle_coeff @angle:49-48-86 harmonic 35.0 120.0
- angle_coeff @angle:48-48-86 harmonic 63.0 120.0
- angle_coeff @angle:56-48-86 harmonic 70.0 124.0
- angle_coeff @angle:49-48-88 harmonic 35.0 128.2
- angle_coeff @angle:101-48-101 harmonic 70.0 111.8
- angle_coeff @angle:56-48-101 harmonic 70.0 124.1
- angle_coeff @angle:48-48-102 harmonic 85.0 120.0
- angle_coeff @angle:48-48-109 harmonic 70.0 124.0
- angle_coeff @angle:25-50-46 harmonic 10.0 90.0
- angle_coeff @angle:19-50-46 harmonic 35.0 120.0
- angle_coeff @angle:25-50-47 harmonic 2.0 90.0
- angle_coeff @angle:46-50-47 harmonic 35.0 120.0
- angle_coeff @angle:3-50-47 harmonic 70.0 118.7
- angle_coeff @angle:13-50-47 harmonic 70.0 124.0
- angle_coeff @angle:46-50-48 harmonic 35.0 123.3
- angle_coeff @angle:47-50-48 harmonic 85.0 117.0
- angle_coeff @angle:25-50-50 harmonic 2.0 90.0
- angle_coeff @angle:46-50-50 harmonic 35.0 120.0
- angle_coeff @angle:13-50-50 harmonic 70.0 124.0
- angle_coeff @angle:47-50-50 harmonic 70.0 124.0
- angle_coeff @angle:50-50-84 harmonic 35.0 106.0
- angle_coeff @angle:46-50-84 harmonic 35.0 122.0
- angle_coeff @angle:46-50-109 harmonic 35.0 120.0
- angle_coeff @angle:13-50-109 harmonic 70.0 124.0
- angle_coeff @angle:47-50-109 harmonic 70.0 124.0
- angle_coeff @angle:6-51-6 harmonic 40.0 109.5
- angle_coeff @angle:5-51-13 harmonic 50.0 109.5
- angle_coeff @angle:13-51-20 harmonic 50.0 109.5
- angle_coeff @angle:2-51-20 harmonic 80.0 109.5
- angle_coeff @angle:6-51-20 harmonic 80.0 109.5
- angle_coeff @angle:5-51-20 harmonic 92.6 111.55
- angle_coeff @angle:20-51-20 harmonic 92.6 111.55
- angle_coeff @angle:46-51-46 harmonic 33.0 109.5
- angle_coeff @angle:5-51-46 harmonic 35.0 109.5
- angle_coeff @angle:20-51-46 harmonic 35.0 109.5
- angle_coeff @angle:13-51-46 harmonic 37.5 110.7
- angle_coeff @angle:46-51-105 harmonic 35.0 109.5
- angle_coeff @angle:13-51-105 harmonic 50.0 109.5
- angle_coeff @angle:20-51-105 harmonic 50.0 109.5
- angle_coeff @angle:13-53-13 harmonic 50.0 113.0
- angle_coeff @angle:13-53-25 harmonic 10.0 100.0
- angle_coeff @angle:45-53-45 harmonic 43.6 109.5
- angle_coeff @angle:25-53-48 harmonic 10.0 100.0
- angle_coeff @angle:13-53-48 harmonic 55.0 114.0
- angle_coeff @angle:2-53-54 harmonic 35.0 109.5
- angle_coeff @angle:6-53-54 harmonic 35.0 109.5
- angle_coeff @angle:13-53-54 harmonic 35.0 109.5
- angle_coeff @angle:48-53-54 harmonic 35.0 109.5
- angle_coeff @angle:54-53-54 harmonic 35.0 109.5
- angle_coeff @angle:25-53-82 harmonic 10.0 100.0
- angle_coeff @angle:13-55-13 harmonic 50.0 118.0
- angle_coeff @angle:45-55-45 harmonic 35.0 113.0
- angle_coeff @angle:13-55-45 harmonic 35.0 118.4
- angle_coeff @angle:45-55-48 harmonic 35.0 120.0
- angle_coeff @angle:2-55-48 harmonic 50.0 123.2
- angle_coeff @angle:6-55-48 harmonic 50.0 123.2
- angle_coeff @angle:13-55-48 harmonic 50.0 123.2
- angle_coeff @angle:2-55-54 harmonic 35.0 118.4
- angle_coeff @angle:13-55-54 harmonic 35.0 118.4
- angle_coeff @angle:48-55-54 harmonic 35.0 120.0
- angle_coeff @angle:54-55-54 harmonic 35.0 120.0
- angle_coeff @angle:45-55-59 harmonic 35.0 120.0
- angle_coeff @angle:3-56-13 harmonic 70.0 120.5
- angle_coeff @angle:13-56-18 harmonic 70.0 120.0
- angle_coeff @angle:25-56-48 harmonic 5.0 120.0
- angle_coeff @angle:45-56-48 harmonic 35.0 113.0
- angle_coeff @angle:13-56-48 harmonic 50.0 118.0
- angle_coeff @angle:48-56-48 harmonic 70.0 117.0
- angle_coeff @angle:3-56-48 harmonic 70.0 120.5
- angle_coeff @angle:13-56-56 harmonic 70.0 117.0
- angle_coeff @angle:48-56-56 harmonic 70.0 117.0
- angle_coeff @angle:25-56-59 harmonic 5.0 119.8
- angle_coeff @angle:48-56-59 harmonic 70.0 118.6
- angle_coeff @angle:59-56-59 harmonic 70.0 118.6
- angle_coeff @angle:59-56-60 harmonic 70.0 111.0
- angle_coeff @angle:48-56-60 harmonic 70.0 112.2
- angle_coeff @angle:59-56-82 harmonic 70.0 111.0
- angle_coeff @angle:48-56-86 harmonic 70.0 117.0
- angle_coeff @angle:13-56-103 harmonic 70.0 114.0
- angle_coeff @angle:3-57-3 harmonic 70.0 126.4
- angle_coeff @angle:3-57-45 harmonic 35.0 116.8
- angle_coeff @angle:45-57-47 harmonic 35.0 119.2
- angle_coeff @angle:3-57-47 harmonic 70.0 121.6
- angle_coeff @angle:45-57-48 harmonic 35.0 118.0
- angle_coeff @angle:3-57-48 harmonic 70.0 125.2
- angle_coeff @angle:48-57-48 harmonic 70.0 125.2
- angle_coeff @angle:45-57-60 harmonic 30.0 125.8
- angle_coeff @angle:13-57-60 harmonic 70.0 125.8
- angle_coeff @angle:60-57-61 harmonic 56.0 113.1
- angle_coeff @angle:45-57-61 harmonic 56.0 118.4
- angle_coeff @angle:13-57-61 harmonic 70.0 118.4
- angle_coeff @angle:48-57-61 harmonic 70.0 118.4
- angle_coeff @angle:45-57-62 harmonic 30.0 128.8
- angle_coeff @angle:60-57-62 harmonic 70.0 105.4
- angle_coeff @angle:48-57-62 harmonic 70.0 109.8
- angle_coeff @angle:13-57-62 harmonic 70.0 128.8
- angle_coeff @angle:45-57-81 harmonic 35.0 123.1
- angle_coeff @angle:45-57-82 harmonic 35.0 120.0
- angle_coeff @angle:61-57-82 harmonic 56.0 113.1
- angle_coeff @angle:60-57-82 harmonic 70.0 109.8
- angle_coeff @angle:45-57-84 harmonic 35.0 120.0
- angle_coeff @angle:61-57-84 harmonic 56.0 113.1
- angle_coeff @angle:60-57-84 harmonic 70.0 109.8
- angle_coeff @angle:82-57-84 harmonic 70.0 109.8
- angle_coeff @angle:84-57-84 harmonic 70.0 109.8
- angle_coeff @angle:81-57-84 harmonic 70.0 111.6
- angle_coeff @angle:45-57-85 harmonic 35.0 120.0
- angle_coeff @angle:82-57-85 harmonic 70.0 109.8
- angle_coeff @angle:24-59-55 harmonic 70.0 116.0
- angle_coeff @angle:49-59-56 harmonic 35.0 115.45
- angle_coeff @angle:13-59-56 harmonic 70.0 115.5
- angle_coeff @angle:55-59-56 harmonic 70.0 119.3
- angle_coeff @angle:24-59-56 harmonic 70.0 123.3
- angle_coeff @angle:56-59-56 harmonic 70.0 129.1
- angle_coeff @angle:56-59-63 harmonic 35.0 115.45
- angle_coeff @angle:13-60-48 harmonic 70.0 120.0
- angle_coeff @angle:48-60-48 harmonic 85.0 134.9
- angle_coeff @angle:56-60-57 harmonic 70.0 126.2
- angle_coeff @angle:57-60-60 harmonic 70.0 106.2
- angle_coeff @angle:20-60-60 harmonic 70.0 110.6
- angle_coeff @angle:16-60-60 harmonic 70.0 111.0
- angle_coeff @angle:13-60-60 harmonic 70.0 120.0
- angle_coeff @angle:24-60-60 harmonic 70.0 127.7
- angle_coeff @angle:56-60-60 harmonic 70.0 127.7
- angle_coeff @angle:48-60-60 harmonic 85.0 117.3
- angle_coeff @angle:3-60-60 harmonic 85.0 119.2
- angle_coeff @angle:60-60-61 harmonic 70.0 111.0
- angle_coeff @angle:24-60-61 harmonic 70.0 126.2
- angle_coeff @angle:3-60-61 harmonic 70.0 130.0
- angle_coeff @angle:48-60-61 harmonic 70.0 132.4
- angle_coeff @angle:12-60-80 harmonic 85.0 134.9
- angle_coeff @angle:48-60-80 harmonic 85.0 134.9
- angle_coeff @angle:80-60-81 harmonic 85.0 108.8
- angle_coeff @angle:12-60-81 harmonic 85.0 116.2
- angle_coeff @angle:48-60-81 harmonic 85.0 116.2
- angle_coeff @angle:3-60-84 harmonic 70.0 130.0
- angle_coeff @angle:60-60-87 harmonic 70.0 107.3
- angle_coeff @angle:57-60-87 harmonic 70.0 107.7
- angle_coeff @angle:81-60-87 harmonic 85.0 108.8
- angle_coeff @angle:12-60-87 harmonic 85.0 134.9
- angle_coeff @angle:48-60-87 harmonic 85.0 134.9
- angle_coeff @angle:60-60-105 harmonic 70.0 106.2
- angle_coeff @angle:56-60-105 harmonic 70.0 126.2
- angle_coeff @angle:48-61-48 harmonic 70.0 125.2
- angle_coeff @angle:25-61-57 harmonic 10.0 125.0
- angle_coeff @angle:25-61-61 harmonic 10.0 125.0
- angle_coeff @angle:60-61-62 harmonic 70.0 103.8
- angle_coeff @angle:25-61-82 harmonic 10.0 125.0
- angle_coeff @angle:61-61-82 harmonic 70.0 109.0
- angle_coeff @angle:60-61-82 harmonic 70.0 110.0
- angle_coeff @angle:82-61-83 harmonic 70.0 110.0
- angle_coeff @angle:57-61-84 harmonic 70.0 104.1
- angle_coeff @angle:82-61-84 harmonic 70.0 110.0
- angle_coeff @angle:57-61-88 harmonic 70.0 104.1
- angle_coeff @angle:20-61-88 harmonic 70.0 105.3
- angle_coeff @angle:49-62-57 harmonic 35.0 120.0
- angle_coeff @angle:49-62-61 harmonic 35.0 120.0
- angle_coeff @angle:57-62-61 harmonic 70.0 113.9
- angle_coeff @angle:57-62-63 harmonic 35.0 123.05
- angle_coeff @angle:61-62-63 harmonic 35.0 123.05
- angle_coeff @angle:49-62-105 harmonic 35.0 120.0
- angle_coeff @angle:63-62-105 harmonic 35.0 123.05
- angle_coeff @angle:61-62-105 harmonic 70.0 113.9
- angle_coeff @angle:5-64-5 harmonic 45.0 102.6
- angle_coeff @angle:4-64-5 harmonic 100.0 108.23
- angle_coeff @angle:4-64-13 harmonic 45.0 109.5
- angle_coeff @angle:5-64-20 harmonic 45.0 102.6
- angle_coeff @angle:20-64-20 harmonic 45.0 102.6
- angle_coeff @angle:13-64-20 harmonic 45.0 109.5
- angle_coeff @angle:4-64-20 harmonic 100.0 108.23
- angle_coeff @angle:4-64-48 harmonic 45.0 109.5
- angle_coeff @angle:5-64-48 harmonic 45.0 109.5
- angle_coeff @angle:20-64-48 harmonic 45.0 109.5
- angle_coeff @angle:5-64-52 harmonic 45.0 108.23
- angle_coeff @angle:13-64-52 harmonic 45.0 109.5
- angle_coeff @angle:20-64-52 harmonic 100.0 108.23
- angle_coeff @angle:52-64-52 harmonic 140.0 119.9
- angle_coeff @angle:25-65-25 harmonic 33.0 109.47
- angle_coeff @angle:25-66-25 harmonic 33.0 109.47
- angle_coeff @angle:78-77-78 harmonic 150.0 180.0
- angle_coeff @angle:6-79-11 harmonic 62.0 98.9
- angle_coeff @angle:13-79-13 harmonic 62.0 102.0
- angle_coeff @angle:5-79-13 harmonic 75.0 96.4
- angle_coeff @angle:5-79-23 harmonic 74.0 108.7
- angle_coeff @angle:13-79-23 harmonic 74.0 108.9
- angle_coeff @angle:23-79-23 harmonic 104.0 119.0
- angle_coeff @angle:13-79-24 harmonic 100.0 103.0
- angle_coeff @angle:23-79-24 harmonic 120.0 107.0
- angle_coeff @angle:13-79-44 harmonic 62.0 102.0
- angle_coeff @angle:23-79-44 harmonic 74.0 108.9
- angle_coeff @angle:13-79-48 harmonic 62.0 102.0
- angle_coeff @angle:23-79-48 harmonic 74.0 107.2
- angle_coeff @angle:5-79-48 harmonic 75.0 96.4
- angle_coeff @angle:24-79-48 harmonic 100.0 103.0
- angle_coeff @angle:13-79-82 harmonic 62.0 102.0
- angle_coeff @angle:46-80-60 harmonic 35.0 126.8
- angle_coeff @angle:2-80-60 harmonic 70.0 128.6
- angle_coeff @angle:13-80-60 harmonic 70.0 128.6
- angle_coeff @angle:46-80-84 harmonic 35.0 126.8
- angle_coeff @angle:2-80-84 harmonic 70.0 125.0
- angle_coeff @angle:13-80-84 harmonic 70.0 125.0
- angle_coeff @angle:60-80-84 harmonic 85.0 106.4
- angle_coeff @angle:12-81-57 harmonic 70.0 132.8
- angle_coeff @angle:48-81-57 harmonic 70.0 132.8
- angle_coeff @angle:57-81-60 harmonic 70.0 104.4
- angle_coeff @angle:12-81-60 harmonic 85.0 122.7
- angle_coeff @angle:48-81-60 harmonic 85.0 122.7
- angle_coeff @angle:13-82-16 harmonic 70.0 125.0
- angle_coeff @angle:16-82-24 harmonic 70.0 125.0
- angle_coeff @angle:16-82-44 harmonic 70.0 120.2
- angle_coeff @angle:20-82-49 harmonic 35.0 117.0
- angle_coeff @angle:16-82-49 harmonic 35.0 125.0
- angle_coeff @angle:49-82-57 harmonic 35.0 120.0
- angle_coeff @angle:57-82-57 harmonic 70.0 120.0
- angle_coeff @angle:13-82-57 harmonic 70.0 125.0
- angle_coeff @angle:48-82-57 harmonic 70.0 125.0
- angle_coeff @angle:56-82-57 harmonic 70.0 126.2
- angle_coeff @angle:49-82-61 harmonic 35.0 120.0
- angle_coeff @angle:16-82-61 harmonic 70.0 115.0
- angle_coeff @angle:20-82-61 harmonic 70.0 115.0
- angle_coeff @angle:57-82-61 harmonic 70.0 120.0
- angle_coeff @angle:13-82-61 harmonic 70.0 125.0
- angle_coeff @angle:44-82-61 harmonic 70.0 126.1
- angle_coeff @angle:24-82-61 harmonic 70.0 126.2
- angle_coeff @angle:57-82-79 harmonic 70.0 120.0
- angle_coeff @angle:61-82-79 harmonic 70.0 120.0
- angle_coeff @angle:20-82-86 harmonic 70.0 122.0
- angle_coeff @angle:61-82-86 harmonic 70.0 130.0
- angle_coeff @angle:57-82-87 harmonic 70.0 106.2
- angle_coeff @angle:56-82-87 harmonic 70.0 127.7
- angle_coeff @angle:49-83-61 harmonic 35.0 120.0
- angle_coeff @angle:48-83-61 harmonic 70.0 111.0
- angle_coeff @angle:13-83-61 harmonic 70.0 124.5
- angle_coeff @angle:49-83-84 harmonic 35.0 128.2
- angle_coeff @angle:61-83-84 harmonic 70.0 111.0
- angle_coeff @angle:13-83-84 harmonic 70.0 130.7
- angle_coeff @angle:13-84-16 harmonic 70.0 125.0
- angle_coeff @angle:13-84-20 harmonic 70.0 121.6
- angle_coeff @angle:16-84-24 harmonic 70.0 125.0
- angle_coeff @angle:20-84-49 harmonic 35.0 113.4
- angle_coeff @angle:16-84-49 harmonic 35.0 125.0
- angle_coeff @angle:48-84-49 harmonic 35.0 130.7
- angle_coeff @angle:49-84-50 harmonic 35.0 130.7
- angle_coeff @angle:20-84-50 harmonic 70.0 110.0
- angle_coeff @angle:49-84-57 harmonic 35.0 121.6
- angle_coeff @angle:13-84-57 harmonic 70.0 121.6
- angle_coeff @angle:48-84-57 harmonic 70.0 121.6
- angle_coeff @angle:3-84-57 harmonic 85.0 120.0
- angle_coeff @angle:57-84-58 harmonic 35.0 120.0
- angle_coeff @angle:13-84-61 harmonic 70.0 118.9
- angle_coeff @angle:49-84-80 harmonic 35.0 120.0
- angle_coeff @angle:57-84-80 harmonic 70.0 108.7
- angle_coeff @angle:49-84-83 harmonic 35.0 130.7
- angle_coeff @angle:57-84-83 harmonic 70.0 106.3
- angle_coeff @angle:20-84-83 harmonic 70.0 108.0
- angle_coeff @angle:16-84-83 harmonic 70.0 111.0
- angle_coeff @angle:13-84-83 harmonic 70.0 130.7
- angle_coeff @angle:13-84-84 harmonic 70.0 120.0
- angle_coeff @angle:57-84-84 harmonic 70.0 120.0
- angle_coeff @angle:61-84-84 harmonic 70.0 120.0
- angle_coeff @angle:20-84-86 harmonic 70.0 121.6
- angle_coeff @angle:57-84-86 harmonic 70.0 121.6
- angle_coeff @angle:49-84-87 harmonic 35.0 132.1
- angle_coeff @angle:57-84-87 harmonic 70.0 107.7
- angle_coeff @angle:20-84-87 harmonic 70.0 110.6
- angle_coeff @angle:16-84-87 harmonic 70.0 111.0
- angle_coeff @angle:61-84-87 harmonic 70.0 111.9
- angle_coeff @angle:13-84-87 harmonic 70.0 132.1
- angle_coeff @angle:48-84-87 harmonic 70.0 132.1
- angle_coeff @angle:86-84-87 harmonic 70.0 132.1
- angle_coeff @angle:3-84-87 harmonic 85.0 120.0
- angle_coeff @angle:49-85-57 harmonic 35.0 120.0
- angle_coeff @angle:13-85-57 harmonic 70.0 121.6
- angle_coeff @angle:49-85-85 harmonic 35.0 130.7
- angle_coeff @angle:57-85-85 harmonic 70.0 106.3
- angle_coeff @angle:13-85-85 harmonic 70.0 130.7
- angle_coeff @angle:48-86-48 harmonic 63.0 120.0
- angle_coeff @angle:48-86-56 harmonic 70.0 124.0
- angle_coeff @angle:48-86-82 harmonic 63.0 120.0
- angle_coeff @angle:48-86-83 harmonic 63.0 120.0
- angle_coeff @angle:48-86-84 harmonic 63.0 120.0
- angle_coeff @angle:48-86-86 harmonic 63.0 120.0
- angle_coeff @angle:56-86-86 harmonic 70.0 124.0
- angle_coeff @angle:48-86-87 harmonic 63.0 120.0
- angle_coeff @angle:48-86-88 harmonic 63.0 120.0
- angle_coeff @angle:49-87-60 harmonic 35.0 120.0
- angle_coeff @angle:46-87-60 harmonic 35.0 126.8
- angle_coeff @angle:13-87-60 harmonic 70.0 128.6
- angle_coeff @angle:49-87-84 harmonic 35.0 125.7
- angle_coeff @angle:46-87-84 harmonic 35.0 126.8
- angle_coeff @angle:84-87-84 harmonic 70.0 103.8
- angle_coeff @angle:82-87-84 harmonic 70.0 110.4
- angle_coeff @angle:2-87-84 harmonic 70.0 125.0
- angle_coeff @angle:13-87-84 harmonic 70.0 125.0
- angle_coeff @angle:3-87-84 harmonic 70.0 130.0
- angle_coeff @angle:60-87-84 harmonic 85.0 106.4
- angle_coeff @angle:84-87-86 harmonic 70.0 125.7
- angle_coeff @angle:49-87-87 harmonic 35.0 127.5
- angle_coeff @angle:60-87-87 harmonic 70.0 107.3
- angle_coeff @angle:84-87-87 harmonic 70.0 107.3
- angle_coeff @angle:86-87-87 harmonic 70.0 127.5
- angle_coeff @angle:84-87-88 harmonic 70.0 103.8
- angle_coeff @angle:48-88-49 harmonic 35.0 128.6
- angle_coeff @angle:49-88-61 harmonic 35.0 118.9
- angle_coeff @angle:13-88-61 harmonic 70.0 118.9
- angle_coeff @angle:19-88-61 harmonic 70.0 118.9
- angle_coeff @angle:61-88-87 harmonic 70.0 111.9
- angle_coeff @angle:4-89-90 harmonic 80.0 134.0
- angle_coeff @angle:90-89-91 harmonic 70.0 91.0
- angle_coeff @angle:4-89-91 harmonic 80.0 134.0
- angle_coeff @angle:13-90-89 harmonic 55.0 127.0
- angle_coeff @angle:89-90-91 harmonic 50.0 94.0
- angle_coeff @angle:13-90-91 harmonic 50.0 126.0
- angle_coeff @angle:24-91-46 harmonic 35.0 108.0
- angle_coeff @angle:13-91-46 harmonic 35.0 114.3
- angle_coeff @angle:44-91-46 harmonic 35.0 114.3
- angle_coeff @angle:46-91-46 harmonic 35.0 114.3
- angle_coeff @angle:16-91-46 harmonic 37.5 108.0
- angle_coeff @angle:46-91-47 harmonic 35.0 109.5
- angle_coeff @angle:46-91-89 harmonic 37.5 110.0
- angle_coeff @angle:24-91-89 harmonic 70.0 117.0
- angle_coeff @angle:46-91-90 harmonic 35.0 111.0
- angle_coeff @angle:16-91-90 harmonic 55.0 109.0
- angle_coeff @angle:91-91-91 harmonic 30.0 79.2
- angle_coeff @angle:13-91-91 harmonic 37.5 117.2
- angle_coeff @angle:44-91-91 harmonic 37.5 117.2
- angle_coeff @angle:46-91-91 harmonic 37.5 117.2
- angle_coeff @angle:24-91-91 harmonic 37.5 126.0
- angle_coeff @angle:16-91-91 harmonic 55.0 128.0
- angle_coeff @angle:89-91-91 harmonic 63.0 85.0
- angle_coeff @angle:47-91-91 harmonic 63.0 114.0
- angle_coeff @angle:90-91-91 harmonic 80.0 89.0
- angle_coeff @angle:13-95-13 harmonic 172.8 120.0
- angle_coeff @angle:13-95-46 harmonic 144.0 120.0
- angle_coeff @angle:13-101-45 harmonic 35.0 109.5
- angle_coeff @angle:45-101-45 harmonic 43.6 106.4
- angle_coeff @angle:45-101-48 harmonic 50.0 112.5
- angle_coeff @angle:13-101-48 harmonic 50.0 120.5
- angle_coeff @angle:13-102-103 harmonic 80.0 117.5
- angle_coeff @angle:48-102-103 harmonic 80.0 117.5
- angle_coeff @angle:103-102-103 harmonic 80.0 125.0
- angle_coeff @angle:25-103-25 harmonic 10.0 109.5
- angle_coeff @angle:25-103-102 harmonic 10.0 109.5
- angle_coeff @angle:13-104-13 harmonic 45.0 109.5
- angle_coeff @angle:3-105-10 harmonic 70.0 117.6
- angle_coeff @angle:3-105-13 harmonic 70.0 117.6
- angle_coeff @angle:3-105-45 harmonic 35.0 119.2
- angle_coeff @angle:45-105-47 harmonic 35.0 119.2
- angle_coeff @angle:13-105-47 harmonic 70.0 121.2
- angle_coeff @angle:3-105-47 harmonic 70.0 121.6
- angle_coeff @angle:3-105-51 harmonic 70.0 117.6
- angle_coeff @angle:47-105-51 harmonic 70.0 121.2
- angle_coeff @angle:45-105-60 harmonic 30.0 125.8
- angle_coeff @angle:6-105-60 harmonic 70.0 125.8
- angle_coeff @angle:10-105-60 harmonic 70.0 125.8
- angle_coeff @angle:13-105-60 harmonic 70.0 125.8
- angle_coeff @angle:51-105-60 harmonic 70.0 125.8
- angle_coeff @angle:45-105-62 harmonic 30.0 128.8
- angle_coeff @angle:60-105-62 harmonic 70.0 105.4
- angle_coeff @angle:6-105-62 harmonic 70.0 128.8
- angle_coeff @angle:10-105-62 harmonic 70.0 128.8
- angle_coeff @angle:13-105-62 harmonic 70.0 128.8
- angle_coeff @angle:51-105-62 harmonic 70.0 128.8
- angle_coeff @angle:4-106-24 harmonic 20.0 109.5
- angle_coeff @angle:24-106-24 harmonic 20.0 109.5
- angle_coeff @angle:13-107-13 harmonic 50.0 118.0
- angle_coeff @angle:3-107-13 harmonic 50.0 121.9
- angle_coeff @angle:1-108-13 harmonic 35.0 110.5
- angle_coeff @angle:13-108-13 harmonic 60.0 110.0
- angle_coeff @angle:13-108-20 harmonic 60.0 100.0
- angle_coeff @angle:20-108-20 harmonic 60.0 110.0
- angle_coeff @angle:13-108-21 harmonic 35.0 110.5
- angle_coeff @angle:45-108-45 harmonic 35.0 109.5
- angle_coeff @angle:13-108-45 harmonic 35.0 110.5
- angle_coeff @angle:46-108-46 harmonic 35.0 109.5
- angle_coeff @angle:13-108-46 harmonic 35.0 110.5
- angle_coeff @angle:13-108-65 harmonic 35.0 110.5
- angle_coeff @angle:13-108-66 harmonic 35.0 110.5
- angle_coeff @angle:13-108-108 harmonic 50.0 112.0
- angle_coeff @angle:46-109-48 harmonic 35.0 123.3
- angle_coeff @angle:46-109-50 harmonic 35.0 120.0
- angle_coeff @angle:13-109-50 harmonic 70.0 124.0
- angle_coeff @angle:46-109-109 harmonic 35.0 120.0
- angle_coeff @angle:13-109-109 harmonic 70.0 124.0
- angle_coeff @angle:50-109-109 harmonic 70.0 124.0
- angle_coeff @angle:48-109-109 harmonic 85.0 117.0
- angle_coeff @angle:4-110-47 harmonic 160.0 180.0
- angle_coeff @angle:47-110-47 harmonic 160.0 180.0
- } #(end of angle_coeffs)
-
- write_once("Data Angles By Type") {
- @angle:25-1-25 @atom:*_b*_a25_d*_i* @atom:*_b*_a1_d*_i* @atom:*_b*_a25_d*_i*
- @angle:1-2-2 @atom:*_b*_a1_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i*
- @angle:2-2-2 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i*
- @angle:2-2-3 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i*
- @angle:2-2-5 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a5_d*_i*
- @angle:2-2-6 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i*
- @angle:6-2-6 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i*
- @angle:5-2-6 @atom:*_b*_a5_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i*
- @angle:2-2-10 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i*
- @angle:3-2-10 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i*
- @angle:6-2-10 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i*
- @angle:10-2-10 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i*
- @angle:5-2-10 @atom:*_b*_a5_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i*
- @angle:10-2-12 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a12_d*_i*
- @angle:6-2-13 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a13_d*_i*
- @angle:10-2-15 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a15_d*_i*
- @angle:2-2-16 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a16_d*_i*
- @angle:10-2-16 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a16_d*_i*
- @angle:2-2-20 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i*
- @angle:6-2-20 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i*
- @angle:10-2-20 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i*
- @angle:3-2-24 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a24_d*_i*
- @angle:2-2-24 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a24_d*_i*
- @angle:2-2-44 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i*
- @angle:6-2-44 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i*
- @angle:10-2-44 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i*
- @angle:13-2-44 @atom:*_b*_a13_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i*
- @angle:3-2-44 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i*
- @angle:2-2-48 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a48_d*_i*
- @angle:10-2-48 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a48_d*_i*
- @angle:2-2-51 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a51_d*_i*
- @angle:6-2-51 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a51_d*_i*
- @angle:2-2-53 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a53_d*_i*
- @angle:2-2-55 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a55_d*_i*
- @angle:10-2-80 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a80_d*_i*
- @angle:2-3-4 @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i*
- @angle:1-3-4 @atom:*_b*_a1_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i*
- @angle:3-3-4 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i*
- @angle:4-3-4 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i*
- @angle:4-3-5 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a5_d*_i*
- @angle:4-3-6 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a6_d*_i*
- @angle:5-3-10 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a10_d*_i*
- @angle:4-3-10 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a10_d*_i*
- @angle:5-3-12 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a12_d*_i*
- @angle:12-3-12 @atom:*_b*_a12_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a12_d*_i*
- @angle:5-3-13 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i*
- @angle:13-3-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i*
- @angle:1-3-13 @atom:*_b*_a1_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i*
- @angle:3-3-13 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i*
- @angle:4-3-13 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i*
- @angle:10-3-20 @atom:*_b*_a10_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i*
- @angle:13-3-20 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i*
- @angle:4-3-20 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i*
- @angle:13-3-21 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a21_d*_i*
- @angle:4-3-21 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a21_d*_i*
- @angle:24-3-24 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:2-3-24 @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:3-3-24 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:6-3-24 @atom:*_b*_a6_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:10-3-24 @atom:*_b*_a10_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:13-3-24 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:4-3-24 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:20-3-24 @atom:*_b*_a20_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i*
- @angle:13-3-44 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a44_d*_i*
- @angle:4-3-44 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a44_d*_i*
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- @angle:84-87-88 @atom:*_b*_a84_d*_i* @atom:*_b*_a87_d*_i* @atom:*_b*_a88_d*_i*
- @angle:48-88-49 @atom:*_b*_a48_d*_i* @atom:*_b*_a88_d*_i* @atom:*_b*_a49_d*_i*
- @angle:49-88-61 @atom:*_b*_a49_d*_i* @atom:*_b*_a88_d*_i* @atom:*_b*_a61_d*_i*
- @angle:13-88-61 @atom:*_b*_a13_d*_i* @atom:*_b*_a88_d*_i* @atom:*_b*_a61_d*_i*
- @angle:19-88-61 @atom:*_b*_a19_d*_i* @atom:*_b*_a88_d*_i* @atom:*_b*_a61_d*_i*
- @angle:61-88-87 @atom:*_b*_a61_d*_i* @atom:*_b*_a88_d*_i* @atom:*_b*_a87_d*_i*
- @angle:4-89-90 @atom:*_b*_a4_d*_i* @atom:*_b*_a89_d*_i* @atom:*_b*_a90_d*_i*
- @angle:90-89-91 @atom:*_b*_a90_d*_i* @atom:*_b*_a89_d*_i* @atom:*_b*_a91_d*_i*
- @angle:4-89-91 @atom:*_b*_a4_d*_i* @atom:*_b*_a89_d*_i* @atom:*_b*_a91_d*_i*
- @angle:13-90-89 @atom:*_b*_a13_d*_i* @atom:*_b*_a90_d*_i* @atom:*_b*_a89_d*_i*
- @angle:89-90-91 @atom:*_b*_a89_d*_i* @atom:*_b*_a90_d*_i* @atom:*_b*_a91_d*_i*
- @angle:13-90-91 @atom:*_b*_a13_d*_i* @atom:*_b*_a90_d*_i* @atom:*_b*_a91_d*_i*
- @angle:24-91-46 @atom:*_b*_a24_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a46_d*_i*
- @angle:13-91-46 @atom:*_b*_a13_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a46_d*_i*
- @angle:44-91-46 @atom:*_b*_a44_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a46_d*_i*
- @angle:46-91-46 @atom:*_b*_a46_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a46_d*_i*
- @angle:16-91-46 @atom:*_b*_a16_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a46_d*_i*
- @angle:46-91-47 @atom:*_b*_a46_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a47_d*_i*
- @angle:46-91-89 @atom:*_b*_a46_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a89_d*_i*
- @angle:24-91-89 @atom:*_b*_a24_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a89_d*_i*
- @angle:46-91-90 @atom:*_b*_a46_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a90_d*_i*
- @angle:16-91-90 @atom:*_b*_a16_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a90_d*_i*
- @angle:91-91-91 @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:13-91-91 @atom:*_b*_a13_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:44-91-91 @atom:*_b*_a44_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:46-91-91 @atom:*_b*_a46_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:24-91-91 @atom:*_b*_a24_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:16-91-91 @atom:*_b*_a16_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:89-91-91 @atom:*_b*_a89_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:47-91-91 @atom:*_b*_a47_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:90-91-91 @atom:*_b*_a90_d*_i* @atom:*_b*_a91_d*_i* @atom:*_b*_a91_d*_i*
- @angle:13-95-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a95_d*_i* @atom:*_b*_a13_d*_i*
- @angle:13-95-46 @atom:*_b*_a13_d*_i* @atom:*_b*_a95_d*_i* @atom:*_b*_a46_d*_i*
- @angle:13-101-45 @atom:*_b*_a13_d*_i* @atom:*_b*_a101_d*_i* @atom:*_b*_a45_d*_i*
- @angle:45-101-45 @atom:*_b*_a45_d*_i* @atom:*_b*_a101_d*_i* @atom:*_b*_a45_d*_i*
- @angle:45-101-48 @atom:*_b*_a45_d*_i* @atom:*_b*_a101_d*_i* @atom:*_b*_a48_d*_i*
- @angle:13-101-48 @atom:*_b*_a13_d*_i* @atom:*_b*_a101_d*_i* @atom:*_b*_a48_d*_i*
- @angle:13-102-103 @atom:*_b*_a13_d*_i* @atom:*_b*_a102_d*_i* @atom:*_b*_a103_d*_i*
- @angle:48-102-103 @atom:*_b*_a48_d*_i* @atom:*_b*_a102_d*_i* @atom:*_b*_a103_d*_i*
- @angle:103-102-103 @atom:*_b*_a103_d*_i* @atom:*_b*_a102_d*_i* @atom:*_b*_a103_d*_i*
- @angle:25-103-25 @atom:*_b*_a25_d*_i* @atom:*_b*_a103_d*_i* @atom:*_b*_a25_d*_i*
- @angle:25-103-102 @atom:*_b*_a25_d*_i* @atom:*_b*_a103_d*_i* @atom:*_b*_a102_d*_i*
- @angle:13-104-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a104_d*_i* @atom:*_b*_a13_d*_i*
- @angle:3-105-10 @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a10_d*_i*
- @angle:3-105-13 @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a13_d*_i*
- @angle:3-105-45 @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a45_d*_i*
- @angle:45-105-47 @atom:*_b*_a45_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a47_d*_i*
- @angle:13-105-47 @atom:*_b*_a13_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a47_d*_i*
- @angle:3-105-47 @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a47_d*_i*
- @angle:3-105-51 @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a51_d*_i*
- @angle:47-105-51 @atom:*_b*_a47_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a51_d*_i*
- @angle:45-105-60 @atom:*_b*_a45_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a60_d*_i*
- @angle:6-105-60 @atom:*_b*_a6_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a60_d*_i*
- @angle:10-105-60 @atom:*_b*_a10_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a60_d*_i*
- @angle:13-105-60 @atom:*_b*_a13_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a60_d*_i*
- @angle:51-105-60 @atom:*_b*_a51_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a60_d*_i*
- @angle:45-105-62 @atom:*_b*_a45_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a62_d*_i*
- @angle:60-105-62 @atom:*_b*_a60_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a62_d*_i*
- @angle:6-105-62 @atom:*_b*_a6_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a62_d*_i*
- @angle:10-105-62 @atom:*_b*_a10_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a62_d*_i*
- @angle:13-105-62 @atom:*_b*_a13_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a62_d*_i*
- @angle:51-105-62 @atom:*_b*_a51_d*_i* @atom:*_b*_a105_d*_i* @atom:*_b*_a62_d*_i*
- @angle:4-106-24 @atom:*_b*_a4_d*_i* @atom:*_b*_a106_d*_i* @atom:*_b*_a24_d*_i*
- @angle:24-106-24 @atom:*_b*_a24_d*_i* @atom:*_b*_a106_d*_i* @atom:*_b*_a24_d*_i*
- @angle:13-107-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a107_d*_i* @atom:*_b*_a13_d*_i*
- @angle:3-107-13 @atom:*_b*_a3_d*_i* @atom:*_b*_a107_d*_i* @atom:*_b*_a13_d*_i*
- @angle:1-108-13 @atom:*_b*_a1_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a13_d*_i*
- @angle:13-108-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a13_d*_i*
- @angle:13-108-20 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a20_d*_i*
- @angle:20-108-20 @atom:*_b*_a20_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a20_d*_i*
- @angle:13-108-21 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a21_d*_i*
- @angle:45-108-45 @atom:*_b*_a45_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a45_d*_i*
- @angle:13-108-45 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a45_d*_i*
- @angle:46-108-46 @atom:*_b*_a46_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a46_d*_i*
- @angle:13-108-46 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a46_d*_i*
- @angle:13-108-65 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a65_d*_i*
- @angle:13-108-66 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a66_d*_i*
- @angle:13-108-108 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a108_d*_i*
- @angle:46-109-48 @atom:*_b*_a46_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a48_d*_i*
- @angle:46-109-50 @atom:*_b*_a46_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a50_d*_i*
- @angle:13-109-50 @atom:*_b*_a13_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a50_d*_i*
- @angle:46-109-109 @atom:*_b*_a46_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i*
- @angle:13-109-109 @atom:*_b*_a13_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i*
- @angle:50-109-109 @atom:*_b*_a50_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i*
- @angle:48-109-109 @atom:*_b*_a48_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i*
- @angle:4-110-47 @atom:*_b*_a4_d*_i* @atom:*_b*_a110_d*_i* @atom:*_b*_a47_d*_i*
- @angle:47-110-47 @atom:*_b*_a47_d*_i* @atom:*_b*_a110_d*_i* @atom:*_b*_a47_d*_i*
- } #(end of angles by type)
-
-
- write_once("In Settings") {
- dihedral_coeff @dihedral:X-2-2-2 opls -2.5 1.25 3.1 0.0
- dihedral_coeff @dihedral:X-2-2-6 opls -2.5 1.25 3.1 0.0
- dihedral_coeff @dihedral:1-2-2-2 opls -2.0 0.7 3.0 0.0
- dihedral_coeff @dihedral:1-2-2-6 opls -2.0 0.7 3.0 0.0
- dihedral_coeff @dihedral:2-2-2-2 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-2-6 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-2-10 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-2-13 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-2-65 opls -2.0 0.5 3.25 0.0
- dihedral_coeff @dihedral:6-2-2-6 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:6-2-2-65 opls -2.0 0.5 3.25 0.0
- dihedral_coeff @dihedral:10-2-2-10 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-5-7 opls 0.3 0.0 1.3 0.0
- dihedral_coeff @dihedral:6-2-5-7 opls 0.3 0.0 1.3 0.0
- dihedral_coeff @dihedral:10-2-5-7 opls 0.3 0.0 1.3 0.0
- dihedral_coeff @dihedral:X-2-10-2 opls -2.5 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-10-2 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:2-2-13-2 opls -3.4 1.25 3.1 0.0
- dihedral_coeff @dihedral:6-2-20-2 opls -7.4 3.0 1.8 0.0
- dihedral_coeff @dihedral:6-2-20-6 opls -8.4 3.0 1.8 0.0
- dihedral_coeff @dihedral:4-3-3-4 opls 1.6 3.2 0.0 0.0
- dihedral_coeff @dihedral:4-3-3-13 opls 0.0 0.5 0.0 0.0
- dihedral_coeff @dihedral:4-3-3-24 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-3-46 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:13-3-3-13 opls 0.7 -1.5 0.0 0.0
- dihedral_coeff @dihedral:13-3-3-24 opls -0.5 0.2 0.0 0.0
- dihedral_coeff @dihedral:13-3-3-46 opls 0.8 -0.76 0.0 0.0
- dihedral_coeff @dihedral:24-3-3-46 opls -0.9 0.3 0.0 0.0
- dihedral_coeff @dihedral:46-3-3-46 opls 0.0 0.0 0.3 0.0
- dihedral_coeff @dihedral:3-3-5-7 opls 3.0 5.5 0.0 0.0
- dihedral_coeff @dihedral:4-3-5-7 opls 0.0 5.0 0.0 0.0
- dihedral_coeff @dihedral:13-3-5-7 opls 1.5 5.5 0.0 0.0
- dihedral_coeff @dihedral:24-3-5-7 opls -2.0 5.0 0.0 0.0
- dihedral_coeff @dihedral:46-3-5-7 opls 1.5 5.5 0.0 0.0
- dihedral_coeff @dihedral:48-3-5-7 opls 4.0 5.0 0.0 0.0
- dihedral_coeff @dihedral:1-3-13-13 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:1-3-13-46 opls 0.0 0.0 0.36 0.0
- dihedral_coeff @dihedral:3-3-13-46 opls 0.0 0.0 0.085 0.0
- dihedral_coeff @dihedral:4-3-13-X opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-13-13 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-13-21 opls -0.65 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-13-44 opls 0.0 0.82 0.0 0.0
- dihedral_coeff @dihedral:4-3-13-24 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-13-46 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-13-48 opls 0.0 0.546 0.0 0.0
- dihedral_coeff @dihedral:5-3-13-13 opls 0.0 1.412 0.0 0.0
- dihedral_coeff @dihedral:5-3-13-44 opls 5.26 0.82 0.0 0.0
- dihedral_coeff @dihedral:5-3-13-46 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:13-3-13-13 opls 1.454 -0.144 -0.775 0.0
- dihedral_coeff @dihedral:13-3-13-46 opls 0.0 0.0 0.275 0.0
- dihedral_coeff @dihedral:20-3-13-13 opls 0.0 0.0 -0.553 0.0
- dihedral_coeff @dihedral:20-3-13-46 opls 0.0 0.0 0.132 0.0
- dihedral_coeff @dihedral:21-3-13-13 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:21-3-13-46 opls 0.0 0.0 0.36 0.0
- dihedral_coeff @dihedral:24-3-13-13 opls 1.173 0.189 -1.2 0.0
- dihedral_coeff @dihedral:24-3-13-21 opls 0.65 0.0 0.0 0.0
- dihedral_coeff @dihedral:24-3-13-24 opls 1.816 1.222 1.581 0.0
- dihedral_coeff @dihedral:24-3-13-46 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:46-3-13-13 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:46-3-13-46 opls 0.0 0.0 0.36 0.0
- dihedral_coeff @dihedral:48-3-13-46 opls 0.0 0.0 0.275 0.0
- dihedral_coeff @dihedral:52-3-13-13 opls 0.0 0.82 0.0 0.0
- dihedral_coeff @dihedral:52-3-13-44 opls 0.0 0.82 0.0 0.0
- dihedral_coeff @dihedral:52-3-13-46 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:65-3-13-13 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:65-3-13-46 opls 0.0 0.0 0.36 0.0
- dihedral_coeff @dihedral:107-3-13-46 opls 0.0 0.0 0.0 0.0
- dihedral_coeff @dihedral:4-3-20-13 opls 0.0 5.124 0.0 0.0
- dihedral_coeff @dihedral:4-3-20-48 opls 0.0 5.0 0.0 0.0
- dihedral_coeff @dihedral:13-3-20-13 opls 4.669 5.124 0.0 0.0
- dihedral_coeff @dihedral:13-3-20-48 opls 1.5 5.0 0.0 0.0
- dihedral_coeff @dihedral:24-3-20-13 opls -2.0 5.0 0.0 0.0
- dihedral_coeff @dihedral:46-3-20-13 opls 4.669 5.124 0.0 0.0
- dihedral_coeff @dihedral:48-3-20-13 opls 4.0 5.0 0.0 0.0
- dihedral_coeff @dihedral:3-3-24-13 opls 0.4 4.9 0.0 0.0
- dihedral_coeff @dihedral:3-3-24-45 opls 0.0 4.9 0.0 0.0
- dihedral_coeff @dihedral:4-3-24-5 opls 0.0 6.603 0.0 0.0
- dihedral_coeff @dihedral:4-3-24-13 opls 0.0 6.089 0.0 0.0
- dihedral_coeff @dihedral:4-3-24-45 opls 0.0 4.9 0.0 0.0
- dihedral_coeff @dihedral:4-3-24-47 opls 0.0 6.089 0.0 0.0
- dihedral_coeff @dihedral:4-3-24-48 opls 0.0 6.089 0.0 0.0
- dihedral_coeff @dihedral:4-3-24-91 opls 0.0 6.089 0.0 0.0
- dihedral_coeff @dihedral:5-3-24-13 opls 2.3 6.089 0.0 0.0
- dihedral_coeff @dihedral:5-3-24-45 opls 0.0 4.9 0.0 0.0
- dihedral_coeff @dihedral:13-3-24-5 opls 4.542 6.603 1.045 0.0
- dihedral_coeff @dihedral:13-3-24-13 opls 2.3 6.089 0.0 0.0
- dihedral_coeff @dihedral:13-3-24-45 opls 0.0 4.9 0.0 0.0
- dihedral_coeff @dihedral:13-3-24-48 opls 2.3 6.089 0.0 0.0
- dihedral_coeff @dihedral:20-3-24-13 opls 2.3 6.089 0.0 0.0
- dihedral_coeff @dihedral:20-3-24-45 opls 0.0 4.9 0.0 0.0
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- } #(end of dihedral_coeffs)
-
- write_once("Data Dihedrals By Type") {
- @dihedral:X-2-2-2 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i*
- @dihedral:X-2-2-6 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i*
- @dihedral:1-2-2-2 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i*
- @dihedral:1-2-2-6 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i*
- @dihedral:2-2-2-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i*
- @dihedral:2-2-2-6 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i*
- @dihedral:2-2-2-10 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i*
- @dihedral:2-2-2-13 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13_i*
- @dihedral:2-2-2-65 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d65_i*
- @dihedral:6-2-2-6 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i*
- @dihedral:6-2-2-65 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d65_i*
- @dihedral:10-2-2-10 @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i*
- @dihedral:2-2-5-7 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:6-2-5-7 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:10-2-5-7 @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:X-2-10-2 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i*
- @dihedral:2-2-10-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i*
- @dihedral:2-2-13-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d2_i*
- @dihedral:6-2-20-2 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d2_i*
- @dihedral:6-2-20-6 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d6_i*
- @dihedral:4-3-3-4 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d4_i*
- @dihedral:4-3-3-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-3-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i*
- @dihedral:4-3-3-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-3-3-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-3-3-24 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i*
- @dihedral:13-3-3-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i*
- @dihedral:24-3-3-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-3-3-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i*
- @dihedral:3-3-5-7 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:4-3-5-7 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:13-3-5-7 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:24-3-5-7 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:46-3-5-7 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:48-3-5-7 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i*
- @dihedral:1-3-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:1-3-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:3-3-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:4-3-13-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*
- @dihedral:4-3-13-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-13-21 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i*
- @dihedral:4-3-13-44 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:4-3-13-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:4-3-13-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:4-3-13-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i*
- @dihedral:5-3-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:5-3-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:5-3-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-3-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-3-13-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:20-3-13-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:20-3-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:21-3-13-13 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:21-3-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:24-3-13-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:24-3-13-21 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i*
- @dihedral:24-3-13-24 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:24-3-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-3-13-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-3-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:48-3-13-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:52-3-13-13 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:52-3-13-44 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:52-3-13-46 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:65-3-13-13 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:65-3-13-46 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:107-3-13-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:4-3-20-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-20-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-3-20-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-3-20-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i*
- @dihedral:24-3-20-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-3-20-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:48-3-20-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:3-3-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:3-3-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:4-3-24-5 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i*
- @dihedral:4-3-24-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-24-45 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:4-3-24-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47_i*
- @dihedral:4-3-24-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i*
- @dihedral:4-3-24-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i*
- @dihedral:5-3-24-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:5-3-24-45 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-3-24-5 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i*
- @dihedral:13-3-24-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-3-24-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-3-24-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i*
- @dihedral:20-3-24-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:20-3-24-45 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:24-3-24-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i*
- @dihedral:24-3-24-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:24-3-24-45 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-3-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-3-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:47-3-24-45 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:48-3-24-45 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:48-3-24-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-3-24-84 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i*
- @dihedral:48-3-24-87 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i*
- @dihedral:84-3-24-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i*
- @dihedral:84-3-24-84 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i*
- @dihedral:84-3-24-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i*
- @dihedral:87-3-24-45 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:87-3-24-48 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i*
- @dihedral:87-3-24-84 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i*
- @dihedral:87-3-24-87 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i*
- @dihedral:X-3-47-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-47-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:4-3-47-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:5-3-47-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:24-3-47-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:24-3-47-47 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:107-3-47-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:107-3-47-47 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:4-3-48-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:5-3-48-48 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-3-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:20-3-48-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:24-3-48-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-3-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-3-50-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-50-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:5-3-50-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-3-50-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-3-56-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*
- @dihedral:13-3-56-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-3-56-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*
- @dihedral:46-3-56-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d45_i*
- @dihedral:X-3-60-X @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:4-3-60-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:4-3-82-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:4-3-82-57 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d57_i*
- @dihedral:4-3-82-61 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:82-3-82-57 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d57_i*
- @dihedral:82-3-82-61 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:4-3-84-20 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i*
- @dihedral:4-3-84-87 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i*
- @dihedral:84-3-84-20 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i*
- @dihedral:84-3-84-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i*
- @dihedral:48-3-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-3-87-X @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:4-3-87-84 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i*
- @dihedral:4-3-87-87 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i*
- @dihedral:24-3-87-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i*
- @dihedral:24-3-87-87 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i*
- @dihedral:4-3-107-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-3-107-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-3-109-109 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:5-3-109-109 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:X-4-106-X @atom:* @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d106_i* @atom:*
- @dihedral:7-5-10-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i*
- @dihedral:7-5-10-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d6_i*
- @dihedral:7-5-13-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d2_i*
- @dihedral:7-5-13-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d6_i*
- @dihedral:7-5-13-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:7-5-13-46 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:7-5-13-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i*
- @dihedral:7-5-13-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i*
- @dihedral:7-5-13-50 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i*
- @dihedral:7-5-44-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i*
- @dihedral:7-5-44-45 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i*
- @dihedral:7-5-24-3 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i*
- @dihedral:7-5-24-45 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:7-5-47-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:7-5-48-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:7-5-51-20 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i*
- @dihedral:7-5-56-3 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i*
- @dihedral:7-5-64-4 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d4_i*
- @dihedral:7-5-64-5 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d5_i*
- @dihedral:7-5-79-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i*
- @dihedral:7-5-79-23 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i*
- @dihedral:7-5-79-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-13-13-3 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i*
- @dihedral:X-13-13-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:X-13-13-24 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:1-13-13-1 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d1_i*
- @dihedral:1-13-13-5 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i*
- @dihedral:1-13-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:1-13-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:3-13-13-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i*
- @dihedral:3-13-13-5 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i*
- @dihedral:3-13-13-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:3-13-13-15 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i*
- @dihedral:3-13-13-16 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i*
- @dihedral:3-13-13-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:3-13-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:3-13-13-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i*
- @dihedral:3-13-13-80 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i*
- @dihedral:5-13-13-5 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i*
- @dihedral:5-13-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:5-13-13-20 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i*
- @dihedral:5-13-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:5-13-13-24 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:5-13-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-13-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-13-15 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i*
- @dihedral:13-13-13-16 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i*
- @dihedral:13-13-13-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i*
- @dihedral:13-13-13-21 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i*
- @dihedral:13-13-13-44 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:13-13-13-24 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:13-13-13-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-13-13-51 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i*
- @dihedral:13-13-13-53 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:13-13-13-65 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d65_i*
- @dihedral:13-13-13-66 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d66_i*
- @dihedral:13-13-13-79 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i*
- @dihedral:13-13-13-107 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i*
- @dihedral:13-13-13-108 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i*
- @dihedral:15-13-13-46 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:16-13-13-46 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:19-13-13-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:20-13-13-20 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i*
- @dihedral:20-13-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:21-13-13-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i*
- @dihedral:21-13-13-44 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:21-13-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:44-13-13-44 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i*
- @dihedral:44-13-13-46 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:44-13-13-48 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i*
- @dihedral:24-13-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:24-13-13-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i*
- @dihedral:24-13-13-80 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i*
- @dihedral:46-13-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-13-13-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-13-13-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-13-13-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i*
- @dihedral:46-13-13-53 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:46-13-13-55 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i*
- @dihedral:46-13-13-59 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i*
- @dihedral:46-13-13-62 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i*
- @dihedral:46-13-13-65 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d65_i*
- @dihedral:46-13-13-66 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d66_i*
- @dihedral:46-13-13-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i*
- @dihedral:46-13-13-80 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i*
- @dihedral:46-13-13-82 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i*
- @dihedral:46-13-13-83 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i*
- @dihedral:46-13-13-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i*
- @dihedral:46-13-13-87 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i*
- @dihedral:46-13-13-88 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i*
- @dihedral:46-13-13-102 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i*
- @dihedral:46-13-13-104 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i*
- @dihedral:46-13-13-107 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i*
- @dihedral:46-13-13-108 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i*
- @dihedral:46-13-13-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i*
- @dihedral:48-13-13-53 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:108-13-13-108 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i*
- @dihedral:13-13-15-17 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i*
- @dihedral:46-13-15-17 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i*
- @dihedral:13-13-16-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-16-16 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i*
- @dihedral:46-13-16-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-16-16 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i*
- @dihedral:46-13-16-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-13-18-19 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i*
- @dihedral:46-13-18-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i*
- @dihedral:X-13-19-18 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i*
- @dihedral:X-13-19-19 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i*
- @dihedral:13-13-19-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i*
- @dihedral:46-13-19-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i*
- @dihedral:X-13-20-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:56-13-20-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:57-13-20-13 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-20-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i*
- @dihedral:13-13-20-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-20-64 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i*
- @dihedral:46-13-20-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*
- @dihedral:46-13-20-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i*
- @dihedral:46-13-20-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-13-20-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-13-20-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i*
- @dihedral:46-13-20-64 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i*
- @dihedral:13-13-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-44-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-44-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-44-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-13-24-45 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:3-13-24-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i*
- @dihedral:3-13-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:3-13-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-13-24-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i*
- @dihedral:13-13-24-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-24-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-13-24-59 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i*
- @dihedral:13-13-24-79 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i*
- @dihedral:13-13-24-91 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i*
- @dihedral:46-13-24-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i*
- @dihedral:46-13-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-24-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-13-24-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i*
- @dihedral:48-13-24-59 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i*
- @dihedral:X-13-47-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:X-13-47-46 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:X-13-47-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:X-13-47-50 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i*
- @dihedral:1-13-47-47 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-13-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-13-47-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i*
- @dihedral:46-13-47-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-13-47-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-13-47-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i*
- @dihedral:46-13-47-110 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i*
- @dihedral:47-13-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:47-13-47-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:X-13-48-48 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:1-13-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-13-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-13-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i*
- @dihedral:21-13-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-13-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:64-13-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:65-13-48-48 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-13-50-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-13-50-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i*
- @dihedral:46-13-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-13-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i*
- @dihedral:46-13-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i*
- @dihedral:13-13-51-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*
- @dihedral:13-13-51-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-13-51-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i*
- @dihedral:13-13-53-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-53-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-53-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-53-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-53-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-13-53-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i*
- @dihedral:13-13-55-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-13-55-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-13-55-54 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i*
- @dihedral:46-13-55-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-55-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-55-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-13-56-18 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d18_i*
- @dihedral:X-13-57-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*
- @dihedral:13-13-57-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*
- @dihedral:13-13-57-62 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i*
- @dihedral:13-13-57-82 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i*
- @dihedral:20-13-57-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*
- @dihedral:20-13-57-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i*
- @dihedral:20-13-57-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i*
- @dihedral:13-13-59-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:*
- @dihedral:13-13-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i*
- @dihedral:46-13-59-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:*
- @dihedral:13-13-62-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* @atom:*
- @dihedral:46-13-62-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* @atom:*
- @dihedral:46-13-64-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i*
- @dihedral:46-13-64-52 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i*
- @dihedral:48-13-64-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i*
- @dihedral:48-13-64-52 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i*
- @dihedral:X-13-79-23 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i*
- @dihedral:X-13-79-24 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i*
- @dihedral:13-13-79-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-79-23 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i*
- @dihedral:46-13-79-5 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d5_i*
- @dihedral:46-13-79-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-79-23 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i*
- @dihedral:46-13-79-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-13-80-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*
- @dihedral:13-13-80-60 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i*
- @dihedral:13-13-80-84 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i*
- @dihedral:46-13-80-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*
- @dihedral:46-13-80-60 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i*
- @dihedral:46-13-80-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i*
- @dihedral:13-13-82-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:46-13-82-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:13-13-83-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* @atom:*
- @dihedral:46-13-83-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* @atom:*
- @dihedral:1-13-84-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:13-13-84-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:13-13-84-57 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i*
- @dihedral:21-13-84-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:46-13-84-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:1-13-87-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:13-13-87-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:21-13-87-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:46-13-87-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:13-13-88-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:46-13-88-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:X-13-90-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d90_i* @atom:*
- @dihedral:46-13-90-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d90_i* @atom:*
- @dihedral:46-13-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:13-13-95-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-95-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-13-102-103 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i*
- @dihedral:46-13-102-103 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i*
- @dihedral:13-13-104-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-104-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13_i*
- @dihedral:X-13-105-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*
- @dihedral:13-13-105-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*
- @dihedral:13-13-105-62 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i*
- @dihedral:13-13-105-82 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i*
- @dihedral:20-13-105-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*
- @dihedral:20-13-105-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i*
- @dihedral:20-13-105-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i*
- @dihedral:3-13-107-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-107-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i*
- @dihedral:13-13-107-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-107-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i*
- @dihedral:46-13-107-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-107-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-13-108-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-13-108-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i*
- @dihedral:46-13-108-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-108-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i*
- @dihedral:46-13-108-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-13-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:46-13-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-13-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-13-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:17-15-48-X @atom:*_b*_a*_d17_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d48_i* @atom:*
- @dihedral:17-15-48-48 @atom:*_b*_a*_d17_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-16-16-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-16-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-16-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i*
- @dihedral:13-16-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i*
- @dihedral:84-16-82-X @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:84-16-82-61 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:82-16-84-49 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:82-16-84-83 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d83_i*
- @dihedral:82-16-84-88 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i*
- @dihedral:X-16-91-X @atom:* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d91_i* @atom:*
- @dihedral:19-18-48-X @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d48_i* @atom:*
- @dihedral:19-18-48-48 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:18-18-56-13 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i*
- @dihedral:18-18-56-46 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d46_i*
- @dihedral:X-19-19-X @atom:* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*
- @dihedral:13-19-19-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-19-19-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-19-19-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-19-19-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i*
- @dihedral:46-19-19-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-19-19-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i*
- @dihedral:19-19-47-13 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:19-19-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:19-19-47-47 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-20-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-20-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-20-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-20-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-20-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-20-47-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i*
- @dihedral:3-20-48-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-20-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-20-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i*
- @dihedral:64-20-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-20-51-5 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d5_i*
- @dihedral:13-20-51-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-20-51-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i*
- @dihedral:13-20-51-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-20-56-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i*
- @dihedral:13-20-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i*
- @dihedral:X-20-64-52 @atom:* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i*
- @dihedral:13-20-64-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-20-64-52 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i*
- @dihedral:48-20-64-4 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d4_i*
- @dihedral:84-20-82-61 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:82-20-84-88 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i*
- @dihedral:84-20-84-49 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:84-20-84-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i*
- @dihedral:108-20-108-13 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i*
- @dihedral:108-20-108-20 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i*
- @dihedral:13-44-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-44-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i*
- @dihedral:45-44-44-45 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i*
- @dihedral:13-44-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:45-44-48-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:59-44-48-48 @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:82-44-48-48 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:84-44-48-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:45-44-82-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i*
- @dihedral:45-44-82-61 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:48-44-82-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i*
- @dihedral:48-44-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:X-24-48-48 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:3-24-48-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-24-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:45-24-48-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:59-24-48-48 @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:82-24-48-48 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:84-24-48-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-24-59-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:*
- @dihedral:X-24-59-49 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d49_i*
- @dihedral:45-24-59-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:*
- @dihedral:X-24-60-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:X-24-79-23 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i*
- @dihedral:13-24-79-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i*
- @dihedral:45-24-79-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-24-82-61 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:45-24-82-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i*
- @dihedral:45-24-82-20 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i*
- @dihedral:45-24-82-61 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:48-24-82-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i*
- @dihedral:48-24-82-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i*
- @dihedral:48-24-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:X-24-84-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:3-24-84-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i*
- @dihedral:45-24-84-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i*
- @dihedral:45-24-84-20 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i*
- @dihedral:48-24-84-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i*
- @dihedral:48-24-84-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i*
- @dihedral:3-24-86-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:3-24-86-56 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i*
- @dihedral:3-24-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i*
- @dihedral:47-24-86-48 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:47-24-86-56 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i*
- @dihedral:X-24-87-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:X-24-88-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:3-24-91-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:3-24-91-89 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i*
- @dihedral:3-24-91-91 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:45-24-91-46 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:45-24-91-89 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i*
- @dihedral:45-24-91-91 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:X-24-106-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d106_i* @atom:*
- @dihedral:47-46-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:47-46-47-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:X-47-47-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*
- @dihedral:X-47-47-19 @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d19_i*
- @dihedral:3-47-47-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i*
- @dihedral:3-47-47-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:5-47-47-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:5-47-47-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-47-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-47-47-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d19_i*
- @dihedral:13-47-47-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d20_i*
- @dihedral:13-47-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:19-47-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:20-47-47-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:21-47-47-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d21_i*
- @dihedral:21-47-47-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-47-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-47-47-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-47-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-47-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-47-48-56 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i*
- @dihedral:47-47-48-48 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-47-50-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-47-50-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-47-50-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-47-50-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i*
- @dihedral:13-47-50-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i*
- @dihedral:24-47-50-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i*
- @dihedral:46-47-50-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-47-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-47-50-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-47-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i*
- @dihedral:46-47-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i*
- @dihedral:X-47-84-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:X-47-86-48 @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:3-47-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i*
- @dihedral:49-47-86-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*
- @dihedral:49-47-86-24 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d24_i*
- @dihedral:X-47-87-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:X-47-88-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:13-47-110-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-47-110-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47_i*
- @dihedral:X-48-48-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*
- @dihedral:X-48-48-13 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i*
- @dihedral:X-48-48-48 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-48-48-49 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:1-48-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:1-48-48-49 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:13-48-48-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-48-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-48-48-49 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:13-48-48-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i*
- @dihedral:21-48-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:21-48-48-49 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:44-48-48-49 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:47-48-48-49 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:48-48-48-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-48-48-49 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:48-48-48-50 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i*
- @dihedral:48-48-48-55 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i*
- @dihedral:48-48-48-60 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i*
- @dihedral:48-48-48-65 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d65_i*
- @dihedral:48-48-48-66 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d66_i*
- @dihedral:48-48-48-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i*
- @dihedral:48-48-48-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i*
- @dihedral:49-48-48-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i*
- @dihedral:49-48-48-50 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i*
- @dihedral:49-48-48-60 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i*
- @dihedral:49-48-48-65 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d65_i*
- @dihedral:49-48-48-66 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d66_i*
- @dihedral:49-48-48-86 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i*
- @dihedral:49-48-48-109 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i*
- @dihedral:56-48-48-86 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i*
- @dihedral:48-48-50-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i*
- @dihedral:48-48-50-47 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:56-48-50-46 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i*
- @dihedral:56-48-50-47 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:48-48-53-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i*
- @dihedral:48-48-53-54 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i*
- @dihedral:X-48-55-45 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i*
- @dihedral:48-48-55-45 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i*
- @dihedral:55-48-55-13 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13_i*
- @dihedral:55-48-55-45 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i*
- @dihedral:60-48-55-45 @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i*
- @dihedral:X-48-56-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*
- @dihedral:48-48-56-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i*
- @dihedral:49-48-56-48 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-48-60-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:X-48-79-23 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i*
- @dihedral:48-48-79-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i*
- @dihedral:48-48-79-24 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i*
- @dihedral:48-48-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-48-86-56 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i*
- @dihedral:48-48-86-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i*
- @dihedral:49-48-86-48 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:49-48-86-56 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i*
- @dihedral:49-48-86-86 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i*
- @dihedral:56-48-86-48 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:56-48-86-86 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i*
- @dihedral:49-48-88-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i*
- @dihedral:56-48-101-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d101_i* @atom:*_b*_a*_d13_i*
- @dihedral:48-48-102-103 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i*
- @dihedral:48-48-109-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i*
- @dihedral:48-48-109-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i*
- @dihedral:48-48-109-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:X-50-50-49 @atom:* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d49_i*
- @dihedral:3-50-50-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i*
- @dihedral:13-50-50-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-50-50-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-50-50-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:46-50-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-50-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:47-50-50-47 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i*
- @dihedral:13-50-109-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-50-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:46-50-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i*
- @dihedral:46-50-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-50-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:47-50-109-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i*
- @dihedral:47-50-109-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i*
- @dihedral:47-50-109-109 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:13-53-82-61 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:48-53-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i*
- @dihedral:45-55-59-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d59_i* @atom:*
