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	diff --git a/tools/moltemplate/LICENSE.TXT b/tools/moltemplate/LICENSE.TXT
	deleted file mode 100644
	index 86812ab32..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) 2012, 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 2e73b6374..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] file.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/common/graphene.lt b/tools/moltemplate/common/graphene.lt
	deleted file mode 100644
	index 6a177c59f..000000000
	--- a/tools/moltemplate/common/graphene.lt
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-# You can use the definitions in this file to
	-# create graphene, graphite, or nanotubes.
	-
	-
	-
	-Graphene {
	-
	- 2AtomCellAlignX {
	-
	- # The 2AtomCellAlignX "molecule" is a minimal basis cell
	- # for any hexagonal arrangement of atoms in 2-dimensions.
	- # The distance between these two atoms is equal to "l", where "l" is
	- # the length of each side of a hexegon, which I set to 1.420 Angstroms.
	- #
	- # l = length of each hexagonal side = 1.42 Angstroms
	- # L = length of each hexagon = 2*l = 2.84 Angstroms
	- # W = width of each hexagon = 2lsqrt(3)/2 = 2.4595121467478056 Angstroms
	- #
	- # The Lattice-cell vectors for graphene (graphite) are
	- # (2.4595121467478, 0, 0) (aligned with X axis)
	- # (1.2297560733739, 2.13, 0) (2.13 = 1.5*l)
	- # ( 0 1.00, 3.35) (3.35 = distance between layers of
	- # graphene sheets in graphite.)
	-
	-
	- # 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
	- }
	-
	- } # 2AtomCellAlignX
	-
	-
	-
	-
	- # Notice that the two atoms in the unit-cell above lie in the XY plane.
	- # (Their z-coord is zero). It's also handy to have a version of this
	- # object which lies in the XZ plan, so we make this below.
	-
	- 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0)
	-
	-
	-
	-
	- # Define properties of the Carbon-Hydrogen graphene atom
	- write_once("Data Masses") {
	- @atom:C 12.0
	- }
	-
	- write_once("In Init") {
	- pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
	- }
	-
	- write_once("In Settings") {
	- # Define a group consisting of only carbon atoms in graphene molecules
	- group Cgraphene type @atom:C
	-
	- # i j epsilon sigma
	- pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 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)
	- }
	-
	-} # Graphene
	-
	-
	-
	diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt
	deleted file mode 100644
	index 3bb7bca40..000000000
	--- a/tools/moltemplate/common/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 200.0 1.0
	- angle_coeff @angle:HOH harmonic 200.0 109.47
	- 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/common/tip3p_attempts/README.TXT b/tools/moltemplate/common/tip3p_attempts/README.TXT
	deleted file mode 100644
	index 13a2626d4..000000000
	--- a/tools/moltemplate/common/tip3p_attempts/README.TXT
	+++ /dev/null
	@@ -1,13 +0,0 @@
	-This directory contains two LT files corresponding to
	-different versions of TIP3P:
	-
	-tip3pcharmm.lt # The implementation of TIP3P used by CHARMM (I think).
	-tip3p2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model
	- # which uses long-range coulombics
	-
	-I have not tested these files so I moved them here.
	-(If you have tested these files, and they work, or if you have other comments
	-or suggestions, feel free to email me at jewett.aij at gmail dot com.)
	-
	-Andrew
	-2012-10-20
	diff --git a/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt b/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt
	deleted file mode 100644
	index f04a161b3..000000000
	--- a/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt
	+++ /dev/null
	@@ -1,88 +0,0 @@
	-# file "tip3p2004.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.
	-
	-TIP3P2004 {
	-
	- write_once("In Init") {
	- # -- Default styles (for solo "TIP3P2004" water) --
	- units real
	- atom_style full
	-
	- pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5
	- 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 -0.830 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/charmm 0.102 3.188
	- #########################################################################
	- #### There are three choices for for the O-H and H-H interactions
	- #########################################################################
	- #### 1) 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
	- #########################################################################
	- #### 2) 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
	- #########################################################################
	- #### 3) The original Jorgensen 1983 parameterization has no OH or HH
	- # lennard-jones 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
	- #########################################################################
	-
	- # 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 fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
	- # (Remember to "unfix" fSHAKE during minimization.)
	-
	- }
	-
	-} # "TIP3P2004" water molecule type
	-
	diff --git a/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt b/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt
	deleted file mode 100644
	index 80ea280fa..000000000
	--- a/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt
	+++ /dev/null
	@@ -1,91 +0,0 @@
	-# file "tip3p_charmm.lt"
	-#
	-# H1 H2
	-# \ /
	-# O
	-#
	-# I think this is the TIP3P water model used by CHARMM (and probably AMBER)
	-# It is (mostly) based on this paper:
	-# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983)
	-
	-TIP3Pcharmm {
	-
	- write_once("In Init") {
	- # -- Default styles (for solo "TIP3Pcharmm" water) --
	- units real
	- atom_style full
	-
	- # I'm not sure exactly which cutoffs distances are traditionally used in
	- # the TIP3P water model used by CHARMM.
	- # (See the Price JCP 2004 paper for a review.)
	- # pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5
	- # Try this instead:
	- pair_style hybrid lj/charmm/coul/charmm 10.0 10.5 10.0 10.5
	-
	- bond_style hybrid harmonic
	- angle_style hybrid harmonic
	- pair_modify mix arithmetic
	- }
	-
	- 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/charmm 0.102 3.188
	- #########################################################################
	- #### There are three choices for for the O-H and H-H interactions
	- #########################################################################
	- #### 1) 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
	- #########################################################################
	- #### 2) 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
	- #########################################################################
	- #### 3) The original Jorgensen 1983 parameterization has no OH or HH
	- # lennard-jones 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
	- #########################################################################
	-
	- # 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 fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
	- # (Remember to "unfix" fSHAKE during minimization.)
	-
	- }
	-
	-} # "TIP3Pcharmm" water molecule type
	-
	diff --git a/tools/moltemplate/common/trappe1998.lt b/tools/moltemplate/common/trappe1998.lt
	deleted file mode 100644
	index 9bcc80cb1..000000000
	--- a/tools/moltemplate/common/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/common/watmw.lt b/tools/moltemplate/common/watmw.lt
	deleted file mode 100644
	index 4728623c2..000000000
	--- a/tools/moltemplate/common/watmw.lt
	+++ /dev/null
	@@ -1,33 +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") {
	- group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group)
	- }
	-
	-} # WatMW
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README.TXT b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README.TXT
	deleted file mode 100644
	index 0aeed79a5..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README.TXT
	+++ /dev/null
	@@ -1,56 +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 new DLPC model is a truncated version of DPPC.)
	- The protein model is described here:
	- G. Bellesia, AI Jewett, and J-E Shea,
	- Protein Science, Vol19 141-154 (2010)
	-
	-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.
	-
	------ 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.
	-Unlike the original "DPPC" molecule model, "DLPC" has 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/CG_membrane_examples/membrane+protein/README_run.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_run.sh
	deleted file mode 100755
	index 18d5b65b6..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_run.sh
	+++ /dev/null
	@@ -1,33 +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.npt # pressure equilibration
	-"$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.npt # pressure equilibration
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_setup.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_setup.sh
	deleted file mode 100755
	index 4414a4a4b..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/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 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 -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/CG_membrane_examples/membrane+protein/README_visualise.txt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_visualise.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/CG_membrane_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg
	deleted file mode 100644
	index 246ee5462..000000000
	Binary files a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index 78f8e6b84..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,2611 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 1685 !NATOM
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	- 2 1 1 1 0.000000 200.0000 0
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	-
	- 1324 !NBOND: bonds
	- 1 2 2 3 3 4 5 6
	- 6 7 7 8 8 9 10 11
	- 11 12 12 13 13 14 15 16
	- 16 17 17 18 19 20 20 21
	- 21 22 23 24 24 25 25 26
	- 27 28 28 29 29 30 31 32
	- 32 33 33 34 34 35 36 37
	- 37 38 38 39 40 41 41 42
	- 42 43 43 44 45 46 46 47
	- 47 48 48 49 50 51 51 52
	- 52 53 54 55 55 56 56 57
	- 57 58 59 60 60 61 61 62
	- 63 64 64 65 65 66 67 68
	- 68 69 69 70 70 71 72 73
	- 73 74 74 75 75 76 77 78
	- 78 79 79 80 80 81 82 83
	- 83 84 84 85 85 86 87 88
	- 88 89 89 90 90 91 92 93
	- 93 94 94 95 96 97 97 98
	- 98 99 99 100 101 102 102 103
	- 103 104 105 106 106 107 107 108
	- 108 109 110 111 111 112 112 113
	- 114 115 115 116 116 117 117 118
	- 119 120 120 121 121 122 123 124
	- 124 125 125 126 126 127 128 129
	- 129 130 130 131 132 133 133 134
	- 134 135 136 137 137 138 138 139
	- 139 140 141 142 142 143 143 144
	- 144 145 146 147 147 148 148 149
	- 149 150 151 152 152 153 153 154
	- 155 156 156 157 157 158 158 159
	- 160 161 161 162 162 163 164 165
	- 165 166 166 167 167 168 169 170
	- 170 171 171 172 173 174 174 175
	- 175 176 176 177 178 179 179 180
	- 180 181 181 182 183 184 184 185
	- 185 186 186 187 188 189 189 190
	- 190 191 191 192 193 194 194 195
	- 195 196 196 197 198 199 199 200
	- 200 201 202 203 203 204 204 205
	- 205 206 207 208 208 209 209 210
	- 211 212 212 213 213 214 214 215
	- 216 217 217 218 218 219 220 221
	- 221 222 222 223 224 225 225 226
	- 226 227 228 229 229 230 230 231
	- 231 232 233 234 234 235 235 236
	- 236 237 238 239 239 240 240 241
	- 241 242 243 244 244 245 245 246
	- 246 247 248 249 249 250 250 251
	- 252 253 253 254 254 255 255 256
	- 257 258 258 259 259 260 260 261
	- 262 263 263 264 264 265 266 267
	- 267 268 268 269 269 270 271 272
	- 272 273 273 274 275 276 276 277
	- 277 278 278 279 280 281 281 282
	- 282 283 283 284 285 286 286 287
	- 287 288 288 289 290 291 291 292
	- 292 293 293 294 295 296 296 297
	- 297 298 299 300 300 301 301 302
	- 302 303 304 305 305 306 306 307
	- 308 309 309 310 310 311 311 312
	- 313 314 314 315 315 316 317 318
	- 318 319 319 320 321 322 322 323
	- 323 324 324 325 326 327 327 328
	- 328 329 329 330 331 332 332 333
	- 333 334 334 335 336 337 337 338
	- 338 339 339 340 341 342 342 343
	- 343 344 345 346 346 347 347 348
	- 349 350 350 351 351 352 352 353
	- 354 355 355 356 356 357 358 359
	- 359 360 360 361 362 363 363 364
	- 364 365 366 367 367 368 368 369
	- 369 370 371 372 372 373 373 374
	- 375 376 376 377 377 378 379 380
	- 380 381 381 382 382 383 384 385
	- 385 386 386 387 388 389 389 390
	- 390 391 391 392 393 394 394 395
	- 395 396 396 397 398 399 399 400
	- 400 401 402 403 403 404 404 405
	- 406 407 407 408 408 409 410 411
	- 411 412 412 413 413 414 415 416
	- 416 417 417 418 418 419 420 421
	- 421 422 422 423 424 425 425 426
	- 426 427 428 429 429 430 430 431
	- 431 432 433 434 434 435 435 436
	- 437 438 438 439 439 440 440 441
	- 442 443 443 444 444 445 445 446
	- 447 448 448 449 449 450 450 451
	- 452 453 453 454 454 455 455 456
	- 457 458 458 459 459 460 460 461
	- 462 463 463 464 464 465 465 466
	- 467 468 468 469 469 470 471 472
	- 472 473 473 474 475 476 476 477
	- 477 478 479 480 480 481 481 482
	- 483 484 484 485 485 486 486 487
	- 488 489 489 490 490 491 492 493
	- 493 494 494 495 496 497 497 498
	- 498 499 500 501 501 502 502 503
	- 503 504 505 506 506 507 507 508
	- 509 510 510 511 511 512 512 513
	- 514 515 515 516 516 517 518 519
	- 519 520 520 521 521 522 523 524
	- 524 525 525 526 526 527 528 529
	- 529 530 530 531 532 533 533 534
	- 534 535 536 537 537 538 538 539
	- 540 541 541 542 542 543 543 544
	- 545 546 546 547 547 548 548 549
	- 550 551 551 552 552 553 553 554
	- 555 556 556 557 557 558 559 560
	- 560 561 561 562 562 563 564 565
	- 565 566 566 567 568 569 569 570
	- 570 571 571 572 573 574 574 575
	- 575 576 577 578 578 579 579 580
	- 581 582 582 583 583 584 585 586
	- 586 587 587 588 589 590 590 591
	- 591 592 592 593 594 595 595 596
	- 596 597 598 599 599 600 600 601
	- 602 603 603 604 604 605 606 607
	- 607 608 608 609 609 610 611 612
	- 612 613 613 614 614 615 616 617
	- 617 618 618 619 620 621 621 622
	- 622 623 624 625 625 626 626 627
	- 627 628 629 630 630 631 631 632
	- 633 634 634 635 635 636 636 637
	- 638 639 639 640 640 641 642 643
	- 643 644 644 645 645 646 647 648
	- 648 649 649 650 650 651 652 653
	- 653 654 654 655 655 656 657 658
	- 658 659 659 660 660 661 662 663
	- 663 664 664 665 665 666 667 668
	- 668 669 669 670 671 672 672 673
	- 673 674 674 675 676 677 677 678
	- 678 679 679 680 681 682 682 683
	- 683 684 684 685 686 687 687 688
	- 688 689 689 690 691 692 692 693
	- 693 694 694 695 696 697 697 698
	- 698 699 700 701 701 702 702 703
	- 703 704 705 706 706 707 707 708
	- 709 710 710 711 711 712 713 714
	- 714 715 715 716 716 717 718 719
	- 719 720 720 721 722 723 723 724
	- 724 725 725 726 727 728 728 729
	- 729 730 730 731 732 733 733 734
	- 734 735 736 737 737 738 738 739
	- 739 740 741 742 742 743 743 744
	- 744 745 746 747 747 748 748 749
	- 750 751 751 752 752 753 754 755
	- 755 756 756 757 758 759 759 760
	- 760 761 762 763 763 764 764 765
	- 766 767 767 768 768 769 769 770
	- 771 772 772 773 773 774 775 776
	- 776 777 777 778 778 779 780 781
	- 781 782 782 783 784 785 785 786
	- 786 787 787 788 789 790 790 791
	- 791 792 792 793 794 795 795 796
	- 796 797 798 799 799 800 800 801
	- 801 802 803 804 804 805 805 806
	- 807 808 808 809 809 810 811 812
	- 812 813 813 814 814 815 816 817
	- 817 818 818 819 819 820 821 822
	- 822 823 823 824 824 825 826 827
	- 827 828 828 829 829 830 831 832
	- 832 833 833 834 835 836 836 837
	- 837 838 839 840 840 841 841 842
	- 843 844 844 845 845 846 847 848
	- 848 849 849 850 850 851 852 853
	- 853 854 854 855 855 856 857 858
	- 858 859 859 860 860 861 862 863
	- 863 864 864 865 865 866 867 868
	- 868 869 869 870 871 872 872 873
	- 873 874 875 876 876 877 877 878
	- 879 880 880 881 881 882 883 884
	- 884 885 885 886 887 888 888 889
	- 889 890 890 891 892 893 893 894
	- 894 895 896 897 897 898 898 899
	- 899 900 901 902 902 903 903 904
	- 905 906 906 907 907 908 908 909
	- 910 911 911 912 912 913 914 915
	- 915 916 916 917 918 919 919 920
	- 920 921 921 922 923 924 924 925
	- 925 926 927 928 928 929 929 930
	- 931 932 932 933 933 934 935 936
	- 936 937 937 938 939 940 940 941
	- 941 942 942 943 944 945 945 946
	- 946 947 948 949 949 950 950 951
	- 951 952 953 954 954 955 955 956
	- 956 957 958 959 959 960 960 961
	- 962 963 963 964 964 965 966 967
	- 967 968 968 969 969 970 971 972
	- 972 973 973 974 975 976 976 977
	- 977 978 979 980 980 981 981 982
	- 982 983 984 985 985 986 986 987
	- 988 989 989 990 990 991 991 992
	- 993 994 994 995 995 996 996 997
	- 998 999 999 1000 1000 1001 1002 1003
	- 1003 1004 1004 1005 1006 1007 1007 1008
	- 1008 1009 1010 1011 1011 1012 1012 1013
	- 1014 1015 1015 1016 1016 1017 1017 1018
	- 1019 1020 1020 1021 1021 1022 1023 1024
	- 1024 1025 1025 1026 1027 1028 1028 1029
	- 1029 1030 1031 1032 1032 1033 1033 1034
	- 1035 1036 1036 1037 1037 1038 1038 1039
	- 1040 1041 1041 1042 1042 1043 1043 1044
	- 1045 1046 1046 1047 1047 1048 1049 1050
	- 1050 1051 1051 1052 1053 1054 1054 1055
	- 1055 1056 1057 1058 1058 1059 1059 1060
	- 1061 1062 1062 1063 1063 1064 1065 1066
	- 1066 1067 1067 1068 1068 1069 1070 1071
	- 1071 1072 1072 1073 1073 1074 1075 1076
	- 1076 1077 1077 1078 1079 1080 1080 1081
	- 1081 1082 1082 1083 1084 1085 1085 1086
	- 1086 1087 1088 1089 1089 1090 1090 1091
	- 1092 1093 1093 1094 1094 1095 1095 1096
	- 1097 1098 1098 1099 1099 1100 1100 1101
	- 1102 1103 1103 1104 1104 1105 1105 1106
	- 1107 1108 1108 1109 1109 1110 1110 1111
	- 1112 1113 1113 1114 1114 1115 1115 1116
	- 1117 1118 1118 1119 1119 1120 1120 1121
	- 1122 1123 1123 1124 1124 1125 1126 1127
	- 1127 1128 1128 1129 1129 1130 1131 1132
	- 1132 1133 1133 1134 1135 1136 1136 1137
	- 1137 1138 1139 1140 1140 1141 1141 1142
	- 1143 1144 1144 1145 1145 1146 1147 1148
	- 1148 1149 1149 1150 1151 1152 1152 1153
	- 1153 1154 1154 1155 1156 1157 1157 1158
	- 1158 1159 1159 1160 1161 1162 1162 1163
	- 1163 1164 1164 1165 1166 1167 1167 1168
	- 1168 1169 1170 1171 1171 1172 1172 1173
	- 1173 1174 1175 1176 1176 1177 1177 1178
	- 1178 1179 1180 1181 1181 1182 1182 1183
	- 1184 1185 1185 1186 1186 1187 1188 1189
	- 1189 1190 1190 1191 1192 1193 1193 1194
	- 1194 1195 1196 1197 1197 1198 1198 1199
	- 1199 1200 1201 1202 1202 1203 1203 1204
	- 1205 1206 1206 1207 1207 1208 1209 1210
	- 1210 1211 1211 1212 1212 1213 1214 1215
	- 1215 1216 1216 1217 1218 1219 1219 1220
	- 1220 1221 1221 1222 1223 1224 1224 1225
	- 1225 1226 1227 1228 1228 1229 1229 1230
	- 1230 1231 1232 1233 1233 1234 1234 1235
	- 1235 1236 1237 1238 1238 1239 1239 1240
	- 1241 1242 1242 1243 1243 1244 1244 1245
	- 1246 1247 1247 1248 1248 1249 1249 1250
	- 1251 1252 1252 1253 1253 1254 1254 1255
	- 1256 1257 1257 1258 1258 1259 1260 1261
	- 1261 1262 1262 1263 1263 1264 1265 1266
	- 1266 1267 1267 1268 1269 1270 1270 1271
	- 1271 1272 1273 1274 1274 1275 1275 1276
	- 1277 1278 1278 1279 1279 1280 1281 1282
	- 1282 1283 1283 1284 1285 1286 1286 1287
	- 1287 1288 1288 1289 1290 1291 1291 1292
	- 1292 1293 1293 1294 1295 1296 1296 1297
	- 1297 1298 1299 1300 1300 1301 1301 1302
	- 1303 1304 1304 1305 1305 1306 1307 1308
	- 1308 1309 1309 1310 1310 1311 1312 1313
	- 1313 1314 1314 1315 1316 1317 1317 1318
	- 1318 1319 1320 1321 1321 1322 1322 1323
	- 1324 1325 1325 1326 1326 1327 1328 1329
	- 1329 1330 1330 1331 1331 1332 1333 1334
	- 1334 1335 1335 1336 1336 1337 1338 1339
	- 1339 1340 1340 1341 1341 1342 1343 1344
	- 1344 1345 1345 1346 1347 1348 1348 1349
	- 1349 1350 1350 1351 1352 1353 1353 1354
	- 1354 1355 1356 1357 1357 1358 1358 1359
	- 1360 1361 1361 1362 1362 1363 1364 1365
	- 1365 1366 1366 1367 1368 1369 1369 1370
	- 1370 1371 1372 1373 1373 1374 1374 1375
	- 1376 1377 1377 1378 1378 1379 1380 1381
	- 1381 1382 1382 1383 1384 1385 1385 1386
	- 1386 1387 1388 1389 1389 1390 1390 1391
	- 1392 1393 1393 1394 1394 1395 1395 1396
	- 1397 1398 1398 1399 1399 1400 1400 1401
	- 1402 1403 1403 1404 1404 1405 1406 1407
	- 1407 1408 1408 1409 1410 1411 1411 1412
	- 1412 1413 1414 1415 1415 1416 1416 1417
	- 1417 1418 1419 1420 1420 1421 1421 1422
	- 1423 1424 1424 1425 1425 1426 1426 1427
	- 1428 1429 1429 1430 1430 1431 1432 1433
	- 1433 1434 1434 1435 1435 1436 1437 1438
	- 1438 1439 1439 1440 1441 1442 1442 1443
	- 1443 1444 1444 1445 1446 1447 1447 1448
	- 1448 1449 1450 1451 1451 1452 1452 1453
	- 1453 1454 1455 1456 1456 1457 1457 1458
	- 1459 1460 1460 1461 1461 1462 1463 1464
	- 1464 1465 1465 1466 1466 1467 1468 1469
	- 1469 1470 1470 1471 1472 1473 1473 1474
	- 1474 1475 1475 1476 1477 1478 1478 1479
	- 1479 1480 1480 1481 1482 1483 1483 1484
	- 1484 1485 1486 1487 1487 1488 1488 1489
	- 1490 1491 1491 1492 1492 1493 1493 1494
	- 1495 1496 1496 1497 1497 1498 1498 1499
	- 1500 1501 1501 1502 1502 1503 1504 1505
	- 1505 1506 1506 1507 1508 1509 1509 1510
	- 1510 1511 1512 1513 1513 1514 1514 1515
	- 1515 1516 1517 1518 1518 1519 1519 1520
	- 1520 1521 1522 1523 1523 1524 1524 1525
	- 1526 1527 1527 1528 1528 1529 1529 1530
	- 1531 1532 1532 1533 1533 1534 1534 1535
	- 1536 1537 1537 1538 1538 1539 1540 1541
	- 1541 1542 1542 1543 1543 1544 1545 1546
	- 1546 1547 1547 1548 1548 1549 1550 1551
	- 1551 1552 1552 1553 1554 1555 1555 1556
	- 1556 1557 1557 1558 1559 1560 1560 1561
	- 1561 1562 1562 1563 1564 1565 1565 1566
	- 1566 1567 1567 1568 1569 1570 1570 1571
	- 1571 1572 1573 1574 1574 1575 1575 1576
	- 1576 1577 1578 1579 1579 1580 1580 1581
	- 1581 1582 1583 1584 1584 1585 1585 1586
	- 1587 1588 1588 1589 1589 1590 1591 1592
	- 1592 1593 1593 1594 1595 1596 1596 1597
	- 1597 1598 1599 1600 1600 1601 1601 1602
	- 1602 1603 1604 1605 1605 1606 1606 1607
	- 1608 1609 1609 1610 1610 1611 1611 1612
	- 1613 1614 1614 1615 1615 1616 1616 1617
	- 1617 1618 1618 1619 1619 1620 1620 1621
	- 1621 1622 1622 1623 1623 1624 1624 1625
	- 1625 1626 1626 1627 1627 1628 1628 1677
	- 1629 1630 1629 1682 1630 1631 1631 1632
	- 1632 1633 1633 1634 1634 1635 1635 1636
	- 1636 1637 1637 1638 1638 1639 1639 1640
	- 1640 1641 1641 1642 1642 1643 1643 1644
	- 1644 1679 1645 1646 1645 1680 1646 1647
	- 1647 1648 1648 1649 1649 1650 1650 1651
	- 1651 1652 1652 1653 1653 1654 1654 1655
	- 1655 1656 1656 1657 1657 1658 1658 1659
	- 1659 1660 1660 1683 1661 1662 1662 1663
	- 1663 1664 1664 1665 1665 1666 1666 1667
	- 1667 1668 1668 1669 1669 1670 1670 1671
	- 1671 1672 1672 1673 1673 1674 1674 1675
	- 1675 1676 1676 1685 1677 1678 1678 1679
	- 1680 1681 1681 1682 1683 1684 1684 1685
	-
	- 963 !NTHETA: angles
	- 1646 1645 1680 1630 1629 1682 1613 1614 1615
	- 1616 1617 1618 1617 1618 1619 1620 1621 1622
	- 1621 1622 1623 1624 1625 1626 1625 1626 1627
	- 1629 1630 1631 1632 1633 1634 1633 1634 1635
	- 1636 1637 1638 1637 1638 1639 1640 1641 1642
	- 1641 1642 1643 1645 1646 1647 1648 1649 1650
	- 1649 1650 1651 1652 1653 1654 1653 1654 1655
	- 1656 1657 1658 1657 1658 1659 1661 1662 1663
	- 1664 1665 1666 1665 1666 1667 1668 1669 1670
	- 1669 1670 1671 1672 1673 1674 1673 1674 1675
	- 1615 1616 1617 1614 1615 1616 1619 1620 1621
	- 1618 1619 1620 1623 1624 1625 1622 1623 1624
	- 1626 1627 1628 1631 1632 1633 1630 1631 1632
	- 1635 1636 1637 1634 1635 1636 1639 1640 1641
	- 1638 1639 1640 1642 1643 1644 1647 1648 1649
	- 1646 1647 1648 1651 1652 1653 1650 1651 1652
	- 1655 1656 1657 1654 1655 1656 1658 1659 1660
	- 1663 1664 1665 1662 1663 1664 1667 1668 1669
	- 1666 1667 1668 1671 1672 1673 1670 1671 1672
	- 1674 1675 1676 1628 1677 1678 1644 1679 1678
	- 1660 1683 1684 1676 1685 1684 1627 1628 1677
	- 1643 1644 1679 1659 1660 1683 1675 1676 1685
	- 1677 1678 1679 1680 1681 1682 1683 1684 1685
	- 1629 1682 1681 1645 1680 1681 1 2 3
	- 2 3 4 5 6 7 6 7 8
	- 7 8 9 10 11 12 11 12 13
	- 12 13 14 15 16 17 16 17 18
	- 19 20 21 20 21 22 23 24 25
	- 24 25 26 27 28 29 28 29 30
	- 31 32 33 32 33 34 33 34 35
	- 36 37 38 37 38 39 40 41 42
	- 41 42 43 42 43 44 45 46 47
	- 46 47 48 47 48 49 50 51 52
	- 51 52 53 54 55 56 55 56 57
	- 56 57 58 59 60 61 60 61 62
	- 63 64 65 64 65 66 67 68 69
	- 68 69 70 69 70 71 72 73 74
	- 73 74 75 74 75 76 77 78 79
	- 78 79 80 79 80 81 82 83 84
	- 83 84 85 84 85 86 87 88 89
	- 88 89 90 89 90 91 92 93 94
	- 93 94 95 96 97 98 97 98 99
	- 98 99 100 101 102 103 102 103 104
	- 105 106 107 106 107 108 107 108 109
	- 110 111 112 111 112 113 114 115 116
	- 115 116 117 116 117 118 119 120 121
	- 120 121 122 123 124 125 124 125 126
	- 125 126 127 128 129 130 129 130 131
	- 132 133 134 133 134 135 136 137 138
	- 137 138 139 138 139 140 141 142 143
	- 142 143 144 143 144 145 146 147 148
	- 147 148 149 148 149 150 151 152 153
	- 152 153 154 155 156 157 156 157 158
	- 157 158 159 160 161 162 161 162 163
	- 164 165 166 165 166 167 166 167 168
	- 169 170 171 170 171 172 173 174 175
	- 174 175 176 175 176 177 178 179 180
	- 179 180 181 180 181 182 183 184 185
	- 184 185 186 185 186 187 188 189 190
	- 189 190 191 190 191 192 193 194 195
	- 194 195 196 195 196 197 198 199 200
	- 199 200 201 202 203 204 203 204 205
	- 204 205 206 207 208 209 208 209 210
	- 211 212 213 212 213 214 213 214 215
	- 216 217 218 217 218 219 220 221 222
	- 221 222 223 224 225 226 225 226 227
	- 228 229 230 229 230 231 230 231 232
	- 233 234 235 234 235 236 235 236 237
	- 238 239 240 239 240 241 240 241 242
	- 243 244 245 244 245 246 245 246 247
	- 248 249 250 249 250 251 252 253 254
	- 253 254 255 254 255 256 257 258 259
	- 258 259 260 259 260 261 262 263 264
	- 263 264 265 266 267 268 267 268 269
	- 268 269 270 271 272 273 272 273 274
	- 275 276 277 276 277 278 277 278 279
	- 280 281 282 281 282 283 282 283 284
	- 285 286 287 286 287 288 287 288 289
	- 290 291 292 291 292 293 292 293 294
	- 295 296 297 296 297 298 299 300 301
	- 300 301 302 301 302 303 304 305 306
	- 305 306 307 308 309 310 309 310 311
	- 310 311 312 313 314 315 314 315 316
	- 317 318 319 318 319 320 321 322 323
	- 322 323 324 323 324 325 326 327 328
	- 327 328 329 328 329 330 331 332 333
	- 332 333 334 333 334 335 336 337 338
	- 337 338 339 338 339 340 341 342 343
	- 342 343 344 345 346 347 346 347 348
	- 349 350 351 350 351 352 351 352 353
	- 354 355 356 355 356 357 358 359 360
	- 359 360 361 362 363 364 363 364 365
	- 366 367 368 367 368 369 368 369 370
	- 371 372 373 372 373 374 375 376 377
	- 376 377 378 379 380 381 380 381 382
	- 381 382 383 384 385 386 385 386 387
	- 388 389 390 389 390 391 390 391 392
	- 393 394 395 394 395 396 395 396 397
	- 398 399 400 399 400 401 402 403 404
	- 403 404 405 406 407 408 407 408 409
	- 410 411 412 411 412 413 412 413 414
	- 415 416 417 416 417 418 417 418 419
	- 420 421 422 421 422 423 424 425 426
	- 425 426 427 428 429 430 429 430 431
	- 430 431 432 433 434 435 434 435 436
	- 437 438 439 438 439 440 439 440 441
	- 442 443 444 443 444 445 444 445 446
	- 447 448 449 448 449 450 449 450 451
	- 452 453 454 453 454 455 454 455 456
	- 457 458 459 458 459 460 459 460 461
	- 462 463 464 463 464 465 464 465 466
	- 467 468 469 468 469 470 471 472 473
	- 472 473 474 475 476 477 476 477 478
	- 479 480 481 480 481 482 483 484 485
	- 484 485 486 485 486 487 488 489 490
	- 489 490 491 492 493 494 493 494 495
	- 496 497 498 497 498 499 500 501 502
	- 501 502 503 502 503 504 505 506 507
	- 506 507 508 509 510 511 510 511 512
	- 511 512 513 514 515 516 515 516 517
	- 518 519 520 519 520 521 520 521 522
	- 523 524 525 524 525 526 525 526 527
	- 528 529 530 529 530 531 532 533 534
	- 533 534 535 536 537 538 537 538 539
	- 540 541 542 541 542 543 542 543 544
	- 545 546 547 546 547 548 547 548 549
	- 550 551 552 551 552 553 552 553 554
	- 555 556 557 556 557 558 559 560 561
	- 560 561 562 561 562 563 564 565 566
	- 565 566 567 568 569 570 569 570 571
	- 570 571 572 573 574 575 574 575 576
	- 577 578 579 578 579 580 581 582 583
	- 582 583 584 585 586 587 586 587 588
	- 589 590 591 590 591 592 591 592 593
	- 594 595 596 595 596 597 598 599 600
	- 599 600 601 602 603 604 603 604 605
	- 606 607 608 607 608 609 608 609 610
	- 611 612 613 612 613 614 613 614 615
	- 616 617 618 617 618 619 620 621 622
	- 621 622 623 624 625 626 625 626 627
	- 626 627 628 629 630 631 630 631 632
	- 633 634 635 634 635 636 635 636 637
	- 638 639 640 639 640 641 642 643 644
	- 643 644 645 644 645 646 647 648 649
	- 648 649 650 649 650 651 652 653 654
	- 653 654 655 654 655 656 657 658 659
	- 658 659 660 659 660 661 662 663 664
	- 663 664 665 664 665 666 667 668 669
	- 668 669 670 671 672 673 672 673 674
	- 673 674 675 676 677 678 677 678 679
	- 678 679 680 681 682 683 682 683 684
	- 683 684 685 686 687 688 687 688 689
	- 688 689 690 691 692 693 692 693 694
	- 693 694 695 696 697 698 697 698 699
	- 700 701 702 701 702 703 702 703 704
	- 705 706 707 706 707 708 709 710 711
	- 710 711 712 713 714 715 714 715 716
	- 715 716 717 718 719 720 719 720 721
	- 722 723 724 723 724 725 724 725 726
	- 727 728 729 728 729 730 729 730 731
	- 732 733 734 733 734 735 736 737 738
	- 737 738 739 738 739 740 741 742 743
	- 742 743 744 743 744 745 746 747 748
	- 747 748 749 750 751 752 751 752 753
	- 754 755 756 755 756 757 758 759 760
	- 759 760 761 762 763 764 763 764 765
	- 766 767 768 767 768 769 768 769 770
	- 771 772 773 772 773 774 775 776 777
	- 776 777 778 777 778 779 780 781 782
	- 781 782 783 784 785 786 785 786 787
	- 786 787 788 789 790 791 790 791 792
	- 791 792 793 794 795 796 795 796 797
	- 798 799 800 799 800 801 800 801 802
	- 803 804 805 804 805 806 807 808 809
	- 808 809 810 811 812 813 812 813 814
	- 813 814 815 816 817 818 817 818 819
	- 818 819 820 821 822 823 822 823 824
	- 823 824 825 826 827 828 827 828 829
	- 828 829 830 831 832 833 832 833 834
	- 835 836 837 836 837 838 839 840 841
	- 840 841 842 843 844 845 844 845 846
	- 847 848 849 848 849 850 849 850 851
	- 852 853 854 853 854 855 854 855 856
	- 857 858 859 858 859 860 859 860 861
	- 862 863 864 863 864 865 864 865 866
	- 867 868 869 868 869 870 871 872 873
	- 872 873 874 875 876 877 876 877 878
	- 879 880 881 880 881 882 883 884 885
	- 884 885 886 887 888 889 888 889 890
	- 889 890 891 892 893 894 893 894 895
	- 896 897 898 897 898 899 898 899 900
	- 901 902 903 902 903 904 905 906 907
	- 906 907 908 907 908 909 910 911 912
	- 911 912 913 914 915 916 915 916 917
	- 918 919 920 919 920 921 920 921 922
	- 923 924 925 924 925 926 927 928 929
	- 928 929 930 931 932 933 932 933 934
	- 935 936 937 936 937 938 939 940 941
	- 940 941 942 941 942 943 944 945 946
	- 945 946 947 948 949 950 949 950 951
	- 950 951 952 953 954 955 954 955 956
	- 955 956 957 958 959 960 959 960 961
	- 962 963 964 963 964 965 966 967 968
	- 967 968 969 968 969 970 971 972 973
	- 972 973 974 975 976 977 976 977 978
	- 979 980 981 980 981 982 981 982 983
	- 984 985 986 985 986 987 988 989 990
	- 989 990 991 990 991 992 993 994 995
	- 994 995 996 995 996 997 998 999 1000
	- 999 1000 1001 1002 1003 1004 1003 1004 1005
	- 1006 1007 1008 1007 1008 1009 1010 1011 1012
	- 1011 1012 1013 1014 1015 1016 1015 1016 1017
	- 1016 1017 1018 1019 1020 1021 1020 1021 1022
	- 1023 1024 1025 1024 1025 1026 1027 1028 1029
	- 1028 1029 1030 1031 1032 1033 1032 1033 1034
	- 1035 1036 1037 1036 1037 1038 1037 1038 1039
	- 1040 1041 1042 1041 1042 1043 1042 1043 1044
	- 1045 1046 1047 1046 1047 1048 1049 1050 1051
	- 1050 1051 1052 1053 1054 1055 1054 1055 1056
	- 1057 1058 1059 1058 1059 1060 1061 1062 1063
	- 1062 1063 1064 1065 1066 1067 1066 1067 1068
	- 1067 1068 1069 1070 1071 1072 1071 1072 1073
	- 1072 1073 1074 1075 1076 1077 1076 1077 1078
	- 1079 1080 1081 1080 1081 1082 1081 1082 1083
	- 1084 1085 1086 1085 1086 1087 1088 1089 1090
	- 1089 1090 1091 1092 1093 1094 1093 1094 1095
	- 1094 1095 1096 1097 1098 1099 1098 1099 1100
	- 1099 1100 1101 1102 1103 1104 1103 1104 1105
	- 1104 1105 1106 1107 1108 1109 1108 1109 1110
	- 1109 1110 1111 1112 1113 1114 1113 1114 1115
	- 1114 1115 1116 1117 1118 1119 1118 1119 1120
	- 1119 1120 1121 1122 1123 1124 1123 1124 1125
	- 1126 1127 1128 1127 1128 1129 1128 1129 1130
	- 1131 1132 1133 1132 1133 1134 1135 1136 1137
	- 1136 1137 1138 1139 1140 1141 1140 1141 1142
	- 1143 1144 1145 1144 1145 1146 1147 1148 1149
	- 1148 1149 1150 1151 1152 1153 1152 1153 1154
	- 1153 1154 1155 1156 1157 1158 1157 1158 1159
	- 1158 1159 1160 1161 1162 1163 1162 1163 1164
	- 1163 1164 1165 1166 1167 1168 1167 1168 1169
	- 1170 1171 1172 1171 1172 1173 1172 1173 1174
	- 1175 1176 1177 1176 1177 1178 1177 1178 1179
	- 1180 1181 1182 1181 1182 1183 1184 1185 1186
	- 1185 1186 1187 1188 1189 1190 1189 1190 1191
	- 1192 1193 1194 1193 1194 1195 1196 1197 1198
	- 1197 1198 1199 1198 1199 1200 1201 1202 1203
	- 1202 1203 1204 1205 1206 1207 1206 1207 1208
	- 1209 1210 1211 1210 1211 1212 1211 1212 1213
	- 1214 1215 1216 1215 1216 1217 1218 1219 1220
	- 1219 1220 1221 1220 1221 1222 1223 1224 1225
	- 1224 1225 1226 1227 1228 1229 1228 1229 1230
	- 1229 1230 1231 1232 1233 1234 1233 1234 1235
	- 1234 1235 1236 1237 1238 1239 1238 1239 1240
	- 1241 1242 1243 1242 1243 1244 1243 1244 1245
	- 1246 1247 1248 1247 1248 1249 1248 1249 1250
	- 1251 1252 1253 1252 1253 1254 1253 1254 1255
	- 1256 1257 1258 1257 1258 1259 1260 1261 1262
	- 1261 1262 1263 1262 1263 1264 1265 1266 1267
	- 1266 1267 1268 1269 1270 1271 1270 1271 1272
	- 1273 1274 1275 1274 1275 1276 1277 1278 1279
	- 1278 1279 1280 1281 1282 1283 1282 1283 1284
	- 1285 1286 1287 1286 1287 1288 1287 1288 1289
	- 1290 1291 1292 1291 1292 1293 1292 1293 1294
	- 1295 1296 1297 1296 1297 1298 1299 1300 1301
	- 1300 1301 1302 1303 1304 1305 1304 1305 1306
	- 1307 1308 1309 1308 1309 1310 1309 1310 1311
	- 1312 1313 1314 1313 1314 1315 1316 1317 1318
	- 1317 1318 1319 1320 1321 1322 1321 1322 1323
	- 1324 1325 1326 1325 1326 1327 1328 1329 1330
	- 1329 1330 1331 1330 1331 1332 1333 1334 1335
	- 1334 1335 1336 1335 1336 1337 1338 1339 1340
	- 1339 1340 1341 1340 1341 1342 1343 1344 1345
	- 1344 1345 1346 1347 1348 1349 1348 1349 1350
	- 1349 1350 1351 1352 1353 1354 1353 1354 1355
	- 1356 1357 1358 1357 1358 1359 1360 1361 1362
	- 1361 1362 1363 1364 1365 1366 1365 1366 1367
	- 1368 1369 1370 1369 1370 1371 1372 1373 1374
	- 1373 1374 1375 1376 1377 1378 1377 1378 1379
	- 1380 1381 1382 1381 1382 1383 1384 1385 1386
	- 1385 1386 1387 1388 1389 1390 1389 1390 1391
	- 1392 1393 1394 1393 1394 1395 1394 1395 1396
	- 1397 1398 1399 1398 1399 1400 1399 1400 1401
	- 1402 1403 1404 1403 1404 1405 1406 1407 1408
	- 1407 1408 1409 1410 1411 1412 1411 1412 1413
	- 1414 1415 1416 1415 1416 1417 1416 1417 1418
	- 1419 1420 1421 1420 1421 1422 1423 1424 1425
	- 1424 1425 1426 1425 1426 1427 1428 1429 1430
	- 1429 1430 1431 1432 1433 1434 1433 1434 1435
	- 1434 1435 1436 1437 1438 1439 1438 1439 1440
	- 1441 1442 1443 1442 1443 1444 1443 1444 1445
	- 1446 1447 1448 1447 1448 1449 1450 1451 1452
	- 1451 1452 1453 1452 1453 1454 1455 1456 1457
	- 1456 1457 1458 1459 1460 1461 1460 1461 1462
	- 1463 1464 1465 1464 1465 1466 1465 1466 1467
	- 1468 1469 1470 1469 1470 1471 1472 1473 1474
	- 1473 1474 1475 1474 1475 1476 1477 1478 1479
	- 1478 1479 1480 1479 1480 1481 1482 1483 1484
	- 1483 1484 1485 1486 1487 1488 1487 1488 1489
	- 1490 1491 1492 1491 1492 1493 1492 1493 1494
	- 1495 1496 1497 1496 1497 1498 1497 1498 1499
	- 1500 1501 1502 1501 1502 1503 1504 1505 1506
	- 1505 1506 1507 1508 1509 1510 1509 1510 1511
	- 1512 1513 1514 1513 1514 1515 1514 1515 1516
	- 1517 1518 1519 1518 1519 1520 1519 1520 1521
	- 1522 1523 1524 1523 1524 1525 1526 1527 1528
	- 1527 1528 1529 1528 1529 1530 1531 1532 1533
	- 1532 1533 1534 1533 1534 1535 1536 1537 1538
	- 1537 1538 1539 1540 1541 1542 1541 1542 1543
	- 1542 1543 1544 1545 1546 1547 1546 1547 1548
	- 1547 1548 1549 1550 1551 1552 1551 1552 1553
	- 1554 1555 1556 1555 1556 1557 1556 1557 1558
	- 1559 1560 1561 1560 1561 1562 1561 1562 1563
	- 1564 1565 1566 1565 1566 1567 1566 1567 1568
	- 1569 1570 1571 1570 1571 1572 1573 1574 1575
	- 1574 1575 1576 1575 1576 1577 1578 1579 1580
	- 1579 1580 1581 1580 1581 1582 1583 1584 1585
	- 1584 1585 1586 1587 1588 1589 1588 1589 1590
	- 1591 1592 1593 1592 1593 1594 1595 1596 1597
	- 1596 1597 1598 1599 1600 1601 1600 1601 1602
	- 1601 1602 1603 1604 1605 1606 1605 1606 1607
	- 1608 1609 1610 1609 1610 1611 1610 1611 1612
	-
	- 70 !NPHI: dihedrals
	- 1616 1617 1618 1619 1620 1621 1622 1623
	- 1624 1625 1626 1627 1632 1633 1634 1635
	- 1636 1637 1638 1639 1640 1641 1642 1643
	- 1648 1649 1650 1651 1652 1653 1654 1655
	- 1656 1657 1658 1659 1664 1665 1666 1667
	- 1668 1669 1670 1671 1672 1673 1674 1675
	- 1614 1615 1616 1617 1618 1619 1620 1621
	- 1622 1623 1624 1625 1630 1631 1632 1633
	- 1634 1635 1636 1637 1638 1639 1640 1641
	- 1646 1647 1648 1649 1650 1651 1652 1653
	- 1654 1655 1656 1657 1662 1663 1664 1665
	- 1666 1667 1668 1669 1670 1671 1672 1673
	- 1613 1614 1615 1616 1617 1618 1619 1620
	- 1615 1616 1617 1618 1621 1622 1623 1624
	- 1619 1620 1621 1622 1625 1626 1627 1628
	- 1623 1624 1625 1626 1629 1630 1631 1632
	- 1633 1634 1635 1636 1631 1632 1633 1634
	- 1637 1638 1639 1640 1635 1636 1637 1638
	- 1641 1642 1643 1644 1639 1640 1641 1642
	- 1645 1646 1647 1648 1649 1650 1651 1652
	- 1647 1648 1649 1650 1653 1654 1655 1656
	- 1651 1652 1653 1654 1657 1658 1659 1660
	- 1655 1656 1657 1658 1661 1662 1663 1664
	- 1665 1666 1667 1668 1663 1664 1665 1666
	- 1669 1670 1671 1672 1667 1668 1669 1670
	- 1673 1674 1675 1676 1671 1672 1673 1674
	- 1626 1627 1628 1677 1642 1643 1644 1679
	- 1658 1659 1660 1683 1674 1675 1676 1685
	- 1680 1645 1646 1647 1682 1629 1630 1631
	- 1646 1645 1680 1681 1630 1629 1682 1681
	- 1680 1681 1682 1629 1645 1680 1681 1682
	- 1677 1678 1679 1644 1628 1677 1678 1679
	- 1683 1684 1685 1676 1660 1683 1684 1685
	- 1627 1628 1677 1678 1643 1644 1679 1678
	- 1659 1660 1683 1684 1675 1676 1685 1684
	-
	- 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
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 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/CG_membrane_examples/membrane+protein/images/membrane+protein_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/membrane+protein_t=0ps_LR.jpg
	deleted file mode 100644
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	deleted file mode 100644
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg
	deleted file mode 100644
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt
	deleted file mode 100644
	index 824fd9659..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt
	+++ /dev/null
	@@ -1,237 +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
	-
	- # -------------- 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 class2
	- 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 6.0 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) = 4eps_ij (K(sig_ij/r)^12 + L(sig_ij/r)^6)
	- #
	- # i j pairstylename eps sig K L
	- #
	- write_once("In Settings") {
	- # Override any pair_coeff and bond_coeff
	- # statements from the 1beadProteSci2010 model
	- # (Because the energies &distances in that model
	- # were in the wrong units.)
	- pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
	- pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 6.0 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 6.0
	- }
	-
	-
	- # 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. Note: If you want the "AF" model,
	- # then change this to "delta60_0".)
	-
	- @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 class2 2.167862 120.0 0 0 2.167862 180.0
	- dihedral_coeff @dihedral:delta65_0 class2 2.167862 115.0 0 0 2.167862 180.0
	- dihedral_coeff @dihedral:turn class2 0 0 0 0 0.361310 180.0
	- # Note: 2.167862=1.2epsilon and 0.361310=0.2epsilon.
	-
	- # 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:delta65_0 class2 mbt 0 0 0 0
	- dihedral_coeff @dihedral:delta65_0 class2 ebt 0 0 0 0 0 0 0 0
	- dihedral_coeff @dihedral:delta65_0 class2 at 0 0 0 0 0 0 0 0
	- dihedral_coeff @dihedral:delta65_0 class2 aat 0 0 0
	- dihedral_coeff @dihedral:delta65_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
	- }
	-
	-
	- # --- 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/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
	deleted file mode 100644
	index a04db1f62..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
	+++ /dev/null
	@@ -1,208 +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
	-
	-} # 1beadProtSci2010 (namespace)
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt
	deleted file mode 100644
	index bb9a732c1..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt
	+++ /dev/null
	@@ -1,186 +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 mixture.
	-
	-
	-
	-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
	- dihedral_style none
	- improper_style none
	- pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15
	-
	- # 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.)
	-
	- pair_modify mix arithmetic
	- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
	-
	- # Optional: The "multi" style could be useful to efficiently simulate
	- # particles different sizes together. The tabular potential has range
	- # 22.5 Angstoms, but the Lennard-Jones forces have range of only
	- # 15.0 Angstroms.
	-
	- neighbor 2.0 multi
	- communicate multi
	- }
	-
	-
	- # Particles shared by all lipid types
	- write_once("Data Masses") {
	- @atom:int 200.0
	- @atom:tail 200.0
	- @atom:head 200.0 #<- Default "head" type. We will override it later
	- }
	-
	-
	-
	- # All force-field parameters appear in the "In Settings" section,
	- # which is later included in the LAMMPS input script.