- @dihedral:13-56-56-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-56-56-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-56-56-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-56-59-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d59_i* @atom:*
- @dihedral:X-56-59-49 @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d49_i*
- @dihedral:X-56-60-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:X-56-62-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d62_i* @atom:*
- @dihedral:X-56-82-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:48-56-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-56-86-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i*
- @dihedral:X-57-60-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:45-57-60-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:X-57-61-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d61_i* @atom:*
- @dihedral:X-57-62-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* @atom:*
- @dihedral:X-57-81-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d81_i* @atom:*
- @dihedral:X-57-82-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:X-57-82-49 @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d49_i*
- @dihedral:45-57-82-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:X-57-84-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:45-57-84-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:61-57-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:84-57-86-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-60-60-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d60_i* @atom:*
- @dihedral:X-60-61-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d61_i* @atom:*
- @dihedral:X-60-80-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d80_i* @atom:*
- @dihedral:X-60-81-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d81_i* @atom:*
- @dihedral:X-60-87-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:48-60-87-84 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i*
- @dihedral:60-60-87-84 @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i*
- @dihedral:X-61-61-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d61_i* @atom:*
- @dihedral:X-61-62-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d62_i* @atom:*
- @dihedral:X-61-82-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*
- @dihedral:X-61-82-49 @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d49_i*
- @dihedral:83-61-82-16 @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i*
- @dihedral:88-61-82-16 @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i*
- @dihedral:88-61-82-20 @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i*
- @dihedral:X-61-83-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*
- @dihedral:82-61-83-49 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d49_i*
- @dihedral:82-61-83-84 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i*
- @dihedral:X-61-84-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:X-61-88-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:82-61-88-84 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d84_i*
- @dihedral:X-80-84-X @atom:* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:X-82-84-X @atom:* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:16-82-86-48 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:20-82-86-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:57-82-86-48 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:61-82-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-82-87-X @atom:* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:X-83-84-X @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:X-83-84-49 @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:49-83-84-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:49-83-84-16 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i*
- @dihedral:49-83-84-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:61-83-84-16 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i*
- @dihedral:61-83-84-20 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i*
- @dihedral:61-83-84-49 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:X-83-86-48 @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:61-83-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:61-83-87-X @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:84-83-87-X @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:X-84-84-X @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*
- @dihedral:X-84-84-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:16-84-84-49 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:49-84-84-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i*
- @dihedral:X-84-86-48 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:16-84-86-48 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:20-84-86-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:57-84-86-48 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:X-84-87-X @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:X-84-87-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i*
- @dihedral:49-84-87-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i*
- @dihedral:X-84-88-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i*
- @dihedral:16-84-88-49 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i*
- @dihedral:16-84-88-61 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i*
- @dihedral:20-84-88-61 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i*
- @dihedral:49-84-88-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:49-84-88-61 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i*
- @dihedral:48-86-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-86-86-56 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i*
- @dihedral:48-86-87-X @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d87_i* @atom:*
- @dihedral:48-86-88-X @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:48-86-88-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i*
- @dihedral:56-86-88-X @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:*
- @dihedral:X-87-87-20 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d20_i*
- @dihedral:X-87-87-57 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d57_i*
- @dihedral:X-87-87-87 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i*
- @dihedral:49-87-87-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i*
- @dihedral:4-89-90-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13_i*
- @dihedral:4-89-90-45 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d45_i*
- @dihedral:4-89-90-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d48_i*
- @dihedral:4-89-90-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i*
- @dihedral:91-89-90-13 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13_i*
- @dihedral:91-89-90-45 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d45_i*
- @dihedral:91-89-90-48 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d48_i*
- @dihedral:91-89-90-91 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i*
- @dihedral:X-89-91-X @atom:* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*
- @dihedral:4-89-91-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:4-89-91-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:90-89-91-46 @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:90-89-91-91 @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:X-90-91-X @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*
- @dihedral:X-90-91-46 @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:X-90-91-91 @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:X-91-91-X @atom:* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*
- @dihedral:X-91-91-24 @atom:* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d24_i*
- @dihedral:13-91-91-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-91-91-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-91-91-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-91-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:91-91-91-91 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i*
- @dihedral:X-109-109-X @atom:* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*
- @dihedral:13-109-109-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i*
- @dihedral:13-109-109-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i*
- @dihedral:13-109-109-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i*
- @dihedral:13-109-109-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i*
- @dihedral:13-109-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:46-109-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i*
- @dihedral:46-109-109-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i*
- @dihedral:46-109-109-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i*
- @dihedral:46-109-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:48-109-109-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i*
- @dihedral:48-109-109-50 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i*
- @dihedral:48-109-109-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:50-109-109-50 @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i*
- @dihedral:50-109-109-109 @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:109-109-109-109 @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i*
- @dihedral:24-3-13-53 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:52-3-13-24 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i*
- @dihedral:3-13-13-53 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:3-13-13-83 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i*
- @dihedral:3-13-13-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i*
- @dihedral:3-13-13-85 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i*
- @dihedral:5-13-13-53 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:15-13-13-53 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:16-13-13-53 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i*
- @dihedral:13-13-13-55 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i*
- @dihedral:24-13-13-83 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i*
- @dihedral:53-13-13-83 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i*
- @dihedral:24-13-13-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i*
- @dihedral:53-13-13-84 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i*
- @dihedral:24-13-13-85 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i*
- @dihedral:46-13-13-85 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i*
- @dihedral:53-13-13-85 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i*
- @dihedral:3-13-53-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i*
- @dihedral:3-13-53-54 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i*
- @dihedral:13-13-53-54 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i*
- @dihedral:46-13-55-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i*
- @dihedral:13-13-85-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:*
- @dihedral:13-13-85-57 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d57_i*
- @dihedral:46-13-85-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:*
- @dihedral:55-48-55-54 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i*
- @dihedral:X-48-81-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d81_i* @atom:*
- @dihedral:X-57-85-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d85_i* @atom:*
- @dihedral:X-85-85-X @atom:* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d85_i* @atom:*
- @dihedral:13-13-13-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i*
- @dihedral:13-13-13-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i*
- } #(end of dihedrals by type)
-
-
- write_once("In Settings") {
- improper_coeff @improper:X-X-3-4 harmonic 10.5 180.0
- improper_coeff @improper:X-X-3-52 harmonic 10.5 180.0
- improper_coeff @improper:X-X-24-X harmonic 2.5 180.0
- improper_coeff @improper:X-X-47-X harmonic 15.0 180.0
- improper_coeff @improper:X-X-48-X harmonic 2.5 180.0
- } #(end of improper_coeffs)
-
- write_once("Data Impropers By Type (opls_imp.py)") {
- @improper:X-X-3-4 @atom:* @atom:* @atom:*_b*_a*_d*_i3 @atom:*_b*_a*_d*_i4
- @improper:X-X-3-52 @atom:* @atom:* @atom:*_b*_a*_d*_i3 @atom:*_b*_a*_d*_i52
- @improper:X-X-24-X @atom:* @atom:* @atom:*_b*_a*_d*_i24 @atom:*
- @improper:X-X-47-X @atom:* @atom:* @atom:*_b*_a*_d*_i47 @atom:*
- @improper:X-X-48-X @atom:* @atom:* @atom:*_b*_a*_d*_i48 @atom:*
- } #(end of impropers by type)
-
-
- # -------- (descriptive comment) --------
- # ---- biologically relevant atom types: ----
- # biotype 1 N "Glycine" 180
- # biotype 2 CA "Glycine" 165
- # biotype 3 C "Glycine" 177
- # biotype 4 HN "Glycine" 183
- # biotype 5 O "Glycine" 178
- # biotype 6 HA "Glycine" 85
- # biotype 7 N "Alanine" 180
- # biotype 8 CA "Alanine" 166
- # biotype 9 C "Alanine" 177
- # biotype 10 HN "Alanine" 183
- # biotype 11 O "Alanine" 178
- # biotype 12 HA "Alanine" 85
- # biotype 13 CB "Alanine" 80
- # biotype 14 HB "Alanine" 85
- # biotype 15 N "Valine" 180
- # biotype 16 CA "Valine" 166
- # biotype 17 C "Valine" 177
- # biotype 18 HN "Valine" 183
- # biotype 19 O "Valine" 178
- # biotype 20 HA "Valine" 85
- # biotype 21 CB "Valine" 82
- # biotype 22 HB "Valine" 85
- # biotype 23 CG1 "Valine" 80
- # biotype 24 HG1 "Valine" 85
- # biotype 25 CG2 "Valine" 80
- # biotype 26 HG2 "Valine" 85
- # biotype 27 N "Leucine" 180
- # biotype 28 CA "Leucine" 166
- # biotype 29 C "Leucine" 177
- # biotype 30 HN "Leucine" 183
- # biotype 31 O "Leucine" 178
- # biotype 32 HA "Leucine" 85
- # biotype 33 CB "Leucine" 81
- # biotype 34 HB "Leucine" 85
- # biotype 35 CG "Leucine" 82
- # biotype 36 HG "Leucine" 85
- # biotype 37 CD1 "Leucine" 80
- # biotype 38 HD1 "Leucine" 85
- # biotype 39 CD2 "Leucine" 80
- # biotype 40 HD2 "Leucine" 85
- # biotype 41 N "Isoleucine" 180
- # biotype 42 CA "Isoleucine" 166
- # biotype 43 C "Isoleucine" 177
- # biotype 44 HN "Isoleucine" 183
- # biotype 45 O "Isoleucine" 178
- # biotype 46 HA "Isoleucine" 85
- # biotype 47 CB "Isoleucine" 82
- # biotype 48 HB "Isoleucine" 85
- # biotype 49 CG1 "Isoleucine" 80
- # biotype 50 HG1 "Isoleucine" 85
- # biotype 51 CG2 "Isoleucine" 81
- # biotype 52 HG2 "Isoleucine" 85
- # biotype 53 CD "Isoleucine" 80
- # biotype 54 HD "Isoleucine" 85
- # biotype 55 N "Serine" 180
- # biotype 56 CA "Serine" 166
- # biotype 57 C "Serine" 177
- # biotype 58 HN "Serine" 183
- # biotype 59 O "Serine" 178
- # biotype 60 HA "Serine" 85
- # biotype 61 CB "Serine" 99
- # biotype 62 HB "Serine" 85
- # biotype 63 OG "Serine" 96
- # biotype 64 HG "Serine" 97
- # biotype 65 N "Threonine" 180
- # biotype 66 CA "Threonine" 166
- # biotype 67 C "Threonine" 177
- # biotype 68 HN "Threonine" 183
- # biotype 69 O "Threonine" 178
- # biotype 70 HA "Threonine" 85
- # biotype 71 CB "Threonine" 100
- # biotype 72 HB "Threonine" 85
- # biotype 73 OG1 "Threonine" 96
- # biotype 74 HG1 "Threonine" 97
- # biotype 75 CG2 "Threonine" 80
- # biotype 76 HG2 "Threonine" 85
- # biotype 77 N "Cysteine (SH)" 180
- # biotype 78 CA "Cysteine (SH)" 166
- # biotype 79 C "Cysteine (SH)" 177
- # biotype 80 HN "Cysteine (SH)" 183
- # biotype 81 O "Cysteine (SH)" 178
- # biotype 82 HA "Cysteine (SH)" 85
- # biotype 83 CB "Cysteine (SH)" 148
- # biotype 84 HB "Cysteine (SH)" 85
- # biotype 85 SG "Cysteine (SH)" 142
- # biotype 86 HG "Cysteine (SH)" 146
- # biotype 87 N "Cystine (SS)" 180
- # biotype 88 CA "Cystine (SS)" 166
- # biotype 89 C "Cystine (SS)" 177
- # biotype 90 HN "Cystine (SS)" 183
- # biotype 91 O "Cystine (SS)" 178
- # biotype 92 HA "Cystine (SS)" 85
- # biotype 93 CB "Cystine (SS)" 156
- # biotype 94 HB "Cystine (SS)" 85
- # biotype 95 SG "Cystine (SS)" 145
- # biotype 96 N "Cysteine (S-)" -1
- # biotype 97 CA "Cysteine (S-)" -1
- # biotype 98 C "Cysteine (S-)" -1
- # biotype 99 HN "Cysteine (S-)" -1
- # biotype 100 O "Cysteine (S-)" -1
- # biotype 101 HA "Cysteine (S-)" -1
- # biotype 102 CB "Cysteine (S-)" -1
- # biotype 103 HB "Cysteine (S-)" -1
- # biotype 104 SG "Cysteine (S-)" -1
- # biotype 105 N "Proline" 181
- # biotype 106 CA "Proline" 188
- # biotype 107 C "Proline" 177
- # biotype 108 O "Proline" 178
- # biotype 109 HA "Proline" 85
- # biotype 110 CB "Proline" 81
- # biotype 111 HB "Proline" 85
- # biotype 112 CG "Proline" 81
- # biotype 113 HG "Proline" 85
- # biotype 114 CD "Proline" 187
- # biotype 115 HD "Proline" 85
- # biotype 116 N "Phenylalanine" 180
- # biotype 117 CA "Phenylalanine" 166
- # biotype 118 C "Phenylalanine" 177
- # biotype 119 HN "Phenylalanine" 183
- # biotype 120 O "Phenylalanine" 178
- # biotype 121 HA "Phenylalanine" 85
- # biotype 122 CB "Phenylalanine" 94
- # biotype 123 HB "Phenylalanine" 85
- # biotype 124 CG "Phenylalanine" 90
- # biotype 125 CD "Phenylalanine" 90
- # biotype 126 HD "Phenylalanine" 91
- # biotype 127 CE "Phenylalanine" 90
- # biotype 128 HE "Phenylalanine" 91
- # biotype 129 CZ "Phenylalanine" 90
- # biotype 130 HZ "Phenylalanine" 91
- # biotype 131 N "Tyrosine" 180
- # biotype 132 CA "Tyrosine" 166
- # biotype 133 C "Tyrosine" 177
- # biotype 134 HN "Tyrosine" 183
- # biotype 135 O "Tyrosine" 178
- # biotype 136 HA "Tyrosine" 85
- # biotype 137 CB "Tyrosine" 94
- # biotype 138 HB "Tyrosine" 85
- # biotype 139 CG "Tyrosine" 90
- # biotype 140 CD "Tyrosine" 90
- # biotype 141 HD "Tyrosine" 91
- # biotype 142 CE "Tyrosine" 90
- # biotype 143 HE "Tyrosine" 91
- # biotype 144 CZ "Tyrosine" 108
- # biotype 145 OH "Tyrosine" 109
- # biotype 146 HH "Tyrosine" 110
- # biotype 147 N "Tyrosine (O-)" -1
- # biotype 148 CA "Tyrosine (O-)" -1
- # biotype 149 C "Tyrosine (O-)" -1
- # biotype 150 HN "Tyrosine (O-)" -1
- # biotype 151 O "Tyrosine (O-)" -1
- # biotype 152 HA "Tyrosine (O-)" -1
- # biotype 153 CB "Tyrosine (O-)" -1
- # biotype 154 HB "Tyrosine (O-)" -1
- # biotype 155 CG "Tyrosine (O-)" -1
- # biotype 156 CD "Tyrosine (O-)" -1
- # biotype 157 HD "Tyrosine (O-)" -1
- # biotype 158 CE "Tyrosine (O-)" -1
- # biotype 159 HE "Tyrosine (O-)" -1
- # biotype 160 CZ "Tyrosine (O-)" -1
- # biotype 161 OH "Tyrosine (O-)" -1
- # biotype 162 N "Tryptophan" 180
- # biotype 163 CA "Tryptophan" 166
- # biotype 164 C "Tryptophan" 177
- # biotype 165 HN "Tryptophan" 183
- # biotype 166 O "Tryptophan" 178
- # biotype 167 HA "Tryptophan" 85
- # biotype 168 CB "Tryptophan" 81
- # biotype 169 HB "Tryptophan" 85
- # biotype 170 CG "Tryptophan" 441
- # biotype 171 CD1 "Tryptophan" 455
- # biotype 172 HD1 "Tryptophan" 91
- # biotype 173 CD2 "Tryptophan" 442
- # biotype 174 NE1 "Tryptophan" 444
- # biotype 175 HE1 "Tryptophan" 445
- # biotype 176 CE2 "Tryptophan" 443
- # biotype 177 CE3 "Tryptophan" 90
- # biotype 178 HE3 "Tryptophan" 91
- # biotype 179 CZ2 "Tryptophan" 90
- # biotype 180 HZ2 "Tryptophan" 91
- # biotype 181 CZ3 "Tryptophan" 90
- # biotype 182 HZ3 "Tryptophan" 91
- # biotype 183 CH2 "Tryptophan" 90
- # biotype 184 HH2 "Tryptophan" 91
- # biotype 185 N "Histidine (+)" 180
- # biotype 186 CA "Histidine (+)" 166
- # biotype 187 C "Histidine (+)" 177
- # biotype 188 HN "Histidine (+)" 183
- # biotype 189 O "Histidine (+)" 178
- # biotype 190 HA "Histidine (+)" 85
- # biotype 191 CB "Histidine (+)" 446
- # biotype 192 HB "Histidine (+)" 85
- # biotype 193 CG "Histidine (+)" 451
- # biotype 194 ND1 "Histidine (+)" 453
- # biotype 195 HD1 "Histidine (+)" 454
- # biotype 196 CD2 "Histidine (+)" 451
- # biotype 197 HD2 "Histidine (+)" 91
- # biotype 198 CE1 "Histidine (+)" 450
- # biotype 199 HE1 "Histidine (+)" 91
- # biotype 200 NE2 "Histidine (+)" 453
- # biotype 201 HE2 "Histidine (+)" 454
- # biotype 202 N "Histidine (HD)" 180
- # biotype 203 CA "Histidine (HD)" 166
- # biotype 204 C "Histidine (HD)" 177
- # biotype 205 HN "Histidine (HD)" 183
- # biotype 206 O "Histidine (HD)" 178
- # biotype 207 HA "Histidine (HD)" 85
- # biotype 208 CB "Histidine (HD)" 446
- # biotype 209 HB "Histidine (HD)" 85
- # biotype 210 CG "Histidine (HD)" 449
- # biotype 211 ND1 "Histidine (HD)" 444
- # biotype 212 HD1 "Histidine (HD)" 445
- # biotype 213 CD2 "Histidine (HD)" 448
- # biotype 214 HD2 "Histidine (HD)" 91
- # biotype 215 CE1 "Histidine (HD)" 447
- # biotype 216 HE1 "Histidine (HD)" 91
- # biotype 217 NE2 "Histidine (HD)" 452
- # biotype 218 N "Histidine (HE)" 180
- # biotype 219 CA "Histidine (HE)" 166
- # biotype 220 C "Histidine (HE)" 177
- # biotype 221 HN "Histidine (HE)" 183
- # biotype 222 O "Histidine (HE)" 178
- # biotype 223 HA "Histidine (HE)" 85
- # biotype 224 CB "Histidine (HE)" 446
- # biotype 225 HB "Histidine (HE)" 85
- # biotype 226 CG "Histidine (HE)" 448
- # biotype 227 ND1 "Histidine (HE)" 452
- # biotype 228 CD2 "Histidine (HE)" 449
- # biotype 229 HD2 "Histidine (HE)" 91
- # biotype 230 CE1 "Histidine (HE)" 447
- # biotype 231 HE1 "Histidine (HE)" 91
- # biotype 232 NE2 "Histidine (HE)" 444
- # biotype 233 HE2 "Histidine (HE)" 445
- # biotype 234 N "Aspartic Acid" 180
- # biotype 235 CA "Aspartic Acid" 166
- # biotype 236 C "Aspartic Acid" 177
- # biotype 237 HN "Aspartic Acid" 183
- # biotype 238 O "Aspartic Acid" 178
- # biotype 239 HA "Aspartic Acid" 85
- # biotype 240 CB "Aspartic Acid" 216
- # biotype 241 HB "Aspartic Acid" 85
- # biotype 242 CG "Aspartic Acid" 213
- # biotype 243 OD "Aspartic Acid" 214
- # biotype 244 N "Aspartic Acid (COOH)" -1
- # biotype 245 CA "Aspartic Acid (COOH)" -1
- # biotype 246 C "Aspartic Acid (COOH)" -1
- # biotype 247 HN "Aspartic Acid (COOH)" -1
- # biotype 248 O "Aspartic Acid (COOH)" -1
- # biotype 249 HA "Aspartic Acid (COOH)" -1
- # biotype 250 CB "Aspartic Acid (COOH)" -1
- # biotype 251 HB "Aspartic Acid (COOH)" -1
- # biotype 252 CG "Aspartic Acid (COOH)" -1
- # biotype 253 OD1 "Aspartic Acid (COOH)" -1
- # biotype 254 OD2 "Aspartic Acid (COOH)" -1
- # biotype 255 HD2 "Aspartic Acid (COOH)" -1
- # biotype 256 N "Asparagine" 180
- # biotype 257 CA "Asparagine" 166
- # biotype 258 C "Asparagine" 177
- # biotype 259 HN "Asparagine" 183
- # biotype 260 O "Asparagine" 178
- # biotype 261 HA "Asparagine" 85
- # biotype 262 CB "Asparagine" 81
- # biotype 263 HB "Asparagine" 85
- # biotype 264 CG "Asparagine" 177
- # biotype 265 OD1 "Asparagine" 178
- # biotype 266 ND2 "Asparagine" 179
- # biotype 267 HD2 "Asparagine" 182
- # biotype 268 N "Glutamic Acid" 180
- # biotype 269 CA "Glutamic Acid" 166
- # biotype 270 C "Glutamic Acid" 177
- # biotype 271 HN "Glutamic Acid" 183
- # biotype 272 O "Glutamic Acid" 178
- # biotype 273 HA "Glutamic Acid" 85
- # biotype 274 CB "Glutamic Acid" 81
- # biotype 275 HB "Glutamic Acid" 85
- # biotype 276 CG "Glutamic Acid" 216
- # biotype 277 HG "Glutamic Acid" 85
- # biotype 278 CD "Glutamic Acid" 213
- # biotype 279 OE "Glutamic Acid" 214
- # biotype 280 N "Glutamic Acid (COOH)" -1
- # biotype 281 CA "Glutamic Acid (COOH)" -1
- # biotype 282 C "Glutamic Acid (COOH)" -1
- # biotype 283 HN "Glutamic Acid (COOH)" -1
- # biotype 284 O "Glutamic Acid (COOH)" -1
- # biotype 285 HA "Glutamic Acid (COOH)" -1
- # biotype 286 CB "Glutamic Acid (COOH)" -1
- # biotype 287 HB "Glutamic Acid (COOH)" -1
- # biotype 288 CG "Glutamic Acid (COOH)" -1
- # biotype 289 HG "Glutamic Acid (COOH)" -1
- # biotype 290 CD "Glutamic Acid (COOH)" -1
- # biotype 291 OE1 "Glutamic Acid (COOH)" -1
- # biotype 292 OE2 "Glutamic Acid (COOH)" -1
- # biotype 293 HE2 "Glutamic Acid (COOH)" -1
- # biotype 294 N "Glutamine" 180
- # biotype 295 CA "Glutamine" 166
- # biotype 296 C "Glutamine" 177
- # biotype 297 HN "Glutamine" 183
- # biotype 298 O "Glutamine" 178
- # biotype 299 HA "Glutamine" 85
- # biotype 300 CB "Glutamine" 81
- # biotype 301 HB "Glutamine" 85
- # biotype 302 CG "Glutamine" 81
- # biotype 303 HG "Glutamine" 85
- # biotype 304 CD "Glutamine" 177
- # biotype 305 OE1 "Glutamine" 178
- # biotype 306 NE2 "Glutamine" 179
- # biotype 307 HE2 "Glutamine" 182
- # biotype 308 N "Methionine" 180
- # biotype 309 CA "Methionine" 166
- # biotype 310 C "Methionine" 177
- # biotype 311 HN "Methionine" 183
- # biotype 312 O "Methionine" 178
- # biotype 313 HA "Methionine" 85
- # biotype 314 CB "Methionine" 81
- # biotype 315 HB "Methionine" 85
- # biotype 316 CG "Methionine" 152
- # biotype 317 HG "Methionine" 85
- # biotype 318 SD "Methionine" 144
- # biotype 319 CE "Methionine" 151
- # biotype 320 HE "Methionine" 85
- # biotype 321 N "Lysine" 180
- # biotype 322 CA "Lysine" 166
- # biotype 323 C "Lysine" 177
- # biotype 324 HN "Lysine" 183
- # biotype 325 O "Lysine" 178
- # biotype 326 HA "Lysine" 85
- # biotype 327 CB "Lysine" 81
- # biotype 328 HB "Lysine" 85
- # biotype 329 CG "Lysine" 81
- # biotype 330 HG "Lysine" 85
- # biotype 331 CD "Lysine" 81
- # biotype 332 HD "Lysine" 85
- # biotype 333 CE "Lysine" 235
- # biotype 334 HE "Lysine" 85
- # biotype 335 NZ "Lysine" 230
- # biotype 336 HZ "Lysine" 233
- # biotype 337 N "Lysine (NH2)" -1
- # biotype 338 CA "Lysine (NH2)" -1
- # biotype 339 C "Lysine (NH2)" -1
- # biotype 340 HN "Lysine (NH2)" -1
- # biotype 341 O "Lysine (NH2)" -1
- # biotype 342 HA "Lysine (NH2)" -1
- # biotype 343 CB "Lysine (NH2)" -1
- # biotype 344 HB "Lysine (NH2)" -1
- # biotype 345 CG "Lysine (NH2)" -1
- # biotype 346 HG "Lysine (NH2)" -1
- # biotype 347 CD "Lysine (NH2)" -1
- # biotype 348 HD "Lysine (NH2)" -1
- # biotype 349 CE "Lysine (NH2)" -1
- # biotype 350 HE "Lysine (NH2)" -1
- # biotype 351 NZ "Lysine (NH2)" -1
- # biotype 352 HZ "Lysine (NH2)" -1
- # biotype 353 N "Arginine" 180
- # biotype 354 CA "Arginine" 166
- # biotype 355 C "Arginine" 177
- # biotype 356 HN "Arginine" 183
- # biotype 357 O "Arginine" 178
- # biotype 358 HA "Arginine" 85
- # biotype 359 CB "Arginine" 81
- # biotype 360 HB "Arginine" 85
- # biotype 361 CG "Arginine" 251
- # biotype 362 HG "Arginine" 85
- # biotype 363 CD "Arginine" 250
- # biotype 364 HD "Arginine" 85
- # biotype 365 NE "Arginine" 246
- # biotype 366 HE "Arginine" 247
- # biotype 367 CZ "Arginine" 245
- # biotype 368 NH "Arginine" 243
- # biotype 369 HH "Arginine" 244
- # biotype 370 N "Ornithine" 180
- # biotype 371 CA "Ornithine" 166
- # biotype 372 C "Ornithine" 177
- # biotype 373 HN "Ornithine" 183
- # biotype 374 O "Ornithine" 178
- # biotype 375 HA "Ornithine" 85
- # biotype 376 CB "Ornithine" 81
- # biotype 377 HB "Ornithine" 85
- # biotype 378 CG "Ornithine" 81
- # biotype 379 HG "Ornithine" 85
- # biotype 380 CD "Ornithine" 235
- # biotype 381 HD "Ornithine" 85
- # biotype 382 NE "Ornithine" 230
- # biotype 383 HE "Ornithine" 233
- # biotype 384 N "MethylAlanine (AIB)" 180
- # biotype 385 CA "MethylAlanine (AIB)" 167
- # biotype 386 C "MethylAlanine (AIB)" 177
- # biotype 387 HN "MethylAlanine (AIB)" 183
- # biotype 388 O "MethylAlanine (AIB)" 178
- # biotype 389 CB "MethylAlanine (AIB)" 80
- # biotype 390 HB "MethylAlanine (AIB)" 85
- # biotype 391 N "Pyroglutamic Acid" 180
- # biotype 392 CA "Pyroglutamic Acid" 166
- # biotype 393 C "Pyroglutamic Acid" 177
- # biotype 394 HN "Pyroglutamic Acid" 183
- # biotype 395 O "Pyroglutamic Acid" 178
- # biotype 396 HA "Pyroglutamic Acid" 85
- # biotype 397 CB "Pyroglutamic Acid" 81
- # biotype 398 HB "Pyroglutamic Acid" 85
- # biotype 399 CG "Pyroglutamic Acid" 216
- # biotype 400 HG "Pyroglutamic Acid" 85
- # biotype 401 CD "Pyroglutamic Acid" 177
- # biotype 402 OE "Pyroglutamic Acid" 178
- # biotype 403 N "N-Terminal GLY" 230
- # biotype 404 CA "N-Terminal GLY" 235
- # biotype 405 C "N-Terminal GLY" 177
- # biotype 406 HN "N-Terminal GLY" 233
- # biotype 407 O "N-Terminal GLY" 178
- # biotype 408 HA "N-Terminal GLY" 85
- # biotype 409 N "N-Terminal ALA" 230
- # biotype 410 CA "N-Terminal ALA" 236
- # biotype 411 C "N-Terminal ALA" 177
- # biotype 412 HN "N-Terminal ALA" 233
- # biotype 413 O "N-Terminal ALA" 178
- # biotype 414 HA "N-Terminal ALA" 85
- # biotype 415 N "N-Terminal VAL" 230
- # biotype 416 CA "N-Terminal VAL" 236
- # biotype 417 C "N-Terminal VAL" 177
- # biotype 418 HN "N-Terminal VAL" 233
- # biotype 419 O "N-Terminal VAL" 178
- # biotype 420 HA "N-Terminal VAL" 85
- # biotype 421 N "N-Terminal LEU" 230
- # biotype 422 CA "N-Terminal LEU" 236
- # biotype 423 C "N-Terminal LEU" 177
- # biotype 424 HN "N-Terminal LEU" 233
- # biotype 425 O "N-Terminal LEU" 178
- # biotype 426 HA "N-Terminal LEU" 85
- # biotype 427 N "N-Terminal ILE" 230
- # biotype 428 CA "N-Terminal ILE" 236
- # biotype 429 C "N-Terminal ILE" 177
- # biotype 430 HN "N-Terminal ILE" 233
- # biotype 431 O "N-Terminal ILE" 178
- # biotype 432 HA "N-Terminal ILE" 85
- # biotype 433 N "N-Terminal SER" 230
- # biotype 434 CA "N-Terminal SER" 236
- # biotype 435 C "N-Terminal SER" 177
- # biotype 436 HN "N-Terminal SER" 233
- # biotype 437 O "N-Terminal SER" 178
- # biotype 438 HA "N-Terminal SER" 85
- # biotype 439 N "N-Terminal THR" 230
- # biotype 440 CA "N-Terminal THR" 236
- # biotype 441 C "N-Terminal THR" 177
- # biotype 442 HN "N-Terminal THR" 233
- # biotype 443 O "N-Terminal THR" 178
- # biotype 444 HA "N-Terminal THR" 85
- # biotype 445 N "N-Terminal CYS (SH)" 230
- # biotype 446 CA "N-Terminal CYS (SH)" 236
- # biotype 447 C "N-Terminal CYS (SH)" 177
- # biotype 448 HN "N-Terminal CYS (SH)" 233
- # biotype 449 O "N-Terminal CYS (SH)" 178
- # biotype 450 HA "N-Terminal CYS (SH)" 85
- # biotype 451 N "N-Terminal CYX (SS)" 230
- # biotype 452 CA "N-Terminal CYX (SS)" 236
- # biotype 453 C "N-Terminal CYX (SS)" 177
- # biotype 454 HN "N-Terminal CYX (SS)" 233
- # biotype 455 O "N-Terminal CYX (SS)" 178
- # biotype 456 HA "N-Terminal CYX (SS)" 85
- # biotype 457 N "N-Terminal CYD (S-)" -1
- # biotype 458 CA "N-Terminal CYD (S-)" -1
- # biotype 459 C "N-Terminal CYD (S-)" -1
- # biotype 460 HN "N-Terminal CYD (S-)" -1
- # biotype 461 O "N-Terminal CYD (S-)" -1
- # biotype 462 HA "N-Terminal CYD (S-)" -1
- # biotype 463 N "N-Terminal PRO" 252
- # biotype 464 CA "N-Terminal PRO" 238
- # biotype 465 C "N-Terminal PRO" 177
- # biotype 466 HN "N-Terminal PRO" 253
- # biotype 467 O "N-Terminal PRO" 178
- # biotype 468 HA "N-Terminal PRO" 85
- # biotype 469 CD "N-Terminal PRO" 239
- # biotype 470 HD "N-Terminal PRO" 85
- # biotype 471 N "N-Terminal PHE" 230
- # biotype 472 CA "N-Terminal PHE" 236
- # biotype 473 C "N-Terminal PHE" 177
- # biotype 474 HN "N-Terminal PHE" 233
- # biotype 475 O "N-Terminal PHE" 178
- # biotype 476 HA "N-Terminal PHE" 85
- # biotype 477 N "N-Terminal TYR" 230
- # biotype 478 CA "N-Terminal TYR" 236
- # biotype 479 C "N-Terminal TYR" 177
- # biotype 480 HN "N-Terminal TYR" 233
- # biotype 481 O "N-Terminal TYR" 178
- # biotype 482 HA "N-Terminal TYR" 85
- # biotype 483 N "N-Terminal TYD (O-)" -1
- # biotype 484 CA "N-Terminal TYD (O-)" -1
- # biotype 485 C "N-Terminal TYD (O-)" -1
- # biotype 486 HN "N-Terminal TYD (O-)" -1
- # biotype 487 O "N-Terminal TYD (O-)" -1
- # biotype 488 HA "N-Terminal TYD (O-)" -1
- # biotype 489 N "N-Terminal TRP" 230
- # biotype 490 CA "N-Terminal TRP" 236
- # biotype 491 C "N-Terminal TRP" 177
- # biotype 492 HN "N-Terminal TRP" 233
- # biotype 493 O "N-Terminal TRP" 178
- # biotype 494 HA "N-Terminal TRP" 85
- # biotype 495 N "N-Terminal HIS (+)" 230
- # biotype 496 CA "N-Terminal HIS (+)" 236
- # biotype 497 C "N-Terminal HIS (+)" 177
- # biotype 498 HN "N-Terminal HIS (+)" 233
- # biotype 499 O "N-Terminal HIS (+)" 178
- # biotype 500 HA "N-Terminal HIS (+)" 85
- # biotype 501 N "N-Terminal HIS (HD)" 230
- # biotype 502 CA "N-Terminal HIS (HD)" 236
- # biotype 503 C "N-Terminal HIS (HD)" 177
- # biotype 504 HN "N-Terminal HIS (HD)" 233
- # biotype 505 O "N-Terminal HIS (HD)" 178
- # biotype 506 HA "N-Terminal HIS (HD)" 85
- # biotype 507 N "N-Terminal HIS (HE)" 230
- # biotype 508 CA "N-Terminal HIS (HE)" 236
- # biotype 509 C "N-Terminal HIS (HE)" 177
- # biotype 510 HN "N-Terminal HIS (HE)" 233
- # biotype 511 O "N-Terminal HIS (HE)" 178
- # biotype 512 HA "N-Terminal HIS (HE)" 85
- # biotype 513 N "N-Terminal ASP" 230
- # biotype 514 CA "N-Terminal ASP" 236
- # biotype 515 C "N-Terminal ASP" 177
- # biotype 516 HN "N-Terminal ASP" 233
- # biotype 517 O "N-Terminal ASP" 178
- # biotype 518 HA "N-Terminal ASP" 85
- # biotype 519 N "N-Terminal ASH (COOH)" -1
- # biotype 520 CA "N-Terminal ASH (COOH)" -1
- # biotype 521 C "N-Terminal ASH (COOH)" -1
- # biotype 522 HN "N-Terminal ASH (COOH)" -1
- # biotype 523 O "N-Terminal ASH (COOH)" -1
- # biotype 524 HA "N-Terminal ASH (COOH)" -1
- # biotype 525 N "N-Terminal ASN" 230
- # biotype 526 CA "N-Terminal ASN" 236
- # biotype 527 C "N-Terminal ASN" 177
- # biotype 528 HN "N-Terminal ASN" 233
- # biotype 529 O "N-Terminal ASN" 178
- # biotype 530 HA "N-Terminal ASN" 85
- # biotype 531 N "N-Terminal GLU" 230
- # biotype 532 CA "N-Terminal GLU" 236
- # biotype 533 C "N-Terminal GLU" 177
- # biotype 534 HN "N-Terminal GLU" 233
- # biotype 535 O "N-Terminal GLU" 178
- # biotype 536 HA "N-Terminal GLU" 85
- # biotype 537 N "N-Terminal GLH (COOH)" -1
- # biotype 538 CA "N-Terminal GLH (COOH)" -1
- # biotype 539 C "N-Terminal GLH (COOH)" -1
- # biotype 540 HN "N-Terminal GLH (COOH)" -1
- # biotype 541 O "N-Terminal GLH (COOH)" -1
- # biotype 542 HA "N-Terminal GLH (COOH)" -1
- # biotype 543 N "N-Terminal GLN" 230
- # biotype 544 CA "N-Terminal GLN" 236
- # biotype 545 C "N-Terminal GLN" 177
- # biotype 546 HN "N-Terminal GLN" 233
- # biotype 547 O "N-Terminal GLN" 178
- # biotype 548 HA "N-Terminal GLN" 85
- # biotype 549 N "N-Terminal MET" 230
- # biotype 550 CA "N-Terminal MET" 236
- # biotype 551 C "N-Terminal MET" 177
- # biotype 552 HN "N-Terminal MET" 233
- # biotype 553 O "N-Terminal MET" 178
- # biotype 554 HA "N-Terminal MET" 85
- # biotype 555 N "N-Terminal LYS" 230
- # biotype 556 CA "N-Terminal LYS" 236
- # biotype 557 C "N-Terminal LYS" 177
- # biotype 558 HN "N-Terminal LYS" 233
- # biotype 559 O "N-Terminal LYS" 178
- # biotype 560 HA "N-Terminal LYS" 85
- # biotype 561 N "N-Terminal LYD (NH2)" -1
- # biotype 562 CA "N-Terminal LYD (NH2)" -1
- # biotype 563 C "N-Terminal LYD (NH2)" -1
- # biotype 564 HN "N-Terminal LYD (NH2)" -1
- # biotype 565 O "N-Terminal LYD (NH2)" -1
- # biotype 566 HA "N-Terminal LYD (NH2)" -1
- # biotype 567 N "N-Terminal ARG" 230
- # biotype 568 CA "N-Terminal ARG" 236
- # biotype 569 C "N-Terminal ARG" 177
- # biotype 570 HN "N-Terminal ARG" 233
- # biotype 571 O "N-Terminal ARG" 178
- # biotype 572 HA "N-Terminal ARG" 85
- # biotype 573 N "N-Terminal ORN" 230
- # biotype 574 CA "N-Terminal ORN" 236
- # biotype 575 C "N-Terminal ORN" 177
- # biotype 576 HN "N-Terminal ORN" 233
- # biotype 577 O "N-Terminal ORN" 178
- # biotype 578 HA "N-Terminal ORN" 85
- # biotype 579 N "N-Terminal AIB" 230
- # biotype 580 CA "N-Terminal AIB" 237
- # biotype 581 C "N-Terminal AIB" 177
- # biotype 582 HN "N-Terminal AIB" 233
- # biotype 583 O "N-Terminal AIB" 178
- # biotype 584 N "C-Terminal GLY" 180
- # biotype 585 CA "C-Terminal GLY" 226
- # biotype 586 C "C-Terminal GLY" 213
- # biotype 587 HN "C-Terminal GLY" 183
- # biotype 588 OXT "C-Terminal GLY" 214
- # biotype 589 HA "C-Terminal GLY" 85
- # biotype 590 N "C-Terminal ALA" 180
- # biotype 591 CA "C-Terminal ALA" 225
- # biotype 592 C "C-Terminal ALA" 213
- # biotype 593 HN "C-Terminal ALA" 183
- # biotype 594 OXT "C-Terminal ALA" 214
- # biotype 595 HA "C-Terminal ALA" 85
- # biotype 596 N "C-Terminal VAL" 180
- # biotype 597 CA "C-Terminal VAL" 225
- # biotype 598 C "C-Terminal VAL" 213
- # biotype 599 HN "C-Terminal VAL" 183
- # biotype 600 OXT "C-Terminal VAL" 214
- # biotype 601 HA "C-Terminal VAL" 85
- # biotype 602 N "C-Terminal LEU" 180
- # biotype 603 CA "C-Terminal LEU" 225
- # biotype 604 C "C-Terminal LEU" 213
- # biotype 605 HN "C-Terminal LEU" 183
- # biotype 606 OXT "C-Terminal LEU" 214
- # biotype 607 HA "C-Terminal LEU" 85
- # biotype 608 N "C-Terminal ILE" 180
- # biotype 609 CA "C-Terminal ILE" 225
- # biotype 610 C "C-Terminal ILE" 213
- # biotype 611 HN "C-Terminal ILE" 183
- # biotype 612 OXT "C-Terminal ILE" 214
- # biotype 613 HA "C-Terminal ILE" 85
- # biotype 614 N "C-Terminal SER" 180
- # biotype 615 CA "C-Terminal SER" 225
- # biotype 616 C "C-Terminal SER" 213
- # biotype 617 HN "C-Terminal SER" 183
- # biotype 618 OXT "C-Terminal SER" 214
- # biotype 619 HA "C-Terminal SER" 85
- # biotype 620 N "C-Terminal THR" 180
- # biotype 621 CA "C-Terminal THR" 225
- # biotype 622 C "C-Terminal THR" 213
- # biotype 623 HN "C-Terminal THR" 183
- # biotype 624 OXT "C-Terminal THR" 214
- # biotype 625 HA "C-Terminal THR" 85
- # biotype 626 N "C-Terminal CYS (SH)" 180
- # biotype 627 CA "C-Terminal CYS (SH)" 225
- # biotype 628 C "C-Terminal CYS (SH)" 213
- # biotype 629 HN "C-Terminal CYS (SH)" 183
- # biotype 630 OXT "C-Terminal CYS (SH)" 214
- # biotype 631 HA "C-Terminal CYS (SH)" 85
- # biotype 632 N "C-Terminal CYX (SS)" 180
- # biotype 633 CA "C-Terminal CYX (SS)" 225
- # biotype 634 C "C-Terminal CYX (SS)" 213
- # biotype 635 HN "C-Terminal CYX (SS)" 183
- # biotype 636 OXT "C-Terminal CYX (SS)" 214
- # biotype 637 HA "C-Terminal CYX (SS)" 85
- # biotype 638 N "C-Terminal CYD (S-)" -1
- # biotype 639 CA "C-Terminal CYD (S-)" -1
- # biotype 640 C "C-Terminal CYD (S-)" -1
- # biotype 641 HN "C-Terminal CYD (S-)" -1
- # biotype 642 OXT "C-Terminal CYD (S-)" -1
- # biotype 643 HA "C-Terminal CYD (S-)" -1
- # biotype 644 N "C-Terminal PRO" 181
- # biotype 645 CA "C-Terminal PRO" 228
- # biotype 646 C "C-Terminal PRO" 213
- # biotype 647 OXT "C-Terminal PRO" 214
- # biotype 648 HA "C-Terminal PRO" 85
- # biotype 649 N "C-Terminal PHE" 180
- # biotype 650 CA "C-Terminal PHE" 225
- # biotype 651 C "C-Terminal PHE" 213
- # biotype 652 HN "C-Terminal PHE" 183
- # biotype 653 OXT "C-Terminal PHE" 214
- # biotype 654 HA "C-Terminal PHE" 85
- # biotype 655 N "C-Terminal TYR" 180
- # biotype 656 CA "C-Terminal TYR" 225
- # biotype 657 C "C-Terminal TYR" 213
- # biotype 658 HN "C-Terminal TYR" 183
- # biotype 659 OXT "C-Terminal TYR" 214
- # biotype 660 HA "C-Terminal TYR" 85
- # biotype 661 N "C-Terminal TYD (O-)" -1
- # biotype 662 CA "C-Terminal TYD (O-)" -1
- # biotype 663 C "C-Terminal TYD (O-)" -1
- # biotype 664 HN "C-Terminal TYD (O-)" -1
- # biotype 665 OXT "C-Terminal TYD (O-)" -1
- # biotype 666 HA "C-Terminal TYD (O-)" -1
- # biotype 667 N "C-Terminal TRP" 180
- # biotype 668 CA "C-Terminal TRP" 225
- # biotype 669 C "C-Terminal TRP" 213
- # biotype 670 HN "C-Terminal TRP" 183
- # biotype 671 OXT "C-Terminal TRP" 214
- # biotype 672 HA "C-Terminal TRP" 85
- # biotype 673 N "C-Terminal HIS (+)" 180
- # biotype 674 CA "C-Terminal HIS (+)" 225
- # biotype 675 C "C-Terminal HIS (+)" 213
- # biotype 676 HN "C-Terminal HIS (+)" 183
- # biotype 677 OXT "C-Terminal HIS (+)" 214
- # biotype 678 HA "C-Terminal HIS (+)" 85
- # biotype 679 N "C-Terminal HIS (HD)" 180
- # biotype 680 CA "C-Terminal HIS (HD)" 225
- # biotype 681 C "C-Terminal HIS (HD)" 213
- # biotype 682 HN "C-Terminal HIS (HD)" 183
- # biotype 683 OXT "C-Terminal HIS (HD)" 214
- # biotype 684 HA "C-Terminal HIS (HD)" 85
- # biotype 685 N "C-Terminal HIS (HE)" 180
- # biotype 686 CA "C-Terminal HIS (HE)" 225
- # biotype 687 C "C-Terminal HIS (HE)" 213
- # biotype 688 HN "C-Terminal HIS (HE)" 183
- # biotype 689 OXT "C-Terminal HIS (HE)" 214
- # biotype 690 HA "C-Terminal HIS (HE)" 85
- # biotype 691 N "C-Terminal ASP" 180
- # biotype 692 CA "C-Terminal ASP" 225
- # biotype 693 C "C-Terminal ASP" 213
- # biotype 694 HN "C-Terminal ASP" 183
- # biotype 695 OXT "C-Terminal ASP" 214
- # biotype 696 HA "C-Terminal ASP" 85
- # biotype 697 N "C-Terminal ASH (COOH)" -1
- # biotype 698 CA "C-Terminal ASH (COOH)" -1
- # biotype 699 C "C-Terminal ASH (COOH)" -1
- # biotype 700 HN "C-Terminal ASH (COOH)" -1
- # biotype 701 OXT "C-Terminal ASH (COOH)" -1
- # biotype 702 HA "C-Terminal ASH (COOH)" -1
- # biotype 703 N "C-Terminal ASN" 180
- # biotype 704 CA "C-Terminal ASN" 225
- # biotype 705 C "C-Terminal ASN" 213
- # biotype 706 HN "C-Terminal ASN" 183
- # biotype 707 OXT "C-Terminal ASN" 214
- # biotype 708 HA "C-Terminal ASN" 85
- # biotype 709 N "C-Terminal GLU" 180
- # biotype 710 CA "C-Terminal GLU" 225
- # biotype 711 C "C-Terminal GLU" 213
- # biotype 712 HN "C-Terminal GLU" 183
- # biotype 713 OXT "C-Terminal GLU" 214
- # biotype 714 HA "C-Terminal GLU" 85
- # biotype 715 N "C-Terminal GLH (COOH)" -1
- # biotype 716 CA "C-Terminal GLH (COOH)" -1
- # biotype 717 C "C-Terminal GLH (COOH)" -1
- # biotype 718 HN "C-Terminal GLH (COOH)" -1
- # biotype 719 OXT "C-Terminal GLH (COOH)" -1
- # biotype 720 HA "C-Terminal GLH (COOH)" -1
- # biotype 721 N "C-Terminal GLN" 180
- # biotype 722 CA "C-Terminal GLN" 225
- # biotype 723 C "C-Terminal GLN" 213
- # biotype 724 HN "C-Terminal GLN" 183
- # biotype 725 OXT "C-Terminal GLN" 214
- # biotype 726 HA "C-Terminal GLN" 85
- # biotype 727 N "C-Terminal MET" 180
- # biotype 728 CA "C-Terminal MET" 225
- # biotype 729 C "C-Terminal MET" 213
- # biotype 730 HN "C-Terminal MET" 183
- # biotype 731 OXT "C-Terminal MET" 214
- # biotype 732 HA "C-Terminal MET" 85
- # biotype 733 N "C-Terminal LYS" 180
- # biotype 734 CA "C-Terminal LYS" 225
- # biotype 735 C "C-Terminal LYS" 213
- # biotype 736 HN "C-Terminal LYS" 183
- # biotype 737 OXT "C-Terminal LYS" 214
- # biotype 738 HA "C-Terminal LYS" 85
- # biotype 739 N "C-Terminal LYD (NH2)" -1
- # biotype 740 CA "C-Terminal LYD (NH2)" -1
- # biotype 741 C "C-Terminal LYD (NH2)" -1
- # biotype 742 HN "C-Terminal LYD (NH2)" -1
- # biotype 743 OXT "C-Terminal LYD (NH2)" -1
- # biotype 744 HA "C-Terminal LYD (NH2)" -1
- # biotype 745 N "C-Terminal ARG" 180
- # biotype 746 CA "C-Terminal ARG" 225
- # biotype 747 C "C-Terminal ARG" 213
- # biotype 748 HN "C-Terminal ARG" 183
- # biotype 749 OXT "C-Terminal ARG" 214
- # biotype 750 HA "C-Terminal ARG" 85
- # biotype 751 N "C-Terminal ORN" 180
- # biotype 752 CA "C-Terminal ORN" 225
- # biotype 753 C "C-Terminal ORN" 213
- # biotype 754 HN "C-Terminal ORN" 183
- # biotype 755 OXT "C-Terminal ORN" 214
- # biotype 756 HA "C-Terminal ORN" 85
- # biotype 757 N "C-Terminal AIB" 180
- # biotype 758 CA "C-Terminal AIB" 227
- # biotype 759 C "C-Terminal AIB" 213
- # biotype 760 HN "C-Terminal AIB" 183
- # biotype 761 OXT "C-Terminal AIB" 214
- # biotype 762 N "Deprotonated N-Terminus" -1
- # biotype 763 H "Deprotonated N-Terminus" -1
- # biotype 764 C "Formyl N-Terminus" 177
- # biotype 765 H "Formyl N-Terminus" 221
- # biotype 766 O "Formyl N-Terminus" 178
- # biotype 767 CH3 "Acetyl N-Terminus" 80
- # biotype 768 H "Acetyl N-Terminus" 85
- # biotype 769 C "Acetyl N-Terminus" 177
- # biotype 770 O "Acetyl N-Terminus" 178
- # biotype 771 C "Protonated C-Terminus" -1
- # biotype 772 O "Protonated C-Terminus" -1
- # biotype 773 OH "Protonated C-Terminus" -1
- # biotype 774 HO "Protonated C-Terminus" -1
- # biotype 775 N "Amide C-Terminus" 179
- # biotype 776 HN "Amide C-Terminus" 182
- # biotype 777 N "N-MeAmide C-Terminus" 180
- # biotype 778 HN "N-MeAmide C-Terminus" 183
- # biotype 779 CH3 "N-MeAmide C-Terminus" 184
- # biotype 780 H "N-MeAmide C-Terminus" 85
- # biotype 2001 O "Water" 63
- # biotype 2002 H "Water" 64
- # biotype 2003 NA "Sodium Ion" -1
- # biotype 2004 K "Potassium Ion" -1
- # biotype 2005 MG "Magnesium Ion" -1
- # biotype 2006 CA "Calcium Ion" -1
- # biotype 2007 CL "Chloride Ion" -1
- # ---------- (end of comment) ----------
-
-
- write_once("In Init") {
- units real
- atom_style full
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid opls
- improper_style hybrid harmonic
- pair_style hybrid lj/cut/coul/long 10.0 10.0
- pair_modify mix geometric
- special_bonds lj/coul 0.0 0.0 0.5
- kspace_style pppm 0.0001
- } #end of init parameters
-
-} # OPLSAA
-
-
-
-
-
-
-############################### NOTES ####################################
-#
-# This file was generated using this script:
-#
-# tinkerparm2lt.py -name OPLSAA -file oplsaa.prm -dihedral-style opls
-#
-# The oplsaa.prm file was downloaded from the TINKER website
-# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-# (You can build a smaller version of this file by editing the oplsaa.prm
-# file and deleting the lines beginning with "atom" that you don't need,
-# and subsequently running tinkerparm2lt.py on the new file. This can
-# help reduce the number of atom types, which can help with visualization,
-# and in some cases may also improve performance.)
-#
-# The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:
-# special_bonds lj/coul 0.0 0.0 0.5
-# (See http://lammps.sandia.gov/doc/special_bonds.html for details)
-#
-# WARNING: All Urey-Bradley interactions have been IGNORED
-#
-# WARNING: Many of these atoms are UNITED-ATOM (UA) atoms (#1-56). This means
-# the hydrogen atoms have been absorbed into the heavy atoms, and the
-# force-field modified accordingly. Moltemplate should complain if
-# you attempt to bond these atoms to hydrogen atoms.
-##########################################################################
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/AUTHOR.TXT b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/AUTHOR.TXT
deleted file mode 100644
index a46bd51d4..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/AUTHOR.TXT
+++ /dev/null
@@ -1,3 +0,0 @@
-OPLSAA force-field conversion tools provided by
-Jason Lambert, Sebastian Echeverri, and Andrew Jewett
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
deleted file mode 100644
index ab7c32530..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
+++ /dev/null
@@ -1,125 +0,0 @@
-NOTE: THE "oplsaa_moltemplate.py" SCRIPT HAS MOVED TO THE "../src/" DIRECTORY.
- (In the past, it was located in this directory.)
-
------------------------------
-Description:
-
-Unfortunately, moltemplate does not come with a file containing OPLSAA
-parameters which is ready to use. You must build it yourself.
-This directory has tools and instructions to explain how to do this.
-
------------------------------
-
-When you want to run a new simulation, you must download the full
-"oplsaa.prm" force-field file (from the TINKER web site) and manually
-delete all the atom types which you do not need. (See below.)
-Then you must use the "oplsaa_moltemplate.py" script to create
-"oplsaa.lt" file which moltemplate.sh needs. Then you must run moltemplate.sh.
-You must do this for each new simulation you plan to run which uses OPLSAA.
-
----- Details: ----
-
- Download the original "oplsaa.prm" file here:
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
- or here:
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-
-and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE
-so that it only contains atom types you plan to have in your simulation
-(see below). Finally, you must run the opls_moltemplate.py script this way:
-
-
-python oplsaa_moltemplate.py oplsaa_subset.prm
-
-
-This will create a file named "oplsaa.lt"
-Look over the newly created "oplsaa.lt" file.
-Then, if necessary, move this file to wherever you plan to run moltemplate.
-
-There is a directory containing an example how to use this code located here:
-examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT
-
------ DETAILS: Editing the "oplsaa_subset.prm" file -------
-
-Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm"
-file (or "oplsaa_subset.prm file) and eliminate atom types which do not
-correspond to any of the atoms in your simulation. This means you must
-look for lines near the beginning of this file which begin with the word "atom"
-and refer to atom types which appear in the simulation you plan to run. All
-other lines (beginning with the word "atom") must be deleted or commented out.
-(Leave the rest of the file alone.)
-
-For example:
-If you were working with ethylene and benzene you would delete every line
-beginning with the word "atom", except for these four lines:
-
-# for ethylene:
-atom 88 47 CM "Alkene H2-C=" 6 12.011 3
-atom 89 46 HC "Alkene H-C=" 1 1.008 1
-# for benzene:
-atom 90 48 CA "Aromatic C" 6 12.011 3
-atom 91 49 HA "Aromatic H-C" 1 1.008 1
-
-
-Then you are ready to run oplsaa_moltemplate.py on this file.
-
-(Note: Atom type numbers, like "88", "89", "47", etc... may vary depending on
- when you downloaded "oplsaa.prm".)
-
-
------ Using the "oplsaa.lt" file -----
-
-Once you have created the "oplsaa.lt" file, you can create files (like
-ethylene.lt) which define molecules that refer to these atom types.
-Here is an excerpt from "ethyelene.lt":
-
-Ethylene inherits OPLSAA {
- write('Data Atoms') {
- list of atoms goes here ...
- }
- write('Data Bond List') {
- list of bonds goes here ...
- }
-}
-
-And then run moltemplate.
-
-
------------ CHARGE: -----------
-
-By default, the OPLSAA force-field assigns atom charge according to atom type.
-When you run moltemplate, it will create a file named "system.in.charges",
-containing commands like:
-
-set type 2 charge -0.42
-set type 3 charge 0.21
-
-(This assumes your main moltemplate file is named "system.lt". If it was
-named something else, eg "polymer.lt", then the file created by moltemplate
-will be named "polymer.in.charges".)
-
-Include these commands somewhere in your LAMMPS input script
-(or use the LAMMPS "include" command to load the commands in system.in.charges)
-
-Note that the atom numbers (eg "2", "3") in this file will not match the
-OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file,
-created by moltemplate, to see a table of "@atom" type numbers translated
-from OPLSAA into LAMMPS.)
-
------------ CREDIT -----------
-
-If you use these tools and you publish a paper using OPLSAA, please also cite
-the TINKER program. (Because the original "oplsaa.prm" file which we depend on
-is distributed with TINKER.) I think these are the relevant citations:
-
-1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
--------------------------------
-
-Jason Lambert and Andrew Jewett
-April, 2014
-
-Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/loplsaa_ext.prm b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/loplsaa_ext.prm
deleted file mode 100644
index ff0e3e445..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/loplsaa_ext.prm
+++ /dev/null
@@ -1,87 +0,0 @@
- ###########################################################################
- ## Extra OPLSAA parameters and atom types for long hydrocarbon chains ##
- ## SOURCE: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 ##
- ## CREDIT: Sebastian Echeverri (file format conversion) ##
- ###########################################################################
- ## This file was used with "tinkerparm2lt.py" to create "loplsaa.lt" ##
- ###########################################################################
-
-atom 80L 13L CT "Alkane CH3- (LOPLS CT_CH3)" 6 12.011 4
-atom 81L 13L CT "Alkane -CH2- (LOPLS CT_CH2)" 6 12.011 4
-atom 85LCH3 46 HC "Alkane H-C CH3 (LOPLS HC_CH3)" 1 1.008 1
-atom 85LCH2 46 HC "Alkane H-C CH2 (LOPLS HC_CH2)" 1 1.008 1
-atom 87L 47L CM "Alkene RH-C= (LOPLS CM_CH)" 6 12.011 3
-atom 89L 46 HC "Alkene H-C= (LOPLS HC_CH)" 1 1.008 1
-atom 86L 47L CM "Alkene R2-C= (LOPLS)" 6 12.011 3
-atom 88L 47L CM "Alkene H2-C= (LOPLS)" 6 12.011 3
-atom 169L 47L CM "Chloroalkene Cl-CH= (LOPLS)" 6 12.011 3
-atom 266L 47L CM "Uracil & Thymine C5 (LOPLS)" 6 12.011 3
-atom 267L 47L CM "Uracil & Thymine C6 (LOPLS)" 6 12.011 3
-atom 280L 47L CM "Cytosine C5 (LOPLS)" 6 12.011 3
-atom 281L 47L CM "Cytosine C6 (LOPLS)" 6 12.011 3
-atom 324L 47L CM "CytosineH+ C5 (LOPLS)" 6 12.011 3
-atom 325L 47L CM "CytosineH+ C6 (LOPLS)" 6 12.011 3
-atom 340L 47L CM "Trifluorothymine CF3- (LOPLS)" 6 12.011 4
-atom 342L 47L CM "Chloroalkene Cl2-C= (LOPLS)" 6 12.011 3
-atom 458L 47L CM "Vinyl Ether =CH-OR (LOPLS)" 6 12.011 3
-atom 459L 47L CM "Vinyl Ether =CR-OR (LOPLS)" 6 12.011 3
-atom 649L 47L CM "Cl..CH3..Cl- Sn2 TS (LOPLS)" 6 12.011 5
-atom 900L 47L CM "Allene/Ketene H2C=C=X (LOPLS)" 6 12.011 3
-atom 901L 47L CM "Allene/Ketene HRC=C=X (LOPLS)" 6 12.011 3
-atom 902L 47L CM "Allene/Ketene R2C=C=X (LOPLS)" 6 12.011 3
-
-vdw 80L 3.5000 0.0660
-vdw 81L 3.5000 0.0660
-vdw 85LCH3 2.5000 0.0300
-vdw 85LCH2 2.5000 0.026290630975
-vdw 87L 3.5500 0.0760
-vdw 89L 2.4200 0.0300
-vdw 86L 3.5500 0.0760
-vdw 88L 3.5500 0.0760
-vdw 169L 3.5500 0.0760
-vdw 266L 3.5000 0.0800
-vdw 267L 3.5000 0.0800
-vdw 280L 3.5000 0.0800
-vdw 281L 3.5000 0.0800
-vdw 324L 3.5000 0.0800
-vdw 325L 3.5000 0.0800
-vdw 340L 3.5000 0.0800
-vdw 342L 3.5500 0.0760
-vdw 458L 3.5500 0.0760
-vdw 459L 3.5500 0.0760
-vdw 649L 3.5500 0.0760
-vdw 900L 3.3000 0.0860
-vdw 901L 3.3000 0.0860
-vdw 902L 3.3000 0.0860
-
-# New torsion angle parameters
-# Taken from table 2 of
-# Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459
-torsion 13L 13L 13L 13L 0.6446926386 0 1 -0.2143420172 180 2 0.1782194073 0 3 0 180 4 # offset V0=-0.0731209369
-torsion 0 47L 47L 0 0.0 0 1 12.2502629063 180 2 0.0 0 3 0 180 4 # offset V0=0.0
-torsion 47L 47L 13L 13L -0.8050121893 0 1 0.3218905354 180 2 -0.1032768881 0 3 0 180 4 # offset V0=-0.3574832696
-torsion 13L 13L 13L 47L 0.4821902486 0 1 0.1343683078 180 2 0.1777461759 0 3 0 180 4 # offset V0=0.4405726577
-
-charge 80L -0.222 #"Alkane CH3- (LOPLS)" "CT_CH3" 3.50 0.0660
-charge 81L -0.148 #"Alkane -CH2- (LOPLS)" "CT_CH2" 3.50 0.0660
-charge 85LCH3 0.074 #"Alkane H-C CH3 (LOPLS)" "HC_CH3" 2.50 0.0300
-charge 85LCH2 0.074 #"Alkane H-C CH2 (LOPLS)" "HC_CH2" 2.50 0.0263
-charge 87L -0.160 #"Alkene RH-C= (LOPLS)" "CM_CH" 3.55 0.0760
-charge 89L 0.160 #"Alkene H-C= (LOPLS)" "HC_CH" 2.42 0.0300
-charge 86L 0.0000
-charge 88L -0.2300
-charge 169L 0.0050
-charge 266L -0.0700
-charge 267L 0.0800
-charge 280L -0.0600
-charge 281L 0.1000
-charge 324L -0.0600
-charge 325L 0.1000
-charge 340L 0.1800
-charge 342L 0.1200
-charge 458L -0.0300
-charge 459L 0.0850
-charge 649L -0.3440
-charge 900L -0.2500
-charge 901L -0.1000
-charge 902L 0.0500
diff --git a/tools/moltemplate/src/moltemplate_force_fields/spce.lt b/tools/moltemplate/src/moltemplate_force_fields/spce.lt
deleted file mode 100644
index 1f0f0f61b..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/spce.lt
+++ /dev/null
@@ -1,52 +0,0 @@
-# file "spce.lt"
-#
-# H1 H2
-# \ /
-# O
-
-SPCE {
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
- $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 600.0 1.0
- angle_coeff @angle:HOH harmonic 75.0 109.47
- pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166
- pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0
- group spce type @atom:O @atom:H
- fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeSPCE during minimization.)
- }
-
- write_once("In Init") {
- # -- Default styles (for solo "SPCE" water) --
- units real
- atom_style full
- # (Hybrid force fields were not necessary but are used for portability.)
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED!
- }
-
-} # end of definition of "SPCE" water molecule type
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect16.lt b/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect16.lt
deleted file mode 100644
index fb431cede..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect16.lt
+++ /dev/null
@@ -1,81 +0,0 @@
-# This ice (1h) unit cell is rectangular and contains 16 water molecules.
-# (Coordinates and cell dimensions converted were from a PDB file.)
-# The dimensions of the unit cell (in Angstroms) are: 9.043 7.832 7.361
-
-
-import "spce.lt" # <-- define the "SPCE" molecule
-
-SpceIceRect16 {
-
- # Create a 3-dimensional array of 16 water molecules
-
- wat = new SPCE[4][2][2]
-
- # Array indices will be correlated with position [xindex][yindex][zindex]
-
- # You can overwrite coordinates of atoms after they were created this way:
- # (Order is not important)
- # atom-ID molecule-ID atomType charge newX newY newZ
-
- write("Data Atoms") {
- $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
- $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970
- $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 3.545 1.970
- $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
- $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711
- $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.371 1.711
- $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300
- $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970
- $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 2.611 3.291
- $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381
- $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711
- $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 1.305 0.390
- $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
- $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711
- $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 5.221 0.390
- $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
- $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970
- $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291
- $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381
- $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711
- $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 4.287 1.711
- $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300
- $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970
- $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970
- $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
- $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391
- $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 2.611 4.070
- $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
- $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651
- $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.972
- $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061
- $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391
- $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 3.545 5.391
- $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981
- $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651
- $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 0.371 5.651
- $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
- $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651
- $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 4.287 5.651
- $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
- $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391
- $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391
- $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981
- $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651
- $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 5.221 6.972
- $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061
- $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391
- $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070
- }
-} # SpceIceRect16
-
-# Credit goes to Martin Chaplin.
-# These coordinates were orignally downloaded from Martin Chaplin's
-# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
-# ... and then they were stretched independently in the xy and z
-# directions in order to match the lattice parameters measured by
-# Rottger et al.,
-# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
-# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
-# I am using the lattice constants measured at temperature 265K
-# (and pressure=100Torr).
diff --git a/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect32.lt b/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect32.lt
deleted file mode 100644
index 7ddcb0adf..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect32.lt
+++ /dev/null
@@ -1,129 +0,0 @@
-# This ice (1h) unit cell is rectangular and contains 32 water molecules.
-# (Coordinates and cell dimensions converted were from a PDB file.)
-# The dimensions of the unit cell (in Angstroms) are: 9.043 15.663 7.361
-
-
-import "spce.lt" # <-- define the "SPCE" molecule
-
-SpceIceRect32 {
-
- # Create a 3-dimensional array of 32 water molecules
-
- wat = new SPCE[4][4][2]
-
- # Array indices will be correlated with position [xindex][yindex][zindex]
-
- # You can overwrite coordinates of atoms after they were created this way:
- # (Order is not important)
- # atom-ID molecule-ID atomType charge newX newY newZ
-
- write("Data Atoms") {
- $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
- $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970
- $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.291
- $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
- $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711
- $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 1.305 0.390
- $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300
- $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970
- $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 3.545 1.970
- $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381
- $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711
- $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 0.371 1.711
- $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
- $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711
- $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.287 1.711
- $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
- $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970
- $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291
- $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381
- $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711
- $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 5.221 0.390
- $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300
- $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970
- $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970
- $atom:wat[0][2][0]/O $mol:wat[0][2][0] @atom:SPCE/O -0.8476 1.131 10.443 2.300
- $atom:wat[0][2][0]/H1 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 0.322 9.976 1.970
- $atom:wat[0][2][0]/H2 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 1.131 11.377 1.970
- $atom:wat[1][2][0]/O $mol:wat[1][2][0] @atom:SPCE/O -0.8476 3.391 9.137 1.381
- $atom:wat[1][2][0]/H1 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 2.582 9.604 1.711
- $atom:wat[1][2][0]/H2 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 3.391 8.203 1.711
- $atom:wat[2][2][0]/O $mol:wat[2][2][0] @atom:SPCE/O -0.8476 5.652 10.443 2.300
- $atom:wat[2][2][0]/H1 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 4.843 9.976 1.970
- $atom:wat[2][2][0]/H2 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 5.652 10.443 3.291
- $atom:wat[3][2][0]/O $mol:wat[3][2][0] @atom:SPCE/O -0.8476 7.912 9.137 1.381
- $atom:wat[3][2][0]/H1 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.103 9.604 1.711
- $atom:wat[3][2][0]/H2 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.912 9.137 0.390
- $atom:wat[0][3][0]/O $mol:wat[0][3][0] @atom:SPCE/O -0.8476 1.131 13.053 1.381
- $atom:wat[0][3][0]/H1 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.940 13.520 1.711
- $atom:wat[0][3][0]/H2 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.131 13.053 0.390
- $atom:wat[1][3][0]/O $mol:wat[1][3][0] @atom:SPCE/O -0.8476 3.391 14.358 2.300
- $atom:wat[1][3][0]/H1 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 4.200 13.891 1.970
- $atom:wat[1][3][0]/H2 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 3.391 15.292 1.970
- $atom:wat[2][3][0]/O $mol:wat[2][3][0] @atom:SPCE/O -0.8476 5.652 13.053 1.381
- $atom:wat[2][3][0]/H1 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 6.461 13.520 1.711
- $atom:wat[2][3][0]/H2 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 5.652 12.119 1.711
- $atom:wat[3][3][0]/O $mol:wat[3][3][0] @atom:SPCE/O -0.8476 7.912 14.358 2.300
- $atom:wat[3][3][0]/H1 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 8.721 13.891 1.970
- $atom:wat[3][3][0]/H2 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 7.912 14.358 3.291
- $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
- $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391
- $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.545 5.391
- $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
- $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651
- $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 0.371 5.651
- $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061
- $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391
- $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 2.611 4.070
- $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981
- $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651
- $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 1.305 6.972
- $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
- $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651
- $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.972
- $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
- $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391
- $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391
- $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981
- $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651
- $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 4.287 5.651
- $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061
- $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391
- $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070
- $atom:wat[0][2][1]/O $mol:wat[0][2][1] @atom:SPCE/O -0.8476 1.131 10.443 5.061
- $atom:wat[0][2][1]/H1 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.940 9.976 5.391
- $atom:wat[0][2][1]/H2 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.131 10.443 4.070
- $atom:wat[1][2][1]/O $mol:wat[1][2][1] @atom:SPCE/O -0.8476 3.391 9.137 5.981
- $atom:wat[1][2][1]/H1 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 4.200 9.604 5.651
- $atom:wat[1][2][1]/H2 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 3.391 9.137 6.972
- $atom:wat[2][2][1]/O $mol:wat[2][2][1] @atom:SPCE/O -0.8476 5.652 10.443 5.061
- $atom:wat[2][2][1]/H1 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 6.461 9.976 5.391
- $atom:wat[2][2][1]/H2 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 5.652 11.377 5.391
- $atom:wat[3][2][1]/O $mol:wat[3][2][1] @atom:SPCE/O -0.8476 7.912 9.137 5.981
- $atom:wat[3][2][1]/H1 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 8.721 9.604 5.651
- $atom:wat[3][2][1]/H2 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 7.912 8.203 5.651
- $atom:wat[0][3][1]/O $mol:wat[0][3][1] @atom:SPCE/O -0.8476 1.131 13.053 5.981
- $atom:wat[0][3][1]/H1 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 0.322 13.520 5.651
- $atom:wat[0][3][1]/H2 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 1.131 12.119 5.651
- $atom:wat[1][3][1]/O $mol:wat[1][3][1] @atom:SPCE/O -0.8476 3.391 14.358 5.061
- $atom:wat[1][3][1]/H1 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 2.582 13.891 5.391
- $atom:wat[1][3][1]/H2 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 3.391 14.358 4.070
- $atom:wat[2][3][1]/O $mol:wat[2][3][1] @atom:SPCE/O -0.8476 5.652 13.053 5.981
- $atom:wat[2][3][1]/H1 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 4.843 13.520 5.651
- $atom:wat[2][3][1]/H2 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 5.652 13.053 6.972
- $atom:wat[3][3][1]/O $mol:wat[3][3][1] @atom:SPCE/O -0.8476 7.912 14.358 5.061
- $atom:wat[3][3][1]/H1 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.103 13.891 5.391
- $atom:wat[3][3][1]/H2 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.912 15.292 5.391
- }
-} # SpceIceRect32
-
-# Credit goes to Martin Chaplin.
-# These coordinates were orignally downloaded from Martin Chaplin's
-# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
-# ... and then they were stretched independently in the xy and z
-# directions in order to match the lattice parameters measured by
-# Rottger et al.,
-# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
-# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
-# I am using the lattice constants measured at temperature 265K
-# (and pressure=100Torr).
diff --git a/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect8.lt b/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect8.lt
deleted file mode 100644
index ccfd2f18c..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/spce_ice_rect8.lt
+++ /dev/null
@@ -1,57 +0,0 @@
-# This ice (1h) unit cell is rectangular and contains 8 water molecules.
-# (Coordinates and cell dimensions converted were from a PDB file.)
-# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362
-
-
-import "spce.lt" # <-- define the "SPCE" molecule
-
-SpceIceRect8 {
-
- # Create a 3-dimensional array of 8 water molecules
-
- wat = new SPCE[2][2][2]
-
- # Array indices will be correlated with position [xindex][yindex][zindex]
-
- # You can overwrite coordinates of atoms after they were created this way:
- # (Order is not important)
- # atom-ID molecule-ID atomType charge newX newY newZ
-
- write("Data Atoms") {
- $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
- $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710
- $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710
- $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
- $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970
- $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652
- $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
- $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289
- $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971
- $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
- $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391
- $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391
- $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
- $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710
- $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710
- $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
- $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970
- $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652
- $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
- $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289
- $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971
- $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
- $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391
- $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391
- }
-} # IceRect8
-
-# Credit goes to Martin Chaplin.
-# These coordinates were orignally downloaded from Martin Chaplin's
-# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
-# ... and then they were stretched independently in the xy and z
-# directions in order to match the lattice parameters measured by
-# Rottger et al.,
-# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
-# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
-# I am using the lattice constants measured at temperature 265K
-# (and pressure=100Torr).
diff --git a/tools/moltemplate/src/moltemplate_force_fields/tip3p_1983.lt b/tools/moltemplate/src/moltemplate_force_fields/tip3p_1983.lt
deleted file mode 100644
index 4a792691e..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/tip3p_1983.lt
+++ /dev/null
@@ -1,119 +0,0 @@
-#############################################################
-# WARNING: THIS FILE HAS NOT BEEN TESTED!
-# (If you use this file in a simulation, please email me to let me know
-# if it worked. -Andrew 2014-5, (jewett dot aij at gmail dot com))
-#########################################################
-# There are two different versions of TIP3P:
-#
-# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think).
-# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model
-# # which uses long-range coulombics
-#########################################################
-
-# file "tip3p_1983.lt"
-#
-# H1 H2
-# \ /
-# O
-#
-# I think this is the TIP3P water model used by CHARMM (and AMBER?). See:
-# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983)
-
-
-TIP3P_1983 {
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766
- $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 450.0 0.9572
- angle_coeff @angle:HOH harmonic 55.0 104.52
-
- #########################################################################
- #### There are two choices for for the O-O interactions
- #########################################################################
- #### O-O nonbonded interactions
-
- # For the 1983 Jorgensen version of TIP3P use:
- pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
-
- # For the 2004 Price & Brooks version of TIP3P use:
- #pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188
-
- #########################################################################
- #### There are three choices for for the O-H and H-H interactions
- #########################################################################
- #### 1) The original Jorgensen 1983 and 2004 Price & Brooks models have no
- # mixed OH or HH interactions. For this behavior, uncomment these lines:
- pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000
- pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753
- #########################################################################
- #### 2) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
- #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
- #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753#arithmetic
- #########################################################################
- #### 3) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
- #### If you want to use this, uncomment the following two lines:
- #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
- #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
- #########################################################################
-
- # Define a group for the tip3p water molecules:
- group tip3p type @atom:O @atom:H
-
- # Optional: Constrain the angles and distances.
- # (Most implementations use this, but it is optional.)
- fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeTIP3P during minimization.)
- }
-
-
- write_once("In Init") {
- # -- Default styles (for solo "TIP3P_1983" water) --
- units real
- atom_style full
-
- # I'm not sure exactly which cutoffs distances are traditionally used in
- # in the 1983 "TIP3P" model by Jorgensen model, (used by CHARMM).
- # (See the Price JCP 2004 paper for a review.)
- # My first guess was this:
- pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5
-
- # However, in the LAMMPS "peptide" example, they use these parameters:
- # pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0
-
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED!
- }
-
-} # "TIP3P_1983" water molecule type
-
-
-
-
-# (note to self:)
-# In the LAMMPS "peptide" example, these (nearly identical) parameters were used
-# and they left the O-H parameters to be determined by the default mixing rules
-#pair_style lj/charmm/coul/long 8.0 10.0 10.0
-#pair_coeff @atom:H @atom:H 0.046 0.400014 0.046 0.400014
-#pair_coeff @atom:O @atom:O 0.1521 3.15057 0.1521 3.15057
-#angle_style charmm
-#angle_coeff @angle:HOH 55.0 104.52 0.0 0.0
diff --git a/tools/moltemplate/src/moltemplate_force_fields/tip3p_1983_charmm.lt b/tools/moltemplate/src/moltemplate_force_fields/tip3p_1983_charmm.lt
deleted file mode 100644
index 1b89435be..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/tip3p_1983_charmm.lt
+++ /dev/null
@@ -1,119 +0,0 @@
-#############################################################
-# WARNING: THIS FILE HAS NOT BEEN TESTED!
-# (If you use this file in a simulation, please email me to let me know
-# if it worked. -Andrew 2014-5, (jewett dot aij at gmail dot com))
-#########################################################
-# There are two different versions of TIP3P:
-#
-# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think).
-# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model
-# # which uses long-range coulombics
-#########################################################
-
-# file "tip3p_1983_charmm.lt"
-#
-# H1 H2
-# \ /
-# O
-#
-# I think this is the TIP3P water model used by CHARMM (and AMBER?). See:
-# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983)
-
-
-TIP3P_1983_CHARMM {
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766
- $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 450.0 0.9572
- angle_coeff @angle:HOH harmonic 55.0 104.52
-
- #########################################################################
- #### There are two choices for for the O-O interactions
- #########################################################################
- #### O-O nonbonded interactions
-
- # For the 1983 Jorgensen version of TIP3P use:
- pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
-
- # For the 2004 Price & Brooks version of TIP3P use:
- #pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188
-
- #########################################################################
- #### There are three choices for for the O-H and H-H interactions
- #########################################################################
- #### 1) The original Jorgensen 1983 and 2004 Price & Brooks models have no
- # mixed OH or HH interactions. For this behavior, uncomment these lines:
- #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000
- #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753
- #########################################################################
- #### 2) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
- pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
- pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
- #########################################################################
- #### 3) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
- #### If you want to use this, uncomment the following two lines:
- #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
- #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
- #########################################################################
-
- # Define a group for the tip3p water molecules:
- group tip3p type @atom:O @atom:H
-
- # Optional: Constrain the angles and distances.
- # (Most implementations use this, but it is optional.)
- fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeTIP3P during minimization.)
- }
-
-
- write_once("In Init") {
- # -- Default styles (for solo "TIP3P_1983_CHARMM" water) --
- units real
- atom_style full
-
- # I'm not sure exactly which cutoffs distances are traditionally used in
- # in the 1983 "TIP3P" model by Jorgensen model, (used by CHARMM).
- # (See the Price JCP 2004 paper for a review.)
- # My first guess was this:
- pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5
-
- # However, in the LAMMPS "peptide" example, they use these parameters:
- # pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0
-
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED!
- }
-
-} # "TIP3P_1983_CHARMM" water molecule type
-
-
-
-
-# (note to self:)
-# In the LAMMPS "peptide" example, these (nearly identical) parameters were used
-# and they left the O-H parameters to be determined by the default mixing rules
-#pair_style lj/charmm/coul/long 8.0 10.0 10.0
-#pair_coeff @atom:H @atom:H 0.046 0.400014 0.046 0.400014
-#pair_coeff @atom:O @atom:O 0.1521 3.15057 0.1521 3.15057
-#angle_style charmm
-#angle_coeff @angle:HOH 55.0 104.52 0.0 0.0
diff --git a/tools/moltemplate/src/moltemplate_force_fields/tip3p_2004.lt b/tools/moltemplate/src/moltemplate_force_fields/tip3p_2004.lt
deleted file mode 100644
index 0c8da1bc5..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/tip3p_2004.lt
+++ /dev/null
@@ -1,107 +0,0 @@
-#########################################################
-# WARNING: THIS FILE HAS NOT BEEN TESTED!
-# (If you use this file in a simulation, please email me to let me know
-# if it worked. -Andrew 2014-5, (jewett dot aij at gmail dot com))
-#########################################################
-# There are two different versions of TIP3P:
-#
-# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think).
-# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model
-# # which uses long-range coulombics
-#########################################################
-
-# file "tip3p_2004.lt"
-#
-# H1 H2
-# \ /
-# O
-#
-# I think this is the TIP3P water described in the paper by
-# Daniel J. Price and Charles L. Brooks III
-# J. Chem. Phys., 121(20): 10096 (2004)
-# Specifically I think it refers to the "Model B" version of long-range TIP3P
-# described in the 3rd-to-last column of "Table I", on p.10099.
-
-TIP3P_2004 {
-
- write("Data Atoms") {
- $atom:O $mol:. @atom:O -0.830 0.0000000 0.00000 0.000000
- $atom:H1 $mol:. @atom:H 0.415 0.756950327 0.00000 0.5858822766
- $atom:H2 $mol:. @atom:H 0.415 -0.756950327 0.00000 0.5858822766
- }
-
- write_once("Data Masses") {
- @atom:O 15.9994
- @atom:H 1.008
- }
-
- write("Data Bonds") {
- $bond:OH1 @bond:OH $atom:O $atom:H1
- $bond:OH2 @bond:OH $atom:O $atom:H2
- }
-
- write("Data Angles") {
- $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
- }
-
- write_once("In Settings") {
- bond_coeff @bond:OH harmonic 450.0 0.9572
- angle_coeff @angle:HOH harmonic 55.0 104.52
-
- #########################################################################
- #### There are two choices for for the O-O interactions
- #########################################################################
- #### O-O nonbonded interactions
-
- # For the 1983 Jorgensen version of TIP3P use:
- #pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
-
- # For the 2004 Price & Brooks version of TIP3P use:
- pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188
-
- #########################################################################
- #### There are three choices for for the O-H and H-H interactions
- #########################################################################
- #### 1) The original Jorgensen 1983 and 2004 Price & Brooks models have no
- # mixed OH or HH interactions. For this behavior, uncomment these lines:
- pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.00 0.4000
- pair_coeff @atom:O @atom:H lj/charmm/coul/long 0.00 1.7753
- #########################################################################
- #### 2) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
- #pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0460 0.4000
- #pair_coeff @atom:O @atom:H lj/charmm/coul/long 0.0836 1.7753 #arithmetic
- #########################################################################
- #### 3) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
- #### If you want to use this, uncomment the following two lines:
- #pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0460 0.4000
- #pair_coeff @atom:O @atom:H lj/charmm/coul/long 0.0836 1.1226 #geometric
- #########################################################################
-
- # Define a group for the tip3p water molecules:
- group tip3p type @atom:O @atom:H
-
- # Optional: Constrain the angles and distances.