	- # These force-field parameters are shared between all lipids by default.
	- # These can be customized and overridden for specific lipid types later.
	-
	-
	- # 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.
	-
	- 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 5epsilon and 10epsilon.
	- bond_coeff @bond:backbone harmonic 116.847 7.5 #<--25000eps/sig^2
	- }
	-
	- write_once("In Settings") {
	- #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
	- angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps
	- }
	-
	- 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 of head beads which all other beads is given by:
	- # epsilon(0.4(sigma/r)^12 - 0.0*(sigma/r)^6),
	-
	- 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
	-
	-
	- } # 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(4K(s/r)^12 + 4L(s/r)^6)
	- # The es4k4l coeffstyle is popular. Using this convention makes it easier
	- # to mix this coarse-grained lipid model with other molecular models.
	-
	-
	- DPPC {
	- write("Data Atoms") {
	- $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # custom "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
	- }
	-
	- } #DPPC
	-
	-
	- DLPC {
	- write("Data Atoms") {
	- $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # custom "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
	- }
	- } #DLPC
	-
	-
	-
	-} # CGLipidBr2005
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
	deleted file mode 100755
	index ae4160531..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
	+++ /dev/null
	@@ -1,34 +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)
	-
	-# The previous version included the repulsive core term
	-def U(r, eps, sigma):
	- return eps* (0.4pow((sigma/r),12) - 3.0sigmasigma/(rr))
	-def F(r, eps, sigma):
	- return eps(120.4pow((sigma/r),13)/sigma - 23.0sigmasigma/(rrr))
	-# We don't want to do that. Instead compute the core repulsion using a
	-# different pair_style and add the attractive term on top of it using the table.
	-# This way it the core repulsion acts as a default interaction with other atom
	-# types (using the new repulsive mixing rules).
	-
	-epsilon = 2.75/4.184 # kCal/mole
	-sigma = 7.5
	-Rmin = 2.6
	-Rmax = 22.6
	-rcut = 22.5
	-N = 1001
	-
	-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/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
	deleted file mode 100755
	index 48f199074..000000000
	--- a/tools/moltemplate/examples/CG_membrane_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 + 2r^2 - 3rc1^2) / (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 + 2.0rsq - 3.0rc1sq) * denom_lj_inv)
	-
	-
	-def U(r, eps, sigma):
	- return eps* (0.4pow((sigma/r),12) - 3.0sigmasigma/(rr))
	-
	-def F(r, eps, sigma):
	- return eps(120.4pow((sigma/r),13)/sigma - 23.0sigmasigma/(rrr))
	-
	-epsilon = 2.75/4.184 # kCal/mole
	-sigma = 7.5
	-Rmin = 2.6
	-Rmax = 22.6
	-Rc1 = 22.0
	-Rc2 = 22.5
	-N = 1001
	-
	-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/CG_membrane_examples/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/system.lt
	deleted file mode 100644
	index efb244255..000000000
	--- a/tools/moltemplate/examples/CG_membrane_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.) 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 6.0 1 -1
	- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	-
	- # We want the interactions between hydrophobic residues and atoms in
	- # the interior of the lipd 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 6.0 1 -1
	-
	- # 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. Probably not 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
	-
	- # All other interactions between proteins and lipids are steric.
	- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	- pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
	-
	-
	- # 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 7.5 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 class2
	- 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/CG_membrane_examples/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/table_int.dat
	deleted file mode 100644
	index 31b9f0c45..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/table_int.dat
	+++ /dev/null
	@@ -1,1010 +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 1001
	-
	-1 2.6 87252.0069441 402763.664479
	-2 2.62 79585.4554502 364574.203947
	-3 2.64 72643.2434671 330255.845328
	-4 2.66 66352.2073932 299391.208536
	-5 2.68 60647.0444312 271610.570248
	-6 2.7 55469.4181565 246586.123584
	-7 2.72 50767.1714483 224026.964698
	-8 2.74 46493.633237 203674.709811
	-9 2.76 42607.0073083 185299.659567
	-10 2.78 39069.8329526 168697.439095
	-11 2.8 35848.5085794 153686.051901
	-12 2.82 32912.8705664 140103.294183
	-13 2.84 30235.8206098 127804.483324
	-14 2.86 27792.9956998 116660.460548
	-15 2.88 25562.4755962 106555.833042
	-16 2.9 23524.5233195 97387.4254387
	-17 2.92 21661.3547409 89062.9145204
	-18 2.94 19956.9338374 81499.6244039
	-19 2.96 18396.7906059 74623.4624292
	-20 2.98 16967.8589974 68367.9785194
	-21 3.0 15658.3325568 62673.5329856
	-22 3.02 14457.5357325 57486.5596649
	-23 3.04 13355.809067 52758.912937
	-24 3.06 12344.4066925 48447.2886046
	-25 3.08 11415.4047444 44512.7098736
	-26 3.1 10561.6194689 40920.0707567
	-27 3.12 9776.5339459 37637.7301715
	-28 3.14 9054.23247117 34637.1508274
	-29 3.16 8389.34175838 31892.5777179
	-30 3.18 7776.97821258 29380.7516608
	-31 3.2 7212.7006167 27080.6538766
	-32 3.22 6692.4676457 24973.2780793
	-33 3.24 6212.59969004 23041.4269669
	-34 3.26 5769.74452856 21269.5303734
	-35 3.28 5360.84644195 19643.4826615
	-36 3.3 4983.1184041 18150.4972204
	-37 3.32 4634.01702836 16778.97618
	-38 3.34 4311.21998136 15518.393672
	-39 3.36 4012.60560869 14359.191159
	-40 3.38 3736.23454428 13292.6835236
	-41 3.4 3480.33310029 12310.9747549
	-42 3.42 3243.27825585 11406.8822043
	-43 3.44 3023.58408279 10573.8684961
	-44 3.46 2819.88946345 9805.98028003
	-45 3.48 2630.94697101 9097.79310596
	-46 3.5 2455.61279669 8444.36177626
	-47 3.52 2292.83761972 7841.17560602
	-48 3.54 2141.65832756 7284.11808108
	-49 3.56 2001.19050257 6769.43046025
	-50 3.58 1870.62160083 6293.67891689
	-51 3.6 1749.20475558 5853.72485855
	-52 3.62 1636.25314534 5446.69810179
	-53 3.64 1531.13487237 5069.97261409
	-54 3.66 1433.26830277 4721.1445646
	-55 3.68 1342.11782445 4398.01245332
	-56 3.7 1257.18998347 4098.55911171
	-57 3.72 1178.02996319 3820.93539003
	-58 3.74 1104.21837425 3563.44536511
	-59 3.76 1035.36832639 3324.53291993
	-60 3.78 971.122756088 3102.76956138
	-61 3.8 911.151986554 2896.84335615
	-62 3.82 855.151498616 2705.54887715
	-63 3.84 802.83989347 2527.77806329
	-64 3.86 753.957029799 2362.51190574
	-65 3.88 708.262319576 2208.81288195
	-66 3.9 665.533168297 2065.81806693
	-67 3.92 625.563546756 1932.73285812
	-68 3.94 588.162682667 1808.82525631
	-69 3.96 553.153861545 1693.42065104
	-70 3.98 520.373327227 1585.89706361
	-71 4.0 489.669273313 1485.68080556
	-72 4.02 460.900917596 1392.24251449
	-73 4.04 433.937652306 1305.09353282
	-74 4.06 408.6582636 1223.78259822
	-75 4.08 384.950214367 1147.89281764
	-76 4.1 362.708984933 1077.03889938
	-77 4.12 341.837466738 1010.86461999
	-78 4.14 322.245404503 949.040505266
	-79 4.16 303.848882793 891.261706073
	-80 4.18 286.569853265 837.246052066
	-81 4.2 270.33569919 786.732267446
	-82 4.22 255.078834164 739.47833469
	-83 4.24 240.736332164 695.259993326
	-84 4.26 227.249586386 653.869362042
	-85 4.28 214.563994495 615.113673492
	-86 4.3 202.628668126 578.814112106
	-87 4.32 191.396164684 544.804746089
	-88 4.34 180.822239621 512.931545605
	-89 4.36 170.865617553 483.051479815
	-90 4.38 161.487780703 455.031686127
	-91 4.4 152.652773286 428.748705595
	-92 4.42 144.327020575 404.087778912
	-93 4.44 136.479161479 380.942197972
	-94 4.46 129.07989358 359.212708377
	-95 4.48 122.101829632 338.806958688
	-96 4.5 115.519364658 319.638992577
	-97 4.52 109.308552789 301.628780369
	-98 4.54 103.446993117 284.701786758
	-99 4.56 97.9137238447 268.788571763
	-100 4.58 92.6891241175 253.824422244
	-101 4.6 87.7548229339 239.749011508
	-102 4.62 83.0936146036 226.506084761
	-103 4.64 78.6893802546 214.043168343
	-104 4.66 74.5270149351 202.31130085
	-105 4.68 70.5923598871 191.264784422
	-106 4.7 66.8721396072 180.860954593
	-107 4.72 63.353903336 171.05996726
	-108 4.74 60.0259706488 161.824601429
	-109 4.76 56.8773808439 153.120076496
	-110 4.78 53.8978458491 144.913882966
	-111 4.8 51.0777063884 137.175625538
	-112 4.82 48.4078911713 129.876877635
	-113 4.84 45.8798788842 122.991046476
	-114 4.86 43.485662782 116.493247913
	-115 4.88 41.2177176913 110.360190267
	-116 4.9 39.0689692529 104.570066494
	-117 4.92 37.0327652428 99.1024540566
	-118 4.94 35.102848823 93.9382219092
	-119 4.96 33.2733335874 89.05944408
	-120 4.98 31.5386802724 84.4493193479
	-121 5.0 29.8936750183 80.0920965658
	-122 5.02 28.3334090704 75.9730052143
	-123 5.04 26.8532598202 72.0781907976
	-124 5.06 25.4488730938 68.3946547294
	-125 5.08 24.116146599 64.9101983786
	-126 5.1 22.8512144543 61.6133709734
	-127 5.12 21.650432722 58.4934210835
	-128 5.14 20.5103658787 55.5402514226
	-129 5.16 19.4277741591 52.7443767307
	-130 5.18 18.3996017121 50.0968845179
	-131 5.2 17.4229655155 47.5893984632
	-132 5.22 16.4951449988 45.2140442802
	-133 5.24 15.6135723236 42.9634178757
	-134 5.26 14.775823281 40.8305556374
	-135 5.28 13.979608762 38.808906703
	-136 5.3 13.2227667648 36.8923070701
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	-818 18.94 -0.0900975756229 -0.0326468987742
	-819 18.96 -0.089445670154 -0.032543720659
	-820 18.98 -0.0887958239027 -0.0324409766249
	-821 19.0 -0.0881480282103 -0.032338664395
	-822 19.02 -0.0875022744633 -0.0322367817064
	-823 19.04 -0.0868585540934 -0.0321353263106
	-824 19.06 -0.0862168585771 -0.0320342959728
	-825 19.08 -0.0855771794356 -0.0319336884725
	-826 19.1 -0.084939508234 -0.0318335016031
	-827 19.12 -0.0843038365819 -0.0317337331714
	-828 19.14 -0.0836701561321 -0.0316343809981
	-829 19.16 -0.0830384585813 -0.0315354429176
	-830 19.18 -0.0824087356692 -0.0314369167774
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	-833 19.24 -0.0805313328034 -0.0311437886765
	-834 19.26 -0.079909426697 -0.031046889041
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	-836 19.3 -0.0786714084036 -0.0308542918291
	-837 19.32 -0.0780552802445 -0.0307585901186
	-838 19.34 -0.0774410621642 -0.0306632836034
	-839 19.36 -0.0768287462793 -0.0305683702482
	-840 19.38 -0.0762183247467 -0.0304738480301
	-841 19.4 -0.0756097897639 -0.0303797149388
	-842 19.42 -0.0750031335683 -0.0302859689762
	-843 19.44 -0.0743983484373 -0.0301926081566
	-844 19.46 -0.0737954266876 -0.0300996305063
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	-846 19.5 -0.0725951427967 -0.0299148168796
	-847 19.52 -0.071997765485 -0.0298229770161
	-848 19.54 -0.0714022212134 -0.0297315125477
	-849 19.56 -0.0708085024932 -0.0296404215602
	-850 19.58 -0.0702166018738 -0.0295497021514
	-851 19.6 -0.0696265119425 -0.0294593524306
	-852 19.62 -0.0690382253245 -0.0293693705184
	-853 19.64 -0.0684517346822 -0.0292797545471
	-854 19.66 -0.0678670327154 -0.0291905026603
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	-857 19.72 -0.0661235864195 -0.02892491311
	-858 19.74 -0.0655459668893 -0.0288370992202
	-859 19.76 -0.0649701000843 -0.0287496402998
	-860 19.78 -0.0643959789228 -0.0286625345588
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	-866 19.9 -0.0609875183786 -0.0281472179874
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	-868 19.94 -0.0598650147059 -0.0279781918096
	-869 19.96 -0.0593062914901 -0.027894185887
	-870 19.98 -0.0587492450313 -0.0278105158248
	-871 20.0 -0.0581938686292 -0.0277271799475
	-872 20.02 -0.0576401556166 -0.0276441765898
	-873 20.04 -0.0570880993599 -0.0275615040963
	-874 20.06 -0.056537693258 -0.0274791608214
	-875 20.08 -0.0559889307431 -0.0273971451294
	-876 20.1 -0.0554418052798 -0.0273154553941
	-877 20.12 -0.0548963103651 -0.0272340899992
	-878 20.14 -0.0543524395283 -0.0271530473379
	-879 20.16 -0.0538101863307 -0.027072325813
	-880 20.18 -0.0532695443654 -0.0269919238365
	-881 20.2 -0.0527305072574 -0.0269118398301
	-882 20.22 -0.0521930686629 -0.0268320722247
	-883 20.24 -0.0516572222695 -0.0267526194605
	-884 20.26 -0.0511229617959 -0.0266734799867
	-885 20.28 -0.0505902809917 -0.0265946522621
	-886 20.3 -0.0500591736373 -0.026516134754
	-887 20.32 -0.0495296335436 -0.0264379259393
	-888 20.34 -0.0490016545518 -0.0263600243033
	-889 20.36 -0.0484752305336 -0.0262824283405
	-890 20.38 -0.0479503553904 -0.0262051365543
	-891 20.4 -0.0474270230535 -0.0261281474567
	-892 20.42 -0.0469052274841 -0.0260514595684
	-893 20.44 -0.0463849626725 -0.0259750714189
	-894 20.46 -0.0458662226388 -0.0258989815462
	-895 20.48 -0.0453490014319 -0.0258231884968
	-896 20.5 -0.0448332931297 -0.0257476908257
	-897 20.52 -0.0443190918392 -0.0256724870964
	-898 20.54 -0.0438063916958 -0.0255975758806
	-899 20.56 -0.0432951868634 -0.0255229557586
	-900 20.58 -0.0427854715342 -0.0254486253186
	-901 20.6 -0.0422772399288 -0.0253745831572
	-902 20.62 -0.0417704862954 -0.0253008278792
	-903 20.64 -0.0412652049103 -0.0252273580972
	-904 20.66 -0.0407613900774 -0.0251541724321
	-905 20.68 -0.040259036128 -0.0250812695126
	-906 20.7 -0.039758137421 -0.0250086479756
	-907 20.72 -0.0392586883422 -0.0249363064654
	-908 20.74 -0.0387606833045 -0.0248642436347
	-909 20.76 -0.0382641167479 -0.0247924581434
	-910 20.78 -0.0377689831387 -0.0247209486595
	-911 20.8 -0.0372752769703 -0.0246497138585
	-912 20.82 -0.036782992762 -0.0245787524235
	-913 20.84 -0.0362921250596 -0.0245080630453
	-914 20.86 -0.0358026684351 -0.0244376444219
	-915 20.88 -0.0353146174863 -0.0243674952592
	-916 20.9 -0.0348279668369 -0.0242976142701
	-917 20.92 -0.0343427111362 -0.0242280001751
	-918 20.94 -0.0338588450591 -0.0241586517019
	-919 20.96 -0.0333763633058 -0.0240895675856
	-920 20.98 -0.0328952606017 -0.0240207465683
	-921 21.0 -0.0324155316974 -0.0239521873994
	-922 21.02 -0.0319371713684 -0.0238838888354
	-923 21.04 -0.0314601744149 -0.0238158496399
	-924 21.06 -0.0309845356618 -0.0237480685835
	-925 21.08 -0.0305102499587 -0.0236805444437
	-926 21.1 -0.0300373121794 -0.0236132760051
	-927 21.12 -0.0295657172219 -0.023546262059
	-928 21.14 -0.0290954600085 -0.0234795014037
	-929 21.16 -0.0286265354851 -0.0234129928442
	-930 21.18 -0.028158938622 -0.0233467351922
	-931 21.2 -0.0276926644126 -0.0232807272662
	-932 21.22 -0.0272277078743 -0.0232149678915
	-933 21.24 -0.0267640640477 -0.0231494558997
	-934 21.26 -0.0263017279969 -0.0230841901292
	-935 21.28 -0.0258406948088 -0.0230191694249
	-936 21.3 -0.0253809595937 -0.0229543926381
	-937 21.32 -0.0249225174848 -0.0228898586266
	-938 21.34 -0.0244653636377 -0.0228255662547
	-939 21.36 -0.0240094932312 -0.0227615143929
	-940 21.38 -0.0235549014661 -0.0226977019182
	-941 21.4 -0.023101583566 -0.0226341277136
	-942 21.42 -0.0226495347765 -0.0225707906687
	-943 21.44 -0.0221987503655 -0.0225076896791
	-944 21.46 -0.021749225623 -0.0224448236465
	-945 21.48 -0.0213009558606 -0.0223821914788
	-946 21.5 -0.020853936412 -0.02231979209
	-947 21.52 -0.0204081626323 -0.0222576244002
	-948 21.54 -0.0199636298985 -0.0221956873354
	-949 21.56 -0.0195203336085 -0.0221339798275
	-950 21.58 -0.0190782691821 -0.0220725008144
	-951 21.6 -0.0186374320597 -0.02201124924
	-952 21.62 -0.0181978177032 -0.0219502240539
	-953 21.64 -0.0177594215953 -0.0218894242115
	-954 21.66 -0.0173222392394 -0.0218288486741
	-955 21.68 -0.0168862661598 -0.0217684964086
	-956 21.7 -0.0164514979014 -0.0217083663878
	-957 21.72 -0.0160179300295 -0.0216484575898
	-958 21.74 -0.0155855581298 -0.0215887689986
	-959 21.76 -0.0151543778082 -0.0215292996039
	-960 21.78 -0.014724384691 -0.0214700484006
	-961 21.8 -0.0142955744243 -0.0214110143895
	-962 21.82 -0.0138679426741 -0.0213521965765
	-963 21.84 -0.0134414851265 -0.0212935939733
	-964 21.86 -0.013016197487 -0.0212352055967
	-965 21.88 -0.0125920754809 -0.0211770304692
	-966 21.9 -0.012169114853 -0.0211190676184
	-967 21.92 -0.0117473113675 -0.0210613160772
	-968 21.94 -0.0113266608076 -0.021003774884
	-969 21.96 -0.0109071589762 -0.0209464430823
	-970 21.98 -0.0104888016947 -0.0208893197208
	-971 22.0 -0.010071584804 -0.0208324038534
	-972 22.02 -0.00965550416359 -0.0207756945391
	-973 22.04 -0.0092405556517 -0.020719190842
	-974 22.06 -0.00882673516534 -0.0206628918315
	-975 22.08 -0.00841403862003 -0.0206067965819
	-976 22.1 -0.0080024619498 -0.0205509041723
	-977 22.12 -0.00759200110698 -0.0204952136871
	-978 22.14 -0.00718265206222 -0.0204397242155
	-979 22.16 -0.00677441080431 -0.0203844348517
	-980 22.18 -0.00636727334011 -0.0203293446947
	-981 22.2 -0.00596123569445 -0.0202744528484
	-982 22.22 -0.00555629391005 -0.0202197584216
	-983 22.24 -0.00515244404737 -0.0201652605278
	-984 22.26 -0.00474968218459 -0.0201109582853
	-985 22.28 -0.00434800441746 -0.0200568508172
	-986 22.3 -0.00394740685922 -0.0200029372512
	-987 22.32 -0.00354788564052 -0.0199492167196
	-988 22.34 -0.0031494369093 -0.0198956883597
	-989 22.36 -0.00275205683071 -0.0198423513132
	-990 22.38 -0.00235574158704 -0.0197892047262
	-991 22.4 -0.00196048737759 -0.0197362477497
	-992 22.42 -0.00156629041861 -0.0196834795391
	-993 22.44 -0.00117314694319 -0.0196308992543
	-994 22.46 -0.000781053201174 -0.0195785060596
	-995 22.48 -0.000390005459079 -0.019526299124
	-996 22.5 0.0 -0.0194742776206
	-997 22.52 0.0 0.0
	-998 22.54 0.0 0.0
	-999 22.56 0.0 0.0
	-1000 22.58 0.0 0.0
	-1001 22.6 0.0 0.0
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.min b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.min
	deleted file mode 100644
	index fce9843aa..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.npt
	deleted file mode 100644
	index af4890aa0..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.npt
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-# -------- REQUIREMENTS: ---------
	-# 1) This example requires the CLASS2 package.
	-# 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-class2" 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 --
	-
	-
	-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
	-
	-# 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
	-
	-
	-#restart 1000000
	-
	-run 2000000
	-
	-write_restart system_after_npt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.nvt
	deleted file mode 100644
	index 54c3d6182..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.nvt
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-# -- Init Section --
	-
	-include system.in.init
	-
	-# -- Atom Definition Section --
	-
	-# read_data system.data <-- commenting out
	-# Use the pressure-equilibrated restart file instead:
	-read_restart system_after_npt.rst
	-
	-
	-# -- 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 20000 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 20000000
	-
	-write_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README.TXT
	deleted file mode 100644
	index 295af3fd1..000000000
	--- a/tools/moltemplate/examples/CG_membrane_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 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/CG_membrane_examples/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_run.sh
	deleted file mode 100755
	index 18d5b65b6..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_run.sh
	+++ /dev/null
	@@ -1,33 +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.npt # pressure equilibration
	-"$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.npt # pressure equilibration
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_setup.sh
	deleted file mode 100755
	index 4414a4a4b..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/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 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 -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/CG_membrane_examples/membrane_BranniganPRE2005/README_visualise.txt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_visualise.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/CG_membrane_examples/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DLPC.jpg
	deleted file mode 100644
	index 637f2f1c7..000000000
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	deleted file mode 100644
	index 14f1a1ed2..000000000
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg
	deleted file mode 100644
	index 757abe268..000000000
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg
	deleted file mode 100644
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC.jpg
	deleted file mode 100644
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005.lt
	deleted file mode 100644
	index bb9a732c1..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005.lt
	+++ /dev/null
	@@ -1,186 +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 mixture.
	-
	-
	-
	-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
	- dihedral_style none
	- improper_style none
	- pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15
	-
	- # 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.)
	-
	- pair_modify mix arithmetic
	- special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
	-
	- # Optional: The "multi" style could be useful to efficiently simulate
	- # particles different sizes together. The tabular potential has range
	- # 22.5 Angstoms, but the Lennard-Jones forces have range of only
	- # 15.0 Angstroms.
	-
	- neighbor 2.0 multi
	- communicate multi
	- }
	-
	-
	- # Particles shared by all lipid types
	- write_once("Data Masses") {
	- @atom:int 200.0
	- @atom:tail 200.0
	- @atom:head 200.0 #<- Default "head" type. We will override it later
	- }
	-
	-
	-
	- # All force-field parameters appear in the "In Settings" section,
	- # which is later included in the LAMMPS input script.
	- # These force-field parameters are shared between all lipids by default.
	- # These can be customized and overridden for specific lipid types later.
	-
	-
	- # 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.
	-
	- 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 5epsilon and 10epsilon.
	- bond_coeff @bond:backbone harmonic 116.847 7.5 #<--25000eps/sig^2
	- }
	-
	- write_once("In Settings") {
	- #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
	- angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps
	- }
	-
	- 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 of head beads which all other beads is given by:
	- # epsilon(0.4(sigma/r)^12 - 0.0*(sigma/r)^6),
	-
	- 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
	-
	-
	- } # 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(4K(s/r)^12 + 4L(s/r)^6)
	- # The es4k4l coeffstyle is popular. Using this convention makes it easier
	- # to mix this coarse-grained lipid model with other molecular models.
	-
	-
	- DPPC {
	- write("Data Atoms") {
	- $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # custom "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
	- }
	-
	- } #DPPC
	-
	-
	- DLPC {
	- write("Data Atoms") {
	- $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # custom "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
	- }
	- } #DLPC
	-
	-
	-
	-} # CGLipidBr2005
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/generate_tables/calc_table.py b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/generate_tables/calc_table.py
	deleted file mode 100755
	index ae4160531..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/generate_tables/calc_table.py
	+++ /dev/null
	@@ -1,34 +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)
	-
	-# The previous version included the repulsive core term
	-def U(r, eps, sigma):
	- return eps* (0.4pow((sigma/r),12) - 3.0sigmasigma/(rr))
	-def F(r, eps, sigma):
	- return eps(120.4pow((sigma/r),13)/sigma - 23.0sigmasigma/(rrr))
	-# We don't want to do that. Instead compute the core repulsion using a
	-# different pair_style and add the attractive term on top of it using the table.
	-# This way it the core repulsion acts as a default interaction with other atom
	-# types (using the new repulsive mixing rules).
	-
	-epsilon = 2.75/4.184 # kCal/mole
	-sigma = 7.5
	-Rmin = 2.6
	-Rmax = 22.6
	-rcut = 22.5
	-N = 1001
	-
	-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/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt
	deleted file mode 100644
	index 81aefe6ff..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-# Description:
	-
	-# This example shows how to build a lipid bilayer composed of a
	-# 50%-50% mixture of two different lipids (DPPC and DLPC).
	-# The DPPC model is described here:
	-# G. Brannigan, P.F. Philips, and F.L.H. Brown,
	-# Physical Review E, Vol 72, 011915 (2005)
	-# The new DLPC model is a truncated version of DPPC,
	-# (Its behaviour has not been rigorously tested.)
	-# Note: 50%/50% mixtures of DPPC & DLPC are commonly used to build liposomes
	-# http://www.ncbi.nlm.nih.gov/pubmed/10620293
	-
	-
	-import "CGLipidBr2005.lt"
	-
	-using namespace CGLipidBr2005
	-
	-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)
	-
	-# 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.
	-
	-
	-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 ( ~= 0.95sigma2^(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) The example we use here is a lipid mixture of DPPC and DLPC, so we 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/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
	deleted file mode 100644
	index 31b9f0c45..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
	+++ /dev/null
	@@ -1,1010 +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 1001
	-
	-1 2.6 87252.0069441 402763.664479
	-2 2.62 79585.4554502 364574.203947
	-3 2.64 72643.2434671 330255.845328
	-4 2.66 66352.2073932 299391.208536
	-5 2.68 60647.0444312 271610.570248
	-6 2.7 55469.4181565 246586.123584
	-7 2.72 50767.1714483 224026.964698
	-8 2.74 46493.633237 203674.709811
	-9 2.76 42607.0073083 185299.659567
	-10 2.78 39069.8329526 168697.439095
	-11 2.8 35848.5085794 153686.051901
	-12 2.82 32912.8705664 140103.294183
	-13 2.84 30235.8206098 127804.483324
	-14 2.86 27792.9956998 116660.460548
	-15 2.88 25562.4755962 106555.833042
	-16 2.9 23524.5233195 97387.4254387
	-17 2.92 21661.3547409 89062.9145204
	-18 2.94 19956.9338374 81499.6244039
	-19 2.96 18396.7906059 74623.4624292
	-20 2.98 16967.8589974 68367.9785194
	-21 3.0 15658.3325568 62673.5329856
	-22 3.02 14457.5357325 57486.5596649
	-23 3.04 13355.809067 52758.912937
	-24 3.06 12344.4066925 48447.2886046
	-25 3.08 11415.4047444 44512.7098736
	-26 3.1 10561.6194689 40920.0707567
	-27 3.12 9776.5339459 37637.7301715
	-28 3.14 9054.23247117 34637.1508274
	-29 3.16 8389.34175838 31892.5777179
	-30 3.18 7776.97821258 29380.7516608
	-31 3.2 7212.7006167 27080.6538766
	-32 3.22 6692.4676457 24973.2780793
	-33 3.24 6212.59969004 23041.4269669
	-34 3.26 5769.74452856 21269.5303734
	-35 3.28 5360.84644195 19643.4826615
	-36 3.3 4983.1184041 18150.4972204
	-37 3.32 4634.01702836 16778.97618
	-38 3.34 4311.21998136 15518.393672
	-39 3.36 4012.60560869 14359.191159
	-40 3.38 3736.23454428 13292.6835236
	-41 3.4 3480.33310029 12310.9747549
	-42 3.42 3243.27825585 11406.8822043
	-43 3.44 3023.58408279 10573.8684961
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	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/calc_table.py
	deleted file mode 100755
	index 48f199074..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/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 + 2r^2 - 3rc1^2) / (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 + 2.0rsq - 3.0rc1sq) * denom_lj_inv)
	-
	-
	-def U(r, eps, sigma):
	- return eps* (0.4pow((sigma/r),12) - 3.0sigmasigma/(rr))
	-
	-def F(r, eps, sigma):
	- return eps(120.4pow((sigma/r),13)/sigma - 23.0sigmasigma/(rrr))
	-
	-epsilon = 2.75/4.184 # kCal/mole
	-sigma = 7.5
	-Rmin = 2.6
	-Rmax = 22.6
	-Rc1 = 22.0
	-Rc2 = 22.5
	-N = 1001
	-
	-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/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/table_int.dat b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/table_int.dat
	deleted file mode 100644
	index d7a16e9bc..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/table_int.dat
	+++ /dev/null
	@@ -1,1020 +0,0 @@
	-# Computed with "calc_table.py"
	-# 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)
	-# where here sigma = 7.5, and epsilon = 2.75/4.184
	-# The interaction is truncated. See below.
	-#
	-# In this version I used the CHARMM switching function
	-# S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2r^2 - 3rc1^2) / (rc2^2-rc1^2)^3
	-# with rc1=22.0 and rc2=22.5
	-# 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 also probably with the later Watson JCP 2011 paper.
	-# (So don't use this.)
	-
	-INT
	-N 1001 R
	-
	-1 2.6 87251.787856 402763.664479
	-2 2.62 79585.2363621 364574.203947
	-3 2.64 72643.024379 330255.845328
	-4 2.66 66351.9883051 299391.208536
	-5 2.68 60646.8253431 271610.570248
	-6 2.7 55469.1990684 246586.123584
	-7 2.72 50766.9523602 224026.964698
	-8 2.74 46493.4141489 203674.709811
	-9 2.76 42606.7882202 185299.659567
	-10 2.78 39069.6138645 168697.439095
	-11 2.8 35848.2894913 153686.051901
	-12 2.82 32912.6514783 140103.294183
	-13 2.84 30235.6015217 127804.483324
	-14 2.86 27792.7766117 116660.460548
	-15 2.88 25562.2565081 106555.833042
	-16 2.9 23524.3042314 97387.4254387
	-17 2.92 21661.1356528 89062.9145204
	-18 2.94 19956.7147493 81499.6244039
	-19 2.96 18396.5715178 74623.4624292
	-20 2.98 16967.6399093 68367.9785194
	-21 3.0 15658.1134687 62673.5329856
	-22 3.02 14457.3166444 57486.5596649
	-23 3.04 13355.5899789 52758.912937
	-24 3.06 12344.1876044 48447.2886046
	-25 3.08 11415.1856563 44512.7098736
	-26 3.1 10561.4003809 40920.0707567
	-27 3.12 9776.3148578 37637.7301715
	-28 3.14 9054.01338308 34637.1508274
	-29 3.16 8389.12267028 31892.5777179
	-30 3.18 7776.75912449 29380.7516608
	-31 3.2 7212.48152861 27080.6538766
	-32 3.22 6692.2485576 24973.2780793
	-33 3.24 6212.38060195 23041.4269669
	-34 3.26 5769.52544046 21269.5303734
	-35 3.28 5360.62735385 19643.4826615
	-36 3.3 4982.89931601 18150.4972204
	-37 3.32 4633.79794027 16778.97618
	-38 3.34 4311.00089327 15518.393672
	-39 3.36 4012.38652059 14359.191159
	-40 3.38 3736.01545619 13292.6835236
	-41 3.4 3480.11401219 12310.9747549
	-42 3.42 3243.05916775 11406.8822043
	-43 3.44 3023.36499469 10573.8684961
	-44 3.46 2819.67037535 9805.98028003
	-45 3.48 2630.72788292 9097.79310596
	-46 3.5 2455.39370859 8444.36177626
	-47 3.52 2292.61853163 7841.17560602
	-48 3.54 2141.43923946 7284.11808108
	-49 3.56 2000.97141448 6769.43046025
	-50 3.58 1870.40251273 6293.67891689
	-51 3.6 1748.98566748 5853.72485855
	-52 3.62 1636.03405724 5446.69810179
	-53 3.64 1530.91578427 5069.97261409
	-54 3.66 1433.04921467 4721.1445646
	-55 3.68 1341.89873635 4398.01245332
	-56 3.7 1256.97089537 4098.55911171
	-57 3.72 1177.8108751 3820.93539003
	-58 3.74 1103.99928616 3563.44536511
	-59 3.76 1035.14923829 3324.53291993
	-60 3.78 970.903667992 3102.76956138
	-61 3.8 910.932898457 2896.84335615
	-62 3.82 854.932410519 2705.54887715
	-63 3.84 802.620805373 2527.77806329
	-64 3.86 753.737941702 2362.51190574
	-65 3.88 708.043231479 2208.81288195
	-66 3.9 665.3140802 2065.81806693
	-67 3.92 625.344458659 1932.73285812
	-68 3.94 587.94359457 1808.82525631
	-69 3.96 552.934773448 1693.42065104
	-70 3.98 520.154239131 1585.89706361
	-71 4.0 489.450185216 1485.68080556
	-72 4.02 460.681829499 1392.24251449
	-73 4.04 433.718564209 1305.09353282
	-74 4.06 408.439175503 1223.78259822
	-75 4.08 384.73112627 1147.89281764
	-76 4.1 362.489896836 1077.03889938
	-77 4.12 341.618378642 1010.86461999
	-78 4.14 322.026316406 949.040505266
	-79 4.16 303.629794696 891.261706073
	-80 4.18 286.350765168 837.246052066
	-81 4.2 270.116611094 786.732267446
	-82 4.22 254.859746067 739.47833469
	-83 4.24 240.517244067 695.259993326
	-84 4.26 227.030498289 653.869362042
	-85 4.28 214.344906398 615.113673492
	-86 4.3 202.409580029 578.814112106
	-87 4.32 191.177076588 544.804746089
	-88 4.34 180.603151525 512.931545605
	-89 4.36 170.646529457 483.051479815
	-90 4.38 161.268692606 455.031686127
	-91 4.4 152.433685189 428.748705595
	-92 4.42 144.107932478 404.087778912
	-93 4.44 136.260073383 380.942197972
	-94 4.46 128.860805483 359.212708377
	-95 4.48 121.882741535 338.806958688
	-96 4.5 115.300276561 319.638992577
	-97 4.52 109.089464693 301.628780369
	-98 4.54 103.22790502 284.701786758
	-99 4.56 97.6946357479 268.788571763
	-100 4.58 92.4700360207 253.824422244
	-101 4.6 87.5357348372 239.749011508
	-102 4.62 82.8745265068 226.506084761
	-103 4.64 78.4702921579 214.043168343
	-104 4.66 74.3079268383 202.31130085
	-105 4.68 70.3732717904 191.264784422
	-106 4.7 66.6530515105 180.860954593
	-107 4.72 63.1348152392 171.05996726
	-108 4.74 59.806882552 161.824601429
	-109 4.76 56.6582927471 153.120076496
	-110 4.78 53.6787577523 144.913882966
	-111 4.8 50.8586182917 137.175625538
	-112 4.82 48.1888030746 129.876877635
	-113 4.84 45.6607907875 122.991046476
	-114 4.86 43.2665746852 116.493247913
	-115 4.88 40.9986295945 110.360190267
	-116 4.9 38.8498811562 104.570066494
	-117 4.92 36.813677146 99.1024540566
	-118 4.94 34.8837607263 93.9382219092
	-119 4.96 33.0542454907 89.05944408
	-120 4.98 31.3195921757 84.4493193479
	-121 5.0 29.6745869215 80.0920965658
	-122 5.02 28.1143209736 75.9730052143
	-123 5.04 26.6341717235 72.0781907976
	-124 5.06 25.229784997 68.3946547294
	-125 5.08 23.8970585023 64.9101983786
	-126 5.1 22.6321263576 61.6133709734
	-127 5.12 21.4313446252 58.4934210835
	-128 5.14 20.291277782 55.5402514226
	-129 5.16 19.2086860624 52.7443767307
	-130 5.18 18.1805136153 50.0968845179
	-131 5.2 17.2038774188 47.5893984632
	-132 5.22 16.2760569021 45.2140442802
	-133 5.24 15.3944842269 42.9634178757
	-134 5.26 14.5567351843 40.8305556374
	-135 5.28 13.7605206653 38.808906703
	-136 5.3 13.003678668 36.8923070701
	-137 5.32 12.2841668048 35.0749554196
	-138 5.34 11.600055277 33.3513905323
	-139 5.36 10.9495202864 31.7164701895
	-140 5.38 10.3308378544 30.1653514539
	-141 5.4 9.7423780233 28.693472236
	-142 5.42 9.182599413 27.2965340593
	-143 5.44 8.65004411217 25.9704859397
	-144 5.46 8.14333288066 24.7115093061
	-145 5.48 7.66116064403 23.5160038893
	-146 5.5 7.20229226095 22.3805745153
	-147 5.52 6.76555854632 21.3020187412
	-148 5.54 6.34985253373 20.2773152771
	-149 5.56 5.95412596195 19.3036131423
	-150 5.58 5.5773859715 18.3782215059
	-151 5.6 5.21869199787 17.4986001669
	-152 5.62 4.87715284909 16.6623506308
	-153 5.64 4.55192395618 15.867207745
	-154 5.66 4.24220478557 15.1110318537
	-155 5.68 3.94723640355 14.3918014404
	-156 5.7 3.66629918323 13.7076062261
	-157 5.72 3.39871064523 13.0566406912
	-158 5.74 3.14382342396 12.4371979973
	-159 5.76 2.90102335163 11.8476642796
	-160 5.78 2.66972765295 11.2865132882
	-161 5.8 2.44938324367 10.7523013555
	-162 5.82 2.23946512673 10.2436626676
	-163 5.84 2.03947488006 9.7593048226
	-164 5.86 1.84893923049 9.2980046552
	-165 5.88 1.66740870871 8.85860431242
	-166 5.9 1.49445638028 8.44000756375
	-167 5.92 1.32967664824 8.04117633127
	-168 5.94 1.17268412303 7.66112742597
	-169 5.96 1.0231125557 7.29892947717
	-170 5.98 0.880613830771 6.9537000433
	-171 6.0 0.744857015106 6.62460289254
	-172 6.02 0.615527459555 6.31084544295
	-173 6.04 0.492325950319 6.01167635216
	-174 6.06 0.374967907076 5.72638324756
	-175 6.08 0.263182625182 5.45429058822
	-176 6.1 0.156712559382 5.19475765055
	-177 6.12 0.0553126466265 4.94717663025
	-178 6.14 -0.0412503342437 4.71097085338
	-179 6.16 -0.133198368078 4.48559308998
	-180 6.18 -0.220742776239 4.27052396409
	-181 6.2 -0.304084758542 4.06527045435
	-182 6.22 -0.383415906069 3.8693644797
	-183 6.24 -0.4589186865 3.68236156522
	-184 6.26 -0.530766903527 3.50383958321
	-185 6.28 -0.599126131804 3.33339756513
	-186 6.3 -0.664154128804 3.17065458013
	-187 6.32 -0.726001224889 3.0152486763
	-188 6.34 -0.784810692795 2.866835881
	-189 6.36 -0.840719097683 2.72508925658
	-190 6.38 -0.893856628836 2.58969800863
	-191 6.4 -0.944347414023 2.46036664323
	-192 6.42 -0.992309817464 2.33681417085
	-193 6.44 -1.03785672233 2.21877335375
	-194 6.46 -1.08109579859 2.10598999469
	-195 6.48 -1.12212975704 1.99822226439
	-196 6.5 -1.16105659023 1.8952400656
	-197 6.52 -1.19796980108 1.79682443166
	-198 6.54 -1.23295861967 1.70276695755
	-199 6.56 -1.26610820912 1.61286926168
	-200 6.58 -1.29749986087 1.52694247655
	-201 6.6 -1.32721118011 1.44480676668
	-202 6.62 -1.35531626183 1.36629087245
	-203 6.64 -1.38188585796 1.29123167801
	-204 6.66 -1.40698753611 1.21947380239
	-205 6.68 -1.43068583041 1.15086921208
	-206 6.7 -1.45304238467 1.08527685416
	-207 6.72 -1.47411608859 1.02256230873
	-208 6.74 -1.493963207 0.962597459596
	-209 6.76 -1.51263750285 0.90526018218
	-210 6.78 -1.53019035404 0.850434047748
	-211 6.8 -1.54667086448 0.798008043011
	-212 6.82 -1.56212596978 0.747876304295
	-213 6.84 -1.57660053762 0.699937865467
	-214 6.86 -1.59013746336 0.654096418865
	-215 6.88 -1.60277776088 0.610260088543
	-216 6.9 -1.61456064906 0.568341215144
	-217 6.92 -1.62552363404 0.528256151786
	-218 6.94 -1.63570258753 0.489925070364
	-219 6.96 -1.64513182134 0.453271777711
	-220 6.98 -1.65384415828 0.418223541087
	-221 7.0 -1.66187099974 0.384710922497
	-222 7.02 -1.66924238997 0.352667621378
	-223 7.04 -1.67598707733 0.322030325194
	-224 7.06 -1.68213257263 0.292738567537
	-225 7.08 -1.68770520468 0.264734593325
	-226 7.1 -1.69273017323 0.237963230734
	-227 7.12 -1.6972315994 0.2123717695
	-228 7.14 -1.70123257376 0.187909845266
	-229 7.16 -1.70475520212 0.16452932965
	-230 7.18 -1.70782064924 0.142184225751
	-231 7.2 -1.71044918037 0.120830568787
	-232 7.22 -1.71266020104 0.100426331626
	-233 7.24 -1.71447229485 0.0809313349308
	-234 7.26 -1.71590325956 0.0623071617066
	-235 7.28 -1.71697014154 0.044517076001
	-236 7.3 -1.71768926862 0.0275259455594
	-237 7.32 -1.71807628139 0.0113001682279
	-238 7.34 -1.71814616312 -0.00419239808778
	-239 7.36 -1.71791326826 -0.0189825020854
	-240 7.38 -1.71739134971 -0.0330995625254
	-241 7.4 -1.71659358478 -0.0465717286462
	-242 7.42 -1.71553260002 -0.0594259376903
	-243 7.44 -1.71422049488 -0.0716879696855
	-244 7.46 -1.71266886435 -0.0833824996199
	-245 7.48 -1.71088882055 -0.0945331471409
	-246 7.5 -1.70889101338 -0.105162523901
	-247 7.52 -1.7066856502 -0.115292278666
	-248 7.54 -1.70428251466 -0.124943140307
	-249 7.56 -1.70169098469 -0.13413495876
	-250 7.58 -1.69892004969 -0.142886744076
	-251 7.6 -1.69597832693 -0.151216703644
	-252 7.62 -1.69287407728 -0.159142277674
	-253 7.64 -1.68961522019 -0.166680173038
	-254 7.66 -1.68620934803 -0.173846395532
	-255 7.68 -1.68266373981 -0.180656280652
	-256 7.7 -1.67898537429 -0.187124522948
	-257 7.72 -1.67518094251 -0.193265204023
	-258 7.74 -1.67125685978 -0.199091819249
	-259 7.76 -1.66721927716 -0.204617303261
	-260 7.78 -1.66307409242 -0.20985405428
	-261 7.8 -1.65882696053 -0.214813957332
	-262 7.82 -1.65448330371 -0.21950840641
	-263 7.84 -1.65004832104 -0.223948325627
	-264 7.86 -1.64552699763 -0.228144189416
	-265 7.88 -1.64092411345 -0.232106041819
	-266 7.9 -1.63624425173 -0.235843514899
	-267 7.92 -1.63149180705 -0.239365846333
	-268 7.94 -1.62667099301 -0.242681896213
	-269 7.96 -1.62178584967 -0.245800163096
	-270 7.98 -1.61684025061 -0.248728799339
	-271 8.0 -1.61183790969 -0.251475625745
	-272 8.02 -1.60678238756 -0.254048145572
	-273 8.04 -1.60167709786 -0.256453557906
	-274 8.06 -1.59652531318 -0.258698770453
	-275 8.08 -1.59133017079 -0.260790411767
	-276 8.1 -1.58609467805 -0.262734842931
	-277 8.12 -1.58082171772 -0.264538168734
	-278 8.14 -1.57551405289 -0.26620624836
	-279 8.16 -1.57017433188 -0.267744705599
	-280 8.18 -1.56480509278 -0.269158938625
	-281 8.2 -1.55940876791 -0.270454129338
	-282 8.22 -1.55398768802 -0.271635252315
	-283 8.24 -1.54854408639 -0.272707083354
	-284 8.26 -1.54308010269 -0.273674207668
	-285 8.28 -1.53759778673 -0.274541027712
	-286 8.3 -1.53209910206 -0.275311770682
	-287 8.32 -1.52658592932 -0.275990495686
	-288 8.34 -1.52106006966 -0.276581100614
	-289 8.36 -1.51552324778 -0.277087328708
	-290 8.38 -1.50997711503 -0.277512774857
	-291 8.4 -1.50442325228 -0.277860891625
	-292 8.42 -1.49886317276 -0.278134995017
	-293 8.44 -1.49329832464 -0.278338270004
	-294 8.46 -1.48773009372 -0.27847377582
	-295 8.48 -1.48215980579 -0.278544451025
	-296 8.5 -1.47658872904 -0.278553118366
	-297 8.52 -1.47101807634 -0.278502489422
	-298 8.54 -1.46544900739 -0.27839516907
	-299 8.56 -1.45988263082 -0.278233659745
	-300 8.58 -1.45432000621 -0.27802036554
	-301 8.6 -1.44876214601 -0.277757596126
	-302 8.62 -1.44321001738 -0.277447570509
	-303 8.64 -1.437664544 -0.277092420635
	-304 8.66 -1.43212660771 -0.276694194842
	-305 8.68 -1.42659705024 -0.276254861174
	-306 8.7 -1.4210766747 -0.275776310556
	-307 8.72 -1.41556624714 -0.275260359835
	-308 8.74 -1.41006649798 -0.274708754702
	-309 8.76 -1.40457812345 -0.274123172492
	-310 8.78 -1.39910178684 -0.273505224869
	-311 8.8 -1.39363811988 -0.272856460401
	-312 8.82 -1.38818772394 -0.272178367032
	-313 8.84 -1.38275117119 -0.271472374453
	-314 8.86 -1.37732900578 -0.270739856375
	-315 8.88 -1.37192174496 -0.269982132713
	-316 8.9 -1.36652988005 -0.269200471678
	-317 8.92 -1.36115387754 -0.26839609179
	-318 8.94 -1.35579418002 -0.267570163805
	-319 8.96 -1.35045120713 -0.266723812565
	-320 8.98 -1.34512535646 -0.26585811878
	-321 9.0 -1.3398170044 -0.264974120729
	-322 9.02 -1.334526507 -0.2640728159
	-323 9.04 -1.32925420074 -0.263155162565
	-324 9.06 -1.32400040334 -0.262222081284
	-325 9.08 -1.31876541444 -0.261274456364
	-326 9.1 -1.31354951637 -0.260313137244
	-327 9.12 -1.3083529748 -0.259338939836
	-328 9.14 -1.3031760394 -0.258352647809
	-329 9.16 -1.2980189445 -0.257355013824
	-330 9.18 -1.29288190964 -0.256346760718
	-331 9.2 -1.28776514023 -0.255328582644
	-332 9.22 -1.28266882805 -0.254301146164
	-333 9.24 -1.27759315183 -0.253265091305
	-334 9.26 -1.27253827775 -0.252221032561
	-335 9.28 -1.26750435995 -0.251169559871
	-336 9.3 -1.262491541 -0.25011123955
	-337 9.32 -1.25749995239 -0.249046615186
	-338 9.34 -1.25252971494 -0.2479762085
	-339 9.36 -1.24758093926 -0.246900520178
	-340 9.38 -1.24265372614 -0.245820030663
	-341 9.4 -1.23774816696 -0.244735200927
	-342 9.42 -1.23286434408 -0.243646473201
	-343 9.44 -1.22800233119 -0.242554271687
	-344 9.46 -1.22316219366 -0.241459003238
	-345 9.48 -1.2183439889 -0.240361058009
	-346 9.5 -1.21354776668 -0.239260810093
	-347 9.52 -1.20877356945 -0.238158618121
	-348 9.54 -1.20402143262 -0.237054825845
	-349 9.56 -1.19929138489 -0.235949762702
	-350 9.58 -1.19458344848 -0.234843744346
	-351 9.6 -1.18989763946 -0.233737073173
	-352 9.62 -1.18523396797 -0.232630038816
	-353 9.64 -1.18059243848 -0.231522918625
	-354 9.66 -1.17597305003 -0.230415978128
	-355 9.68 -1.17137579646 -0.229309471477
	-356 9.7 -1.16680066665 -0.228203641873
	-357 9.72 -1.16224764472 -0.22709872198
	-358 9.74 -1.15771671022 -0.225994934317
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	-1000 22.58 -0.0 -0.0
	-1001 22.6 -0.0 -0.0
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.min b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.min
	deleted file mode 100644
	index aaf17a456..000000000
	--- a/tools/moltemplate/examples/CG_membrane_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.npt
	deleted file mode 100644
	index b309e3fb8..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.npt
	+++ /dev/null
	@@ -1,56 +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 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
	-
	-# 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_restart system_after_npt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.nvt
	deleted file mode 100644
	index 54c14b7ce..000000000
	--- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.nvt
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-# -- Init Section --
	-
	-include system.in.init
	-
	-# -- Atom Definition Section --
	-
	-# read_data system.data #<-- commenting out
	-# Use the pressure-equilibrated restart file instead:
	-read_restart system_after_npt.rst
	-
	-
	-# -- 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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT
	deleted file mode 100644
	index c3173a1e1..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh
	deleted file mode 100755
	index 4dd3eea8f..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh
	+++ /dev/null
	@@ -1,22 +0,0 @@
	-# This is just an example.