- # (Most implementations use this, but it is optional.)
- fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
- # (Remember to "unfix" fShakeTIP3P during minimization.)
- }
-
-
- write_once("In Init") {
- # -- Default styles (for solo "TIP3P_2004" water) --
- units real
- atom_style full
-
- pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5
-
- # Note: in the LAMMPS "peptide" example, they use these parameters:
- # pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0
-
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- kspace_style pppm 0.0001
- #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED!
- }
-
-} # "TIP3P_2004" water molecule type
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/trappe1998.lt b/tools/moltemplate/src/moltemplate_force_fields/trappe1998.lt
deleted file mode 100644
index 1227b2aeb..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/trappe1998.lt
+++ /dev/null
@@ -1,53 +0,0 @@
-# This file stores complete LAMMPS data for the TraPPE model of saturated
-# hydrocarbon chains. In this "united-atom" model, each methyl group is
-# represented by a single atom. Forces between "atoms" are taken from the
-# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577)
-
-TraPPE {
-
- write_once("Data Masses") {
- @atom:CH2 14.1707
- @atom:CH3 15.2507
- @atom:CH4 16.3307
- }
-
- write_once("Data Angles By Type") {
- @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated
- }
-
- write_once("Data Dihedrals By Type") {
- @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated
- }
-
- write_once("In Settings") {
- pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95
- pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75
- pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73
- bond_coeff @bond:saturated harmonic 120.0 1.54
- angle_coeff @angle:backbone harmonic 62.0022 114
- dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0
- }
-
- # Optional: Create a group corresponding to atoms used by the TraPPE force-
- # field. (This is useful if you mix force-fields together.)
-
- write_once("In Settings") {
- group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4
- }
-
- write_once("In Init") {
- # -- Default styles for "TraPPE" --
- units real
- atom_style full
- # (Hybrid force field styles were used for portability.)
- bond_style hybrid harmonic
- angle_style hybrid harmonic
- dihedral_style hybrid opls
- improper_style none
- pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
- pair_modify mix arithmetic
- special_bonds lj 0.0 0.0 0.0
- }
-
-} # class TraPPE
-
diff --git a/tools/moltemplate/src/moltemplate_force_fields/watmw.lt b/tools/moltemplate/src/moltemplate_force_fields/watmw.lt
deleted file mode 100644
index f4eedc404..000000000
--- a/tools/moltemplate/src/moltemplate_force_fields/watmw.lt
+++ /dev/null
@@ -1,77 +0,0 @@
-# This file stores LAMMPS data for the "mW" water model.
-# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016)
-#
-# In this model, each water molecule is represented by a single "mW" particle.
-# These particles interact with their neighbors via 3-body Stillinger-Weber
-# forces whose parameters are tuned to mimic directional hydrogen-bonding
-# in liquid water (as well as hexagonal ice, type II ice, and
-# low-density super-cooled liquid/amorphous water phases).
-
-####
-#
-# NOTE: THIS FILE IS INTENDED FOR SIMULATIONS OF PURE WATER ONLY.
-# IF YOU HAVE OTHER ATOMS IN YOUR SYSTEM (BESIDES WATER),
-# YOU MUST REPLACE THIS LINE:
-#
-# pair_coeff * * sw system.in.sw mW
-#
-# WITH THIS LINE:
-#
-# pair_coeff * * sw system.in.sw mW NULL NULL NULL
-#
-# ...IN THE FILE BELOW.
-#
-# (Note:The number of "NULL" entries in the list should match the
-# number of other atom types defined somewhere in your simulation.
-# In the "3bodyWater+hydrocarbons_MW+TraPPE" example, there are 3
-# types of carbon defined in "trappe1998.lt", so "NULL" appears 3 times.
-####
-
-
-
-
-WatMW {
- write("Data Atoms") {
- $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0
- }
-
- write_once("Data Masses") {
- @atom:mW 18.02
- }
-
- write_once("system.in.sw") {
- mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0
- }
-
- write_once("In Init") {
- # -- Default styles for "WatMW" --
- units real
- pair_style sw
- }
-
- write_once("In Settings") {
- # --Now indicate which atom type(s) are simulated using the "sw" pair style
- # -- In this case only one of the atom types is used (the mW water "atom").
-
- pair_coeff * * sw system.in.sw mW # SEE COMMENT ABOVE
-
- # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
- # -- the atoms are identified by order in the list, not by name. (The "mW"
- # -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
- # -- This command says that the first atom type corresponds to the "mW"
- # -- atom in system.in.sw, and to ignore the remaining three atom types
- # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
- # -- We don't want to use the "sw" force field for interactions involving
- # -- these atom types, so we put "NULL" there.)
- # -- Note: For this to work, you should probably run moltemplate this way:
- # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
- # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom)
- }
-
- # -- optional --
-
- write_once("In Settings") {
- group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group)
- }
-
-} # WatMW
diff --git a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py b/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
deleted file mode 100755
index 5a2ce05c4..000000000
--- a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
+++ /dev/null
@@ -1,489 +0,0 @@
-#! /usr/bin/env python
-#
-# The purpose of this script is to create a moltemplate lt file for the oplsaa.
-# forcefield. This will assist researchers in building complex simulations using
-# this OPLS-UA and the OPLS-AA forcefields.
-
-__author__="Jason Lambert"
-# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu, and Andrew Jewett)
-__version__="0.21"
-
-
-
-import sys
-import os
-from operator import itemgetter
-
-g_program_name = __file__.split('/')[-1]
-
-# First make a copy of the \"oplsaa.prm\" file
-# (which can be downloaded from the TINKER web site).
-# The lines in this file beginning with the word \"atoms\" should
-# define the atoms which you plan to put in your simulation. All other
-# lines beginning with the word \"atoms\" should be deleted.
-# (Leave the other sections of this file alone.)
-#""")
-
-
-if sys.version > '3':
- import io
-else:
- import cStringIO
-
-try:
- if sys.version < '2.7':
- raise Exception('Error: Using python '+sys.version+'\n'+
- ' Alas, your version of python is too old.\n'
- ' You must upgrade to a newer version of python (2.7 or later).')
-except Exception as err:
- sys.stderr.write('\n\n'+str(err)+'\n')
- sys.exit(-1)
-
-
-
-#input data from file containing oplsaa force field parameters.
-try:
- f=open(sys.argv[1],"r")
-except:
- sys.stderr.write("Error: \n"
- " You need to specify a file name as an input argument:\n"
- " python oplsaa_moltemplate.py <forcefield file name>\n"
- " (or the file name is specified incorrectly)\n")
- sys.exit()
-
-
-sys.stderr.write(g_program_name+", version "+__version__+"\n"
- "Reading parameter file...\n")
-
-
-#output lt file
-g=open("oplsaa.lt","w")
-
-
-
-lines = f.readlines()
-
-
-
-# Ignore/Comment out lines before the "## Atom Type Definitions ##" section.
-
-for i in range(0, len(lines)):
- if (lines[i].find("## Atom Type Definitions ##") != -1):
- break
- else:
- lines[i] = '# ' + lines[i]
-
-
-# As of late 2014, there appear to be 906 atom types, but we don't assume this.
-# First try to infer out how many atom types there were in the original
-# oplsaa.prm file, or at least find an upper bound on the atom-type numbers.
-# (Keep track of the maximum value of the first column in the "atom" section.)
-max_atomType = 0
-num_atomTypes = 0
-for line in lines:
- # skip over text after a # comment character
- ic = line.find('#')
- if ic != -1:
- line = (line[:ic]).strip()
- else:
- line = line.strip()
- # now look for lines beginning with the word "atom"
- tokens = line.split()
- if ((len(tokens)>2) and (tokens[0] == "atom")):
- num_atomTypes += 1
- if (int(tokens[1]) > max_atomType):
- max_atomType = int(tokens[1])
-
-if num_atomTypes > 25:
- sys.stderr.write("\n"
- "(Note: If your computer freezes while running "+g_program_name+",\n"
- " it could be because you forgot to edit the .prm file.\n"
- " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n"
- " types. If you run "+g_program_name+" on this file, it may freeze or\n"
- " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n"
- " relevant to your problem. To do that, delete the lines from the .prm\n"
- " file beginning with \"atom\" which you do not need.)\n\n")
-
-#temporary storage file
-atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key
-#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms
-atom=[[-10000,-10000] for i in range(0,max_atomType+1)]
-#charge_by_type={} # lookup charge by atom type
-#vdw_by_type={} # lookup epsilon & sigma parameters by atom type
-charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom
-vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma
-
-
-
-#atom is declared this way so for sorting purposes.
-#atom contains the following data upon allocation
-#atom[][0]=atom_id( Important for partial charges and non_bonded interactions)
-#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers)
-#atom[][2]=atom_mass
-#atom[][3]=partial charge
-#atom[][4]=non_bonding sigma
-#atom[][5]=non_bonding epsilon
-#atom[][6]=atom comment
-bond=[]
-#bond contains the following data
-#bond[0]=atom 1 ffid
-#bond[1]=atom 2 ffid
-#bond[2]=bond spring constant(OPLS-aa compatible)
-#bond[3]=equilibrium bond distance(Angstrom)
-angle=[]
-#angle contains the following data
-#angle[0]=atom 1 ffid
-#angle[1]=atom 2 ffid
-#angle[2]=atom 3 ffid
-#angle[3]=spring constant
-#angle[4]=equilibrium angle (degrees)
-dihedral=[]
-#dihedral contains the following data
-#dihedral[0]=atom 1 ffid
-#dihedral[1]=atom 2 ffid
-#dihedral[2]=atom 3 ffid
-#dihedral[3]=atom 4 ffid
-#dihedral[4]=v1
-#dihedral[5]=v2
-#dihedral[6]=v3
-#dihedral[7]=v4
-improper=[]
-#improper[0]=atom 1 ffid
-#improper[1]=atom 2 ffid(central atom)
-#improper[2]=atom 3 ffid
-#improper[3]=atom 4 ffid
-#improper[4]=spring coefficient
-#improper[5]=equilibrium angle
-
-
-#This section gets all the parameters from the force field file
-for line in lines:
-
- # skip over text after a # comment character
- ic = line.find('#')
- if ic != -1:
- line = (line[:ic]).strip()
- else:
- line = line.strip()
-
- if line.find("atom") == 0:
- line=line.split()
- atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]),
- 0.0,0.0,0.0," ".join(line[3:-2])]
- elif line.find("vdw") == 0:
- line=line.split()
- #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])])
- if (int(line[1]) <= max_atomType):
- vdw_by_type[int(line[1])] = (float(line[2]),float(line[3]))
- elif line.find("bond") == 0:
- line=line.split()
- bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])])
- elif line.find("angle") == 0:
- line=line.split()
- angle.append([int(line[1]),int(line[2]),int(line[3]),
- float(line[4]),float(line[5])])
- elif line.find("torsion") == 0:
- line=line.split()
- dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]),
- float(line[5]),float(line[8]), float(line[11]), 0.0])
- elif line.find("charge") == 0:
- line=line.split()
- #charge_temp.append([int(line[1]),float(line[2])])
- if (int(line[1]) <= max_atomType):
- charge_by_type[int(line[1])] = float(line[2])
- elif line.find("imptors") == 0:
- line=line.split()
- improper.append([int(line[1]), int(line[2]),
- int(line[3]), int(line[4]), float(line[5]), float(line[6])])
-
-
-#if len(atom) > 600:
-# sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n"
-# " (You were supposed to edit out the atoms you don't need.\n"
-# " Not doing this may crash your computer.)\n"
-# "\n"
-# " Proceed? (Y/N): ")
-# reply = sys.stdin.readline()
-# if find(reply.strip().lower(), 'y') != 0:
-# exit(0)
-
-
-
-#adding the charge and Lennard Jones parameters to
-#to each atom type.
-#----------------------------------------------#
-
-system_is_charged = False
-
-for i in range(0,len(atom)):
- atom_type_num = atom[i][0]
- #q = charge_by_type.get(atomTypeNum)
- #if q:
- # atom[i][3] = q
- if atom_type_num != -10000:
- q = charge_by_type[atom_type_num]
- atom[i][3] = q
- if q != 0.0:
- # the system has some charged atoms
- system_is_charged = True
-
-for i in range(0,len(atom)):
- atom_type_num = atom[i][0]
- #vdw_params = vdw_by_type.get(atomTypeNum)
- #if vdw_params:
- # atom[i][4] = vdw_params[0]
- # atom[i][5] = vdw_params[1]
- if atom_type_num != -10000:
- vdw_params = vdw_by_type[atom_type_num]
- atom[i][4] = vdw_params[0]
- atom[i][5] = vdw_params[1]
-
-del(charge_by_type)
-del(vdw_by_type)
-
-
-
-if system_is_charged:
- pair_style = "lj/cut/coul/long"
- pair_style_params = "10.0 10.0"
- kspace_style = " kspace_style pppm 0.0001\n"
-else:
- pair_style = "lj/cut"
- pair_style_params = "10.0"
- kspace_style = ""
-
-pair_style_command = " pair_style hybrid "+pair_style+" "+pair_style_params+"\n"
-
-
-
-#----------------------------------------------------------#
-#begin writing content to lt file
-g.write("# NOTE: This file was created automatically using:\n"
- "# "+g_program_name+" \""+sys.argv[1]+"\"\n\n\n")
-
-g.write("OPLSAA {\n\n" )
-
-#write out the atom masses
-#----------------------------------------------------------#
-g.write(" write_once(\"Data Masses\"){\n")#checked with gaff
-for i,x in enumerate(atom):
- if x[0] != -10000:
- g.write(" @atom:{} {} #{} partial charge={}\n".format(
- x[0],x[2],x[6],x[3]))
-g.write(" } #(end of atom masses)\n\n")
-#----------------------------------------------------------#
-
-
-#write out the pair coefficients
-#----------------------------------------------------------#
-g.write(" write_once(\"In Settings\"){\n")#checked with gaff
-for i,x in enumerate(atom):
- if x[0] != -10000:
- fmt = " pair_coeff @atom:{0} @atom:{0} "+pair_style+" {1} {2}\n"
- g.write(fmt.format(x[0],x[5],x[4]))
-g.write(" } #(end of pair coeffs)\n\n")
-
-g.write(" write_once(\"In Charges\"){\n")#checked with gaff
-for i,x in enumerate(atom):
- if x[0] != -10000:
- g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3]))
-g.write(" } #(end of atom charges)\n\n")
-
-#-----------------------------------------------------------#
-
-# This part of the code creates a lookup dictionary
-# that allows you to find every type of atom by its
-# force field id. force field id is the id number
-# relevant to bonds, angles, dihedrals, and impropers.
-# This greatly increases the speed of angle, bond, dihedral
-# and improper assignment.
-#------------------------------------------------------------#
-atom=sorted(atom,key=itemgetter(1))
-atom_ffid=0
-for x in atom:
- if x[1]==atom_ffid:
- atom_lookup[x[1]].append(x[0])
- elif x[1]>atom_ffid:
- atom_lookup[x[1]]=[x[0]]
- atom_ffid=x[1]
-atom_lookup[0]=["*"]
-
-#-------------------------------------------------------------#
-#writing out the bond coefficients and bond parameters#
-#-------------------------------------------------------------#
-
-# First check if the atoms in system can potentially form bonds
-might_have_bonds = False
-for x in bond:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- might_have_bonds = True
-
-if might_have_bonds:
- h=open("temp.txt","w+")
- g.write(" write_once(\"In Settings\") {\n")
- index1=0
- for x in bond:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3]))
- # Miguel Gonzales corrected this line to:
- g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3]))
- h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z))
- g.write(" } #(end of bond_coeffs)\n\n")
- h.seek(0,0)
- g.write(" write_once(\"Data Bonds By Type\") {\n")
- for line in h.readlines():
- g.write(line)
- g.write(" } #(end of bonds by type)\n\n")
- del(bond)
- h.close()
-
-
-#-----------------------------------------------------------#
-#writing out angle coefficients and angles by type.---------#
-#-----------------------------------------------------------#
-
-# First check if the atoms in system can potentially form angle interactions
-might_have_angles = False
-for x in angle:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- for u in atom_lookup.get(x[2],[]):
- might_have_angles = True
-
-if might_have_angles:
- h=open("temp.txt","w+")
- g.write(" write_once(\"Data Angles By Type\"){\n")
- for x in angle:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- for u in atom_lookup.get(x[2],[]):
- #print(y,z,u,x)
- #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4]))
- # Miguel Gonzales corrected this line:
- h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4]))
- g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u))
-
- g.write(" } #(end of angles by type)\n\n")
- h.seek(0,0)
- g.write(" write_once(\"In Settings\" ){\n")
- for line in h.readlines():
- g.write(line)
- g.write(" } #(end of angle_coeffs)\n\n")
- del(angle)
- h.close()
-
-#----------------------------------------------------------#
-#writing dihedrals by type and dihedral coefficients-------#
-#----------------------------------------------------------#
-
-# First check if the atoms in system can potentially form dihedral interactions
-might_have_dihedrals = False
-for x in dihedral:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- for u in atom_lookup.get(x[2],[]):
- for v in atom_lookup.get(x[3],[]):
- might_have_dihedrals = True
-
-if might_have_dihedrals:
- h=open("temp.txt","w+")
- g.write(" write_once(\"Data Dihedrals By Type\") {\n")
- #print(atom_lookup)
- for x in dihedral:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- for u in atom_lookup.get(x[2],[]):
- for v in atom_lookup.get(x[3],[]):
- if x[0]!=0 and x[3]!=0:
- g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
- h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format(y,z,u,v,x[4],x[5],x[6],x[7]))
- elif x[0]==0 and x[3]!=0:
- g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(
- y,z,u,v))
- h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format(z,u,v,x[4],x[5],x[6],x[7]))
- elif x[0]==0 and x[3]==0:
- g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
- #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7]))
- h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7]))
-
- del(dihedral)
- g.write(" } #(end of Dihedrals by type)\n\n")
- h.seek(0,0)
- g.write(" write_once(\"In Settings\") {\n")
- for line in h.readlines():
- g.write(line)
- g.write(" } #(end of dihedral_coeffs)\n\n")
- h.close()
-
-#-----------------------------------------------------------------------#
-#----writing out improper coefficients and impropers by type------------#
-#-----------------------------------------------------------------------#
-
-# First check if the atoms in system can potentially form improper interactions
-might_have_impropers = False
-for x in improper:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- for u in atom_lookup.get(x[2],[]):
- for v in atom_lookup.get(x[3],[]):
- might_have_impropers = True
-
-if might_have_impropers:
- h=open("temp.txt","w+")
- g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n")
- for x in improper:
- for y in atom_lookup.get(x[0],[]):
- for z in atom_lookup.get(x[1],[]):
- for u in atom_lookup.get(x[2],[]):
- for v in atom_lookup.get(x[3],[]):
- # Notation: let I,J,K,L denote the atom types ("biotypes")
- # listed in the order they appear in the "oplsaa.prm" file.
- # (I think J and L are represented by "u" and "v" in the code here.)
- # It looks like the "oplsaa.prm" file distributed with tinker
- # treats the third atom ("K") as the central atom.
- # After checking the code, it appears that the improper angle is
- # calculated as the angle between the I,J,K and the J,K,L planes
- if x[0]==0 and x[1]==0 and x[3]==0:
- g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
- h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180))
- else:
- g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
- h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180))
-
-
- g.write(" } #(end of impropers by type)\n\n")
- h.seek(0,0)
- g.write(" write_once(\"In Settings\") {\n")
- for line in h.readlines():
- g.write(line)
- g.write(" } #(end of improp_coeffs)\n\n")
- h.close()
-
-#-----------------------------------------------------------------------#
-
-#This section writes out the input parameters required for an opls-aa simulation
-# lammps.
-
-
-g.write(" write_once(\"In Init\") {\n")
-g.write(" units real\n")
-g.write(" atom_style full\n")
-g.write(" bond_style hybrid harmonic\n")
-g.write(" angle_style hybrid harmonic\n")
-g.write(" dihedral_style hybrid opls\n")
-g.write(" improper_style hybrid harmonic\n")
-g.write(pair_style_command)
-g.write(" pair_modify mix geometric\n")
-g.write(" special_bonds lj/coul 0.0 0.0 0.5\n")
-g.write(kspace_style)
-g.write(" } #end of init parameters\n\n")
-g.write("} # OPLSAA\n")
-f.close()
-g.close()
-os.remove("temp.txt")
-
-
-sys.stderr.write("...finished.\n")
-
diff --git a/tools/moltemplate/src/nbody_Angles.py b/tools/moltemplate/src/nbody_Angles.py
deleted file mode 100644
index 66775743d..000000000
--- a/tools/moltemplate/src/nbody_Angles.py
+++ /dev/null
@@ -1,52 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how 3-body angle interactions are generated by moltemplate
-# by default. It can be overridden by supplying your own custom file.
-
-# To find 3-body "angle" interactions, we would use this subgraph:
-#
-#
-# *---*---* => 1st bond connects atoms 0 and 1
-# 0 1 2 2nd bond connects atoms 1 and 2
-#
-
-bond_pattern = Ugraph([(0,1), (1,2)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-# The next function eliminates the redundancy between 0-1-2 and 2-1-0:
-def canonical_order(match):
- """
- Before defining a new interaction, we must check to see if an
- interaction between these same 3 atoms has already been created
- (perhaps listed in a different, but equivalent order).
- If we don't check for this this, we will create many unnecessary redundant
- interactions (which can slow down he simulation).
- To avoid this, I define a "canonical_order" function which sorts the atoms
- and bonds in a way which is consistent with the symmetry of the interaction
- being generated... Later the re-ordered list of atom and bond ids will be
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far. Note that
- the energy of an angle interaction is a function of the angle between.
- three consecutively bonded atoms (referred to here as: 0,1,2).
- This angle does not change when swapping the atoms at either end (0 and 2).
- So it does not make sense to define a separate 3-body angle
- interaction between atoms 0,1,2 AS WELL AS an interaction between 2,1,0.
- So we sort the atoms and bonds so that the first atom has a always has
- a lower atomID than the third atom. (Later we will check to see if we
- have already defined an interaction between these 3 atoms. If not then
- we create a new one.)
-
- """
- # match[0][0:2] contains the ID numbers for the 3 atoms in the match
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- # match[1][0:1] contains the ID numbers for the 2 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- if atom0 < atom2:
- #return ((atom0, atom1, atom2), (bond0, bond1)) same thing as:
- return match
- else:
- return ((atom2, atom1, atom0), (bond1, bond0))
diff --git a/tools/moltemplate/src/nbody_Bonds.py b/tools/moltemplate/src/nbody_Bonds.py
deleted file mode 100644
index ec1ac2232..000000000
--- a/tools/moltemplate/src/nbody_Bonds.py
+++ /dev/null
@@ -1,31 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# To find 2-body "bond" interactions, we would use this subgraph:
-#
-#
-# *---* => one bond connects atoms 0 and 1
-# 0 1
-#
-
-bond_pattern = Ugraph([(0,1)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-# The next function eliminates the redundancy between 0-1 and 1-0:
-def canonical_order(match):
- """
- It does not make sense to define a separate bond between atoms 1 and 2,
- and between atoms 2 and 1. This function will swap the atoms in the bond
- if the first atom > second atom.
-
- """
- # match[0][0:2] contains the ID numbers for the 2 atoms in the match
- atom0 = match[0][0]
- atom1 = match[0][1]
- # match[1][0:1] contains the ID numbers for the 1 bond
- bond0 = match[1][0]
- if atom0 < atom1:
- #return ((atom0, atom1), (bond0)) same thing as:
- return match
- else:
- return ((atom1, atom0), (bond0))
diff --git a/tools/moltemplate/src/nbody_Dihedrals.py b/tools/moltemplate/src/nbody_Dihedrals.py
deleted file mode 100644
index 2c8194885..000000000
--- a/tools/moltemplate/src/nbody_Dihedrals.py
+++ /dev/null
@@ -1,53 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how dihedral interactions are generated by moltemplate.sh
-# by default. It can be overridden by supplying your own custom file.
-
-# To find 4-body "dihedral" interactions, we would use this subgraph:
-#
-# 1st bond connects atoms 0 and 1
-# *---*---*---* => 2nd bond connects atoms 1 and 2
-# 0 1 2 3 3rd bond connects atoms 2 and 3
-#
-
-bond_pattern = Ugraph([(0,1), (1,2), (2,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- Before defining a new interaction, we must check to see if an
- interaction between these same 4 atoms has already been created
- (perhaps listed in a different, but equivalent order).
- If we don't check for this this, we will create many unnecessary redundant
- interactions (which can slow down he simulation).
- To avoid this, I define a "canonical_order" function which sorts the atoms
- and bonds in a way which is consistent with the symmetry of the interaction
- being generated... Later the re-ordered list of atom and bond ids will be
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far. Note that
- the energy of a dihedral interaction is a function of the dihedral-angle.
- The dihedral-angle is usually defined as the angle between planes formed
- by atoms 0,1,2 & 1,2,3. This angle does not change when reversing the
- order of the atoms. So it does not make sense to define a separate
- dihedral interaction between atoms 0,1,2,3 AS WELL AS between 3,2,1,0.
- So we sort the atoms so that the first atom has a lower atomID than the
- last atom. (Later we will check to see if we have already defined an
- interaction between these 4 atoms. If not then we create a new one.)
-
- """
-
- # match[0][0:3] contains the ID numbers of the 4 atoms in the match
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- # match[1][0:2] contains the ID numbers of the the 3 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- bond2 = match[1][2]
- if atom0 < atom3:
- #return ((atom0, atom1, atom2, atom3), (bond0, bond1, bond2)) same as:
- return match
- else:
- return ((atom3, atom2, atom1, atom0), (bond2, bond1, bond0))
diff --git a/tools/moltemplate/src/nbody_Impropers.py b/tools/moltemplate/src/nbody_Impropers.py
deleted file mode 100644
index 587ab4a44..000000000
--- a/tools/moltemplate/src/nbody_Impropers.py
+++ /dev/null
@@ -1,62 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how improper interactions are generated by moltemplate.sh
-# by default. It can be overridden by supplying your own custom file
-# (for example, see "opls_imp.py")
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 3
-# * 1st bond connects atoms 0 and 1
-# | => 2nd bond connects atoms 0 and 2
-# _.*._ 3rd bond connects atoms 0 and 3
-# *' 0 `*
-# 1 2
-#
-
-bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- Before defining a new interaction, we must check to see if an
- interaction between these same 4 atoms has already been created
- (perhaps listed in a different, but equivalent order).
- If we don't check for this this, we will create many unnecessary redundant
- interactions (which can slow down he simulation).
- To avoid this, I define a "canonical_order" function which sorts the atoms
- and bonds in a way which is consistent with the symmetry of the interaction
- being generated... Later the re-ordered list of atom and bond ids will be
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far. Note that
- the energy of an improper interactions is a function of the improper angle.
- The improper-angle is usually defined as the angle between planes formed
- by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the
- angle between the 0,1,2 plane and atom 3.)
- This angle does not change when swapping the MIDDLE pair of atoms (1 and 2)
- (except for a change of sign, which does not matter since the energy functions
- used are typically sign invariant. Furthermore, neither of MIDDLE pair of atoms
- are the central atom, and there are 3!=6 ways of ordering the remaining 3 atoms.)
- Consequently it does not make sense to define a separate 4-body improper
- interaction between atoms 0,1,2,3 AS WELL AS between 0,2,1,3.
- So we sort the atoms and bonds so that the second atom has a always has
- a lower atomID than the third atom. (Later we will check to see if we
- have already defined an interaction between these 4 atoms. If not then
- we create a new one.)
-
- """
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- # match[1][0:2] contains the ID numbers for the 3 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- bond2 = match[1][2]
- if atom1 <= atom2:
- #return ((atom0,atom1,atom2,atom3), (bond0,bond1,bond2))
- # But this is the same thing as:
- return match
- else:
- return ((atom0,atom2,atom1,atom3), (bond1,bond0,bond2))
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/class2_dih.py b/tools/moltemplate/src/nbody_alternate_symmetry/class2_dih.py
deleted file mode 100644
index 4d7185e5f..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/class2_dih.py
+++ /dev/null
@@ -1,40 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how improper interactions are generated in class2 files.
-# To use it, add "(class2_dih.py)" to the name of the "Data Dihedrals By Type"
-# section, and make sure this file is located in the "common" directory.
-# For example:
-# write_once("Data Dihedrals By Type (class2_dih.py)") {
-# ...
-# }
-
-# To find 4-body "dihedral" interactions, we would use this subgraph:
-#
-# 1st bond connects atoms 0 and 1
-# *---*---*---* => 2nd bond connects atoms 1 and 2
-# 0 1 2 3 3rd bond connects atoms 2 and 3
-#
-
-bond_pattern = Ugraph([(0,1), (1,2), (2,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- When searching for atoms with matching bond patterns GraphMatcher
- often returns redundant results. We must define a "canonical_order"
- function which sorts the atoms and bonds in a way which is consistent
- with the type of N-body interaction being considered.
- However, some dihedral_styles (such as dihedral_style class2)
- have no symmetry (at least not for arbitrary choices of parameters).
- These force-field styles, the different permulations of atom-order
- are not equivalent. So we do not want to rearrange the order of
- the atoms (and bonds) in the match, because the formula for the
- interaction between atoms 1,2,3,4 is not the same as the formula
- for the interaction between atoms 4,3,2,1.
- In this case, this function returns
- the original "match" argument unmodified.
-
- """
-
- return match
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/class2_imp.py b/tools/moltemplate/src/nbody_alternate_symmetry/class2_imp.py
deleted file mode 100644
index fec6dcb15..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/class2_imp.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how improper interactions are generated in class2 files.
-# To use it, add "(class2_imp.py)" to the name of the "Data Impropers By Type"
-# section, and make sure this file is located in the "common" directory.
-# For example:
-# write_once("Data Impropers By Type (class2_imp.py)") {
-# ...
-# }
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 3
-# * 1st bond connects atoms 0 and 1
-# | => 2nd bond connects atoms 0 and 2
-# _.*._ 3rd bond connects atoms 0 and 3
-# *' 0 `*
-# 1 2
-#
-
-bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- When searching for atoms with matching bond patterns GraphMatcher
- often returns redundant results. We must define a "canonical_order"
- function which sorts the atoms and bonds in a way which is consistent
- with the type of N-body interaction being considered.
- However, some improper_styles (such as improper_style class2)
- have no symmetry (at least not for arbitrary choices of parameters).
- These force-field styles, the different permulations of atom-order
- are not equivalent. So we do not want to rearrange the order of
- the atoms (and bonds) in the match, because the resulting interaction
- is not equivalent. In this case, this function returns
- the original "match" argument unmodified.
-
- """
-
- return match
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/gaff_imp.py b/tools/moltemplate/src/nbody_alternate_symmetry/gaff_imp.py
deleted file mode 100644
index 5e9fe2689..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/gaff_imp.py
+++ /dev/null
@@ -1,74 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how improper interactions are generated in AMBER (GAFF).
-# To use it, add "(gaff_imp.py)" to the name of the "Data Impropers By Type"
-# section, and make sure this file is located in the "common" directory.
-# For example:
-# write_once("Data Impropers By Type (gaff_imp.py)") {
-# ...
-# }
-
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 0
-# * 1st bond connects atoms 2 and 0
-# | => 2nd bond connects atoms 2 and 1
-# _.*._ 3rd bond connects atoms 2 and 3
-# *' 2 `*
-# 1 3
-#
-# In AMBER/GAFF, the central atom is the third atom ("2").
-# http://archive.ambermd.org/201307/0519.html
-# This differs from other force-fields.
-# We take this detail into account in the line below:
-
-bond_pattern = Ugraph([(2,0), (2,1), (2,3)])
-
-# As with other force-fields, the improper-angle is the angle between the planes
-# defined by the first three atoms (0,1,2) and last three atoms (1,2,3).
-# (This is implemented in LAMMPS using an improper_style which requires
-# that the atoms in the interaction will be listed in this order: 0,1,2,3.)
-
-def canonical_order(match):
- """
- Before defining a new interaction, we must check to see if an
- interaction between these same 4 atoms has already been created
- (perhaps listed in a different, but equivalent order).
- If we don't check for this this, we will create many unnecessary redundant
- interactions (which can slow down he simulation).
- To avoid this, I define a "canonical_order" function which sorts the atoms
- and bonds in a way which is consistent with the symmetry of the interaction
- being generated... Later the re-ordered list of atom and bond ids will be
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far. Note that
- the energy of an improper interactions is a function of the improper angle.
- The improper-angle is usually defined as the angle between planes formed
- by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the
- angle between the 0,1,2 plane and atom 3.)
- This angle does not change when swapping the OUTER pair of atoms (0 and 3)
- (except for a change of sign, which does not matter since the energy functions
- used are typically sign invariant. Furthermore, neither of OUTER pair of atoms
- are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.)
- Consequently it does not make sense to define a separate 4-body improper-
- interaction between atoms 0,1,2,3 AS WELL AS between 3,1,2,0.
- So we sort the atoms and bonds so that the first atom has a always has
- a lower atomID than the last atom. (Later we will check to see if we
- have already defined an interaction between these 4 atoms. If not then
- we create a new one.)
-
- """
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- # match[1][0:2] contains the ID numbers for the 3 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- bond2 = match[1][2]
- if atom0 <= atom3:
- #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2))
- # But this is the same thing as:
- return match
- else:
- return ((atom3,atom1,atom2,atom0), (bond2,bond1,bond0))
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py b/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py
deleted file mode 100644
index d3f9513d3..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py
+++ /dev/null
@@ -1,32 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# To find 4-body "dihedral" interactions, we would use this subgraph:
-#
-# 1st bond connects atoms 0 and 1
-# *---*---*---* => 2nd bond connects atoms 1 and 2
-# 0 1 2 3 3rd bond connects atoms 2 and 3
-#
-
-bond_pattern = Ugraph([(0,1), (1,2), (2,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- When searching for atoms with matching bond patterns GraphMatcher
- often returns redundant results. We must define a "canonical_order"
- function which sorts the atoms and bonds in a way which is consistent
- with the type of N-body interaction being considered.
- However, some dihedral_styles (such as dihedral_style class2)
- have no symmetry (at least not for arbitrary choices of parameters).
- These force-field styles, the different permulations of atom-order
- are not equivalent. So we do not want to rearrange the order of
- the atoms (and bonds) in the match, because the formula for the
- interaction between atoms 1,2,3,4 is not the same as the formula
- for the interaction between atoms 4,3,2,1.
- In this case, this function returns
- the original "match" argument unmodified.
-
- """
-
- return match
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Icenter_swapJK.py b/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Icenter_swapJK.py
deleted file mode 100644
index 938de21b4..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Icenter_swapJK.py
+++ /dev/null
@@ -1,49 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 3
-# * 1st bond connects atoms 0 and 1
-# | => 2nd bond connects atoms 0 and 2
-# _.*._ 3rd bond connects atoms 0 and 3
-# *' 0 `*
-# 1 2
-#
-
-bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- When searching for atoms with matching bond patterns GraphMatcher
- often returns redundant results. We must define a "canonical_order"
- function which sorts the atoms and bonds in a way which is consistent
- with the type of N-body interaction being considered.
- The atoms (and bonds) in a candidate match are rearranged by the
- canonical_order(). Then the re-ordered list of atom and bond ids is
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far.
- (For example, it does not make sense to define a separate 4-body improper-
- angle interaction between atoms 1, 2, 3, 4 AND 1, 3, 2, 4.
- The improper-angle is usually defined as the angle between planes formed
- by atoms 1,2,3 & 2,3,4. Alternately, it may instead be defined as the
- angle between the 1,2,3 plane and atom 4. Either way, this angle does
- not change when swapping the middle pair of atoms so we arbitrarily
- sort them so that the second atom has a lower atomID than the third atom.)
-
- """
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- # match[1][0:2] contains the ID numbers for the 3 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- bond2 = match[1][2]
- if atom1 <= atom2:
- #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2))
- # But this is the same thing as:
- return match
- else:
- return ((atom0,atom2,atom1,atom3), (bond1, bond0, bond2))
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Icenter_swapJKL.py b/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Icenter_swapJKL.py
deleted file mode 100644
index 2432769dc..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Icenter_swapJKL.py
+++ /dev/null
@@ -1,43 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# To find 4-body "improper" interactions, we would use this subgraph:
-# 3
-# * 1st bond connects atoms 0 and 1
-# | => 2nd bond connects atoms 0 and 2
-# _.*._ 3rd bond connects atoms 0 and 3
-# *' 0 `*
-# 1 2
-#
-
-bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
-# (Note: Ugraph atom-index counters begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- When searching for atoms with matching bond patterns GraphMatcher
- often returns redundant results. We must define a "canonical_order"
- function which sorts the atoms and bonds in a way which is consistent
- with the type of N-body interaction being considered.
- The atoms (and bonds) in a candidate match are rearranged by the
- canonical_order(). Then the re-ordered list of atom and bond ids is
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far.
- (For example, it does not make sense to define a separate 4-body improper-
- angle interaction between atoms 1,2,3,4 AND 1,4,2,3,
- or 1,3,4,2, or 1,4,3,2 or 1,2,4,3, or 1,3,2,4, for that matter.)
- In some cases, the second atom is the central atom (the "hub"), and the
- potential is invariant with respect to permutations of the other 3 atoms.
- So we arbitrarily sort these other 3 atoms in increasing order
- (as well as the bonds which connect the central atom to them).
-
- """
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- bonds = match[1]
- ab=[(atom1,0), (atom2,1), (atom3,2)]
- ab.sort()
- return ((atom0, ab[0][0], ab[1][0], ab[2][0]),
- (bonds[ab[0][1]], bonds[ab[1][1]], bonds[ab[2][1]]))
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Jcenter.py b/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Jcenter.py
deleted file mode 100644
index 17c5966ee..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Jcenter.py
+++ /dev/null
@@ -1,64 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 0
-# * 1st bond connects atoms 1 and 0
-# | => 2nd bond connects atoms 1 and 2
-# _.*._ 3rd bond connects atoms 1 and 3
-# *' 1 `*
-# 2 3
-#
-# In OPLS, the central atom is the second atom ("1").
-# This differs from other force-fields.
-# We take this detail into account in the line below:
-
-bond_pattern = Ugraph([(1,0), (1,2), (1,3)])
-
-# As with other force-fields, the improper-angle is the angle between the planes
-# defined by the first three atoms (0,1,2) and last three atoms (1,2,3).
-# (This is implemented in LAMMPS using an improper_style which requires
-# that the atoms in the interaction will be listed in this order: 0,1,2,3.)
-
-def canonical_order(match):
- """
- Before defining a new interaction, we must check to see if an
- interaction between these same 4 atoms has already been created
- (perhaps listed in a different, but equivalent order).
- If we don't check for this this, we will create many unnecessary redundant
- interactions (which can slow down he simulation).
- To avoid this, I define a "canonical_order" function which sorts the atoms
- and bonds in a way which is consistent with the symmetry of the interaction
- being generated... Later the re-ordered list of atom and bond ids will be
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far. Note that
- the energy of an improper interactions is a function of the improper angle.
- The improper-angle is usually defined as the angle between planes formed
- by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the
- angle between the 0,1,2 plane and atom 3.)
- This angle does not change when swapping the OUTER pair of atoms (0 and 3)
- (except for a change of sign, which does not matter since the energy functions
- used are typically sign invariant. Furthermore, neither of OUTER pair of atoms
- are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.)
- Consequently it does not make sense to define a separate 4-body improper-
- interaction between atoms 0,1,2,3 AS WELL AS between 3,1,2,0.
- So we sort the atoms and bonds so that the first atom has a always has
- a lower atomID than the last atom. (Later we will check to see if we
- have already defined an interaction between these 4 atoms. If not then
- we create a new one.)
-
- """
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- # match[1][0:2] contains the ID numbers for the 3 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- bond2 = match[1][2]
- if atom0 <= atom3:
- #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2))
- # But this is the same thing as:
- return match
- else:
- return ((atom3,atom1,atom2,atom0), (bond2,bond1,bond0))
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Jcenter_nosym.py b/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Jcenter_nosym.py
deleted file mode 100644
index 8ef6e8f34..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/nbody_Impropers_Jcenter_nosym.py
+++ /dev/null
@@ -1,33 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 3
-# * 1st bond connects atoms 0 and 1
-# | => 2nd bond connects atoms 0 and 2
-# _.*._ 3rd bond connects atoms 0 and 3
-# *' 0 `*
-# 1 2
-#
-
-bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
-# (Ugraph atom indices begin at 0, not 1)
-
-
-def canonical_order(match):
- """
- When searching for atoms with matching bond patterns GraphMatcher
- often returns redundant results. We must define a "canonical_order"
- function which sorts the atoms and bonds in a way which is consistent
- with the type of N-body interaction being considered.
- However, some improper_styles (such as improper_style class2)
- have no symmetry (at least not for arbitrary choices of parameters).
- These force-field styles, the different permulations of atom-order
- are not equivalent. So we do not want to rearrange the order of
- the atoms (and bonds) in the match, because the resulting interaction
- is not equivalent. In this case, this function returns
- the original "match" argument unmodified.
-
- """
-
- return match
diff --git a/tools/moltemplate/src/nbody_alternate_symmetry/opls_imp.py b/tools/moltemplate/src/nbody_alternate_symmetry/opls_imp.py
deleted file mode 100644
index 3ee661760..000000000
--- a/tools/moltemplate/src/nbody_alternate_symmetry/opls_imp.py
+++ /dev/null
@@ -1,72 +0,0 @@
-from nbody_graph_search import Ugraph
-
-# This file defines how improper interactions are generated in OPLS.
-# To use it, add "(opls_imp.py)" to the name of the "Data Impropers By Type"
-# section, and make sure this file is located in the "common" directory.
-# For example:
-# write_once("Data Impropers By Type (opls_imp.py)") {
-# ...
-# }
-
-
-# To find 4-body "improper" interactions,
-# (by default, most of the time), we would use this subgraph:
-# 0
-# * 1st bond connects atoms 2 and 0
-# | => 2nd bond connects atoms 2 and 1
-# _.*._ 3rd bond connects atoms 2 and 3
-# *' 2 `*
-# 1 3
-#
-# In OPLS (as implemented in TINKER .PRM files), the central atom
-# is the third atom ("2").
-
-bond_pattern = Ugraph([(2,0), (2,1), (2,3)])
-
-# As with other force-fields, the improper-angle is the angle between the planes
-# defined by the first three atoms (0,1,2) and last three atoms (1,2,3).
-# (This is implemented in LAMMPS using an improper_style which requires
-# that the atoms in the interaction will be listed in this order: 0,1,2,3.)
-
-def canonical_order(match):
- """
- Before defining a new interaction, we must check to see if an
- interaction between these same 4 atoms has already been created
- (perhaps listed in a different, but equivalent order).
- If we don't check for this this, we will create many unnecessary redundant
- interactions (which can slow down he simulation).
- To avoid this, I define a "canonical_order" function which sorts the atoms
- and bonds in a way which is consistent with the symmetry of the interaction
- being generated... Later the re-ordered list of atom and bond ids will be
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added to the list of interactions found so far. Note that
- the energy of an improper interactions is a function of the improper angle.
- The improper-angle is usually defined as the angle between planes formed
- by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the
- angle between the 0,1,2 plane and atom 3.)
- This angle does not change when swapping the OUTER pair of atoms (0 and 3)
- (except for a change of sign, which does not matter since the energy functions
- used are typically sign invariant. Furthermore, neither of OUTER pair of atoms
- are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.)
- Consequently it does not make sense to define a separate 4-body improper-
- interaction between atoms 0,1,2,3 AS WELL AS between 3,1,2,0.
- So we sort the atoms and bonds so that the first atom has a always has
- a lower atomID than the last atom. (Later we will check to see if we
- have already defined an interaction between these 4 atoms. If not then
- we create a new one.)
-
- """
- atom0 = match[0][0]
- atom1 = match[0][1]
- atom2 = match[0][2]
- atom3 = match[0][3]
- # match[1][0:2] contains the ID numbers for the 3 bonds
- bond0 = match[1][0]
- bond1 = match[1][1]
- bond2 = match[1][2]
- if atom0 <= atom3:
- #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2))
- # But this is the same thing as:
- return match
- else:
- return ((atom3,atom1,atom2,atom0), (bond2,bond1,bond0))
diff --git a/tools/moltemplate/src/nbody_by_type.py b/tools/moltemplate/src/nbody_by_type.py
deleted file mode 100644
index 13fc01201..000000000
--- a/tools/moltemplate/src/nbody_by_type.py
+++ /dev/null
@@ -1,665 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2011, Regents of the University of California
-# All rights reserved.
-
-man_page_text = """
-
- nbody_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS)
- data file containing bonded many-body interactions by atom type
- (and bond type), and generates a list of additional interactions
- in LAMMPS format consistent with those type (to the standard out).
-
- Typical Usage:
-
- nbody_by_type.py X < old.data > new.data
-
- --or--
-
- nbody_by_type.py X \\
- -atoms atoms.data \\
- -bonds bonds.data \\
- -nbody X.data \\
- -nbodybytype X_by_type.data \\
- > new_X.data
-
- In both cases "X" denotes the interaction type, which
- is either "Angles", "Dihedrals", or "Impropers".
- (Support for other interaction types can be added by the user. See below.)
-
- -------- Example 1 -------
-
- nbody_by_type.py X < old.data > new.data
-
- In this example, nbody_by_type.py reads a LAMMPS data file
- "orig.data", and extracts the relevant section ("Angles",
- "Dihedrals", or "Impropers"). It also looks a section named "X By Type",
- (eg. "Angles By type", "Impropers By type", "Impropers By type")
- which contains a list of criteria for automatically defining additional
- interactions of that type. For example, this file might contain:
-
- Angle By Type
-
- 7 1 2 1 * *
- 8 2 2 * * *
- 9 3 4 3 * *
-
- The first column is an interaction type ID.
- The next 3 columns are atom type identifiers.
- The final 2 columns are bond type identifiers.
- The * is a wildcard symbol indicating there is no preference for bond types
- in this example. (Optionally, regular expressions can also be used to
- define a type match, by enclosing the atom or bond type in / slashes.)
-
- The first line tells us to that there should be a 3-body "Angle"
- interaction of type "7" whenever an atom of type 1 is bonded to an atom
- of type "2", which is bonded to another atom of type "1" again.
- The second line tells us that an angle is defined whenever three atoms
- are bonded together and the first two are of type "2".
- (Redundant angle interactions are filtered.)
-
- New interactions are created for every group of bonded
- atoms which match these criteria if they are bonded together
- in the relevant way for that interaction type (as determined by
- nbody_X.py), and printed to the standard output. For example,
- suppose you are automatically generating 3-body "Angle" interactions using:
-
- nbody_by_type Angles < old.data > new.data
-
- The file "new.data" will be identical to "old.data", however the
- "Angles By Type" section will be deleted, and the following lines of
- text will be added to the "Angles" section:
-
- 394 7 5983 5894 5895
- 395 7 5984 5895 5896
- 396 7 5985 5896 5897
- : : : : :
- 847 9 14827 14848 14849
-
- The numbers in the first column are counters which assign a ID to
- every interaction of that type, and start where the original "Angles"
- data left off (New angle ID numbers do not overlap with old ID numbers).
- The text in the second column ("7", "9", ...) matches the text from the
- first column of the "Angle By Type" section of the input file.
-
- -------- Example 2 -------
-
- nbody_by_type.py X \\
- -atoms atoms.data \\
- -bonds bonds.data \\
- -nbody X.data \\
- -nbodybytype X_by_type.data \\
- -prefix "SOMESTRING" -suffix "ANOTHERSTRING" \\
- > new_X.data
-
- In particular, for Angle interactions:
-
- nbody_by_type.py Angles \\
- -atoms atoms.data \\
- -bonds bonds.data \\
- -nbody angles.data \\
- -nbodybytype angles_by_type.data \\
- > new_Angles.data
-
- When run this way, nbody_by_type.py behaves exactly the same way
- as in Example 1, however only the lines of text corresponding to
- the new generated interactions are printed, (not the entire data file).
- Also note, that when run this way, nbody_by_type.py does not read the
- LAMMPS data from the standard input. Instead, it reads each section of
- the data file from a different file indicated by the arguments following
- the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags.
-
- "Angles" is a 3-body interaction style. So when run this way,
- nbody_by_type.py will create a 5 (=3+2) column file (new_Angles.data).
-
-Note: the atom, bond and other IDs/types in need not be integers.
-
-Note: This program must be distributed with several python modules, including:
- nbody_Angles.py, nbody_Dihedrals.py, and nbody_Impropers.py. These
- contain bond definitions for angular, dihedral, and improper interactions.
- (In case any new interaction types are ever added to LAMMPS, with only
- a few lines of python it is easy to edit to define new bonded
- interaction types by supplying new "nbody_X.py" python module.
- Refer to the modules listed above for examples.)
-
-Note: Optional "-prefix" and "-suffix" arguments can be included to decorate
- the interaction IDs (first column). For example, -prefix "auto_" and
- -suffix "_angle", causes "new_Angles.data" to contain the following text:
-
- auto_394_angle 7 5983 5894 5895
- auto_395_angle 7 5984 5895 5896
- auto_396_angle 7 5985 5896 5897
- : : : : :
- auto_847_angle 9 14827 14848 14849
-
-"""
-
-
-import sys
-from extract_lammps_data import *
-from nbody_by_type_lib import GenInteractions_str
-from ttree_lex import *
-from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid
-import os, inspect # <- Needed to import modules in subdirectories (see below)
-
-if sys.version < '2.6':
- raise InputError('Error: Using python '+sys.version+'\n'
- ' Alas, you must upgrade to a newer version of python (2.6 or later).')
-elif sys.version < '2.7':
- sys.stderr.write('--------------------------------------------------------\n'
- '----------------- WARNING: OLD PYTHON VERSION ----------\n'
- ' This program is untested on your python version ('+sys.version+').\n'
- ' PLEASE LET ME KNOW IF THIS PROGRAM CRASHES (and upgrade python).\n'
- ' -Andrew 2013-10-25\n'
- '--------------------------------------------------------\n'
- '--------------------------------------------------------\n')
- from ordereddict import OrderedDict
-else:
- from collections import OrderedDict
-
-
-
-def GenInteractions_lines(lines_atoms,
- lines_bonds,
- lines_nbody,
- lines_nbodybytype,
- atom_style,
- g_bond_pattern,
- canonical_order, #function to sort atoms and bonds
- prefix='',
- suffix='',
- report_progress = False):
-
- column_names = AtomStyle2ColNames(atom_style)
- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
-
- atomids_str = []
- atomtypes_str = []
-
- for iv in range(0, len(lines_atoms)):
- line = lines_atoms[iv].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = SplitQuotedString(line)
- if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
- raise(InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.'))
- tokens = SplitQuotedString(line)
- atomids_str.append(EscCharStrToChar(tokens[i_atomid]))
- atomtypes_str.append(EscCharStrToChar(tokens[i_atomtype]))
-
- bondids_str = []
- bondtypes_str = []
- bond_pairs = []
- for ie in range(0, len(lines_bonds)):
- line = lines_bonds[ie].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = SplitQuotedString(line)
- if len(tokens) < 4:
- raise(InputError('Error not enough columns on line '+str(ie+1)+' of \"Bonds\" section.'))
- bondids_str.append(EscCharStrToChar(tokens[0]))
- bondtypes_str.append(EscCharStrToChar(tokens[1]))
- bond_pairs.append( (EscCharStrToChar(tokens[2]),
- EscCharStrToChar(tokens[3])) )
-
- typepattern_to_coefftypes = []
-
- for i in range(0, len(lines_nbodybytype)):
- line = lines_nbodybytype[i].strip()
- if '#' in line:
- icomment = line.find('#')
- line = (line[:icomment]).strip()
- if len(line) > 0:
- tokens = SplitQuotedString(line)
-
- if ((len(tokens) != 1 + g_bond_pattern.GetNumVerts()) and
- (len(tokens) != 1 + g_bond_pattern.GetNumVerts()
- + g_bond_pattern.GetNumEdges())):
- raise(InputError('Error: Wrong number of columns in \"By Type\" section of data file.\n'
- 'Offending line:\n'+
- '\"'+line+'\"\n'
- 'Expected either '+
- str(1 + g_bond_pattern.GetNumVerts()) + ' or ' +
- str(1 + g_bond_pattern.GetNumVerts() +
- g_bond_pattern.GetNumEdges())
- + ' colunms.'))
-
- coefftype = EscCharStrToChar(tokens[0])
- typepattern = []
-
- for typestr in tokens[1:]:
- if ((len(typestr) >= 2) and
- (typestr[0] == '/') and (typestr[-1] == '/')):
- regex_str = typestr[1:-1]
- typepattern.append( re.compile(regex_str) )
- else:
- typepattern.append(EscCharStrToChar(typestr))
-
- # If the user neglected to specify the bond types, assume '*'
- if len(tokens) == 1 + g_bond_pattern.GetNumVerts():
- typepattern += ['*'] * g_bond_pattern.GetNumEdges()
-
- typepattern_to_coefftypes.append([typepattern, coefftype])
-
- coefftype_to_atomids_str = GenInteractions_str(bond_pairs,
- g_bond_pattern,
- typepattern_to_coefftypes,
- canonical_order,
- atomids_str,
- atomtypes_str,
- bondids_str,
- bondtypes_str,
- report_progress)
- lines_nbody_new = []
- for coefftype, atomids_list in coefftype_to_atomids_str.items():
- for atomids_found in atomids_list:
- n = len(lines_nbody) + len(lines_nbody_new) + 1
- line = prefix+str(n)+suffix+' '+ \
- coefftype+' '+(' '.join(atomids_found))+'\n'
- lines_nbody_new.append(line)
-
- return lines_nbody_new
-
-
-
-def GenInteractions_files(lines_data,
- src_bond_pattern,
- fname_atoms,
- fname_bonds,
- fname_nbody,
- fname_nbodybytype,
- section_name,
- section_name_bytype,
- atom_style,
- prefix='',
- suffix='',
- report_progress = False):
-
- if fname_atoms == None:
- lines_atoms = [line for line in ExtractDataSection(lines_data, 'Atoms')]
- else:
- try:
- f = open(fname_atoms, 'r')
- except:
- sys.stderr.write('Error: Unable to open file \"'+fname_atoms+'\" for reading.\n')
- sys.exit(-1)
- lines_atoms = [line for line in f.readlines()
- if ((len(line.strip())>0) and (line.strip()[0] != '#'))]
- f.close()
-
-
- if fname_bonds == None:
- lines_bonds = [line for line in ExtractDataSection(lines_data, 'Bonds')]
- else:
- try:
- f = open(fname_bonds, 'r')
- except IOError:
- sys.stderr.write('Error: Unable to open file \"'+fname_bonds+'\" for reading.\n')
- sys.exit(-1)
- lines_bonds = [line for line in f.readlines()
- if ((len(line.strip())>0) and (line.strip()[0] != '#'))]
- f.close()
-
-
- if fname_nbody == None:
- lines_nbody = [line for line in ExtractDataSection(lines_data, section_name)]
- else:
- try:
- f = open(fname_nbody, 'r')
- lines_nbody = [line for line in f.readlines()
- if ((len(line.strip())>0) and (line.strip()[0] != '#'))]
- f.close()
- except IOError:
- #sys.stderr.write(' (omitting optional file \"'+fname_nbody+'\")\n')
- lines_nbody = []
-
-
- if fname_nbodybytype == None:
- lines_nbodybytype=[line for
- line in ExtractDataSection(lines_data,
- section_name_bytype)]
-
- else:
- try:
- f = open(fname_nbodybytype, 'r')
- except:
- sys.stderr.write('Error: Unable to open file \"'+fname_nbodybytype+'\" for reading.\n')
- sys.exit(-1)
- lines_nbodybytype = [line for line in f.readlines()
- if((len(line.strip())>0)and(line.strip()[0]!='#'))]
- f.close()
-
-
- try:
- g = __import__(src_bond_pattern) #defines g.bond_pattern, g.canonical_order
- except:
- # If not found, look for it in the "nbody_alternate_symmetry" directory
- #http://stackoverflow.com/questions/279237/import-a-module-from-a-relative-path
- cmd_subfolder = os.path.realpath(os.path.abspath(os.path.join(os.path.split(inspect.getfile( inspect.currentframe() ))[0],"nbody_alternate_symmetry")))
- if cmd_subfolder not in sys.path:
- sys.path.insert(0, cmd_subfolder)
- try:
- g = __import__(src_bond_pattern) #defines g.bond_pattern, g.canonical_order
- except:
- sys.stderr.write('Error: Unable to locate file \"'+src_bond_pattern+'\"\n'
- ' (Did you mispell the file name?\n'
- ' Check the \"nbody_alternate_symmetry/\" directory.)\n')
- sys.exit(-1)
-
-
-
-
- return GenInteractions_lines(lines_atoms,
- lines_bonds,
- lines_nbody,
- lines_nbodybytype,
- atom_style,
- g.bond_pattern,
- g.canonical_order,
- prefix,
- suffix,
- report_progress)
-
-
-
-
-
-
-if __name__ == "__main__":
-
- g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py'
- g_date_str = '2014-12-19'
- g_version_str = '0.18'
-
- bond_pattern_module_name = ""
-
- ####### Main Code Below: #######
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
- if sys.version < '3':
- sys.stderr.write(' (python version < 3)\n')
- else:
- sys.stderr.write('\n')
-
- try:
-
- fname_atoms = None
- fname_bonds = None
- fname_nbody = None
- fname_nbodybytype = None
- atom_style = 'full'
- prefix=''
- suffix=''
-
- argv = [arg for arg in sys.argv]
-
- if len(argv) == 1:
- raise InputError('Error: Missing argument required.\n'
- ' The \"'+g_program_name+'\" program requires an argument containing the\n'
- ' name of a section from a LAMMPS data file storing bonded interactions.\n'
- ' (For example: "Angles", "Dihedrals", or "Impropers".)\n'
- #' Note: The first letter of each section is usually capitalized.)\n'
- '\n'
- '--------------- general documentation -------------\n'
- '\n' + man_page_text + '\n')
-
- section_name = '' # (This will be replaced later.)
- section_name_bytype = '' # (This will be replaced later.)
-
- # Loop over the remaining arguments not processed yet.
- # These arguments are specific to the lttree.py program
- # and are not understood by ttree.py:
- i = 1
- while i < len(argv):
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
- if ((argv[i].lower() == '-?') or
- (argv[i].lower() == '--?') or
- (argv[i].lower() == '-help') or
- (argv[i].lower() == '-help')):
- if i+1 >= len(argv):
- sys.stdout.write(man_page_text+'\n')
- sys.exit(0)
-
- elif argv[i].lower() == '-atoms':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- ' text which might appear in the "Atoms" section of a LAMMPS data file.\n')
- fname_atoms = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-bonds':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- ' text which might appear in the "Bonds" section of a LAMMPS data file.\n')
- fname_bonds = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-nbody':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
-
- #raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
- # ' text which might appear in the "'+section_name+' section of a LAMMPS data file.\n')
- fname_nbody = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-nbodybytype':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
-
- #raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n'
- # ' text which might appear in the "'+section_name+' By Type" section\n'
- # ' of a LAMMPS data file.\n')
- fname_nbodybytype = argv[i+1]
- del(argv[i:i+2])
-
- elif ((argv[i].lower() == '-atom-style') or
- (argv[i].lower() == '-atom_style')):
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n'
- ' (Or single quoted string which includes a space-separated\n'
- ' list of column names.)\n')
- atom_style = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-prefix':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a prefix string\n'
- ' (a string you want to appear to the left of the integer\n'
- ' which counts the bonded interactions you have generated.)\n')
- prefix = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-suffix':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by a suffix string\n'
- ' (a string you want to appear to the right of the integer\n'
- ' which counts the bonded interactions you have generated.)\n')
- prefix = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-subgraph':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by the name of a python file\n'
- ' containing the definition of the subgraph you are searching for\n'
- ' and it\'s symmetry properties.\n'
- ' (See nbody_Dihedrals.py for example.)\n')
- bond_pattern_module_name = argv[i+1]
- # If the file name ends in ".py", then strip off this suffix.
- # For some reason, the next line does not work:
- #bond_pattern_module_name=bond_pattern_module_name.rstrip('.py')
- # Do this instead
- pc = bond_pattern_module_name.rfind('.py')
- if pc != -1:
- bond_pattern_module_name = bond_pattern_module_name[0:pc]
-
- del(argv[i:i+2])
-
- elif argv[i].lower() == '-section':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by the name of the LAMMPS\n'
- ' Data section describing the type of interaction being generated.\n'
- ' (For example: \"Angles\", \"Dihedrals\", \"Impropers\", etc...)\n')
- section_name = argv[i+1]
- del(argv[i:i+2])
-
-
- elif argv[i].lower() == '-sectionbytype':
- if i+1 >= len(argv):
- raise InputError('Error: '+argv[i]+' flag should be followed by the name of the\n'
-
- ' write_once(\"???? By Type\") section describing how to create the\n'
- ' interactions. (For example: \"Angles By Type\", \"Dihedrals By Type\",\n'
- ' \"Impropers By Type\", etc... Note that this argument\n'
- ' will contain spaces, so surround it with quotes.)\n')
-
- section_name_bytype = argv[i+1]
- del(argv[i:i+2])
-
- elif argv[i][0] == '-':
- raise InputError('Error('+g_program_name+'):\n'
- 'Unrecognized command line argument \"'+argv[i]+'\"\n')
- else:
- i += 1
-
- #if len(argv) == 1:
- # raise InputError('Error: Missing argument required.\n'
- # ' The \"'+g_program_name+'\" program requires an argument containing the\n'
- # ' name of a section from a LAMMPS data file storing bonded interactions.\n'
- # ' (For example: "Angles", "Dihedrals", or "Impropers".)\n')
- # #' Note: The first letter of each section is usually capitalized.)\n'
-
- if len(argv) == 1:
- pass
- elif len(argv) == 2:
- section_name = argv[1]
- section_name_bytype = section_name + ' By Type'
- # default bond_pattern_module name
- if bond_pattern_module_name == "": #<--if not set by user
- bond_pattern_module_name = 'nbody_'+section_name
- del(argv[1:2])
- else:
- # if there are more than 2 remaining arguments,
- problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
- raise InputError('Syntax Error('+g_program_name+'):\n\n'
- ' Problem with argument list.\n'
- ' The remaining arguments are:\n\n'
- ' '+(' '.join(problem_args))+'\n\n'
- ' (The actual problem may be earlier in the argument list.)\n')
-
- if ((section_name == '') or
- (section_name_bytype == '') or
- (bond_pattern_module_name == '')):
- raise InputError('Syntax Error('+g_program_name+'):\n\n'
- ' You have not defined the following arguments:\n'
- ' -section name\n'
- ' -sectionbytype namebytype\n'
- ' -subgraph pythonfile.py\n')
-
- # ------------ Done parsing argument list ----------
-
- if (fname_atoms or fname_bonds or fname_nbody or fname_nbodybytype):
- output_full_DATA_file = False
- lines_data = []
- else:
- output_full_DATA_file = True
- lines_data = sys.stdin.readlines()
-
- # Calculate the interactions and generate a list of lines of text
-
- lines_new_interactions = \
- GenInteractions_files(lines_data,
- bond_pattern_module_name,
- fname_atoms,
- fname_bonds,
- fname_nbody,
- fname_nbodybytype,
- section_name,
- section_name_bytype,
- atom_style,
- prefix,
- suffix,
- report_progress=True)
-
- # Print this text to the standard out.
-
- # Question: Do we write out the entire DATA file,
- # or just the portion that was generated by this program?
-
- if not output_full_DATA_file:
- # ...then only print out the interactions which were generated
- # by this program, omitting any lines from the original data file:
-
- # (This is the way I usually run this program.)
- for line in lines_new_interactions:
- sys.stdout.write(line)
-
-
- else:
-
-
- # ...then print out the entire data file, deleting the "By Type"
- # section, and adding the generated lines of text to the corresponding
-
- # If present, update the interaction counter at the beginning
- # of the LAMMPS data file. (For example, if if 100 new "Angles"
- # interactions were generated, replace "2 Angles" with "102 Angles")
- #
- for i in range(0, len(lines_data)):
- line = lines_data[i].strip()
- tokens = SplitQuotedString(line)
-
- # updating the interaction counter
- if ((len(tokens) == 2) and (tokens[1] == (section_name).lower())):
- tokens[0] = str(int(tokens[0]) + len(lines_new_interactions))
- lines_data[i] = ' '.join(tokens) + '\n'
-
- # stop when you come to a section header
- elif line in lammps_data_sections:
- #"lammps_data_sections" is defined in "extract_lammps_data.py"
- break
-
-
- # locate the appropriate section of the data file
- # (storing the type of interactions we just created)
- i_nbody_a, i_nbody_b = \
- FindDataSection(lines_data, section_name)
-
- if i_nbody_a == -1:
- if len(lines_new_interactions) > 0:
- # If not found, create a new section at the end of the file,
- # containing a section name followed by the list of lines
- lines_data += ['\n', section_name+'\n', '\n'] + \
- lines_new_interactions + ['\n']
- else:
- # Insert the new lines into the existing section
- lines_data[i_nbody_b:i_nbody_b] = lines_new_interactions
-
- # Figure out where the "By Type" section is located
- # (so we skip over it)
- i_bytype_a, i_bytype_b = \
- FindDataSection(lines_data, section_name_bytype)
-
- in_bytype_section = False
- for i in range(0, len(lines_data)):
- line = lines_data[i].strip()
- # Omit all lines of text in the 'By Type' section (including the
- # header and commments or blank lines which immediately follow it.)
- if line == section_name_bytype:
- in_bytype_section = True
- elif i == i_bytype_b:
- in_bytype_section = False
-
- if not in_bytype_section:
- sys.stdout.write(lines_data[i])
-
- except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/nbody_by_type_lib.py b/tools/moltemplate/src/nbody_by_type_lib.py
deleted file mode 100644
index eca4ff344..000000000
--- a/tools/moltemplate/src/nbody_by_type_lib.py
+++ /dev/null
@@ -1,394 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-
-import sys
-from nbody_graph_search import *
-#from collections import namedtuple
-if sys.version < '2.7':
- sys.stderr.write('--------------------------------------------------------\n'
- '----------------- WARNING: OLD PYTHON VERSION ----------\n'
- ' This program is untested on your python version ('+sys.version+').\n'
- ' PLEASE LET ME KNOW IF THIS PROGRAM CRASHES (and upgrade python).\n'
- ' -Andrew 2013-10-25\n'
- '--------------------------------------------------------\n'
- '--------------------------------------------------------\n')
- from ordereddict import OrderedDict
-else:
- from collections import OrderedDict
-from collections import defaultdict
-from ttree_lex import MatchesPattern, MatchesAll, InputError
-#import gc
-
-
-def GenInteractions_int(G_system,
- g_bond_pattern,
- typepattern_to_coefftypes,
- canonical_order, #function to sort atoms and bonds
- atomtypes_int2str,
- bondtypes_int2str,
- report_progress = False): #print messages to sys.stderr?
- """
- GenInteractions() automatically determines a list of interactions
- present in a system of bonded atoms (argument "G_system"),
- which satisfy the bond topology present in "g_bond_pattern", and
- satisfy the atom and bond type requirements in "typepattern_to_coefftypes".
-
- Whenever a set of atoms in "G_system" are bonded together in a way which
- matches "g_bond_pattern", and when the atom and bond types is consistent
- with one of the entries in "typepattern_to_coefftypes", the corresponding
- list of atoms from G_system is appended to the list of results.
-
- These results (the list of lists of atoms participating in an interaction)
- are organized according their corresponding "coefftype", a string
- which identifies the type of interaction they obey as explained above.
- results are returned as a dictionary using "coefftype" as the lookup key.
-
- Arguments:
-
- -- typepattern_to_coefftypes is a list of 2-tuples --
- The first element of the 2-tuple is the "typepattern".
- It contains a string describing a list of atom types and bond types.
- The typepattern is associated with a "coefftype",
- which is the second element of the 2-tuple. This is a string
- which identifies the type of interaction between the atoms.
- Later on, this string can be used to lookup the force field
- parameters for this interaction elsewhere.)
-
- -- Arguments: G_system, g_bond_pattern, atomtypes_int2str, bondtypes_int2str --
-
- G_system stores a list of atoms and bonds, and their attributes in
- "Ugraph" format. In this format:
- Atom ID numbers are represented by indices into the G_system.verts[] list.
- Bond ID numbers are represented by indices into the G_system.edges[] list.
- Atom types are represented as integers in the G_system.verts[i].attr list.
- Bond types are represented as integers in the G_system.edges[i].attr list.
- They are converted into strings using
- atomtypes_int2str, and bondtypes_int2str.
-
- g_bond_pattern is a graph which specifies the type of bonding between
- the atoms required for a match. It is in Ugraph format (however the
- atom and bond types are left blank.)
-
- Atom and bond types are supplied by the user in string format. (These
- strings typically encode integers, but could be any string in principle.)
- The string-version of the ith atom type is stored in
- atomtypes_int2str[ G_system.verts[i].attr ]
- The string-version of the ith bond type is stored in
- bondtypes_int2str[ G_system.edges[i].attr ]
-
- -- The "canonical_order" argument: --
-
- The search for atoms with a given bond pattern often yields
- redundant matches. There is no difference for example
- between the angle formed between three consecutively
- bonded atoms (named, 1, 2, 3, for example), and the
- angle between the same atoms in reverse order (3, 2, 1).
- However both triplets of atoms will be returned by the subgraph-
- matching algorithm when searching for ALL 3-body interactions.)
-
- To eliminate this redundancy, the caller must supply a "canonical_order"
- argument. This is a function which sorts the atoms and bonds in a way
- which is consistent with the type of N-body interaction being considered.
- The atoms (and bonds) in a candidate match are rearranged by the
- canonical_order(). Then the re-ordered list of atom and bond ids is
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added.
-
- """
-
- if report_progress:
- startatomid = 0
- sys.stderr.write(' searching for matching bond patterns:\n')
- sys.stderr.write(' 0%')
-
- # Figure out which atoms from "G_system" bond together in a way which
- # matches the "g_bond_pattern" argument. Organize these matches by
- # atom and bond types and store all of the non-redundant ones in
- # the "interactions_by_type" variable.
-
- gm = GraphMatcher(G_system, g_bond_pattern)
-
- interactions_by_type = defaultdict(list)
-
- for atombondids in gm.Matches():
- # "atombondids" is a tuple.
- # atombondids[0] has atomIDs from G_system corresponding to g_bond_pattern
- # (These atomID numbers are indices into the G_system.verts[] list.)
- # atombondids[1] has bondIDs from G_system corresponding to g_bond_pattern
- # (These bondID numbers are indices into the G_system.edges[] list.)
-
- # It's convenient to organize the list of interactions-between-
- # atoms in a dictionary indexed by atomtypes and bondtypes.
- # (Because many atoms and bonds typically share the same type,
- # organizing the results this way makes it faster to check
- # whether a given interaction matches a "typepattern" defined
- # by the user. We only have to check once for the whole group.)
-
- atombondtypes = \
- (tuple([G_system.GetVert(Iv).attr for Iv in atombondids[0]]),
- tuple([G_system.GetEdge(Ie).attr for Ie in atombondids[1]]))
-
- interactions_by_type[atombondtypes].append(atombondids)
-
- if report_progress:
- # GraphMatcher.Matches() searches for matches in an order
- # that selects a different atomid number from G_system,
- # starting at 0, and continuing up to the number of atoms (-1)
- # in the system (G_system.nv-1), and using this as the first
- # atom in the match (ie match[0][0]). This number can be used
- # to guess much progress has been made so far.
- oldatomid = startatomid
- startatomid = atombondids[0][0]
- percent_complete = (100 * startatomid) // G_system.GetNumVerts()
- # report less often as more progress made
- if percent_complete <= 4:
- old_pc = (100 * oldatomid) // G_system.GetNumVerts()
- if percent_complete > old_pc:
- sys.stderr.write(' '+str(percent_complete)+'%')
- elif percent_complete <= 8:
- pc_d2 = (100 * startatomid) // (2*G_system.GetNumVerts())
- oldpc_d2 = (100 * oldatomid) // (2*G_system.GetNumVerts())
- if pc_d2 > oldpc_d2:
- sys.stderr.write(' '+str(percent_complete)+'%')
- elif percent_complete <= 20:
- pc_d4 = (100 * startatomid) // (4*G_system.GetNumVerts())
- oldpc_d4 = (100 * oldatomid) // (4*G_system.GetNumVerts())
- if pc_d4 > oldpc_d4:
- sys.stderr.write(' '+str(percent_complete)+'%')
- else:
- pc_d10 = (100 * startatomid) // (10*G_system.GetNumVerts())
- oldpc_d10 = (100 * oldatomid) // (10*G_system.GetNumVerts())
- if pc_d10 > oldpc_d10:
- sys.stderr.write(' '+str(percent_complete)+'%')
-
- if report_progress:
- sys.stderr.write(' 100%\n')
- #sys.stderr.write(' ...done\n')
- #sys.stderr.write(' Looking up available atom and bond types...')
-
- #coefftype_to_atomids = defaultdict(list)
- #abids_to_coefftypes = defaultdict(list)
- coefftype_to_atomids = OrderedDict()
- abids_to_coefftypes = OrderedDict()
-
-
-
-
- # -------------------- reporting progress -----------------------
- if report_progress:
- # The next interval of code is not technically necessary, but it makes
- # the printed output easier to read by excluding irrelevant interactions
- # Now, test each match to see if the atoms and bonds involved match
- # any of the type-patterns in the "typepattern_to_coefftypes" argument.
-
- types_atoms_all_str = set([])
- types_bonds_all_str = set([])
- for typepattern, coefftype in typepattern_to_coefftypes:
- for atombondtypes, abidslist in interactions_by_type.items():
- for Iv in atombondtypes[0]:
- types_atoms_all_str.add(atomtypes_int2str[Iv])
- for Ie in atombondtypes[1]:
- types_bonds_all_str.add(bondtypes_int2str[Ie])
- # ------------------ reporting progress (end) -------------------
-
-
-
- count = 0
- for typepattern, coefftype in typepattern_to_coefftypes:
-
-
- # ------------------ reporting progress -----------------------
- # The next interval of code is not technically necessary, but it makes
- # the printed output easier to read by excluding irrelevant interactions
-
- if report_progress:
-
- # Check to see if the atoms or bonds referred to in typepattern
- # are (potentially) satisfied by any of the atoms present in the system.
- # If any of the required atoms for this typepattern are not present
- # in this system, then skip to the next typepattern.