	-#
	-# Note: The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which
	-# refer to the input scripts and data files you created earlier:
	-# 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/CG_misc/2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh
	deleted file mode 100755
	index acc5fbbaa..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/2bead_heteropolymer/README_visualise.txt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualise.txt
	deleted file mode 100644
	index 5d97ea56a..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualise.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/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg
	deleted file mode 100644
	index a57d0309c..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg
	deleted file mode 100644
	index c77d7ee9d..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index a30fdf733..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,1728 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 756 !NATOM
	- 1 1 1 1 0.000000 13.0000 0
	- 2 1 3 3 0.000000 50.0000 0
	- 3 1 1 1 0.000000 13.0000 0
	- 4 1 3 3 0.000000 50.0000 0
	- 5 1 1 1 0.000000 13.0000 0
	- 6 1 2 2 0.000000 50.0000 0
	- 7 1 1 1 0.000000 13.0000 0
	- 8 1 2 2 0.000000 50.0000 0
	- 9 1 1 1 0.000000 13.0000 0
	- 10 1 2 2 0.000000 50.0000 0
	- 11 1 1 1 0.000000 13.0000 0
	- 12 1 2 2 0.000000 50.0000 0
	- 13 1 1 1 0.000000 13.0000 0
	- 14 1 3 3 0.000000 50.0000 0
	- 15 1 1 1 0.000000 13.0000 0
	- 16 1 3 3 0.000000 50.0000 0
	- 17 1 1 1 0.000000 13.0000 0
	- 18 1 3 3 0.000000 50.0000 0
	- 19 1 1 1 0.000000 13.0000 0
	- 20 1 2 2 0.000000 50.0000 0
	- 21 1 1 1 0.000000 13.0000 0
	- 22 1 2 2 0.000000 50.0000 0
	- 23 1 1 1 0.000000 13.0000 0
	- 24 1 2 2 0.000000 50.0000 0
	- 25 1 1 1 0.000000 13.0000 0
	- 26 1 3 3 0.000000 50.0000 0
	- 27 1 1 1 0.000000 13.0000 0
	- 28 1 3 3 0.000000 50.0000 0
	- 29 2 1 1 0.000000 13.0000 0
	- 30 2 3 3 0.000000 50.0000 0
	- 31 2 1 1 0.000000 13.0000 0
	- 32 2 3 3 0.000000 50.0000 0
	- 33 2 1 1 0.000000 13.0000 0
	- 34 2 2 2 0.000000 50.0000 0
	- 35 2 1 1 0.000000 13.0000 0
	- 36 2 2 2 0.000000 50.0000 0
	- 37 2 1 1 0.000000 13.0000 0
	- 38 2 2 2 0.000000 50.0000 0
	- 39 2 1 1 0.000000 13.0000 0
	- 40 2 2 2 0.000000 50.0000 0
	- 41 2 1 1 0.000000 13.0000 0
	- 42 2 3 3 0.000000 50.0000 0
	- 43 2 1 1 0.000000 13.0000 0
	- 44 2 3 3 0.000000 50.0000 0
	- 45 2 1 1 0.000000 13.0000 0
	- 46 2 3 3 0.000000 50.0000 0
	- 47 2 1 1 0.000000 13.0000 0
	- 48 2 2 2 0.000000 50.0000 0
	- 49 2 1 1 0.000000 13.0000 0
	- 50 2 2 2 0.000000 50.0000 0
	- 51 2 1 1 0.000000 13.0000 0
	- 52 2 2 2 0.000000 50.0000 0
	- 53 2 1 1 0.000000 13.0000 0
	- 54 2 3 3 0.000000 50.0000 0
	- 55 2 1 1 0.000000 13.0000 0
	- 56 2 3 3 0.000000 50.0000 0
	- 57 3 1 1 0.000000 13.0000 0
	- 58 3 3 3 0.000000 50.0000 0
	- 59 3 1 1 0.000000 13.0000 0
	- 60 3 3 3 0.000000 50.0000 0
	- 61 3 1 1 0.000000 13.0000 0
	- 62 3 2 2 0.000000 50.0000 0
	- 63 3 1 1 0.000000 13.0000 0
	- 64 3 2 2 0.000000 50.0000 0
	- 65 3 1 1 0.000000 13.0000 0
	- 66 3 2 2 0.000000 50.0000 0
	- 67 3 1 1 0.000000 13.0000 0
	- 68 3 2 2 0.000000 50.0000 0
	- 69 3 1 1 0.000000 13.0000 0
	- 70 3 3 3 0.000000 50.0000 0
	- 71 3 1 1 0.000000 13.0000 0
	- 72 3 3 3 0.000000 50.0000 0
	- 73 3 1 1 0.000000 13.0000 0
	- 74 3 3 3 0.000000 50.0000 0
	- 75 3 1 1 0.000000 13.0000 0
	- 76 3 2 2 0.000000 50.0000 0
	- 77 3 1 1 0.000000 13.0000 0
	- 78 3 2 2 0.000000 50.0000 0
	- 79 3 1 1 0.000000 13.0000 0
	- 80 3 2 2 0.000000 50.0000 0
	- 81 3 1 1 0.000000 13.0000 0
	- 82 3 3 3 0.000000 50.0000 0
	- 83 3 1 1 0.000000 13.0000 0
	- 84 3 3 3 0.000000 50.0000 0
	- 85 4 1 1 0.000000 13.0000 0
	- 86 4 3 3 0.000000 50.0000 0
	- 87 4 1 1 0.000000 13.0000 0
	- 88 4 3 3 0.000000 50.0000 0
	- 89 4 1 1 0.000000 13.0000 0
	- 90 4 2 2 0.000000 50.0000 0
	- 91 4 1 1 0.000000 13.0000 0
	- 92 4 2 2 0.000000 50.0000 0
	- 93 4 1 1 0.000000 13.0000 0
	- 94 4 2 2 0.000000 50.0000 0
	- 95 4 1 1 0.000000 13.0000 0
	- 96 4 2 2 0.000000 50.0000 0
	- 97 4 1 1 0.000000 13.0000 0
	- 98 4 3 3 0.000000 50.0000 0
	- 99 4 1 1 0.000000 13.0000 0
	- 100 4 3 3 0.000000 50.0000 0
	- 101 4 1 1 0.000000 13.0000 0
	- 102 4 3 3 0.000000 50.0000 0
	- 103 4 1 1 0.000000 13.0000 0
	- 104 4 2 2 0.000000 50.0000 0
	- 105 4 1 1 0.000000 13.0000 0
	- 106 4 2 2 0.000000 50.0000 0
	- 107 4 1 1 0.000000 13.0000 0
	- 108 4 2 2 0.000000 50.0000 0
	- 109 4 1 1 0.000000 13.0000 0
	- 110 4 3 3 0.000000 50.0000 0
	- 111 4 1 1 0.000000 13.0000 0
	- 112 4 3 3 0.000000 50.0000 0
	- 113 5 1 1 0.000000 13.0000 0
	- 114 5 3 3 0.000000 50.0000 0
	- 115 5 1 1 0.000000 13.0000 0
	- 116 5 3 3 0.000000 50.0000 0
	- 117 5 1 1 0.000000 13.0000 0
	- 118 5 2 2 0.000000 50.0000 0
	- 119 5 1 1 0.000000 13.0000 0
	- 120 5 2 2 0.000000 50.0000 0
	- 121 5 1 1 0.000000 13.0000 0
	- 122 5 2 2 0.000000 50.0000 0
	- 123 5 1 1 0.000000 13.0000 0
	- 124 5 2 2 0.000000 50.0000 0
	- 125 5 1 1 0.000000 13.0000 0
	- 126 5 3 3 0.000000 50.0000 0
	- 127 5 1 1 0.000000 13.0000 0
	- 128 5 3 3 0.000000 50.0000 0
	- 129 5 1 1 0.000000 13.0000 0
	- 130 5 3 3 0.000000 50.0000 0
	- 131 5 1 1 0.000000 13.0000 0
	- 132 5 2 2 0.000000 50.0000 0
	- 133 5 1 1 0.000000 13.0000 0
	- 134 5 2 2 0.000000 50.0000 0
	- 135 5 1 1 0.000000 13.0000 0
	- 136 5 2 2 0.000000 50.0000 0
	- 137 5 1 1 0.000000 13.0000 0
	- 138 5 3 3 0.000000 50.0000 0
	- 139 5 1 1 0.000000 13.0000 0
	- 140 5 3 3 0.000000 50.0000 0
	- 141 6 1 1 0.000000 13.0000 0
	- 142 6 3 3 0.000000 50.0000 0
	- 143 6 1 1 0.000000 13.0000 0
	- 144 6 3 3 0.000000 50.0000 0
	- 145 6 1 1 0.000000 13.0000 0
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	- 165 6 1 1 0.000000 13.0000 0
	- 166 6 3 3 0.000000 50.0000 0
	- 167 6 1 1 0.000000 13.0000 0
	- 168 6 3 3 0.000000 50.0000 0
	- 169 7 1 1 0.000000 13.0000 0
	- 170 7 3 3 0.000000 50.0000 0
	- 171 7 1 1 0.000000 13.0000 0
	- 172 7 3 3 0.000000 50.0000 0
	- 173 7 1 1 0.000000 13.0000 0
	- 174 7 2 2 0.000000 50.0000 0
	- 175 7 1 1 0.000000 13.0000 0
	- 176 7 2 2 0.000000 50.0000 0
	- 177 7 1 1 0.000000 13.0000 0
	- 178 7 2 2 0.000000 50.0000 0
	- 179 7 1 1 0.000000 13.0000 0
	- 180 7 2 2 0.000000 50.0000 0
	- 181 7 1 1 0.000000 13.0000 0
	- 182 7 3 3 0.000000 50.0000 0
	- 183 7 1 1 0.000000 13.0000 0
	- 184 7 3 3 0.000000 50.0000 0
	- 185 7 1 1 0.000000 13.0000 0
	- 186 7 3 3 0.000000 50.0000 0
	- 187 7 1 1 0.000000 13.0000 0
	- 188 7 2 2 0.000000 50.0000 0
	- 189 7 1 1 0.000000 13.0000 0
	- 190 7 2 2 0.000000 50.0000 0
	- 191 7 1 1 0.000000 13.0000 0
	- 192 7 2 2 0.000000 50.0000 0
	- 193 7 1 1 0.000000 13.0000 0
	- 194 7 3 3 0.000000 50.0000 0
	- 195 7 1 1 0.000000 13.0000 0
	- 196 7 3 3 0.000000 50.0000 0
	- 197 8 1 1 0.000000 13.0000 0
	- 198 8 3 3 0.000000 50.0000 0
	- 199 8 1 1 0.000000 13.0000 0
	- 200 8 3 3 0.000000 50.0000 0
	- 201 8 1 1 0.000000 13.0000 0
	- 202 8 2 2 0.000000 50.0000 0
	- 203 8 1 1 0.000000 13.0000 0
	- 204 8 2 2 0.000000 50.0000 0
	- 205 8 1 1 0.000000 13.0000 0
	- 206 8 2 2 0.000000 50.0000 0
	- 207 8 1 1 0.000000 13.0000 0
	- 208 8 2 2 0.000000 50.0000 0
	- 209 8 1 1 0.000000 13.0000 0
	- 210 8 3 3 0.000000 50.0000 0
	- 211 8 1 1 0.000000 13.0000 0
	- 212 8 3 3 0.000000 50.0000 0
	- 213 8 1 1 0.000000 13.0000 0
	- 214 8 3 3 0.000000 50.0000 0
	- 215 8 1 1 0.000000 13.0000 0
	- 216 8 2 2 0.000000 50.0000 0
	- 217 8 1 1 0.000000 13.0000 0
	- 218 8 2 2 0.000000 50.0000 0
	- 219 8 1 1 0.000000 13.0000 0
	- 220 8 2 2 0.000000 50.0000 0
	- 221 8 1 1 0.000000 13.0000 0
	- 222 8 3 3 0.000000 50.0000 0
	- 223 8 1 1 0.000000 13.0000 0
	- 224 8 3 3 0.000000 50.0000 0
	- 225 9 1 1 0.000000 13.0000 0
	- 226 9 3 3 0.000000 50.0000 0
	- 227 9 1 1 0.000000 13.0000 0
	- 228 9 3 3 0.000000 50.0000 0
	- 229 9 1 1 0.000000 13.0000 0
	- 230 9 2 2 0.000000 50.0000 0
	- 231 9 1 1 0.000000 13.0000 0
	- 232 9 2 2 0.000000 50.0000 0
	- 233 9 1 1 0.000000 13.0000 0
	- 234 9 2 2 0.000000 50.0000 0
	- 235 9 1 1 0.000000 13.0000 0
	- 236 9 2 2 0.000000 50.0000 0
	- 237 9 1 1 0.000000 13.0000 0
	- 238 9 3 3 0.000000 50.0000 0
	- 239 9 1 1 0.000000 13.0000 0
	- 240 9 3 3 0.000000 50.0000 0
	- 241 9 1 1 0.000000 13.0000 0
	- 242 9 3 3 0.000000 50.0000 0
	- 243 9 1 1 0.000000 13.0000 0
	- 244 9 2 2 0.000000 50.0000 0
	- 245 9 1 1 0.000000 13.0000 0
	- 246 9 2 2 0.000000 50.0000 0
	- 247 9 1 1 0.000000 13.0000 0
	- 248 9 2 2 0.000000 50.0000 0
	- 249 9 1 1 0.000000 13.0000 0
	- 250 9 3 3 0.000000 50.0000 0
	- 251 9 1 1 0.000000 13.0000 0
	- 252 9 3 3 0.000000 50.0000 0
	- 253 10 1 1 0.000000 13.0000 0
	- 254 10 3 3 0.000000 50.0000 0
	- 255 10 1 1 0.000000 13.0000 0
	- 256 10 3 3 0.000000 50.0000 0
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	-
	- 729 !NBOND: bonds
	- 1 2 1 3 3 4 3 5
	- 5 6 5 7 7 8 7 9
	- 9 10 9 11 11 12 11 13
	- 13 14 13 15 15 16 15 17
	- 17 18 17 19 19 20 19 21
	- 21 22 21 23 23 24 23 25
	- 25 26 25 27 27 28 29 30
	- 29 31 31 32 31 33 33 34
	- 33 35 35 36 35 37 37 38
	- 37 39 39 40 39 41 41 42
	- 41 43 43 44 43 45 45 46
	- 45 47 47 48 47 49 49 50
	- 49 51 51 52 51 53 53 54
	- 53 55 55 56 57 58 57 59
	- 59 60 59 61 61 62 61 63
	- 63 64 63 65 65 66 65 67
	- 67 68 67 69 69 70 69 71
	- 71 72 71 73 73 74 73 75
	- 75 76 75 77 77 78 77 79
	- 79 80 79 81 81 82 81 83
	- 83 84 85 86 85 87 87 88
	- 87 89 89 90 89 91 91 92
	- 91 93 93 94 93 95 95 96
	- 95 97 97 98 97 99 99 100
	- 99 101 101 102 101 103 103 104
	- 103 105 105 106 105 107 107 108
	- 107 109 109 110 109 111 111 112
	- 113 114 113 115 115 116 115 117
	- 117 118 117 119 119 120 119 121
	- 121 122 121 123 123 124 123 125
	- 125 126 125 127 127 128 127 129
	- 129 130 129 131 131 132 131 133
	- 133 134 133 135 135 136 135 137
	- 137 138 137 139 139 140 141 142
	- 141 143 143 144 143 145 145 146
	- 145 147 147 148 147 149 149 150
	- 149 151 151 152 151 153 153 154
	- 153 155 155 156 155 157 157 158
	- 157 159 159 160 159 161 161 162
	- 161 163 163 164 163 165 165 166
	- 165 167 167 168 169 170 169 171
	- 171 172 171 173 173 174 173 175
	- 175 176 175 177 177 178 177 179
	- 179 180 179 181 181 182 181 183
	- 183 184 183 185 185 186 185 187
	- 187 188 187 189 189 190 189 191
	- 191 192 191 193 193 194 193 195
	- 195 196 197 198 197 199 199 200
	- 199 201 201 202 201 203 203 204
	- 203 205 205 206 205 207 207 208
	- 207 209 209 210 209 211 211 212
	- 211 213 213 214 213 215 215 216
	- 215 217 217 218 217 219 219 220
	- 219 221 221 222 221 223 223 224
	- 225 226 225 227 227 228 227 229
	- 229 230 229 231 231 232 231 233
	- 233 234 233 235 235 236 235 237
	- 237 238 237 239 239 240 239 241
	- 241 242 241 243 243 244 243 245
	- 245 246 245 247 247 248 247 249
	- 249 250 249 251 251 252 253 254
	- 253 255 255 256 255 257 257 258
	- 257 259 259 260 259 261 261 262
	- 261 263 263 264 263 265 265 266
	- 265 267 267 268 267 269 269 270
	- 269 271 271 272 271 273 273 274
	- 273 275 275 276 275 277 277 278
	- 277 279 279 280 281 282 281 283
	- 283 284 283 285 285 286 285 287
	- 287 288 287 289 289 290 289 291
	- 291 292 291 293 293 294 293 295
	- 295 296 295 297 297 298 297 299
	- 299 300 299 301 301 302 301 303
	- 303 304 303 305 305 306 305 307
	- 307 308 309 310 309 311 311 312
	- 311 313 313 314 313 315 315 316
	- 315 317 317 318 317 319 319 320
	- 319 321 321 322 321 323 323 324
	- 323 325 325 326 325 327 327 328
	- 327 329 329 330 329 331 331 332
	- 331 333 333 334 333 335 335 336
	- 337 338 337 339 339 340 339 341
	- 341 342 341 343 343 344 343 345
	- 345 346 345 347 347 348 347 349
	- 349 350 349 351 351 352 351 353
	- 353 354 353 355 355 356 355 357
	- 357 358 357 359 359 360 359 361
	- 361 362 361 363 363 364 365 366
	- 365 367 367 368 367 369 369 370
	- 369 371 371 372 371 373 373 374
	- 373 375 375 376 375 377 377 378
	- 377 379 379 380 379 381 381 382
	- 381 383 383 384 383 385 385 386
	- 385 387 387 388 387 389 389 390
	- 389 391 391 392 393 394 393 395
	- 395 396 395 397 397 398 397 399
	- 399 400 399 401 401 402 401 403
	- 403 404 403 405 405 406 405 407
	- 407 408 407 409 409 410 409 411
	- 411 412 411 413 413 414 413 415
	- 415 416 415 417 417 418 417 419
	- 419 420 421 422 421 423 423 424
	- 423 425 425 426 425 427 427 428
	- 427 429 429 430 429 431 431 432
	- 431 433 433 434 433 435 435 436
	- 435 437 437 438 437 439 439 440
	- 439 441 441 442 441 443 443 444
	- 443 445 445 446 445 447 447 448
	- 449 450 449 451 451 452 451 453
	- 453 454 453 455 455 456 455 457
	- 457 458 457 459 459 460 459 461
	- 461 462 461 463 463 464 463 465
	- 465 466 465 467 467 468 467 469
	- 469 470 469 471 471 472 471 473
	- 473 474 473 475 475 476 477 478
	- 477 479 479 480 479 481 481 482
	- 481 483 483 484 483 485 485 486
	- 485 487 487 488 487 489 489 490
	- 489 491 491 492 491 493 493 494
	- 493 495 495 496 495 497 497 498
	- 497 499 499 500 499 501 501 502
	- 501 503 503 504 505 506 505 507
	- 507 508 507 509 509 510 509 511
	- 511 512 511 513 513 514 513 515
	- 515 516 515 517 517 518 517 519
	- 519 520 519 521 521 522 521 523
	- 523 524 523 525 525 526 525 527
	- 527 528 527 529 529 530 529 531
	- 531 532 533 534 533 535 535 536
	- 535 537 537 538 537 539 539 540
	- 539 541 541 542 541 543 543 544
	- 543 545 545 546 545 547 547 548
	- 547 549 549 550 549 551 551 552
	- 551 553 553 554 553 555 555 556
	- 555 557 557 558 557 559 559 560
	- 561 562 561 563 563 564 563 565
	- 565 566 565 567 567 568 567 569
	- 569 570 569 571 571 572 571 573
	- 573 574 573 575 575 576 575 577
	- 577 578 577 579 579 580 579 581
	- 581 582 581 583 583 584 583 585
	- 585 586 585 587 587 588 589 590
	- 589 591 591 592 591 593 593 594
	- 593 595 595 596 595 597 597 598
	- 597 599 599 600 599 601 601 602
	- 601 603 603 604 603 605 605 606
	- 605 607 607 608 607 609 609 610
	- 609 611 611 612 611 613 613 614
	- 613 615 615 616 617 618 617 619
	- 619 620 619 621 621 622 621 623
	- 623 624 623 625 625 626 625 627
	- 627 628 627 629 629 630 629 631
	- 631 632 631 633 633 634 633 635
	- 635 636 635 637 637 638 637 639
	- 639 640 639 641 641 642 641 643
	- 643 644 645 646 645 647 647 648
	- 647 649 649 650 649 651 651 652
	- 651 653 653 654 653 655 655 656
	- 655 657 657 658 657 659 659 660
	- 659 661 661 662 661 663 663 664
	- 663 665 665 666 665 667 667 668
	- 667 669 669 670 669 671 671 672
	- 673 674 673 675 675 676 675 677
	- 677 678 677 679 679 680 679 681
	- 681 682 681 683 683 684 683 685
	- 685 686 685 687 687 688 687 689
	- 689 690 689 691 691 692 691 693
	- 693 694 693 695 695 696 695 697
	- 697 698 697 699 699 700 701 702
	- 701 703 703 704 703 705 705 706
	- 705 707 707 708 707 709 709 710
	- 709 711 711 712 711 713 713 714
	- 713 715 715 716 715 717 717 718
	- 717 719 719 720 719 721 721 722
	- 721 723 723 724 723 725 725 726
	- 725 727 727 728 729 730 729 731
	- 731 732 731 733 733 734 733 735
	- 735 736 735 737 737 738 737 739
	- 739 740 739 741 741 742 741 743
	- 743 744 743 745 745 746 745 747
	- 747 748 747 749 749 750 749 751
	- 751 752 751 753 753 754 753 755
	- 755 756
	-
	- 1026 !NTHETA: angles
	- 1 3 5 3 5 7 5 7 9
	- 7 9 11 9 11 13 11 13 15
	- 13 15 17 15 17 19 17 19 21
	- 19 21 23 21 23 25 23 25 27
	- 29 31 33 31 33 35 33 35 37
	- 35 37 39 37 39 41 39 41 43
	- 41 43 45 43 45 47 45 47 49
	- 47 49 51 49 51 53 51 53 55
	- 57 59 61 59 61 63 61 63 65
	- 63 65 67 65 67 69 67 69 71
	- 69 71 73 71 73 75 73 75 77
	- 75 77 79 77 79 81 79 81 83
	- 85 87 89 87 89 91 89 91 93
	- 91 93 95 93 95 97 95 97 99
	- 97 99 101 99 101 103 101 103 105
	- 103 105 107 105 107 109 107 109 111
	- 113 115 117 115 117 119 117 119 121
	- 119 121 123 121 123 125 123 125 127
	- 125 127 129 127 129 131 129 131 133
	- 131 133 135 133 135 137 135 137 139
	- 141 143 145 143 145 147 145 147 149
	- 147 149 151 149 151 153 151 153 155
	- 153 155 157 155 157 159 157 159 161
	- 159 161 163 161 163 165 163 165 167
	- 169 171 173 171 173 175 173 175 177
	- 175 177 179 177 179 181 179 181 183
	- 181 183 185 183 185 187 185 187 189
	- 187 189 191 189 191 193 191 193 195
	- 197 199 201 199 201 203 201 203 205
	- 203 205 207 205 207 209 207 209 211
	- 209 211 213 211 213 215 213 215 217
	- 215 217 219 217 219 221 219 221 223
	- 225 227 229 227 229 231 229 231 233
	- 231 233 235 233 235 237 235 237 239
	- 237 239 241 239 241 243 241 243 245
	- 243 245 247 245 247 249 247 249 251
	- 253 255 257 255 257 259 257 259 261
	- 259 261 263 261 263 265 263 265 267
	- 265 267 269 267 269 271 269 271 273
	- 271 273 275 273 275 277 275 277 279
	- 281 283 285 283 285 287 285 287 289
	- 287 289 291 289 291 293 291 293 295
	- 293 295 297 295 297 299 297 299 301
	- 299 301 303 301 303 305 303 305 307
	- 309 311 313 311 313 315 313 315 317
	- 315 317 319 317 319 321 319 321 323
	- 321 323 325 323 325 327 325 327 329
	- 327 329 331 329 331 333 331 333 335
	- 337 339 341 339 341 343 341 343 345
	- 343 345 347 345 347 349 347 349 351
	- 349 351 353 351 353 355 353 355 357
	- 355 357 359 357 359 361 359 361 363
	- 365 367 369 367 369 371 369 371 373
	- 371 373 375 373 375 377 375 377 379
	- 377 379 381 379 381 383 381 383 385
	- 383 385 387 385 387 389 387 389 391
	- 393 395 397 395 397 399 397 399 401
	- 399 401 403 401 403 405 403 405 407
	- 405 407 409 407 409 411 409 411 413
	- 411 413 415 413 415 417 415 417 419
	- 421 423 425 423 425 427 425 427 429
	- 427 429 431 429 431 433 431 433 435
	- 433 435 437 435 437 439 437 439 441
	- 439 441 443 441 443 445 443 445 447
	- 449 451 453 451 453 455 453 455 457
	- 455 457 459 457 459 461 459 461 463
	- 461 463 465 463 465 467 465 467 469
	- 467 469 471 469 471 473 471 473 475
	- 477 479 481 479 481 483 481 483 485
	- 483 485 487 485 487 489 487 489 491
	- 489 491 493 491 493 495 493 495 497
	- 495 497 499 497 499 501 499 501 503
	- 505 507 509 507 509 511 509 511 513
	- 511 513 515 513 515 517 515 517 519
	- 517 519 521 519 521 523 521 523 525
	- 523 525 527 525 527 529 527 529 531
	- 533 535 537 535 537 539 537 539 541
	- 539 541 543 541 543 545 543 545 547
	- 545 547 549 547 549 551 549 551 553
	- 551 553 555 553 555 557 555 557 559
	- 561 563 565 563 565 567 565 567 569
	- 567 569 571 569 571 573 571 573 575
	- 573 575 577 575 577 579 577 579 581
	- 579 581 583 581 583 585 583 585 587
	- 589 591 593 591 593 595 593 595 597
	- 595 597 599 597 599 601 599 601 603
	- 601 603 605 603 605 607 605 607 609
	- 607 609 611 609 611 613 611 613 615
	- 617 619 621 619 621 623 621 623 625
	- 623 625 627 625 627 629 627 629 631
	- 629 631 633 631 633 635 633 635 637
	- 635 637 639 637 639 641 639 641 643
	- 645 647 649 647 649 651 649 651 653
	- 651 653 655 653 655 657 655 657 659
	- 657 659 661 659 661 663 661 663 665
	- 663 665 667 665 667 669 667 669 671
	- 673 675 677 675 677 679 677 679 681
	- 679 681 683 681 683 685 683 685 687
	- 685 687 689 687 689 691 689 691 693
	- 691 693 695 693 695 697 695 697 699
	- 701 703 705 703 705 707 705 707 709
	- 707 709 711 709 711 713 711 713 715
	- 713 715 717 715 717 719 717 719 721
	- 719 721 723 721 723 725 723 725 727
	- 729 731 733 731 733 735 733 735 737
	- 735 737 739 737 739 741 739 741 743
	- 741 743 745 743 745 747 745 747 749
	- 747 749 751 749 751 753 751 753 755
	- 1 3 4 2 1 3 4 3 5
	- 11 13 14 13 15 16 14 13 15
	- 15 17 18 16 15 17 18 17 19
	- 23 25 26 25 27 28 26 25 27
	- 29 31 32 30 29 31 32 31 33
	- 39 41 42 41 43 44 42 41 43
	- 43 45 46 44 43 45 46 45 47
	- 51 53 54 53 55 56 54 53 55
	- 57 59 60 58 57 59 60 59 61
	- 67 69 70 69 71 72 70 69 71
	- 71 73 74 72 71 73 74 73 75
	- 79 81 82 81 83 84 82 81 83
	- 85 87 88 86 85 87 88 87 89
	- 95 97 98 97 99 100 98 97 99
	- 99 101 102 100 99 101 102 101 103
	- 107 109 110 109 111 112 110 109 111
	- 113 115 116 114 113 115 116 115 117
	- 123 125 126 125 127 128 126 125 127
	- 127 129 130 128 127 129 130 129 131
	- 135 137 138 137 139 140 138 137 139
	- 141 143 144 142 141 143 144 143 145