- atoms_available_Iv = [False for Iv in range(0, g_bond_pattern.GetNumVerts())]
- for Iv in range(0, g_bond_pattern.GetNumVerts()):
- for type_atom_str in types_atoms_all_str:
- if MatchesPattern(type_atom_str, typepattern[Iv]):
- atoms_available_Iv[Iv] = True
- atoms_available = True
- for Iv in range(0, g_bond_pattern.GetNumVerts()):
- if not atoms_available_Iv[Iv]:
- atoms_available = False
-
- bonds_available_Ie = [False for Ie in range(0, g_bond_pattern.GetNumEdges())]
- for Ie in range(0, g_bond_pattern.GetNumEdges()):
- for type_bond_str in types_bonds_all_str:
- if MatchesPattern(type_bond_str,
- typepattern[g_bond_pattern.GetNumVerts()+Ie]):
- bonds_available_Ie[Ie] = True
- bonds_available = True
- for Ie in range(0, g_bond_pattern.GetNumEdges()):
- if not bonds_available_Ie[Ie]:
- bonds_available = False
-
- if atoms_available and bonds_available:
-
- # Explanation:
- # (Again) only if ALL of the atoms and bond requirements for
- # this typepattern are satisfied by at least SOME of the atoms
- # present in the this system, ...THEN print a status message.
- # (Because for complex all-atom force-fields, the number of
- # possible atom types, and typepatterns far exceeds the number
- # of atom types typically present in the system. Otherwise
- # hundreds of kB of irrelevant information can be printed.)
-
- sys.stderr.write(' checking '+coefftype+' type requirements:'
- #' (atom-types,bond-types) '
- '\n '+str(typepattern)+'\n')
-
- # ------------------ reporting progress (end) -------------------
-
-
-
-
-
- for atombondtypes, abidslist in interactions_by_type.items():
- # express atom & bond types in a tuple of the original string format
- types_atoms = [atomtypes_int2str[Iv] for Iv in atombondtypes[0]]
- types_bonds = [bondtypes_int2str[Ie] for Ie in atombondtypes[1]]
- type_strings = types_atoms + types_bonds
- # use string comparisons to check for a match with typepattern
- if MatchesAll(type_strings, typepattern): #<-see "ttree_lex.py"
- for abids in abidslist:
-
- # Re-order the atoms (and bonds) in a "canonical" way.
- # Only add new interactions to the list after re-ordering
- # them and checking that they have not been added earlier.
- # (...well not when using the same coefftype at least.
- # This prevents the same triplet of atoms from
- # being used to calculate the bond-angle twice:
- # once for 1-2-3 and 3-2-1, for example.)
- abids = canonical_order(abids)
- redundant = False
- if abids in abids_to_coefftypes:
- coefftypes = abids_to_coefftypes[abids]
- if coefftype in coefftypes:
- redundant = True
-
- if not redundant:
- # (It's too bad python does not
- # have an Ordered defaultdict)
- if coefftype in coefftype_to_atomids:
- coefftype_to_atomids[coefftype].append(abids[0])
- else:
- coefftype_to_atomids[coefftype]=[abids[0]]
- if abids in abids_to_coefftypes:
- abids_to_coefftypes[abids].append(coefftype)
- else:
- abids_to_coefftypes[abids] = [coefftype]
- count += 1
-
- if report_progress:
- sys.stderr.write(' (found '+
- str(count)+' non-redundant matches)\n')
-
- return coefftype_to_atomids
-
-
-
-
-
-
-
-
-def GenInteractions_str(bond_pairs,
- g_bond_pattern,
- typepattern_to_coefftypes,
- canonical_order, #function to sort atoms and bonds
- atomids_str,
- atomtypes_str,
- bondids_str,
- bondtypes_str,
- report_progress = False): #print messages to sys.stderr?
-
-
- assert(len(atomids_str) == len(atomtypes_str))
- assert(len(bondids_str) == len(bondtypes_str))
- # The atomids and atomtypes and bondtypes are strings.
- # First we assign a unique integer id to each string.
-
- atomids_str2int = {}
- atomtypes_str2int = {}
- atomtypes_int2str = []
- atomtype_int = 0
- for i in range(0, len(atomids_str)):
- if atomids_str[i] in atomids_str2int:
- raise InputError('Error: multiple atoms have the same id ('+
- str(atomids_str[i])+')')
- atomids_str2int[atomids_str[i]] = i
- #atomtypes_int = len(atomtypes_int)+1
- if (not (atomtypes_str[i] in atomtypes_str2int)):
- atomtypes_str2int[atomtypes_str[i]] = atomtype_int
- atomtypes_int2str.append(atomtypes_str[i])
- atomtype_int += 1
- #atomtypes_int.append(atomtype_int)
-
- bondids_str2int = {}
- bondtypes_str2int = {}
- bondtypes_int2str = []
- bondtype_int = 0
- for i in range(0, len(bondids_str)):
- if bondids_str[i] in bondids_str2int:
- raise InputError('Error: multiple bonds have the same id ('+
- str(bondids_str[i])+')')
- bondids_str2int[bondids_str[i]] = i
- #bondtype_int = len(bondtypes_int)+1
- if (not (bondtypes_str[i] in bondtypes_str2int)):
- bondtypes_str2int[bondtypes_str[i]] = bondtype_int
- bondtypes_int2str.append(bondtypes_str[i])
- bondtype_int += 1
-
- # Now convert "bond_pairs" into the UGraph format
- G_system = Ugraph()
- for iv in range(0, len(atomtypes_str)):
- G_system.AddVertex(iv, atomtypes_str2int[atomtypes_str[iv]])
-
- for ie in range(0, len(bond_pairs)):
- atomid1_str = bond_pairs[ie][0]
- atomid2_str = bond_pairs[ie][1]
- if (atomid1_str not in atomids_str2int):
- raise InputError('Error in Bonds Section:\n'
- ' '+atomid1_str+' is not defined in Atoms section\n')
- if (atomid2_str not in atomids_str2int):
- raise InputError('Error in Bonds Section:\n'
- ' '+atomid2_str+' is not defined in Atoms section\n')
- G_system.AddEdge(atomids_str2int[atomid1_str],
- atomids_str2int[atomid2_str],
- bondtypes_str2int[bondtypes_str[ie]])
-
- coefftype_to_atomids_int = GenInteractions_int(G_system,
- g_bond_pattern,
- typepattern_to_coefftypes,
- canonical_order,
- atomtypes_int2str,
- bondtypes_int2str,
- report_progress)
- coefftype_to_atomids_str = OrderedDict()
- for coefftype, atomidss_int in coefftype_to_atomids_int.items():
- if report_progress:
- sys.stderr.write(' processing coefftype: '+str(coefftype)+'\n')
- for atomids_int in atomidss_int:
- if coefftype in coefftype_to_atomids_str:
- coefftype_to_atomids_str[coefftype].append(
- [atomids_str[iv] for iv in atomids_int])
- else:
- coefftype_to_atomids_str[coefftype] = \
- [[atomids_str[iv] for iv in atomids_int]]
- #gc.collect()
-
- return coefftype_to_atomids_str
-
-
diff --git a/tools/moltemplate/src/nbody_fix_ttree_assignments.py b/tools/moltemplate/src/nbody_fix_ttree_assignments.py
deleted file mode 100644
index 46f9efa33..000000000
--- a/tools/moltemplate/src/nbody_fix_ttree_assignments.py
+++ /dev/null
@@ -1,149 +0,0 @@
-#!/usr/bin/env python
-
-"""
-nbody_fix_ttree_assignments.py
-
-This is an ugly little script which was not intended to be run by end users.
-
-Typical usage:
-
-nbody_fix_ttree_assignments.py "angles" new_Angles.template \
- < ttree_assignments.txt > ttree_assigmnents_new.txt
-
-What it does:
-
-In this example, this program extracts the first column from
-"new_Angles.template", and appends to it the first column from
-the lines in ttree_assignments.txt containing "@angle:".
-Then it adds a second column which is just a sequence of integers
-counting upwards.
-Finally it inserts this 2-column text into the appropriate place in a
-ttree_assignments.txt file, replacing the original @angle variables
-with the new ones (followed by the renumbered original).
-
-
- AWK/GREP equivalent
-This program is roughly equivalent to the following lines of awk/grep:
-
-awk 'BEGIN{i=-1} {if(substr($0,0,8)=="$/angle") i=NR; if (i==-1){print $0}}'\
- < ttree_assignments.txt > ttree_assignments_new.txt
-
-awk '{print $1}' < new_Angles.template > Angles_column1.txt
-grep '$/angle:' ttree_assignments.txt | awk '{print $1}' >> Angles_column1.txt
-awk '{print $1 " " NR}' < Angles_column1.txt >> ttree_assignments_new.txt
-
-awk 'BEGIN{found=0;passed=0} {if(substr($0,0,8)=="$/angle") found=1;
- else {if (found) {passed=1}}
- if (passed) print $0}' \
- < ttree_assignments.txt >> ttree_assignments_new.txt
-
-I wrote this python script (instead of using awk) just to handle quoted stings
-(and strings with other fancy characters and escape sequences).
-
-"""
-
-import sys
-from ttree_lex import SplitQuotedString, EscCharStrToChar, SafelyEncodeString, InputError
-
-g_program_name = __file__.split('/')[-1]
-
-try:
- if (len(sys.argv) != 3):
- raise InputError('Error running \"'+g_program_name+'\"\n'
- ' Wrong number of arguments.\n'
- ' (This is likely a programmer error.\n'
- ' This script was not intended to be run by end users.)\n')
-
- cat_name = sys.argv[1]
- f = open(sys.argv[2])
- lines_generated = f.readlines()
- f.close()
-
- # Selections are simply lists of 2-tuples (pairs)
- #f = open('ttree_assignments.txt','r')
- #lines_bindings = f.readlines()
- #f.close()
- lines_bindings = sys.stdin.readlines()
-
- # Figure out which lines in the 'ttree_assignments.txt' file
- # contain the variables of the type you are looking for.
- # Make note of the relevant line numbers
- i_preexisting_begin = -1
- i_preexisting_end = -1
- in_section = False
- possible_cat_names = set(['$'+cat_name, '$/'+cat_name, '${'+cat_name, '${/'+cat_name])
-
- preexisting_interaction_list = []
- for i in range(0, len(lines_bindings)):
- line = lines_bindings[i].strip()
- tokens = SplitQuotedString(line) #strip comments, handle quotes
- if len(tokens) == 2:
- before_colon = tokens[0].split(':')[0]
- if before_colon in possible_cat_names:
- if i_preexisting_begin == -1:
- i_preexisting_begin = i
- in_section = True
- else:
- if in_section:
- i_preexisting_end = i
- in_section = False
-
- if i_preexisting_end == -1:
- i_preexisting_end = len(lines_bindings)
-
- if i_preexisting_begin == -1:
- for line in lines_bindings:
- sys.stdout.write(line)
- else:
- # write out all the lines in the original file up until the point where
- # the variables in the category we are looking for were encountered
- for i in range(0, i_preexisting_begin):
- sys.stdout.write(lines_bindings[i])
-
- sys.stderr.write(' (adding new lines)\n')
-
- # Now add some new lines (2-column format).
- # As with any ttree_assignment.txt file:
- # The first column has our generated variable names
- # The second column has the counter assigned to that variable
- new_counter = 1
- for line_orig in lines_generated:
- line = line_orig.strip()
- if len(line) > 0:
- tokens = SplitQuotedString(line) #strip comments, handle quotes
- sys.stdout.write(tokens[0]+' '+str(new_counter)+'\n')
- new_counter += 1
-
- sys.stderr.write(' (adding pre-exisiting lines)\n')
- if i_preexisting_begin != -1:
- # Append the original pre-existing interactions of that type, but assign
- # them to higher numbers. (Hopefully this helps to make sure that these
- # assignments will override any of the automatic/generated assignments.)
- # As with any ttree_assignment.txt file:
- # The first column has our generated variable names
- # The second column has the counter assigned to that variable
-
- #sys.stderr.write(' i_preexisting_begin='+
- # str(i_preexisting_begin)+
- # ' i_preexisting_end='+str(i_preexisting_end)+'\n')
-
- for i in range(i_preexisting_begin, i_preexisting_end):
- line = lines_bindings[i].strip()
- tokens = SplitQuotedString(line) #strip comments, handle quotes
- if len(tokens) == 2:
- sys.stdout.write(tokens[0]+' '+str(new_counter)+'\n')
- new_counter += 1
-
- #sys.stderr.write(' (writing pre-exisiting lines)\n')
-
- # write out all the lines in the original file after this point.
- for i in range(i_preexisting_end, len(lines_bindings)):
- sys.stdout.write(lines_bindings[i])
-
- sys.exit(0)
-
-
-except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/nbody_graph_search.py b/tools/moltemplate/src/nbody_graph_search.py
deleted file mode 100644
index 06f06b7d6..000000000
--- a/tools/moltemplate/src/nbody_graph_search.py
+++ /dev/null
@@ -1,976 +0,0 @@
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-
-#__all__ = ['Ugraph', 'GraphMatcher', 'DFS', 'GenError', 'GraphError', 'Disconnected', 'NotUndirected']
-
-
-import sys
-import copy
-from operator import itemgetter
-
-
-class GenError(Exception):
- """
- An exception class containing string for error reporting.
-
- """
- def __init__(self, err_msg):
- self.err_msg = err_msg
- def __str__(self):
- return self.err_msg
- def __repr__(self):
- return str(self)
-
-class GraphError(GenError):
- """
- An exception class containing a graph and a string for error reporting.
-
- """
- def __init__(self, g, err_msg):
- GenError.__init__(self, err_msg)
- self.g = g
- def __str__(self):
- g_str = str(g)
- # If the string representation of the graph is too
- # large to fit in one screen, truncate it
- g_str_lines = g_str.split('\n')
- if (len(g_str_lines) > 12):
- g_str_lines = g_str_lines[0:12] + [' ...(additional lines not shown)]']
- g_str = '\n'.join(g_str_lines)
- return 'Problem with graph:\n'+g_str+'\n'+self.err_msg
- def __repr__(self):
- return str(self)
-
-class Disconnected(GraphError):
- def __init__(self, g, err_msg):
- GraphError.__init__(self, g, err_msg)
-
-class NotUndirected(GraphError):
- def __init__(self, g, err_msg):
- GraphError.__init__(self, g, err_msg)
-
-
-
-class Edge(object):
- __slots__=["start","stop","attr"]
- def __init__(self,
- iv_start, # edge starts here (index into vertex list)
- iv_stop, # edge ends here (index into vertex list)
- attr=None): # edges have an optional type attribute
- self.start = iv_start
- self.stop = iv_stop
- self.attr = attr
- def __str__(self):
- return '('+str(self.start)+','+str(self.stop)+')'
- def __repr__(self):
- return str(self)
-
-
-class Vertex(object):
- __slots__=["attr"]
- def __init__(self, attr=None):
- self.attr = attr
-
-
-
-
-class Dgraph(object):
- """
- This class is a minimal implementation of a directed graph.
- Vertices and edges are accessed by integer index only (beginning at 0).
- Multiple edges connecting the same pair of vertices are allowed.
- (One would use the AddEdge() member function to accomplish this.)
- Both vertices and edges have an optional "attr" attribute.
-
- """
-
- NULL = -1 # forbidden vertex id number (used several places)
-
- def __init__(self, edgelist=None):
- """
- The constructor accepts an optional neighborlist argument.
- This is a simple list of neighbors for every vertex in the graph
- and it completely defines the topology of the graph.
- (Vertex and edge attributes can be specified later.)
-
- Alternatley, you can leave the neighborlist argument blank,
- and build the graph one vertex at a time later
- using the "AddVertex()" and "AddEdge()" commands.
- (AddEdge() commands must be issued strictly after
- all vertices have been defined.)
-
- """
-
- if edgelist == None:
- self.verts = []
- self.edges = []
- self.nv = 0 #integer keeps track of # of vertices = len(self.verts)
- self.ne = 0 #integer keeps track of # of edges = len(self.edges)
- self.neighbors = [] # The adjacency list.
-
- else:
- # Parse the edge-list format:
- iv_max = 0 # <-- what's the vertex with the maximum id number?
- for i in range(0, len(edgelist)):
- iv = edgelist[i][0]
- jv = edgelist[i][1]
- if ((iv < 0) or (jv < 0)):
- raise(GenError('Error in Dgraph.__init__: Negative vertex number pair encountered: ('+str(iv)+','+str(jv)+')'))
- if iv > iv_max:
- iv_max = iv
- if jv > iv_max:
- iv_max = jv
-
- self.nv = iv_max+1
- self.verts = [Vertex() for iv in range(0, self.nv)]
- self.edges = []
- self.ne = 0
- self.neighbors = [[] for iv in range(0, self.nv)]
-
- for i in range(0, len(edgelist)):
- iv = edgelist[i][0]
- jv = edgelist[i][1]
- self.neighbors[iv].append(self.ne)
- self.edges.append(Edge(iv, jv))
- self.ne += 1
- assert(self.ne == len(self.edges))
-
- self.SortNeighborLists()
-
-
- def AddVertex(self, iv=-1, attr=None):
- """
- Add a vertex to the graph.
- (Edges connected to this vertex must be added later using "AddEdge()"
- All vertices should be added before "AddEdge()" is ever invoked.)
-
- Optional "attr" argument allows you to set the attribute of this vertex.
- (for example, in a molecule this might correspond to the type of atom
- in the molecule).
-
- Optional "iv" argument allows you to specify the index of that vertex.
- Vertices can be added in any order, but thei vertex id numbers
- should eventually fill the range from 0 to self.nv-1.
-
- """
- if iv == -1: # if iv unspecified, put the vertex at the end of the list
- iv = self.nv
-
- if iv < self.nv:
- self.verts[iv].attr = attr
- else:
- # In case there is a gap between iv and nv, fill it with blanks
- self.verts += ([Vertex()] * ((1 + iv) - self.nv))
- self.neighbors += ([[]] * ((1 + iv) - self.nv))
- self.verts[iv].attr = attr
- self.nv = iv+1
- assert(self.nv == len(self.verts))
- assert(self.nv == len(self.neighbors))
-
-
- def AddEdge(self, iv, jv, attr=None, remove_duplicates=False):
- """
- Add an edge to graph connecting vertex iv to jv.
- (both are integers from 0 to self.nv-1)
- This function must not be called until all vertices have been added.
- If the edge is already present (and remove_duplicates==True),
- no new edge will be added.
-
- """
- if remove_duplicates:
- for je in self.neighbors[iv]:
- if jv == self.edges[je].stop:
- return # In that case, do nothing, the edge is already present
- self.edges.append(Edge(iv, jv, attr))
- self.neighbors[iv].append(self.ne)
- self.ne += 1
- assert(self.ne == len(self.edges))
-
-
- def ReorderVerts(self, vpermutation, invert=False):
- """
- This function allows the user to re-order (relabel) the vertices
- in a graph, making the necessary changes to the
- self.verts, self.edges, and self.neighbors lists.
- By default (invert=False). The vpermutation is a list
- from 1 to self.nv which is interpreted this way:
- iv = vpermutation[iv_orig]
- where "iv" and "iv_orig" are the vertex id numbers before
- and after the mapping (which also corresponds to its
- position in the self.verts and self.neighbors arrays).
-
- """
- assert(len(self.verts) == self.nv)
- assert(len(self.edges) == self.ne)
- assert(len(vpermutation) == self.nv)
-
- if (invert):
- vperm = [-1 for iv in vpermutation]
- for iv in range(0, self.nv):
- vperm[ vpermutation[iv] ] = iv
- else:
- vperm = vpermutation
-
- orig_verts = [vert for vert in self.verts]
- for iv_old in range(0, self.nv):
- iv = vperm[iv_old]
- self.verts[iv] = orig_verts[iv_old]
-
- for ie in range(0, self.ne):
- self.edges[ie].start = vperm[self.edges[ie].start]
- self.edges[ie].stop = vperm[self.edges[ie].stop]
-
- orig_neighbors = [nlist for nlist in self.neighbors]
- # self.neighbors is a 2-d array.
- # We need to re-sort "self.neighbors" because the first index is
- # a vertex id number, and these id numbers have been permuted.
- # However, there's no need to sort the contents of each sub-array
- # (self.neighbors[iv]), because these are edge id numbers (indices into
- # the self.edges[] array). These edge index numbers are never altered.
- # (However the entries stored in self.edges were modified earlier.)
- for iv_old in range(0, self.nv):
- iv = vperm[iv_old]
- self.neighbors[iv] = orig_neighbors[iv_old]
-
- # Optional:
- self.SortNeighborLists()
-
-
- def ReorderEdges(self, epermutation, invert=False):
- """
- This function allows the user to re-order (relabel) the
- edges in a graph, making the necessary changes to the
- self.edges and self.neighbors lists.
- By default (invert=False). The epermutation is a list
- from 1 to self.ne which is interpreted this way:
- ie = epermutation[ie_orig]
- where "ie" and "ie_orig" are the edge id numbers before
- and after the mapping (which also corresponds to that edge's
- position in the self.edges array).
- (Minor detail: Recall that in this code, Ugraphs
- are implemented by placing two (directed) edges between each pair of
- connected, adjacent vertices, which point back-and-forth between them.
- Consequently the list of edges in self.edges is often typically
- twice as large you might expect.)
-
- """
- assert(len(self.verts) == self.nv)
- assert(len(self.edges) == self.ne)
- assert(len(epermutation) == self.ne)
-
- if (invert):
- eperm = [-1 for ie in epermutation]
- for ie in range(0, self.ne):
- eperm[ epermutation[ie] ] = ie
- else:
- eperm = epermutation
-
- orig_edges = [edge for edge in self.edges]
- for ie_old in range(0, self.ne):
- ie = eperm[ie_old]
- self.edges[ie] = orig_edges[ie_old]
-
- for iv in range(0, self.nv):
- for j in range(0, len(self.neighbors[iv])):
- je_old = self.neighbors[iv][j]
- self.neighbors[iv][j] = eperm[je_old]
-
- def SortNeighborLists(self):
- assert(self.nv == len(self.neighbors))
- for iv in range(0, self.nv):
- #Back when self.neighbors was just a 2-dimensional list of
- #vertex id numbers, then the following line would have worked:
- # self.neighbors[iv].sort()
-
- # ugly python code alert:
- #Unfortunately, we had to change the format of self.neighbors. Now
- #it is a list of indices into the self.edges array ("ie" numbers).
- #We want to sort the "ie" numbers by the vertices they point to.
- #self.edge[ie].start should point to the current vertex (hopefully).
- #self.edge[ie].stop should point to the vertex it's attached to.
- #So we want to sort the ie's in self.neighbors by self.edge[ie].stop
- #Create a temporary array of 2-tuples (ie, jv)
- nlist = [(ie, self.edges[ie].stop)
- for ie in self.neighbors[iv]]
- self.neighbors[iv] = [ie for ie,jv in sorted(nlist,
- key=itemgetter(1))]
-
- def FindEdge(self, istart, istop):
- """
- A simple function looks up the edge id number
- corresponding to an edge connecting vertex istart to istop.
- If not present returns Dgraph.NULL.
-
- """
- iv = istart
- for je in self.neighbors[iv]:
- jv = self.edges[je].stop
- if jv == istop:
- return je
- return Dgraph.NULL
-
- def GetVert(self, iv):
- return self.verts[iv]
-
- def GetEdge(self, ie):
- return self.edges[ie]
-
- def GetNumVerts(self):
- return self.nv
-
- def GetNumEdges(self):
- return self.ne
-
- # Commenting out. I think it's clearer to use python's deepcopy instead
- #def makecopy(self):
- # new_copy = Ugraph()
- # new_copy.verts = [vertex for vertex in self.verts]
- # new_copy.edges = [ edge for edge in self.edges]
- # new_copy.neighbors = [nlist for nlist in self.neighbors]
- # new_copy.nv = self.nv
- # new_copy.ne = self.ne
- # return new_copy
-
-
- def __str__(self):
- # Print the graph as a list of neighbor-lists.
- # (Note: This is the same format as the first argument to __init__().
- # The Vertex.attr and Edge.attr attributes are not printed.)
- l = ['([']
- for iv in range(0, self.nv):
- l.append('[')
- for j in range(0, len(self.neighbors[iv])):
- je = self.neighbors[iv][j]
- jv = self.edges[je].stop
- l.append(str(jv))
- if j < len(self.neighbors[iv])-1:
- l.append(', ')
- else:
- l.append(']')
- if iv < self.nv-1:
- l.append(',\n ')
- else:
- l.append(']')
- l.append(',\n [')
- for ie in range(0, self.ne):
- l.append(str(self.edges[ie]))
- if ie < self.ne-1:
- l.append(', ')
- else:
- l.append('])\n')
- return ''.join(l)
-
- def __repr__(self):
- return str(self)
-
-
-
-
-
-
-class Ugraph(Dgraph):
- """
- This class is a minimal implementation of an undirected graph.
- Vertices and edges are accessed by integer index only (beginning at 0).
- Multiple edges connecting the same pair of vertices are allowed.
- (One would use the AddEdge() member function to accomplish this.)
- Both vertices and edges have an optional "attr" attribute.
-
- Undirected graphs (Ugraphs) are represented internally as
- directed graphs. This means that for every edge in the Ugraph,
- connecting vertex 2 to 3, for example, two edges are stored
- internally, (2 -> 3, and 3 -> 2),
- Edges which begin and end at the same vertex are stored only once.)
-
- """
-
- def __init__(self, edgelist=None):
- Dgraph.__init__(self, edgelist)
-
- # Now add the extra edges which point in the reverse direction.
- neu = self.ne
- ned = self.ne
- for ieu in range(0, self.ne):
- iv = self.edges[ieu].start
- jv = self.edges[ieu].stop
- if iv != jv:
- ned += 1
-
- self.ieu_to_ied = [Dgraph.NULL for ieu in range(0, neu)]
- self.ied_to_ieu = [Dgraph.NULL for ied in range(0, ned)]
-
- ied_redundant = neu
- for ie in range(0, neu):
- iv = self.edges[ie].start
- jv = self.edges[ie].stop
- attr = self.edges[ie].attr
- self.ieu_to_ied[ie] = ie
- self.ied_to_ieu[ie] = ie
-
- if iv != jv:
- # Then create another edge which points in the reverse direction
- Dgraph.AddEdge(self, jv, iv, attr) # <--this increments self.ne
- self.ied_to_ieu[ied_redundant] = ie
- ied_redundant += 1
-
- self.neu = neu
- assert(self.ne == ned)
-
-
- def AddEdge(self, iv, jv, attr=None, remove_duplicates=False):
- """
- Add an edge to an undirected graph connecting vertices iv and jv.
- If the edge is already present (and remove_duplicates==True),
- no new edge will be added.
-
- Note: Undirected Ugraphs are implemented by creating two separate
- digraph edges that conect iv->jv and jv->iv.
-
- """
-
- self.ieu_to_ied.append( len(self.edges) )
- Dgraph.AddEdge(self, iv, jv, attr, remove_duplicates)
- self.ied_to_ieu.append( self.neu )
- if jv != iv:
- Dgraph.AddEdge(self, jv, iv, attr, remove_duplicates)
- self.ied_to_ieu.append( self.neu )
- self.neu += 1
-
- assert(len(self.ieu_to_ied) == self.neu)
- assert(len(self.ied_to_ieu) == len(self.edges))
-
-
-
- def ReorderEdges(self, epermutation, invert=False):
- Dgraph.ReorderEdges(self, epermutation, invert)
-
- # Now update the
- # self.ieu_to_ied and
- # self.ied_to_ieu lookup tables:
-
- if (invert): # (first invert the permutation if necessary)
- eperm = [-1 for ie in epermutation]
- for ie in range(0, self.ne):
- eperm[ epermutation[ie] ] = ie
- else:
- eperm = epermutation
- #epermutation.reverse()
-
- ieu_to_ied_orig = [ied for ied in self.ieu_to_ied]
- ied_to_ieu_orig = [ieu for ieu in self.ied_to_ieu]
-
- for ieu in range(0, self.neu):
- ied_old = ieu_to_ied_orig[ieu]
- ied = eperm[ied_old]
- self.ieu_to_ied[ieu] = ied
- for ied_old in range(0, self.ne):
- ieu = ied_to_ieu_orig[ied_old]
- ied = eperm[ied_old]
- self.ied_to_ieu[ied] = ieu
-
- eperm = epermutation
-
-
- def LookupDirectedEdgeIdx(self, ieu):
- return self.ieu_to_ied[ieu]
-
-
- def LookupUndirectedEdgeIdx(self, ied):
- return self.ied_to_ieu[ied]
-
- #def GetVert(self, iv): <-- (inherited from parent)
- # return self.verts[iv]
-
- def GetEdge(self, ieu):
- ied = self.ieu_to_ied[ieu]
- return self.edges[ied]
-
- #def GetNumVerts(self): <-- (inherited from parent)
- # return self.nv
-
- def GetNumEdges(self):
- return self.neu
-
- def FindEdge(self, istart, istop):
- """
- A simple function looks up the (undirected) edge id number
- corresponding to an edge connecting vertices istart and istop.
- If not present returns Dgraph.NULL.
-
- To find the corresponding entry in the self.edges[] list,
- you can either:
- use the LookupDirectedEdge() lookup function
- or
- you can use the parent-class' version of this function
- Dgraph.FindEdge(self, istart, istop) which returns
- this number by default.
-
- """
- ied = Dgraph.FindEdge(self, istart, istop)
- ieu = self.LookupUndirectedEdgeIdx(ied)
- return ieu
-
-
- def CalcEdgeLookupTable(self):
- """
- COMMENT: THIS NEXT FUNCTION IS PROBABLY NOT NECESSARY AND MIGHT BE
- REMOVED AT A LATER TIME WHEN I FIGURE OUT A BETTER WAY.
-
- Because undirected graphs (Ugraphs) are implemented as directed graphs
- (Dgraphs) with redundant edges, they may have some extra edges which
- the user never explicitly asked for.
- There is some confusion about whether the i'th edge refers to
- the i'th undirected edge that the user explicitly added, or
- the i'th directed edge which is stored internally.
-
- (The number of directed edges is usually twice the number of
- edges that the user asked for. But not always, because edges
- wich start and end at the same vertex are only represented once.)
-
- This function calculates lookup tables to translate between
- the two edge numbering systems:
-
- self.ieu_to_ied[ieu] returns a directed edge id number,
- (which is an index into the self.edges list)
- corresponding to the ieu'th undirected edge
- which was explicitly added by the caller.
-
- self.ied_to_ieu[ied] takes a directed edge id number (ied,
- an index into the self.edges list)
- and returns the undirected edge number,
- which is allways <= ied
-
- """
-
- self.ieu_to_ied = []
- self.ied_to_ieu = [Ugraph.NULL for ied in range(0, self.ne)]
- for ied in range(0, self.ne):
- iv = self.edges[ied].start
- jv = self.edges[ied].stop
- ieu = len(self.ieu_to_ied)
- self.ied_to_ieu[ied] = ieu
- if iv <= jv:
- self.ieu_to_ied.append(ied)
-
-
-
-
-def SortVertsByDegree(g):
- vert_numneighbors = [(iv, len(g.neighbors[iv])) for iv in range(0, g.nv)]
- vert_numneighbors.sort(key=itemgetter(1))
- order = [vert_numneighbors[iv][0] for iv in range(0, g.nv)]
- g.ReorderVerts(order, invert=True)
-
-
-
-class DFS(object):
- """
- This class contains a member function (Order()) calculates the order
- of vertices visited in a depth-first-search over a connected graph.
-
- """
-
- def __init__(self, g):
- self.g = g
- self.sv = 0 #integer sv keeps track of how many vertices visited so far
- self.se = 0 #integer se keeps track of how many edges visited so far
- self.vvisited=[False for iv in range(0, self.g.nv)] # verts visited
- self.vorder =[Dgraph.NULL for iv in range(0, self.g.nv)] #search order
- self.evisited=[False for ie in range(0, self.g.ne)] # edges visited
- self.eorder =[Dgraph.NULL for ie in range(0, self.g.ne)] #search order
-
- def Reset(self):
- self.sv = 0
- self.se = 0
- for iv in range(0, self.g.nv):
- self.vvisited[iv] = False
- self.vorder[iv] = Dgraph.NULL
- for ie in range(0, self.g.ne):
- self.evisited[ie] = False
- self.eorder[ie] = Dgraph.NULL
-
- def Order(self, starting_node=0):
- """
- VisitOrder(starting_node)
- generates a list of integers from 0 to self.g.nv-1 (=#vertices minus 1)
- which represents the order in which the vertices would be visited
- during a Depth-First-Search.
-
- The first vertex visited is specified by the "starting_node" argument
- (an integer (from 0 to g.nv-1)).
-
- """
- self.Reset()
- # The first vertex to be visited should be the starting_node
- self.vorder[0] = starting_node
- self.vvisited[starting_node] = True
- self.sv = 1
- self._Order(starting_node)
- if self.sv != self.g.nv:
- raise(Disconnected(self.g, "Error(Order): "+
- "The input graph is not connected."))
- assert(self.se == self.g.ne)
- return ([iv for iv in self.vorder], [ie for ie in self.eorder])
- #return self.order
-
- def _Order(self, iv):
- """
- _Order() is a recursive function which carries out a
- Depth-First-Search over the graph "self.g", starting with vertex iv.
-
- """
- for je in self.g.neighbors[iv]:
- jv = self.g.edges[je].stop
- if not self.evisited[je]:
- self.eorder[self.se] = je
- self.se += 1
- self.evisited[je] = True
- if not self.vvisited[jv]:
- self.vorder[self.sv] = jv
- self.sv += 1
- self.vvisited[jv] = True
- self._Order(jv)
-
- def IsConnected(self):
- self.Reset()
- self._Order(0)
- return (self.sv == self.g.nv)
-
- def IsCyclic(self):
- """
- IsCyclic() returns True if the graph is cyclic (and connected).
- (An exception is raised on disconnected graphs.)
- This function quits early as soon as a cycle is found.
-
- """
- self.Reset()
- if (type(self.g) is Ugraph):
- is_cyclic = self._IsCyclicUgraph(0, Dgraph.NULL)
- else:
- is_cyclic = self._IsCyclic(0)
- if ((self.sv != self.g.nv) and (not is_cyclic)):
- raise(Disconnected(self.g, "Error(IsCyclic): "+
- "The input graph is not connected."))
- return is_cyclic
-
- def _IsCyclicUgraph(self, iv, ivprev):
- """
- _IsCyclicUgraph() is a recursive function which carries out a
- Depth-First-Search over the graph "self.g" to determine whether the
- graph is cyclic. This function works on undirected graphs (Ugraphs).
-
- Indirected graphs (Ugraphs) are a special case.
- Ugraphs are implemented by using two (redundant) forward/backward edges
- connecting each pair of adjacent vertices. This creates trivial loops.
- This version of _IsCyclicUgraph() only counts loops between more
- distantly connected vertices.
-
- """
- self.sv += 1
- self.vvisited[iv] = True
- for je in self.g.neighbors[iv]:
- jv = self.g.edges[je].stop
- if self.vvisited[jv]:
- if jv != ivprev:
- return True
- elif self._IsCyclicUgraph(jv, iv):
- return True
-
- return False
-
-
- def _IsCyclic(self, iv):
- """
- _IsCyclic() is a recursive function which carries out a
- Depth-First-Search over the graph "self.g" to determine whether
- the graph is cyclic.
- This function works on directed graphs.
-
- """
- self.sv += 1
- self.vvisited[iv] = True
- for je in self.g.neighbors[iv]:
- jv = self.g.edges[je].stop
- if self.vvisited[jv]:
- return True
- elif self._IsCyclic(jv):
- return True
-
- return False
-
-
-
-class GraphMatcher(object):
- """
- This class is a variant of the VF2 algorithm for searching
- for small connected subgraphs (g) within a larger graph (G).
- GraphMatcher works on directed or underected graphs (Dgraph or Ugraph).
- This particular version is better optimized for detecting subgraph
- isomorphisms between two graphs of highly unequal size. It should be
- faster in these situations because, the computation required for
- each step is independent of the number of vertices in the larger graph
- In the original VF2 algorithm, the computation time for each step
- is proportional to the number of vertices in the larger graph.
- (The distinction matters when one graph is much smaller than the other.)
-
- Limitations: At the moment, the matching process uses a simple
- depth-first-search to search the vertices of the small graph "g".
- Hence this approach fails when the smaller graph g is disconnected.
- (but it can probably be fixed by picking a different algorithm to search
- the small graph).
-
- """
-
- def __init__(self,
- G, # The "big" graph
- g): # The little graph (number of vertices in g must be <= G)
-
- self.G = G
- self.g = copy.deepcopy(g)
-
- if (type(self.G) is Ugraph):
- assert(type(self.g) is Ugraph)
- # self.G.CalcEdgeLookupTable() <-- not needed anymore
-
- self.sv = 0
- self.se = 0
- self.voccupiedG = [False for iv in range(0, G.nv)]
- self.eoccupiedG = [False for ie in range(0, G.ne)]
- self.G_is_too_small = False
- if ((g.nv > G.nv) or
- (g.ne > G.ne)):
- self.G_is_too_small = True
- #raise GenErr('Error: The first argument of GraphMatcher(G,g),\n'+
- # ' must be at least as large as the second.')
-
-
- # The list self.iv_to_Iv is the mapping between the graph vertices.
- # Iv is an index into the large graph's list of vertices.
- # iv is an index into the small graph's list of vertices.
- # The mapping is stored in the iv_to_Iv list.
- self.iv_to_Iv = [Dgraph.NULL for Iv in range(0, self.g.nv)]
- self.ie_to_Ie = [Dgraph.NULL for Ie in range(0, self.g.ne)]
- # (This used to be called "core_2" in the VF2 algorithm)
-
- # Due to the large number of recursion limit
- self.old_recursion_limit = sys.getrecursionlimit()
- expected_max_recursion = self.g.nv
-
- if self.old_recursion_limit < 1.5 * expected_max_recursion:
- # Give some breathing room.
- sys.setrecursionlimit(int(1.5 * expected_max_recursion))
-
- subgraph_searcher = DFS(self.g)
- # Perform a Depth-First-Search on the small graph.
- self.vorder_g, self.eorder_g = subgraph_searcher.Order()
- # Then re-order the vertices and edgers to
- # match the order they were visited.
-
- # Note on permutation order:
- # (The DFS.Order() function returns the permutation in this format
- # old_index[ new_index ]
- # where new_index is the DFS iteration when the vertex/edge was visited
- # and old_index is the original vertex/edge order.
- # However the ReorderVerts() and ReorderEdges() functions expect
- # the permutation to have the opposite order: new_index[ old_index ]
- # Hence we set "invert=True", when we invoke these functions.)
- self.g.ReorderVerts(self.vorder_g, invert=True)
- self.g.ReorderEdges(self.eorder_g, invert=True)
-
- # Initialize state
- self.Reset()
-
-
- def Reset(self):
- """Reinitializes the state of the match-search algorithm.
-
- """
- for iv in range(0, self.g.nv):
- self.iv_to_Iv[iv] = Dgraph.NULL
- for ie in range(0, self.g.ne):
- self.ie_to_Ie[ie] = Dgraph.NULL
- for Iv in range(0, self.G.nv):
- self.voccupiedG[Iv] = False
- for Ie in range(0, self.G.ne):
- self.eoccupiedG[Ie] = False
-
- self.se = 0
- self.sv = 0
-
- # OPTIONAL: First, do a partial sort for the vertices in the graphs
- # based on number of edges emanating from each vertex.
- # (This is probably unnecessary for small subgraphs.)
- #SortVertsByDegree(self.g)
-
-
-
- def Matches(self):
- """
- Iterator over all matches between G and g.
- Each "match" corresponds to a subgraph of G which is isomorphic to g.
- Matches is formatted as a 2-tuple of lists:
- (list of vertex ids from G, list of edge ids from G)
- The vertex ids in the list are a subset of the integers from 0 to G.nv.
- The edge ids in the list are a subset of the integers from 0 to G.ne.
-
- (The corresponding vertices and edges from g are indicated by the order)
-
- """
-
- self.Reset()
- if self.G_is_too_small:
- # Then there are fewer verts and edges in G than in g.
- # Thus it is impossible for a subgraph of G to be isomorphic to g.
- return # return no matches
-
- for Iv in range(0, self.G.nv):
-
- # match vertex Iv from G with vertex 0 from graph g
- self.iv_to_Iv[0] = Iv
- self.voccupiedG[Iv] = True
-
- # Implementation:
- # In this loop we begin the search process
- # starting with a different vertex (Iv) from big graph G,
- # and matching it with the first vertex (iv=0) from small graph g.
- # In this way the match "begins" from vertex Iv in G.
- #
- # Any matches found which begin from vertex Iv are distinct
- # from matches beginning from any other vertex in G.
- # Looping over all Iv in G is necessary and sufficient
- # to insure that all possible subgraphs of G
- # (which are isomorphic to g) are considered.
-
- self.sv = 1 # we have matched one vertex already
- self.se = 0 # we haven't matched any edges yet
- for match in self.Match():
- yield match
- self.voccupiedG[Iv] = False
-
- def Match(self):
-
- # self.se represents how many vertices have been matched so far.
- # We are done searching if all of the edges from 0 to self.se-1
- # from graph g have been selected (matched with edges from graph G).
- if self.se == self.g.ne:
- # Note: This also gaurantees that all vertices have been visited.
- assert(self.sv == self.g.nv)
- yield self.ReformatMatch()
-
- else:
- # VF2-style recursive loop:
-
- # We know the next edge to be matched is connected to at least
- # one previously visited vertex from g which has already been
- # been added to the the current match-in-progress.
- iv = self.g.edges[self.se].start
- Iv = self.iv_to_Iv[iv]
- assert(iv < self.sv) # <-- check to verify this is so
-
- # The other vertex may or may not have been visited (matched) yet.
- iv_neighbor = self.g.edges[self.se].stop
-
- # Two cases:
- # Case 1: edge self.se points to a previously visited vertex from g
- # This means we have a loop.
- if iv_neighbor < self.sv:
- # In that case, then the corresponding edge in G must
- # connect the corresponding pair of vertices from G.
- # (Which we know have already been assigned to vertices in g
- # because both iv and iv_neighbor are < self.sv)
- Iv_neighbor = self.iv_to_Iv[iv_neighbor]
- # Loop over all of the edges in G which connect this pair
- # of vertices (Iv --> Iv_neighbor)
- for Je in self.G.neighbors[Iv]:
- Jv = self.G.edges[Je].stop
- if ((Jv == Iv_neighbor) and
- (not self.eoccupiedG[Je])):
-
- # Match edge Je from big graph G with
- # edge self.se from small graph g
- self.ie_to_Ie[self.se] = Je
- self.se += 1
- self.eoccupiedG[Je] = True
- for match in self.Match():
- yield match
- self.eoccupiedG[Je] = False
- self.se -= 1
- self.ie_to_Ie[self.se] = Dgraph.NULL
-
- # Case 2:
- else: # this would mean that iv_neighbor >= self.sv
-
- # If iv_neighbor>=self.sv, then this edge points to to a vertex
- # in g which has not yet been paired with a vertex from G.
-
- # Loop over all of the edges in G which connect vertex
- # Iv from G to new (unvisited) vertices in G
- for Je in self.G.neighbors[Iv]:
- Jv = self.G.edges[Je].stop
- if (not self.voccupiedG[Jv]):
-
- assert(not self.eoccupiedG[Je])
- # Match both edge Je with je
- # AND vertex Jv with jv
- self.ie_to_Ie[self.se] = Je
- self.se += 1
- self.eoccupiedG[Je] = True
- self.iv_to_Iv[self.sv] = Jv
- self.sv += 1
- self.voccupiedG[Jv] = True
- # Then continue the recursion
- for match in self.Match():
- yield match
- self.voccupiedG[Jv] = False
- self.sv -= 1
- self.iv_to_Iv[self.sv] = Dgraph.NULL
- self.eoccupiedG[Je] = False
- self.se -= 1
- self.ie_to_Ie[self.se] = Dgraph.NULL
-
- def ReformatMatch(self):
- # (This is because we are assuming g is connected.
- # IT should not have any orphanned vertices.)
- # Now return the match:
- #
- # There are different ways of doing this
- # version 1:
- #match = (self.iv_to_Iv, self.ie_to_Ie) <-return a pointer to array
- # version 2:
- #match = ([Iv for Iv in self.iv_to_Iv], <-return a copy of the array
- # [Ie for Ie in self.ie_to_Ie])
- # version 3:
- # Recall that the vertices and edges and g have been re-ordered,
- # so sort the list of Iv indices in the order they would be
- # matched with the original vertices from the original graph g:
- #match = ([self.iv_to_Iv[self.vorder_g[iv]]
- # for iv in range(0,self.g.nv)],
- # [self.ie_to_Ie[self.eorder_g[ie]]
- # for ie in range(0,self.g.ne)])
- # version 4: Similar to version 3 above, but we also translate
- # the directed edge id list into a shorter undirected
- # edge id list.
- match_verts = [self.iv_to_Iv[self.vorder_g[iv]]
- for iv in range(0,self.g.nv)]
-
- if type(self.g) is Dgraph:
- match_edges = [self.ie_to_Ie[self.eorder_g[ie]]
- for ie in range(0, self.g.ne)]
- else:
- #assert(atype(self.g) is Ugraph)
- match_edges = [Dgraph.NULL for ieu in range(0, self.g.neu)]
-
- for ie in range(0, self.g.ne):
- iv = self.g.edges[ie].start
- jv = self.g.edges[ie].stop
- if iv <= jv: # <-- avoid duplicating edges (iv,jv) and (jv,iv)
- ieu = self.g.LookupUndirectedEdgeIdx(ie)
- Ie = self.ie_to_Ie[ie]
- Ieu = self.G.LookupUndirectedEdgeIdx(Ie)
- match_edges[ieu] = Ieu
-
- return (tuple(match_verts), tuple(match_edges))
diff --git a/tools/moltemplate/src/nbody_reorder_atoms.py b/tools/moltemplate/src/nbody_reorder_atoms.py
deleted file mode 100644
index f2027bd09..000000000
--- a/tools/moltemplate/src/nbody_reorder_atoms.py
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env python
-
-"""
- Reorder the atoms in the Angles section of a data file to make sure that
- atoms have a "canonical order" (for example the first atom has a lower
- id than the last atom, for angle and dihedral interactions.
- (This helps us detect potential problems like dupicate Angle interactions.)
-
-"""
-
-import sys
-from operator import itemgetter
-
-g_program_name = __file__.split('/')[-1]
-
-in_stream = sys.stdin
-
-
-section_name = ''
-if len(sys.argv) == 3:
- section_name = sys.argv[1]
- module_name = sys.argv[2].rstrip('.py')
-else:
- sys.stderr.write('Usage Example:\n\n'
- ' '+g_program_name+' Angles nbody_angles.py < angles.txt > new_angles.txt\n\n'
- ' In this example \"angles.txt\" contains only the \"Angles\" section of\n'
- ' a LAMMPS DATA file. (Either a text-editor, or the \n'
- ' \"extract_lammps_data.py\" script can be used to select a section from\n'
- ' a LAMMPS DATA file\n\n'
- 'Error('+g_program_name+'): expected exactly one argument:\n'
- ' \"Angles\", \"Dihedrals\", or \"Impropers\"\n')
- exit(-1)
-
-# Ordering rules are defined in a seperate module named
-# nbody_angles.py, nbody_dihedrals.py, nbody_impropers.py
-# Load that now.
-
-g = __import__(module_name) #defines g.bond_pattern, g.canonical_order
-
-# This module defines the graph representing the bond pattern for this type
-# of interaction. (The number of vertices and edges for the graph corresponds
-# to the number of atoms and bonds in this type of interaction.)
-natoms = g.bond_pattern.GetNumVerts()
-nbonds = g.bond_pattern.GetNumEdges()
-
-
-for line_orig in in_stream:
- line = line_orig.rstrip('\n')
- comment = ''
- if '#' in line_orig:
- ic = line.find('#')
- line = line_orig[:ic]
- comment = ' '+line_orig[ic:].rstrip('\n')
-
- tokens = line.strip().split()
- swapped = False
- if len(tokens) == 2+natoms:
- all_integers = True
- abids_l = [[0 for i in range(0, natoms)],
- [0 for i in range(0, nbonds)]]
- for i in range(0, natoms):
- if not tokens[2+i].isdigit():
- all_integers = False
- if all_integers:
- for i in range(0, natoms):
- abids_l[0][i] = int(tokens[2+i])
- else:
- for i in range(0, natoms):
- abids_l[0][i] = tokens[2+i]
- abids = g.canonical_order( (tuple(abids_l[0]), tuple(abids_l[1])) )
- for i in range(0, natoms):
- tokens[2+i] = str(abids[0][i])
-
- sys.stdout.write(' '.join(tokens)+comment+'\n')
diff --git a/tools/moltemplate/src/ordereddict.py b/tools/moltemplate/src/ordereddict.py
deleted file mode 100644
index d8177973b..000000000
--- a/tools/moltemplate/src/ordereddict.py
+++ /dev/null
@@ -1,258 +0,0 @@
-# Backport of OrderedDict() class that runs on Python 2.4, 2.5, 2.6, 2.7 and pypy.
-# Passes Python2.7's test suite and incorporates all the latest updates.
-
-try:
- from thread import get_ident as _get_ident
-except ImportError:
- from dummy_thread import get_ident as _get_ident
-
-try:
- from _abcoll import KeysView, ValuesView, ItemsView
-except ImportError:
- pass
-
-
-class OrderedDict(dict):
- 'Dictionary that remembers insertion order'
- # An inherited dict maps keys to values.
- # The inherited dict provides __getitem__, __len__, __contains__, and get.
- # The remaining methods are order-aware.
- # Big-O running times for all methods are the same as for regular dictionaries.
-
- # The internal self.__map dictionary maps keys to links in a doubly linked list.
- # The circular doubly linked list starts and ends with a sentinel element.
- # The sentinel element never gets deleted (this simplifies the algorithm).
- # Each link is stored as a list of length three: [PREV, NEXT, KEY].
-
- def __init__(self, *args, **kwds):
- '''Initialize an ordered dictionary. Signature is the same as for
- regular dictionaries, but keyword arguments are not recommended
- because their insertion order is arbitrary.
-
- '''
- if len(args) > 1:
- raise TypeError('expected at most 1 arguments, got %d' % len(args))
- try:
- self.__root
- except AttributeError:
- self.__root = root = [] # sentinel node
- root[:] = [root, root, None]
- self.__map = {}
- self.__update(*args, **kwds)
-
- def __setitem__(self, key, value, dict_setitem=dict.__setitem__):
- 'od.__setitem__(i, y) <==> od[i]=y'
- # Setting a new item creates a new link which goes at the end of the linked
- # list, and the inherited dictionary is updated with the new key/value pair.
- if key not in self:
- root = self.__root
- last = root[0]
- last[1] = root[0] = self.__map[key] = [last, root, key]
- dict_setitem(self, key, value)
-
- def __delitem__(self, key, dict_delitem=dict.__delitem__):
- 'od.__delitem__(y) <==> del od[y]'
- # Deleting an existing item uses self.__map to find the link which is
- # then removed by updating the links in the predecessor and successor nodes.
- dict_delitem(self, key)
- link_prev, link_next, key = self.__map.pop(key)
- link_prev[1] = link_next
- link_next[0] = link_prev
-
- def __iter__(self):
- 'od.__iter__() <==> iter(od)'
- root = self.__root
- curr = root[1]
- while curr is not root:
- yield curr[2]
- curr = curr[1]
-
- def __reversed__(self):
- 'od.__reversed__() <==> reversed(od)'
- root = self.__root
- curr = root[0]
- while curr is not root:
- yield curr[2]
- curr = curr[0]
-
- def clear(self):
- 'od.clear() -> None. Remove all items from od.'
- try:
- for node in self.__map.itervalues():
- del node[:]
- root = self.__root
- root[:] = [root, root, None]
- self.__map.clear()
- except AttributeError:
- pass
- dict.clear(self)
-
- def popitem(self, last=True):
- '''od.popitem() -> (k, v), return and remove a (key, value) pair.
- Pairs are returned in LIFO order if last is true or FIFO order if false.
-
- '''
- if not self:
- raise KeyError('dictionary is empty')
- root = self.__root
- if last:
- link = root[0]
- link_prev = link[0]
- link_prev[1] = root
- root[0] = link_prev
- else:
- link = root[1]
- link_next = link[1]
- root[1] = link_next
- link_next[0] = root
- key = link[2]
- del self.__map[key]
- value = dict.pop(self, key)
- return key, value
-
- # -- the following methods do not depend on the internal structure --
-
- def keys(self):
- 'od.keys() -> list of keys in od'
- return list(self)
-
- def values(self):
- 'od.values() -> list of values in od'
- return [self[key] for key in self]
-
- def items(self):
- 'od.items() -> list of (key, value) pairs in od'
- return [(key, self[key]) for key in self]
-
- def iterkeys(self):
- 'od.iterkeys() -> an iterator over the keys in od'
- return iter(self)
-
- def itervalues(self):
- 'od.itervalues -> an iterator over the values in od'
- for k in self:
- yield self[k]
-
- def iteritems(self):
- 'od.iteritems -> an iterator over the (key, value) items in od'
- for k in self:
- yield (k, self[k])
-
- def update(*args, **kwds):
- '''od.update(E, **F) -> None. Update od from dict/iterable E and F.
-
- If E is a dict instance, does: for k in E: od[k] = E[k]
- If E has a .keys() method, does: for k in E.keys(): od[k] = E[k]
- Or if E is an iterable of items, does: for k, v in E: od[k] = v
- In either case, this is followed by: for k, v in F.items(): od[k] = v
-
- '''
- if len(args) > 2:
- raise TypeError('update() takes at most 2 positional '
- 'arguments (%d given)' % (len(args),))
- elif not args:
- raise TypeError('update() takes at least 1 argument (0 given)')
- self = args[0]
- # Make progressively weaker assumptions about "other"
- other = ()
- if len(args) == 2:
- other = args[1]
- if isinstance(other, dict):
- for key in other:
- self[key] = other[key]
- elif hasattr(other, 'keys'):
- for key in other.keys():
- self[key] = other[key]
- else:
- for key, value in other:
- self[key] = value
- for key, value in kwds.items():
- self[key] = value
-
- __update = update # let subclasses override update without breaking __init__
-
- __marker = object()
-
- def pop(self, key, default=__marker):
- '''od.pop(k[,d]) -> v, remove specified key and return the corresponding value.
- If key is not found, d is returned if given, otherwise KeyError is raised.
-
- '''
- if key in self:
- result = self[key]
- del self[key]
- return result
- if default is self.__marker:
- raise KeyError(key)
- return default
-
- def setdefault(self, key, default=None):
- 'od.setdefault(k[,d]) -> od.get(k,d), also set od[k]=d if k not in od'
- if key in self:
- return self[key]
- self[key] = default
- return default
-
- def __repr__(self, _repr_running={}):
- 'od.__repr__() <==> repr(od)'
- call_key = id(self), _get_ident()
- if call_key in _repr_running:
- return '...'
- _repr_running[call_key] = 1
- try:
- if not self:
- return '%s()' % (self.__class__.__name__,)
- return '%s(%r)' % (self.__class__.__name__, self.items())
- finally:
- del _repr_running[call_key]
-
- def __reduce__(self):
- 'Return state information for pickling'
- items = [[k, self[k]] for k in self]
- inst_dict = vars(self).copy()
- for k in vars(OrderedDict()):
- inst_dict.pop(k, None)
- if inst_dict:
- return (self.__class__, (items,), inst_dict)
- return self.__class__, (items,)
-
- def copy(self):
- 'od.copy() -> a shallow copy of od'
- return self.__class__(self)
-
- @classmethod
- def fromkeys(cls, iterable, value=None):
- '''OD.fromkeys(S[, v]) -> New ordered dictionary with keys from S
- and values equal to v (which defaults to None).
-
- '''
- d = cls()
- for key in iterable:
- d[key] = value
- return d
-
- def __eq__(self, other):
- '''od.__eq__(y) <==> od==y. Comparison to another OD is order-sensitive
- while comparison to a regular mapping is order-insensitive.
-
- '''
- if isinstance(other, OrderedDict):
- return len(self)==len(other) and self.items() == other.items()
- return dict.__eq__(self, other)
-
- def __ne__(self, other):
- return not self == other
-
- # -- the following methods are only used in Python 2.7 --
-
- def viewkeys(self):
- "od.viewkeys() -> a set-like object providing a view on od's keys"
- return KeysView(self)
-
- def viewvalues(self):
- "od.viewvalues() -> an object providing a view on od's values"
- return ValuesView(self)
-
- def viewitems(self):
- "od.viewitems() -> a set-like object providing a view on od's items"
- return ItemsView(self)
diff --git a/tools/moltemplate/src/pdbsort.py b/tools/moltemplate/src/pdbsort.py
deleted file mode 100644
index 7d735a975..000000000
--- a/tools/moltemplate/src/pdbsort.py
+++ /dev/null
@@ -1,138 +0,0 @@
-#!/usr/bin/env python
-"""
- Unfortunately, the lines in a PDB files are not always listed in the
- correct order. Software that reads PDB files is expected to re-sort this
- data before interpreting it. (One reason I don't like them.)
- This script reads a PDB file from the standard input, sorts the lines
- according to ChainID, SeqNum (residue-number), Icode (insert-code),
- and AtomID (in that order) and prints the result to the standard-out.
- Only the ATOM and HETATM records are effected.
- All other lines in the PDB file are printed back to the user verbatim.
- Note: the "altLoc" column (character #17 on each line) is ignored
- and is not used for sorting purposes.
-
-"""
-
-from collections import defaultdict
-
-
-# In order to specify any amino acid in a PDB file, you must provide 3
-# identifiers:
-# the ChainID a single letter specifying
-# the SeqNum an integer indicating the location within that chain
-# the ICode ("insert code" usually 0. I don't know why this number is
-# necessary. ..For the record, I never loved the PDB file format.)
-
-
-class AtomDescr:
- def __init__(self, setChainID, setSeqNum, setICode, setAtomID):
- self.chainID = setChainID
- self.seqNum = setSeqNum
- self.iCode = setICode
- self.atomID = setAtomID
-
- #I plan to store this information in a python dictionary.
- #Unfortunately, in order to use such classes as keys in python dictionaries
- #I must define comparison operators, and a hash function.
- #In retrospect I figured out it would have been easier just to use tuples
- #as dictionary keys. I suppose it was a good excercise to try to do it
- #using python classes instead. I'm sorry it made the code so long.
-
- def __le__(self, other):
- #return ((self.chainID < other.chainID) or ((self.chainID == other.chainID) and ((self.seqNum < other.seqNum) or ((self.seqNum == other.seqNum) and (self.iCode <= other.iCode)))))))
- # instead I'll exploit python's ability to compare tuples
- return (self.chainID, self.seqNum, self.iCode, self.atomID) <= (other.chainID, other.seqNum, other.iCode, other.atomID)
-
- def __lt__(self, other):
- return (self.chainID, self.seqNum, self.iCode, self.atomID) < (other.chainID, other.seqNum, other.iCode, other.atomID)
-
- def __eq__(self, other):
- #return ((self.chainID == x.chainID) and (self.seqNum == x.seqNum) and (self.iCode == x.iCode))
- return (self.chainID, self.seqNum, self.iCode, self.atomID) == (other.chainID, other.seqNum, other.iCode, other.atomID)
-
- def __ne__(self, other):
- return not __eq__(self, other)
-
- def __gt__(self, other):
- return not __le__(self, other)
-
- def __ge__(self, other):
- return not __lt__(self, other)
-
- def __cmp__(self, other):
- if __lt__(self, other):
- return -1
- elif __gt__(self, other):
- return 1
- else:
- return 0
-
- def __hash__(self):
- numChainIDs = 128
- numICodes = 128
- i = self.seqNum
- i *= numChainIDs
- i += ord(self.chainID)
- i *= numICodes
- i += ord(self.iCode)
- i *=10
- i += self.atomID
- return i
-
-
-
-
-import sys
-from operator import attrgetter
-g_program_name = __file__.split('/')[-1]
-g_version_str = 0.11
-g_date_str = 2013-9-18
-
-if len(sys.argv) == 1:
- use_all_residues = True
-elif len(sys.argv) == 7:
- use_all_residues = False
- first = AtomDescr(sys.argv[1], int(sys.argv[2]), sys.argv[3], 0)
- last = AtomDescr(sys.argv[4], int(sys.argv[5]), sys.argv[6], 2147483647)
-else:
- sys.stderr.write("Error("+g_program_name+"): This program requires either 0 or 6 arguments.\n"
- " By default, the the sequence is extracted from the entire PDB file.\n"
- " In that case, no arguments are required.\n"
- " Alternately, you can limit the selection to a single interval of\n"
- " residues from one of the chains in the PDB file.\n"
- " To specify an interval, you must passing 6 arguments to this program.\n"
- " This program requires a pair of residues to designate the first and\n"
- " last members of the interval. Each residue requires 3 identifiers.\n"
- " Consequently the six arguments needed are:\n"
- "ChainID_first SeqNum_first ICode_first ChainID_last SeqNum_last ICode_last\n")
- exit(-1)
-
-
-atoms2lines = defaultdict(list)
-
-for line in sys.stdin:
- if (line[0:6] == "ATOM ") or (line[0:6] == "HETATM"):
- atomID = int(line[6:11])
- #atomType = line[12:16]
- #altLoc = line[16:17]
- iCode = line[26:27]
- #resType = line[17:20]
- chainID = line[21:22]
- seqNumStr = line[22:26]
- seqNum = int(seqNumStr)
- atomdescr = AtomDescr(chainID, int(seqNumStr), iCode, int(atomID))
- atoms2lines[atomdescr].append(line.rstrip('\n'))
- else:
- sys.stdout.write(line)
-
-# Extract an (unordered) list of the atomdescrs of the atoms in the sequence
-atomdescrs = [atomdescr for atomdescr in atoms2lines]
-
-# Residues in PDB files are often not listed in order.
-# Consequently, we must sort the list by chainID, seqNum, and finnaly iCode:
-sequence_of_atomdescrs = sorted(atomdescrs, key=attrgetter('chainID','seqNum','iCode','atomID'))
-
-for atomdescr in sequence_of_atomdescrs:
- for line in atoms2lines[atomdescr]:
- sys.stdout.write(line+'\n')
-
diff --git a/tools/moltemplate/src/postprocess_input_script.py b/tools/moltemplate/src/postprocess_input_script.py
deleted file mode 100644
index 5d414eadb..000000000
--- a/tools/moltemplate/src/postprocess_input_script.py
+++ /dev/null
@@ -1,147 +0,0 @@
-#!/usr/bin/env python
-
-"""
- Reorder the integer arguments to the commands in a LAMMPS input
- file if these arguments violate LAMMPS order requirements.
- We have to do this because the moltemplate.sh script will automatically
- assign these integers in a way which may violate these restrictions
- and the user has little control over this.
-
- This script:
- swaps the I and J integers in "pair_coeff I J ..." commands when I > J
-
- Other features may be added later
-
-"""
-
-
-import sys
-lines_orig = []
-f = None
-fname = None
-num_lines_ignore = 0
-
-
-# Lines from files passed as arguments are read and processed silently.
-# (Why? Sometimes it's necessary to read the contents of previous input scripts
-# in order to be able to understand a script command which appears later.
-# I'm assuming these files will be processed by lammps in the same order. So I
-# must insure that moltemplate.sh passes them to this program in that order.
-# I'm too lazy to read the "include" commands in input scripts correctly.)
-if len(sys.argv) > 1:
- for fname in sys.argv[1:]:
- f = open(fname, 'r')
- in_stream = f
- lines_orig += in_stream.readlines()
- num_lines_ignore += len(lines_orig)
- f.close()
-
-
-# Lines read from the standard input are read, processed, and printed to stdout
-in_stream = sys.stdin
-lines_orig += in_stream.readlines()
-
-pair_style_list=[]
-swap_occured = False
-warn_wildcard = False
-
-i=0
-while i < len(lines_orig):
- # Read the next logical line
- # Any lines ending in '&' should be merged with the next line before breaking
- line_orig = ''
- while i < len(lines_orig):
- line_counter = 1 + i - num_lines_ignore
- line_orig += lines_orig[i]
- if ((len(line_orig) < 2) or (line_orig[-2:] != '&\n')):
- break
- i += 1
- line = line_orig.replace('&\n','\n').rstrip('\n')
-
- comment = ''
- if '#' in line_orig:
- ic = line.find('#')
- line = line_orig[:ic]
- comment = line_orig[ic:] # keep track of comments (put them back later)
-
- tokens = line.strip().split()
- if ((len(tokens) >= 2) and (tokens[0] == 'pair_style')):
- pair_style_list = tokens[1:]
-
- if ((len(tokens) >= 3) and (tokens[0] == 'pair_coeff')):
-
- if ((tokens[1].isdigit() and (tokens[2].isdigit())) and
- (int(tokens[1]) > int(tokens[2]))):
-
- swap_occured = True
- tmp = tokens[2]
- tokens[2] = tokens[1]
- tokens[1] = tmp
-
- if i >= num_lines_ignore:
-
- # polite warning:
- sys.stderr.write('swapped pair_coeff order on line '+str(line_counter))
- #if (fname != None):
- # sys.stderr.write(' of file \"'+fname+'\"')
- sys.stderr.write('\n')
-
- # Deal with the "hbond/" pair coeffs.
- #
- # The hbond/dreiding pair style designates one of the two atom types
- # as a donor, and the other as an acceptor (using the 'i','j' flags)
- # If swapped atom types eariler, we also need to swap 'i' with 'j'.
- #
- # If "hbond/dreiding.." pair style is used with "hybrid" or
- # "hybrid/overlay" then tokens[3] is the name of the pair style
- # and tokens[5] is either 'i' or 'j'.
- if len(pair_style_list) > 0:
- if ((pair_style_list[0] == 'hybrid') or
- (pair_style_list[0] == 'hybrid/overlay')):
- if ((len(tokens) > 5) and (tokens[5] == 'i') and (tokens[3][0:6]=='hbond/')):
- tokens[5] = 'j'
- sys.stderr.write(' (and replaced \"i\" with \"j\")\n')
- elif ((len(tokens) > 5) and (tokens[5] == 'j') and (tokens[3][0:6]=='hbond/')):
- tokens[5] = 'i'
- sys.stderr.write(' (and replaced \"j\" with \"i\")\n')
- elif (pair_style_list[0][0:6] == 'hbond/'):
- if ((len(tokens) > 4) and (tokens[4] == 'i')):
- tokens[4] = 'j'
- sys.stderr.write(' (and replaced \"i\" with \"j\")\n')
- elif ((len(tokens) > 4) and (tokens[4] == 'j')):
- tokens[4] = 'i'
- sys.stderr.write(' (and replaced \"j\" with \"i\")\n')
-
- sys.stdout.write((' '.join(tokens)+comment).replace('\n','&\n')+'\n')
-
- else:
- if ((('*' in tokens[1]) or ('*' in tokens[2]))
- and
- (not (('*' == tokens[1]) and ('*' == tokens[2])))):
- warn_wildcard = True
- if i >= num_lines_ignore:
- sys.stdout.write(line_orig)
- else:
- if i >= num_lines_ignore:
- sys.stdout.write(line_orig)
-
- i += 1
-
-
-
-if swap_occured:
- sys.stderr.write('\n'
- ' WARNING: Atom order in some pair_coeff commands was swapped to pacify LAMMPS.\n'
- ' For some exotic pair_styles such as hbond/dreiding, this is not enough. If you\n'
- ' use exotic pair_styles, please verify the \"pair_coeff\" commands are correct.\n')
-
-if warn_wildcard:
- sys.stderr.write('\n'
- ' WARNING: The use of wildcard characters (\"*\") in your \"pair_coeff\"\n'
- ' commands is not recommended.\n'
- ' (It is safer to specify each interaction pair manually.\n'
- ' Check every pair_coeff command. Make sure that every atom type in\n'
- ' the first group is <= atom types in the second group.\n'
- ' Moltemplate does NOT do this when wildcards are used.)\n'
- ' If you are using a many-body pair style then ignore this warning.\n')
-
diff --git a/tools/moltemplate/src/raw2data.py b/tools/moltemplate/src/raw2data.py
deleted file mode 100644
index 5f9149d6f..000000000
--- a/tools/moltemplate/src/raw2data.py
+++ /dev/null
@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from dump2data import *
-
-g_program_name = 'raw2data.py'
-g_date_str = '2014-12-19'
-g_version_str = 'v0.43'
-
-####### Main Code Below: #######
-sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str)
-sys.stderr.write('\n')
-
-try:
- data_settings = DataSettings()
- misc_settings = MiscSettings()
- misc_settings.multi = False
-
- warning_strings = []
- ParseArgs(sys.argv,
- misc_settings,
- data_settings,
- warning_strings)
-
- frame_coords = defaultdict(list)
- frame_coords_ixiyiz = defaultdict(list)
- frame_vects = defaultdict(list)
- frame_velocities = defaultdict(list)
- frame_xlo_str = frame_xhi_str = None
- frame_ylo_str = frame_yhi_str = None
- frame_zlo_str = frame_zhi_str = None
- frame_xy_str = frame_xz_str = frame_yz_str = None
- frame_natoms = -1
- frame_timestep_str = ''
- i_atomid = i_atomtype = i_molid = -1
- i_x = i_y = i_z = i_xu = i_yu = i_zu = -1
- i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1
-
- dump_column_names = []
-
- #num_frames_in = -1
- num_frames_out = 0
- finished_reading_frame = False
- read_last_frame = False
-
- #in_coord_file = open('traj.raw','r')
- #in_coord_file = open('tmp_atom_coords.dat','r')
- in_coord_file = sys.stdin
- read_last_frame = False
- while True:
-
- line = '\n'
- while (line != '') and (line.strip() == ''):
- line = in_coord_file.readline()
-
- if line == '': # if EOF
- break
-
- frame_coords = defaultdict(list)
- while line.strip() != '':
- n_crds = len(frame_coords)
- #sys.stdout.write("n_crds="+str(n_crds)+": \""+line.strip()+"\"\n")
- frame_coords[str(n_crds+1)] = line.split()
- line = in_coord_file.readline()
-
- # Check to see if there are any blank lines at this location in the file
- # If there are, it means we are at a new "frame" (in the trajectory).
- # Skip over any blank line(s) separating this frame from the next frame
- # so that the next time we enter the loop, we are at the beginning
- # of a new frame.
- while (line != '') and (line.strip() == ''):
- line = in_coord_file.readline()
-
- # Parse the DATA file specified by the user
- # and replace appropriate lines or fields with
- # the corresponding text from the input file.
- if misc_settings.multi:
- out_file_name = data_settings.file_name + '.'\
- + str(num_frames_out)
- sys.stderr.write(' (creating file \"'+out_file_name+'\")\n')
- out_file = open(out_file_name, 'w')
- else:
- out_file = sys.stdout
-
- WriteFrameToData(out_file,
- None,
- misc_settings,
- data_settings,
- frame_natoms,
- frame_coords,
- frame_coords_ixiyiz,
- frame_vects,
- frame_velocities,
- None,
- None,
- frame_xlo_str, frame_xhi_str,
- frame_ylo_str, frame_yhi_str,
- frame_zlo_str, frame_zhi_str,
- frame_xy_str, frame_xz_str, frame_yz_str)
-
-except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)
diff --git a/tools/moltemplate/src/remove_duplicate_atoms.py b/tools/moltemplate/src/remove_duplicate_atoms.py
deleted file mode 100644
index d7f7d5ed3..000000000
--- a/tools/moltemplate/src/remove_duplicate_atoms.py
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/env python
-
-"""
- Get rid of lines containing duplicate copies of the same atom in the "Atoms"
- section of a LAMMPS data file. Duplicate lines which occur later are
- preserved and the earlier lines are erased.
- The file is read from sys.stdin. This program does not parse the entire
- data file. The text from the "Atoms" section of the LAMMPS file must
- be extracted in advance before it is sent to this program.)
-
-"""
-
-import sys
-in_stream = sys.stdin
-f = None
-fname = None
-if len(sys.argv) == 2:
- fname = sys.argv[1]
- f = open(fname, 'r')
- in_stream = f
-
-atom_ids_in_use = set([])
-
-lines = in_stream.readlines()
-
-# Start at the end of the file and read backwards.
-# If duplicate lines exist, eliminate the ones that occur earlier in the file.
-i = len(lines)
-while i > 0:
- i -= 1
- line_orig = lines[i]
- line = line_orig.rstrip('\n')
- if '#' in line_orig:
- ic = line.find('#')
- line = line_orig[:ic]
-
- tokens = line.strip().split()
- if len(tokens) > 0:
- atom_id = tokens[0]
- if atom_id in atom_ids_in_use:
- del lines[i]
- else:
- atom_ids_in_use.add(atom_id)
- else:
- del lines[i]
-
-
-for line in lines:
- sys.stdout.write(line)
-
-if f != None:
- f.close()
-
diff --git a/tools/moltemplate/src/remove_duplicates_nbody.py b/tools/moltemplate/src/remove_duplicates_nbody.py
deleted file mode 100644
index 100998abe..000000000
--- a/tools/moltemplate/src/remove_duplicates_nbody.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python
-
-"""
- Get rid of lines containing duplicate bonded nbody interactions in the
- corresponding section of a LAMMPS data file (such as bonds, angles,
- dihedrals and impropers). Duplicate lines which occur later are
- preserved and the earlier lines are erased.
- (This program reads from sys.stdin. This program does not parse the entire
- data file. The text from the relevant section of the LAMMPS file should be
- extracted in advance before it is sent to this program.)
-
-"""
-
-import sys
-in_stream = sys.stdin
-
-if len(sys.argv) == 2:
- n = int(sys.argv[1])
-if (len(sys.argv) != 2) or (n < 1):
- sys.stderr.write('Error (remove_duplicates_nbody.py): expected a positive integer argument.\n')
- sys.exit(-1)
-
-atom_ids_in_use = set([])
-
-lines = in_stream.readlines()
-
-# Start at the end of the file and read backwards.
-# If duplicate lines exist, eliminate the ones that occur earlier in the file.
-i = len(lines)
-while i > 0:
- i -= 1
- line_orig = lines[i]
- line = line_orig.rstrip('\n')
- if '#' in line_orig:
- ic = line.find('#')
- line = line_orig[:ic]
-
- tokens = line.strip().split()
- if len(tokens) == 2+n:
- atom_ids = tuple(tokens[2:2+n])
- if atom_ids in atom_ids_in_use:
- del lines[i]
- else:
- atom_ids_in_use.add(atom_ids)
- elif len(tokens) == 0:
- del lines[i]
-
-for line in lines:
- sys.stdout.write(line)
diff --git a/tools/moltemplate/src/renumber_DATA_first_column.py b/tools/moltemplate/src/renumber_DATA_first_column.py
deleted file mode 100644
index 69b6477de..000000000
--- a/tools/moltemplate/src/renumber_DATA_first_column.py
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env python
-
-"""
- renumber the integers at the beginning of ever line in the file
- to make sure these numbers are contiguous.
- The file is read from sys.stdin.
- This program does not parse an entire LAMMPS data file.
- The text from the "Atoms" section
- (or "Bonds", or "Angles", or "Dihedrals", or "Impropers" sections)
- of the LAMMPS file must be extracted in advance.