	- 151 153 154 153 155 156 154 153 155
	- 155 157 158 156 155 157 158 157 159
	- 163 165 166 165 167 168 166 165 167
	- 169 171 172 170 169 171 172 171 173
	- 179 181 182 181 183 184 182 181 183
	- 183 185 186 184 183 185 186 185 187
	- 191 193 194 193 195 196 194 193 195
	- 197 199 200 198 197 199 200 199 201
	- 207 209 210 209 211 212 210 209 211
	- 211 213 214 212 211 213 214 213 215
	- 219 221 222 221 223 224 222 221 223
	- 225 227 228 226 225 227 228 227 229
	- 235 237 238 237 239 240 238 237 239
	- 239 241 242 240 239 241 242 241 243
	- 247 249 250 249 251 252 250 249 251
	- 253 255 256 254 253 255 256 255 257
	- 263 265 266 265 267 268 266 265 267
	- 267 269 270 268 267 269 270 269 271
	- 275 277 278 277 279 280 278 277 279
	- 281 283 284 282 281 283 284 283 285
	- 291 293 294 293 295 296 294 293 295
	- 295 297 298 296 295 297 298 297 299
	- 303 305 306 305 307 308 306 305 307
	- 309 311 312 310 309 311 312 311 313
	- 319 321 322 321 323 324 322 321 323
	- 323 325 326 324 323 325 326 325 327
	- 331 333 334 333 335 336 334 333 335
	- 337 339 340 338 337 339 340 339 341
	- 347 349 350 349 351 352 350 349 351
	- 351 353 354 352 351 353 354 353 355
	- 359 361 362 361 363 364 362 361 363
	- 365 367 368 366 365 367 368 367 369
	- 375 377 378 377 379 380 378 377 379
	- 379 381 382 380 379 381 382 381 383
	- 387 389 390 389 391 392 390 389 391
	- 393 395 396 394 393 395 396 395 397
	- 403 405 406 405 407 408 406 405 407
	- 407 409 410 408 407 409 410 409 411
	- 415 417 418 417 419 420 418 417 419
	- 421 423 424 422 421 423 424 423 425
	- 431 433 434 433 435 436 434 433 435
	- 435 437 438 436 435 437 438 437 439
	- 443 445 446 445 447 448 446 445 447
	- 449 451 452 450 449 451 452 451 453
	- 459 461 462 461 463 464 462 461 463
	- 463 465 466 464 463 465 466 465 467
	- 471 473 474 473 475 476 474 473 475
	- 477 479 480 478 477 479 480 479 481
	- 487 489 490 489 491 492 490 489 491
	- 491 493 494 492 491 493 494 493 495
	- 499 501 502 501 503 504 502 501 503
	- 505 507 508 506 505 507 508 507 509
	- 515 517 518 517 519 520 518 517 519
	- 519 521 522 520 519 521 522 521 523
	- 527 529 530 529 531 532 530 529 531
	- 533 535 536 534 533 535 536 535 537
	- 543 545 546 545 547 548 546 545 547
	- 547 549 550 548 547 549 550 549 551
	- 555 557 558 557 559 560 558 557 559
	- 561 563 564 562 561 563 564 563 565
	- 571 573 574 573 575 576 574 573 575
	- 575 577 578 576 575 577 578 577 579
	- 583 585 586 585 587 588 586 585 587
	- 589 591 592 590 589 591 592 591 593
	- 599 601 602 601 603 604 602 601 603
	- 603 605 606 604 603 605 606 605 607
	- 611 613 614 613 615 616 614 613 615
	- 617 619 620 618 617 619 620 619 621
	- 627 629 630 629 631 632 630 629 631
	- 631 633 634 632 631 633 634 633 635
	- 639 641 642 641 643 644 642 641 643
	- 645 647 648 646 645 647 648 647 649
	- 655 657 658 657 659 660 658 657 659
	- 659 661 662 660 659 661 662 661 663
	- 667 669 670 669 671 672 670 669 671
	- 673 675 676 674 673 675 676 675 677
	- 683 685 686 685 687 688 686 685 687
	- 687 689 690 688 687 689 690 689 691
	- 695 697 698 697 699 700 698 697 699
	- 701 703 704 702 701 703 704 703 705
	- 711 713 714 713 715 716 714 713 715
	- 715 717 718 716 715 717 718 717 719
	- 723 725 726 725 727 728 726 725 727
	- 729 731 732 730 729 731 732 731 733
	- 739 741 742 741 743 744 742 741 743
	- 743 745 746 744 743 745 746 745 747
	- 751 753 754 753 755 756 754 753 755
	- 3 5 6 5 7 8 6 5 7
	- 7 9 10 8 7 9 9 11 12
	- 10 9 11 12 11 13 17 19 20
	- 19 21 22 20 19 21 21 23 24
	- 22 21 23 24 23 25 31 33 34
	- 33 35 36 34 33 35 35 37 38
	- 36 35 37 37 39 40 38 37 39
	- 40 39 41 45 47 48 47 49 50
	- 48 47 49 49 51 52 50 49 51
	- 52 51 53 59 61 62 61 63 64
	- 62 61 63 63 65 66 64 63 65
	- 65 67 68 66 65 67 68 67 69
	- 73 75 76 75 77 78 76 75 77
	- 77 79 80 78 77 79 80 79 81
	- 87 89 90 89 91 92 90 89 91
	- 91 93 94 92 91 93 93 95 96
	- 94 93 95 96 95 97 101 103 104
	- 103 105 106 104 103 105 105 107 108
	- 106 105 107 108 107 109 115 117 118
	- 117 119 120 118 117 119 119 121 122
	- 120 119 121 121 123 124 122 121 123
	- 124 123 125 129 131 132 131 133 134
	- 132 131 133 133 135 136 134 133 135
	- 136 135 137 143 145 146 145 147 148
	- 146 145 147 147 149 150 148 147 149
	- 149 151 152 150 149 151 152 151 153
	- 157 159 160 159 161 162 160 159 161
	- 161 163 164 162 161 163 164 163 165
	- 171 173 174 173 175 176 174 173 175
	- 175 177 178 176 175 177 177 179 180
	- 178 177 179 180 179 181 185 187 188
	- 187 189 190 188 187 189 189 191 192
	- 190 189 191 192 191 193 199 201 202
	- 201 203 204 202 201 203 203 205 206
	- 204 203 205 205 207 208 206 205 207
	- 208 207 209 213 215 216 215 217 218
	- 216 215 217 217 219 220 218 217 219
	- 220 219 221 227 229 230 229 231 232
	- 230 229 231 231 233 234 232 231 233
	- 233 235 236 234 233 235 236 235 237
	- 241 243 244 243 245 246 244 243 245
	- 245 247 248 246 245 247 248 247 249
	- 255 257 258 257 259 260 258 257 259
	- 259 261 262 260 259 261 261 263 264
	- 262 261 263 264 263 265 269 271 272
	- 271 273 274 272 271 273 273 275 276
	- 274 273 275 276 275 277 283 285 286
	- 285 287 288 286 285 287 287 289 290
	- 288 287 289 289 291 292 290 289 291
	- 292 291 293 297 299 300 299 301 302
	- 300 299 301 301 303 304 302 301 303
	- 304 303 305 311 313 314 313 315 316
	- 314 313 315 315 317 318 316 315 317
	- 317 319 320 318 317 319 320 319 321
	- 325 327 328 327 329 330 328 327 329
	- 329 331 332 330 329 331 332 331 333
	- 339 341 342 341 343 344 342 341 343
	- 343 345 346 344 343 345 345 347 348
	- 346 345 347 348 347 349 353 355 356
	- 355 357 358 356 355 357 357 359 360
	- 358 357 359 360 359 361 367 369 370
	- 369 371 372 370 369 371 371 373 374
	- 372 371 373 373 375 376 374 373 375
	- 376 375 377 381 383 384 383 385 386
	- 384 383 385 385 387 388 386 385 387
	- 388 387 389 395 397 398 397 399 400
	- 398 397 399 399 401 402 400 399 401
	- 401 403 404 402 401 403 404 403 405
	- 409 411 412 411 413 414 412 411 413
	- 413 415 416 414 413 415 416 415 417
	- 423 425 426 425 427 428 426 425 427
	- 427 429 430 428 427 429 429 431 432
	- 430 429 431 432 431 433 437 439 440
	- 439 441 442 440 439 441 441 443 444
	- 442 441 443 444 443 445 451 453 454
	- 453 455 456 454 453 455 455 457 458
	- 456 455 457 457 459 460 458 457 459
	- 460 459 461 465 467 468 467 469 470
	- 468 467 469 469 471 472 470 469 471
	- 472 471 473 479 481 482 481 483 484
	- 482 481 483 483 485 486 484 483 485
	- 485 487 488 486 485 487 488 487 489
	- 493 495 496 495 497 498 496 495 497
	- 497 499 500 498 497 499 500 499 501
	- 507 509 510 509 511 512 510 509 511
	- 511 513 514 512 511 513 513 515 516
	- 514 513 515 516 515 517 521 523 524
	- 523 525 526 524 523 525 525 527 528
	- 526 525 527 528 527 529 535 537 538
	- 537 539 540 538 537 539 539 541 542
	- 540 539 541 541 543 544 542 541 543
	- 544 543 545 549 551 552 551 553 554
	- 552 551 553 553 555 556 554 553 555
	- 556 555 557 563 565 566 565 567 568
	- 566 565 567 567 569 570 568 567 569
	- 569 571 572 570 569 571 572 571 573
	- 577 579 580 579 581 582 580 579 581
	- 581 583 584 582 581 583 584 583 585
	- 591 593 594 593 595 596 594 593 595
	- 595 597 598 596 595 597 597 599 600
	- 598 597 599 600 599 601 605 607 608
	- 607 609 610 608 607 609 609 611 612
	- 610 609 611 612 611 613 619 621 622
	- 621 623 624 622 621 623 623 625 626
	- 624 623 625 625 627 628 626 625 627
	- 628 627 629 633 635 636 635 637 638
	- 636 635 637 637 639 640 638 637 639
	- 640 639 641 647 649 650 649 651 652
	- 650 649 651 651 653 654 652 651 653
	- 653 655 656 654 653 655 656 655 657
	- 661 663 664 663 665 666 664 663 665
	- 665 667 668 666 665 667 668 667 669
	- 675 677 678 677 679 680 678 677 679
	- 679 681 682 680 679 681 681 683 684
	- 682 681 683 684 683 685 689 691 692
	- 691 693 694 692 691 693 693 695 696
	- 694 693 695 696 695 697 703 705 706
	- 705 707 708 706 705 707 707 709 710
	- 708 707 709 709 711 712 710 709 711
	- 712 711 713 717 719 720 719 721 722
	- 720 719 721 721 723 724 722 721 723
	- 724 723 725 731 733 734 733 735 736
	- 734 733 735 735 737 738 736 735 737
	- 737 739 740 738 737 739 740 739 741
	- 745 747 748 747 749 750 748 747 749
	- 749 751 752 750 749 751 752 751 753
	-
	- 648 !NPHI: dihedrals
	- 1 3 5 7 3 5 7 9
	- 5 7 9 11 7 9 11 13
	- 9 11 13 15 11 13 15 17
	- 13 15 17 19 15 17 19 21
	- 17 19 21 23 19 21 23 25
	- 21 23 25 27 29 31 33 35
	- 31 33 35 37 33 35 37 39
	- 35 37 39 41 37 39 41 43
	- 39 41 43 45 41 43 45 47
	- 43 45 47 49 45 47 49 51
	- 47 49 51 53 49 51 53 55
	- 57 59 61 63 59 61 63 65
	- 61 63 65 67 63 65 67 69
	- 65 67 69 71 67 69 71 73
	- 69 71 73 75 71 73 75 77
	- 73 75 77 79 75 77 79 81
	- 77 79 81 83 85 87 89 91
	- 87 89 91 93 89 91 93 95
	- 91 93 95 97 93 95 97 99
	- 95 97 99 101 97 99 101 103
	- 99 101 103 105 101 103 105 107
	- 103 105 107 109 105 107 109 111
	- 113 115 117 119 115 117 119 121
	- 117 119 121 123 119 121 123 125
	- 121 123 125 127 123 125 127 129
	- 125 127 129 131 127 129 131 133
	- 129 131 133 135 131 133 135 137
	- 133 135 137 139 141 143 145 147
	- 143 145 147 149 145 147 149 151
	- 147 149 151 153 149 151 153 155
	- 151 153 155 157 153 155 157 159
	- 155 157 159 161 157 159 161 163
	- 159 161 163 165 161 163 165 167
	- 169 171 173 175 171 173 175 177
	- 173 175 177 179 175 177 179 181
	- 177 179 181 183 179 181 183 185
	- 181 183 185 187 183 185 187 189
	- 185 187 189 191 187 189 191 193
	- 189 191 193 195 197 199 201 203
	- 199 201 203 205 201 203 205 207
	- 203 205 207 209 205 207 209 211
	- 207 209 211 213 209 211 213 215
	- 211 213 215 217 213 215 217 219
	- 215 217 219 221 217 219 221 223
	- 225 227 229 231 227 229 231 233
	- 229 231 233 235 231 233 235 237
	- 233 235 237 239 235 237 239 241
	- 237 239 241 243 239 241 243 245
	- 241 243 245 247 243 245 247 249
	- 245 247 249 251 253 255 257 259
	- 255 257 259 261 257 259 261 263
	- 259 261 263 265 261 263 265 267
	- 263 265 267 269 265 267 269 271
	- 267 269 271 273 269 271 273 275
	- 271 273 275 277 273 275 277 279
	- 281 283 285 287 283 285 287 289
	- 285 287 289 291 287 289 291 293
	- 289 291 293 295 291 293 295 297
	- 293 295 297 299 295 297 299 301
	- 297 299 301 303 299 301 303 305
	- 301 303 305 307 309 311 313 315
	- 311 313 315 317 313 315 317 319
	- 315 317 319 321 317 319 321 323
	- 319 321 323 325 321 323 325 327
	- 323 325 327 329 325 327 329 331
	- 327 329 331 333 329 331 333 335
	- 337 339 341 343 339 341 343 345
	- 341 343 345 347 343 345 347 349
	- 345 347 349 351 347 349 351 353
	- 349 351 353 355 351 353 355 357
	- 353 355 357 359 355 357 359 361
	- 357 359 361 363 365 367 369 371
	- 367 369 371 373 369 371 373 375
	- 371 373 375 377 373 375 377 379
	- 375 377 379 381 377 379 381 383
	- 379 381 383 385 381 383 385 387
	- 383 385 387 389 385 387 389 391
	- 393 395 397 399 395 397 399 401
	- 397 399 401 403 399 401 403 405
	- 401 403 405 407 403 405 407 409
	- 405 407 409 411 407 409 411 413
	- 409 411 413 415 411 413 415 417
	- 413 415 417 419 421 423 425 427
	- 423 425 427 429 425 427 429 431
	- 427 429 431 433 429 431 433 435
	- 431 433 435 437 433 435 437 439
	- 435 437 439 441 437 439 441 443
	- 439 441 443 445 441 443 445 447
	- 449 451 453 455 451 453 455 457
	- 453 455 457 459 455 457 459 461
	- 457 459 461 463 459 461 463 465
	- 461 463 465 467 463 465 467 469
	- 465 467 469 471 467 469 471 473
	- 469 471 473 475 477 479 481 483
	- 479 481 483 485 481 483 485 487
	- 483 485 487 489 485 487 489 491
	- 487 489 491 493 489 491 493 495
	- 491 493 495 497 493 495 497 499
	- 495 497 499 501 497 499 501 503
	- 505 507 509 511 507 509 511 513
	- 509 511 513 515 511 513 515 517
	- 513 515 517 519 515 517 519 521
	- 517 519 521 523 519 521 523 525
	- 521 523 525 527 523 525 527 529
	- 525 527 529 531 533 535 537 539
	- 535 537 539 541 537 539 541 543
	- 539 541 543 545 541 543 545 547
	- 543 545 547 549 545 547 549 551
	- 547 549 551 553 549 551 553 555
	- 551 553 555 557 553 555 557 559
	- 561 563 565 567 563 565 567 569
	- 565 567 569 571 567 569 571 573
	- 569 571 573 575 571 573 575 577
	- 573 575 577 579 575 577 579 581
	- 577 579 581 583 579 581 583 585
	- 581 583 585 587 589 591 593 595
	- 591 593 595 597 593 595 597 599
	- 595 597 599 601 597 599 601 603
	- 599 601 603 605 601 603 605 607
	- 603 605 607 609 605 607 609 611
	- 607 609 611 613 609 611 613 615
	- 617 619 621 623 619 621 623 625
	- 621 623 625 627 623 625 627 629
	- 625 627 629 631 627 629 631 633
	- 629 631 633 635 631 633 635 637
	- 633 635 637 639 635 637 639 641
	- 637 639 641 643 645 647 649 651
	- 647 649 651 653 649 651 653 655
	- 651 653 655 657 653 655 657 659
	- 655 657 659 661 657 659 661 663
	- 659 661 663 665 661 663 665 667
	- 663 665 667 669 665 667 669 671
	- 673 675 677 679 675 677 679 681
	- 677 679 681 683 679 681 683 685
	- 681 683 685 687 683 685 687 689
	- 685 687 689 691 687 689 691 693
	- 689 691 693 695 691 693 695 697
	- 693 695 697 699 701 703 705 707
	- 703 705 707 709 705 707 709 711
	- 707 709 711 713 709 711 713 715
	- 711 713 715 717 713 715 717 719
	- 715 717 719 721 717 719 721 723
	- 719 721 723 725 721 723 725 727
	- 729 731 733 735 731 733 735 737
	- 733 735 737 739 735 737 739 741
	- 737 739 741 743 739 741 743 745
	- 741 743 745 747 743 745 747 749
	- 745 747 749 751 747 749 751 753
	- 749 751 753 755 6 5 7 8
	- 8 7 9 10 10 9 11 12
	- 20 19 21 22 22 21 23 24
	- 34 33 35 36 36 35 37 38
	- 38 37 39 40 48 47 49 50
	- 50 49 51 52 62 61 63 64
	- 64 63 65 66 66 65 67 68
	- 76 75 77 78 78 77 79 80
	- 90 89 91 92 92 91 93 94
	- 94 93 95 96 104 103 105 106
	- 106 105 107 108 118 117 119 120
	- 120 119 121 122 122 121 123 124
	- 132 131 133 134 134 133 135 136
	- 146 145 147 148 148 147 149 150
	- 150 149 151 152 160 159 161 162
	- 162 161 163 164 174 173 175 176
	- 176 175 177 178 178 177 179 180
	- 188 187 189 190 190 189 191 192
	- 202 201 203 204 204 203 205 206
	- 206 205 207 208 216 215 217 218
	- 218 217 219 220 230 229 231 232
	- 232 231 233 234 234 233 235 236
	- 244 243 245 246 246 245 247 248
	- 258 257 259 260 260 259 261 262
	- 262 261 263 264 272 271 273 274
	- 274 273 275 276 286 285 287 288
	- 288 287 289 290 290 289 291 292
	- 300 299 301 302 302 301 303 304
	- 314 313 315 316 316 315 317 318
	- 318 317 319 320 328 327 329 330
	- 330 329 331 332 342 341 343 344
	- 344 343 345 346 346 345 347 348
	- 356 355 357 358 358 357 359 360
	- 370 369 371 372 372 371 373 374
	- 374 373 375 376 384 383 385 386
	- 386 385 387 388 398 397 399 400
	- 400 399 401 402 402 401 403 404
	- 412 411 413 414 414 413 415 416
	- 426 425 427 428 428 427 429 430
	- 430 429 431 432 440 439 441 442
	- 442 441 443 444 454 453 455 456
	- 456 455 457 458 458 457 459 460
	- 468 467 469 470 470 469 471 472
	- 482 481 483 484 484 483 485 486
	- 486 485 487 488 496 495 497 498
	- 498 497 499 500 510 509 511 512
	- 512 511 513 514 514 513 515 516
	- 524 523 525 526 526 525 527 528
	- 538 537 539 540 540 539 541 542
	- 542 541 543 544 552 551 553 554
	- 554 553 555 556 566 565 567 568
	- 568 567 569 570 570 569 571 572
	- 580 579 581 582 582 581 583 584
	- 594 593 595 596 596 595 597 598
	- 598 597 599 600 608 607 609 610
	- 610 609 611 612 622 621 623 624
	- 624 623 625 626 626 625 627 628
	- 636 635 637 638 638 637 639 640
	- 650 649 651 652 652 651 653 654
	- 654 653 655 656 664 663 665 666
	- 666 665 667 668 678 677 679 680
	- 680 679 681 682 682 681 683 684
	- 692 691 693 694 694 693 695 696
	- 706 705 707 708 708 707 709 710
	- 710 709 711 712 720 719 721 722
	- 722 721 723 724 734 733 735 736
	- 736 735 737 738 738 737 739 740
	- 748 747 749 750 750 749 751 752
	- 4 3 5 6 12 11 13 14
	- 18 17 19 20 24 23 25 26
	- 32 31 33 34 40 39 41 42
	- 46 45 47 48 52 51 53 54
	- 60 59 61 62 68 67 69 70
	- 74 73 75 76 80 79 81 82
	- 88 87 89 90 96 95 97 98
	- 102 101 103 104 108 107 109 110
	- 116 115 117 118 124 123 125 126
	- 130 129 131 132 136 135 137 138
	- 144 143 145 146 152 151 153 154
	- 158 157 159 160 164 163 165 166
	- 172 171 173 174 180 179 181 182
	- 186 185 187 188 192 191 193 194
	- 200 199 201 202 208 207 209 210
	- 214 213 215 216 220 219 221 222
	- 228 227 229 230 236 235 237 238
	- 242 241 243 244 248 247 249 250
	- 256 255 257 258 264 263 265 266
	- 270 269 271 272 276 275 277 278
	- 284 283 285 286 292 291 293 294
	- 298 297 299 300 304 303 305 306
	- 312 311 313 314 320 319 321 322
	- 326 325 327 328 332 331 333 334
	- 340 339 341 342 348 347 349 350
	- 354 353 355 356 360 359 361 362
	- 368 367 369 370 376 375 377 378
	- 382 381 383 384 388 387 389 390
	- 396 395 397 398 404 403 405 406
	- 410 409 411 412 416 415 417 418
	- 424 423 425 426 432 431 433 434
	- 438 437 439 440 444 443 445 446
	- 452 451 453 454 460 459 461 462
	- 466 465 467 468 472 471 473 474
	- 480 479 481 482 488 487 489 490
	- 494 493 495 496 500 499 501 502
	- 508 507 509 510 516 515 517 518
	- 522 521 523 524 528 527 529 530
	- 536 535 537 538 544 543 545 546
	- 550 549 551 552 556 555 557 558
	- 564 563 565 566 572 571 573 574
	- 578 577 579 580 584 583 585 586
	- 592 591 593 594 600 599 601 602
	- 606 605 607 608 612 611 613 614
	- 620 619 621 622 628 627 629 630
	- 634 633 635 636 640 639 641 642
	- 648 647 649 650 656 655 657 658
	- 662 661 663 664 668 667 669 670
	- 676 675 677 678 684 683 685 686
	- 690 689 691 692 696 695 697 698
	- 704 703 705 706 712 711 713 714
	- 718 717 719 720 724 723 725 726
	- 732 731 733 734 740 739 741 742
	- 746 745 747 748 752 751 753 754
	- 2 1 3 4 14 13 15 16
	- 16 15 17 18 26 25 27 28
	- 30 29 31 32 42 41 43 44
	- 44 43 45 46 54 53 55 56
	- 58 57 59 60 70 69 71 72
	- 72 71 73 74 82 81 83 84
	- 86 85 87 88 98 97 99 100
	- 100 99 101 102 110 109 111 112
	- 114 113 115 116 126 125 127 128
	- 128 127 129 130 138 137 139 140
	- 142 141 143 144 154 153 155 156
	- 156 155 157 158 166 165 167 168
	- 170 169 171 172 182 181 183 184
	- 184 183 185 186 194 193 195 196
	- 198 197 199 200 210 209 211 212
	- 212 211 213 214 222 221 223 224
	- 226 225 227 228 238 237 239 240
	- 240 239 241 242 250 249 251 252
	- 254 253 255 256 266 265 267 268
	- 268 267 269 270 278 277 279 280
	- 282 281 283 284 294 293 295 296
	- 296 295 297 298 306 305 307 308
	- 310 309 311 312 322 321 323 324
	- 324 323 325 326 334 333 335 336
	- 338 337 339 340 350 349 351 352
	- 352 351 353 354 362 361 363 364
	- 366 365 367 368 378 377 379 380
	- 380 379 381 382 390 389 391 392
	- 394 393 395 396 406 405 407 408
	- 408 407 409 410 418 417 419 420
	- 422 421 423 424 434 433 435 436
	- 436 435 437 438 446 445 447 448
	- 450 449 451 452 462 461 463 464
	- 464 463 465 466 474 473 475 476
	- 478 477 479 480 490 489 491 492
	- 492 491 493 494 502 501 503 504
	- 506 505 507 508 518 517 519 520
	- 520 519 521 522 530 529 531 532
	- 534 533 535 536 546 545 547 548
	- 548 547 549 550 558 557 559 560
	- 562 561 563 564 574 573 575 576
	- 576 575 577 578 586 585 587 588
	- 590 589 591 592 602 601 603 604
	- 604 603 605 606 614 613 615 616
	- 618 617 619 620 630 629 631 632
	- 632 631 633 634 642 641 643 644
	- 646 645 647 648 658 657 659 660
	- 660 659 661 662 670 669 671 672
	- 674 673 675 676 686 685 687 688
	- 688 687 689 690 698 697 699 700
	- 702 701 703 704 714 713 715 716
	- 716 715 717 718 726 725 727 728
	- 730 729 731 732 742 741 743 744
	- 744 743 745 746 754 753 755 756
	-
	- 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
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 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/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt
	deleted file mode 100644
	index eb1820ec7..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt
	+++ /dev/null
	@@ -1,173 +0,0 @@
	-# In this example, we define two types of molecules: "H" and "P",
	-# both containing two atoms, named "CA" and "R".
	-#
	-# @R
	-# \|
	-# @CA
	-#
	-# Eventually, we will connect multiple "H" and "P" molecules
	-# together to form a polymer, as shown below:
	-#
	-# @R @R
	-# \| \|
	-# _@CA_ _@CA_
	-# ... -.@CA-' `-@CA-' ` ...
	-# \| \|
	-# @R @R
	-#
	-# Suppose that the "H" and "P" molecules both use the same
	-# type of backbone atom ("CA"), but have their own custom "R"
	-# sidechain atoms with different properties:
	-# The "R" atoms belonging to "H" molecules are attracted to each other.
	-# The "R" atoms in "P" molecules are not.
	-#
	-# (Note: There is no reason the "H" and "P" molecules in this example need
	-# to contain the same number of atoms, or the same atom names.
	-# The point of this example is to illustrate how to share atom types
	-# and also the difference between local and global atom types.)
	-#
	-# By default, all counter variables are local. This means that whenever
	-# an atom type (or other counter variable) appears inside a molecule
	-# definition using the normal syntax "@atom:R", that atom type is a local
	-# property of the the "H" or "P" molecule in which it appears.
	-# Any properties assigned to the "R" atoms in either molecule are unique
	-# to that molecule.
	-#
	-# However in order to share "CA" atom types, we will override this behavior
	-# using the "@atom:../CA" syntax instead of "@atom:CA". This will define
	-# the "CA" atom in the outer (global) environment, and any properties
	-# (mass, radius, etc...) assigned to the "@atom:../CA" atom apply to
	-# "CA" atoms in both the the "H" and "P" molecules (and everywhere else).
	-#
	-# This might not be a desirable. "CA" is a popular name for carbon
	-# atoms in different types of molecules. We don't want to prevent other
	-# molecules from using this atom name. So we enclose the "CA" atom,
	-# (along with the definitions of the "H" and "P" molecules) within a
	-# namespace/environment object ("2bead"). This makes the definition
	-# of "H" and "P" more portable. Later on we can combine "H" and "P"
	-# molecules with other molecules without worrying whether they contain
	-# "CA" atoms with different properties.
	-#
	-# Note: In this example "2bead" is NOT a molecule. (Because it contains no
	-# "write("Data Atoms")" section of its own.) "2bead" is simply the
	-# name of an environment in which other molecules (H,P) are defined.
	-
	-
	-
	-
	-2bead {
	-
	- # 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" --
	- units real
	- 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/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
	- }
	-
	-
	- # Define H (the "hydrophobic" residue)
	- H {
	- # atom-id 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:R 0.0 0.000 4.4000 0.0000000
	- }
	- write("Data Bonds") {
	- $bond:CR @bond:../sidechain $atom:CA $atom:R
	- }
	- }
	-
	-
	- # Define P (the "polar" residue)
	- P {
	- # atom-id 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:R 0.0 0.000 4.4000 0.0000000
	- }
	- write("Data Bonds") {
	- $bond:CR @bond:../sidechain $atom:CA $atom:R
	- }
	- }
	-
	- # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc)
	- # can be shared. The ".." in "@atom:../CA" tells moltemplate that
	- # atom type CA is defined in the parent's environment. (We are
	- # sharing the CA atom type between both the H and P residues.
	- # The same is true of the ".." in "@bond:../sidechain".
	- #
	- #
	- # Note: The "..." in "$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.
	-
	-
	-
	- # There are 3 atom types: the R sidechain (belonging to the H and P residues)
	- # and the CA sidechain atom (shared by both residues)
	-
	- write_once("Data Masses") {
	- @atom:CA 13.0
	- @atom:H/R 50.0
	- @atom:P/R 50.0
	- }
	-
	-
	- # --------------------------------------------------------------------
	- # -- 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) = 4eps_ij ( (sig_ij/r)^12 - (sig_ij/r)^6 )
	- #
	- # Hydrophobic side-chains 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:H/R @atom:H/R lj/cut 2.50 3.6
	- pair_coeff @atom:P/R @atom:P/R lj/cut 0.10 3.6
	- }
	- #
	- # (Interactions between different atom types use "arithmetic" 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:sidechain harmonic 30.0 3.4
	- bond_coeff @bond:backbone harmonic 30.0 3.7
	- }
	-
	-} # 2bead
	-
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt
	deleted file mode 100644
	index c378609ac..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt
	+++ /dev/null
	@@ -1,61 +0,0 @@
	-# Although there's no need to define angular interactions (because the "H"
	-# and "P" molecules only contains two atoms), we define the settings for angles
	-# or dihedrals which might be present later when we connect multiple "H" and "P"
	-# molecules together to build a polymer.
	-
	-2bead {
	-
	- # OPTIONAL: Enclose these angle settings within the 2bead {...} environment.
	- # We do this for the same reason we enclosed "H" and "P" in "2bead".
	- # This does not overwrite the definition of 2bead. Here we are only
	- # augmenting "2bead" to include definitions of the following angles
	-
	- # 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:*
	- }
	-
	- # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3
	-
	- write_once("Data Dihedrals By Type") {
	- @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:*
	- @dihedral:RCCR @atom:/R @atom:CA @atom:CA @atom:/R @bond:* @bond:* @bond:*
	- }
	-
	- # 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
	- # "w" is the weight for 1-4 pair interactions, which we set to 0.0
	-
	- 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")
	-
	-}
	\ No newline at end of file
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh
	deleted file mode 100755
	index 7604a672c..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh
	+++ /dev/null
	@@ -1,20 +0,0 @@
	-# The version of "2bead.lt" in this directory is defines two types of
	-# molecules (named "2bead/H" and "2bead/P").
	-#
	-# However, there is another version of this file which is easier to understand.
	-# I recommend reading that file first.
	-# It is located at "simplified_version_one_residue/2bead.lt".
	-# It defines only one type of molecule (named "2bead")
	-# It is much simpler.
	-
	-# ------
	-
	-# Use these commands to generate the LAMMPS input script and data file
	-# (and other auxilliary files):
	-
	-# run moltemplate
	-
	-moltemplate.sh system.lt
	-
	-# This will generate various files with names ending in .in and *.data.
	-
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
	deleted file mode 100644
	index 6c7089244..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-import "2bead.lt"
	-import "2bead_angles.lt"
	-
	-Peptide {
	-
	- # A polymer of alternating "H" and "P" beads:
	-
	- res1 = new 2bead/P
	- res2 = new 2bead/P.rot(180.0, 1,0,0).move(3.2,0,0)
	- res3 = new 2bead/H.rot( 0.0, 1,0,0).move(6.4,0,0)
	- res4 = new 2bead/H.rot(180.0, 1,0,0).move(9.6,0,0)
	- res5 = new 2bead/H.rot( 0.0, 1,0,0).move(12.8,0,0)
	- res6 = new 2bead/H.rot(180.0, 1,0,0).move(16.0,0,0)
	- res7 = new 2bead/P.rot( 0.0, 1,0,0).move(19.2,0,0)
	- res8 = new 2bead/P.rot(180.0, 1,0,0).move(22.4,0,0)
	- res9 = new 2bead/P.rot( 0.0, 1,0,0).move(25.6,0,0)
	- res10 = new 2bead/H.rot(180.0, 1,0,0).move(28.8,0,0)
	- res11 = new 2bead/H.rot( 0.0, 1,0,0).move(32.0,0,0)
	- res12 = new 2bead/H.rot(180.0, 1,0,0).move(35.2,0,0)
	- res13 = new 2bead/P.rot( 0.0, 1,0,0).move(38.4,0,0)
	- res14 = new 2bead/P.rot(180.0, 1,0,0).move(41.6,0,0)
	-
	- # Now, link the residues together this way:
	- write("Data Bonds") {
	- $bond:backbone1 @bond:2bead/backbone $atom:res1/CA $atom:res2/CA
	- $bond:backbone2 @bond:2bead/backbone $atom:res2/CA $atom:res3/CA
	- $bond:backbone3 @bond:2bead/backbone $atom:res3/CA $atom:res4/CA
	- $bond:backbone4 @bond:2bead/backbone $atom:res4/CA $atom:res5/CA
	- $bond:backbone5 @bond:2bead/backbone $atom:res5/CA $atom:res6/CA
	- $bond:backbone6 @bond:2bead/backbone $atom:res6/CA $atom:res7/CA
	- $bond:backbone7 @bond:2bead/backbone $atom:res7/CA $atom:res8/CA
	- $bond:backbone8 @bond:2bead/backbone $atom:res8/CA $atom:res9/CA
	- $bond:backbone9 @bond:2bead/backbone $atom:res9/CA $atom:res10/CA
	- $bond:backbone10 @bond:2bead/backbone $atom:res10/CA $atom:res11/CA
	- $bond:backbone11 @bond:2bead/backbone $atom:res11/CA $atom:res12/CA
	- $bond:backbone12 @bond:2bead/backbone $atom:res12/CA $atom:res13/CA
	- $bond:backbone13 @bond:2bead/backbone $atom:res13/CA $atom:res14/CA
	- }
	-
	- create_var { $mol } # <--create a molecule ID number for this peptide
	-
	- # This causes res1,res2,res3,...,res14 to share the same molecule counter
	- # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks
	- # for a counter of that type in a parent molecule or earlier ancestor.
	-
	-} # Peptide
	-
	-
	-
	-# Angle, dihedral and improper interactions will be generated
	-# according to the instructions in "2bead_angles.lt"
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt
	deleted file mode 100644
	index eea38da04..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt
	+++ /dev/null
	@@ -1,122 +0,0 @@
	-# This file contains the definition of "2-bead", a simple molecule
	-# containing two atoms:
	-#
	-# @R
	-# \|
	-# @CA
	-#
	-#
	-# Later on, we may connect them together to form a polymer:
	-#
	-#
	-# @R @R
	-# \| \|
	-# _@CA_ _@CA_
	-# ... -.@CA-' `-@CA-' ` ...
	-# \| \|
	-# @R @R
	-#
	-# THERE ARE TWO VERSIONS OF THIS FILE:
	-# In the simple version, shown here, there is only one type of side-chain "R".
	-# More complex examples have multiple types of molecules
	-# each with different side-chain properties.
	-
	-2bead {
	-
	- # atom-id mol-id atom-type charge x y z
	-
	- write("Data Atoms") {
	- $atom:CA $mol:... @atom:CA 0.0 0.000 0.0000 0.0000000
	- $atom:R $mol:... @atom:R 0.0 0.000 3.4000 0.0000000
	- }
	-
	- write_once("Data Masses") {
	- @atom:C 14.0
	- @atom:R 50.0
	- }
	-
	- write("Data Bonds") {
	- $bond:CR @bond:sidechain $atom:CA $atom:R
	- }
	-
	- 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:*
	- }
	-
	- write_once("Data Dihedrals By Type") {
	- @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:*
	- @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:*
	- }
	-
	-
	- write_once("In Settings") {
	- # 2-body (bonded) interaction parameters are listed by bondType:
	- #
	- # Ubond(r) = (k/2)*(r-0)^2
	- #
	- # The corresponding command is:
	- #
	- # bond_coeff bondType harmonic k r0
	- #
	- bond_coeff @bond:sidechain harmonic 30.0 3.4
	- bond_coeff @bond:backbone harmonic 30.0 3.7
	-
	- # 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
	- #
	- # The corresponding command is:
	- #
	- # angle_coeff angleType harmonic k theta0
	- # (The theta0 parameter is in degrees, k is in kcal/mol/rad^2)
	-
	- angle_coeff @angle:backbone harmonic 30.0 104
	- angle_coeff @angle:sidechain harmonic 30.0 127
	-
	-
	- # 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 corresponding command is
	- # dihedral_coeff dihedralType charmm K d w
	- #
	- # The d parameter is in degrees, K is in kcal/mol/rad^2.
	- # "w" is the weight for 1-4 pair interactions, which we set to 0.0.
	- # This should turn off pairwise interactions between 1-4 bonded atoms
	- # which are also involved in any of the dihedral interactions below:
	- #
	- dihedral_coeff @dihedral:CCCC charmm -0.5 1 180 0.0
	- dihedral_coeff @dihedral:RCCR charmm -1.5 1 -90 0.0
	-
	-
	- # 2-body (non-bonded) interactions are listed by atom type:
	-
	- # interaction between atoms of the same type:
	- # epsilon signma
	- pair_coeff @atom:CA @atom:CA lj/charmm/coul/charmm 0.010 2.0
	- pair_coeff @atom:R @atom:R lj/charmm/coul/charmm 2.50 3.6
	- #
	- # interactions between different atom types use arithmetic mixing rules
	-
	- } # write_once("In Settings")
	-
	-
	- write_once("In Init") {
	- # -- Default styles for "2bead" --
	- 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
	- pair_modify mix arithmetic
	- special_bonds lj 0.0 0.0 0.0
	- }
	-} # 2bead
	-
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt
	deleted file mode 100644
	index 567ec3ae5..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,25 +0,0 @@
	-import "peptide.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 peptides in a rectangular grid
	-peptides = new Peptide [3].move(0, 0, 60.0)
	- [3].move(0, 60.0, 0)
	- [3].move(60.0, 0, 0)
	-
	-# Now (for fun) shift some of the peptides
	-# in the x direction by a distance of 25.0
	-# Suppose we want to move the middle slice
	-# (which has constant Z). We do that this way:
	-peptides[1][][].move(25,0,0)
	-# more examples:
	-peptides[][1][].move(0,0,25)
	-peptides[][][1].move(0,25,0)
	-
	-
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.min b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.min
	deleted file mode 100644
	index 351da8231..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/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 2500 traj_min.lammpstrj id mol type x y z ix iy iz
	-
	-minimize 1.0e-5 1.0e-7 500 2000
	-
	-write_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt
	deleted file mode 100644
	index eb864e049..000000000
	--- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt
	+++ /dev/null
	@@ -1,38 +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 read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-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
	-
	-restart 1000000 restart_nvt
	-
	-run 1000000
	-
	-write_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT
	deleted file mode 100644
	index 1a077178e..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-This is a very crude attempt to create a polymer melt
	-consisting of 150 copies of the same polymer.
	-
	-THE FORCE FIELD PARAMETERS AND CONFORMATION FOR THIS SYSTEM ARE COMPLETELY WRONG
	-
	-The purpose of this example is to demonstrate one way to create a
	-large number of randomly generated polymers, and to use
	-an NPT simulation to pack them all into a small box.
	-(Smaller than their initial outstretched length.)
	-
	-Each polymer is a random heteropolymer of length 200 monomers.
	-This polymer is a polymoer of PVDF and PCTFE monomers
	-selected randomly in a 1:3 ratio.
	-Again, this is not a realistic simulation of PVDV or PCTFE polymers,
	-
	-Furthermore, even after the simulation is done, the arrangement of the
	-polymers in the box is not characteristic of a truly random polymer melt.
	-
	-
	----- A note on size ---
	-
	-This is a large system with nearly 200000 atoms.
	-It takes several minutes to compile this example
	-and (currently requiring at least 4.0 Gb of memory).
	-(I'm working on reducing that requirement. -Andrew 2012-9-12)
	-
	------------------------
	-
	-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/CG_misc/random_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh
	deleted file mode 100755
	index e8e13dec7..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh
	+++ /dev/null
	@@ -1,19 +0,0 @@
	-# This is just an example.