-
-"""
-
-import sys
-from operator import itemgetter
-
-in_stream = sys.stdin
-f = None
-fname = None
-if len(sys.argv) == 2:
- fname = sys.argv[1]
- f = open(fname, 'r')
- in_stream = f
-
-
-lines = in_stream.readlines()
-column1_iorig_columnsAfter1 = []
-
-# Start at the end of the file and read backwards.
-# If duplicate lines exist, eliminate the ones that occur earlier in the file.
-i = 0
-while i < len(lines):
- line_orig = lines[i]
- line = line_orig.rstrip('\n')
- comment = ''
- if '#' in line_orig:
- ic = line.find('#')
- line = line_orig[:ic]
- comment = ' '+line_orig[ic:].rstrip('\n')
-
- tokens = line.strip().split()
- if len(tokens) > 0:
- if str.isdigit(tokens[0]):
- column1 = int(tokens[0])
- else:
- column1 = tokens[0]
- column1_iorig_columnsAfter1.append([column1, i, ' '.join(tokens[1:])+comment])
- i += 1
-
-# Sort the list of lines by the first number on each line
-
-column1_iorig_columnsAfter1.sort(key=itemgetter(0))
-
-# Change all of these numbers so that they are consecutive starting at 1
-for i in range(0, len(column1_iorig_columnsAfter1)):
- column1_iorig_columnsAfter1[i][0] = i+1
-
-# Sort the list of lines so they are back in the original order
-
-column1_iorig_columnsAfter1.sort(key=itemgetter(1))
-
-for i in range(0, len(column1_iorig_columnsAfter1)):
- column1 = column1_iorig_columnsAfter1[i][0]
- columnsAfter1 = column1_iorig_columnsAfter1[i][2]
- sys.stdout.write(str(column1) +' ' + columnsAfter1 + '\n')
-
-if f != None:
- f.close()
-
diff --git a/tools/moltemplate/src/tinkerparm2lt.py b/tools/moltemplate/src/tinkerparm2lt.py
deleted file mode 100644
index 03367b1cf..000000000
--- a/tools/moltemplate/src/tinkerparm2lt.py
+++ /dev/null
@@ -1,581 +0,0 @@
-#! /usr/bin/env python
-#
-# The purpose of this script is to create a moltemplate lt file for the opls.
-# and oplsaa forcefields.
-
-__author__ = 'Jason Lambert and Andrew Jewett'
-# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others)
-__version__ = '0.1'
-__date__ = '2016-11-20'
-
-
-
-import sys
-import os
-from sets import Set
-from operator import itemgetter
-
-
-g_program_name = __file__.split('/')[-1]
-
-
-doc_msg = \
- "Typical Usage:\n\n" + \
- " "+g_program_name+" -name OPLS < oplsaa.prm > oplsaa.lt\n\n" + \
- " where \"oplsaa.prm\" is a force-field file downloaded from the TINKER website,\n" + \
- " \"oplsaa.lt\" is the corresponding file converted into moltemplate (.lt) format.\n" + \
- " and \"OPLS\" is the name that future moltemplate users will use to refer to\n" + \
- " this force-field (optional).\n" + \
- "Optional Arguments\n" + \
- " -name FORCEFIELDNAME # Give the force-field a name\n" + \
- " -file FILE_NAME # Read force field parameters from a file\n" + \
- " -url URL # Read force field parameters from a file on the web\n" + \
- " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n"
-
-
-
-
-def SplitQuotedString(string,
- quotes='\'\"',
- delimiters=' \t\r\f\n',
- escape='\\',
- comment_char='#'):
- tokens = []
- token = ''
- reading_token = True
- escaped_state = False
- quote_state = None
- for c in string:
-
- if (c in comment_char) and (not escaped_state) and (quote_state==None):
- tokens.append(token)
- return tokens
-
- elif (c in delimiters) and (not escaped_state) and (quote_state==None):
- if reading_token:
- tokens.append(token)
- token = ''
- reading_token = False
-
- elif c in escape:
- if escaped_state:
- token += c
- reading_token = True
- escaped_state = False
- else:
- escaped_state = True
- # and leave c (the '\' character) out of token
- elif (c in quotes) and (not escaped_state):
- if (quote_state != None):
- if (c == quote_state):
- quote_state = None
- else:
- quote_state = c
- token += c
- reading_token = True
- else:
- if (c == 'n') and (escaped_state == True):
- c = '\n'
- elif (c == 't') and (escaped_state == True):
- c = '\t'
- elif (c == 'r') and (escaped_state == True):
- c = '\r'
- elif (c == 'f') and (escaped_state == True):
- c = '\f'
- token += c
- reading_token = True
- escaped_state = False
-
- if len(string) > 0:
- tokens.append(token)
- return tokens
-
-
-
-
-def RemoveOuterQuotes(text, quotes='\"\''):
- if ((len(text)>=2) and (text[0] in quotes) and (text[-1]==text[0])):
- return text[1:-1]
- else:
- return text
-
-
-
-
-
-
-try:
- sys.stderr.write(g_program_name+", version "+__version__+", "+__date__+"\n")
- if sys.version < '2.6':
- raise Exception('Error: Using python '+sys.version+'\n'+
- ' Alas, your version of python is too old.\n'
- ' You must upgrade to a newer version of python (2.6 or later).')
-
- if sys.version < '2.7':
- from ordereddict import OrderedDict
- else:
- from collections import OrderedDict
-
- if sys.version > '3':
- import io
- else:
- import cStringIO
-
-
- # defaults:
- ffname = "TINKER_FORCE_FIELD"
- type_subset = Set([])
- filename_in = ""
- file_in = sys.stdin
- dihedral_style_name = "fourier"
- special_bonds_command = "special_bonds lj/coul 0.0 0.0 0.5"
- mixing_style = "geometric"
- contains_united_atoms = False
-
- argv = [arg for arg in sys.argv]
-
- i = 1
-
- while i < len(argv):
-
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
-
- if argv[i] == '-atoms':
- if i+1 >= len(argv):
- raise Exception('Error: the \"'+argv[i]+'\" argument should be followed by a quoted string\n'
- ' which contains a space-delimited list of of a subset of atom types\n'
- ' you want to use from the original force-field.\n'
- ' Make sure you enclose the entire list in quotes.\n');
- type_subset = Set(argv[i+1].strip('\"\'').strip().split())
- del argv[i:i+2]
-
- elif argv[i] == '-name':
- if i+1 >= len(argv):
- raise Exception('Error: '+argv[i]+' flag should be followed by the name of the force-field\n')
- ffname = argv[i+1]
- del argv[i:i+2]
-
- elif argv[i] in ('-file','-in-file'):
- if i+1 >= len(argv):
- raise Exception('Error: '+argv[i]+' flag should be followed by the name of a force-field file\n')
- filename_in = argv[i+1]
- try:
- file_in = open(filename_in, 'r')
- except IOError:
- sys.stderr.write('Error: Unable to open file\n'
- ' \"'+filename_in+'\"\n'
- ' for reading.\n')
- sys.exit(1)
- del argv[i:i+2]
-
- elif argv[i] == '-dihedral-style':
- if i+1 >= len(argv):
- raise Exception('Error: '+argv[i]+' flag should be followed by either \"opls\" or \"fourier\"\n')
- dihedral_style_name = argv[i+1]
- if dihedral_style_name not in ('fourier','opls'):
- raise Exception('Error: '+argv[i]+' '+dihedral_style_name+' not supported.\n')
- del argv[i:i+2]
-
-
- elif argv[i] in ('-url','-in-url'):
- import urllib2
- if i+1 >= len(argv):
- raise Exception('Error: '+argv[i]+' flag should be followed by the name of a force-field file.\n')
- url = argv[i+1]
- try:
- request = urllib2.Request(url)
- file_in = urllib2.urlopen(request)
- except urllib2.URLError:
- sys.stdout.write("Error: Unable to open link:\n"+url+"\n")
- sys.exit(1)
- del argv[i:i+2]
-
- elif argv[i] in ('-help','--help','-?','--?'):
- sys.stderr.write(doc_msg)
- sys.exit(0)
- del argv[i:i+1]
-
- else:
- i += 1
-
- if len(argv) != 1:
- raise Exception('Error: Unrecongized arguments: ' +' '.join(argv[1:]) +
- '\n\n'+ doc_msg)
-
-
- #sys.stderr.write("Reading parameter file...\n")
-
-
- lines = file_in.readlines()
-
- atom2charge = OrderedDict() # lookup charge from atom type
- atom2mass = OrderedDict() # lookup mass from atom type
- atom2vdw_e = OrderedDict() # lookup Lennard-Jones "epsilon" parameter
- atom2vdw_s = OrderedDict() # lookup Lennard-Jones "sigma" parameter
- atom2descr = OrderedDict()
- atom2ffid = OrderedDict() # lookup force-field-ID from atom type
- # force-field-ID is an id number/string used to assign
- # bonds, angles, dihedrals, and impropers.
-
- bonds_by_type = OrderedDict() # lookup bond parameters by force-field-ID
- angles_by_type = OrderedDict() # lookup angle parameters by force-field-ID
- dihedrals_by_type = OrderedDict() # lookup dihedral parameters by force-field-ID
- impropers_by_type = OrderedDict() # lookup improper parameters by force-field-ID
- lines_ureybrad = []
- lines_biotype = []
-
-
- for iline in range(0, len(lines)):
- line = lines[iline]
- tokens = SplitQuotedString(line.strip(),
- comment_char='#')
-
- if (len(tokens)>1) and (tokens[0] == 'atom'):
- tokens = map(RemoveOuterQuotes,
- SplitQuotedString(line.strip(),
- comment_char=''))
- if (len(tokens) > 6):
- if ((len(type_subset) == 0) or (tokens[1] in type_subset)):
- atom2ffid[tokens[1]] = tokens[2]
- #atom2mass[tokens[1]] = float(tokens[6])
- #Some atoms in oplsaa.prm have zero mass. Unfortunately this
- #causes LAMMPS to crash, even if these atoms are never used,
- #so I give the mass a non-zero value instead.
- atom2mass[tokens[1]] = max(float(tokens[6]), 1e-30)
- atom2descr[tokens[1]] = tokens[4]
- if tokens[4].find('(UA)') != -1:
- contains_united_atoms = True
- else:
- raise Exception('Error: Invalid atom line:\n'+line)
- elif (len(tokens) > 2) and (tokens[0] == 'charge'):
- if ((len(type_subset) == 0) or (tokens[1] in type_subset)):
- atom2charge[tokens[1]] = float(tokens[2])
- elif (len(tokens) > 3) and (tokens[0] == 'vdw'):
- if ((len(type_subset) == 0) or (tokens[1] in type_subset)):
- atom2vdw_e[tokens[1]] = float(tokens[3]) # "epsilon"
- atom2vdw_s[tokens[1]] = float(tokens[2]) # "sigma"
- elif (len(tokens) > 4) and (tokens[0] == 'bond'):
- k = float(tokens[3])
- r0 = float(tokens[4])
- bonds_by_type[tokens[1],tokens[2]] = (k, r0)
- elif (len(tokens) > 5) and (tokens[0] == 'angle'):
- k = float(tokens[4])
- angle0 = float(tokens[5])
- angles_by_type[tokens[1],tokens[2],tokens[3]] = (k, angle0)
- elif (len(tokens) > 11) and (tokens[0] == 'torsion'):
- if dihedral_style_name == 'fourier':
- # http://lammps.sandia.gov/doc/dihedral_fourier.html
- m = (len(tokens) - 5) / 3
- K = [0.0 for i in range(0,m)]
- n = [0.0 for i in range(0,m)]
- d = [0.0 for i in range(0,m)]
- for i in range(0,m):
- K[i] = float(tokens[5+3*i])
- d[i] = float(tokens[5+3*i+1])
- n[i] = float(tokens[5+3*i+2])
- dihedrals_by_type[tokens[1],tokens[2],tokens[3],tokens[4]]=(K,n,d)
- elif dihedral_style_name == 'opls':
- # http://lammps.sandia.gov/doc/dihedral_opls.html
- K1 = float(tokens[5])
- K2 = float(tokens[8])
- K3 = float(tokens[11])
- K4 = 0.0
- if len(tokens) > 14:
- K4 = float(tokens[14])
- if ((float(tokens[6]) != 0.0) or (float(tokens[7]) != 1.0) or
- (float(tokens[9]) not in (180.0,-180.0)) or (float(tokens[10]) != 2.0) or
- (float(tokens[12]) != 0.0) or (float(tokens[13]) != 3.0) or
- ((K4 != 0.0) and
- ((len(tokens) <= 16) or
- (float(tokens[15]) not in (180.0,-180.0)) or
- (float(tokens[16]) != 4.0)))):
- raise Exception("Error: This parameter file is incompatible with -dihedral-style \""+dihedral_style_name+"\"\n"+
- " (See line number "+str(iline+1)+" of parameter file.)\n")
- dihedrals_by_type[tokens[1],tokens[2],tokens[3],tokens[4]]=(K1,K2,K3,K4)
- else:
- assert(False)
-
- elif (len(tokens) > 7) and (tokens[0] == 'imptors'):
- k = float(tokens[5])
- angle0 = float(tokens[6])
- multiplicity = float(tokens[7])
- impropers_by_type[tokens[1],tokens[2],tokens[3],tokens[4]] = (k/multiplicity, angle0)
- elif ((len(tokens) > 0) and (tokens[0] == 'biotype')):
- # I'm not sure what to do with these, so I'll store them for now and
- # append them as comments to the .lt file generated by the program.
- lines_biotype.append(line.rstrip())
- elif ((len(tokens) > 0) and (tokens[0] == 'ureybrad')):
- # I'm not sure what to do with these, so I'll store them for now and
- # append them as comments to the .lt file generated by the program.
- lines_ureybrad.append(line.rstrip())
- elif ((len(tokens) > 1) and (tokens[0] == 'radiusrule')):
- if tokens[1] == 'GEOMETRIC':
- mixing_style = 'geometric'
- elif tokens[1] == 'ARITHMETIC':
- mixing_style = 'arithmetic'
- else:
- raise Exception("Error: Unrecognized mixing style: "+tokens[1]+", found here:\n" +
- line)
- elif ((len(tokens) > 1) and (tokens[0] == 'epsilonrule')):
- if tokens[1] != 'GEOMETRIC':
- raise Exception("Error: As of 2016-9-21, LAMMPS only supports GEOMETRIC mixing of energies\n" +
- " This force field simply cannot be used with LAMMPS in a general way.\n" +
- " One way around this is to manually change the \"epsilonrule\" back to\n" +
- " GEOMETRIC, and limit the number of atom types considered by this\n" +
- " program by using the -atoms \"LIST OF ATOMS\" argument,\n" +
- " to only include the atoms you care about, and then explicitly\n" +
- " define pair_coeffs for all possible pairs of these atom types.\n" +
- " If this is a popular force-field, then lobby the LAMMPS developers\n" +
- " to consider alternate mixing rules.\n\n" +
- "The offending line from the file is line number "+str(iline)+":\n" +
- line+"\n")
-
-except Exception as err:
- sys.stderr.write('\n\n'+str(err)+'\n')
- sys.exit(1)
-
-
-
-
-
-
-
-
-#sys.stderr.write(" done.\n")
-#sys.stderr.write("Converting to moltemplate format...\n")
-
-
-
-
-
-
-
-system_is_charged = False
-for atom_type in atom2charge:
- if atom2charge[atom_type] != 0.0:
- system_is_charged = True
-
-if system_is_charged:
- pair_style_name = "lj/cut/coul/long"
- pair_style_params = "10.0 10.0"
- kspace_style = " kspace_style pppm 0.0001\n"
-else:
- pair_style_name = "lj/cut"
- pair_style_params = "10.0"
- kspace_style = ""
-
-pair_style_command = " pair_style hybrid "+pair_style_name+" "+pair_style_params+"\n"
-
-bond_style_name = "harmonic"
-angle_style_name = "harmonic"
-improper_style_name = "harmonic"
-
-
-
-
-
-
-
-sys.stdout.write("# This file was generated automatically using:\n")
-sys.stdout.write("# "+g_program_name+" "+" ".join(sys.argv[1:])+"\n")
-if contains_united_atoms:
- sys.stdout.write("#\n"
- "# WARNING: Many of these atoms are probably UNITED-ATOM (UA) atoms.\n"
- "# The hydrogen atoms have been absorbed into the heavy atoms, and the\n"
- "# force-field modified accordingly. Do not mix with ordinary atoms.\n")
-sys.stdout.write("#\n"
- "# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:\n")
-sys.stdout.write("# "+special_bonds_command+"\n")
-sys.stdout.write("# (See http://lammps.sandia.gov/doc/special_bonds.html for details)\n")
-if len(lines_ureybrad) > 0:
- sys.stdout.write("#\n"
- "# WARNING: All Urey-Bradley interactions have been IGNORED including:\n")
- sys.stdout.write("# ffid1 ffid2 ffid3 K r0\n# ")
- sys.stdout.write("\n# ".join(lines_ureybrad))
- sys.stdout.write("\n\n")
-sys.stdout.write("\n\n")
-sys.stdout.write(ffname+" {\n\n")
-
-
-sys.stdout.write(" write_once(\"In Charges\") {\n")
-for atype in atom2mass:
- assert(atype in atom2descr)
- sys.stdout.write(" set type @atom:" + atype + " charge " + str(atom2charge[atype]) +
- " # \"" + atom2descr[atype] + "\"\n")
-sys.stdout.write(" } #(end of atom partial charges)\n\n\n")
-
-
-sys.stdout.write(" write_once(\"Data Masses\") {\n")
-for atype in atom2mass:
- sys.stdout.write(" @atom:" + atype + " " + str(atom2mass[atype]) + "\n")
-sys.stdout.write(" } #(end of atom masses)\n\n\n")
-
-
-sys.stdout.write(" write_once(\"In Settings\") {\n")
-for atype in atom2vdw_e:
- assert(atype in atom2vdw_s)
- assert(atype in atom2ffid)
-
- sys.stdout.write(" pair_coeff " +
- "@atom:"+atype+"_b"+atom2ffid[atype]+"_a"+atom2ffid[atype]+"_d"+atom2ffid[atype]+"_i"+atom2ffid[atype]+" "
- "@atom:"+atype+"_b"+atom2ffid[atype]+"_a"+atom2ffid[atype]+"_d"+atom2ffid[atype]+"_i"+atom2ffid[atype]+" "+
- pair_style_name +
- " " + str(atom2vdw_e[atype]) +
- " " + str(atom2vdw_s[atype]) + "\n")
-sys.stdout.write(" } #(end of pair_coeffs)\n\n\n")
-
-
-
-sys.stdout.write(" # ------- force-field-IDs for bonded interaction lookup -------\n")
-sys.stdout.write(" # (First append the \"force-field-ID\" to the atom type name.\n")
-sys.stdout.write(" # Later use these expanded names for force-field lookup.)\n")
-for atype in atom2ffid:
- ffid = atype + "_ffid" + atom2ffid[atype]
- sys.stdout.write(" replace{ @atom:" + atype +
- " @atom:"+atype+"_b"+atom2ffid[atype]+"_a"+atom2ffid[atype]+"_d"+atom2ffid[atype]+"_i"+atom2ffid[atype]+" }\n")
-sys.stdout.write(" #(end of force-field-IDs)\n\n\n")
-
-
-
-sys.stdout.write(" write_once(\"In Settings\") {\n")
-for btype in bonds_by_type:
- ffid1 = btype[0] if btype[0] != "0" else "X"
- ffid2 = btype[1] if btype[1] != "0" else "X"
- (k,r0) = bonds_by_type[btype]
- sys.stdout.write(" bond_coeff @bond:" + ffid1 + "-" + ffid2 + " " +
- bond_style_name +" "+ str(k) + " " +str(r0) + "\n")
-sys.stdout.write(" } #(end of bond_coeffs)\n\n")
-
-sys.stdout.write(" write_once(\"Data Bonds By Type\") {\n")
-for btype in bonds_by_type:
- ffid1 = btype[0] if btype[0] != "0" else "X"
- ffid2 = btype[1] if btype[1] != "0" else "X"
- sys.stdout.write(" @bond:" + ffid1 + "-" + ffid2)
- ffid1 = "@atom:*_b"+btype[0]+"_a*_d*_i*" if btype[0] != "0" else "@atom:*"
- ffid2 = "@atom:*_b"+btype[1]+"_a*_d*_i*" if btype[1] != "0" else "@atom:*"
- sys.stdout.write(" " + ffid1 + " " + ffid2 + "\n")
-sys.stdout.write(" } #(end of bonds by type)\n\n\n")
-
-
-
-sys.stdout.write(" write_once(\"In Settings\") {\n")
-for atype in angles_by_type:
- ffid1 = atype[0] if atype[0] != "0" else "X"
- ffid2 = atype[1] if atype[1] != "0" else "X"
- ffid3 = atype[2] if atype[2] != "0" else "X"
- (k,angle0) = angles_by_type[atype]
- sys.stdout.write(" angle_coeff @angle:"+ffid1+"-"+ffid2+"-"+ffid3+" "+
- angle_style_name +" "+ str(k) + " " +str(angle0) + "\n")
-sys.stdout.write(" } #(end of angle_coeffs)\n\n")
-
-sys.stdout.write(" write_once(\"Data Angles By Type\") {\n")
-for atype in angles_by_type:
- ffid1 = atype[0] if atype[0] != "0" else "X"
- ffid2 = atype[1] if atype[1] != "0" else "X"
- ffid3 = atype[2] if atype[2] != "0" else "X"
- sys.stdout.write(" @angle:" + ffid1 + "-" + ffid2 + "-" + ffid3)
- ffid1 = "@atom:*_b*_a"+atype[0]+"_d*_i*" if atype[0] != "0" else "@atom:*"
- ffid2 = "@atom:*_b*_a"+atype[1]+"_d*_i*" if atype[1] != "0" else "@atom:*"
- ffid3 = "@atom:*_b*_a"+atype[2]+"_d*_i*" if atype[2] != "0" else "@atom:*"
- sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + "\n")
-sys.stdout.write(" } #(end of angles by type)\n\n\n")
-
-
-
-sys.stdout.write(" write_once(\"In Settings\") {\n")
-for dtype in dihedrals_by_type:
- ffid1 = dtype[0] if dtype[0] != "0" else "X"
- ffid2 = dtype[1] if dtype[1] != "0" else "X"
- ffid3 = dtype[2] if dtype[2] != "0" else "X"
- ffid4 = dtype[3] if dtype[3] != "0" else "X"
- sys.stdout.write(" dihedral_coeff @dihedral:"+
- ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " +
- dihedral_style_name +" ")
- if dihedral_style_name == 'fourier':
- # http://lammps.sandia.gov/doc/dihedral_fourier.html
- (K,n,d) = dihedrals_by_type[dtype]
- m = len(K)
- assert((m == len(n)) and (m == len(d)))
- sys.stdout.write(str(m))
- for i in range(0,m):
- sys.stdout.write(" " + str(K[i]) + " " + str(n[i]) + " " + str(d[i]))
- sys.stdout.write("\n")
- elif dihedral_style_name == 'opls':
- # http://lammps.sandia.gov/doc/dihedral_opls.html
- (K1,K2,K3,K4) = dihedrals_by_type[dtype]
- sys.stdout.write(str(K1) +" "+ str(K2) +" "+ str(K3) +" "+ str(K4)+"\n")
- else:
- assert(False)
-sys.stdout.write(" } #(end of dihedral_coeffs)\n\n")
-
-sys.stdout.write(" write_once(\"Data Dihedrals By Type\") {\n")
-for dtype in dihedrals_by_type:
- ffid1 = dtype[0] if dtype[0] != "0" else "X"
- ffid2 = dtype[1] if dtype[1] != "0" else "X"
- ffid3 = dtype[2] if dtype[2] != "0" else "X"
- ffid4 = dtype[3] if dtype[3] != "0" else "X"
- sys.stdout.write(" @dihedral:"+ffid1+"-"+ffid2+"-"+ffid3+"-"+ffid4)
- ffid1 = "@atom:*_b*_a*_d"+dtype[0]+"_i*" if dtype[0] != "0" else "@atom:*"
- ffid2 = "@atom:*_b*_a*_d"+dtype[1]+"_i*" if dtype[1] != "0" else "@atom:*"
- ffid3 = "@atom:*_b*_a*_d"+dtype[2]+"_i*" if dtype[2] != "0" else "@atom:*"
- ffid4 = "@atom:*_b*_a*_d"+dtype[3]+"_i*" if dtype[3] != "0" else "@atom:*"
- sys.stdout.write(" "+ffid1+" "+ffid2+" "+ffid3+" "+ffid4+"\n")
-sys.stdout.write(" } #(end of dihedrals by type)\n\n\n")
-
-
-
-sys.stdout.write(" write_once(\"In Settings\") {\n")
-for itype in impropers_by_type:
- ffid1 = itype[0] if itype[0] != "0" else "X"
- ffid2 = itype[1] if itype[1] != "0" else "X"
- ffid3 = itype[2] if itype[2] != "0" else "X"
- ffid4 = itype[3] if itype[3] != "0" else "X"
- (k,angle0) = impropers_by_type[itype]
- sys.stdout.write(" improper_coeff @improper:"+
- ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " +
- improper_style_name +" "+ str(k) +" "+ str(angle0) +"\n")
-sys.stdout.write(" } #(end of improper_coeffs)\n\n")
-
-sys.stdout.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n")
-for itype in impropers_by_type:
- ffid1 = itype[0] if itype[0] != "0" else "X"
- ffid2 = itype[1] if itype[1] != "0" else "X"
- ffid3 = itype[2] if itype[2] != "0" else "X"
- ffid4 = itype[3] if itype[3] != "0" else "X"
- sys.stdout.write(" @improper:"+ffid1+"-"+ffid2+"-"+ffid3+"-"+ffid4)
- ffid1 = "@atom:*_b*_a*_d*_i"+itype[0] if itype[0] != "0" else "@atom:*"
- ffid2 = "@atom:*_b*_a*_d*_i"+itype[1] if itype[1] != "0" else "@atom:*"
- ffid3 = "@atom:*_b*_a*_d*_i"+itype[2] if itype[2] != "0" else "@atom:*"
- ffid4 = "@atom:*_b*_a*_d*_i"+itype[3] if itype[3] != "0" else "@atom:*"
- sys.stdout.write(" "+ffid1+" "+ffid2+" "+ffid3+" "+ffid4+"\n")
-sys.stdout.write(" } #(end of impropers by type)\n\n\n")
-
-sys.stdout.write(" # -------- (descriptive comment) --------\n")
-sys.stdout.write(" # ---- biologically relevant atom types: ----\n # ")
-sys.stdout.write("\n # ".join(lines_biotype))
-sys.stdout.write("\n # ---------- (end of comment) ----------\n")
-sys.stdout.write("\n\n")
-
-sys.stdout.write(" write_once(\"In Init\") {\n")
-sys.stdout.write(" units real\n")
-sys.stdout.write(" atom_style full\n")
-sys.stdout.write(" bond_style hybrid "+bond_style_name+"\n")
-sys.stdout.write(" angle_style hybrid "+angle_style_name+"\n")
-sys.stdout.write(" dihedral_style hybrid "+dihedral_style_name+"\n")
-sys.stdout.write(" improper_style hybrid "+improper_style_name+"\n")
-sys.stdout.write(pair_style_command)
-sys.stdout.write(" pair_modify mix "+mixing_style+"\n")
-sys.stdout.write(" "+special_bonds_command+"\n")
-sys.stdout.write(kspace_style)
-sys.stdout.write(" } #end of init parameters\n\n")
-
-sys.stdout.write("} # "+ffname+"\n\n")
-
-
-
-
-#sys.stderr.write(" done.\n")
-
-if filename_in != "":
- file_in.close()
-
diff --git a/tools/moltemplate/src/ttree.py b/tools/moltemplate/src/ttree.py
deleted file mode 100644
index dda1880c1..000000000
--- a/tools/moltemplate/src/ttree.py
+++ /dev/null
@@ -1,5383 +0,0 @@
-#!/usr/bin/env python
-
-# Authors: Andrew Jewett (jewett.aij at g mail)
-# http://www.moltemplate.org
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2011, Regents of the University of California
-# All rights reserved.
-
-"""
- ttree.py is a simple program for recursively generating large redundant
- text files (such as data files read by molecular simulation programs)
- from small (non-redundant) text files (such as molecule definitions
- and force-field parameters).
-
- By default, the large number of unique template variables generated
- in the process are automatically substituted with integers
- (or other numeric counters, all of which can be overridden),
- rendered, and the rendered templates are written to a file.
-
-BasicUI This section of the code contains the user interface for ttree
- when run as a stand-alone program, as described above. (This
- section of code contains the "if __name__ == __main__:" code block.)
-
--- Data Types --
-
-StaticObj Static nodes are data structures used to store ttree class definitions.
- (Static nodes are useful for defining molecule types or
- namespaces in LAMMPS or other molecular simulation programs.)
- The nodes themselves are stored in a tree of nested class definitions.
- Static variables (such as "@atom:C") are also associated with
- StaticObjs.
-
-InstanceObj Instance nodes are created when a user creates one (or many)
- copies of a class, using the "new" command.
- These classes in turn may instantiate other classes.
- (Example: A user may manually instantiate several copies of a
- molecule, such as a protein, however each of those
- molecules may contain molecular subunits, such as
- amino acids, which are automatically instantiated.)
- Instance variables (such as "$atom:CA") are also associated with
- InstanceObjs.
-
-"""
-
-import sys
-from collections import defaultdict
-import operator
-import random
-#import gc
-
-try:
- unicode
-except NameError:
- # Python 3
- basestring = unicode = str
-
-
-# -- ttree_lex.py --
-# TtreeShlex is a backwards-compatible version of python's standard shlex module
-# It has the additional member: "self.wordterminators", which overrides
-# the "self.wordchars" member. This enables better handling of unicode
-# characters by allowing a much larger variety of characters to appear
-# in words or tokens parsed by TtreeShlex. Otherwise it is identical to shlex.
-from ttree_lex import *
-
-
-if sys.version < '2.6':
- raise InputError('Error: Using python '+sys.version+'\n'
- ' Alas, you must upgrade to a newer version of python (2.7 or later).')
-elif sys.version < '2.7':
- sys.stderr.write('--------------------------------------------------------\n'
- '----------------- WARNING: OLD PYTHON VERSION ----------\n'
- ' This program is untested on your python version ('+sys.version+').\n'
- ' PLEASE LET ME KNOW IF THIS PROGRAM CRASHES (and upgrade python).\n'
- ' -Andrew 2016-9-21\n'
- '--------------------------------------------------------\n'
- '--------------------------------------------------------\n')
- from ordereddict import OrderedDict
-else:
- from collections import OrderedDict
-
-
-if sys.version > '3':
- import io
-else:
- import cStringIO
-
-
-# We keep track of the program name and version.
-# (This is only used for generating error messages.)
-#g_filename = 'ttree.py'
-g_filename = __file__.split('/')[-1]
-g_module_name = g_filename
-if g_filename.rfind('.py') != -1:
- g_module_name = g_filename[:g_filename.rfind('.py')]
-g_date_str = '2016-9-21'
-g_version_str = '0.84'
-
-
-
-
-
-
-
-class ClassReference(object):
- """ Every class defined by the user (stored in an StaticObj data structure)
- may contain references to other classes (ie. other StaticObjs).
- (Note: All of these StaticObjs are stored in the same tree, the
- global static tree.)
- Examples:
- Whenever an instance of a class is created, this may automatically spawn
- the creation of additional classes (which are instantiated because a 'new'
- command appeared within the first class's definition). These are stored in
- the "StaticObj.instance_commands[i].class_ref" attribute.
- Similarly, each class (StaticObj) can optionally inherit some of its
- traits (consisting of write() and new commands) from one or more
- "class_parents" (also StaticObjs). A list of these parents is stored in the
- "StaticObj.class_parents" attribute. In both cases (self.instance_commands
- or self.class_parents) we need to store a pointer to the StaticObj(s)
- corresponding to the instance-childen or class-parents.
- (This stored in self.statobj).
- However, for the purposes of debugging and interactivity, it is also
- convenient to permanently keep track of the string that the user used to
- specify the name/location of that class/StaticObj
- (stored in self.statobj_str), in addition to the location
- in the file where that string occurs (stored in self.srcloc)."""
-
- __slots__=["statobj_str","srcloc","statobj"]
-
- def __init__(self,
- statobj_str=None,
- srcloc=None,
- statobj=None):
- self.statobj_str = statobj_str
- if srcloc is None:
- self.srcloc = OSrcLoc('', -1)
- else:
- self.srcloc = srcloc
- self.statobj = statobj
-
- #def __repr__(self):
- # return repr((self.statobj_str, self.srcloc))
-
-
-
-# "Command"s are tasks to carry out.
-# (...either immediately, or later during instantiation)
-# Commands are used to write to files, create new instances, delete instances,
-# or custom commands to modify an instance of a class.
-# (For example "instance = new Class.move(1,0,0).rot(45,0,0,1)"
-# The ".move(1,0,0)" and ".rot(45,0,0,1)" commands are "stackable" and
-# have similar syntax to member functions in C++, JAVA, Python.)
-
-class Command(object):
- __slots__=["srcloc"]
-
- def __init__(self, srcloc=None):
- self.srcloc = srcloc
-
- # COMMENTING OUT: "COUNT" AND "ORDER" ARE NO LONGER NEEDED
-
- #count = 0
- #def __init__(self, srcloc=None):
- # self.srcloc = srcloc
- # # The "order" member is a counter that keeps track of the order
- # # in which the Command data types are created (issued by the user).
- # Command.count += 1
- # self.order = Command.count
- #def __lt__(self, x):
- # return self.order < x.order
-
-
-
-class WriteFileCommand(Command):
- """ WriteFileCommand
-
- filename This is the name of the file that will be written to
- when the command is executed.
- tmpl_list This is the contents of what will be written to the file.
- Text strings are often simple strings, however more
- generally, they can be strings which include other variables
- (ie templates). In general, templates are lists of alternating
- TextBlocks and VarRefs, (with additional tags and data to
- identify where they occur in in the original user's files).
-
- """
- __slots__=["filename", "tmpl_list"]
-
- def __init__(self,
- filename = None,
- tmpl_list = None,
- srcloc = None):
- self.filename = filename
- if tmpl_list is None:
- self.tmpl_list = []
- else:
- Command.__init__(self, srcloc)
- self.tmpl_list = tmpl_list
- def __str__(self):
- if self.filename:
- return 'WriteFileCommand(\"'+self.filename+'\")'
- else:
- return 'WriteFileCommand(NULL)'
- def __copy__(self):
- tmpl_list = []
- CopyTmplList(self.tmpl_list, tmpl_list) #CHECK:IS_MEMORY_WASTED_HERE?
- return WriteFileCommand(self.filename, tmpl_list, self.srcloc)
-
-
-class InstantiateCommand(Command):
- """ InstantiateCommand is a simple tuple-like datatype used to
- store pairs of names (strings, stored in self.name),
- and ClassReferences (see above, stored in self.class_ref).n
- The "suffix" argument is an optional string which may contain
- additional instructions how to instantiate the object.
-
- """
-
- __slots__=["name",
- "class_ref",
- "instobj"]
-
- def __init__(self,
- name = None,
- class_ref = None,
- srcloc = None,
- instobj = None):
- Command.__init__(self, srcloc)
- self.name = name
- #if class_ref is None:
- # self.class_ref = ClassReference()
- #else:
- self.class_ref = class_ref
- self.instobj = instobj
-
- def __str__(self):
- return 'InstantiateCommand('+self.name+')'
-
- def __copy__(self):
- return InstantiateCommand(self.name,
- self.class_ref,
- self.srcloc,
- self.instobj)
-
-
-class DeleteCommand(Command):
- __slots__=[]
- def __init__(self,
- srcloc = None):
- Command.__init__(self, srcloc)
-
- def __str__(self):
- return 'DeleteCommand()'
-
- def __copy__(self):
- return DeleteCommand(self.srcloc)
-
-
-
-
-class StackableCommand(Command):
- """ StackableCommand is a class for storing commands
- that effect the environment of the object being created.
- The combined effect of these commands can be thought of as a "stack"
- Commands can be pushed on the stack, or popped off
-
- The actual commands themselves are represented by the "contents" member
- which is usually a text string.
- ttree.py does not attempt to understand the content of these commands.
- That job is left up to the __main___ module. (IE. whatever script that
- happens to be importing ttree.py. If there is no script, and
- ttree.py IS the main module, then it simply ignores these commands.)
-
- """
-
- __slots__=["context_node"]
-
- def __init__(self,
- srcloc,
- context_node=None):
- Command.__init__(self, srcloc)
- self.context_node = context_node # if multiple stacks are present, then use "context_node"
- # as a key to identify which stack you want
- # the command to modify
-
-class PushCommand(StackableCommand):
-
- __slots__=["contents"]
-
- def __init__(self,
- contents,
- srcloc,
- context_node=None):
- StackableCommand.__init__(self, srcloc, context_node)
- self.contents = contents
-
- def __copy__(self):
- return PushCommand(self.contents, self.srcloc, self.context_node)
-
- def __str__(self):
- return 'PushCommand('+str(self.contents)+')'
-
-class PushRightCommand(PushCommand):
- __slots__=[]
- def __init__(self,
- contents,
- srcloc,
- context_node=None):
- PushCommand.__init__(self, contents, srcloc, context_node)
-
- def __copy__(self):
- return PushRightCommand(self.contents, self.srcloc, self.context_node)
-
- def __str__(self):
- return 'PushRightCommand('+str(self.contents)+')'
-
-class PushLeftCommand(PushCommand):
- __slots__=[]
- def __init__(self,
- contents,
- srcloc,
- context_node=None):
- PushCommand.__init__(self, contents, srcloc, context_node)
-
- def __copy__(self):
- return PushLeftCommand(self.contents, self.srcloc, self.context_node)
-
- def __str__(self):
- return 'PushLeftCommand('+str(self.contents)+')'
-
-class PopCommand(StackableCommand):
- __slots__=["partner"]
- def __init__(self,
- partner,
- srcloc,
- context_node=None):
- StackableCommand.__init__(self, srcloc, context_node)
- self.partner = partner
-
- def __copy__(self):
- return PopCommand(self.partner, self.srcloc, self.context_node)
-
- def __str__(self):
- return 'PopCommand('+str(self.partner.contents)+')'
-
-class PopRightCommand(PopCommand):
- __slots__=[]
- def __init__(self,
- partner,
- srcloc,
- context_node=None):
- PopCommand.__init__(self, partner, srcloc, context_node)
- assert((partner is None) or isinstance(partner, PushRightCommand))
-
- def __copy__(self):
- return PopRightCommand(self.partner, self.srcloc, self.context_node)
-
- def __str__(self):
- return 'PopRightCommand('+str(self.partner.contents)+')'
-
-class PopLeftCommand(PopCommand):
- __slots__=[]
- def __init__(self,
- partner,
- srcloc,
- context_node=None):
- PopCommand.__init__(self, partner, srcloc, context_node)
- assert((partner is None) or isinstance(partner, PushLeftCommand))
-
- def __copy__(self):
- return PopLeftCommand(self.partner, self.srcloc, self.context_node)
-
- def __str__(self):
- return 'PopLeftCommand('+str(self.partner.contents)+')'
-
-
-
-
-
-# The ScopeCommand, ScopeBegin, and ScopeEnd commands are useful to designate
-# which commands belong to a particular class definition (or class instance).
-# (This is useful later on, when a linear list of commands has been created.)
-# They are simply markers an do not do anything. These classes can be ignored.
-class ScopeCommand(Command):
- __slots__=["node"]
-
- def __init__(self,
- node,
- srcloc):
- Command.__init__(self, srcloc)
- self.node = node
- #self.srcloc = srcloc
-
- def __copy__(self):
- return ScopeCommand(self.node, self.srcloc)
-
- def __str__(self):
- if self.node:
- return 'ScopeCommand('+self.node.name+')'
- else:
- return 'ScopeCommand(None)'
-
-class ScopeBegin(ScopeCommand):
- __slots__=[]
- def __init__(self, node, srcloc):
- ScopeCommand.__init__(self, node, srcloc)
- def __copy__(self):
- return ScopeBegin(self.node, self.srcloc)
- def __str__(self):
- if self.node:
- return 'ScopeBegin('+NodeToStr(self.node)+')'
- else:
- return 'ScopeBegin(None)'
-
-class ScopeEnd(ScopeCommand):
- __slots__=[]
- def __init__(self, node, srcloc):
- ScopeCommand.__init__(self, node, srcloc)
- def __copy__(self):
- return ScopeEnd(self.node, self.srcloc)
- def __str__(self):
- if self.node:
- return 'ScopeEnd('+NodeToStr(self.node)+')'
- else:
- return 'ScopeEnd(None)'
-
-
-
-# COMMENTING OUT: NOT NEEDED AT THE MOMENT
-#class VarAssignCommand(Command):
-# """ VarAssignCommand
-#
-# This class is used whenever the user makes an explicit request to assign
-# a variable to a value (values are text strings).
-#
-# var_ref The variable name (tecnically speaking, I call this
-# a variable descriptor string and it includes at least one of
-# the following: the name of a leaf node, a category node name,
-# and category name)
-# the location in the file where variable appears, and (eventually
-# after subsequent lookup), references to the leaf_node, cat_node,
-# "Category", and "VarBinding" data structures associated with it.
-# text_tmpl Text strings are often simple strings, however more
-# generally, they can be strings which include other variables
-# (ie templates). In general, templates are lists of alternating
-# TextBlocks and VarRefs, (with additional tags and data to
-# identify where they occur in in the original user's files).
-#
-# """
-# __slots__=["var_ref","text_tmpl"]
-#
-# def __init__(self,
-# #command_name = '=', <-- ?!?
-# var_ref = None,
-# text_tmpl=None):
-# Command.__init__(self, srcloc)
-# self.var_ref = var_ref
-# self.text_tmpl = text_tmpl
-
-
-
-class ModCommand(object):
- __slots__=["command","multi_descr_str"]
- def __init__(self,
- command,
- multi_descr_str):
- self.command = command
- self.multi_descr_str = multi_descr_str
-
- def __str__(self):
- return 'ModCommand('+str(self.command)+')'
-
- def __copy__(self):
- return ModCommand(self.command.__copy__(), self.multi_descr_str)
-
-
-
-
-def CopyTmplList(source_tmpl_list, dest_cpy):
- for entry in source_tmpl_list:
- if isinstance(entry, TextBlock):
- dest_cpy.append(entry) # Then make a shallow copy
- # (pointer assignment) to the text
- # block (Text blocks do not change
- # during instantiation.)
- elif isinstance(entry, VarRef):
- assert(len(entry.prefix)>0)
- if entry.prefix[0] == '@': # '@' vars refer to static data
- dest_cpy.append(entry) # Then make a shallow copy
- # pointer assignment) to the static
- # variable. (Static variables do
- # not change during instantiation.)
-
- elif entry.prefix[0] == '$': # new '$' vars are created
- # during every instantiation.
-
- # var_refs do change when you instantiate them. So
- # create a new VarRef object, and copy the attributes.
- var_ref = VarRef(entry.prefix,
- entry.descr_str,
- entry.suffix,
- entry.srcloc)
- # Note: for instance variables ('$' vars)
- # "entry.nptr" should not contain
- # any data yet, so we just ignore it.
- # I assert this below:
- assert((entry.nptr.cat_node is None) and
- (entry.nptr.leaf_node is None))
-
- dest_cpy.append(var_ref)
- else:
- assert(False) # prefix[0] should be either '@' or '$'
- else:
- assert(False) # type(entry) should be either TextBlock or VarRef
-
-
-
-
-
-
-
-def RecursiveJoin(tokens_expr, delimiter = ''):
- """ RecursiveJoin() converts a tree-like list/tuple of tokens, for example:
- ['a ', ('tree', '-', ['like', 'container']), [[' '], 'of'], ' strings']
- to an ordinary string, eg:
- 'a tree-like container of strings'
- This behavees similarly to "reduce(lambda a, b: a+b, tokens)",
- except that it works with arbitrarily nested lists/tuples."""
- text = ''
- if isinstance(tokens_expr, basestring):
- return tokens_expr
- else:
- text_lstr = []
- for i in range(0, len(tokens_expr)):
- text.append( TokensToStr(tokens_expr[i]) )
- return ''.join(text_lstr, delimiter)
-
-
-
-
-
-
-#----------------------------------------------------------
-#----------------------------------------------------------
-# The following code is specific to ttree.
-#
-# (Up until this point, we have only defined
-# a few simple general text parsing routines.)
-#----------------------------------------------------------
-#----------------------------------------------------------
-
-
-
-def PtknsToStr(path_tokens):
- """
- There are three ways to store paths:
- As a single string: '/Protein/Phe/Ca' <- the format entered by the user
- As a list of tokens ['Protein', 'Phe', 'Ca'] <- split into tokens
- As a list of nodes in a tree (pointers to nodes in a tree hierarchy)
- This function converts between the first two formats.
- """
- text = ''
- if len(path_tokens) > 0:
- text = path_tokens[0]
- for i in range(1, len(path_tokens)):
- text += '/' + path_tokens[i]
- else:
- text = ''
- return text
-
-
-
-def StrToPtkns(path_string):
- """ The inverse of PtknsToStr(), this function splits a string like
- '/usr/local/../bin/awk' into ['usr','local','..','bin','awk'].
- For illustrative purposes only. Use text.split('/') directly instead."""
- return orig_text.split('/')
-
-
-
-def FindChild(name, node, dbg_loc):
- """ FindChild looks over the list of node.children to find a child
- which matches the name given in the first argument.
- If it is not found, it returns None.
- Note: I have not yet specified what kind of nodes FindChild() operates
- on. Both StaticObjs and InstanceObjs have self.children and self.parent.
- However only StaticObjs have "self.class_parents".
- ("class_parents" are "parents" in the object-oriented sense.)
- If "node" (2nd argument) happens t be an StaticObj, this means it also
- We must search over the children of these class_parents as well.
-
- Terminology used here differs from Object Oriented Programming
-
- Children in node.children are not children in the object-oriented
- programming sense. However, in OOP, "children" are objects that share all
- of the traits of their ancestors (and may have additionl traits as well).
- I have implemented OOP style children and parents, but this informtion
- is stored in "node.class_parents", instead of "node.parents".
- For comparison, instantiated nodes (InstanceObjs) are different. Altough
- instantiated classes (InstanceObjs) have access to the attributes of the
- class_parents of the StaticObjs that define them, they do not remember the
- ownership of that data. (It just gets merged with their own member data,
- including their .children.)
- Hence we must treat StaticObjs carefully because their are two ways we can
- access child data. We should loop over both of them. We do that below:
- """
-
- child = node.children.get(name)
-
- if child:
- return child
-
- if isinstance(node, StaticObj):
-
- # The object-oriented inheritance stuff appears here.
- # If you don't care about OOP or inheritance,
- # then comment out the loop that follows:
-
- # Search recursively over the "children" (ie attributes or members)
- # belonging to any OOP ancestors of this node.
- for class_parent in node.class_parents:
- child = FindChild(name, class_parent, dbg_loc)
- if child != None:
- return child
- for namespace_node in node.namespaces:
- child = FindChild(name, namespace_node, dbg_loc)
- if child != None:
- return child
- else:
- assert(isinstance(node, InstanceObjBasic))
-
- # Otherwise, a child name match was not found
- return None
-
-
-
-
-
-def FollowPath(path_tokens, starting_node, dbg_loc):
- """ FollowPath() returns the "last_node", a node whose position in the
- tree is indicated by a list of path_tokens, describing the names
- of nodes connecting "starting_node" to "last_node".
- If it one of the strings in the list of path_tokens turns out
- not to match then names of classes in the tree, then this function
- returns the last_node that did match before the error occurred,
- as well as an integer which stores the number of tokens in
- the path_tokens list which were successfully processed.
- In other words, the list of node naes is not a full path, but the
- relative path that takes you from one node (not necessarily the root)
- to another. Return Value:
- Ideally, each node in the list should be a parent or a child of the
- previous node. (See comment for PathTokensToStr(), for more details.)
- This function returns the number of path_tokens successfully
- parsed. Under normal termination, this is len(path_tokens).
- If the path can not be followed (because at some point, a child
- or parent does not exist), then this function returns a number
- smaller than len(path_tokens).
- We let the caller handle undefined paths. """
-
- #print(' FollowPath() invoked on: ', path_tokens)
-
- if len(path_tokens) == 0:
- return 0, starting_node
-
- node = starting_node
- # Is this path a relative path, or a full path?
- # If the path-string began with '/', then it's a full path. This means
- # that after processing by split('/'), the first token will be ''
- # Example: path_tokens='/Prot/Alanine'.split('/')
- # --> path_tokens[0] == ''
- if path_tokens[0] == '':
- # In that case, then take us to the root node:
- while node.parent != None:
- node = node.parent
- #sys.stdout.write('FollowPath(): Retreating to node \"'+node.name+'\"\n')
- i0 = 1 # <- We've just processed the first token. Skip over it later.
- else:
- i0 = 0
-
-
- i = i0
- while i < len(path_tokens):
-
- if path_tokens[i] == '..':
- if node.parent is None:
- return i, node # <-return the index into the token list
- # Caller will know that something went awry
- # if the return value is not equal to the
- # length of the token list
- else:
- node = node.parent
- i += 1
-
- elif path_tokens[i] == '...':
-
- node_before_ellipsis = node
- if i == len(path_tokens)-1:
- return i, node_before_ellipsis
-
- search_target = path_tokens[i+1]
- # Now search over the "children" of this node
- # for one who's name matches path_tokens[i].
- # If not found, then move up to the parent node's children.
- # (This is not an exhaustive tree search. Only the nodes which
- # are immediate children of this node's parents are searched.)
- while node != None:
- child = FindChild(search_target, node, dbg_loc)
- if child is None:
- node = node.parent
- else:
- node = child
- break
-
- if node is None:
- # Caller will know that something went awry if the return
- # value is not equal to the length of the token list.
- return i, node_before_ellipsis
-
- i += 2
-
- elif path_tokens[i] in ('','.'): # <-Note we ignore empty tokens from now on.
- # (Same convention is used in specifying a
- # directory in a filesystem, eg. using /usr/local
- # or /usr//local or /usr/./local. These are all equivalent.)
- i += 1
-
- else:
-
- # Now search over the "children" of this
- # node for one who's name matches path_tokens[i].
- child = FindChild(path_tokens[i], node, dbg_loc)
-
- if child is None:
- # In that case, return with the node_list incomplete.
- # Let the caller check to see if something went wrong.
- return i, node # <-return the index into the token list (i)
- # Caller will know that something went awry
- # if the return value is not equal to the
- # length of the token list
- else:
- node = child
-
- i += 1
-
- if node.IsDeleted():
- #sys.stderr.write('(debug_msg: encountered deleted node: \"'+node.name+'\")\n')
- break
-
- return len(path_tokens), node
-
-
-
-
-
-def PtknsToNode(path_tokens, starting_node, dbg_loc):
- """ PtknsToNode() is identical to def FollowPath() except
- that it raises syntax-error exceptions if the path is undefined."""
-
- i_last_ptkn, last_node = FollowPath(path_tokens, starting_node, dbg_loc)
-
- if i_last_ptkn < len(path_tokens):
- #assert(isinstance(last_node,StaticObj)) <--why did I assert this? seems wrong
-
- if (last_node.parent is None) and (path_tokens[i_last_ptkn] == '..'):
- #In that case, we tried to back out beyond the root of the tree.
- raise InputError('Error('+g_module_name+'.PtknsToNode()):\n'
- ' Invalid variable/class name:\n'
- ' \"'+PtknsToStr(path_tokens)+'\" located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
- ' There are too many \"..\" tokens in the path string.')
-
- elif path_tokens[i_last_ptkn] == '...':
- if i_last_ptkn+1 == len(path_tokens):
- raise InputError('Error('+g_module_name+'.PtknsToNode()):\n'
- ' Error in '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
- ' Expected name following \"...\"\n')
- else:
- search_target = path_tokens[i_last_ptkn+1]
- #In that case, we were unable to find the node referenced by "..."
- raise InputError('Error('+g_module_name+'.PtknsToNode()):\n'
- ' Class or variable \"'+search_target+'\" not found\n'
- ' in this context: \"'+PtknsToStr(path_tokens)+'\"\n'
- ' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno))
-
- else:
- #Then the reason is: The string in path_tokens[i_last_ptkn]
- #was supposed to be a child of last_node but a child
- #of that name was not found.
- err_msg = 'Error('+g_module_name+'.PtknsToNode()):\n'+\
- ' Undefined variable/class name:\n'+\
- ' \"'+PtknsToStr(path_tokens)+'\",\n'+\
- ' This occured near or before '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'+\
- ' (Specifically \"'+path_tokens[i_last_ptkn]+\
- '\" is not a subordinate of \"'+MaxLenStr(last_node.name,'/')+'\".)\n'+\
- ' This may be due to a typo located here or earlier.\n'+\
- ' It may also occur if you deleted the object earlier. (Referring to a\n'+\
- ' deleted object is only forgiven when using [0-9] or [0:10] notation.)\n'+\
- ' If this object refers to an array you must use brackets []\n'+\
- ' to explicitly specify the element(s) you want from that array.\n'+\
- ' (To select multiple elements, you can use [*] or [0-9] or [0:10].)\n'
-
- if (path_tokens[i_last_ptkn] in NodeToPtkns(last_node)):
- err_msg += '\nIn this case:\n'+\
- ' It seems like you may have omitted a } character somewhere before:\n'+\
- ' '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)
- raise InputError(err_msg)
- assert(False) # One of the two conditions above should be true.
-
- return last_node
-
-
-
-
-
-def StrToNode(obj_name, starting_node, dbg_loc):
- path_tokens = obj_name.split('/')
- return PtknsToNode(path_tokens, starting_node, dbg_loc)
-
-
-
-def NodeListToPtkns(node_list, dbg_loc=None):
- assert(len(node_list) > 0) #The path must contain at least the starting node
- path_tokens = [node_list[0].name]
- for i in range(1, len(node_list)):
- if node_list[i] == node_list[i-1].parent:
- path_tokens.append('..')
- else:
- path_tokens.append(node_list[i].name)
- # Now check to make sure the user supplied consistent information:
- if (node_list[i] not in node_list[i-1].children.values()):
- raise InputError('Error('+g_module_name+'.NodeListToPtkns()):\n'
- ' Undefined variable/class name:\n'
- ' \"'+PtknsToStr(path_tokens)+'\" located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
- ' (\"'+path_tokens[i]+'\" is not subordinate to \"'+MaxLenStr(node_list[i-1].name,'/')+'\")\n'
- ' This could be an internal error.')
- return path_tokens
-
-
-
-def NodeListToStr(node_list, dbg_loc=None):
- assert(len(node_list) > 0) #The path must contain at least the starting node
- path_str = node_list[0].name
- for i in range(1, len(node_list)):
- if node_list[i] == node_list[i-1].parent:
- path_str += '/..'
- else:
- path_str += '/' + node_list[i].name
- # Now check to make sure the user supplied consistent information:
- if (node_list[i] not in node_list[i-1].children.values()):
- err_msg = 'Error('+g_module_name+'.NodeListToStr()):\n'+\
- ' Invalid variable/class name:\n' +\
- ' \"'+PtknsToStr(path_tokens)+'\"'
- if dbg_loc != None:
- err_msg += ' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)
- err_msg += '\n' +\
- ' (\"'+node_list[i].name+'\" is not a subordinate of \"'+MaxLenStr(node_list[i-1].name,'/')+'\")\n'+\
- ' This could be an internal error.'
- raise InputError(err_msg)
- return path_str
-
-
-
-def NodeToPtkns(node):
- ptkns = []
- nd = node
- while nd != None:
- ptkns.append(nd.name)
- nd = nd.parent
- ptkns.reverse()
- return ptkns
-
-
-
-def NodeToStr(node):
- ptkns = NodeToPtkns(node)
- assert(len(ptkns) > 0)
- if node.parent is None:
- assert(node.name == '')
- return '/'
- path_str = ptkns[0]
- i = 1
- while i < len(ptkns):
- path_str += '/'+ptkns[i]
- i += 1
- return path_str
-
-
-
-def CatLeafNodesToTkns(cat_name, cat_node, leaf_node, dbg_loc):
- assert((cat_node != None) and (leaf_node != None))
- assert((cat_name != None) and (cat_name != ''))
-
- # Determine the path of the cat node
- cat_node_ptkns = NodeToPtkns(cat_node)
- cat_node_ptkns.append(cat_name+':')
-
- # Determine the path of the leaf node (which should inherit from cat)
- deleted = False
- leaf_node_ptkns = []
- if cat_node != leaf_node:
- node = leaf_node
- while node.parent != None:
- if node.IsDeleted():
- deleted = True
- leaf_node_ptkns.append('DELETED_'+node.name)
- break
- leaf_node_ptkns.append(node.name)
- if node.parent == cat_node:
- break
- node = node.parent
- leaf_node_ptkns.reverse()
-
- if not deleted:
- # Check that leaf inherits from cat. If not, print error.
- if ((node.parent != cat_node) and (node != cat_node)):
- err_msg = 'Error('+g_module_name+'.CatLeafNodesToPtkns()):\n'+\
- ' Invalid variable (category:leaf) pair\n'
- if dbg_loc != None:
- cat_node_str = NodeToStr(cat_node)
- leaf_node_str = NodeToStr(leaf_node)
- err_msg += ' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'+\
- ' (\"'+leaf_node.name+'\" is not in the scope of \"'+cat_node_str+'/'+cat_name+':\")\n'+\
- ' This will happen if you used the \"category\" command to manually\n'+\
- ' create a category/counter which is not defined globally.\n'+\
- '\n'+\
- ' Note: Using the analogy of a unix style file system, \n'+\
- ' the problem is that \"'+leaf_node_str+'\"\n'+\
- ' is not a subdirectory of \"'+cat_node_str+'\".\n'+\
- '\n'+\
- ' Note: This often occurs when \".../\" is used. In that case, you may\n'+\
- ' be able to avoid this error by referring to your variable explicitly\n'+\
- ' by using chains of \"../\" tokens in the path instead of \".../\".\n'
- #' Make sure that your variable you are using is defined in \n'+\
- #' an environment (currently \"'+leaf_node_str+'\")\n'+\
- #' which lies WITHIN the environment where the category was defined.\n'+\
- #' (currently \"'+cat_node_str+'\").\n'
- raise InputError(err_msg)
- else:
- err_msg = 'Warning: Strange variable path'
- if dbg_loc != None:
- err_msg += ' near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)
- err_msg += '\n' +\
- ' The category and leaf nodes for variable \"'+cat_name+':'+leaf_node.name+'\" are the same.\n'+\
- ' Check to see that this variable is behaving the way you intended.\n'+\
- ' (It\'s possible this could be an internal error in the program.)\n'
- sys.stderr.write(err_msg)
-
- # Merge the list of strings together into a single string:
- return cat_node_ptkns + leaf_node_ptkns
-
-
-
-def CanonicalCatName(cat_name, cat_node, dbg_loc=None):
- # Determine the path of the cat node
- tkns = NodeToPtkns(cat_node)
- tkns.append(cat_name)
- #full_cat_name = tkns[0]
- #for i in range(1,len(tkns)):
- # full_cat_name += '/'+tkns[i]
- # better way:
- return '/'.join(tkns)
-
-
-
-def CanonicalDescrStr(cat_name, cat_node, leaf_node, dbg_loc=None):
- tkns = CatLeafNodesToTkns(cat_name, cat_node, leaf_node, dbg_loc)
- descr_str = tkns[0]
- for i in range(1, len(tkns)):
- if (len(descr_str)>0) and (descr_str[-1] == ':'):
- descr_str += tkns[i]
- else:
- descr_str += '/'+tkns[i]
- return descr_str
-
-
-
-def CollapsePath(path_tokens):
- """
- CollapsePath() takes a list of Strings argument representing a
- directory-like path string
- (for example '/SUB1A/Sub2A/../Sub2B/sub3b/../sub3c/entry'),
- and replaces it with a version which should contain no '..' patterns.
- (In the example above, it returns /SUB1A/Sub2B/sub3c/entry')
- """
- new_ptkns = []
- ndelete = 0
- i = len(path_tokens)-1
- while i >= 0:
- if path_tokens[i] == '..':
- ndelete += 1
- else:
- if (ndelete > 0) and (path_tokens[i] != ''):
- # Note: "path_tokens[i] != '')" means "/a/b//c" <-> "/a/b/c"
- ndelete -= 1
- else:
- if len(path_tokens[i]) > 0:
- new_ptkns.append(path_tokens[i])
- i -= 1
- new_ptkns.reverse()
-
- if ndelete > 0:
- return ndelete # <-- useful to let caller know an error ocurred
-
- return new_ptkns
-
-
-
-
-
-def FindCatNode(category_name, current_node, srcloc):
- """ Search upwards (toward the ancester nodes), looking for a node
- containing a category matching category_name (first argument).
- Useful when the user specifies a category name, but neglects to
- specify which node it was defined in.
- Note: there is no gaurantee that the category node returned by this function
- contains an entry in it's "categories" list corresponding to this
- category name. You must check for this condition and handle it."""
- cat_node = None
- node = current_node
- while True:
- if category_name in node.categories:
- cat_node = node
- break
- elif node.parent != None:
- node = node.parent
- else:
- # node.parent is None, ... we're done
- break
-
- if cat_node is None:
- assert(node.parent is None)
- #sys.stderr.write('Warning near ' +
- # ErrorLeader(srcloc.infile,
- # srcloc.lineno)+'\n'+
- # ' no category named \"'+category_name+'\" found.\n'+
- # ' Creating a new global category: /'+
- # category_name+':\n')
- cat_node = node # the global node
-
- assert(cat_node != None)
-
- return cat_node
-
-
-def RemoveNullTokens(in_ptkns):
- """This function just gets rid of useless empty tokens in the path ('', '.')
- (However if '' appears at the beginning of a path, we leave it alone.)
-
- """
- out_ptkns = []
- for i in range(0,len(in_ptkns)):
- if ((in_ptkns[i] != '.') and
- ((in_ptkns[i] != '') or (i==0))):
- out_ptkns.append(in_ptkns[i])
- # (I'm sure there are ways to write this in python
- # using fewer lines of code. Sigh.)
- return out_ptkns
-
-
-
-def DescrToCatLeafPtkns(descr_str, dbg_loc):
- """
- Review: Variables in this program have three parts:
- 1) A variable category name (designating the type of variable).
- 2) A variable category path, which consists of a node which is an ancestor
- of the variable leaf (1) in the tree
- 3) A variable name ("leaf"), which refers to a node in the tree
- (either a static type tree or instance tree)
-
- DescrToCatLeafPtkns() takes a string describing a variable,
- as it appears in a template (ie, a write() command, once it has been
- stripped of it's '$' or '@' prefix, and surrounding {} brackets)
- ...and divides it into strings which specify the location of that leaf in
- a static or instance tree, in addition to the name and location of the
- category node. Descriptor examples for atoms in water:
- "AtomType:/Water/O", There are only 2 --types-- of atoms in
- "AtomType:/Water/H", a water molecule. We identify them this way.
- "AtomID:O" However each water molecule has 3 atoms, and we
- "AtomID:H1" can give each atom in each water molecule a unique
- "AtomID:H2" AtomID number. "AtomID:H2" is the id number of the
- second hydrogen atom in the current water molecule.
-
- ---- Output: This function returns a 3-tuple: ----
-
- leaf_ptkns The name of the variable's leaf node, as well as the list of
- tokens denoting the path (named list of nodes) which lead to it.
- cat_name The name of the variable category (no path information)
- cat_ptkns A --suggestion-- for where to find the node containing the
- category mentioned in "cat_name". Same format as leaf_ptkns.
-
- Examples:
- "AtomType:/Water/O" cat_name='AtomType', cat_path=[], leaf_ptkns=['','Water','O']
- "AtomType:/Water/H" cat_name='AtomType', cat_path=[], leaf_ptkns=['','Water','H']
-
- "AtomID:O" cat_name='AtomID', cat_path=[], leaf_ptkns=['O']
- "AtomID:H1" cat_name='AtomID', cat_path=[], leaf_ptkns=['H1']
- "AtomID:H2" cat_name='AtomID', cat_path=[], leaf_ptkns=['H2']
- "mol:/" cat_name='mol', cat_path=[], leaf_ptkns=['']
- "mol:" cat_name='mol', cat_path=[], leaf_ptkns=[]
- "mol:../" cat_name='mol', cat_path=[], leaf_ptkns=['..']
- "../mol" cat_name='mol', cat_path=[], leaf_ptkns=['..']
- "$/peptide[3]/ResID:res[25]" cat_name='ResID', cat_path=['', 'peptide[3]'], leaf_ptkns=['res[25]']
-
- """
-
- split_colon = descr_str.split(':')
- if len(split_colon) > 2:
- raise InputError('Error('+g_module_name+'.DescrToCatLeafPtkns())\n'
- ' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n\n'
- ' Bad variable descriptor: \"'+descr_str+'\"\n'+
- ' There can be at most one \':\' character in a variable descriptor.\n')
- # ---- Are we using colon syntax (example '$atom:H1')?
- elif len(split_colon) == 2:
- # The category name = text after the last '/' (if present)and before ':'
- cat_ptkns = split_colon[0].split('/')
- cat_name = cat_ptkns[-1]
- # The text before that is the suggested (category) path
- cat_ptkns = cat_ptkns[:-1]
- # if len(cat_ptkns) == 0:
- # cat_ptkns.append('.')
-
- # The remaining text is the path leading to the leaf node.
- if split_colon[1] != '':
- leaf_ptkns = split_colon[1].split('/')
- else:
- leaf_ptkns = []
-
- if (cat_name == ''):
- raise InputError('Error('+g_module_name+'.DescrToCatLeafPtkns()):\n'
- ' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n\n'
- ' Bad variable descriptor: \"'+descr_str+'\"\n')
- else:
- # ---- Are we using colon-less syntax (example: "$../mol") ?
- ptkns = split_colon[0].split('/')
- cat_name = ptkns[-1] # last token (eg. "mol") is the cat_name
- leaf_ptkns = ptkns[:-1] # the rest is the leaf's path ("..")
- if len(leaf_ptkns) == 0:
- leaf_ptkns.append('.')
- #cat_ptkns = ptkns[:-1] # the same goes for the cat path suggestion
- #if len(cat_ptkns) == 0:
- # cat_ptkns.append('.')
- cat_ptkns = []
-
-
-
- # On 2012-8-22, I commented out this line:
- #return cat_name, RemoveNullTokens(cat_ptkns), RemoveNullTokens(leaf_ptkns)
- # and replaced it with:
-
- return cat_name, RemoveNullTokens(cat_ptkns), leaf_ptkns
-
-
-
-
-
-
-
-
-def DescrToCatLeafNodes(descr_str,
- context_node,
- dbg_loc,
- create_missing_nodes=False):
- """
- Variables in ttree correspond to nodes in a tree
- (and also categories to which they belong).
- DescrToCatLeafNodes() reads the name of a variable,
- (its descriptor) and determines where in the tree
- does this variable reside, and what is it's category?
- This function is the heart of ttree because it is
- the function used to interpret ttree variable syntax.
- (It is very messy right now. I will clean up the code later. AJ 2011-9-06)
-
- Arguments:
- descr_str The complete name that the user gave
- to the variable. (Excluding '$' or '@')
-
- context_node The class (node) in which the variable
- was used. descr_str is interpeted
- relative to this context. (This argument
- is similar to the current directory
- in which a command was issued in unix.)
-
- dbg_loc The location in the user's input file(s)
- where this variable is referred to.
-
- create_missing_nodes
- If we lookup a variable whose leaf node
- does not exist yet, should we create it?
- Setting this argument to "True" allows
- us to augment the tree to add nodes
- corresponding to variables.
-
-
-
- -- Here is a greatly simplified version of DescrToCatLeafNodes(): --
-
- def DescrToCatLeafNodes(descr_str, context_node, dbg_loc):
- cat_name, cat_ptkns, leaf_ptkns = DescrToCatLeafPtkns(descr_str, dbg_loc)
- cat_node = PtknsToNode(cat_ptkns, context_node, dbg_loc)
- if len(cat_ptkns) > 0:
- leaf_node = PtknsToNode(leaf_ptkns, cat_node, dbg_loc)
- else:
- leaf_node = PtknsToNode(leaf_ptkns, context_node, dbg_loc)
- return cat_name, cat_node, leaf_node
-
- (This version works, but it does not handle "..." corectly,
- and it does not create missing nodes when needed.)
-
-
- -- Here is a (probably unnecessary) review of terminology: --
-
- Descriptor String:
- The first argument ("descr_str") is a descriptor string.
- A descriptor string typically contains ":" and "/"
- characters to to divide the string into pieces in order
- to identify a category name, category node, and leaf node.
- Conceptually, the variable's NAME is the leaf node.
- The variable's TYPE is the category (node and name).
-
- Node:
- Nodes are used to represent both class objects and variable names
- 1) class objects
- Each type of class objects is represented by an StaticObj.
- Each instantiated object is represented by an InstanceObj.
- 2) variable names (leaf nodes)
- However variable names are also represented using either
- StaticObjs (for @ static variables) or
- InstanceObjs (for $ instance variables)
- Again, all variables in ttree are members of a class object.
- In this case, the name of the node corresponds to the variable's
- name, and it's position in the tree refers to the class to which
- it belongs.
- However "leaf nodes" do not uniquely identify the
- actual variable itself. A single node can refer to two different
- variables if they are in different categories.
- All 3 identifiers (leaf node, category node, category name)
- are needed to uniquely identify a ttree variable. See below.
-
- Ptkn (Path Token)
- Strings containing multiple '/' characters are typically used
- to identify the location of the category and leaf nodes in the
- tree (ie the path to the node). The '/' characters are
- delimiters which break up the string into small pieces, (which
- are usually the names of classes).
- These pieces are called "path tokens" or "ptkns"
-
- Leaf Node:
- It exists as a node in a tree (instead of a simple string)
- because, just like member variables in a class in an
- object oriented programming language (or in a C struct)
- language, variables in ttree belong to the class in
- which they are defined. The node's location in the
- tree represents which class it belongs to.
- If a variable's leaf node name
- refers to a node which does no exist yet, then we create it
- (assuming the "create_missing_nodes" argument is "True").
-
- Category Node/Name:
- Categories are a peculiar feature of ttree. Categories
- are groups of variables that share the same counter when
- numeric values are automatically given to each variable.
- So you can think of a category as a counter with a name.
- Variables in different categories have different counters,
- and are assigned numeric values independently.
- Consequently two variables in different categories
- may be assigned the same number. But two variables
- in the same category are always given unique values.
- Counters are typically global, but can have local scope.
- (ie, only defined within a Class, or an instantiated
- class, and whatever other classes are nested or
- instantiated beneath it.)
- Therefore to identify a counter/category you must specify
- both a name AND a node. The node identifies the class where
- the scope is defined. It is assumed that the Leaf Node
- (see above) lies within this scope (ie. somewhere after
- it in the tree).
- Example: local counters are used to keep track of the
- residues within in a protein chain. If we use a class to
- represent the protein, we can create a local residue-
- counter (category) within that protein. Then when we
- instantiate the protein multiple times, this counter
- is reset for every new instance of of the protein.
-
- """
-
- cat_name, cat_ptkns, leaf_ptkns = DescrToCatLeafPtkns(descr_str, dbg_loc)
-
-
-
- # ---- ellipsis hack ----
- #
- # Search for class:
- # Most users expect ttree.py to behave like a
- # standard programming language: If the class they are
- # instantiating was not defined in this specific
- # location, they expect ttree.py to search for
- # it outwards, first in the parent's environment,
- # and then in the parent's parent's environment,
- # and so on, until the object is found.
- # For example, most users expect this to work:
- # class Res{
- # write("Atoms") {
- # $atom:CA @atom:CA 0.123 1.234 2.345
- # $atom:CB @atom:CB 1.234 2.345 3.456
- # }
- # }
- # class Protein{
- # write_once("AnglesByType") {
- # @angle:backbone @atom:Res/CA @atom:Res/CA @atom:Res/CA
- # }
- # Notice that in class Protein, we did not have to specify
- # where "Res" was defined because it is defined in the parent
- # environment (ie. immediately outside Proteins's environment).
- # The general way to do this in ttree.py, is to
- # use ellipsis syntax "@atom:.../Res/CA" symbol. The
- # ellipsis ".../" tells ttree.py to search upwards
- # for the object to the right of it ("Res")
- # In order to make ttree.py behave the way
- # most users are expecting, we artificially insert a
- # ".../" before the class name here. (Later on, the
- # code that processes the ".../" symbol will take
- # care of finding A. We don't have to worry about
- # about doing that now.)
- #
- # I think we only want to do this for variables with path information
- # such as "@atom:Res/CA" (which means that leaf_ptkns = ['Res', 'CA']).
- # For simple variables like "@atom:CA", we don't automatically look upwards
- # unless the user eplicitly requests it.
- # (That's why we check to make sure that len(leaf_ptkns) > 1 below
- # before we insert '...' into the leaf_ptkns.)
- # In other words, the two variables "@atom:CA" below are treated differently
- #
- # A {
- # write("Atoms") {
- # @atom:CA
- # }
- # class B {
- # write("Atoms") {
- # @atom:CA
- # }
- # }
- # }
- #
- if ((descr_str.find(':') != -1) and
- #(not ((len(leaf_ptkns) == 1) and
- # (leaf_ptkns[0] == context_node.name))) and
- #(len(leaf_ptkns) > 0) and
- (len(leaf_ptkns) > 1) and
- (len(leaf_ptkns[0]) > 0) and
- (leaf_ptkns[0][0] not in ('.','*','?'))):
-
- leaf_ptkns.insert(0, '...')
- # ---- Done with "ellipsis hack" -----
-
-
-
- #sys.stderr.write(' DescrToCatLeafNodes(): (cat_ptkns, cat_name, lptkns) = ('+
- # str(cat_ptkns)+', \"'+cat_name+'\", '+str(leaf_ptkns)+')\n')
-
- cat_node = None
- cat_start_node = context_node
- leaf_start_node = context_node
-
- if (len(cat_ptkns) > 0):
- if cat_ptkns[-1] == '...':
- # The "..." in this position means trace the path from the
- # current node (context_node) up to cat_ptkns[:-1].
- cat_start_node = PtknsToNode(cat_ptkns[:-1], context_node, dbg_loc)
- # Later on, we will search upwards until we find an ancestor
- # node containing a category matching cat_name. This will
- # be taken care of later. (See "if cat_node is None:" below.)
- else:
- # In this case, the user supplied an explicit path
- # for the category node. Find it now.
- cat_node = PtknsToNode(cat_ptkns, context_node, dbg_loc)
- # Whenever the user supplies an explicit path, then
- # the cat node should be the starting location from
- # which the leaf path is interpreted. This nearly
- # insures that the leaf node will be an ancestor
- # of the category node, which is what we want.
- leaf_start_node = cat_node
-
- if cat_node is None:
- # Otherwise, the user did not indicate where the category
- # node is defined, but only supplied the category name.
- # (This is the most common scenario.)
- # In this case, climb up the tree to the parent
- # until you find an ancestor with a category whose
- # name matches cat_name.
- cat_node = FindCatNode(cat_name, cat_start_node, dbg_loc)
-
- if (cat_name not in cat_node.categories):
- if create_missing_nodes:
- # If this is the first time we encountered a variable in this
- # category (ie if it's the first time we encountered a variable
- # with this category's name and node), then we must create a
- # new entry in the cat_node.categories associative container
- # (using cat_name as the dictionary key).
- cat_node.categories[cat_name] = Category(cat_name)
- else:
- raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
- ' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
- ' Category named \"'+cat_name+'\" not found at\n'
- ' position '+NodeToStr(cat_node)+'\n')
-
-
- # ---------- Now look up the leaf node -----------
-
-
-
- if (len(leaf_ptkns) > 0) and (leaf_ptkns[-1] == 'query()'):
- # Special case: "query()"
- # Variables named "query()" are not really variables.
- # (They are a way for users to query a category's counter.)
- # But we treat them as such internally. Consequently we
- # give them unique names to avoid clashes (just in case
- # "query()" appears multiple times in the same context).
- #leaf_ptkns[-1] = '__query__'+dbg_loc.infile+'_'+str(dbg_loc.lineno)
- leaf_ptkns[-1] = '__query__' + str(dbg_loc.order)
-
-
-
- # Lookup the path for the leaf:
- #
- # Often, the leaf that the path refers to does not
- # exist yet. For example, it is common for a template to
- # contain a reference to "$atom:CA". If the current context_node
- # is "/protein1/res22", this means that the leaf should be
- # at "/protein1/res22/CA". (However in this example, "CA"
- # is not a class that has been defined yet. It is the name
- # of a variable which which may not have even been mentioned
- # before. Think of "CA" as a variable placeholder.
- #
- # So we follow the path tokens as far as we can:
- i_last_ptkn, last_node = FollowPath(leaf_ptkns,
- leaf_start_node,
- dbg_loc)
-
- # Did we find the node?
- if i_last_ptkn == len(leaf_ptkns):
-
- leaf_node = last_node
-
- else:
-
- # If we are here, then we did not find the node.
- # The unrecognized token is stored in
- # leaf_ptkns[i_last_ptkn]
-
- if leaf_ptkns[i_last_ptkn] == '...':
- # ----------------------------------------------
- # ---- UGHH I hate dealing with '...' ----
- # ----(Messy code to follow in this section)----
- # ----------------------------------------------
- # The "..." means different things depending on
- # whether or not it is the last token in leaf_ptkns.
-
- if i_last_ptkn+1 < len(leaf_ptkns):
- # If "..." is NOT the last token in leaf_ptkns, we
- # should search for an ancestor of this node who has
- # a child whose name matches a the requested target
- # string (located in leaf_ptkns[i_last_ptkn+1])
- search_target = leaf_ptkns[i_last_ptkn+1]
- # If such an ancestor exists, then FollowPath()
- # should have already found it for us.
- # This means it was not found.
- # So if there is only one more token in the
- # list of tokens, then create the needed node
- if (create_missing_nodes and
- (i_last_ptkn+1 == len(leaf_ptkns)-1)):
- # Create a new leaf node and link it:
- new_leaf_name = leaf_ptkns[-1]
- parent_node = last_node
- # Is this parent_node an StaticObj? (..or inherit from StaticObj?)
- if isinstance(parent_node, StaticObj):
- parent_node.children[new_leaf_name] = StaticObj(new_leaf_name, parent_node)
- elif isinstance(parent_node, InstanceObj):
- parent_node.children[new_leaf_name] = InstanceObjBasic(new_leaf_name, parent_node)
- else:
- assert(False) # (only 2 types of nodes are possible)
- # Now assign the pointer
- leaf_node = parent_node.children[new_leaf_name]
- else:
- #In that case, we were unable to find the node referenced by "..."
- raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
- ' Broken path.\n' # containing ellipsis (...)\n'
- ' class/variable \"'+search_target+'\" not found in this\n'
- ' context: \"'
- #+var_ref.prefix + var_ref.descr_str + var_ref.suffix+'\"\n'
- +descr_str+'\"\n'
- ' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno))
-
-
- else: # if i_last_ptkn+1 < len(leaf_ptkns):
-
-
- # If "..." IS the last token, then it means:
- # we want to search for the CATEGORY NAME,
- # This is very different.
- # It means we need to:
- # search backwards up the ancestor tree until
- # we find an ancestor variable (of last_node)
- # which has the right category, (ie until you
- # find an ancestor node with a variable (VarRef)
- # pointing to it with belonging to the correct
- # category node and name (determined above).)
- # If not found, then use the current context_node.
-
- assert(cat_name in cat_node.categories)
- var_bindings = cat_node.categories[cat_name].bindings
-
- node = last_node
- while (node != None):
- # Recall that cat_node.categories[cat_name]
- # is a dictionary whose keys are leaf nodes
- # corresponding to the variables in this category.
- if node in var_bindings:
- # then we found it, and we're done
- break
- else:
- node = node.parent
-
- if node != None:
- leaf_node = node
-
- else:
- # If not found, have it point to the
- # current (context) node.
- leaf_node = context_node
-
- # -----------------------------------------------
- # -- Finished dealing with '...' in leaf_ptkns --
- # -----------------------------------------------
-
-
- elif (create_missing_nodes and
- ((i_last_ptkn == len(leaf_ptkns)-1) or
- HasWildCard('/'.join(leaf_ptkns)))):
-
- #elif (create_missing_nodes and
- # (i_last_ptkn == len(leaf_ptkns)-1)):
-
- # Again, another reason the leaf-node was not found is
- # that it refers to a leaf node which has not yet been
- # created. If the path was valid until up to the last
- # token, then we sould create a new node with this name.
- # -- This is a common scenario. --
- # -- This is how all new variables are created. --
- # Anyway, we handle that here:
-
- # Create a new leaf node and link it:
- new_leaf_name = leaf_ptkns[-1]
- new_leaf_name = '/'.join(leaf_ptkns[i_last_ptkn:])
- parent_node = last_node
- # Is this parent_node an StaticObj? (..or does it inherit from StaticObj?)
- if isinstance(parent_node, StaticObj):
- parent_node.children[new_leaf_name] = StaticObj(new_leaf_name, parent_node)
- elif isinstance(parent_node, InstanceObj):
- parent_node.children[new_leaf_name] = InstanceObjBasic(new_leaf_name, parent_node)
- else:
- assert(False) # (only 2 types of nodes are possible)
- # Now assign the pointer
- leaf_node = parent_node.children[new_leaf_name]
-
-
- else:
-
- # Otherwise, the user made a mistake in the path.
- # Figure out which kind of mistake and print an error.
-
- if (last_node.parent is None) and (leaf_ptkns[i_last_ptkn] == '..'):
- #In that case, we tried to back out beyond the root of the tree.
- raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
- ' Broken path in variable:\n'
- #' \"'+var_ref.prefix + var_ref.descr_str + var_ref.suffix+'\"\n'
- ' \"'+ descr_str + '\"\n'
- ' located near '+
- ErrorLeader(dbg_loc.infile,
- dbg_loc.lineno)+'\n'
- ' There are too many \"..\" tokens in the path string.')
-
-
- else:
-
- #Then the reason is: The string in leaf_ptkns[i_last_ptkn]
- #was supposed to be a child of last_node but a child
- #of that name was not found.
- raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
- ' Broken path / Undefined variable:\n'
- #' \"'+var_ref.prefix + var_ref.descr_str + var_ref.suffix+'\"\n'
- ' \"'+ descr_str + '\"\n'
- ' located near '+
- ErrorLeader(dbg_loc.infile,
- dbg_loc.lineno)+'\n'
- ' Undefined: \"'+PtknsToStr(leaf_ptkns)+'\"\n'
- ' (Specifically \"'+leaf_ptkns[i_last_ptkn]+
- '\" is not a subordinate of \"'+MaxLenStr(last_node.name,'/')+'\")')
- #'\n This could be a typo or spelling error.')
-
- return cat_name, cat_node, leaf_node
-
-
-
-
-
-
-
-def DescrToVarBinding(descr_str, context_node, dbg_loc):
- """ DescrToVarBinding() is identical to LookupVar(), but it has a name
- that is harder to remember. See comment for LookupVar() below.
-
- """
- cat_name, cat_node, leaf_node = DescrToCatLeafNodes(descr_str,
- context_node,
- dbg_loc)
-
- if cat_name in cat_node.categories:
- category = cat_node.categories[cat_name]
- var_bindings = category.bindings
- if leaf_node in var_bindings:
- var_binding = var_bindings[leaf_node]
- else:
- raise InputError('Error('+g_module_name+'.DescrToVarBinding()):\n'
- ' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
- ' Bad variable reference: \"'+descr_str+'\". There is\n'
- ' There no category named \"'+cat_name+'\" defined for "'+NodeToStr(cat_node)+'\".\n')
- else:
- raise InputError('Error('+g_module_name+'.DescrToVarBinding()):\n'
- ' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
- ' Bad variable reference: \"'+descr_str+'\". There is\n'
- ' no category named \"'+cat_name+'\" defined for "'+NodeToStr(cat_node)+'\".\n')
-
- return var_binding
-
-
-
-
-
-# Wrappers:
-
-def LookupVar(descr_str, context_node, dbg_loc):
- """ LookupVar() looks up a string (a variable descriptor, which is the
- variable's name, excluding the '$', '@' prefixes and any '{}' brackets.)
- This function returns the variable's "VarBinding" (the variable-name:value
- pair). This is useful for querying or changing the value of a variable.
- Because nearly all variables are local, you must specify the starting
- node (ie. the node corresponding to the class in which this class
- or variable was referred to). This is typically the global node.
-
- """
- return DescrToVarBinding(descr_str, context_node, dbg_loc)
-
-
-
-
-def LookupNode(obj_name, starting_node, dbg_loc):
- """ LookupNode() parses through a string like
- '../ClassA/NestedClassB'
- and returns the corresponding node.
- Nodes are data types used for representing a class or class instance.
- They are also used for storing variables.
- 'ClassA/NestedClassB/VariableC'
- Because nearly all variables are local, you must specify the starting
- node (ie. the node corresponding to the class in which this class
- or variable was referred to). This is typically the global node.
-
- """
- return StrToNode(obj_name, starting_node, dbg_loc)
-
-
-
-
-
-class SimpleCounter(object):
- __slots__=["n","nincr"]
-
- # static data attributes:
- default_n0 = 1
- default_nincr = 1
-
- def __init__(self, n0 = None, nincr = None):
- if n0 == None:
- n0 = SimpleCounter.default_n0
- if nincr == None:
- nincr = SimpleCounter.default_nincr
- self.n = n0 - nincr
- self.nincr = nincr
-
- def query(self):
- return self.n
-
- def incr(self):
- self.n += self.nincr
-
- def __copy__(self): #makes a (deep) copy of the counter in its current state
- return SimpleCounter(self.n + self.nincr, self.nincr)
-
-
-
-
-class Category(object):
- """
- Category contains a list of all of the variables which belong
- to the same category, as well as some supporting information.
-
- Attributes:
-
- name The name of the category (a string)
-
- bindings An OrderedDict() containing leaf_node:VarBinding
- (key:value) pairs. Variables are looked up by their leaf node.
- The actual variable name (which simply refers to the leaf node)
- and values are both stored in the VarBinding data structure.
-
- counter A counter object like "SimpleCounter". Each time counter.incr()
- is invoked it should return a unique string (typically this is
- simply a string representing an integer which is incremented).
-
- """
-
- __slots__=["name","bindings","counter","manual_assignments","reserved_values"]
-
- def __init__(self,
- name = '',
- bindings = None,
- counter = None,
- manual_assignments = None,
- reserved_values = None):
-
- self.name = name
-
- if bindings is None:
- self.bindings = OrderedDict()
- else:
- self.bindings = bindings
-
- if counter is None:
- self.counter = SimpleCounter()
- else:
- self.counter = counter
-
- if manual_assignments is None:
- self.manual_assignments = OrderedDict()
- else:
- self.manual_assignments = manual_assignments
-
- if reserved_values is None:
- self.reserved_values = OrderedDict()
- else:
- self.reserved_values = reserved_values
-
-
-
-
-
-class StaticObj(object):
- """ StaticObjs and InstanceObjs:
-
- The state of the system is stored in two different trees:
- 1) The static tree:
- StaticObj trees are similar "class" definitions in an OOP language.
- These trees contains class definitions, and their nested classes,
- and instructions for how to create new instances (copies) of this class.
- Nodes in this tree are stored using StaticObjs:
- 2) The instance tree:
- This tree contains classes that have been instantiated, and any sub-
- classes (members or attributes) that are instantiated as a result.
- This tree is automatically generated by instantiating the root
- StaticObj. Nodes in this tree are stored using InstanceObjs.
-
- StaticObjs and InstanceObjs both contain
- "commands" (commands which usually involve instructions
- for writing templates)
- "categories" (local counters used to assign variables. See below.)
- "children" (Nested class definitions -NOT- OOP child classes. See below.)
- StaticObjs also contain
- "instance_commands"
- "instance_categories"
- These three members contain information to create a new instance/copy
- of this class (how to construct an InstanceObj from an StaticObj).
-
- StaticObj contains the member function Parse() which builds the global static
- tree by parsing the contents of a text file supplied by the user.
-
- The external function BuildInstanceTree(), creates the global instance tree
- from the global static tree (a tree of StaticObjs).
-
- ----- CLASS MEMBERS OF StaticObj: ----
- 0) Name:
- Every class (object type) has a name. It is stored in self.name.
- To make it easier to distinguish the names of classes from the names of
- individual instances of that class, I recommend using a capital letter
- for the name of a class type (and lower-case letters for instances).
-
- 1) Commands
- Commands are usually instructions for writing templates.
- Templates are blocks of ordinary text which contain variables.
- (Variables in this program consist of variable names, categories,
- and (eventually) bound values (usually generated automatically),
- which will be substituted into the template to generate a text file.)
- A class can contain multiple templates, each one having a unique name
- which also happens to be the name of the file that will be created when
- the template is written.
- Variants:
-
- self.commands:
- Some templates are written immediate after the class is defined
- (stored in "self.commands").
- Example: The "write_once()" command.
-
- self.instance_commands:
- Other templates are written when an instance/copy of the class is created
- (stored in "self.instance_commands".
- Example: The "write()" command.
-
- 2) Children
- self.children:
- Class definitions can be defined from within the definition of other
- ("parent") classes. These nested classes are referred to as "children".
- These sub-classes are not "children" in the OOP sense of the word at
- all (they do not have any of the the traits of their "parents").
- However in the source code I refer to them as "children" because here
- they are implemented as "child" nodes (branches) in the tree-like
- data-structure used to store class definitions (the static tree).
-
- 3) Categories
- This is a new concept and is difficult to explain.
- Recall that each class contains a list of templates containing raw text,
- interspersed with variables (whose values will determined later).
- In most cases, variables are assigned to integer values which are
- automatically generated by incrementing a counter. Simply put,
- "categories" are collections of variables which share the same counter.
- Within a category, the goal is to assign a unique integer (or other
- symbol) to each distinct variable in this category.
- To avoid name-clashes, variable names have local "scope".
- This scope is the "leaf_token"
-
- Categories can be specific to a particular class (node), and any of the
- classes (nodes) which are nested within it, but by default are global.
- (This means they "belong" to the global (outermost) node by default.)
- All the various categories which are defined within a particular
- StaticObj are stored in self.categories.
- Static variables (ie. variables with a '@' prefix) are stored this way.
-
- "self.categories"
- If a class contains a new category, it means that if any nested
- classes defined within that class definition contain (static, '@')
- variables whose categories match the category name, their values will
- be determined by looking up the couter associated with this category
- stored locally (here) in self.categories. All variables belonging
- to this category are stored in "self.categories[category_name]".
- "self.instance_categories"
- Recall that creating a new copy (instance) of a class automatically
- creates an InstanceObj in the instance-tree. InstanceObj's have a
- ".categories" attribute of their own, the contents of which are
- copied from this StaticObj's "self.instance_categories" attribute.
- Instantiating a new class also spawns the instantiation of any
- sub-classes.
- If any of these "instance children" contain variables whose category
- names match a category stored in the parent InstanceObj's .categories
- dictionary, then their values will be determined by that InstanceObj's
- counter for that category name.
- 4) Parent:
- A link to the parent StaticObj is stored in self.parent.
-
- """
-
-
- __slots__=["name",
- "parent",
- "children",
- "categories",
- "commands",
- "srcloc_begin",
- "srcloc_end",
- "deleted",
- "class_parents",
- "namespaces",
- "instname_refs",
- "instance_categories",
- "instance_commands_push",
- "instance_commands",
- "instance_commands_pop"]
-
- def __init__(self,
- name='',
- parent=None):
- """
- The members/attributes of StaticObj are defined in the comment
- for StaticObj above. """
-
- # The following members are shared by both InstanceObj and StaticObj:
-
- self.name = name
-
- self.parent = parent #For traversing the global static template tree
-
- self.children = OrderedDict() # Nested class definitions.
-
- self.categories=OrderedDict() #<- new variable categories that are only defined
- # in the context of this molecule's type definition
- self.commands=[] # Commands to carry out (only once)
-
- ##vb##self.var_bindings=[] # List of variables assigned to this object.
-
- self.srcloc_begin = None # Keep track of location in user files
- self.srcloc_end = None # (useful for error message reporting)
-
- self.deleted = False # Users can delete static objects?
- # (why not?)
-
- # The following members are not shared with InstanceObj:
-
- self.class_parents = [] # classes we inherit traits from (this is
- # similar to the parent/child relationship
- # in an object-oriented-programming language)
-
- self.namespaces = [] # A list of classes we also look in when searching
- # for other static nodes or variables. (similar to
- # class_parents, but only used for searches.)
-
- self.instname_refs = {} # <-- used for debugging to insure that
- # two instances do not have the same name
-
- self.instance_categories=OrderedDict()#<-new variable categories that are defined
- #within the scope of this molecule's instance
- self.instance_commands_push=[] #1)process these commands first by adding
- # these commands to InstanceObj.commands
- # (before you deal with class_parents)
- self.instance_commands=[] #2) then add this to InstanceObj.commands
- self.instance_commands_pop=[] #3) finally add these commands
-
-
-
- def DeleteSelf(self):
- for child in self.children.values():
- child.DeleteSelf()
- self.deleted = True
-
-
-
- def IsDeleted(self):
- return self.deleted
-
-
- ##vb##def AddVarBinding(self, var_binding):
- ##vb## if self.var_bindings is None:
- ##vb## self.var_bindings = [var_binding]
- ##vb## else:
- ##vb## self.var_bindings.append(var_binding)
-
-
- def Parse(self, lex):
-
- """ Parse() builds a static tree of StaticObjs by parsing text file.
- -The "lex" argument is a file or input stream which has been converted
- to a "TemplateLexer" object (similar to the python's built-in shlex lexer).
- """
-
- # The next two variables store a stack of commands the user wants
- # to manually add to the list of stackable instance_commands.
- # (Allowing the users to directly manipulate the transformation stack
- # is an experimental feature as of 2015- Most users don't need this.)
- user_push_left_commands = []
- user_push_right_commands = []
-
- #sys.stdout.write(' -- Parse() invoked --\n')
-
- # Keep track of the location in the users' input files where this
- # class object is first defined. (Keep in mind that the user might
- # augment their original class definition, adding new content to an
- # existing class. In that case self.srcloc_begin will have already
- # been assigned. We don't want to overwrite it in that case.)
- if self.srcloc_begin is None: # <-- not defined yet?
- self.srcloc_begin = lex.GetSrcLoc()
-
- while True:
-
- cmd_token = lex.get_token()
-
- #print('Parse(): token = \"'+cmd_token+'\", '+lex.error_leader())
-
- if cmd_token == lex.eof:
- #print('Parse(): EOF encountered\n')
- break
-
-
- if ((cmd_token == 'write') or
- (cmd_token == 'write_once') or
- (cmd_token == 'create_var') or
- (cmd_token == 'replace')):
- open_paren = lex.get_token()
-
- #print('Parse(): open_paren=\"'+open_paren+'\"')
- if open_paren=='{':
- # ..then the user neglected to specify the "dest" file-name
- # argument. In that case, supply the default, ''.
- # (which is shorthand for the standard out in this case)
- open_curly = open_paren[0]
- open_paren = ''
- close_paren = ''
- tmpl_filename = ''
- srcloc = lex.GetSrcLoc()
- else:
- tmpl_filename = lex.get_token()
- if tmpl_filename == ')':
- tmpl_filename = ''
- close_paren = ')'
- else:
- close_paren = lex.get_token()
- open_curly = lex.get_token()
- srcloc = lex.GetSrcLoc()
-
- if (cmd_token == 'create_var'):
- tmpl_filename = None
- # This means: define the template without attaching
- # a file name to it. (IE., don't write the contents
- # of what's enclosed in the curly brackets { } to a file.)
-
- if (cmd_token == 'replace'):
- tmpl_filename = "ttree_replacements.txt"
-
- if ((open_curly != '{') or
- ((open_paren == '') and (close_paren != '')) or
- ((open_paren == '(') and (close_paren != ')'))):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error in '+lex.error_leader()+'\n\n'
- 'Syntax error at the beginning of the \"'+cmd_token+'\" command.')
- if tmpl_filename != None:
- tmpl_filename = RemoveOuterQuotes(tmpl_filename, lex.quotes)
- # ( The previous line is similar to:
- # tmpl_filename = tmpl_filename.strip(lex.quotes) )
-
- tmpl_contents = lex.ReadTemplate()
- StaticObj.CleanupReadTemplate(tmpl_contents, lex)
-
- #sys.stdout.write(' Parse() after ReadTemplate, tokens:\n\n')
- #print(tmpl_contents)
- #sys.stdout.write('\n----------------\n')
-
-
- if (cmd_token == 'write_once' or
- cmd_token == 'replace'):
-
- # Check for a particular bug:
- # Ordinary instance variables (preceded by a '$')
- # should never appear in a write_once() statement.
- for entry in tmpl_contents:
- if (isinstance(entry, VarRef) and
- (entry.prefix[0]=='$')):
- err_msg = ('Error('+g_module_name+'.StaticObj.Parse()):\n'+
- ' Error near '+ErrorLeader(entry.srcloc.infile,
- entry.srcloc.lineno)+'\n'+
- ' Illegal variable: \"'+entry.prefix+entry.descr_str+entry.suffix+'\"\n'+
- ' All variables in a \"'+cmd_token+'\" statement must be statically\n'+
- ' defined, and hence they must begin with a \'@\' prefix character.\n'+
- ' (not a \'$\' character).\n')
- if (cmd_token == 'write_once'):
- err_msg += ' Suggestion: Use the \"write()\" command instead.\n'
- raise InputError(err_msg)
-
-
-
- if cmd_token == 'write':
- commands = self.instance_commands
- elif (cmd_token == 'write_once' or
- cmd_token == 'replace'):
- commands = self.commands
- elif (cmd_token == 'create_var'):
- commands = self.instance_commands
- else:
- assert(False)
-
- command = WriteFileCommand(tmpl_filename,
- tmpl_contents,
- srcloc)
- commands.append(command)
-
- # end of "if (cmd_token == 'write') or (cmd_token == 'write_once'):"
-
- elif cmd_token == 'delete':
-
- instobj_descr_str = lex.get_token()
- instobj_srcloc = lex.GetSrcLoc()
- delete_command = DeleteCommand(instobj_srcloc)
- mod_command = ModCommand(delete_command,
- instobj_descr_str)
- self.instance_commands.append(mod_command)
-
- elif cmd_token == 'using':
-
- namespacecom_str = lex.get_token()
- if namespacecom_str != 'namespace':
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' The \"'+cmd_token+'\" command must be followed by the \"namespace\" keyword.')
- namespace_str = lex.get_token()
-
- stnode = StrToNode(namespace_str,
- self,
- lex.GetSrcLoc())
-
- self.namespaces.append(stnode)
-
- elif cmd_token == 'category':
-
- cat_name = lex.get_token()
-
- cat_count_start = 1
- cat_count_incr = 1
-
- open_paren = lex.get_token()
- if (open_paren == '('):
- token = lex.get_token()
- if token == ',':
- token = lex.get_token()
- if token != ')':
- # Interpret token as an integer, float, or string
- try:
- cat_count_start = int(token)
- except ValueError:
- try:
- cat_count_start = float(token)
- except ValueError:
- cat_count_start = RemoveOuterQuotes(token, '\'\"')
- token = lex.get_token()
- if token == ',':
- token = lex.get_token()
- if token != ')':
- # Interpret token as an integer,float,or string
- try:
- cat_count_incr = int(token)
- except ValueError:
- try:
- cat_count_incr = float(token)
- except ValueError:
- cat_count_incr = RemoveOuterQuotes(token, '\'\"')
- token = lex.get_token()
- if token != ')':
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"'+cmd_token+' '+cat_name+'...\" has too many arguments,\n'
- ' or lacks a close-paren \')\'.\n')
- else:
- lex.push_token(open_paren)
-
- if (isinstance(cat_count_start, basestring) or
- isinstance(cat_count_incr, basestring)):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"'+cmd_token+' '+cat_name+'('+
- str(cat_count_start)+','+
- str(cat_count_incr)+')\"\n'
- ' Only numeric counters are currently supported.\n')
-
- # check for really stupid and unlikely errors:
- if type(cat_count_start) is not type(cat_count_incr):
- if ((isinstance(cat_count_start, int) or
- isinstance(cat_count_start, float))
- and
- (isinstance(cat_count_incr, int) or
- isinstance(cat_count_incr, float))):
- cat_count_start = float(cat_count_start)
- cat_count_incr = float(cat_count_incr)
- else:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' Problem with \"'+cmd_token+'\" command.\n')
-
- prefix = cat_name[0]
- cat_name = cat_name[1:]
- # Add this category to the list.
- if prefix == '@':
- self.categories[cat_name] = Category(cat_name)
- self.categories[cat_name].counter=SimpleCounter(cat_count_start,
- cat_count_incr)
- elif prefix == '$':
- self.instance_categories[cat_name] = Category(cat_name)
- self.instance_categories[cat_name].counter=SimpleCounter(cat_count_start,
- cat_count_incr)
- else:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' category name = \"'+cat_name+'\" lacks a \'$\' or \'&\' prefix.\n'
- ' This one-character prefix indicates whether the variables in this\n'
- ' new category will be static or dynamics variables\n')
-
-
-
- elif (cmd_token == '}') or (cmd_token == ''):
- # a '}' character means we have reached the end of our scope.
- # Stop parsing and let the caller deal with the remaining text.
- # (And a '' means we reached the end of the file... I think.)
- break
-
-
- #elif (cmd_token == 'include'):
- # "include filename" loads a file (adds it to the file stack)
- # The "TtreeShlex" class (from which "lex" inherits) handles
- # "include" statements (ie. "source" statements) automatically.
-
- elif ((cmd_token == 'push') or
- (cmd_token == 'push_left') or
- (cmd_token == 'push_right')):
-
- push_cmd_src_loc = lex.GetSrcLoc()
- push_cmd_text = lex.GetParenExpr()
- if ((len(push_cmd_text) < 2) or
- (push_cmd_text[0] != '(') or
- (push_cmd_text[-1] != ')')):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' Bad \"push\" command. Expected an expression in parenthesis.\n')
- push_cmd_text = push_cmd_text[1:-1]
-
- if (cmd_token == 'push_right'):
- push_command = PushRightCommand(push_cmd_text,
- push_cmd_src_loc)
- user_push_right_commands.append(push_command)
- else:
- push_command = PushLeftCommand(push_cmd_text,
- push_cmd_src_loc)
- user_push_left_commands.append(push_command)
- self.instance_commands.append(push_command)
-
- elif ((cmd_token == 'pop') or
- (cmd_token == 'pop_left') or
- (cmd_token == 'pop_right')):
-
- pop_cmd_text = lex.GetParenExpr()
- pop_cmd_src_loc = lex.GetSrcLoc()
- if (cmd_token == 'pop_right'):
- if len(user_push_right_commands) > 0:
- push_command = user_push_right_commands.pop()
- else:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' Too many \"pop_right\" commands.\n')
- pop_command = PopRightCommand(push_command,
- pop_cmd_src_loc)
- else:
- if len(user_push_left_commands) > 0:
- push_command = user_push_left_commands.pop()
- else:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' Too many pop, (or pop_left) commands.\n')
- pop_command = PopLeftCommand(push_command,
- pop_cmd_src_loc)
- self.instance_commands.append(pop_command)
-
-
-
- else:
-
- # Otherwise, 'cmd_token' is not a command at all.
- # Instead it's the name of an object which needs to be
- # defined or instantiated.
- # First, let's figure out which.
-
- # (small detail: The "class" keyword is optional
- # and can be skipped.)
- if cmd_token == 'class':
- object_name = lex.get_token()
- else:
- object_name = cmd_token
-
- next_symbol = lex.get_token()
- #print('Parse(): next_token=\"'+next_symbol+'\"')
-
- class_parents = []
-
- if next_symbol == 'inherits':
-
- # Then read in the list of classes which are parents of
- # of this class. (Multiple inheritance is allowed.)
- # (We don't yet check to insure that these are valid class
- # names. We'll do this later in LookupStaticRefs().)
-
- syntax_err_inherits = False
-
- while True:
- next_symbol = lex.get_token()
- if ((next_symbol == '{') or
- (next_symbol == lex.eof)):
- break
- elif (next_symbol == '='):
- syntax_err_inherits = True
- break
- else:
- class_parents.append(StrToNode(next_symbol,
- self,
- lex.GetSrcLoc()))
- if len(class_parents) == 0:
- syntax_err_inherits = True
-
- if syntax_err_inherits:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"inherits\" should be followed by one or more class names.\n')
-
-
- if next_symbol == '{':
- child_name = object_name
-
- # Check to see if this class has already been defined.
- # (IE. check if it present in the list of children.)
- # If the name (child_name) matches another class (child),
- # then the contents of the new class will be appended to
- # the old. This way, class definitions can be augmented
- # later. (This is the way "namespaces" work in C++.)
- child = self.children.get(child_name)
- # If found, we refer to it as "child".
- # If not, then we create a new StaticObj named "child".
- if child is None:
- child = StaticObj(child_name, self)
- self.children[child_name] = child
- assert(child.name == child_name)
-
- # Either way we invoke child.Parse(), to
- # add contents (class commands) to child.
- child.Parse(lex)
- child.class_parents += class_parents
-
-
-
- elif next_symbol == '=':
- next_symbol = lex.get_token()
- if next_symbol == 'new':
- base_name = object_name
- base_srcloc = lex.GetSrcLoc()
- array_slice_str = ''
- if base_name.find('/') != -1:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+ErrorLeader(base_srcloc.infile,
- base_srcloc.lineno)+'\n'
- ' (You can not instantiate some other object\'s members.)\n'
- ' Invalid instance name: \"'+base_name+'\"\n')
-
- elif base_name in self.instname_refs:
- ref_srcloc = self.instname_refs[base_name]
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Duplicate class/array \"'+base_name+'\"\n'
- ' This occurs near:\n'
- ' '+ErrorLeader(ref_srcloc.infile,
- ref_srcloc.lineno)+'\n'
- ' and also near:\n'
- ' '+ErrorLeader(base_srcloc.infile,
- base_srcloc.lineno)+'\n')
- else:
- self.instname_refs[base_name] = base_srcloc
-
-
-
-
-
- # Check for syntax allowing the user to instantiate
- # PART of an array. For example, check for this syntax:
- # "monomers[20-29] = new ...". This only fills in a
- # portion of the array from: monomers[20]...monomers[29]
- #
- # We also have to deal with multidimensional syntax
- # like this: "cells[3][2-3][1][4-7] = new..."
- # Split the "cells[3][2-3][2][4-7][2]" string into
- # "cells[3][", "][1][", and "]".
- # Later, we will instantiate InstanceObjs with names:
- # "cells[3][2][1][4]"
- # "cells[3][2][1][5]"
- # "cells[3][2][1][6]"
- # "cells[3][2][1][7]"
- # "cells[3][3][1][4]"
- # "cells[3][3][1][5]"
- # "cells[3][3][1][6]"
- # "cells[3][3][1][7]"
-
-
- p1 = base_name.find('[')
- if p1 == -1:
- p1 = len(base_name)
- else:
- p1 += 1
- array_name_tkns = [ base_name[0:p1] ]
- array_name_offsets = []
-
- p2 = -1
- p4 = p1
- while p4 < len(base_name):
- p3 = base_name.find(']', p1)
-
- if p3 == -1:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Expected a \']\' character following:\n'
- ' \"'+base_name[0:p1]+'\", located near:\n'
- ' '+ErrorLeader(ref_srcloc.infile,
- ref_srcloc.lineno)+'\n')
-
- # Search for a '-', ':', or '*' character between []
- # For example "monomers[20-29] = "
- # If present, the user wants us to fill a range
- # inside an array. This could be a multi-dimensional
- # array, (eg "cells[3][2-6][4-11] = "), so we must
- # figure out which entries in the array the user
- # wants us to fill (in this case, "[2-6][4-11]")
- p2 = base_name.find('-', p1)
- if p2 == -1:
- p2 = len(base_name)
- if p2 > p3:
- p2 = base_name.find(':', p1)
- if p2 == -1:
- p2 = len(base_name)
- if p2 > p3:
- p2 = base_name.find('*', p1)
- if p2 == -1:
- p2 = len(base_name)
-
- p4 = p3 + 1
- if p4 < len(base_name):
- if base_name[p4] == '[':
- p4 += 1 # skip over it
- else:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Expected a \'[\' character forllowing a \']\' character in\n'
- ' \"'+base_name[0:p2+1]+'\", located near:\n'
- ' '+ErrorLeader(ref_srcloc.infile,
- ref_srcloc.lineno)+'\n')
-
-
-
-
- if p2 > p3:
- # Then no '-', ':', or '*' character was found
- # between '[' and the subsequent ']' character
- # In that case, ignore this token
-
- token = base_name[p1:p4]
- # append all this text to the previous token
- if len(array_name_tkns) == 0:
- array_name_tkns.append(token)
- else:
- array_name_tkns[-1] = array_name_tkns[-1]+token
- array_slice_str = 'slice '
- else:
-
- assert((p1 < p2) and (p2 < p3))
- index_offset_str = base_name[p1:p2]
- if len(index_offset_str) == 0:
- index_offset = 0
-
- elif (not str.isdigit(index_offset_str)):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Expected a nonnegative integer preceding the \''+base_name[p2]+'\' character in:\n'
- ' \"'+base_name[0:p2+1]+'\", located near:\n'
- ' '+ErrorLeader(ref_srcloc.infile,
- ref_srcloc.lineno)+'\n')
- else:
- index_offset = int(index_offset_str)
- token=base_name[p3:p4]
- array_name_tkns.append(token)
- array_name_offsets.append(index_offset)
-
- p1 = p4
-
-
-
- # If the statobj_str token contains a ']' character
- # then this means the user wants us to make multiple
- # copies of this template. The number of copies
- # to instantiate is enclosed in the [] characters
- # (Example wat = new Water[3000] creates
- # 3000 instantiations of the Water template
- # named wat[1], wat[2], wat[3], ... wat[3000]).
-
- # Note: Here '[' and ']' have a special meaning.
- # So lex.get_token() should not treat them as
- # ordinary word characters. To prevent this:
- orig_wordterminators = lex.wordterminators
- lex.wordterminators += '[],'
-
- class_name_str = lex.get_token()
- if ((class_name_str == lex.eof) or
- (class_name_str == '}')):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- 'Class ends prematurely. (Incomplete \"new\" statement.)')
-
- assert(len(class_name_str) > 0)
-
- if (class_name_str[0] == '['):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' new '+class_name_str+'\n'
- 'Bracketed number should be preceded by a class name.')
- class_names = []
- weights = []
- num_by_type = []
- if class_name_str == 'random':
- class_names, weights, num_by_type = self._ParseRandom(lex)
- tmp_token = lex.get_token()
- if len(tmp_token)>0:
- if tmp_token[0]=='.':
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"'+tmp_token+'\" should not follow random()\n'
- '\n'
- ' Coordinate transformations and other commands (such as \"'+tmp_token+'\")\n'
- ' should appear after each class name inside the random() statement,\n'
- ' not after it. For example, do not use:\n'
- ' \"lipids=new random([DPPC,DLPC],[0.5,0.5]).move(0,0,23.6)\"\n'
- ' Use this instead:\n'
- ' \"lipids=new random([DPPC.move(0,0,23.6),DLPC.move(0,0,23.6)],[0.5,0.5])\"\n')
- lex.push_token(tmp_token)
- else:
- class_name, class_suffix, class_suffix_srcloc = \
- self._ProcessClassName(class_name_str, lex)
-
- array_size = []
- array_suffixes = []
- array_srclocs = []
-
- # A general "new" statement could look like this:
- # "m = new Mol.scale(3) [2].trans(0,4.5,0).rotate(30,0,0,1)
- # [3].trans(0,0,4.5)"
- # So far we have processed "m = new Mol.scale(3)".
- # Now, we need to deal with:
- # "[2].trans(0,4.5,0).rotate(30,0,0,1) [3].trans(0,0,4.5)"
- while True:
- new_token = lex.get_token()
- #if ((new_token == '') or (new_token == lex.eof)):
- # break
- if new_token == '[':
- number_str = lex.get_token()
- close_bracket = lex.get_token()
- if ((not str.isdigit(number_str)) or
- (close_bracket != ']')):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error in \"new\" statement near '+lex.error_leader()+'\n'
- ' A \'[\' character should be followed by a number and a \']\' character.')
- array_size.append(int(number_str))
- suffix = lex.get_token()
-
- if ((suffix == '') or (suffix == lex.eof)):
- array_suffixes.append('')
- array_srclocs.append(base_srcloc)
- break
- if suffix[0] == '.':
- lex.push_token(suffix[1:])
- suffix_func = lex.GetParenExpr()
- suffix = '.' + suffix_func
- array_suffixes.append(suffix)
- array_srclocs.append(lex.GetSrcLoc())
- else:
- array_suffixes.append('')
- array_srclocs.append(base_srcloc)
- lex.push_token(suffix)
- if suffix != '[':
- break
- else:
- lex.push_token(new_token)
- break
- srcloc_final = lex.GetSrcLoc()
-
- lex.wordterminators = orig_wordterminators
-
- assert(len(array_size) == len(array_suffixes))
-
- if len(array_size) > 0:
- if len(array_name_offsets) == 0:
- assert(len(array_name_tkns) == 1)
- array_name_offsets = [0] * len(array_size)
- array_name_tkns[0] = array_name_tkns[0] + '['
- for d in range(0, len(array_size)-1):
- array_name_tkns.append('][')
- array_name_tkns.append(']')
-
- if len(array_name_offsets) != len(array_size):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error in \"new\" statement near/before '+lex.error_leader()+'\n'
- ' Array '+array_slice_str+'dimensionality on the left side of the \'=\' character ('+str(len(array_name_offsets))+')\n'
- ' does not match the array dimensionality on the right side ('+str(len(array_size))+').\n')
-
-
-
-
-
- # If the user wants us to instantiate a
- # multidimensional array of class instances
- # then we must loop through this multidimensional
- # array and create a new instance for each entry.
- # For example fill a 3 dimensional volume
- # with 1000 water molecules
- # Example 1:
- # solvent = new Water [10][10][10]
- # (The coordinates must be read separately.)
- # In this example array_size = [10,10,10]
- # array_suffixes = ['','','']
- # Example 2:
- # solvent = new Water.transcm(0,0,0)
- # [10].trans(0,0,4)
- # [10].trans(0,4,0).rot(45,0,0,1)
- # [10].trans(4,0,0)
- # (This command generates a 10x10x10 lattice
- # simple cubic lattice of regularly spaced
- # water molecules pointing the same direction.)
- # In this example array_size = [10,10,10]
- # and
- # class_suffix = 'transcm(0,0,0)'
- # and
- # array_suffixes = ['trans(0,0,4)',
- # 'trans(0,4,0).rot(45,0,0,1)',
- # 'trans(4,0,0)']
- # Note that tree ignores the "trans()"
- # commands, it stores them so that inherited
- # classes can attempt to process them.
-
-
- D = len(array_size)
- if D > 0:
-
- i_elem = 0 #(used to look up selection_list[])
- if len(num_by_type) > 0:
- selection_list = []
- for i in range(0, len(num_by_type)):
- selection_list += [i]*num_by_type[i]
- random.shuffle(selection_list)
-
- num_elements = 1
- for d in range(0,D):
- num_elements *= array_size[d]
- err_msg_str = str(array_size[0])
- for d in range(1,D):
- err_msg_str += '*'+str(array_size[d])
- if num_elements != len(selection_list):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near or before '+lex.error_leader()+'\n'
- ' The sum of the numbers in the \"new random([],[])\" command ('+str(len(selection_list))+')\n'
- ' does not equal the number of elements in the array ('+err_msg_str+')\n')
-
-
- digits = [0 for d in range(0, D)]
- table_filled = False
- pushed_commands = []
- while (not table_filled):
- instance_name = array_name_tkns[0]
- for d in range(0, D):
- i = digits[d]
- instance_name+=str(i+
- array_name_offsets[d])+\
- array_name_tkns[d+1]
-
-
- # Does the user want us to select
- # a class at random?
- if len(class_names) > 0:
-
- if len(num_by_type) > 0:
- class_name_str = class_names[selection_list[i_elem]]
- else:
- class_name_str = RandomSelect(class_names,
- weights)
- class_name, class_suffix, class_suffix_srcloc= \
- self._ProcessClassName(class_name_str, lex)
-
- if class_suffix != '':
- class_suffix_command = \
- PushRightCommand(class_suffix.lstrip('.'),
- class_suffix_srcloc)
- self.instance_commands.append(class_suffix_command)
- command = \
- InstantiateCommand(instance_name,
- ClassReference(class_name,
- base_srcloc),
- base_srcloc)
- self.instance_commands.append(command)
-
- if class_suffix != '':
- command = \
- PopRightCommand(class_suffix_command,
- srcloc_final)
- self.instance_commands.append(command)
-
-
- # Now go to the next entry in the table.
- # The indices of this table are similar to
- # a D-digit integer. We increment this d-digit number now.
- d_carry = D-1
- while True:
- digits[d_carry] += 1
- if digits[d_carry] >= array_size[d_carry]:
- digits[d_carry] = 0
- if array_suffixes[d_carry] != '':
- for i in range(0, array_size[d_carry]-1):
- partner = pushed_commands.pop()
- command = PopRightCommand(partner,
- srcloc_final)
- self.instance_commands.append(command)
- d_carry -= 1
- else:
- if array_suffixes[d_carry] != '':
- command = PushRightCommand(array_suffixes[d_carry].lstrip('.'),
- array_srclocs[d_carry])
- pushed_commands.append(command)
- self.instance_commands.append(command)
- break
- if d_carry < 0:
- table_filled = True
- break
-
- i_elem += 1 #(used to look up selection_list[])
- pass
-
-
- else:
- if len(class_names) > 0:
- assert(len(num_by_type) == 0)
- #if len(num_by_type) > 0:
- # class_name_str = class_names[selection_list[i_elem]]
- #else:
- # class_name_str = RandomSelect(class_names,
- # weights)
- class_name_str = RandomSelect(class_names,
- weights)
- class_name, class_suffix, class_suffix_srcloc= \
- self._ProcessClassName(class_name_str, lex)
- if class_suffix != '':
- class_suffix_command = \
- PushRightCommand(class_suffix.lstrip('.'),
- class_suffix_srcloc)
- self.instance_commands.append(class_suffix_command)
- command = \
- InstantiateCommand(base_name,
- ClassReference(class_name,
- base_srcloc),
- base_srcloc)
- self.instance_commands.append(command)
-
- if class_suffix != '':
- command = \
- PopRightCommand(class_suffix_command,
- srcloc_final)
- self.instance_commands.append(command)
-
- else:
-
- # Now check for commands using this syntax:
- #
- # "MolNew = MolOld.rot(45,1,0,0).scale(100.0)"
- # /|\ /|\ `-----------.------------'
- # | | |
- # child_name parent_name optional suffix
-
- child_name = object_name
- parent_name_str = next_symbol
-
- child = StaticObj(child_name, self)
-
- parent_name, suffix, suffix_srcloc = \
- self._ProcessClassName(parent_name_str, lex)
-
- child.class_parents.append(StrToNode(parent_name,
- self,
- lex.GetSrcLoc()))
-
- if suffix != '':
- # Assume the command is a StackableCommand. (This
- # way it will enclose the commands of the parents.)
- # Stackable commands come in (Push...Pop) pairs.
- push_command = PushLeftCommand(suffix,
- suffix_srcloc)
- pop_command = PopLeftCommand(push_command,
- suffix_srcloc)
- push_mod_command = ModCommand(push_command, './')
- pop_mod_command = ModCommand(pop_command, './')
- child.instance_commands_push.append(push_mod_command)
- child.instance_commands_pop.insert(0,pop_mod_command)
-
- #sys.stderr.write('child.instance_commands_push = '+str(child.instance_commands_push)+'\n')
-
- #sys.stderr.write('child.instance_commands_pop = '+str(child.instance_commands_pop)+'\n')
-
- # Check to see if this class has already been defined.
- if self.children.get(child_name) is not None:
- if self.children[i].IsDeleted():
- del self.children[child_name]
- else:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' The name \"'+child_name+'\" is already in use.')
-
- self.children[child_name] = child
-
-
-
- else:
-
- # Otherwise hopefully this is a post-instance command
- # (a command applied to a class which has been instantiated)
- # In that case, the object_name would be followed by
- # a dot and a function-call containing a '(' paren (which
- # would have ended up stored in the next_symbol variable).
-
- open_paren_encountered = False
- if (next_symbol == '('):
- open_paren_encountered = True
- lex.push_token(next_symbol) #put '(' back in the stream
-
- i_dot = object_name.rfind('.')
- i_slash = object_name.rfind('/')
- dot_encountered = ((i_dot != -1) and
- ((i_slash == -1) or (i_slash < i_dot)))
-
- if (open_paren_encountered and dot_encountered and
- (object_name[:1] != '[')):
-
- obj_descr_str, suffix, suffix_srcloc = \
- self._ExtractSuffix(object_name, lex)
-
- path_tokens = obj_descr_str.split('/')
- i_last_ptkn, staticobj = FollowPath(path_tokens,
- self,
- lex.GetSrcLoc())
- instobj_descr_str = './'+'/'.join(path_tokens[i_last_ptkn:])
-
- # I still support the "object_name.delete()" syntax for
- # backwards compatibility. (However newer input files
- # use this equivalent syntax: "delete object_name")
- if suffix == 'delete()':
- delete_command = DeleteCommand(suffix_srcloc)
- mod_command = ModCommand(delete_command,
- instobj_descr_str)
- staticobj.instance_commands.append(mod_command)
- else:
- push_command = PushLeftCommand(suffix,
- suffix_srcloc,
- '.')
- pop_command = PopLeftCommand(push_command,
- suffix_srcloc,
- '.')
- push_mod_command = ModCommand(push_command,
- instobj_descr_str)
- pop_mod_command = ModCommand(pop_command,
- instobj_descr_str)
- if instobj_descr_str != './':
- #sys.stderr.write('DEBUG: Adding '+str(push_command)+' to '+
- # staticobj.name+'.instance_commands\n')
- staticobj.instance_commands.append(push_mod_command)
- staticobj.instance_commands.append(pop_mod_command)
- else:
- #sys.stderr.write('DEBUG: Adding '+str(push_command)+' to '+
- # staticobj.name+'.instance_commands_push\n')
- # Question: Should I make these PushRight commands and
- # append them in the opposite order?
- # If so I also have to worry about the case above.
- staticobj.instance_commands_push.append(push_mod_command)
- staticobj.instance_commands_pop.insert(0,pop_mod_command)
-
- else:
- # Otherwise, the cmd_token is not any of these:
- # "write", "write_once", "replace", "create_vars"
- # "delete", or "category".
- # ... and it is ALSO not any of these:
- # the name of a class (StaticObj), or
- # the name of an instance (InstanceObj)
- # followed by either a '.' or "= new"
- #
- # In that case, it is a syntax error:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Syntax error at or before '+lex.error_leader()+'\n'
- ' \"'+object_name+' '+next_symbol+'\".')
-
- # Keep track of the location in the user's input files
- # where the definition of this object ends.
- self.srcloc_end = lex.GetSrcLoc()
-
-
-
-
- # Finally, if there are any remaining user_push_left_commands or
- # user_push_right_commands, deal with them (by popping them).
- for push_command in user_push_left_commands:
- push_command = user_push_left_commands.pop()
- pop_command = PopLeftCommand(push_command,
- self.srcloc_end)
- self.instance_commands.append(pop_command)
-
- for push_command in user_push_right_commands:
- push_command = user_push_right_commands.pop()
- pop_command = PopRightCommand(push_command,
- self.srcloc_end)
- self.instance_commands.append(pop_command)
-
-
-
- @staticmethod
- def CleanupReadTemplate(tmpl_contents, lex):
- #1) Remove any newlines at the beginning of the first text block
- # in tmpl_content.(Sometimes they cause ugly extra blank lines)
- assert(len(tmpl_contents) > 0)
- if isinstance(tmpl_contents[0], TextBlock):
- first_token_strip = tmpl_contents[0].text.lstrip(' ')
- if ((len(first_token_strip) > 0) and
- (first_token_strip[0] in lex.newline)):
- tmpl_contents[0].text = first_token_strip[1:]
- tmpl_contents[0].srcloc.lineno += 1
-
- #2) Remove any trailing '}' characters, and complain if absent.
- # The last token
- assert(isinstance(tmpl_contents[-1], TextBlock))
- assert(tmpl_contents[-1].text in ['}',''])
- if tmpl_contents[-1].text == '}':
- del tmpl_contents[-1]
- else:
- tmpl_begin = None
- if isinstance(tmpl_contents[0], TextBlock):
- tmpl_begin = tmpl_contents[0].srcloc
- elif isinstance(tmpl_contents[0], VarRef):
- tmpl_begin = tmpl_contents[0].srcloc
- else:
- assert(False)
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n\n'
- ' Premature end to template.\n'
- '(Missing terminator character, usually a \'}\'.) The\n'
- 'incomplete template begins near '+ErrorLeader(tmpl_begin.infile, tmpl_begin.lineno)+'\n')
- #3) Finally, if there is nothing but whitespace between the
- # last newline and the end, then strip that off too.
- if isinstance(tmpl_contents[-1], TextBlock):
- i = len(tmpl_contents[-1].text)-1
- if i >= 0:
- while ((i >= 0) and
- (tmpl_contents[-1].text[i] in lex.whitespace) and
- (tmpl_contents[-1].text[i] not in lex.newline)):
- i -= 1
- if (tmpl_contents[-1].text[i] in lex.newline):
- tmpl_contents[-1].text = tmpl_contents[-1].text[0:i+1]
-
-
-
- def LookupStaticRefs(self):
- """ Whenever the user requests to instantiate a new copy of a class,
- the name of that class is stored in self.instance_commands.
- This name is stored as a string. After all of the classes have been
- defined, then we go back through the tree and replace these names
- with pointers to actual StaticObjs which correspond to those classes.
- (This was deferred until all of the classes have been defined so
- that users can refer to classes that they will define later on.)
-
- """
-
- # Now do the same for any children which
- # are created during instantiation:
- for command in self.instance_commands:
- # Does this command create/instantiate a new copy of a class?
- if isinstance(command, InstantiateCommand):
- # If so, figure out which statobj is referred to by statobj_str.
- assert(isinstance(command.class_ref.statobj_str, basestring))
- command.class_ref.statobj = StrToNode(command.class_ref.statobj_str,
- self,
- command.class_ref.srcloc)
-
- # Now recursively resolve StaticObj pointers for the "children"
- # (in this case, "children" refers to classes whose definitions
- # are nested within this one).
- for child in self.children.values():
- child.LookupStaticRefs()
-
-
-
-
- def _ExtractSuffix(self, class_name_str, lex):
- """
-
- This ugly function helps process "new" commands such as:
- mola = new ForceFieldA/../MoleculeA.move(30,0,0).rot(45,0,0,1)
- This function expects a string,
- (such as "ForceFieldA/../MoleculeA.move(30,0,0).rot(45,0,0,1)")
- It extracts the class name "ForceFieldA/../MoleculeA"
- and suffix "move(30,0,0).rot(45,0,0,1)"
- """
- # Dots in class names can appear for 2 reasons:
- # 1) as part of a path like "../" describing the location
- # where this class was defined relative to the caller.
- # In that case it will be preceded or followed by
- # either another dot '.', or a slash '/'
- # 2) as part of a "suffix" which appears after the name
- # containing instructions which modify how to
- # instantiate that class.
- # Case 1 is handled elsewhere. Case 2 is handled here.
- i_dot = 0
- while i_dot < len(class_name_str):
-
- i_dot = class_name_str.find('.', i_dot)
-
- if i_dot == -1:
- break
- # Is the '.' character followed by another '.', as in ".."?
- # If so, it's part of a path such as "../Parent/Mol', (if
- # so, it's not what we're looking for, so keep searching)
- if i_dot < len(class_name_str)-1:
- if class_name_str[i_dot+1] == '.':
- i_dot += 1
- #otherwise, check to see if it is followed by a '/'?
- elif class_name_str[i_dot+1] != '/':
- # if not, then it must be part of a function name
- break;
-
- class_suffix = ''
- class_name = class_name_str
- class_suffix_srcloc = None
-
- if ((i_dot != -1) and
- (i_dot < len(class_name_str))):
- class_suffix = class_name_str[i_dot:]
- class_name = class_name_str[:i_dot]
- if class_name_str[-1] != ')':
- # If it does not already contains the parenthesis?
- class_suffix += lex.GetParenExpr()
- class_suffix_srcloc = lex.GetSrcLoc()
- #sys.stderr.write(' splitting class name into class_name.suffix\n'
- # ' class_name=\"'+class_name+'\"\n'
- # ' suffix=\"'+class_suffix+'\"\n')
-
- return class_name, class_suffix.lstrip('.'), class_suffix_srcloc
-
-
-
-
- def _ProcessClassName(self, class_name_str, lex):
- """
-
- This function does some additional
- processing (occasionaly inserting "..." before class_name).
- """
-
- class_name, class_suffix, class_suffix_srcloc = \
- self._ExtractSuffix(class_name_str, lex)
-
- # ---- ellipsis hack ----
- # (Note-to-self 2012-4-15)
- # Most users expect ttree.py to behave like a
- # standard programming language: If the class they are
- # instantiating was not defined in this specific
- # location, they expect ttree.py to search for
- # it outwards, first in the parent's environment,
- # and then in the parent's parent's environment,
- # and so on, until the object is found.
- # For example, most users expect this to work:
- # class A{
- # <definition_of_a_goes_here...>
- # }
- # class B{
- # a = new A
- # }
- # Notice in the example above we did not have to specify where "A"
- # was defined, because it is defined in the parent's
- # environment (ie. immediately outside B's environment).
- #
- # One can obtain the equivalent behavior in ttree.py
- # using ellipsis syntax: "a = new .../A" symbol.
- # The ellipsis ".../" tells ttree.py to search upwards
- # for the object to the right of it ("A")
- # In order to make ttree.py behave the way
- # most users are expecting, we artificially insert a
- # ".../" before the class name here. (Later on, the
- # code that processes the ".../" symbol will take
- # care of finding A.)
-
- if (len(class_name)>0) and (class_name[0] not in ('.','/','*','?')):
- class_name = '.../' + class_name
-
- return class_name, class_suffix, class_suffix_srcloc
-
-
-
-
-
- def _ParseRandom(self, lex):
- bracket1 = lex.get_token()
- bracket2 = lex.get_token()
- if ((bracket1 != '(') and (bracket1 != '[')):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- 'Expected a \"([\" following '+class_name+'.')
- class_names = []
- token = ''
- prev_token = '['
- while True:
- token = lex.get_token()
- if (token == '('):
- lex.push_token(token)
- token = lex.GetParenExpr()
- if (prev_token not in (',','[','(')):
- assert(len(class_names) > 0)
- class_names[-1] = prev_token + token
- prev_token = prev_token + token
- else:
- class_names.append(token)
- prev_token = token
- else:
- if ((token == ']') or
- (token == lex.eof) or
- (token == '}') or
- ((token in lex.wordterminators) and
- (token != ','))):
- if (prev_token in (',','[','(')):
- class_names.append('')
- break
- if token != ',':
- class_names.append(token)
- elif (prev_token in (',','[','(')):
- class_names.append('')
- prev_token = token
-
-
- token_comma = lex.get_token()
- bracket1 = lex.get_token()
- if ((token != ']') or
- (token_comma != ',') or
- (bracket1 != '[')):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- 'Expected a list of class names enclosed in [] brackets, followed by\n'
- 'a comma, and then a list of probabilities also enclosed in [] brackets.\n'
- '(A random-seed following another comma is optional.)')
-
- weights = []
- while True:
- token = lex.get_token()
- if ((token == ']') or
- (token == lex.eof) or
- (token == '}') or
- ((token in lex.wordterminators) and
- (token != ','))):
- break
- if token != ',':
- try:
- weight = float(token)
- except ValueError:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"'+token+'\"\n'
- 'Expected a list of numbers enclosed in [] brackets.')
- if (weight < 0.0):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' Negative numbers are not allowed in \"random(\" argument list.\n')
- weights.append(weight)
-
- bracket2 = lex.get_token()
- if ((token != ']') or
- (bracket2 not in (')',','))):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- 'Expected a \")\" or a \",\" following the list of numeric weights.')
-
- if len(class_names) != len(weights):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- 'Unequal number of entries in object list and probability list.\n')
-
- # Are all the entries in the "weights" array integers?
- # If they are then, treat them as molecule counters,
- # ot probabilities
- num_by_type = []
- for i in range(0, len(weights)):
- # are the weights all positive integers?
- n = int(weights[i])
- if n == weights[i]:
- num_by_type.append(n)
- if len(num_by_type) < len(weights):
- num_by_type = []
-
- tot_weight = sum(weights)
- if (tot_weight <= 0.0):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' The numbers in the \"random(\" argument list can not all be zero.\n')
- for i in range(0,len(weights)):
- weights[i] /= tot_weight
-
-
- if bracket2 == ',':
- try:
- token = lex.get_token()
- seed = int(token)
- random.seed(seed)
- except ValueError:
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"'+token+'\"\n'
- 'Expected an integer (a seed) following the list of weights.')
- bracket2 = lex.get_token()
- if (bracket2 != ')'):
- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
- ' Error near '+lex.error_leader()+'\n'
- ' \"'+token+'\"\n'
- 'Expected a \")\".')
- else:
- random.seed()
-
- return (class_names, weights, num_by_type)
-
-
-
-
-
- def BuildCommandList(self, command_list):
- """
- Search the commands in the tree and make a linear list of commands
- in the order they should be carried out.
-
- """
-
- if self.IsDeleted():
- return
-
- # Add a special note to the list of commands to indicate which object
- # the commands refer to. (This might be useful one day.)
- # Later we can loop through this command list and still be able to tell
- # whether or not we are within the scope of a particular class or instance
- # (by seeing if we are between a "ScopeBegin" and "ScopeEnd" pair).
- command_list.append(ScopeBegin(self, self.srcloc_begin))
-
- # We want to append commands to the command_list in the same order
- # that these commands appear in the user's input files.
-
- # Unfortunately the commands may be interspersed with the creation of
- # new StaticObjs which have their own commands which we have to explore
- # recursively.
- # Fortunately each child (StaticObj) has a srcloc_begin member, so we
- # can infer the correct order of all the commands belonging to the
- # children and correctly insert them into the correct place in between
- # the commands of the parent.
-
- srcloc2command_or_child = {}
-
- for command in self.commands:
- srcloc2command_or_child[command.srcloc] = command
-
- for child in self.children.values():
- srcloc = child.srcloc_begin
- # special case: Some children do not have a srcloc because
- # they were generated automatically. These children should
- # not have any commands either so we can ignore them.
- if srcloc != None:
- srcloc2command_or_child[srcloc] = child
- else:
- assert(len(child.commands) == 0)
-
- for srcloc in sorted(srcloc2command_or_child.keys()):
- entry = srcloc2command_or_child[srcloc]
- if isinstance(entry, StaticObj):
- child = entry
- child_commands = []
- child.BuildCommandList(child_commands)
- command_list += child_commands
- else:
- command_list.append(entry)
-
- command_list.append(ScopeEnd(self, self.srcloc_end))
-
-
-
-
- def __str__(self):
- out_str = self.name
- if len(self.children) > 0:
- out_str += '('
- i = 0
- for child in self.children.values():
- if i+1 < len(self.children):
- out_str += str(child)+', '
- else:
- out_str += str(child)+')'
- i += 1
-
- return out_str
-
-
-
-
-
-
-def RandomSelect(entries, weights):
- """ Return an entry from a list at random using
- a (normalized) list of probabilities. """
- assert(len(entries) == len(weights))
- x = random.random()
- i = 0
- tot_probability = 0.0
- while i < len(weights)-1:
- tot_probability += weights[i]
- if x <= tot_probability:
- break
- i += 1
- return entries[i]
-
-
-
-
-class InstanceObjBasic(object):
- """ A simplified version of InstanceObj.
- See the documentation/comments for InstanceObj for more details.
- (Leaf nodes (variables) are typically stored as InstanceObjBasic objects
- More general, non-leaf nodes are stored using InstanceObj objects.)
-
- """
-
- __slots__=["name","parent"]
-
- def __init__(self,
- name = '',
- parent = None):
- self.parent = parent # the environment/object which created this object
- # Example:
- # Suppose this "molecule" is an amino acid monomer
- # belonging to a protein. The "parent" refers to
- # the InstanceObj for the protein. ".parent" is
- # useful for traversing the global instance tree.
- # (use InstanceObj.statobj.parent for
- # traversing the global static tree)
-
- self.name = name # A string uniquely identifying this object in
- # in it's "parent" environment.
- # (It is always the same for every instance
- # of the parent object. It would save memory to
- # get rid of this member. Andrew 2012/9/13)
-
- #self.deleted = False
-
- ##vb##self.var_bindings=None # List of variables assigned to this object
- ##vb## # or None (None takes up less space than an
- ##vb## # empty list.)
-
-
- ##vb##def AddVarBinding(self, var_binding):
- ##vb## if self.var_bindings is None:
- ##vb## self.var_bindings = [var_binding]
- ##vb## else:
- ##vb## self.var_bindings.append(var_binding)
-
-
- #def DeleteSelf(self):
- # self.deleted = True
-
- def DeleteSelf(self):
- #self.Dealloc()
- self.parent = self # This condition (normally never true)
- # flags the node as "deleted". (Nodes are never
- # actually deleted, just flagged.)
- # I used to have a separate boolean member variable
- # which was set True when deleted, but I started
- # eliminated unnecessary data members to save space.
-
-
- #def IsDeleted(self):
- # return self.deleted
-
- def IsDeleted(self):
- # Return true if self.deleted == True or self.parent == self
- # for this node (or for any ancestor node).
- node = self
- while node.parent != None:
- if hasattr(node, 'deleted'):
- if node.deleted:
- return True
- elif node.parent == node:
- return True
- node = node.parent
- return False
-
-
-
-
- #def Dealloc(self):
- # pass
- ##vb##if self.var_bindings is None:
- ##vb## return
- ##vb##N = len(self.var_bindings)-1
- ##vb##for i in range(0,len(self.var_bindings)):
- ##vb## vb = self.var_bindings[N-i]
- ##vb## cat = vb.category
- ##vb## assert(self in cat.bindings)
- ##vb## del cat.bindings[self]
- ##vb## del self.var_bindings[N-i]
- ##vb##self.var_bindings = None
-
-
-
-
-
-
-
-class InstanceObj(InstanceObjBasic):
- """ InstanceObjs are used to store nodes in the global
- "instance tree", the tree of all classes (molecules) which have
- been instantiated. Recall that whenever a class is instantiated,
- it's members will be instantiated as well. Since these
- members can also be classes, this relationship is hierarchical,
- and can be represented as a tree.
- "InstanceObjs" are the data type used to store the nodes in that tree."""
-
- __slots__=["statobj",
- "children",
- "categories",
- "commands",
- "commands_push",
- "commands_pop",
- "srcloc_begin",
- "srcloc_end",
- "deleted"]
- #"LookupMultiDescrStr",
- ##"Dealloc",
- ##"DeleteSelf",
- ##"IsDeleted",
- ##"UndeleteSelf",
- ##"DeleteProgeny",
- #"BuildInstanceTree",
- #"ProcessCommand",
- #"ProcessContextNodes",
- #"BuildCommandList"]
-
-
- def __init__(self,
- name = '',
- parent = None):
-
- InstanceObjBasic.__init__(self, name, parent)
-
- self.statobj = None # The statobj node refered to by this instance
- self.children = {} # A list of statobjs corresponding to
- # constituent parts (members) of the
- # current class instance.
- # The typical example is to consider the
- # multiple amino acids (child-molecules)
- # which must be created in order to create a
- # new protein (instance) to which they belong
- # (which would be "self" in this example)
-
- self.categories = {} # This member stores the same data as the
- # Instance variables (ie. variables
- # with a '$' prefix) are stored in a
- # category belonging to node.categories
- # where "node" is of type InstanceObj.
- # (There is a long explanation of
- # "categories" in the comments
- # of class StaticObj.)
-
- self.commands = [] # An ordered list of commands to carry out
- # during instantiation
-
- self.commands_push = [] # Stackable commands to carry out (first, before children)
- self.commands_pop = [] # Stackable commands to carry out (last, after children)
-
-
- self.srcloc_begin = None # Keep track of location in user files
- self.srcloc_end = None # (useful for error message reporting)
- self.deleted = False
-
-
-
- def LookupMultiDescrStr(self,
- multi_descr_str,
- srcloc,
- null_list_warning=False,
- null_list_error=False):
- """
- Post-Instance (PI) modifiers/commands are commands which modify
- an instance of a class after it has already been instantiated.
-
- Simple Example:
-
- class A {
- ...
- }
- class B {
- a = new A.command_1()
- a.command_2()
- }
-
- In the example above "command_2()" is a ModCommand, and
- "a" is the multi_descr_str (string describing the correspond InstanceObj).
- The "command_2()" command will be retroactively pushed onto the
- list of commands to execute once "a" is instantiated.
- (This is somewhat counter-intuitive.)
-
- When array brackets [] and wildcards are used, a single ModCommand
- can modify many different instances, for example suppose:
-
- a = new A [2][5][3]
-
- then "a[1][2][*].command_3()" is equivalent to
-
- a[0][2][0].command_3()
- a[0][2][1].command_3()
- a[0][2][2].command_3()
-
- In this example "a[1][2][*]" is the multi_descr_str
-
- "a[*][3][*].command_4()" is equivalent to
-
- a[0][3][0].command_4()
- a[0][3][1].command_4()
- a[1][3][0].command_4()
- a[1][3][1].command_4()
-
- In this function, we interpret strings like "a" and "a[*][3][*]"
- in the examples above, and figure out which InstanceObjs they refer to,
- and push the corresponding command into that InstanceObjs instance
- command stack retroactively.
-
- In addition to [*], you can use [a-b] and [a:b] syntax. For example:
- "a[0][1-2][0-1].command_3()" and
- "a[0][1:3][0:2].command_3()" are both equivalent to:
-
- a[0][1][0].command_3()
- a[0][1][1].command_3()
- a[0][2][0].command_3()
- a[0][2][1].command_3()
-
- """
-
- pattern_str = multi_descr_str
-
- # Suppose pattern_str = 'a[1][*][3]/b[**][2]'
- # We want to split this string into a list of string fragments
- # which omits the '*' characters: [ 'a[', '][3]/b', '][2]' ]
- # However, we only want to do this when * is enclosed in [].
- pattern_fragments = []
- ranges_ab = []
- i_close_prev = 0
- i_close = 0
- i_open = 0
- while True:
- i_open = pattern_str.find('[', i_open+1)
- if i_open == -1:
- pattern_fragments.append(pattern_str[i_close_prev:])
- break
- else:
- i_close = pattern_str.find(']', i_open+1)
- if i_close == -1:
- pattern_fragments.append(pattern_str[i_close_prev:])
- break
-
- # If there is a '*' or a ':' character between
- # the [] brackets, then split the string at '['
- # (at i_open) and resume reading again at ']'
- # (at i_close) (and create a new entry in the
- # pattern_fragments[] and ranges_ab[] lists)
- wildcard_here = True
- range_ab = [0,-1]
- for j in range(i_open+1, i_close):
- if ((pattern_str[j] == ':') or
- ((pattern_str[j] == '-') and (j > i_open+1)) or
- (pattern_str[j] == '*')):
- i_wildcard = len(pattern_fragments)
- range_a_str = pattern_str[i_open+1 : j]
- range_b_str = pattern_str[j+1 : i_close]
- if (range_a_str != ''):
- if str.isdigit(range_a_str):
- range_ab[0] = int(range_a_str)
- else:
- raise InputError('Error near '+
- ErrorLeader(srcloc.infile,
- srcloc.lineno)+'\n'
- ' Expected colon-separated integers.\n')
- if (range_b_str != ''):
- if str.isdigit(range_b_str):
- range_ab[1] = int(range_b_str)
- # special case: When [a-b] type syntax is
- # used, it selects from a to b inclusive.
- # (IE. b is not a strict upper bound.)
- if pattern_str[j] == '-':
- range_ab[1] += 1
- else:
- raise InputError('Error near '+
- ErrorLeader(srcloc.infile,
- srcloc.lineno)+'\n'
- ' Expected colon-separated integers.\n')
- break
- elif j == i_close-1:
- wildcard_here = False
-
- if wildcard_here:
- pattern_fragments.append(pattern_str[i_close_prev:i_open+1])
- ranges_ab.append(range_ab)
- i_close_prev = i_close
-
- assert(len(pattern_fragments)-1==len(ranges_ab))
- # Now figure out which InstanceObj or InstanceObjs correspond to
- # the name or set of names suggested by the multi_descr_str,
- # (after wildcard characters have been substituted with integers).
-
- instobj_list = []
- if len(pattern_fragments) == 1:
- # commenting out:
- # instobj_list.append(StrToNode(pattern_str, self, srcloc))
- #
- # Line above will print an error message if the node is not found.
- # However sometimes we don't want this. Use this code instead:
- path_tokens = pattern_str.split('/')
- i_last_ptkn, instobj = FollowPath(path_tokens,
- self,
- srcloc)
-
- # If found add to instobj_list
-
- if ((i_last_ptkn == len(path_tokens))
- and (not instobj.IsDeleted())):
- instobj_list.append(instobj)
-
- else:
- # num_counters equals the number of bracket-enclosed wildcards
- num_counters= len(pattern_fragments)-1
- multi_counters = [ranges_ab[i][0] for i in range(0, num_counters)]
- all_matches_found = False
- d_carry = 0
- while d_carry < num_counters:
-
- # Find the next InstanceObj in the set of InstanceObjs which
- # satisfy the wild-card pattern in pattern_fragments.
-
- while d_carry < num_counters:
-
- candidate_descr_str = ''.join([pattern_fragments[i] +
- str(multi_counters[i])
- for i in range(0,num_counters)] \
- + \
- [pattern_fragments[num_counters]])
-
- #sys.stderr.write('DEBUG: /'+self.name+
- # '.LookupMultiDescrStr()\n'
- # ' looking up \"'+
- # candidate_descr_str+'\"\n')
-
- path_tokens = candidate_descr_str.split('/')
- i_last_ptkn, instobj = FollowPath(path_tokens,
- self,
- srcloc)
-
- # If there is an InstanceObj with that name,
- # then add it to the list of InstanceObjs to
- # which we will apply this modifier function,
- # and increment the counters
-
- # If found (and if the counter is within the range)...
- if ((i_last_ptkn == len(path_tokens)) and
- ((ranges_ab[d_carry][1] == -1) or
- (multi_counters[d_carry]<ranges_ab[d_carry][1]))):
- # (make sure it has not yet been "deleted")
- if (not instobj.IsDeleted()):
- instobj_list.append(instobj)
- d_carry = 0
- multi_counters[0] += 1
- #sys.stderr.write('DEBUG: InstanceObj found.\n')
- break
-
-
- # If there is no InstanceObj with that name,
- # then perhaps it is because we have incremented
- # the counter too high. If there are multiple
- # counters, increment the next most significant
- # counter, and reset this counter to 0.
- # Keep looking
- # (We only do this if the user neglected to explicitly
- # specify an upper bound --> ranges_ab[d_carry[1]==-1)
- elif ((ranges_ab[d_carry][1] == -1) or
- (multi_counters[d_carry]>=ranges_ab[d_carry][1])):
- #sys.stderr.write('DEBUG: InstanceObj not found.\n')
- multi_counters[d_carry] = ranges_ab[d_carry][0]
- d_carry += 1
- if d_carry >= num_counters:
- break
- multi_counters[d_carry] += 1
- else:
- # Object was not found but we keep going. Skip
- # to the next entry in the multi-dimensional list.
- d_carry = 0
- multi_counters[0] += 1
- break
-
- if (null_list_warning and (len(instobj_list) == 0)):
- sys.stderr.write('WARNING('+g_module_name+'.LookupMultiDescrStr()):\n'
- ' Potential problem near '+
- ErrorLeader(srcloc.infile,
- srcloc.lineno)+'\n'
- ' No objects (yet) matching name \"'+pattern_str+'\".\n')
- if (null_list_error and
- (len(instobj_list) == 0)):
- if len(pattern_fragments) == 1:
- raise InputError('Error('+g_module_name+'.LookupMultiDescrStr()):\n'
- ' Syntax error near '+
- ErrorLeader(srcloc.infile,
- srcloc.lineno)+'\n'
- ' No objects matching name \"'+pattern_str+'\".')
- else:
- sys.stderr.write('WARNING('+g_module_name+'.LookupMultiDescrStr()):\n'
- ' Potential problem near '+
- ErrorLeader(srcloc.infile,
- srcloc.lineno)+'\n'
- ' No objects (yet) matching name \"'+pattern_str+'\".\n')
-
-
- return instobj_list
-
-
-
-
- def __str__(self):
- out_str = self.name
- if len(self.children) > 0:
- out_str += '('
- i = 0
- for child in self.children.values():
- if i+1 < len(self.children):
- out_str += str(child)+', '
- else:
- out_str += str(child)+')'
- i += 1
-
- return out_str
-
-
-
-
-
- def DeleteSelf(self):
- self.deleted = True
-
- # COMMENT1: Don't get rid of pointers to yourself. Knowing which
- # objects you instantiated and destroyed might be useful
- # in case you want to apply multiple delete [*] commands
- # COMMENT2: Don't delete all the child nodes, and commands. These are
- # needed later (so that text-templates containing references
- # to these nodes don't cause moltemplate to crash.)
-
- #def UndeleteSelf(self):
- # self.deleted = False
- #
- #
- #def DeleteProgeny(self):
- # for child in self.children.values():
- # if hasattr(child, 'DeleteProgeny'):
- # child.DeleteProgeny()
- # else:
- # child.DeleteSelf()
- # self.DeleteSelf();
-
-
-
-
-
- def BuildInstanceTree(self,
- statobj,
- class_parents_in_use):
- """
- This takes care of the details of copying relevant data from an StaticObj
- into a newly-created InstanceObj. It allocates space for and performs
- a deep-copy of any instance variables (and new instance categories), but
- it performs a shallow copy of everything else (template text, etc..).
- This is done recursively for every child that this class instantiates.
-
- """
-
- if self.IsDeleted():
- return
-
- #sys.stderr.write(' DEBUG: '+self.name+
- # '.BuildInstanceTree('+statobj.name+')\n')
-
- #instance_refs = {}
- # Keep track of which line in the file (and which file) we were
- # in when we began parsing the class which defines this instance,
- # as well as when we stopped parsing.
- # (Don't do this if you are recusively searching class_parents because
- # in that case you would be overwritting .statobj with with the parent.)
- if len(class_parents_in_use) == 0:
- self.statobj = statobj
- self.srcloc_begin = statobj.srcloc_begin
- self.srcloc_end = statobj.srcloc_end
-
- # Make copies of the class_parents' StaticObj data.
-
- # First deal with the "self.instance_commands_push"
- # These commands should be carried out before any of the commands
- # in "self.instance_commands".
- for command in statobj.instance_commands_push:
- #self.commands.append(command)
- self.ProcessCommand(command)
-
- # Then deal with class parents
- for class_parent in statobj.class_parents:
- # Avoid the "Diamond of Death" multiple inheritance problem
- if class_parent not in class_parents_in_use:
- #sys.stderr.write(' DEBUG: '+self.name+'.class_parent = '+
- # class_parent.name+'\n')
- self.BuildInstanceTree(class_parent,
- class_parents_in_use)
- class_parents_in_use.add(class_parent)
-
- # Now, deal with the data in THIS object and its children
- assert((self.commands != None) and (self.categories != None))
-
- # "instance_categories" contains a list of new "categories" (ie new
- # types of variables) to create whenever this class is instantiated.
- # (This is used whenever we create a local counter variable: Suppose we
- # want to count the residues within a particular protein, when there
- # are multiple copies of the same protein in the simulation.)
- for cat_name, cat in statobj.instance_categories.items():
- assert(len(cat.bindings) == 0)
- self.categories[cat_name] = Category(cat_name)
- self.categories[cat_name].counter = cat.counter.__copy__()
- # Note: Later on we will generate leaf nodes corresponding to
- # variables, and put references to them in this category.
-
- # Deal with the "instance_commands",
- for command in statobj.instance_commands:
- #self.commands.append(command)
- self.ProcessCommand(command)
-
-
- # Finally deal with the "self.instance_commands_pop"
- # These commands should be carried out after all of the commands
- # in "self.instance_commands".
- for command in statobj.instance_commands_pop:
- #self.commands.append(command)
- self.ProcessCommand(command)
-
-
-
-
-
- def ProcessCommand(self, command):
-
- if isinstance(command, ModCommand):
-
- sys.stderr.write(' processing command \"'+str(command)+'\"\n')
- mod_command = command
- instobj_list = self.LookupMultiDescrStr(mod_command.multi_descr_str,
- mod_command.command.srcloc)
-
- if isinstance(mod_command.command, DeleteCommand):
-
- # Delete any objects we have created so far
- # whose name matches mod_command.multi_descr_str:
- for instobj in instobj_list:
- instobj.DeleteSelf()
- #instobj.DeleteProgeny()
-
- elif len(instobj_list) == 0:
-
- raise InputError('Error('+g_module_name+'.ProcessCommand()):\n'
- ' Syntax error at or before '+
- ErrorLeader(mod_command.command.srcloc.infile,
- mod_command.command.srcloc.lineno)+'\n'
- ' No objects matching name \"'+
- mod_command.multi_descr_str+'\"\n'
- ' (If the object is an array, include brackets. Eg. \"molecules[*][*][*]\")')
-
- else:
- for instobj in instobj_list:
- assert(not isinstance(mod_command.command, DeleteCommand))
- command = mod_command.command.__copy__()
- self.ProcessContextNodes(command)
- if isinstance(command, PushCommand):
- instobj.commands_push.append(command)
- elif isinstance(mod_command.command, PopCommand):
- instobj.commands_pop.insert(0, command)
- else:
- # I don't know if any other types commands will ever
- # occur but I handle them below, just in case...
- assert(not isinstance(command, InstantiateCommand))
- instobj.commands.append(command.__copy__())
-
- return # ends "if isinstance(command, ModCommand):"
-
-
- # Otherwise:
- command = command.__copy__()
- self.ProcessContextNodes(command)
-
-
- if isinstance(command, InstantiateCommand):
- sys.stderr.write(' processing command \"'+str(command)+'\"\n')
- self.commands.append(command) #<- useful later to keep track of the
- # order that children were created
-
- # check to make sure no child of that name was previously defined
- prev_child = self.children.get(command.name)
- if ((prev_child != None) and (not prev_child.IsDeleted())):
- raise InputError('Error near '+
- ErrorLeader(command.srcloc.infile,
- command.srcloc.lineno)+'\n'
- ' Object \"'+command.name+'\" is already defined.\n')
-
- child = InstanceObj(command.name, self)
- command.instobj = child
-
- if command.class_ref.statobj_str == '':
- child.DeleteSelf()
-
- # Why? This if-then check handles the case when the user
- # wants to create an array of molecules with random vacancies.
- # When this happens, some of the instance commands will
- # contain instructions to create a copy of a molecule with
- # an empty molecule-type-string (class_ref.statobj_str).
- # Counter-intuitively, ...
- # ...we DO want to create something here so that the user can
- # safely loop over the array without generating an error.
- # (Such as to delete elements, or move the remaining
- # members in the array.) We just want to mark it as
- # 'deleted'. (That's what "DeleteSelf()" does.)
- else:
-
- # This is the heart of "BuildInstanceTree()"
- # (which implements object composition)
- new_class_parents_in_use = set([])
- child.BuildInstanceTree(command.class_ref.statobj,
- new_class_parents_in_use)
-
- self.children[child.name] = child
-
-
- elif isinstance(command, WriteFileCommand):
- #sys.stderr.write(' processing command \"'+str(command)+'\"\n')
-
- self.commands.append(command)
-
- for var_ref in command.tmpl_list:
- # Process the VarRef entries in the tmpl_list,
- # (and check they have the correct prefix: either '$' or '@')
- # Ignore other entries (for example, ignore TextBlocks).
-
-
- if (isinstance(var_ref, VarRef) and (var_ref.prefix[0] == '$')):
-
- if (var_ref.descr_str[:4] == 'mol:'):
- pass
-
- var_ref.nptr.cat_name, var_ref.nptr.cat_node, var_ref.nptr.leaf_node = \
- DescrToCatLeafNodes(var_ref.descr_str,
- self,
- var_ref.srcloc,
- True)
-
-
- categories = var_ref.nptr.cat_node.categories
-
- # "categories" is a dictionary storing "Category" objects
- # indexed by category names.
-
- # Note to self: Always use the ".categories" member,
- # (never the ".instance_categories" member.
- # ".instance_categories" are only used temporarilly before
- # we instantiate, ie. before we build the tree of InstanceObjs.)
-
- category = categories[var_ref.nptr.cat_name]
- # "category" is a Category object containing a
- # dictionary of VarBinding objects, and an internal counter.
-
- var_bindings = category.bindings
- # "var_bindings" is a dictionary storing "VarBinding"
- # objects, indexed by leaf nodes. Each leaf node
- # corresponds to a unique variable in this category.
-
- # --- Now update "var_bindings" ---
-
- # Search for the "VarBinding" object that
- # corresponds to this leaf node.
- # If not found, then create one.
-
- if var_ref.nptr.leaf_node in var_bindings:
- var_binding = var_bindings[var_ref.nptr.leaf_node]
- # "var_binding" stores the information for a variable,
- # including pointers to all of the places the variable
- # is rerefenced, the variable's (full) name, and value.
- #
- # Keep track of all the places that varible is
- # referenced by updating the ".refs" member
- var_binding.refs.append(var_ref)
- else:
- # Not found, so we create a new binding.
- var_binding = VarBinding()
-
- # var_binding.refs contains a list of all the places
- # this variable is referenced. Start with this var_ref:
- var_binding.refs = [var_ref]
-
- # keep track of the cat_node, cat_name, leaf_node:
- var_binding.nptr = var_ref.nptr
-
- # "var_binding.full_name" stores a unique string like
- # '@/atom:Water/H' or '$/atom:water[1423]/H2',
- # which contains the full path for the category and leaf
- # nodes, and uniquely identifies this variable globally.
- # Thus these strings correspond uniquely (ie. in a
- # one-to-one fashion) with the nodes they represent.
-
-
- var_binding.full_name = var_ref.prefix[0] + \
- CanonicalDescrStr(var_ref.nptr.cat_name,
- var_ref.nptr.cat_node,
- var_ref.nptr.leaf_node,
- var_ref.srcloc)
- # (These names can always be generated later when needed
- # but it doesn't hurt to keep track of it here too.)
-
-
- # Now add this binding to the other
- # bindings in this category:
- var_bindings[var_ref.nptr.leaf_node] = var_binding
-
- ##vb## var_ref.nptr.leaf_node.AddVarBinding(var_binding)
-
- var_binding.category = category
-
-
- # It's convenient to add a pointer in the opposite direction
- # so that later if we find the var_ref, we can find its
- # binding and visa-versa. (Ie. two-way pointers)
- var_ref.binding = var_binding
-
- assert(var_ref.nptr.leaf_node in var_bindings)
-
-
-
- else:
- # Otherwise, we don't know what this command is yet.
- # Append it to the list of commands and process it/ignore it later.
- self.commands.append(command)
-
-
-
- def ProcessContextNodes(self, command):
- if hasattr(command, 'context_node'):
- # Lookup any nodes pointers to instobjs
- if command.context_node != None:
- if type(command.context_node) is str:
- command.context_node = StrToNode(command.context_node,
- self,
- command.srcloc)
- # (Otherwise, just leave it as None)
-
-
-
- def BuildCommandList(self, command_list):
- """
- Search the commands in the tree and make a linear list of commands
- in the order they should be carried out.
-
- """
-
- if self.IsDeleted():
- return
-
- if (len(self.commands) == 0):
- assert(len(self.children) == 0)
- # To save memory don't generate any commands
- # for trivial (leaf) nodes
- return
-
- # Add a special note to the list of commands to indicate which object
- # the commands refer to. (This might be useful one day.)
- # Later we can loop through this command list and still be able to tell
- # whether or not we are within the scope of a particular class or instance
- # (by seeing if we are between a "ScopeBegin" and "ScopeEnd" pair).
-
- command_list.append(ScopeBegin(self, self.srcloc_begin))
- # Note:
- # The previous version looped over all commands in this node, and then
- # recursively invoke BuildCommandList() on all the children of this node
- # We don't do that anymore because it does not take into account the
- # order that various child objects were created/instantiated
- # which potentially could occur in-between other commands. Instead,
- # now we loop through the command_list and recursively visit child
- # nodes only when we encounter them in the command list.
-
- for command in self.commands_push:
- assert(isinstance(command, InstantiateCommand) == False)
- command_list.append(command)
-
- for command in self.commands:
- if isinstance(command, InstantiateCommand):
- #child = self.children[command.name]
- # the above line does not work because you may have
- # deleted that child after you created and then
- # replaced it by somebody else. Store the node.
- child = command.instobj
- child.BuildCommandList(command_list)
- else:
- command_list.append(command)
-
- for command in self.commands_pop:
- assert(isinstance(command, InstantiateCommand) == False)
- command_list.append(command)
-
- command_list.append(ScopeEnd(self, self.srcloc_begin))
-
-
-
-
-
-
-
-def AssignTemplateVarPtrs(tmpl_list, context_node):
- """
- Now scan through all the variables within the templates defined
- for this context_node (either static or dynamic depending on var_filter).
- Each reference to a variable in the template has a descriptor which
- indicates the variable's type, and in which molecule it is defined (ie
- where it is located in the molecule instance tree or type definition tree).
- (See comments for "class VarNPtr(object):" above for details.)
-
- Eventually we want to assign a value to each variable.
- This same variable (node) may appear multiple times in diffent templates.
- So we also create a place to store this variable's value, and also assign
- (two-way) pointers from the VarRef in the template, to this storage area so
- that later on when we write out the contents of the template to a file, we
- can substitute this variable with it's value, in all the places it appears.
-
- """
-
- for var_ref in tmpl_list:
- # Process the VarRef entries in the tmpl_list,
- # (and check they have the correct prefix: either '$' or '@')
- # Ignore other entries (for example, ignore TextBlocks).
-
-
- if (isinstance(var_ref, VarRef) and
- ((isinstance(context_node, StaticObj) and
- (var_ref.prefix[0] == '@'))
- or
- (isinstance(context_node, InstanceObjBasic) and
- (var_ref.prefix[0] == '$')))):
-
-
-
- var_ref.nptr.cat_name, var_ref.nptr.cat_node, var_ref.nptr.leaf_node = \
- DescrToCatLeafNodes(var_ref.descr_str,
- context_node,
- var_ref.srcloc,
- True)
-
-
- categories = var_ref.nptr.cat_node.categories
-
- # "categories" is a dictionary storing "Category" objects
- # indexed by category names.
-
- # Note to self: Always use the ".categories" member,
- # (never the ".instance_categories" member.
- # ".instance_categories" are only used temporarilly before
- # we instantiate, ie. before we build the tree of InstanceObjs.)
-
-
- category = categories[var_ref.nptr.cat_name]
- # "category" is a Category object containing a
- # dictionary of VarBinding objects, and an internal counter.
-
- var_bindings = category.bindings
- # "var_bindings" is a dictionary storing "VarBinding"
- # objects, indexed by leaf nodes. Each leaf node
- # corresponds to a unique variable in this category.
-
- # --- Now update "var_bindings" ---
-
- # Search for the "VarBinding" object that
- # corresponds to this leaf node.
- # If not found, then create one.
-
- if var_ref.nptr.leaf_node in var_bindings:
- var_binding = var_bindings[var_ref.nptr.leaf_node]
- # "var_binding" stores the information for a variable,
- # including pointers to all of the places the variable
- # is rerefenced, the variable's (full) name, and value.
- #
- # Keep track of all the places that varible is
- # referenced by updating the ".refs" member
- var_binding.refs.append(var_ref)
- else:
- # Not found, so we create a new binding.
- var_binding = VarBinding()
-
- # var_binding.refs contains a list of all the places
- # this variable is referenced. Start with this var_ref:
- var_binding.refs = [var_ref]
-
- # keep track of the cat_node, cat_name, leaf_node:
- var_binding.nptr = var_ref.nptr
-
- # "var_binding.full_name" stores a unique string like
- # '@/atom:Water/H' or '$/atom:water[1423]/H2',
- # which contains the full path for the category and leaf
- # nodes, and uniquely identifies this variable globally.
- # Thus these strings correspond uniquely (ie. in a
- # one-to-one fashion) with the nodes they represent.
-
-
- var_binding.full_name = var_ref.prefix[0] + \
- CanonicalDescrStr(var_ref.nptr.cat_name,
- var_ref.nptr.cat_node,
- var_ref.nptr.leaf_node,
- var_ref.srcloc)
- # (These names can always be generated later when needed
- # but it doesn't hurt to keep track of it here too.)
-
-
- # Now add this binding to the other
- # bindings in this category:
- var_bindings[var_ref.nptr.leaf_node] = var_binding
-
- ##vb## var_ref.nptr.leaf_node.AddVarBinding(var_binding)
-
- var_binding.category = category
-
- # It's convenient to add a pointer in the opposite direction
- # so that later if we find the var_ref, we can find its
- # binding and visa-versa. (Ie. two-way pointers)
- var_ref.binding = var_binding
-
- assert(var_ref.nptr.leaf_node in var_bindings)
-
-
-
-
-
-def AssignStaticVarPtrs(context_node, search_instance_commands = False):
-
- #sys.stdout.write('AssignVarPtrs() invoked on node: \"'+NodeToStr(context_node)+'\"\n')
-
- if search_instance_commands:
- assert(isinstance(context_node, StaticObj))
- commands = context_node.instance_commands
- else:
- # Note: Leaf nodes contain no commands, so skip them
- if (not hasattr(context_node, 'commands')):
- return
- # Otherwise process their commands
- commands = context_node.commands
-
-
- for command in commands:
-
- if isinstance(command, WriteFileCommand):
- AssignTemplateVarPtrs(command.tmpl_list, context_node)
-
- # Recursively invoke AssignVarPtrs() on all (non-leaf) child nodes:
- for child in context_node.children.values():
- AssignStaticVarPtrs(child, search_instance_commands)
-
-
-
-
-
-def AssignVarOrderByCommand(command_list, prefix_filter):
- """
- For each category in context_node, and each variable in that category,
- set the order of each variable according to the position of the
- write(), write_once(), or other command that created it.
- Only variables with the correct prefix ('$' or '@') are affected.
-
- """
- count = 0
- for command in command_list:
- if isinstance(command, WriteFileCommand):
- tmpl_list = command.tmpl_list
- for var_ref in tmpl_list:
- if isinstance(var_ref, VarRef):
- if var_ref.prefix in prefix_filter:
- count += 1
- if ((var_ref.binding.order is None) or
- (var_ref.binding.order > count)):
- var_ref.binding.order = count
-
-
-#def AssignVarOrderByFile(command_list, prefix_filter):
-# """
-# For each category in context_node, and each variable in that category,
-# set the order of each variable equal to the position of that variable
-# in the user's input file.
-#
-# """
-#
-# for command in command_list:
-# if isinstance(command, WriteFileCommand):
-# tmpl_list = command.tmpl_list
-# for var_ref in tmpl_list:
-# if isinstance(var_ref, VarRef):
-# if var_ref.prefix in prefix_filter:
-# if ((var_ref.binding.order is None) or
-# (var_ref.binding.order > var_ref.srcloc.order)):
-# var_ref.binding.order = var_ref.srcloc.order
-
-
-def AssignVarOrderByFile(context_node, prefix_filter, search_instance_commands=False):
- """
- For each category in context_node, and each variable in that category,
- set the order of each variable equal to the position of that variable
- in the user's input file.
-
- """
-
- commands = context_node.commands
- if search_instance_commands:
- assert(isinstance(context_node, StaticObj))
- commands.append(context_node.instance_commands_push + \
- context_node.instance_commands + \
- context_node.instance_commands_pop)
-
- for command in commands:
- if isinstance(command, WriteFileCommand):
- tmpl_list = command.tmpl_list
- for var_ref in tmpl_list:
- if (isinstance(var_ref, VarRef) and
- (var_ref.prefix in prefix_filter)):
- if ((var_ref.binding.order == -1) or
- (var_ref.binding.order > var_ref.srcloc.order)):
- var_ref.binding.order = var_ref.srcloc.order
-
- for child in context_node.children.values():
- AssignVarOrderByFile(child, prefix_filter, search_instance_commands)
-
-
-
-
-
-
-def AutoAssignVals(cat_node,
- sort_variables,
- reserved_values = None,
- ignore_prior_values = False):
- """
- This function automatically assigns values to all the variables
- belonging to all the categories in cat_node.categories.
- Each category has its own internal counter. For every variable in that
- category, query the counter (which usually returns an integer),
- and assign the variable to it. Exceptions can be made if the integer
- is reserved by some other variable, or if it has been already assigned.
- Afterwards, we recursively search the child nodes recursively
- (in a depth-first-search order).
-
- sort_variables: Sorting the variables according to their "binding.order"
- counters is optional.
-
- """
-
- if (not hasattr(cat_node, 'categories')):
- # (sometimes leaf nodes lack a 'categories' member, to save memory)
- return
-
- # Search the tree in a depth-first-search manner.
- # For each node, examine the "categories" associated with that node
- # (ie the list of variables whose counters lie within that node's scope).
- for cat_name, cat in cat_node.categories.items():
-
- # Loop through all the variables in this category.
-
- if sort_variables:
-
- # Sort the list of variables according to var_binding.order
-
- # First, print a progress indicator (this could be slow)
- prefix = '$'
- # Is this parent_node an StaticObj? (..or inherit from StaticObj?)
- if isinstance(cat_node, StaticObj):
- prefix = '@'
- sys.stderr.write(' sorting variables in category: '+prefix+
- CanonicalCatName(cat_name, cat_node)+':\n')
-
- var_bind_iter = iter(sorted(cat.bindings.items(),
- key=operator.itemgetter(1)))
- else:
- # Just iterate through them in the order that they were added
- # to the category list. (This happens to be the same order as
- # we found it earlier when searching the tree.)
- var_bind_iter = iter(cat.bindings.items())
-
-
- for leaf_node,var_binding in var_bind_iter:
-
- if ((var_binding.value is None) or ignore_prior_values):
-
- if var_binding.nptr.leaf_node.name[:9] == '__query__':
- # -- THE "COUNT" HACK --
- # '__query__...' variables are not really variables.
- # They are a mechanism to allow the user to query the
- # category counter without incrementing it.
- var_binding.value = str(cat.counter.query())
-
- elif HasWildCard(var_binding.full_name):
- # -- The wildcard hack ---
- # Variables containing * or ? characters in their names
- # are not allowed. These are not variables, but patterns
- # to match with other variables. Represent them by the
- # (full-path-expanded) string containing the * or ?.
- var_binding.value = var_binding.full_name
-
- else:
-
- if ((not var_binding.nptr.leaf_node.IsDeleted()) and
- (len(var_binding.refs) > 0)):
-
- # For each (regular) variable, query this category's counter
- # (convert it to a string), and see if it is already in use
- # (in this category). If not, then set this variable's value
- # to the counter's value. Either way, increment the counter.
- while True:
- cat.counter.incr()
- value = str(cat.counter.query())
- if ((reserved_values is None) or
- ((cat, value) not in reserved_values)):
- break
-
- var_binding.value = value
-
- # Recursively invoke AssignVarValues() on all child nodes
- for child in cat_node.children.values():
- AutoAssignVals(child,
- sort_variables,
- reserved_values,
- ignore_prior_values)
-
-
-
-
-
-
-# Did the user ask us to reformat the output string?
-# This information is encoded in the variable's suffix.
-def ExtractFormattingCommands(suffix):
- if (len(suffix) <= 1):
- return None, None
- if suffix[-1] == '}': # Get rid of any trailing '}' characters
- suffix = suffix[:-1]
- if suffix[-1] != ')': # Format functions are always followed by parens
- return None, None
- else:
- idot = suffix.find('.') # Format functions usually preceded by '.'
- ioparen = suffix.find('(')
- icparen = suffix.find(')')
- format_fname = suffix[idot+1:ioparen]
- args = suffix[ioparen+1:icparen]
- args = args.split(',')
- for i in range(0, len(args)):
- args[i] = RemoveOuterQuotes(args[i].strip(), '\"\'')
- return format_fname, args
-
-
-
-
-def Render(tmpl_list, substitute_vars=True):
- """
- This function converts a TextBlock,VarRef list into a string.
- It is invoked by WriteTemplatesValue() in order to print
- out the templates stored at each node of the tree.
-
- """
-
- out_str_list = []
- i = 0
- while i < len(tmpl_list):
- entry = tmpl_list[i]
- if isinstance(entry, VarRef):
- var_ref = entry
- var_bindings = var_ref.nptr.cat_node.categories[var_ref.nptr.cat_name].bindings
- #if var_ref.nptr.leaf_node not in var_bindings:
- #assert(var_ref.nptr.leaf_node in var_bindings)
- if var_ref.nptr.leaf_node.IsDeleted():
- raise InputError('Error near '+
- ErrorLeader(var_ref.srcloc.infile,
- var_ref.srcloc.lineno)+'\n'
- ' The variable you referred to does not exist:\n\n'
- ' '+var_ref.prefix+var_ref.descr_str+var_ref.suffix+'\n\n'
- ' (You probably deleted it or something it belonged to earlier.)\n')
- else:
- if substitute_vars:
- value = var_bindings[var_ref.nptr.leaf_node].value
- format_fname, args = ExtractFormattingCommands(var_ref.suffix)
- if format_fname == 'ljust':
- if len(args) == 1:
- value = value.ljust(int(args[0]))
- else:
- value = value.ljust(int(args[0]), args[1])
- elif format_fname == 'rjust':
- if len(args) == 1:
- value = value.rjust(int(args[0]))
- else:
- value = value.rjust(int(args[0]), args[1])
- out_str_list.append(value)
-
- else:
- out_str_list.append(var_ref.prefix +
- SafelyEncodeString(var_bindings[var_ref.nptr.leaf_node].full_name[1:]) +
- var_ref.suffix)
-
- else:
- assert(isinstance(entry, TextBlock))
- out_str_list.append(entry.text)
- i += 1
-
- return ''.join(out_str_list)
-
-def IgnoreThis(a):
- pass
-
-
-
-
-def FindReplacementVarPairs(context_node,
- replace_var_pairs):
- #search_instance_commands = False):
-
- #####################
- #if search_instance_commands:
- # assert(isinstance(context_node, StaticObj))
- # commands = context_node.instance_commands
- #else:
- # # Note: Leaf nodes contain no commands, so skip them
- # if (not hasattr(context_node, 'commands')):
- # return
- # # Otherwise process their commands
- # commands = context_node.commands
- #####################
-
- commands = context_node.commands
-
- for command in commands:
-
- if (isinstance(command, WriteFileCommand) and
- command.filename == 'ttree_replacements.txt'):
- tmpl_list = command.tmpl_list
- var_alias = None
- for entry in tmpl_list:
- # Each successive pair of variables indicates a
- # variable you wish to replace.
- # (Any ordinary text in between variable names is ignored.)
- if isinstance(entry, VarRef):
- if var_alias == None:
- var_alias = (entry.nptr.cat_name,
- entry.nptr.cat_node,
- entry.nptr.leaf_node)
- else:
- var_replace = (entry.nptr.cat_name,
- entry.nptr.cat_node,
- entry.nptr.leaf_node)
-
- replace_var_pairs[var_alias] = var_replace
- var_alias = None
-
- # Recursively invoke AssignVarPtrs() on all (non-leaf) child nodes:
- for child in context_node.children.values():
- FindReplacementVarPairs(child,
- replace_var_pairs)
- #search_instance_commands)
-
-
-
-
-
-def ReplaceVars(context_node,
- replace_var_pairs,
- search_instance_commands = False):
-
- if len(replace_var_pairs) == 0:
- return
-
- #sys.stdout.write('AssignVarPtrs() invoked on node: \"'+NodeToStr(context_node)+'\"\n')
-
- if search_instance_commands:
- assert(isinstance(context_node, StaticObj))
- commands = context_node.instance_commands
- else:
- # Note: Leaf nodes contain no commands, so skip them
- if (not hasattr(context_node, 'commands')):
- return
- # Otherwise process their commands
- commands = context_node.commands
-
-
- if len(replace_var_pairs) > 0:
- for command in commands:
- if isinstance(command, WriteFileCommand):
- ReplaceVarsInTmpl(command.tmpl_list,
- replace_var_pairs)
-
- # Recursively invoke ReplaceVars() on all (non-leaf) child nodes:
- for child in context_node.children.values():
- ReplaceVars(child,
- replace_var_pairs,
- search_instance_commands)
-
-
-
-
-
-def ReplaceVarsInTmpl(tmpl_list, replace_var_pairs):
- """ replace any references to specific variables with other variables """
-
- if len(replace_var_pairs) == 0:
- return
-
- i = 0
- while i < len(tmpl_list):
- entry = tmpl_list[i]
- if isinstance(entry, VarRef):
- var_ref = entry
- #full_name = var_bindings[var_ref.nptr.leaf_node].full_name
- if (var_ref.nptr.cat_name,
- var_ref.nptr.cat_node,
- var_ref.nptr.leaf_node) in replace_var_pairs:
- # optional: (since we will eventually delete the variable)
- # delete the reference to this variable from "bindings"
-
- nptr_old = var_ref.nptr
-
- # swap the old variable with the new one
- (nptr_new_cat_name, nptr_new_cat_node, nptr_new_leaf_node) = \
- replace_var_pairs[(nptr_old.cat_name,
- nptr_old.cat_node,
- nptr_old.leaf_node)]
-
- var_bindings = var_ref.nptr.cat_node.categories[nptr_old.cat_name].bindings
-
- assert(nptr_new_leaf_node in var_bindings)
-
- # Copy the things we need from the old variable.
- # References to the old variable should be added to the new one
- # (since they are the same variable)
- #for ref in var_bindings[nptr_old.leaf_node].refs:
- # ref.nptr.cat_name = nptr_new_cat_name
- # ref.nptr.cat_node = nptr_new_cat_node
- # ref.nptr.leaf_node = nptr_new_leaf_node
- if nptr_old.leaf_node in var_bindings:
- var_bindings[nptr_new_leaf_node].refs += var_bindings[nptr_old.leaf_node].refs
- del var_bindings[nptr_old.leaf_node]
-
- var_ref.nptr.cat_name = nptr_new_cat_name
- var_ref.nptr.cat_node = nptr_new_cat_node
- var_ref.nptr.leaf_node = nptr_new_leaf_node # <-- this will...
- # ... update all places where that nptr is used, including
- # all of the varrefs from the old variable. In other words,
- # there is no need to manually update the leaf_nodes in
- # the var_bindings[nptr_new_leaf_node].refs
- # (It's better to do it this way instead.)
-
- #var_ref.prefix = (...no need to modify)
- #var_ref.suffix = (...no need to modify)
-
- var_ref.descr_str = \
- CanonicalDescrStr(var_ref.nptr.cat_name,
- var_ref.nptr.cat_node,
- var_ref.nptr.leaf_node,
- var_ref.srcloc)
-
- var_bindings[nptr_new_leaf_node].full_name = var_ref.prefix[0] + var_ref.descr_str
-
- i += 1
-
-
-
-
-def MergeWriteCommands(command_list):
- """ Write commands are typically to the same file.
- We can improve performance by appending all of
- commands that write to the same file together before
- carrying out the write operation.
-
- """
- file_templates = defaultdict(list)
- for command in command_list:
- if isinstance(command, WriteFileCommand):
- if command.filename != None:
- file_templates[command.filename] += \
- command.tmpl_list
-
- return file_templates
-
-
-
-def WriteTemplatesValue(file_templates):
- """ Carry out the write() and write_once() commands (which
- write out the contents of the templates contain inside them).
-
- """
- for filename, tmpl_list in file_templates.items():
- if filename == '':
- out_file = sys.stdout
- else:
- out_file = open(filename, 'a')
-
- out_file.write(Render(tmpl_list, substitute_vars=True))
- if filename != '':
- out_file.close()
-
- # Alternate (old method):
- #for command in command_list:
- # if isinstance(command, WriteFileCommand):
- # if command.filename != None:
- # if command.filename == '':
- # out_file = sys.stdout
- # else:
- # out_file = open(command.filename, 'a')
- #
- # out_file.write(Render(command.tmpl_list))
- #
- # if command.filename != '':
- # out_file.close()
-
-
-
-def WriteTemplatesVarName(file_templates):
- """ Carry out the write() and write_once() commands (which
- write out the contents of the templates contain inside them).
- However variables within the templates are represented by their
- full name instead of their assigned value.
-
- """
-
- for filename, tmpl_list in file_templates.items():
- if filename != '':
- out_file = open(filename + '.template', 'a')
- out_file.write(Render(tmpl_list, substitute_vars=False))
- out_file.close()
-
-
-
-def EraseTemplateFiles(command_list):
- filenames = set([])
- for command in command_list:
- if isinstance(command, WriteFileCommand):
- if (command.filename != None) and (command.filename != ''):
- if command.filename not in filenames:
- filenames.add(command.filename)
- # Openning the files (in mode 'w') and closing them again
- # erases their contents.
- out_file = open(command.filename, 'w')
- out_file.close()
- out_file = open(command.filename + '.template', 'w')
- out_file.close()
-
-#def ClearTemplates(file_templates):
-# for filename in file_templates:
-# if filename != '':
-# out_file = open(filename, 'w')
-# out_file.close()
-# out_file = open(filename + '.template', 'w')
-# out_file.close()
-
-
-
-def WriteVarBindingsFile(node):
- """ Write out a single file which contains a list of all
- of the variables defined (regardless of which class they
- were defined in). Next to each variable name is the corresponding
- information stored in that variable (a number) that variable.
-
- """
- if (not hasattr(node, 'categories')):
- # (sometimes leaf nodes lack a 'categories' member, to save memory)
- return
-
- out = open('ttree_assignments.txt', 'a')
- for cat_name in node.categories:
- var_bindings = node.categories[cat_name].bindings
- for nd, var_binding in var_bindings.items():
- if nd.IsDeleted():
- continue # In that case, skip this variable
-
- if len(var_binding.refs) == 0: #check2016-6-07
- continue
-
- #if type(node) is type(nd):
- if ((isinstance(node, InstanceObjBasic) and isinstance(nd, InstanceObjBasic))
- or
- (isinstance(node, StaticObj) and isinstance(nd, StaticObj))):
-
- # Now omit variables whos names contain "*" or "?"
- # (these are actually not variables, but wildcard patterns)
- if not HasWildCard(var_binding.full_name):
- if len(var_binding.refs) > 0:
- usage_example = ' #'+\
- ErrorLeader(var_binding.refs[0].srcloc.infile, \
- var_binding.refs[0].srcloc.lineno)
- else:
- usage_example = ''
- out.write(SafelyEncodeString(var_binding.full_name) +' '+
- SafelyEncodeString(var_binding.value)
- +usage_example+'\n')
- out.close()
- for child in node.children.values():
- WriteVarBindingsFile(child)
-
-
-
-
-
-
-def CustomizeBindings(bindings,
- objectdefs,
- objects):
-
- var_assignments = set()
-
- for name,vlpair in bindings.items():
-
- prefix = name[0]
- var_descr_str = name[1:]
-
- value = vlpair.val
- dbg_loc = vlpair.loc
-
- if prefix == '@':
- var_binding = LookupVar(var_descr_str,
- objectdefs,
- dbg_loc)
-
- elif prefix == '$':
- var_binding = LookupVar(var_descr_str,
- objects,
- dbg_loc)
- else:
- # If the user neglected a prefix, this should have generated
- # an error earlier on.
- assert(False)
-
- # Change the assignment:
- var_binding.value = value
- var_assignments.add((var_binding.category, value))
-
- #sys.stderr.write(' CustomizeBindings: descr=' + var_descr_str +
- # ', value=' + value + '\n')
-
- return var_assignments
-
-
-
-def ReplaceVarsInCustomBindings(bindings,
- objectdefs,
- objects,
- replace_var_pairs):
-
- if len(replace_var_pairs) == 0:
- return
-
- list_of_pairs = bindings.items()
-
- for name,vlpair in list_of_pairs:
-
- prefix = name[0]
- var_descr_str = name[1:]
-
- value = vlpair.val
- dbg_loc = vlpair.loc
-
- if prefix == '@':
- # At this point, we have probably already binding associated
- # with any replaced variables. Instead lookup the nodes directly:
-
- cat_name, cat_node, leaf_node = DescrToCatLeafNodes(var_descr_str,
- objectdefs,
- dbg_loc)
- # If this triplet corresponds to a variable we want to replace
- # then lookup the corrected triplet
- if (cat_name, cat_node, leaf_node) in replace_var_pairs:
- (new_cat_name,
- new_cat_node,
- new_leaf_node) = replace_var_pairs[(cat_name,
- cat_node,
- leaf_node)]
-
- # now reconstruct the string representing that variable
- new_name = prefix + CanonicalDescrStr(new_cat_name,
- new_cat_node,
- new_leaf_node)
- bindings[new_name] = bindings[name]
- del bindings[name]
-
-
-##############################################################
-##################### BasicUI functions #####################
-# These functions are examples of how to use the StaticObj
-# and InstanceObj data structures above, and to read a ttree file.
-# These are examples only. New programs based on ttree_lib.py
-# will probably require their own settings and functions.
-##############################################################
-
-
-def BasicUIReadBindingsFile(bindings_so_far, filename):
- try:
- f = open(filename, 'r')
- except IOError:
- sys.stderr.write('Error('+g_filename+'):\n'' : unable to open file\n'
- '\n'
- ' \"'+filename+'\"\n'
- ' for reading.\n'
- '\n'
- ' (If you were not trying to open a file with this name, then this could\n'
- ' occur if you forgot to enclose your command-line-argument in quotes,\n'
- ' For example, use: \'$atom:wat[2]/H1 20\' or "\$atom:wat[2]/H1 to 20"\n'
- ' to set the variable $atom:wat[2]/H1 to 20.)\n')
- sys.exit(1)
-
- BasicUIReadBindingsStream(bindings_so_far, f, filename)
- f.close()
-
-
-
-
-def BasicUIReadBindingsText(bindings_so_far, text, source_name=''):
- if sys.version > '3':
- in_stream = io.StringIO(text)
- else:
- in_stream = cStringIO.StringIO(text)
- return BasicUIReadBindingsStream(bindings_so_far, in_stream, source_name)
-
-
-
-class ValLocPair(object):
- __slots__=["val","loc"]
- def __init__(self,
- val = None,
- loc = None):
- self.val = val
- self.loc = loc
-
-
-def BasicUIReadBindingsStream(bindings_so_far, in_stream, source_name=''):
-
- # EXAMPLE (simple version)
- # The simple version of this function commented out below
- # does not handle variable whose names or values
- # contain strange or escaped characters, quotes or whitespace.
- # But I kept it in for illustrative purposes:
- #
- #for line in f:
- # line = line.strip()
- # tokens = line.split()
- # if len(tokens) == 2:
- # var_name = tokens[0]
- # var_value = tokens[1]
- # var_assignments[var_name] = var_value
- #f.close()
-
-
- lex = TemplateLexer(in_stream, source_name)
- tmpllist = lex.ReadTemplate()
- i = 0
- if isinstance(tmpllist[0], TextBlock):
- i += 1
- while i+1 < len(tmpllist):
- # process one line at a time (2 entries per line)
- var_ref = tmpllist[i]
- text_block = tmpllist[i+1]
- assert(isinstance(var_ref, VarRef))
- if (not isinstance(text_block, TextBlock)):
- raise InputError('Error('+g_filename+'):\n'
- ' This is not a valid name-value pair:\n'
- ' \"'+var_ref.prefix+var_ref.descr_str+' '+text_block.text.rstrip()+'\"\n'
- ' Each variable asignment should contain a variable name (beginning with\n'
- ' @ or $) followed by a space, and then a string you want to assign to it.\n'
- ' (Surrounding quotes are optional and will be removed.)\n')
-
- # Variables in the ttree_assignments.txt file use "full-path" style.
- # In other words, the full name of the variable, (including all
- # path information) is stored var_ref.descr_str,
- # and the first character of the prefix stores either a @ or $
- var_name = var_ref.prefix[:1] + var_ref.descr_str
- text = SplitQuotedString(text_block.text.strip())
- var_value = EscCharStrToChar(RemoveOuterQuotes(text, '\'\"'))
- bindings_so_far[var_name] = ValLocPair(var_value, lex.GetSrcLoc())
- i += 2
-
-
-
-
-class BasicUISettings(object):
- """
- BasicUISettings() contains several run-time user customisations
- for ttree. (These effect the order and values assigned to variables
- in a ttreee file).
- This object, along with the other "UI" functions below are examples only.
- (New programs based on ttree_lib.py will probably have their own settings
- and functions.)
-
- Members:
- user_bindings
- user_bindings_x
- These are lists containing pairs of variable names,
- and the string values they are bound to (which are typically numeric).
- Values specified in the "user_bindings_x" list are "exclusive".
- This means their values are reserved, so that later on, when other
- variables (in the same category) are automatically assigned to values, care
- care will be taken to avoid duplicating the values in user_bindings_x.
- However variables in the "user_bindings" list are assigned without regard
- to the values assigned to other variables, and may or may not be unique.
-
- order_method
- The order_method specifies the order in which values will be automatically
- assigned to variables. (In the context of building molecular simulation
- input files, this helps the user to insure that the order of the atoms
- created by the ttree file matches the order they appear in other files
- created by other programs.)
-
- """
- def __init__(self,
- user_bindings_x=None,
- user_bindings=None,
- order_method='by_command',
- lex=None):
- if user_bindings_x:
- self.user_bindings_x = user_bindings_x
- else:
- self.user_bindings_x = OrderedDict()
- if user_bindings:
- self.user_bindings = user_bindings
- else:
- self.user_bindings = OrderedDict()
- self.order_method = order_method
- self.lex = lex
-
-
-
-
-def BasicUIParseArgs(argv, settings):
- """
- BasicUIParseArgs()
- The following function contains part of the user interface for a
- typical ttree-based program. This function processes an argument list
- and extracts the common ttree user settings.
- This function, along with the other "UI" functions below are examples only.
- (New programs based on ttree_lib.py will probably have their own UI.)
-
- """
-
- #argv = [arg for arg in orig_argv] # (make a deep copy of "orig_argv")
-
- # This error message is used in multiple places:
-
- bind_err_msg = 'should either be followed by a 2-column\n'+\
- ' file (containing variable-value pairs on each line).\n'+\
- ' --OR-- a quoted string (such as \"@atom:x 2\")\n'+\
- ' with the full variable name and its desired value.'
- bind_err_msg_var = 'Missing value, or space needed separating variable\n'+\
- ' and value. (Remember to use quotes to surround the argument\n'+\
- ' containing the variable name, and it\'s assigned value.)'
-
- i = 1
-
-
- while i < len(argv):
- #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
- if argv[i] == '-a':
- if ((i+1 >= len(argv)) or (argv[i+1][:1] == '-')):
- raise InputError('Error('+g_filename+'):\n'
- ' Error in -a \"'+argv[i+1]+' argument.\"\n'
- ' The -a flag '+bind_err_msg)
- if (argv[i+1][0] in '@$'):
- #tokens = argv[i+1].strip().split(' ')
- tokens = SplitQuotedString(argv[i+1].strip())
- if len(tokens) < 2:
- raise InputError('Error('+g_filename+'):\n'
- ' Error in -a \"'+argv[i+1]+'\" argument.\n'
- ' '+bind_err_msg_var)
- BasicUIReadBindingsText(settings.user_bindings_x,
- argv[i+1],
- '__command_line_argument__')
- else:
- BasicUIReadBindingsFile(settings.user_bindings_x,
- argv[i+1])
- #i += 2
- del(argv[i:i+2])
- elif argv[i] == '-b':
- if ((i+1 >= len(argv)) or (argv[i+1][:1] == '-')):
- raise InputError('Error('+g_filename+'):\n'
- ' Error in -b \"'+argv[i+1]+' argument.\"\n'
- ' The -b flag '+bind_err_msg)
- if (argv[i+1][0] in '@$'):
- #tokens = argv[i+1].strip().split(' ')
- tokens = SplitQuotedString(argv[i+1].strip())
- if len(tokens) < 2:
- raise InputError('Error('+g_filename+'):\n'
- ' Error in -b \"'+argv[i+1]+'\" argument.\n'
- ' '+bind_err_msg_var)
- BasicUIReadBindingsText(settings.user_bindings,
- argv[i+1],
- '__command_line_argument__')
- else:
- BasicUIReadBindingsFile(settings.user_bindings,
- argv[i+1])
- #i += 2
- del(argv[i:i+2])
- elif argv[i] == '-order-command':
- settings.order_method = 'by_command'
- #i += 1
- del(argv[i:i+1])
- elif argv[i] == '-order-file':
- settings.order_method = 'by_file'
- #i += 1
- del(argv[i:i+1])
- elif ((argv[i] == '-order-tree') or (argv[i] == '-order-dfs')):
- settings.order_method = 'by_tree'
- del(argv[i:i+1])
- elif ((argv[i] == '-importpath') or
- (argv[i] == '-import-path') or
- (argv[i] == '-import_path')):
- if ((i+1 >= len(argv)) or (argv[i+1][:1] == '-')):
- raise InputError('Error('+g_filename+'):\n'
- ' Error in \"'+argv[i]+'\" argument.\"\n'
- ' The \"'+argv[i]+'\" argument should be followed by the name of\n'
- ' an environment variable storing a path for including/importing files.\n')
- TtreeShlex.custom_path = RemoveOuterQuotes(argv[i+1])
- del(argv[i:i+2])
-
- elif ((argv[i][0] == '-') and (__name__ == "__main__")):
- #elif (__name__ == "__main__"):
- raise InputError('Error('+g_filename+'):\n'
- 'Unrecognized command line argument \"'+argv[i]+'\"\n')
- else:
- i += 1
-
-
- if __name__ == "__main__":
-
- # Instantiate the lexer we will be using.
- # (The lexer's __init__() function requires an openned file.
- # Assuming __name__ == "__main__", then the name of that file should
- # be the last remaining (unprocessed) argument in the argument list.
- # Otherwise, then name of that file will be determined later by the
- # python script which imports this module, so we let them handle it.)
-
- if len(argv) == 1:
- raise InputError('Error('+g_filename+'):\n'
- ' This program requires at least one argument\n'
- ' the name of a file containing ttree template commands\n')
- elif len(argv) == 2:
- try:
- settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file
- except IOError:
- sys.stderr.write('Error('+g_filename+'):\n'
- ' unable to open file\n'
- ' \"'+argv[1]+'\"\n'
- ' for reading.\n')
- sys.exit(1)
- del(argv[1:2])
-
- else:
- # if there are more than 2 remaining arguments,
- problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
- raise InputError('Syntax Error ('+g_filename+'):\n'
- ' Problem with argument list.\n'
- ' The remaining arguments are:\n\n'
- ' '+(' '.join(problem_args))+'\n\n'
- ' (The actual problem may be earlier in the argument list.\n'
- ' If these arguments are source files, then keep in mind\n'
- ' that this program can not parse multiple source files.)\n'
- ' Check the syntax of the entire argument list.\n')
-
-
-
-
-
-
-def BasicUI(settings,
- static_tree_root,
- instance_tree_root,
- static_commands,
- instance_commands):
- """
- BasicUI()
- This function loads a ttree file and optional custom bindings for it,
- creates a "static" tree (of defined ttree classes),
- creates an "instance" tree (of instantiated ttree objects),
- automatically assigns values to unbound variables,
- substitutes them into text templates (renders the template).
- The actual writing of the templates to a file is not handled here.
-
- """
-
- # Parsing, and compiling is a multi-pass process.
-
- # Step 1: Read in the StaticObj (class) definitions, without checking
- # whether or not the instance_children refer to valid StaticObj types.
- sys.stderr.write('parsing the class definitions...')
- static_tree_root.Parse(settings.lex)
- #gc.collect()
-
-
- #sys.stderr.write('static = ' + str(static_tree_root) + '\n')
-
- # Step 2: Now that the static tree has been constructed, lookup
- # any references to classes (StaticObjs), contained within
- # the instance_children or class_parents of each node in
- # static_tree_root. Replace them with (pointers to)
- # the StaticObjs they refer to (and check validity).
- # (Note: Variables stored within the templates defined by write()
- # and write_once() statements may also refer to StaticObjs in
- # the tree, but we leave these references alone. We handle
- # these assignments later using "AssignVarPtrs()" below.)
- sys.stderr.write(' done\nlooking up classes...')
- static_tree_root.LookupStaticRefs()
- #gc.collect()
-
-
- # Step 3: Now scan through all the (static) variables within the templates
- # and replace the (static) variable references to pointers
- # to nodes in the StaticObj tree:
- sys.stderr.write(' done\nlooking up @variables...')
-
- # Step 3a)
- # Here we assign pointers for @variables in "write_once(){text}" templates:
- AssignStaticVarPtrs(static_tree_root, search_instance_commands=False)
-
- # Step 3b) Replace any @variables with their equivalents (if applicable)
- replace_var_pairs = {}
- FindReplacementVarPairs(static_tree_root, replace_var_pairs)
- ReplaceVars(static_tree_root, replace_var_pairs,
- search_instance_commands=False)
-
- # Step 3c)
- # Here we assign pointers for @variables in "write(){text}" templates:
- AssignStaticVarPtrs(static_tree_root, search_instance_commands=True)
- ReplaceVars(static_tree_root, replace_var_pairs,
- search_instance_commands=True)
-
- sys.stderr.write(' done\nconstructing the tree of class definitions...')
- sys.stderr.write(' done\n\nclass_def_tree = ' + str(static_tree_root) + '\n\n')
- #gc.collect()
-
-
- # Step 4: Construct the instance tree (the tree of instantiated
- # classes) from the static tree of type definitions.
- sys.stderr.write('constructing the instance tree...\n')
- class_parents_in_use = set([])
- instance_tree_root.BuildInstanceTree(static_tree_root, class_parents_in_use)
- #sys.stderr.write('done\n garbage collection...')
- #gc.collect()
- sys.stderr.write(' done\n')
- #sys.stderr.write('instance_tree = ' + str(instance_tree_root) + '\n')
-
-
- # Step 5: The commands must be carried out in a specific order.
- # (for example, the "write()" and "new" commands).
- # Search through the tree, and append commands to a command list.
- # Then re-order the list in the order the commands should have
- # been executed in. (We don't carry out the commands yet,
- # we just store them and sort them.)
- class_parents_in_use = set([])
- static_tree_root.BuildCommandList(static_commands)
- instance_tree_root.BuildCommandList(instance_commands)
- #sys.stderr.write('static_commands = '+str(static_commands)+'\n')
- #sys.stderr.write('instance_commands = '+str(instance_commands)+'\n')
-
-
- # Step 6: Replace any $variables with their equivalents (if applicable)
- ReplaceVars(instance_tree_root, replace_var_pairs)
-
-
- # Step 7: We are about to assign numbers to the variables.
- # We need to decide the order in which to assign them.
- # By default static variables (@) are assigned in the order
- # they appear in the file.
- # And, by default instance variables ($)
- # are assigned in the order they are created during instantiation.
- #sys.stderr.write(' done\ndetermining variable count order...')
- AssignVarOrderByFile(static_tree_root, '@', search_instance_commands=True)
- AssignVarOrderByCommand(instance_commands, '$')
-
-
- # Step 8: Assign the variables.
- # (If the user requested any customized variable bindings,
- # load those now.)
- if len(settings.user_bindings_x) > 0:
- if len(replace_var_pairs) > 0:
- ReplaceVarsInCustomBindings(settings.user_bindings_x,
- static_tree_root,
- instance_tree_root,
- replace_var_pairs)
- reserved_values = CustomizeBindings(settings.user_bindings_x,
- static_tree_root,
- instance_tree_root)
- else:
- reserved_values = None
-
- sys.stderr.write('sorting variables...\n')
- AutoAssignVals(static_tree_root,
- (settings.order_method != 'by_tree'),
- reserved_values)
-
- AutoAssignVals(instance_tree_root,
- (settings.order_method != 'by_tree'),
- reserved_values)
-
- if len(settings.user_bindings) > 0:
- if len(replace_var_pairs) > 0:
- ReplaceVarsInCustomBindings(settings.user_bindings,
- static_tree_root,
- instance_tree_root,
- replace_var_pairs)
- CustomizeBindings(settings.user_bindings,
- static_tree_root,
- instance_tree_root)
-
- sys.stderr.write(' done\n')
-
-
-
-
-
-if __name__ == "__main__":
-
- """
- This is is a "main module" wrapper for invoking ttree.py
- as a stand alone program. This program:
-
- 1)reads a ttree file,
- 2)constructs a tree of class definitions (g_objectdefs)
- 3)constructs a tree of instantiated class objects (g_objects),
- 4)automatically assigns values to the variables,
- 5)and carries out the "write" commands to write the templates a file(s).
-
- """
-
- ####### Main Code Below: #######
- g_program_name = g_filename
- sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
- sys.stderr.write('\n(python version '+str(sys.version)+')\n')
-
- try:
-
- settings = BasicUISettings()
- BasicUIParseArgs(sys.argv, settings)
-
-
- # Data structures to store the class definitionss and instances
- g_objectdefs = StaticObj('', None) # The root of the static tree
- # has name '' (equivalent to '/')
- g_objects = InstanceObj('', None) # The root of the instance tree
- # has name '' (equivalent to '/')
-
- # A list of commands to carry out
- g_static_commands = []
- g_instance_commands = []
-
-
- BasicUI(settings,
- g_objectdefs,
- g_objects,
- g_static_commands,
- g_instance_commands)
-
- # Now write the files
- # (Finally carry out the "write()" and "write_once()" commands.)
-
- # Optional: Multiple commands to write to the same file can be merged to
- # reduce the number of times the file is openned and closed.
- sys.stderr.write('writing templates...\n')
- # Erase the files that will be written to:
- EraseTemplateFiles(g_static_commands)
- EraseTemplateFiles(g_instance_commands)
-
- g_static_commands = MergeWriteCommands(g_static_commands)
- g_instance_commands = MergeWriteCommands(g_instance_commands)
-
- # Write the files with the original variable names present
- WriteTemplatesVarName(g_static_commands)
- WriteTemplatesVarName(g_instance_commands)
- # Write the files with the variable names substituted by values
- WriteTemplatesValue(g_static_commands)
- WriteTemplatesValue(g_instance_commands)
-
- sys.stderr.write(' done\n')
-
- # Step 11: Now write the variable bindings/assignments table.
- sys.stderr.write('writing \"ttree_assignments.txt\" file...')
- open('ttree_assignments.txt', 'w').close() # <-- erase previous version.
- WriteVarBindingsFile(g_objectdefs)
- WriteVarBindingsFile(g_objects)
-
- sys.stderr.write(' done\n')
-
- except (ValueError, InputError) as err:
- sys.stderr.write('\n\n'+str(err)+'\n')
- sys.exit(-1)
-
diff --git a/tools/moltemplate/src/ttree_lex.py b/tools/moltemplate/src/ttree_lex.py
deleted file mode 100644
index d0938047c..000000000
--- a/tools/moltemplate/src/ttree_lex.py
+++ /dev/null
@@ -1,2088 +0,0 @@
-# -*- coding: iso-8859-1 -*-
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-"""A lexical analyzer class for simple shell-like syntaxes.
- This version has been modified slightly to work better with unicode.
- It was forked from the version of shlex that ships with python 3.2.2.
- A few minor features and functions have been added. """
-
-# Module and documentation by Eric S. Raymond, 21 Dec 1998
-# Input stacking and error message cleanup added by ESR, March 2000
-# push_source() and pop_source() made explicit by ESR, January 2001.
-# Posix compliance, split(), string arguments, and
-# iterator interface by Gustavo Niemeyer, April 2003.
-# ("wordterminators" (unicode support) hack by Andrew Jewett September 2011)
-
-import os.path
-import sys
-from collections import deque
-import re, fnmatch
-import string
-#import gc
-
-
-try:
- from cStringIO import StringIO
-except ImportError:
- try:
- from StringIO import StringIO
- except ImportError:
- from io import StringIO
-
-__all__ = ["TtreeShlex",
- "split",
- "LineLex",
- "SplitQuotedString",
- "EscCharStrToChar",
- "SafelyEncodeString",
- "RemoveOuterQuotes",
- "MaxLenStr",
- "HasWildCard",
- #"IsRegex",
- "InputError",
- "ErrorLeader",
- "SrcLoc",
- "OSrcLoc",
- "TextBlock",
- "VarRef",
- "VarNPtr",
- "VarBinding",
- "SplitTemplate",
- "SplitTemplateMulti",
- "TableFromTemplate",
- "ExtractCatName",
- #"_TableFromTemplate",
- #"_DeleteLineFromTemplate",
- "DeleteLinesWithBadVars",
- "TemplateLexer"]
-
-
-
-
-class TtreeShlex(object):
- """ A lexical analyzer class for simple shell-like syntaxes.
- TtreeShlex is a backwards-compatible version of python's standard shlex
- module. It has the additional member: "self.wordterminators", which
- overrides the "self.wordchars" member. This enables better handling of
- unicode characters by allowing a much larger variety of characters to
- appear in words or tokens parsed by TtreeShlex.
-
- """
-
- custom_path = None
-
- def __init__(self,
- instream=None,
- infile=None,
- custom_include_path=None,
- posix=False):
- if isinstance(instream, str):
- instream = StringIO(instream)
- if instream is not None:
- self.instream = instream
- self.infile = infile
- else:
- self.instream = sys.stdin
- self.infile = None
- self.posix = posix
- if posix:
- self.eof = None
- else:
- self.eof = ''
- self.commenters = '#'
- self.wordchars = ('abcdfeghijklmnopqrstuvwxyz'
- 'ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_')
- if self.posix:
- self.wordchars += ('ßàáâãäåæçèéêëìíîïðñòóôõöøùúûüýþÿ'
- 'ÀÁÂÃÄÅÆÇÈÉÊËÌÍÎÏÐÑÒÓÔÕÖØÙÚÛÜÝÞ')
-
- self.wordterminators = set([]) #WORDTERMINATORS
- self.prev_space_terminator = '' #WORDTERMINATORS
- self.whitespace = ' \t\r\f\n'
- self.whitespace_split = False
- self.quotes = '\'"'
- self.escape = '\\'
- self.escapedquotes = '"'
- self.state = ' '
- self.pushback = deque()
- self.lineno = 1
- self.debug = 0
- self.token = ''
- self.filestack = deque()
- # self.source_triggers
- # are tokens which allow the seamless insertion of other
- # files into the file being read.
- self.source_triggers=set(['source'])
- self.source_triggers_x=set([])
- #Note: self.source_triggers_x
- # This is a subset of self.source_triggers.
- # In this case file inclusion is exclusive.
- # In other words, if one of these tokens
- # is encountered, the file is only included
- # if it has not been included already.
- self.source_files_restricted = set([])
- self.include_path = []
- if TtreeShlex.custom_path:
- include_path_list = TtreeShlex.custom_path.split(':')
- self.include_path += [d for d in include_path_list if len(d)>0]
- if 'TTREE_PATH' in os.environ:
- include_path_list = os.environ['TTREE_PATH'].split(':')
- self.include_path += [d for d in include_path_list if len(d)>0]
- if self.debug:
- print('TtreeShlex: reading from %s, line %d' \
- % (self.instream, self.lineno))
- self.end_encountered = False
-
-
- @staticmethod #WORDTERMINATORS
- def _belongs_to(char, include_chars, exclude_chars): #WORDTERMINATORS
- if ((not exclude_chars) or (len(exclude_chars)==0)): #WORDTERMINATORS
- return char in include_chars #WORDTERMINATORS
- else: #WORDTERMINATORS
- return char not in exclude_chars #WORDTERMINATORS
-
- def push_raw_text(self, text):
- """Push a block of text onto the stack popped by the ReadLine() method.
- (If multiple lines are present in the text, (which is determined by
- self.line_terminators), then the text is split into multiple lines
- and each one of them is pushed onto this stack individually.
- The "self.lineno" counter is also adjusted, depending on the number
- of newline characters in "line".
- Do not strip off the newline, or other line terminators
- at the end of the text block before using push_raw_text()!
-
- """
- if self.debug >= 1:
- print("TtreeShlex: pushing token " + repr(text))
- for c in reversed(text): #WORDTERMINATORS
- self.pushback.appendleft(c) #WORDTERMINATORS
- if c == '\n': #WORDTERMINATORS
- self.lineno -= 1 #WORDTERMINATORS
- if len(text) > 0: #WORDTERMINATORS
- self.end_encountered = False #WORDTERMINATORS
-
- def push_token(self, text):
- "Push a token onto the stack popped by the get_token method"
- self.push_raw_text(text+self.prev_space_terminator)
-
- def push_source(self, newstream, newfile=None):
- "Push an input source onto the lexer's input source stack."
- if isinstance(newstream, str):
- newstream = StringIO(newstream)
- self.filestack.appendleft((self.infile, self.instream, self.lineno))
- self.infile = newfile
- self.instream = newstream
- self.lineno = 1
- if self.debug:
- if newfile is not None:
- print('TtreeShlex: pushing to file %s' % (self.infile,))
- else:
- print('TtreeShlex: pushing to stream %s' % (self.instream,))
-
- def pop_source(self):
- "Pop the input source stack."
- self.instream.close()
- (self.infile, self.instream, self.lineno) = self.filestack.popleft()
- if self.debug:
- print('TtreeShlex: popping to %s, line %d' \
- % (self.instream, self.lineno))
- self.state = ' '
-
- def get_token(self):
- "Get a token from the input stream (or from stack if it's nonempty)"
- #### #CHANGING: self.pushback is now a stack of characters, not tokens #WORDTERMINATORS
- #### if self.pushback: #WORDTERMINATORS
- #### tok = self.pushback.popleft() #WORDTERMINATORS
- #### if self.debug >= 1: #WORDTERMINATORS
- #### print("TtreeShlex: popping token " + repr(tok)) #WORDTERMINATORS
- #### return tok #WORDTERMINATORS
- #### No pushback. Get a token. #WORDTERMINATORS
- raw = self.read_token()
- # Handle inclusions
- if self.source_triggers is not None:
- while raw in self.source_triggers:
- fname=self.read_token()
- spec = self.sourcehook(fname)
- if spec:
- (newfile, newstream) = spec
- if ((raw not in self.source_triggers_x) or
- (newfile not in self.source_files_restricted)):
- self.push_source(newstream, newfile)
- if raw in self.source_triggers_x:
- self.source_files_restricted.add(newfile)
- else:
- if self.debug >= 1:
- sys.stderr.write('\ndebug warning: duplicate attempt to import file:\n \"'+newfile+'\"\n')
- raw = self.get_token()
-
- # Maybe we got EOF instead?
- while raw == self.eof:
- if not self.filestack:
- return self.eof
- else:
- self.pop_source()
- raw = self.get_token()
- # Neither inclusion nor EOF
- if self.debug >= 1:
- if raw != self.eof:
- print("TtreeShlex: token=" + repr(raw))
- else:
- print("TtreeShlex: token=EOF")
-
- if raw == self.eof: #WORDTERMINATORS
- self.end_encountered = True #WORDTERMINATORS
-
- return raw
-
-
- def read_char(self):
- if self.pushback: #WORDTERMINATORS
- nextchar = self.pushback.popleft() #WORDTERMINATORS
- assert((type(nextchar) is str) and (len(nextchar)==1)) #WORDTERMINATORS
- else: #WORDTERMINATORS
- nextchar = self.instream.read(1) #WORDTERMINATORS
- return nextchar
-
-
- def read_token(self):
- self.prev_space_terminator = '' #WORDTERMINATORS
- quoted = False
- escapedstate = ' '
- while True:
- #### self.pushback is now a stack of characters, not tokens #WORDTERMINATORS
- nextchar = self.read_char()
- if nextchar == '\n':
- self.lineno = self.lineno + 1
- if self.debug >= 3:
- print("TtreeShlex: in state", repr(self.state), \
- "I see character:", repr(nextchar))
- if self.state is None:
- self.token = '' # past end of file
- break
- elif self.state == ' ':
- if not nextchar:
- self.state = None # end of file
- break
- elif nextchar in self.whitespace:
- if self.debug >= 2:
- print("TtreeShlex: I see whitespace in whitespace state")
- if self.token or (self.posix and quoted):
- # Keep track of which whitespace
- # character terminated the token.
- self.prev_space_terminator = nextchar #WORDTERMINATORS
- break # emit current token
- else:
- continue
- elif nextchar in self.commenters:
- self.instream.readline()
- self.lineno = self.lineno + 1
- elif self.posix and nextchar in self.escape:
- escapedstate = 'a'
- self.state = nextchar
- elif TtreeShlex._belongs_to(nextchar, #WORDTERMINATORS
- self.wordchars, #WORDTERMINATORS
- self.wordterminators):#WORDTERMINATORS
- self.token = nextchar
- self.state = 'a'
- elif nextchar in self.quotes:
- if not self.posix:
- self.token = nextchar
- self.state = nextchar
- elif self.whitespace_split:
- self.token = nextchar
- self.state = 'a'
- else:
- self.token = nextchar
- if self.token or (self.posix and quoted):
- break # emit current token
- else:
- continue
- elif self.state in self.quotes:
- quoted = True
- if not nextchar: # end of file
- if self.debug >= 2:
- print("TtreeShlex: I see EOF in quotes state")
- # XXX what error should be raised here?
- raise ValueError("Error at or before "+self.error_leader()+"\n"
- " No closing quotation.")
- if nextchar == self.state:
- if not self.posix:
- self.token = self.token + nextchar
- self.state = ' '
- break
- else:
- self.state = 'a'
- elif self.posix and nextchar in self.escape and \
- self.state in self.escapedquotes:
- escapedstate = self.state
- self.state = nextchar
- else:
- self.token = self.token + nextchar
- elif self.state in self.escape:
- if not nextchar: # end of file
- if self.debug >= 2:
- print("TtreeShlex: I see EOF in escape state")
- # XXX what error should be raised here?
- raise ValueError("No escaped character")
- # In posix shells, only the quote itself or the escape
- # character may be escaped within quotes.
- if escapedstate in self.quotes and \
- nextchar != self.state and nextchar != escapedstate:
- self.token = self.token + self.state
- self.token = self.token + nextchar
- self.state = escapedstate
- elif self.state == 'a':
- if not nextchar:
- self.state = None # end of file
- break
- elif nextchar in self.whitespace:
- if self.debug >= 2:
- print("TtreeShlex: I see whitespace in word state")
- self.state = ' '
- if self.token or (self.posix and quoted):
- # Keep track of which whitespace
- # character terminated the token.
- self.prev_space_terminator = nextchar #WORDTERMINATORS
- break # emit current token
- else:
- continue
- elif nextchar in self.commenters:
- comment_contents = self.instream.readline()
- self.lineno = self.lineno + 1
- if self.posix:
- self.state = ' '
- if self.token or (self.posix and quoted):
- # Keep track of which character(s) terminated
- # the token (including whitespace and comments).
- self.prev_space_terminator = nextchar + comment_contents #WORDTERMINATORS
- break # emit current token
- else:
- continue
- elif self.posix and nextchar in self.quotes:
- self.state = nextchar
- elif self.posix and nextchar in self.escape:
- escapedstate = 'a'
- self.state = nextchar
- elif (TtreeShlex._belongs_to(nextchar, #WORDTERMINATORS
- self.wordchars, #WORDTERMINATORS
- self.wordterminators)#WORDTERMINATORS
- or (nextchar in self.quotes) #WORDTERMINATORS
- or (self.whitespace_split)): #WORDTERMINATORS
- self.token = self.token + nextchar
- else:
- self.pushback.appendleft(nextchar)
- if self.debug >= 2:
- print("TtreeShlex: I see punctuation in word state")
- self.state = ' '
- if self.token:
- break # emit current token
- else:
- continue
- result = self.token
- self.token = ''
- if self.posix and not quoted and result == '':
- result = None
- if self.debug > 1:
- if result:
- print("TtreeShlex: raw token=" + repr(result))
- else:
- print("TtreeShlex: raw token=EOF")
- return result
-
- def sourcehook(self, newfile):
- "Hook called on a filename to be sourced."
- newfile = RemoveOuterQuotes(newfile)
- # This implements cpp-like semantics for relative-path inclusion.
- if isinstance(self.infile, str) and not os.path.isabs(newfile):
- newfile_full = os.path.join(os.path.dirname(self.infile), newfile)
- try:
- f = open(newfile_full, "r")
- except IOError:
- # If not found,
- err = True
- # ...then check to see if the file is in one of the
- # directories in the self.include_path list.
- for d in self.include_path:
- newfile_full = os.path.join(d, newfile)
- try:
- f = open(newfile_full, "r")
- err = False
- break
- except IOError:
- err=True
- if err:
- raise InputError('Error at '+self.error_leader()+'\n'
- ' unable to open file \"'+newfile+'\"\n'
- ' for reading.\n')
- return (newfile, f)
-
- def error_leader(self, infile=None, lineno=None):
- "Emit a C-compiler-like, Emacs-friendly error-message leader."
- if infile is None:
- infile = self.infile
- if lineno is None:
- lineno = self.lineno
- return "\"%s\", line %d: " % (infile, lineno)
-
- def __iter__(self):
- return self
-
- def __next__(self):
- token = self.get_token()
- if token == self.eof:
- raise StopIteration
- return token
-
- def __bool__(self):
- return not self.end_encountered
-
- # For compatibility with python 2.x, I must also define:
- def __nonzero__(self):
- return self.__bool__()
-
-
-# The split() function was originally from shlex
-# It is included for backwards compatibility.
-def split(s, comments=False, posix=True):
- lex = TtreeShlex(s, posix=posix)
- lex.whitespace_split = True
- if not comments:
- lex.commenters = ''
- return list(lex)
-
-
-
-##################### NEW ADDITIONS (may be removed later) #################
-
-#"""
-# -- linelex.py --
-#linelex.py defines the LineLex class, which inherits from, and further
-#augments the capabilities of TtreeShlex by making it easier to parse
-#individual lines one at a time. (The original shlex's "source" inclusion
-#ability still works when reading entire lines, and lines are still counted.)
-#
-#"""
-
-#import sys
-
-
-class InputError(Exception):
- """ A generic exception object containing a string for error reporting.
- (Raising this exception implies that the caller has provided
- a faulty input file or argument.)
-
- """
-
- def __init__(self, err_msg):
- self.err_msg = err_msg
- def __str__(self):
- return self.err_msg
- def __repr__(self):
- return str(self)
-
-
-def ErrorLeader(infile, lineno):
- return '\"'+infile+'\", line '+str(lineno)
-
-
-class SrcLoc(object):
- """ SrcLoc is essentially nothing more than a 2-tuple containing the name
- of a file (str) and a particular line number inside that file (an integer).
-
- """
- __slots__=["infile","lineno"]
- def __init__(self, infile='', lineno=-1):
- self.infile = infile
- self.lineno = lineno
-
-
-
-
-def SplitQuotedString(string,
- quotes='\'\"',
- delimiters=' \t\r\f\n',
- escape='\\',
- comment_char='#'):
- tokens = []
- token = ''
- reading_token = True
- escaped_state = False
- quote_state = None
- for c in string:
-
- if (c in comment_char) and (not escaped_state) and (quote_state==None):
- tokens.append(token)
- return tokens
-
- elif (c in delimiters) and (not escaped_state) and (quote_state==None):
- if reading_token:
- tokens.append(token)
- token = ''
- reading_token = False
-
- elif c in escape:
- if escaped_state:
- token += c
- reading_token = True
- escaped_state = False
- else:
- escaped_state = True
- # and leave c (the '\' character) out of token
- elif (c in quotes) and (not escaped_state):
- if (quote_state != None):
- if (c == quote_state):
- quote_state = None
- else:
- quote_state = c
- token += c
- reading_token = True
- else:
- if (c == 'n') and (escaped_state == True):
- c = '\n'
- elif (c == 't') and (escaped_state == True):
- c = '\t'
- elif (c == 'r') and (escaped_state == True):
- c = '\r'
- elif (c == 'f') and (escaped_state == True):
- c = '\f'
- token += c
- reading_token = True
- escaped_state = False
-
- if len(string) > 0:
- tokens.append(token)
- return tokens
-
-
-def EscCharStrToChar(s_in, escape='\\'):
- """
- EscCharStrToChar() replaces any escape sequences
- in a string with their 1-character equivalents.
-
- """
- assert(len(escape) > 0)
- out_lstr = []
- escaped_state = False
- for c in s_in:
- if escaped_state:
- if (c == 'n'):
- out_lstr.append('\n')
- elif (c == 't'):
- out_lstr.append('\t')
- elif (c == 'r'):
- out_lstr.append('\r')
- elif (c == 'f'):
- out_lstr.append('\f')
- elif (c == '\''):
- out_lstr.append('\'')
- elif (c == '\"'):
- out_lstr.append('\"')
- elif c in escape:
- out_lstr.append(c)
- else:
- out_lstr.append(escape+c) # <- keep both characters
- escaped_state = False
- else:
- if c in escape:
- escaped_state = True
- else:
- out_lstr.append(c)
-
- return ''.join(out_lstr)
-
-
-
-def SafelyEncodeString(in_str,
- quotes='\'\"',
- delimiters=' \t\r\f\n',
- escape='\\',
- comment_char='#'):
- """
- SafelyEncodeString(in_str) scans through the input string (in_str),
- and returns a new string in which probletic characters
- (like newlines, tabs, quotes, etc), are replaced by their two-character
- backslashed equivalents (like '\n', '\t', '\'', '\"', etc).
- The escape character is the backslash by default, but it too can be
- overridden to create custom escape sequences
- (but this does not effect the encoding for characters like '\n', '\t').
-
- """
- assert(len(escape) > 0)
- out_lstr = []
- use_outer_quotes = False
- for c in in_str:
- if (c == '\n'):
- c = '\\n'
- elif (c == '\t'):
- c = '\\t'
- elif (c == '\r'):
- c = '\\r'
- elif (c == '\f'):
- c = '\\f'
- elif c in quotes:
- c = escape[0]+c
- elif c in escape:
- c = c+c
- elif c in delimiters:
- use_outer_quotes = True
- # hmm... that's all that comes to mind. Did I leave anything out?
- out_lstr.append(c)
-
- if use_outer_quotes:
- out_lstr = ['\"'] + out_lstr + ['\"']
-
- return ''.join(out_lstr)
-
-
-def RemoveOuterQuotes(text, quotes='\"\''):
- if ((len(text)>=2) and (text[0] in quotes) and (text[-1]==text[0])):
- return text[1:-1]
- else:
- return text
-
-
-
-def MaxLenStr(s1, s2):
- if len(s2) > len(s1):
- return s2
- else:
- return s1
-
-
-#def IsRegex(pat):
-# """
-# Check to see if string (pat) is bracketed by slashes.
-#
-# """
-# return (len(pat)>=2) and (pat[0]=='/') and (pat[-1] == '/')
-
-def HasWildCard(pat):
- """
- Returns true if a string (pat) contains a '*' or '?' character.
-
- """
- return (pat.find('*') != -1) or (pat.find('?') != -1)
-
-
-#def HasWildCard(pat):
-# """
-# Returns true if a string (pat) contains a non-backslash-protected
-# * or ? character.
-#
-# """
-# N=len(pat)
-# i=0
-# while i < N:
-# i = pat.find('*', i, N)
-# if i == -1:
-# break
-# elif (i==0) or (pat[i-1] != '\\'):
-# return True
-# i += 1
-# i=0
-# while i < N:
-# i = pat.find('?', i, N)
-# if i == -1:
-# break
-# elif (i==0) or (pat[i-1] != '\\'):
-# return True
-# i += 1
-# return False
-
-
-def MatchesPattern(s, pattern):
- if type(pattern) is str:
- #old code:
- #if ((len(s) > 1) and (s[0] == '/') and (s[-1] == '/'):
- # re_string = p[1:-1] # strip off the slashes '/' and '/'
- # if not re.search(re_string, s):
- # return False
- #new code:
- # uses precompiled regular expressions (See "pattern.search" below)
- if HasWildCard(pattern):
- if not fnmatch.fnmatchcase(s, pattern):
- return False
- elif s != pattern:
- return False
- else:
- #assert(type(p) is _sre.SRE_Match)
- # I assume pattern = re.compile(some_reg_expr)
- if not pattern.search(s):
- return False
- return True
-
-
-
-def MatchesAll(multi_string, pattern):
- assert(len(multi_string) == len(pattern))
- for i in range(0, len(pattern)):
- if not MatchesPattern(multi_string[i], pattern[i]):
- return False
- return True
-
-
-
-class LineLex(TtreeShlex):
- """ This class extends the TtreeShlex module (a slightly modified
- version of the python 3.2.2 version of shlex). LineLex has the
- ability to read one line at a time (in addition to one token at a time).
- (Many files and scripts must be parsed one line at a time instead of one
- token at a time. In these cases, the whitespace position also matters.)
-
- Arguably, this class might not be necessary.
- I could get rid of this class completely. That would be nice. To do that
- we would need to augment and generalize shlex's get_token() member function
- to make it read lines, not just tokens. Of course, you can always
- change the wordchars (or wordterminators). Even so, there are two other
- difficulties using the current version of shlex.get_token() to read lines:
- 1) File inclusion happen whenever the beginning of a line/token matches one
- of the "source_triggers" (not the whole line as required by get_token()).
- 2) Lines ending in a special character (by default the backslash character)
- continue on to the next line.
- This code seems to work on our test files, but I'm sure there are bugs.
- Andrew 2012-3-25
-
- """
- def __init__(self,
- instream=None,
- infile=None,
- posix=False):
- TtreeShlex.__init__(self, instream, infile, posix)
- self.line_terminators = '\n'
- self.line_extend_chars = '\\'
- self.skip_comments_during_readline = True
-
-
- def _StripComments(self, line):
- if self.skip_comments_during_readline:
- for i in range(0, len(line)):
- if ((line[i] in self.commenters) and
- ((i==0) or (line[i-1] not in self.escape))):
- return line[:i]
- return line
-
-
-
- def _ReadLine(self,
- recur_level=0):
- """
- This function retrieves a block of text, halting at a
- terminal character. Escape sequences are respected.
- The self.lineno (newline counter) is also maintained.
-
- The main difference between Readline and get_token()
- is the way they handle the "self.source_triggers" member.
- Both Readline() and get_token() insert text from other files when they
- encounter a string in "self.source_triggers" in the text they read.
- However ReadLine() ONLY inserts text from other files if the token which
- matches with self.source_triggers appears at the beginning of the line.
- get_token() inserts text only if lex.source matches the entire token.
-
- comment-to-self:
- At some point, once I'm sure this code is working, I should replace
- shlex.get_token() with the code from ReadLine() which is more general.
- It would be nice to get rid of "class LineLex" entirely. ReadLine()
- is the only new feature that LineLex which was lacking in shlex.
-
- To do this I would need to add a couple optional arguments to
- "get_token()", allowing it to mimic ReadLine(), such as:
- "override_wordterms" argument (which we can pass a '\n'), and
- "token_extender" argument (like '\' for extending lines)
-
- """
- first_token=''
- line = ''
- escaped_state = False
- found_space = False
- while True:
- nextchar = self.read_char()
- #sys.stderr.write('nextchar=\"'+nextchar+'\"\n')
- while nextchar == '':
- if not self.filestack:
- return self._StripComments(line), '', first_token, found_space
- else:
- self.pop_source()
- nextchar = self.read_char()
- if nextchar == '\n':
- self.lineno += 1
-
- if escaped_state:
- escaped_state = False
- else:
- if nextchar in self.escape:
- line += nextchar
- escaped_state = True
- else:
- escaped_state = False
-
- if not escaped_state:
- if (nextchar in self.whitespace):
- found_space = True
- while first_token in self.source_triggers:
- fname = RemoveOuterQuotes(self.get_token())
- if (fname == '') or (fname in self.source_triggers):
- raise InputError('Error: near '+self.error_leader()+'\n'
- ' Nonsensical file inclusion request.\n')
- if self.debug >= 0:
- sys.stderr.write( (' ' * recur_level) +
- 'reading file \"'+fname+'\"\n')
- spec = self.sourcehook(fname)
- if spec:
- (fname, subfile) = spec
- if ((first_token not in self.source_triggers_x) or
- (fname not in self.source_files_restricted)):
- self.push_source(subfile, fname)
- if first_token in self.source_triggers_x:
- self.source_files_restricted.add(fname)
- else:
- if self.debug >= 0:
- sys.stderr.write('\nWarning at '+self.error_leader()+':\n'
- ' duplicate attempt to import file:\n \"'+fname+'\"\n')
-
- line, nextchar, first_token, found_space = \
- self._ReadLine(recur_level+1)
-
-
- if nextchar in self.line_terminators:
- line_nrw = line.rstrip(self.whitespace)
- #sys.stderr.write('line_nrw=\"'+line_nrw+'\"\n')
- if ((len(line_nrw) > 0) and
- (line_nrw[-1] in self.line_extend_chars) and
- ((len(line_nrw) < 2) or (line_nrw[-2] not in self.escape))):
- line = line_nrw[:-1] #delete the line_extend character
- # from the end of that line and keep reading...
- else:
- return self._StripComments(line), nextchar, first_token, found_space
- else:
- line += nextchar
- if not found_space:
- first_token += nextchar
-
-
-
- def ReadLine(self, recur_level=0):
- line, nextchar, first_token, found_space = \
- self._ReadLine(recur_level)
- if nextchar == self.eof:
- self.end_encountered = True
- return line + nextchar
-
-
- @staticmethod
- def TextBlock2Lines(text, delimiters, keep_delim=True):
- """ This splits a string into a list of sub-strings split by delimiter
- characters. This function is different from the standard str.split()
- function: The string is split at every character which belongs to the
- "delimiters" argument (which can be a string or some other container).
- This character is included at the end of every substring. Example:
- TextBlock2Lines('\nabc\nde^fg\nhi j\n', '^\n')
- returns:
- ['\n', 'abc\n', 'de^', 'fg\n', 'hi j\n']
-
- """
- ls = []
- i = 0
- i_prev = 0
- while i < len(text):
- if text[i] in delimiters:
- if keep_delim:
- ls.append(text[i_prev:i+1])
- else:
- ls.append(text[i_prev:i])
- i_prev = i+1
- i += 1
- if (i_prev < len(text)):
- ls.append(text[i_prev:i+1])
- return ls
-
- def __iter__(self):
- return self
-
- def __next__(self):
- line = self.ReadLine()
- if line == self.eof:
- raise StopIteration
- return line
-
-
-class OSrcLoc(object):
- """ OSrcLoc is barely more than a 2-tuple containing the name of a file
- (a string) and a particular line number inside that file (an integer).
- These objects are passed around and stored in the nodes of
- every tree, so that if a syntax error or broken link in that node
- is discovered, an error message can be provided to the user.
-
- """
-
- __slots__ = ["infile","lineno","order"]
- count = 0
-
- def __init__(self, infile='', lineno=-1):
- self.infile = infile
- self.lineno = lineno
- OSrcLoc.count += 1
- self.order = OSrcLoc.count # keep track of how many times it was called
-
- def __lt__(self, x):
- return self.order < x.order
-
- #def __repr__(self):
- # return repr((self.infile, self.lineno, self.order))
-
-
-
-class TextBlock(object):
- """TextBlock is just a 3-tuple consisting of a string, and an OSrcLoc
- to help locate it in the original file from which it was read."""
-
- __slots__=["text","srcloc"]
-
- def __init__(self, text, srcloc): #srcloc_end):
- self.text = text
- if srcloc == None:
- self.srcloc = OSrcLoc()
- else:
- self.srcloc = srcloc
- #if srcloc_end == None:
- # self.srcloc_end = OSrcLoc()
- #else:
- # self.srcloc_end = srcloc_end
-
- def __repr__(self):
- return '\"'+self.text+'\"'
-
-
-
-class VarRef(object):
- """VarRef stores variable names, and paths, and other attribute information,
- as well as a "OSrcLoc" to keep track of the file it was defined in."""
-
- __slots__=["prefix","descr_str","suffix","srcloc","binding","nptr"]
-
- def __init__(self,
- prefix = '', # '$' or '${'
- descr_str = '', # <- descriptor string: "cpath/category:lpath"
- suffix = '', # '}'
- srcloc = None,# location in file where defined
- binding = None,# a pointer to a tuple storing the value
- nptr = None):# <- see class VarNPtr
-
- self.prefix = prefix #Any text before the descriptor string goes here
- self.suffix = suffix #Any text after the descriptor string goes here
- self.descr_str = descr_str
- if srcloc == None: # <- Location in text file where variable appears
- self.srcloc = OSrcLoc()
- else:
- self.srcloc = srcloc
-
- self.binding = binding
-
- if nptr == None:
- self.nptr = VarNPtr()
- else:
- self.nptr = nptr
-
- def __lt__(self, x):
- return self.order < x.order
-
- #def __repr__(self):
- # return repr((self.prefix + self.descr_str + self.suffix, srcloc))
-
-
-class VarNPtr(object):
- """
- Every time a variable appears in a template, it has has a "descriptor".
- For example, consider the variable
- "$atom:CA"
- This is a string which encodes 3 pieces of information.
- 1) the category name: This is essentialy indicates the variable's type.
- (ie "atom", in the example above)
- 2) the category node: Some TYPES have limited scope. Users can
- specify the root node of the portion of the tree
- in which this variable's type makes sense.
- If this node is the root node, then that category
- is relevant everywhere, and is not molecule or class
- specific. All variables have a category node, which
- is often not explicitly defined to by the user.
- (Category node = the root "/", in the example above.)
- 3) the leaf node: This is a node whose ".name" member matches the name
- of a variable. This node is created for this purpose
- and it's position in the tree is a reflection of
- that variable's intended scope.
- In a molecule this "name" might be the name
- of a type of atom, or an atom ID, or a bond type,
- which is found in a particular molecule.
- (Leaf node would be named "CA" in the example above.)
-
- The VarNPtr class is simply a 3-tuple which
- keeps these 3 pieces of data together.
-
- """
-
- __slots__=["cat_name","cat_node","leaf_node"]
-
- def __init__(self, cat_name='', cat_node=None, leaf_node=None):
- self.cat_name = cat_name
- self.cat_node = cat_node
- self.leaf_node = leaf_node
-
- #def __repr__(self):
- # return repr((self.cat_name, self.cat_node.name, self.leaf_node.name))
-
-
-class VarBinding(object):
- """ VarBinding is essentially a tuple consistng of (full_name, binding, refs):
-
- "self.full_name" is canonical name for this variable. This is a string
- which specifies full path leading to the category node (beginning with '/'),
- the category name (followed by a ':'),
- as well as the leaf node (including the path leading up to it from cat_node)
- This triplet identifies the variable uniquely.
-
- "self.value" is the data that the variable refers to (usually a string).
-
- "self.refs" stores a list of VarRefs which mention the same variable
- from the various places inside various templates in the tree.
-
- """
-
- __slots__=["full_name","nptr","value","refs","order","category"]
-
- def __init__(self,
- full_name = '',
- nptr = None,
- value = None,
- refs = None,
- order = -1,
- category = None):
- self.full_name = full_name
- self.nptr = nptr
- self.value = value
- self.refs = refs
- self.order = order
- self.category = category
-
- def __lt__(self, x):
- return self.order < x.order
-
- def __repr__(self):
- return repr((self.full_name, self.value, self.order))
-
-
-def ExtractCatName(descr_str):
- """ When applied to a VarRef's "descr_str" member,
- this function will extract the "catname" of it's corresponding
- "nptr" member. This can be useful for error reporting.
- (I use it to insure that the user is using the correct counter
- variable types at various locations in their input files.)
-
- """
-
- ib = descr_str.find(':')
- if ib == -1:
- ib = len(descr_str)
- ia = descr_str.rfind('/')
- if ia == -1:
- ia = 0
- return descr_str[ia:ib]
- else:
- str_before_colon = descr_str[0:ib]
- ia = str_before_colon.rfind('/')
- if ia == -1:
- return str_before_colon
- else:
- return str_before_colon[ia+1:]
-
-
-
-def _DeleteLineFromTemplate(tmpl_list,
- i_entry, # index into tmpl_list
- newline_delimiter='\n'):
- """ Delete a single line from tmpl_list.
- tmpl_list is an alternating list of VarRefs and TextBlocks.
- To identify the line, the index corresponding to one of the
- entries in the tmpl_list is used. (Usually it is a VarRef)
- The text after the preceding newline, and the text up to the next newline
- (starting from the beginning of the current entry, if a TextBlock)
- is deleted, including any VarRef (variables) located in between.
-
- It returns the index corresponding to the next
- entry in the list (after deletion).
-
- """
-
- i_prev_newline = i_entry
- while i_prev_newline >= 0:
- entry = tmpl_list[i_prev_newline]
- if isinstance(entry, TextBlock):
- i_char_newline = entry.text.rfind(newline_delimiter)
- if i_char_newline != -1: # then newline found
- # Delete the text after this newline
- entry.text = entry.text[:i_char_newline+1]
- break
- i_prev_newline -= 1
-
- first_var = True
- #i_next_newline = i_entry
- i_next_newline = i_prev_newline+1
- while i_next_newline < len(tmpl_list):
- entry = tmpl_list[i_next_newline]
- if isinstance(entry, TextBlock):
- i_char_newline = entry.text.find(newline_delimiter)
- if i_char_newline != -1: # then newline found
- # Delete the text before this newline (including the newline)
- entry.text = entry.text[i_char_newline+1:]
- break
- # Invoke DeleteSelf() on the first variables on this line. This will
- # insure that it is deleted from the ttree_assignments.txt file.
- elif isinstance(entry, VarRef):
- if first_var:
- entry.nptr.leaf_node.DeleteSelf()
- first_var = False
- i_next_newline += 1
-
- del tmpl_list[i_prev_newline + 1 : i_next_newline]
- return i_prev_newline + 1
-
-
-
-def DeleteLinesWithBadVars(tmpl_list,
- delete_entire_template = False,
- newline_delimiter = '\n'):
- """
- Loop through the entries in a template,
- an alternating list of TextBlocks and VarRefs (tmpl_list).
- If a VarRef points to a leaf_node which no longer exists
- (ie. no longer in the corresponding category's .bindings list).
- Then delete the line it came from from the template (tmpl_list).
-
- """
-
- out_str_list = []
- i = 0
- while i < len(tmpl_list):
- entry = tmpl_list[i]
- if isinstance(entry, VarRef):
- var_ref = entry
- var_bindings = var_ref.nptr.cat_node.categories[var_ref.nptr.cat_name].bindings
- #if var_ref.nptr.leaf_node not in var_bindings:
- if var_ref.nptr.leaf_node.IsDeleted():
- if delete_entire_template:
- del tmpl_list[:]
- return 0
- else:
- i = _DeleteLineFromTemplate(tmpl_list,
- i,
- newline_delimiter)
- else:
- i += 1
- else:
- i += 1
-
-
-
-
-
-
-
-def SplitTemplate(ltmpl, delim, delete_blanks = False):
- """
- Split a template "ltmpl" into a list of "tokens" (sub-templates)
- using a single delimiter string "delim".
-
- INPUT arguments:
- "ltmpl" should be an list of TextBlocks and VarRefs.
- "delim" should be a simple string (type str)
- "delete_blanks" should be a boolean True/False value.
- When true, successive occurrences of the delimiter
- should not create blank entries in the output list.
-
- OUTPUT:
- A list of tokens.
- Each "token" is either a TextBlock, a VarRef,
- or a (flat, 1-dimensional) list containing more than one of these objects.
- The number of "tokens" returned equals the number of times the delimiter
- is encountered in any of the TextBlocks in the "ltmpl" argument, plus one.
- (... Unless "delete_blanks" is set to True.
- Again, in that case, empty entries in this list are deleted.)
-
- """
- assert(type(delim) is str)
- if not hasattr(ltmpl, '__len__'):
- ltmpl = [ltmpl]
-
- tokens_lltmpl = []
- token_ltmpl = []
- i = 0
- while i < len(ltmpl):
- entry = ltmpl[i]
- if isinstance(entry, TextBlock):
- #if hasattr(entry, 'text'):
- prev_src_loc = entry.srcloc
-
- tokens_str = entry.text.split(delim)
-
- lineno = entry.srcloc.lineno
-
- j = 0
- while j < len(tokens_str):
- token_str = tokens_str[j]
-
- delim_found = False
- if (j < len(tokens_str)-1):
- delim_found = True
-
- if token_str == '':
- if delete_blanks:
- if delim == '\n':
- lineno += 1
- if len(token_ltmpl) > 0:
- if len(token_ltmpl) == 1:
- tokens_lltmpl.append(token_ltmpl[0])
- else:
- tokens_lltmpl.append(token_ltmpl)
- del token_ltmpl
- token_ltmpl = []
- j += 1
- continue
-
- new_src_loc = OSrcLoc(prev_src_loc.infile, lineno)
- new_src_loc.order = prev_src_loc.order
-
- for c in token_str:
- # Reminder to self: c != delim (so c!='\n' if delim='\n')
- # (We keep track of '\n' characters in delimiters above.)
- if c == '\n':
- lineno +=1
-
- new_src_loc.lineno = lineno
-
- text_block = TextBlock(token_str,
- new_src_loc)
-
- prev_src_loc = new_src_loc
-
- if len(token_ltmpl) == 0:
- if delim_found:
- tokens_lltmpl.append(text_block)
- del token_ltmpl
- token_ltmpl = []
- else:
- token_ltmpl.append(text_block)
- else:
- if delim_found:
- if len(token_str) > 0:
- token_ltmpl.append(text_block)
- tokens_lltmpl.append(token_ltmpl)
- del token_ltmpl
- token_ltmpl = []
- else:
- assert(not delete_blanks)
- if (isinstance(token_ltmpl[-1], VarRef)
- and
- ((j>0)
- or
- ((j == len(tokens_str)-1) and
- (i == len(ltmpl)-1))
- )):
- # In that case, this empty token_str corresponds
- # to a delimiter which was located immediately
- # after the variable name,
- # AND
- # -there is more text to follow,
- # OR
- # -we are at the end of the template.
- token_ltmpl.append(text_block)
- if len(token_ltmpl) == 1:
- tokens_lltmpl.append(token_ltmpl[0])
- else:
- tokens_lltmpl.append(token_ltmpl)
- del token_ltmpl
- token_ltmpl = []
- else:
- token_ltmpl.append(text_block)
-
- if (delim_found and (delim == '\n')):
- lineno += 1
-
- j += 1
-
- elif isinstance(entry, VarRef):
- #elif hasattr(entry, 'descr_str'):
- lineno = entry.srcloc.lineno
- if ((len(token_ltmpl) == 1) and
- isinstance(token_ltmpl[0], TextBlock) and
- (len(token_ltmpl[0].text) == 0)):
- # special case: if the previous entry was "", then it means
- # the delimeter appeared at the end of the previous text block
- # leading up to this variable. It separates the variable from
- # the previous text block. It is not a text block of length 0.
- token_ltmpl[0] = entry
- else:
- token_ltmpl.append(entry)
- elif entry == None:
- token_ltmpl.append(entry)
- else:
- assert(False)
-
- i += 1
-
- # Append left over remains of the last token
- if len(token_ltmpl) == 1:
- tokens_lltmpl.append(token_ltmpl[0])
- elif len(token_ltmpl) > 1:
- tokens_lltmpl.append(token_ltmpl)
- del token_ltmpl
-
- return tokens_lltmpl
-
-
-
-
-
-
-def SplitTemplateMulti(ltmpl, delims, delete_blanks=False):
- """
- Split a template "ltmpl" into a list of templates using a
- single one or more delimiter strings "delim_list".
- If multiple delimiter strings are provided, splitting
- begins using the first delimiter string in the list.
- Then each token in the resulting list of templates
- is split using the next delimiter string
- and so on until we run out of delimiter strings.
-
- "ltmpl" should be an list of TextBlocks and VarRefs.
- "delims" should be a simple string (type str) or a list of strings
- "delete_blanks" is either True or False
- If True, then any blank entries in the resulting list of
- tokens (sub-templates) will be deleted.
-
- """
-
- if hasattr(delims, '__len__'): # then it hopefully is a list of strings
- delim_list = delims
- else:
- delim_list = [delims] # then it hopefully is a string
-
- tokens = [ltmpl]
- for delim in delim_list:
- assert(type(delim) is str)
- tokens_il = []
- for t in tokens:
- sub_tokens = SplitTemplate(t, delim, delete_blanks)
- for st in sub_tokens:
- if hasattr(st, '__len__'):
- if (len(st) > 0) or (not delete_blanks):
- tokens_il.append(st)
- else:
- tokens_il.append(st)
- tokens = tokens_il
- del tokens_il
-
- return tokens
-
-
-
-def _TableFromTemplate(d, ltmpl, delimiters, delete_blanks):
- """
- See the docstring for the TableFromTemplate() function for an explanation.
- (This _TableFromTemplate() and SplitTemplate() are the workhorse functions
- for TableFromTemplate().)
-
- """
-
- output = SplitTemplateMulti(ltmpl, delimiters[d], delete_blanks[d])
-
- if d > 0:
- i = 0
- while i < len(output):
- output[i] = _TableFromTemplate(d-1,
- output[i],
- delimiters,
- delete_blanks)
- # Delete empty LISTS?
- if (delete_blanks[d] and
- hasattr(output[i], '__len__') and
- (len(output[i]) == 0)):
- del output[i]
- else:
- i += 1
-
- return output
-
-
-def TableFromTemplate(ltmpl, delimiters, delete_blanks=True):
- """
- This function can be used to split a template
- (a list containing TextBlocks and VarRefs) into a table
- into a multidimensional table, with an arbitrary number of dimensions.
-
- Arguments:
-
- ltmpl
-
- An alternating list of TextBlocks and VarRefs containing
- the contents of this text template.
-
- delimiters
-
- The user must supply a list or tuple of delimiters: one delimiter for
- each dimension in the table, with low-priority delimiters
- (such as spaces ' ') appearing first, and higher-priority delimiters
- (sich as newlines '\n') appearing later on in the list.
- This function will divide the entire "ltmpl" into an n-dimensional
- table. Initially the text is split into a list of text using the
- highest-priority delimiter. Then each entry in the resulting list is
- split into another list according to the next highest-priority delimiter.
- This continues until all of the delimiters are used up and an
- n-dimensional list-of-lists is remaining.
-
- delete_blanks
-
- The optional "delete_blanks" argument can be used to indicate whether
- or not to delete blank entries in the table (which occur as a result
- of placing two delimiters next to each other). It should be either
- None (default), or it should be an array of booleans matching the
- size of the "delimiters" argument. This allows the caller to customize
- the merge settings separately for each dimension (for example: to allow
- merging of whitespace within a line, without ignoring blank lines).
-
-
- ---- Details: ----
-
- 1) Multi-character delimiters ARE allowed (like '\n\n').
-
- 2) If a delimiter in the "delimiters" argument is not a string
- but is a tuple (or a list) of strings, then the text is split according
- to any of the delimiters in that tuple/list (starting from the last entry).
- This way, users can use this feature to split text according to multiple
- different kinds of whitespace characters (such as ' ' and '\t'), for
- example, buy setting delimiters[0] = (' ','\t'). If, additionally,
- delete_blanks[0] == True, then this will cause this function to
- divide text in without regard to whitespace on a given line (for example).
-
- Detailed example:
-
- table2D = TableFromTmplList(ltmpl,
- delimiters = ((' ','\t'), '\n'),
- delete_blanks = (True, False))
-
- This divides text in a similar way that the "awk" program does by default,
- ie, by ignoring various kinds of whitespace between text fields, but NOT
- ignoring blank lines.
-
- 3) Any text contained in variable-names is ignored.
-
- """
-
- # Make a copy of ltmpl
- # (The workhorse function "_TableFromTemplate()" makes in-place changes to
- # its "ltmpl" argument. I don't want to modify "ltmpl", so I make a copy
- # of it before I invoke "_TableFromTemplate()" on it.)
-
- output = [ltmpl[i] for i in range(0, len(ltmpl))]
-
- d = len(delimiters) - 1
- output = _TableFromTemplate(d, output, delimiters, delete_blanks)
- return output
-
-
-
-
-
-
-
-
-
-
-class TemplateLexer(TtreeShlex):
- """ This class extends the standard python lexing module, shlex, adding a
- new member function (ReadTemplate()), which can read in a block of raw text,
- (halting at an (non-escaped) terminal character), and split the text into
- alternating blocks of text and variables. (As far as this lexer is
- concerned, "variables" are simply tokens preceded by $ or @ characters,
- and surrounded by optional curly-brackets {}.)
-
- """
- def __init__(self,
- instream=None,
- infile=None,
- posix=False):
- TtreeShlex.__init__(self, instream, infile, posix)
- self.var_delim = '$@' #characters which can begin a variable name
- self.var_open_paren = '{' #optional parenthesis surround a variable
- self.var_close_paren = '}' #optional parenthesis surround a variable
- self.newline = '\n'
- self.comment_skip_var = '#'
-
- # Which characters belong in words?
- #
- # We want to allow these characters:
- # ./$@&%^!*~`-_:;?<>[]()
- # to appear inside the tokens that TtreeShlex.get_token()
- # retrieves (TtreeShlex.get_token() is used to read class
- # names, and instance names, and variable names)
- #
- # settings.lex.wordchars+='./$@&%^!*~`-_+:;?<>[]' #Allow these chars
- #
- # Ommisions:
- # Note: I left out quotes, whitespace, comment chars ('#'), and escape
- # characters ('\\') because they are also dealt with separately.
- # Those characters should not overlap with settings.lex.wordchars.
- #
- # Enabling unicode support requires that we override this choice
- # by specifying "lex.wordterminators" instead of "wordchars".
- #
- # lex.wordterminators should be the (printable) set inverse of lex.wordchars
- # I'm not sure which ascii characters are NOT included in the string above
- # (We need to figure that out, and put them in settings.lex.wordterminators)
- # To figure that out, uncomment the 8 lines below:
- #
- #self.wordterminators=''
- #for i in range(0,256):
- # c = chr(i)
- # if c not in self.wordchars:
- # self.wordterminators += c
- #sys.stderr.write('-------- wordterminators = --------\n')
- #sys.stderr.write(self.wordterminators+'\n')
- #sys.stderr.write('-----------------------------------\n')
- #
- # Here is the result:
- self.wordterminators = '(){|}' + \
- self.whitespace + \
- self.quotes + \
- self.escape + \
- self.commenters
- # Note:
- # self.whitespace = ' \t\r\f\n'
- # self.quotes = '\'"'
- # self.escape = '\\'
- # self.commenters = '#'
- # Note: I do not terminate on these characters: +-=*'"`
- # because they appear in the names of atom types in many force-fields.
- # Also * characters are needed for variables containing wildcards
- # in the name (which will be dealt with later).
-
-
- self.source_triggers=set(['include','import'])
- self.source_triggers_x=set(['import'])
-
-
-
-
- def GetSrcLoc(self):
- return OSrcLoc(self.infile, self.lineno)
-
-
- def ReadTemplate(self,
- simplify_output=False,
- terminators='}',
- other_esc_chars='{',
- keep_terminal_char = True):
- """
- ReadTemplate() reads a block of text (between terminators)
- and divides it into variables (tokens following a '$' or '@' character)
- and raw text. This is similar to pythons string.Template(),
- however it reads from streams (files), not strings, and it allows use
- of more complicated variable names with multiple variable delimiters
- (eg '$' and '@').
- This readline()-like member function terminates when reaching a
- user-specified terminator character character (second argument),
- or when variable (eg: "$var"$ is encountered). The result is
- a list of variable-separated text-blocks (stored in the first
- argument). For example, the string:
- "string with $var1 and $var2 variables.}" contains:
- "string with ",
- $var1,
- " and ",
- $var2,
- " variables.}"
- This simplifies the final process of rendering
- (substituting text into) the text blocks later on.
- Output:
- This function returns a list of (alternating) blocks of
- text, and variable names. Each entry in the list is either:
- 1) a text block:
- Raw text is copied from the source, verbatim, along with
- some additional data (filename and line numbers), to
- help retroactively identify where the text came from
- (in case a syntax error in the text is discovered later).
- In this case, the list entry is stored as a list
- The format (TextBlock) is similar to:
- [text_string, ((filenameA,lineBegin), (filenameB,lineEnd))],
- where the tuples, (filenameA,lineBegin) and (filenameB,lineEnd)
- denote the source file(s) from which the text was read, and
- line number at the beginning and ending of the text block.
- (This information is useful for generating helpful error
- messages. Note that the "TtreeShlex" class allows users to
- combine multiple files transparently into one stream using
- the "source" (or "sourcehook()") member. For this reason, it
- is possible, although unlikely, that the text-block
- we are reading could span multiple different files.)
- 2) a variable (for example "$var" or "${var}"):
- In this case, the list entry is stored in the "VarRef" format
- which is essentialy shown below:
- [[var_prefix, var_nptr, var_suffix], (filename,lineno)]
- where var_prefix and var_suffix are strings containing brackets
- and other text enclosing the variable name (and may be empty).
-
- As an example, we consider a file named "datafile" which
- contains the text containing 2 text blocks and 1 variable:
- "some\n text\n before ${var}. Text after\n".
- ReadTemplate() will read this and return a list with 3 entries:
- [ ['some\n text\n before', (('datafile', 1), ('datafile', 3))],
- [['${', 'var', '}'], ('datafile', 3, 3)],
- ['Text after\n', (('datafile', 3), ('datafile', 4))] ]
-
- Note that while parsing the text, self.lineno counter is
- incremented whenever a newline character is encountered.
- (Also: Unlike shlex.get_token(), this function does not
- delete commented text, or insert text from other files.)
-
- Exceptional Cases:
- Terminator characters are ignored if they are part of a variable
- reference. (For example, the '}' in "${var}", is used to denote a
- bracketed variable, and does not cause ReadTemplate() to stop reading)
- OR if they are part of a two-character escape sequence
- (for example, '}' in "\}" does not cause terminate parsing).
- In that case, the text is considered normal text. (However the
- '\' character is also stripped out. It is also stripped out if it
- precedes any characters in "other_esc_chars", which is
- the second argument. Otherwise it is left in the text block.)
-
- """
- #print(' ReadTemplate('+terminators+') invoked at '+self.error_leader())
-
- # The main loop of the parser reads only one variable at time.
- # The following variables keep track of where we are in the template.
- reading_var=False # Are we currently reading in the name of a variable?
-
- prev_char_delim=False #True iff we just read a var_delim character like '$'
- escaped_state=False #True iff we just read a (non-escaped) esc character '\'
- commented_state=False #True iff we are in a region of text where vars should be ignored
- var_paren_depth=0 # This is non-zero iff we are inside a
- # bracketed variable's name for example: "${var}"
- var_terminators = self.whitespace + self.newline + self.var_delim + '{}'
-
- tmpl_list = [] # List of alternating tuples of text_blocks and
- # variable names (see format comment above)
- # This list will be returned to the caller.
-
- #sys.stderr.write('report_progress='+str(report_progress))
-
- prev_filename = self.infile
- prev_lineno = self.lineno
- var_prefix = ''
- var_descr_plist = []
- var_suffix = ''
- text_block_plist = []
-
- done_reading = False
-
- while not done_reading:
-
- terminate_text = False
- terminate_var = False
- #delete_prior_escape = False
-
- nextchar = self.read_char()
-
-
- #print(' ReadTemplate() nextchar=\''+nextchar+'\' at '+self.error_leader()+' esc='+str(escaped_state)+', pvar='+str(prev_char_delim)+', paren='+str(var_paren_depth))
-
-
-
- # Count newlines:
- if nextchar in self.newline:
- commented_state = False
- self.lineno += 1
-
- elif ((nextchar in self.comment_skip_var) and
- (not escaped_state)):
- commented_state = True
-
- # Check for end-of-file:
- if nextchar == '':
-
- if escaped_state:
- raise InputError('Error: in '+self.error_leader()+'\n\n'
- 'No escaped character.')
- if reading_var:
- terminate_var = True
- else:
- terminate_text = True
-
- done_reading = True
-
-
- # --- Now process the character: ---
-
-
- # What we do next depends on which "mode" we are in.
- # If we are reading a regular text block (reading_var == False),
- # then we keep appending characters onto the end of "text_block",
- # checking for terminal characters, or variable delimiters.
- # If we are reading a variable name (reading_var == True),
- # then we append characters to the end of "var_descr_plist[]",
- # checking for variable terminator characters, as well as
- # parenthesis (some variables are surrounded by parenthesis).
-
- elif reading_var:
-
- if nextchar in terminators:
- #sys.stdout.write(' ReadTemplate() readmode found terminator.\n')
- if escaped_state:
- # In this case, the '\' char was only to prevent terminating
- # string prematurely, so delete the '\' character.
- #delete_prior_escape = True
- if not (nextchar in self.var_close_paren):
- del var_descr_plist[-1]
- var_descr_plist.append(nextchar)
-
- elif not ((var_paren_depth>0) and (nextchar in self.var_close_paren)):
- terminate_var = True
- done_reading = True
-
- if nextchar in self.var_open_paren: # eg: nextchar == '{'
- #sys.stdout.write(' ReadTemplate() readmode found {.\n')
- if escaped_state:
- # In this case, the '\' char was only to prevent
- # interpreting '{' as a variable prefix
- #delete_prior_escape=True # so delete the '\' character
- del var_descr_plist[-1]
- var_descr_plist.append(nextchar)
- else:
- # "${var}" is a valid way to refer to a variable
- if prev_char_delim:
- var_prefix += nextchar
- var_paren_depth = 1
- # "${{var}}" is also a valid way to refer to a variable,
- # (although strange), but "$va{r}" is not.
- # Parenthesis (in bracketed variable names) must
- # immediately follow the '$' character (as in "${var}")
- elif var_paren_depth > 0:
- var_paren_depth += 1
-
- elif nextchar in self.var_close_paren:
- #sys.stdout.write(' ReadTemplate() readmode found }.\n')
- if escaped_state:
- # In this case, the '\' char was only to prevent
- # interpreting '}' as a variable suffix,
- #delete_prior_escape=True #so skip the '\' character
- if (nextchar not in terminators):
- del var_descr_plist[-1]
- var_descr_plist.append(nextchar)
- else:
- if var_paren_depth > 0:
- var_paren_depth -= 1
- if var_paren_depth == 0:
- var_suffix = nextchar
- terminate_var = True
-
- elif nextchar in var_terminators:
- #sys.stdout.write(' ReadTemplate() readmode found var_terminator \"'+nextchar+'\"\n')
- if (escaped_state or (var_paren_depth>0)):
- # In this case, the '\' char was only to prevent
- # interpreting nextchar as a variable terminator
- #delete_prior_escape = True # so skip the '\' character
- del var_descr_plist[-1]
- var_descr_plist.append(nextchar)
- else:
- terminate_var = True
-
- elif nextchar in self.var_delim: # such as '$'
- #sys.stdout.write(' ReadTemplate() readmode found var_delim.\n')
- if escaped_state:
- # In this case, the '\' char was only to prevent
- # interpreting '$' as a new variable name
- #delete_prior_escape = True # so skip the '\' character
- del var_descr_plist[-1]
- var_descr_plist.append(nextchar)
- else:
- prev_var_delim = True
- # Then we are processing a new variable name
- terminate_var = True
- else:
- var_descr_plist.append(nextchar)
- prev_char_delim = False
-
-
- else: # begin else clause for "if reading_var:"
-
- # Then we are reading a text_block
-
- if nextchar in terminators:
- if escaped_state:
- # In this case, the '\' char was only to prevent terminating
- # string prematurely, so delete the '\' character.
- #delete_prior_escape = True
- del text_block_plist[-1]
- text_block_plist.append(nextchar)
- elif commented_state:
- text_block_plist.append(nextchar)
- else:
- terminate_text = True
- done_reading = True
-
- elif nextchar in self.var_delim: # such as '$'
- if escaped_state:
- # In this case, the '\' char was only to prevent
- # interpreting '$' as a variable prefix.
- #delete_prior_escape=True #so delete the '\' character
- del text_block_plist[-1]
- text_block_plist.append(nextchar)
- elif commented_state:
- text_block_plist.append(nextchar)
- else:
- prev_char_delim = True
- reading_var = True
- var_paren_depth = 0
- terminate_text = True
- else:
- text_block_plist.append(nextchar)
- #TO DO: use "list_of_chars.join()" instead of '+='
- prev_char_delim = False # the previous character was not '$'
-
-
- # Now deal with "other_esc_chars"
- #if escaped_state and (nextchar in other_esc_chars):
-
- if escaped_state and (nextchar in other_esc_chars):
- if reading_var:
- #sys.stdout.write(' ReadTemplate: var_descr_str=\''+''.join(var_descr_plist)+'\'\n')
- assert(var_descr_plist[-2] in self.escape)
- del var_descr_plist[-2]
- else:
- #sys.stdout.write(' ReadTemplate: text_block=\''+''.join(text_block_plist)+'\'\n')
- assert(text_block_plist[-2] in self.escape)
- del text_block_plist[-2]
-
-
- if terminate_text:
- #sys.stdout.write('ReadTemplate() appending: ')
- #sys.stdout.write(text_block)
-
- #tmpl_list.append( [text_block,
- # ((prev_filename, prev_lineno),
- # (self.infile, self.lineno))] )
-
- if simplify_output:
- tmpl_list.append(''.join(text_block_plist))
- else:
- tmpl_list.append(TextBlock(''.join(text_block_plist),
- OSrcLoc(prev_filename, prev_lineno)))
- #, OSrcLoc(self.infile, self.lineno)))
- if not done_reading:
- # The character that ended the text block
- # was a variable delimiter (like '$'), in which case
- # we should put it (nextchar) in the variable's prefix.
- var_prefix = nextchar
- else:
- var_prefix = ''
- var_descr_plist = []
- var_suffix = ''
- prev_filename = self.infile
- prev_lineno = self.lineno
- del text_block_plist
- text_block_plist = []
- #gc.collect()
-
-
- elif terminate_var:
- # Print an error if we terminated in the middle of
- # an incomplete variable name:
- if prev_char_delim:
- raise InputError('Error: near '+self.error_leader()+'\n\n'
- 'Null variable name.')
- if var_paren_depth > 0:
- raise InputError('Error: near '+self.error_leader()+'\n\n'
- 'Incomplete bracketed variable name.')
-
- var_descr_str = ''.join(var_descr_plist)
-
- # Now check for variable format modifiers,
- # like python's ".rjust()" and ".ljust()".
- # If present, then put these in the variable suffix.
- if ((len(var_descr_plist)>0) and (var_descr_plist[-1]==')')):
- #i = len(var_descr_plist)-1
- #while i >= 0:
- # if var_descr_plist[i] == '(':
- # break
- # i -= 1
- i = var_descr_str.rfind('(')
- if (((i-6) >= 0) and
- ((var_descr_str[i-6:i] == '.rjust') or
- (var_descr_str[i-6:i] == '.ljust'))):
- var_suffix =''.join(var_descr_plist[i-6:])+var_suffix
- #var_descr_plist = var_descr_plist[:i-6]
- var_descr_str = var_descr_str[:i-6]
-
- # Process any special characters in the variable name
- var_descr_str = EscCharStrToChar(var_descr_str)
-
- #tmpl_list.append( [[var_prefix, var_descr_str, var_suffix],
- # (self.infile, self.lineno)] )
- if simplify_output:
- tmpl_list.append(var_prefix + var_descr_str + var_suffix)
- else:
- tmpl_list.append( VarRef(var_prefix, var_descr_str, var_suffix,
- OSrcLoc(self.infile, self.lineno)) )
-
- #if report_progress:
- #sys.stderr.write(' parsed variable '+var_prefix+var_descr_str+var_suffix+'\n')
-
- #sys.stdout.write('ReadTemplate() appending: ')
- #print(var_prefix + var_descr_str + var_suffix)
-
- del var_descr_plist
- del var_descr_str
-
- prev_filename = self.infile
- prev_lineno = self.lineno
- var_prefix = ''
- var_descr_plist = []
- var_suffix = ''
- # Special case: Variable delimiters like '$'
- # terminate the reading of variables,
- # but they also signify that a new
- # variable is being read.
- if nextchar in self.var_delim:
- # Then we are processing a new variable name
- prev_var_delim = True
- reading_var = True
- var_paren_depth = 0
- var_prefix = nextchar
-
- elif nextchar in self.var_close_paren:
- del text_block_plist
- text_block_plist = []
- #gc.collect()
- prev_var_delim = False
- reading_var = False
-
- else:
- # Generally, we don't want to initialize the next text block
- # with the empty string. Consider that whatever character
- # caused us to stop reading the previous variable and append
- # it to the block of text that comes after.
- del text_block_plist
- text_block_plist = [nextchar]
- #gc.collect()
- prev_var_delim = False
- reading_var = False
-
-
- # If we reached the end of the template (and the user requests it),
- # then the terminal character can be included in the list
- # of text_blocks to be returned to the caller.
- if done_reading and keep_terminal_char:
- #sys.stdout.write('ReadTemplate() appending: \''+nextchar+'\'\n')
- # Here we create a new text block which contains only the
- # terminal character (nextchar).
- #tmpl_list.append( [nextchar,
- # ((self.infile, self.lineno),
- # (self.infile, self.lineno))] )
- if simplify_output:
- tmpl_list.append(nextchar)
- else:
- tmpl_list.append(TextBlock(nextchar,
- OSrcLoc(self.infile, self.lineno)))
- #, OSrcLoc(self.infile, self.lineno)))
-
-
- if escaped_state:
- escaped_state = False
- else:
- if nextchar in self.escape:
- escaped_state = True
-
- #print("*** TMPL_LIST0 = ***", tmpl_list)
- return tmpl_list # <- return value stored here
-
-
-
-
- def GetParenExpr(self, prepend_str='', left_paren='(', right_paren=')'):
- """ GetParenExpr() is useful for reading in strings
- with nested parenthesis and spaces.
- This function can read in the entire string:
-
- .trans(0, 10.0*sin(30), 10.0*cos(30))
-
- (Because I was too lazy to write this correctly...)
- Spaces are currently stripped out of the expression.
- (...unless surrounded by quotes) The string above becomes:
-
- ".trans(0,10.0*sin(30),10.0*cos(30))"
-
- Sometimes the caller wants to prepend some text to the beginning
- of the expression (which may contain parenthesis). For this
- reason, an optional first argument ("prepend_str") can be
- provided. By default it is empty.
-
- """
-
- src_loc_begin = SrcLoc(self.infile, self.lineno)
- orig_wordterm = self.wordterminators
- self.wordterminators = self.wordterminators.replace(left_paren,'').replace(right_paren,'')
-
- token = self.get_token()
- if ((token == '') or
- (token == self.eof)):
- return prepend_str
-
-
- expr_str = prepend_str + token
-
- #if (expr_str.find(left_paren) == -1):
- # raise InputError('Error near or before '+self.error_leader()+'\n'
- # 'Expected an open-paren (\"'+prepend_str+left_paren+'\") before this point.\n')
- # return expr_str
-
- paren_depth = expr_str.count(left_paren) - expr_str.count(right_paren)
- while ((len(expr_str) == 0) or (paren_depth > 0)):
- token = self.get_token()
- if ((type(token) is not str) or
- (token == '')):
- raise InputError('Error somewhere between '+
- self.error_leader(src_loc_begin.infile,
- src_loc_begin.lineno)
- + 'and ' + self.error_leader()+'\n'
- 'Invalid expression: \"'+expr_str[0:760]+'\"')
- expr_str += token
- paren_depth = expr_str.count(left_paren) - expr_str.count(right_paren)
- if (paren_depth != 0):
- raise InputError('Error somewhere between '+
- self.error_leader(src_loc_begin.infile,
- src_loc_begin.lineno)
- + 'and ' + self.error_leader()+'\n'
- 'Invalid expression: \"'+expr_str[0:760]+'\"')
- self.wordterminators = orig_wordterm
- return expr_str
-
-
-
-
-
-
-
-
-
-
-if __name__ == '__main__':
- if len(sys.argv) == 1:
- lexer = TtreeShlex()
- else:
- file = sys.argv[1]
- lexer = TtreeShlex(open(file), file)
- while 1:
- tt = lexer.get_token()
- if tt:
- print("Token: " + repr(tt))
- else:
- break
diff --git a/tools/moltemplate/src/ttree_matrix_stack.py b/tools/moltemplate/src/ttree_matrix_stack.py
deleted file mode 100644
index 18649cfb0..000000000
--- a/tools/moltemplate/src/ttree_matrix_stack.py
+++ /dev/null
@@ -1,710 +0,0 @@
-# Author: Andrew Jewett (jewett.aij@gmail.com)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-from collections import deque
-from array import array
-from ttree_lex import *
-#import sys
-
-def MultMat(dest, A, B):
- """ Multiply two matrices together. Store result in "dest".
-
- """
- I = len(A)
- J = len(B[0])
- K = len(B) # or len(A[0])
- for i in range(0,I):
- for j in range(0,J):
- dest[i][j] = 0.0
- for k in range(0,K):
- dest[i][j] += A[i][k] * B[k][j]
-
-
-def MatToStr(M):
- strs = []
- for i in range(0, len(M)):
- for j in range(0, len(M[i])):
- strs.append(str(M[i][j])+' ')
- strs.append('\n')
- return(''.join(strs))
-
-
-def LinTransform(dest, M, x):
- """ Multiply matrix M by 1-dimensioal array (vector) "x" (from the right).
- Store result in 1-dimensional array "dest".
- In this function, wetreat "x" and "dest" as a column vectors.
- (Not row vectors.)
-
- """
- I = len(A)
- J = len(x)
- for i in range(0,I):
- dest[i] = 0.0
- for j in range(0,J):
- dest[i] += M[i][j] * x[j]
-
-
-def AffineTransform(dest, M, x):
- """ This function performs an affine transformation on vector "x".
- Multiply 3-dimensional vector "x" by first three columns of 3x4
- matrix M. Add to this the final column of M. Store result in "dest":
- dest[0] = M[0][0]*x[0] + M[0][1]*x[1] + M[0][2]*x[2] + M[0][3]
- dest[1] = M[1][0]*x[0] + M[1][1]*x[1] + M[1][2]*x[2] + M[1][3]
- dest[2] = M[2][0]*x[0] + M[2][1]*x[1] + M[2][2]*x[2] + M[2][3]
-
- """
- D = len(M)
- #assert(len(M[0]) == D+1)
- for i in range(0,D):
- dest[i] = 0.0
- for j in range(0,D):
- dest[i] += M[i][j] * x[j]
- dest[i] += M[i][D] #(translation offset stored in final column)
-
-
-def AffineCompose(dest, M2, M1):
- """
- Multiplication for pairs of 3x4 matrices is technically undefined.
- However what we want to do is compose two affine transformations: M1 and M2
-
- 3x4 matrices are used to define rotations/translations
- x' = M[0][0]*x + M[0][1]*y + M[0][2]*z + M[0][3]
- y' = M[1][0]*x + M[1][1]*y + M[1][2]*z + M[1][3]
- z' = M[2][0]*x + M[2][1]*y + M[2][2]*z + M[2][3]
-
- We want to create a new 3x4 matrix representing an affine transformation
- (M2 M1), defined so that when (M2 M1) is applied to vector x, the result is
- M2 (M1 x). In other words:
- first, affine transformation M1 is applied to to x
- then, affine transformation M2 is applied to (M1 x)
-
- """
-
- D = len(M1)
- #assert(len(M1[0]) == D+1)
- #assert(len(M2[0]) == D+1)
- for i in range(0, D):
- dest[i][D] = 0.0
- for j in range(0, D+1):
- dest[i][j] = 0.0
- for k in range(0, D):
- dest[i][j] += M2[i][k] * M1[k][j]
- dest[i][D] += M2[i][D]
-
-def CopyMat(dest, source):
- for i in range(0, len(source)):
- for j in range(0, len(source[i])):
- dest[i][j] = source[i][j]
-
-
-class AffineStack(object):
- """
- This class defines a matrix stack used to define compositions of affine
- transformations of 3 dimensional coordinates (rotation and translation).
- Affine transformations are represented using 3x4 matrices.
- (Coordinates of atoms are thought of as column vectors: [[x],[y],[z]],
- although they are represented internally in the more ordinary way [x,y,z].
- To aplly an affine transformation to a vector, multiply the vector
- by the matrix, from the left-hand side, as explained in the comments for:
- AffineTransform(dest, M, x)
- Note: The last column of the 3x4 matrix stores a translational offset.
- This bears similarity with the original OpenGL matrix stack
- http://content.gpwiki.org/index.php/OpenGL:Tutorials:Theory
- (OpenGL uses 4x4 matrices. We don't need the final row of these matrices,
- because in OpenGL, these rows are used for perspective transformations.)
- http://en.wikipedia.org/wiki/Homogeneous_coordinates#Use_in_computer_graphics
-
- """
- def __init__(self):
- self.stack = None
- self.M = None
- self._tmp = None
- self.Clear()
-
- def Clear(self):
- self.stack = deque([])
- self.M = [[1.0, 0.0, 0.0, 0.0],
- [0.0, 1.0, 0.0, 0.0],
- [0.0, 0.0, 1.0, 0.0]] # (identity, initially)
- self._tmp = [[1.0, 0.0, 0.0, 0.0],
- [0.0, 1.0, 0.0, 0.0],
- [0.0, 0.0, 1.0, 0.0]]
-
- def PushRight(self, M):
- #Push a copy of matrix self.M onto the stack
- # We make no distinction between "right" and "left" here.
- # All transformations are pushed onto the stack in the same way.
- # (The "right" and "left" refer to whether the matrix is multiplied
- # on the right of left hand side. Because not all matrices need be
- # invertible, we require that matrices be popped from the stack
- # in the reverse order they were pushed. This prevents the ability
- # to push and pop matrices to either end of the stack in an arbitrary
- # order (like append(), appendleft(), pop(), popleft()).)
- self.stack.append([[self.M[i][j] for j in range(0,len(self.M[i]))]
- for i in range(0,len(self.M))])
- # The "Right" and "Left" refer to whether the new matrix is multiplied
- # on the right or left side of the culmulatie matrix product.
- AffineCompose(self._tmp, self.M, M) # Afterwards, self._tmp = self.M * M
-
- #sys.stderr.write('DEBUG: PushLeft()\n' +
- # MatToStr(self._tmp) + '\n = \n' +
- # MatToStr(M) + '\n * \n' +
- # MatToStr(self.M) + '\n')
-
- CopyMat(self.M, self._tmp) # Copy self._tmp into self.M
-
-
- def PushLeft(self, M):
- #Push a copy of matrix self.M onto the stack
- # We make no distinction between right and left here.
- # All transformations are pushed onto the stack in the same way.
- # (The "right" and "left" refer to whether the matrix is multiplied
- # on the right of left hand side. Because not all matrices need be
- # invertible, we require that matrices be popped from the stack
- # in the reverse order they were pushed. This prevents the ability
- # to push and pop matrices to either end of the stack in an arbitrary
- # order (like append(), appendleft(), pop(), popleft()).)
- self.stack.append([[self.M[i][j] for j in range(0,len(self.M[i]))]
- for i in range(0,len(self.M))])
- # The "Right" and "Left" refer to whether the new matrix is multiplied
- # on the right or left side of the culmulatie matrix product.
- AffineCompose(self._tmp, M, self.M) # Afterwards, self._tmp = M * self.M
-
- #sys.stderr.write('DEBUG: PushLeft()\n' +
- # MatToStr(self._tmp) + '\n = \n' +
- # MatToStr(M) + '\n * \n' +
- # MatToStr(self.M) + '\n')
-
- CopyMat(self.M, self._tmp) # Copy self.tmp into self.M
-
-
- def Pop(self):
- CopyMat(self.M, self.stack.pop())
- # (No need to return a matrix,"self.M",after popping.
- # The caller can directly access self.M later.)
- #return self.M
-
-
- def PopRight(self):
- self.Pop()
-
-
- def PopLeft(self):
- self.Pop()
-
- def PushCommandsRight(self,
- text, # text containing affine transformation commands
- # The next two arguments are optional:
- src_loc = OSrcLoc(), # for debugging
- xcm = None): # position of center of object
- """Generate affine transformation matrices from simple text commands
- (such as \"rotcm(90,0,0,1)\" and \"move(0,5.0,0)".
- Chains of "rotcm", "movecm", "rot", and "move" commands
- can also be strung together:
- \"rotcm(90,0,0,1).move(0,5.0,0)\"
- Commands ending in \"cm\" are carried out relative to center-of-mass
- (average position) of the object, and consequently require
- an additional argument (\"xcm\").
-
- """
- self.PushRight(AffineStack.CommandsToMatrix(text, src_loc, xcm))
-
- def PushCommandsLeft(self,
- text, # text containing affine transformation commands
- # The next two arguments are optional:
- src_loc = OSrcLoc(), # for debugging
- xcm = None): # position of center of object
- self.PushLeft(AffineStack.CommandsToMatrix(text, src_loc, xcm))
-
-
- def __len__(self):
- return 1 + len(self.stack)
-
-
- @staticmethod
- def CommandsToMatrix(text, # text containing affine transformation commands
- src_loc = OSrcLoc(), # for debugging
- xcm = None): # position of center of object
- Mdest=[[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0]]
- M =[[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0]]
- Mtmp =[[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0]]
-
- transform_commands = text.split(').')
- for transform_str in transform_commands:
- if transform_str.find('move(') == 0:
- i_paren_close = transform_str.find(')')
- if i_paren_close == -1:
- i_paren_close = len(transform_str)
- args = transform_str[5:i_paren_close].split(',')
- if (len(args) != 3):
- raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- ' Invalid command: \"'+transform_str+'\"\n'
- ' This command requires 3 numerical arguments.')
- M = [[1.0, 0.0, 0.0, float(args[0])],
- [0.0, 1.0, 0.0, float(args[1])],
- [0.0, 0.0, 1.0, float(args[2])]]
- AffineCompose(Mtmp, M, Mdest)
- CopyMat(Mdest, Mtmp)
-
- #if transform_str.find('movecm(') == 0:
- # # assert(xcm != None)
- # i_paren_close = transform_str.find(')')
- # if i_paren_close == -1:
- # i_paren_close = len(transform_str)
- # args = transform_str[8:i_paren_close].split(',')
- # if (len(args) != 3):
- # raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- # ' Invalid command: \"'+transform_str+'\"\n'
- # ' This command requires 3 numerical arguments.')
- # M = [[1.0, 0.0, 0.0, float(args[0])-(xcm[0])],
- # [0.0, 1.0, 0.0, float(args[1])-(xcm[1])],
- # [0.0, 0.0, 1.0, float(args[2])-(xcm[2])]]
- # AffineCompose(Mtmp, M, Mdest)
- # CopyMat(Mdest, Mtmp)
-
- elif transform_str.find('rot(') == 0:
- i_paren_close = transform_str.find(')')
- if i_paren_close == -1:
- i_paren_close = len(transform_str)
- args = transform_str[4:i_paren_close].split(',')
- center_v = None
- if (len(args) == 7):
- center_v = [float(args[4]), float(args[5]), float(args[6])]
- elif (len(args) != 4):
- raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- ' Invalid command: \"'+transform_str+'\"\n'
- ' This command requires either 4 or 7 numerical arguments. Either:\n'
- ' rot(angle, axisX, axisY, axiZ) or \n'
- ' rot(angle, axisX, axisY, axiZ, centerX, centerY, centerZ)')
- M[0][3] = 0.0 #RotMatAXYZ() only modifies 3x3 submatrix of M
- M[1][3] = 0.0 #The remaining final column must be zeroed by hand
- M[2][3] = 0.0
- RotMatAXYZ(M,
- float(args[0])*math.pi/180.0,
- float(args[1]),
- float(args[2]),
- float(args[3]))
- if (center_v == None):
- AffineCompose(Mtmp, M, Mdest)
- CopyMat(Mdest, Mtmp)
- else:
- # Move "center_v" to the origin
- moveCentToOrig = [[1.0, 0.0, 0.0, -center_v[0]],
- [0.0, 1.0, 0.0, -center_v[1]],
- [0.0, 0.0, 1.0, -center_v[2]]]
- AffineCompose(Mtmp, moveCentToOrig, Mdest)
- CopyMat(Mdest, Mtmp)
- # Rotate the coordinates (relative to the origin)
- AffineCompose(Mtmp, M, Mdest) # M is the rotation matrix
- CopyMat(Mdest, Mtmp)
- # Move the origin back to center_v
- moveCentBack = [[1.0, 0.0, 0.0, center_v[0]],
- [0.0, 1.0, 0.0, center_v[1]],
- [0.0, 0.0, 1.0, center_v[2]]]
- AffineCompose(Mtmp, moveCentBack, Mdest)
- CopyMat(Mdest, Mtmp)
-
- # # elif transform_str.find('rotcm(') == 0:
- # # assert(xcm != None)
- # # i_paren_close = transform_str.find(')')
- # # if i_paren_close == -1:
- # # i_paren_close = len(transform_str)
- # # args = transform_str[6:i_paren_close].split(',')
- # # if (len(args) != 4):
- # # raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- # # ' Invalid command: \"'+transform_str+'\"\n'
- # # ' This command requires 4 numerical arguments.')
- # #
- # # moveCMtoOrig = [[1.0, 0.0, 0.0, -xcm[0]],
- # # [0.0, 1.0, 0.0, -xcm[1]],
- # # [0.0, 0.0, 1.0, -xcm[2]]]
- # # AffineCompose(Mtmp, moveCMtoOrig, Mdest)
- # # CopyMat(Mdest, Mtmp)
- # # M[0][3] = 0.0#RotMatAXYZ() only modifies 3x3 submatrix of M
- # # M[1][3] = 0.0#The remaining final column must be zeroed by hand
- # # M[2][3] = 0.0
- # # RotMatAXYZ(M,
- # # float(args[0])*math.pi/180.0,
- # # float(args[1]),
- # # float(args[2]),
- # # float(args[3]))
- # # AffineCompose(Mtmp, M, Mdest)
- # # CopyMat(Mdest, Mtmp)
- # # moveCmBack = [[1.0, 0.0, 0.0, xcm[0]],
- # # [0.0, 1.0, 0.0, xcm[1]],
- # # [0.0, 0.0, 1.0, xcm[2]]]
- # # AffineCompose(Mtmp, moveCmBack, Mdest)
- # # CopyMat(Mdest, Mtmp)
-
- elif transform_str.find('rotvv(') == 0:
- i_paren_close = transform_str.find(')')
- if i_paren_close == -1:
- i_paren_close = len(transform_str)
- args = transform_str[6:i_paren_close].split(',')
- center_v = None
- if (len(args) == 9):
- center_v = [float(args[6]), float(args[7]), float(args[8])]
- elif (len(args) != 6):
- raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- ' Invalid command: \"'+transform_str+'\"\n'
- ' This command requires either 6 or 9 numerical arguments. Either:\n'
- ' rotvv(Xold,Yold,Zold,Xnew,Ynew,Znew) or \n'
- ' rotvv(Xold,Yold,Zold,Xnew,Ynew,Znew,centerX,centerY,centerZ)')
- M[0][3] = 0.0 #RotMatXYZXYZ() only modifies 3x3 submatrix of M
- M[1][3] = 0.0 #The remaining final column must be zeroed by hand
- M[2][3] = 0.0
- RotMatXYZXYZ(M,
- float(args[0]),
- float(args[1]),
- float(args[2]),
- float(args[3]),
- float(args[4]),
- float(args[5]))
- if (center_v == None):
- AffineCompose(Mtmp, M, Mdest)
- CopyMat(Mdest, Mtmp)
- else:
- # Move "center_v" to the origin
- moveCentToOrig = [[1.0, 0.0, 0.0, -center_v[0]],
- [0.0, 1.0, 0.0, -center_v[1]],
- [0.0, 0.0, 1.0, -center_v[2]]]
- AffineCompose(Mtmp, moveCentToOrig, Mdest)
- CopyMat(Mdest, Mtmp)
- # Rotate the coordinates (relative to the origin)
- AffineCompose(Mtmp, M, Mdest) # M is the rotation matrix
- CopyMat(Mdest, Mtmp)
- # Move the origin back to center_v
- moveCentBack = [[1.0, 0.0, 0.0, center_v[0]],
- [0.0, 1.0, 0.0, center_v[1]],
- [0.0, 0.0, 1.0, center_v[2]]]
- AffineCompose(Mtmp, moveCentBack, Mdest)
- CopyMat(Mdest, Mtmp)
-
- elif transform_str.find('scale(') == 0:
- i_paren_close = transform_str.find(')')
- if i_paren_close == -1:
- i_paren_close = len(transform_str)
- args = transform_str[6:i_paren_close].split(',')
-
- if (len(args) == 1):
- scale_v = [float(args[0]), float(args[0]), float(args[0])]
- center_v = [0.0, 0.0, 0.0]
- elif (len(args) == 3):
- scale_v = [float(args[0]), float(args[1]), float(args[2])]
- center_v = [0.0, 0.0, 0.0]
- elif (len(args) == 4):
- scale_v = [float(args[0]), float(args[0]), float(args[0])]
- center_v = [float(args[1]), float(args[2]), float(args[3])]
- elif (len(args) == 6):
- scale_v = [float(args[0]), float(args[1]), float(args[2])]
- center_v = [float(args[3]), float(args[4]), float(args[5])]
- else:
- raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- ' Invalid command: \"'+transform_str+'\"\n'
- ' This command requires either 1, 3, 4, or 6 numerical arguments. Either:\n'
- ' scale(ratio), or \n'
- ' scale(ratioX, ratioY, ratioZ),\n'
- ' scale(ratio, centerX, centerY, centerZ), or\n'
- ' scale(ratioX, ratioY, ratioZ, centerX, centerY, centerZ)')
-
- ScaleMat(M, scale_v)
-
- # Now worry about translation:
- for d in range(0, 3):
- M[d][3] = center_v[d] * (1.0 - scale_v[d])
-
- AffineCompose(Mtmp, M, Mdest)
- CopyMat(Mdest, Mtmp)
-
- # # elif transform_str.find('scalecm(') == 0:
- # # assert(xcm != None)
- # # i_paren_close = transform_str.find(')')
- # # if i_paren_close == -1:
- # # i_paren_close = len(transform_str)
- # # args = transform_str[8:i_paren_close].split(',')
- # #
- # # moveCMtoOrig = [[1.0, 0.0, 0.0, -xcm[0]],
- # # [0.0, 1.0, 0.0, -xcm[1]],
- # # [0.0, 0.0, 1.0, -xcm[2]]]
- # # AffineCompose(Mtmp, moveCMtoOrig, Mdest)
- # # CopyMat(Mdest, Mtmp)
- # #
- # # M[0][3] = 0.0 #ScaleMat() only modifies 3x3 submatrix of M
- # # M[1][3] = 0.0 #The remaining final column must be zeroed by hand
- # # M[2][3] = 0.0
- # # if (len(args) == 1):
- # # ScaleMat(M, args[0])
- # # elif (len(args) == 3):
- # # ScaleMat(M, args)
- # # else:
- # # raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- # # ' Invalid command: \"'+transform_str+'\"\n'
- # # ' This command requires either 1 or 3 numerical arguments.')
- # #
- # # AffineCompose(Mtmp, M, Mdest)
- # # CopyMat(Mdest, Mtmp)
- # # moveCmBack = [[1.0, 0.0, 0.0, xcm[0]],
- # # [0.0, 1.0, 0.0, xcm[1]],
- # # [0.0, 0.0, 1.0, xcm[2]]]
- # # AffineCompose(Mtmp, moveCmBack, Mdest)
- # # CopyMat(Mdest, Mtmp)
-
- else:
- raise InputError('Error near '+ErrorLeader(src_loc.infile, src_loc.lineno)+':\n'
- ' Unknown transformation command: \"'+transform_str+'\"\n')
-
-
- return Mdest
-
-
-
-
-class MultiAffineStack(object):
- def __init__(self, which_stack=None):
- self.tot_stack = None
- self.stack_lookup = None
- self.stack_keys = None
- self.stacks = None
- self.M = None
- self.error_if_substack_empty = False
- self.Clear()
-
- def Clear(self):
- self.tot_stack = AffineStack()
- self.stack_lookup = {}
- self.stack_keys = deque([])
- self.stacks = deque([])
- self.M = self.tot_stack.M
- self.error_if_substack_empty = False
-
- def _Update(self):
- self.tot_stack.Clear()
- self.M = self.tot_stack.M
- assert(len(self.stacks) > 0)
- for stack in self.stacks:
- self.tot_stack.PushRight(stack.M)
-
- def PushStack(self, which_stack):
- stack = AffineStack()
- self.stack_keys.append(which_stack)
- self.stack_lookup[which_stack] = stack
- self.stacks.append(stack)
- self.tot_stack.PushRight(stack.M)
-
- def PopStack(self):
- assert(len(self.stacks) > 0)
- self.tot_stack.PopRight()
- which_stack = self.stack_keys.pop()
- del self.stack_lookup[which_stack]
- self.stacks.pop()
-
- def Push(self, M, which_stack=None, right_not_left = True):
- if len(self.stacks) == 0:
- self.PushStack(which_stack)
- if which_stack == None:
- stack = self.stacks[-1]
- if right_not_left:
- stack.PushRight(M) # This should copy the matrix M into stack.M
- else:
- stack.PushLeft(M)
- else:
- stack = self.stack_lookup[which_stack]
- if right_not_left:
- stack.PushRight(M)
- else:
- stack.PushLeft(M)
- if stack == self.stacks[-1]:
- self.tot_stack.PopRight() #Replace the last matrix on self.tot_stack
- # Note: Always use tot_stack.PopRight (even if right_not_left=False)
- self.tot_stack.PushRight(stack.M) # with the the updated version.
- # Note: We could call self._Update(M) here, but that is slower.
- else:
- self._Update()
-
- def PushRight(self, M, which_stack=None):
- self.Push(M, which_stack, right_not_left=True)
-
- def PushLeft(self, M, which_stack=None):
- self.Push(M, which_stack, right_not_left=False)
-
- def PushCommandsRight(self,
- text, # text containing affine transformation commands
- # The next two arguments are optional:
- src_loc = OSrcLoc(), # for debugging
- xcm = None,
- which_stack=None): # position of center of object
- """Generate affine transformation matrices from simple text commands
- (such as \"rotcm(90,0,0,1)\" and \"move(0,5.0,0)".
- Chains of "rotcm", "movecm", "rot", and "move" commands
- can also be strung together:
- \"rotcm(90,0,0,1).move(0,5.0,0)\"
- Commands ending in \"cm\" are carried out relative to center-of-mass
- (average position) of the object, and consequently require
- an additional argument (\"xcm\").
-
- """
- self.PushRight(AffineStack.CommandsToMatrix(text, src_loc, xcm),
- which_stack)
-
- def PushCommandsLeft(self,
- text, # text containing affine transformation commands
- # The next two arguments are optional:
- src_loc = OSrcLoc(), # for debugging
- xcm = None, # position of center of object
- which_stack = None):
- self.PushLeft(AffineStack.CommandsToMatrix(text, src_loc, xcm),
- which_stack)
-
-
-
- def Pop(self, which_stack=None, right_not_left=True):
- #empty_stack_error = False
-
- if which_stack == None:
- stack = self.stacks[-1]
- if len(stack) >= 1:
- if right_not_left:
- stack.PopRight()
- else:
- stack.PopLeft()
- # Note: We could call self._Update(M) here, but that is slower
- self.tot_stack.PopRight() #Replace the last matrix on self.tot_stack
- # Note: Always use tot_stack.PopRight (even if right_not_left=False)
- self.tot_stack.PushRight(stack.M) # with the the updated version.
- else:
- assert(False)
- # OPTIONAL CODE BELOW AUTOMATICALLY INVOKES self.PopStack() WHEN
- # THE stacks[-1].stack IS EMPTY. PROBABLY DOES NOT WORK. IGNORE
- # if (not self.error_if_substack_empty):
- # if right_not_left:
- # assert(len(self.stacks) > 0)
- # self.PopStack()
- # else:
- # assert(False)
- # else:
- # empty_stack_error = True
-
- else:
- stack = self.stack_lookup[which_stack]
- if len(stack) > 1:
- if right_not_left:
- stack.PopRight()
- else:
- stack.PopLeft()
- self._Update()
- else:
- assert(False)
- #empty_stack_error = True
-
- def PopRight(self, which_stack=None):
- self.Pop(which_stack, right_not_left=True)
-
- def PopLeft(self, which_stack=None):
- self.Pop(which_stack, right_not_left=True)
-
-
-
-
-
-
-import math
-
-
-def ScaleMat(dest, scale):
- for i in range(0, len(dest)):
- for j in range(0, len(dest[i])):
- dest[i][j] = 0.0
- if ((type(scale) is float) or (type(scale) is int)):
- for i in range(0, len(dest)):
- dest[i][i] = scale
- else:
- for i in range(0, len(dest)):
- dest[i][i] = scale[i]
-
-
-def RotMatAXYZ(dest, angle, axis_x, axis_y, axis_z):
-
- r = math.sqrt(axis_x*axis_x + axis_y*axis_y + axis_z*axis_z)
-
- X = 1.0
- Y = 0.0
- Z = 0.0
- if r > 0.0: # check for non-sensical input
- X = axis_x / r
- Y = axis_y / r
- Z = axis_z / r
- else:
- angle = 0.0
-
- #angle *= math.pi/180.0 # "angle" is assumed to be in degrees
- # on second thought, let the caller worry about angle units.
- c = math.cos(angle)
- s = math.sin(angle)
-
- dest[0][0] = X*X*(1-c) + c
- dest[1][1] = Y*Y*(1-c) + c
- dest[2][2] = Z*Z*(1-c) + c
-
- dest[0][1] = X*Y*(1-c) - Z*s
- dest[0][2] = X*Z*(1-c) + Y*s
-
- dest[1][0] = Y*X*(1-c) + Z*s
- dest[2][0] = Z*X*(1-c) - Y*s
-
- dest[1][2] = Y*Z*(1-c) - X*s
- dest[2][1] = Z*Y*(1-c) + X*s
-
- # formula from these sources:
- # http://inside.mines.edu/~gmurray/ArbitraryAxisRotation/
- # also check
- # http://www.manpagez.com/man/3/glRotate/
- # some pdb test commands:
- # from lttree_matrixstack import *
- # r = [[1.0,0.0,0.0], [0.0,1.0,0.0], [0.0,0.0,1.0]]
- # RotMatAXYZ(r, 90.0, 0.0, 0.0, 1.0)
-
-def CrossProd(dest, A, B):
- dest[0] = (A[1]*B[2] - B[1]*A[2])
- dest[1] = (A[2]*B[0] - B[2]*A[0])
- dest[2] = (A[0]*B[1] - B[0]*A[1])
-
-def DotProd(A, B):
- c = 0.0
- for d in range(0, len(A)):
- c += A[d]*B[d]
- return c
-
-def Length(A):
- L = 0.0
- for x in A:
- L += x*x
- return math.sqrt(L)
-
-def Normalize(dest, source):
- assert(len(dest) == len(source))
- L = Length(source)
- for d in range(0, len(source)):
- dest[d] = source[d] / L
-
-def RotMatXYZXYZ(dest,
- xold, yold, zold,
- xnew, ynew, znew):
- A = [xold, yold, zold]
- B = [xnew, ynew, znew]
- axis = [0.0, 0.0, 0.0]
- CrossProd(axis, A, B)
- La = Length(A)
- Lb = Length(B)
- Lc = Length(axis)
- sinAng = Lc / (La*Lb)
- cosAng = DotProd(A,B) / (La*Lb)
- if Lc > 0.0:
- Normalize(axis, axis)
- angle = math.atan2(sinAng, cosAng)
- else:
- axis = [1.0, 0.0, 0.0]
- angle = 0.0
- RotMatAXYZ(dest, angle, axis[0], axis[1], axis[2])
diff --git a/tools/moltemplate/src/ttree_render.py b/tools/moltemplate/src/ttree_render.py
deleted file mode 100644
index 48ea7af04..000000000
--- a/tools/moltemplate/src/ttree_render.py
+++ /dev/null
@@ -1,115 +0,0 @@
-#!/usr/bin/env python
-
-man_page_text = """
-Usage (example):
-
-ttree_render.py ttree_assignments.txt < file.template > file.rendered
-
-The argument (ttree_assignments.txt) should be a 2-column file containing
-ttree-style variables (1st column), and their values (bindings, 2nd column).
-
-This program reads a text file containing ttree-style variables,
-substitutes the corresponding values stored in ttree_assignments.txt,
-and prints out the new (rendered) text to the standard-out.
-
-"""
-
-
-import sys
-from ttree_lex import *
-from ttree import *
-import gc
-
-
-g_filename = __file__.split('/')[-1]
-g_module_name = g_filename
-if g_filename.rfind('.py') != -1:
- g_module_name = g_filename[:g_filename.rfind('.py')]
-g_date_str = '2012-9-06'
-g_version_str = '0.1'
-g_program_name = g_filename
-#sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
-
-
-
-try:
-
- if (len(sys.argv) != 2):
- raise InputError('Error running \"'+g_program_name+'\"\n'
- ' Typical usage:\n'
- ' ttree_render.py ttree_assignments.txt < file.template > file.rendered\n'
- '\n'
- ' Missing argument.\n'
- ' Expected the name of a 2-column file containing\n'
- ' variable names and their bindings (values).\n'
- ' (This is likely a programmer error.\n'
- ' This script was not intended to be run by end users.)\n')
-
- bindings_filename = sys.argv[1]
- f = open(bindings_filename)
- assignments = {}
-
- #BasicUIReadBindingsStream(assignments, f, bindings_filename)
-
- # The line above is robust but it uses far too much memory.
- # This for loop below works for most cases.
- for line in f:
- #tokens = lines.strip().split()
- tokens = SplitQuotedString(line.strip()) # like split but handles quotes
- if len(tokens) < 2:
- continue
- assignments[tokens[0]] = tokens[1]
-
- f.close()
- gc.collect()
-
- lex = TemplateLexer(sys.stdin, '__standard_input_for_ttree_render__')
- lex.var_delim = '$@'
-
- text_block_list = lex.ReadTemplate(simplify_output=True)
-
- output = []
-
- for entry in text_block_list:
- assert(isinstance(entry, str))
-
- if ((len(entry) > 1) and (entry[0] in lex.var_delim)):
- if '.' in entry:
- ic = entry.find('.')
- var_name = entry[:ic]
- var_suffix = entry[ic:]
- else:
- var_name = entry
- var_suffix = ''
-
- var_name = entry
- if var_name not in assignments:
- raise(InputError('Error('+g_program_name+')'
- #' at '+ErrorLeader(var_ref.src_loc.infile,
- # var_ref.src_loc.lineno)+
- ' unknown variable:\n'
- ' \"'+var_name+'\"\n'))
- else:
- var_value = assignments[var_name]
-
- format_fname, args = ExtractFormattingCommands(var_suffix)
- if format_fname == 'ljust':
- if len(args) == 1:
- var_value = var_value.ljust(int(args[0]))
- else:
- var_value = var_value.ljust(int(args[0]), args[1])
- elif format_fname == 'rjust':
- if len(args) == 1:
- var_value = var_value.rjust(int(args[0]))
- else:
- var_value = var_value.rjust(int(args[0]), args[1])
- output.append(var_value)
- else:
- output += entry
-
- sys.stdout.write(''.join(output))
-
-
-except (ValueError, InputError) as err:
- sys.stderr.write('\n'+str(err)+'\n')
- sys.exit(-1)

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