	-#
	-# Note: The "run.in.nvt" file is a LAMMPS input script which attempts to read
	-# the input scripts and data files you created with 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.nvt
	-
	-# Alternately, if you have MPI installed, try something like this:
	-
	-#NUMPROCS=4
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh
	deleted file mode 100755
	index acc5fbbaa..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/random_heteropolymer/README_visualise.txt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualise.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/CG_misc/random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg
	deleted file mode 100644
	index f67da797f..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg
	deleted file mode 100644
	index 15d7b2967..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index 6915e2739..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,277 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 116 !NATOM
	- 1 1 3 3 0.000000 12.0000 0
	- 2 1 4 4 0.000000 17.0000 0
	- 3 1 4 4 0.000000 17.0000 0
	- 4 1 3 3 0.000000 12.0000 0
	- 5 1 4 4 0.000000 17.0000 0
	- 6 1 4 4 0.000000 17.0000 0
	- 7 1 1 1 0.000000 12.0000 0
	- 8 1 2 2 0.000000 17.0000 0
	- 9 1 1 1 0.000000 12.0000 0
	- 10 1 2 2 0.000000 17.0000 0
	- 11 1 1 1 0.000000 12.0000 0
	- 12 1 2 2 0.000000 17.0000 0
	- 13 1 3 3 0.000000 12.0000 0
	- 14 1 4 4 0.000000 17.0000 0
	- 15 1 4 4 0.000000 17.0000 0
	- 16 1 1 1 0.000000 12.0000 0
	- 17 1 2 2 0.000000 17.0000 0
	- 18 1 1 1 0.000000 12.0000 0
	- 19 1 2 2 0.000000 17.0000 0
	- 20 1 1 1 0.000000 12.0000 0
	- 21 1 2 2 0.000000 17.0000 0
	- 22 1 1 1 0.000000 12.0000 0
	- 23 1 2 2 0.000000 17.0000 0
	- 24 1 1 1 0.000000 12.0000 0
	- 25 1 2 2 0.000000 17.0000 0
	- 26 1 1 1 0.000000 12.0000 0
	- 27 1 2 2 0.000000 17.0000 0
	- 28 1 1 1 0.000000 12.0000 0
	- 29 1 2 2 0.000000 17.0000 0
	- 30 1 3 3 0.000000 12.0000 0
	- 31 1 4 4 0.000000 17.0000 0
	- 32 1 4 4 0.000000 17.0000 0
	- 33 1 1 1 0.000000 12.0000 0
	- 34 1 2 2 0.000000 17.0000 0
	- 35 1 3 3 0.000000 12.0000 0
	- 36 1 4 4 0.000000 17.0000 0
	- 37 1 4 4 0.000000 17.0000 0
	- 38 1 1 1 0.000000 12.0000 0
	- 39 1 2 2 0.000000 17.0000 0
	- 40 1 3 3 0.000000 12.0000 0
	- 41 1 4 4 0.000000 17.0000 0
	- 42 1 4 4 0.000000 17.0000 0
	- 43 1 3 3 0.000000 12.0000 0
	- 44 1 4 4 0.000000 17.0000 0
	- 45 1 4 4 0.000000 17.0000 0
	- 46 1 1 1 0.000000 12.0000 0
	- 47 1 2 2 0.000000 17.0000 0
	- 48 1 1 1 0.000000 12.0000 0
	- 49 1 2 2 0.000000 17.0000 0
	- 50 1 3 3 0.000000 12.0000 0
	- 51 1 4 4 0.000000 17.0000 0
	- 52 1 4 4 0.000000 17.0000 0
	- 53 1 1 1 0.000000 12.0000 0
	- 54 1 2 2 0.000000 17.0000 0
	- 55 1 1 1 0.000000 12.0000 0
	- 56 1 2 2 0.000000 17.0000 0
	- 57 1 3 3 0.000000 12.0000 0
	- 58 1 4 4 0.000000 17.0000 0
	- 59 1 4 4 0.000000 17.0000 0
	- 60 1 1 1 0.000000 12.0000 0
	- 61 1 2 2 0.000000 17.0000 0
	- 62 1 3 3 0.000000 12.0000 0
	- 63 1 4 4 0.000000 17.0000 0
	- 64 1 4 4 0.000000 17.0000 0
	- 65 1 1 1 0.000000 12.0000 0
	- 66 1 2 2 0.000000 17.0000 0
	- 67 1 1 1 0.000000 12.0000 0
	- 68 1 2 2 0.000000 17.0000 0
	- 69 1 1 1 0.000000 12.0000 0
	- 70 1 2 2 0.000000 17.0000 0
	- 71 1 3 3 0.000000 12.0000 0
	- 72 1 4 4 0.000000 17.0000 0
	- 73 1 4 4 0.000000 17.0000 0
	- 74 1 3 3 0.000000 12.0000 0
	- 75 1 4 4 0.000000 17.0000 0
	- 76 1 4 4 0.000000 17.0000 0
	- 77 1 1 1 0.000000 12.0000 0
	- 78 1 2 2 0.000000 17.0000 0
	- 79 1 1 1 0.000000 12.0000 0
	- 80 1 2 2 0.000000 17.0000 0
	- 81 1 3 3 0.000000 12.0000 0
	- 82 1 4 4 0.000000 17.0000 0
	- 83 1 4 4 0.000000 17.0000 0
	- 84 1 1 1 0.000000 12.0000 0
	- 85 1 2 2 0.000000 17.0000 0
	- 86 1 1 1 0.000000 12.0000 0
	- 87 1 2 2 0.000000 17.0000 0
	- 88 1 1 1 0.000000 12.0000 0
	- 89 1 2 2 0.000000 17.0000 0
	- 90 1 1 1 0.000000 12.0000 0
	- 91 1 2 2 0.000000 17.0000 0
	- 92 1 3 3 0.000000 12.0000 0
	- 93 1 4 4 0.000000 17.0000 0
	- 94 1 4 4 0.000000 17.0000 0
	- 95 1 1 1 0.000000 12.0000 0
	- 96 1 2 2 0.000000 17.0000 0
	- 97 1 1 1 0.000000 12.0000 0
	- 98 1 2 2 0.000000 17.0000 0
	- 99 1 1 1 0.000000 12.0000 0
	- 100 1 2 2 0.000000 17.0000 0
	- 101 1 3 3 0.000000 12.0000 0
	- 102 1 4 4 0.000000 17.0000 0
	- 103 1 4 4 0.000000 17.0000 0
	- 104 1 1 1 0.000000 12.0000 0
	- 105 1 2 2 0.000000 17.0000 0
	- 106 1 1 1 0.000000 12.0000 0
	- 107 1 2 2 0.000000 17.0000 0
	- 108 1 3 3 0.000000 12.0000 0
	- 109 1 4 4 0.000000 17.0000 0
	- 110 1 4 4 0.000000 17.0000 0
	- 111 1 1 1 0.000000 12.0000 0
	- 112 1 2 2 0.000000 17.0000 0
	- 113 1 1 1 0.000000 12.0000 0
	- 114 1 2 2 0.000000 17.0000 0
	- 115 1 1 1 0.000000 12.0000 0
	- 116 1 2 2 0.000000 17.0000 0
	-
	- 115 !NBOND: bonds
	- 1 2 1 3 1 4 4 5
	- 4 6 4 7 7 8 7 9
	- 9 10 9 11 11 12 11 13
	- 13 14 13 15 13 16 16 17
	- 16 18 18 19 18 20 20 21
	- 20 22 22 23 22 24 24 25
	- 24 26 26 27 26 28 28 29
	- 28 30 30 31 30 32 30 33
	- 33 34 33 35 35 36 35 37
	- 35 38 38 39 38 40 40 41
	- 40 42 40 43 43 44 43 45
	- 43 46 46 47 46 48 48 49
	- 48 50 50 51 50 52 50 53
	- 53 54 53 55 55 56 55 57
	- 57 58 57 59 57 60 60 61
	- 60 62 62 63 62 64 62 65
	- 65 66 65 67 67 68 67 69
	- 69 70 69 71 71 72 71 73
	- 71 74 74 75 74 76 74 77
	- 77 78 77 79 79 80 79 81
	- 81 82 81 83 81 84 84 85
	- 84 86 86 87 86 88 88 89
	- 88 90 90 91 90 92 92 93
	- 92 94 92 95 95 96 95 97
	- 97 98 97 99 99 100 99 101
	- 101 102 101 103 101 104 104 105
	- 104 106 106 107 106 108 108 109
	- 108 110 108 111 111 112 111 113
	- 113 114 113 115 115 116
	-
	- 193 !NTHETA: angles
	- 1 4 7 38 40 43 40 43 46
	- 69 71 74 71 74 77 30 33 35
	- 35 38 40 57 60 62 4 7 9
	- 9 11 13 13 16 18 26 28 30
	- 43 46 48 46 48 50 50 53 55
	- 53 55 57 62 65 67 67 69 71
	- 74 77 79 77 79 81 81 84 86
	- 88 90 92 92 95 97 97 99 101
	- 101 104 106 104 106 108 108 111 113
	- 7 9 11 16 18 20 18 20 22
	- 20 22 24 22 24 26 24 26 28
	- 65 67 69 84 86 88 86 88 90
	- 95 97 99 111 113 115 11 13 16
	- 28 30 33 33 35 38 48 50 53
	- 55 57 60 60 62 65 79 81 84
	- 90 92 95 99 101 104 106 108 111
	- 5 4 7 6 4 7 11 13 14
	- 11 13 15 14 13 16 15 13 16
	- 28 30 31 28 30 32 31 30 33
	- 32 30 33 33 35 36 33 35 37
	- 36 35 38 37 35 38 38 40 41
	- 38 40 42 44 43 46 45 43 46
	- 48 50 51 48 50 52 51 50 53
	- 52 50 53 55 57 58 55 57 59
	- 58 57 60 59 57 60 60 62 63
	- 60 62 64 63 62 65 64 62 65
	- 69 71 72 69 71 73 75 74 77
	- 76 74 77 79 81 82 79 81 83
	- 82 81 84 83 81 84 90 92 93
	- 90 92 94 93 92 95 94 92 95
	- 99 101 102 99 101 103 102 101 104
	- 103 101 104 106 108 109 106 108 110
	- 109 108 111 110 108 111 7 9 10
	- 8 7 9 9 11 12 10 9 11
	- 16 18 19 17 16 18 18 20 21
	- 19 18 20 20 22 23 21 20 22
	- 22 24 25 23 22 24 24 26 27
	- 25 24 26 26 28 29 27 26 28
	- 46 48 49 47 46 48 53 55 56
	- 54 53 55 65 67 68 66 65 67
	- 67 69 70 68 67 69 77 79 80
	- 78 77 79 84 86 87 85 84 86
	- 86 88 89 87 86 88 88 90 91
	- 89 88 90 95 97 98 96 95 97
	- 97 99 100 98 97 99 104 106 107
	- 105 104 106 111 113 114 112 111 113
	- 113 115 116 114 113 115 1 4 5
	- 1 4 6 2 1 4 3 1 4
	- 40 43 44 40 43 45 41 40 43
	- 42 40 43 71 74 75 71 74 76
	- 72 71 74 73 71 74 4 7 8
	- 12 11 13 13 16 17 29 28 30
	- 30 33 34 34 33 35 35 38 39
	- 39 38 40 43 46 47 49 48 50
	- 50 53 54 56 55 57 57 60 61
	- 61 60 62 62 65 66 70 69 71
	- 74 77 78 80 79 81 81 84 85
	- 91 90 92 92 95 96 100 99 101
	- 101 104 105 107 106 108 108 111 112
	- 2 1 3 5 4 6 14 13 15
	- 31 30 32 36 35 37 41 40 42
	- 44 43 45 51 50 52 58 57 59
	- 63 62 64 72 71 73 75 74 76
	- 82 81 83 93 92 94 102 101 103
	- 109 108 110
	-
	- 47 !NPHI: dihedrals
	- 38 40 43 46 69 71 74 77
	- 1 4 7 9 40 43 46 48
	- 67 69 71 74 71 74 77 79
	- 35 38 40 43 30 33 35 38
	- 28 30 33 35 33 35 38 40
	- 57 60 62 65 55 57 60 62
	- 4 7 9 11 7 9 11 13
	- 13 16 18 20 24 26 28 30
	- 62 65 67 69 65 67 69 71
	- 81 84 86 88 86 88 90 92
	- 92 95 97 99 95 97 99 101
	- 108 111 113 115 16 18 20 22
	- 18 20 22 24 20 22 24 26
	- 22 24 26 28 84 86 88 90
	- 9 11 13 16 11 13 16 18
	- 26 28 30 33 46 48 50 53
	- 53 55 57 60 48 50 53 55
	- 60 62 65 67 77 79 81 84
	- 79 81 84 86 88 90 92 95
	- 90 92 95 97 97 99 101 104
	- 104 106 108 111 99 101 104 106
	- 106 108 111 113 43 46 48 50
	- 50 53 55 57 74 77 79 81
	- 101 104 106 108
	-
	- 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
	-
	- 1 0 !NGRP
	- 0 0 0
	-
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg
	deleted file mode 100644
	index cc6822e7b..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg
	deleted file mode 100644
	index efcaa76c0..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt
	deleted file mode 100644
	index 9ebf85461..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt
	+++ /dev/null
	@@ -1,123 +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. --
	- # ----------------------------------------------------------------------
	-
	-
	-MonomerTypes {
	-
	-
	- 2bead {
	- # atom-id mol-id atom-type charge x y z
	-
	- write("Data Atoms") {
	- $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.0000
	- $atom:R $mol:... @atom:R 0.0 0.000 4.400 0.0000
	- }
	-
	- # bond-id bond-type atom-id1 atom-id2
	-
	- write("Data Bonds") {
	- $bond:CR @bond:../sidechain $atom:CA $atom:R
	- }
	-
	- # atom-type mass
	-
	- write_once("Data Masses") {
	- @atom:CA 12.0
	- @atom:R 17.0
	- }
	-
	- # atom-type atom-type epsilon sigma
	-
	- write_once("In Settings") {
	- pair_coeff @atom:CA @atom:CA 0.10 2.0
	- pair_coeff @atom:R @atom:R 0.50 3.0
	- }
	-
	- } # 2bead
	-
	-
	- 3bead {
	- # atom-id mol-id atom-type charge x y z
	-
	- write("Data Atoms") {
	- $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.000
	- $atom:R1 $mol:... @atom:R 0.0 0.000 2.700 2.950
	- $atom:R2 $mol:... @atom:R 0.0 0.000 2.700 -2.950
	- }
	-
	- # 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
	- }
	-
	- # atom-type mass
	-
	- write_once("Data Masses") {
	- @atom:CA 12.0
	- @atom:R 17.0
	- }
	-
	- # atom-type atom-type epsilon sigma
	-
	- write_once("In Settings") {
	- pair_coeff @atom:CA @atom:CA 0.10 2.0
	- pair_coeff @atom:R @atom:R 0.50 3.0
	- }
	- } # 3bead
	-
	-
	-
	-
	- # bond-type k r0
	-
	- write_once("Data Bond Coeffs") {
	- @bond:sidechain 20.0 3.4
	- @bond:bb 20.0 3.4 # "bb" shorthand for "backbone"
	- }
	-
	- # Although there's no need to define angular interactions (because this
	- # "molecule" only contains two atoms), we define the settings for angles
	- # or dihedrals which might be present later when we build a polymer.
	-
	- # angle-type k theta0
	-
	- write_once("Data Angle Coeffs") {
	- @angle:backbone 10.00 160
	- @angle:sidechain 10.00 120
	- @angle:RCR 10.00 120
	- }
	-
	- # dihedral-type K1 K2 K3 K4
	-
	- write_once("Data Dihedral Coeffs") {
	- @dihedral:backbn 0.10 -0.271016 3.145034 0.0
	- }
	-
	- # 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:*
	- }
	-
	- # 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 * * *
	- }
	-
	-} # MonomerTypes
	-
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt
	deleted file mode 100644
	index 9497dcc39..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-import "monomers.lt"
	-
	-using namespace MonomerTypes
	-
	-RandomHeteropolymer {
	-
	- # Make a chain of monomers with random composition:
	-
	- monomers = new random([2bead,3bead],
	- [0.6,0.4],
	- 123456) # <-- optional random seed
	- [50].rot(180,1,0,0).move(2.95, 0, 0)
	-
	- # Now, link the monomers together this way:
	-
	- write("Data Bonds") {
	- $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/CA $atom:monomers[1]/CA
	- $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/CA $atom:monomers[2]/CA
	- $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/CA $atom:monomers[3]/CA
	- $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/CA $atom:monomers[4]/CA
	- $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/CA $atom:monomers[5]/CA
	- $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/CA $atom:monomers[6]/CA
	- $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/CA $atom:monomers[7]/CA
	- $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/CA $atom:monomers[8]/CA
	- $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/CA $atom:monomers[9]/CA
	- $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/CA $atom:monomers[10]/CA
	- $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/CA $atom:monomers[11]/CA
	- $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/CA $atom:monomers[12]/CA
	- $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/CA $atom:monomers[13]/CA
	- $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/CA $atom:monomers[14]/CA
	- $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/CA $atom:monomers[15]/CA
	- $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/CA $atom:monomers[16]/CA
	- $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/CA $atom:monomers[17]/CA
	- $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/CA $atom:monomers[18]/CA
	- $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/CA $atom:monomers[19]/CA
	- $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/CA $atom:monomers[20]/CA
	- $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/CA $atom:monomers[21]/CA
	- $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/CA $atom:monomers[22]/CA
	- $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/CA $atom:monomers[23]/CA
	- $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/CA $atom:monomers[24]/CA
	- $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/CA $atom:monomers[25]/CA
	- $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/CA $atom:monomers[26]/CA
	- $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/CA $atom:monomers[27]/CA
	- $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/CA $atom:monomers[28]/CA
	- $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/CA $atom:monomers[29]/CA
	- $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/CA $atom:monomers[30]/CA
	- $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/CA $atom:monomers[31]/CA
	- $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/CA $atom:monomers[32]/CA
	- $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/CA $atom:monomers[33]/CA
	- $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/CA $atom:monomers[34]/CA
	- $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/CA $atom:monomers[35]/CA
	- $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/CA $atom:monomers[36]/CA
	- $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/CA $atom:monomers[37]/CA
	- $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/CA $atom:monomers[38]/CA
	- $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/CA $atom:monomers[39]/CA
	- $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/CA $atom:monomers[40]/CA
	- $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/CA $atom:monomers[41]/CA
	- $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/CA $atom:monomers[42]/CA
	- $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/CA $atom:monomers[43]/CA
	- $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/CA $atom:monomers[44]/CA
	- $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/CA $atom:monomers[45]/CA
	- $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/CA $atom:monomers[46]/CA
	- $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/CA $atom:monomers[47]/CA
	- $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/CA $atom:monomers[48]/CA
	- $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/CA $atom:monomers[49]/CA
	- }
	-
	- # These lines of moltemplate script above were generated in python:
	- # for i in range(0,49):
	- # print(' $bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers['
	- # +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA')
	-
	- # Finally, create a molecule ID number for this large polymer object
	-
	- create_var { $mol }
	-
	-} # RandomHeteropolymer
	-
	-
	-
	-# Angle, dihedral and improper interactions will be generated
	-# automatically according to the instructions in "monomers.lt"
	diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt
	deleted file mode 100644
	index 11f2d48fa..000000000
	--- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,33 +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") {
	- 0.0 150.0 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/CG_misc/random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt
	deleted file mode 100644
	index 5e08f03cb..000000000
	--- a/tools/moltemplate/examples/CG_misc/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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_misc/translocation/README.TXT b/tools/moltemplate/examples/CG_misc/translocation/README.TXT
	deleted file mode 100644
	index b9bac96d5..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/translocation/README_run.sh b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh
	deleted file mode 100755
	index e8e13dec7..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh
	+++ /dev/null
	@@ -1,19 +0,0 @@
	-# This is just an example.
	-#
	-# Note: The "run.in.nvt" file is a LAMMPS input script which attempts to read
	-# the input scripts and data files you created with 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.nvt
	-
	-# Alternately, if you have MPI installed, try something like this:
	-
	-#NUMPROCS=4
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt
	diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh
	deleted file mode 100755
	index acc5fbbaa..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/translocation/README_visualise.txt b/tools/moltemplate/examples/CG_misc/translocation/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/README_visualise.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/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index 74e373532..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,1995 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 1716 !NATOM
	- 1 1 1 1 0.000000 10.0000 0
	- 2 2 1 1 0.000000 10.0000 0
	- 3 3 1 1 0.000000 10.0000 0
	- 4 4 1 1 0.000000 10.0000 0
	- 5 5 1 1 0.000000 10.0000 0
	- 6 6 1 1 0.000000 10.0000 0
	- 7 7 1 1 0.000000 10.0000 0
	- 8 8 1 1 0.000000 10.0000 0
	- 9 9 1 1 0.000000 10.0000 0
	- 10 10 1 1 0.000000 10.0000 0
	- 11 11 1 1 0.000000 10.0000 0
	- 12 12 1 1 0.000000 10.0000 0
	- 13 13 1 1 0.000000 10.0000 0
	- 14 14 1 1 0.000000 10.0000 0
	- 15 15 1 1 0.000000 10.0000 0
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	- 20 20 1 1 0.000000 10.0000 0
	- 21 21 1 1 0.000000 10.0000 0
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	- 23 23 1 1 0.000000 10.0000 0
	- 24 24 1 1 0.000000 10.0000 0
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	- 1447 1447 2 2 0.000000 10.0000 0
	- 1448 1448 2 2 0.000000 10.0000 0
	- 1449 1449 2 2 0.000000 10.0000 0
	- 1450 1450 2 2 0.000000 10.0000 0
	- 1451 1451 2 2 0.000000 10.0000 0
	- 1452 1452 2 2 0.000000 10.0000 0
	- 1453 1453 2 2 0.000000 10.0000 0
	- 1454 1454 2 2 0.000000 10.0000 0
	- 1455 1455 2 2 0.000000 10.0000 0
	- 1456 1456 2 2 0.000000 10.0000 0
	- 1457 1457 2 2 0.000000 10.0000 0
	- 1458 1458 2 2 0.000000 10.0000 0
	- 1459 1459 2 2 0.000000 10.0000 0
	- 1460 1460 2 2 0.000000 10.0000 0
	- 1461 1461 2 2 0.000000 10.0000 0
	- 1462 1462 2 2 0.000000 10.0000 0
	- 1463 1463 2 2 0.000000 10.0000 0
	- 1464 1464 2 2 0.000000 10.0000 0
	- 1465 1465 2 2 0.000000 10.0000 0
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	- 1467 1467 2 2 0.000000 10.0000 0
	- 1468 1468 2 2 0.000000 10.0000 0
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	- 1470 1470 2 2 0.000000 10.0000 0
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	- 1474 1474 2 2 0.000000 10.0000 0
	- 1475 1475 2 2 0.000000 10.0000 0
	- 1476 1476 2 2 0.000000 10.0000 0
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	- 1483 1483 2 2 0.000000 10.0000 0
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	- 1488 1488 2 2 0.000000 10.0000 0
	- 1489 1489 2 2 0.000000 10.0000 0
	- 1490 1490 2 2 0.000000 10.0000 0
	- 1491 1491 2 2 0.000000 10.0000 0
	- 1492 1492 2 2 0.000000 10.0000 0
	- 1493 1493 2 2 0.000000 10.0000 0
	- 1494 1494 2 2 0.000000 10.0000 0
	- 1495 1495 2 2 0.000000 10.0000 0
	- 1496 1496 2 2 0.000000 10.0000 0
	- 1497 1497 2 2 0.000000 10.0000 0
	- 1498 1498 2 2 0.000000 10.0000 0
	- 1499 1499 2 2 0.000000 10.0000 0
	- 1500 1500 2 2 0.000000 10.0000 0
	- 1501 1501 2 2 0.000000 10.0000 0
	- 1502 1502 2 2 0.000000 10.0000 0
	- 1503 1503 2 2 0.000000 10.0000 0
	- 1504 1504 2 2 0.000000 10.0000 0
	- 1505 1505 2 2 0.000000 10.0000 0
	- 1506 1506 2 2 0.000000 10.0000 0
	- 1507 1507 2 2 0.000000 10.0000 0
	- 1508 1508 2 2 0.000000 10.0000 0
	- 1509 1509 2 2 0.000000 10.0000 0
	- 1510 1510 2 2 0.000000 10.0000 0
	- 1511 1511 2 2 0.000000 10.0000 0
	- 1512 1512 2 2 0.000000 10.0000 0
	- 1513 1513 2 2 0.000000 10.0000 0
	- 1514 1514 2 2 0.000000 10.0000 0
	- 1515 1515 2 2 0.000000 10.0000 0
	- 1516 1516 2 2 0.000000 10.0000 0
	- 1517 1517 2 2 0.000000 10.0000 0
	- 1518 1518 2 2 0.000000 10.0000 0
	- 1519 1519 2 2 0.000000 10.0000 0
	- 1520 1520 2 2 0.000000 10.0000 0
	- 1521 1521 2 2 0.000000 10.0000 0
	- 1522 1522 2 2 0.000000 10.0000 0
	- 1523 1523 2 2 0.000000 10.0000 0
	- 1524 1524 2 2 0.000000 10.0000 0
	- 1525 1525 2 2 0.000000 10.0000 0
	- 1526 1526 2 2 0.000000 10.0000 0
	- 1527 1527 2 2 0.000000 10.0000 0
	- 1528 1528 2 2 0.000000 10.0000 0
	- 1529 1529 2 2 0.000000 10.0000 0
	- 1530 1530 2 2 0.000000 10.0000 0
	- 1531 1531 2 2 0.000000 10.0000 0
	- 1532 1532 2 2 0.000000 10.0000 0
	- 1533 1533 2 2 0.000000 10.0000 0
	- 1534 1534 2 2 0.000000 10.0000 0
	- 1535 1535 2 2 0.000000 10.0000 0
	- 1536 1536 2 2 0.000000 10.0000 0
	- 1537 1537 2 2 0.000000 10.0000 0
	- 1538 1538 2 2 0.000000 10.0000 0
	- 1539 1539 2 2 0.000000 10.0000 0
	- 1540 1540 2 2 0.000000 10.0000 0
	- 1541 1541 2 2 0.000000 10.0000 0
	- 1542 1542 2 2 0.000000 10.0000 0
	- 1543 1543 2 2 0.000000 10.0000 0
	- 1544 1544 2 2 0.000000 10.0000 0
	- 1545 1545 2 2 0.000000 10.0000 0
	- 1546 1546 2 2 0.000000 10.0000 0
	- 1547 1547 2 2 0.000000 10.0000 0
	- 1548 1548 2 2 0.000000 10.0000 0
	- 1549 1549 2 2 0.000000 10.0000 0
	- 1550 1550 2 2 0.000000 10.0000 0
	- 1551 1551 2 2 0.000000 10.0000 0
	- 1552 1552 2 2 0.000000 10.0000 0
	- 1553 1553 2 2 0.000000 10.0000 0
	- 1554 1554 2 2 0.000000 10.0000 0
	- 1555 1555 2 2 0.000000 10.0000 0
	- 1556 1556 2 2 0.000000 10.0000 0
	- 1557 1557 2 2 0.000000 10.0000 0
	- 1558 1558 2 2 0.000000 10.0000 0
	- 1559 1559 2 2 0.000000 10.0000 0
	- 1560 1560 2 2 0.000000 10.0000 0
	- 1561 1561 2 2 0.000000 10.0000 0
	- 1562 1562 2 2 0.000000 10.0000 0
	- 1563 1563 2 2 0.000000 10.0000 0
	- 1564 1564 2 2 0.000000 10.0000 0
	- 1565 1565 2 2 0.000000 10.0000 0
	- 1566 1566 2 2 0.000000 10.0000 0
	- 1567 1567 2 2 0.000000 10.0000 0
	- 1568 1568 2 2 0.000000 10.0000 0
	- 1569 1569 2 2 0.000000 10.0000 0
	- 1570 1570 2 2 0.000000 10.0000 0
	- 1571 1571 2 2 0.000000 10.0000 0
	- 1572 1572 2 2 0.000000 10.0000 0
	- 1573 1573 2 2 0.000000 10.0000 0
	- 1574 1574 2 2 0.000000 10.0000 0
	- 1575 1575 2 2 0.000000 10.0000 0
	- 1576 1576 2 2 0.000000 10.0000 0
	- 1577 1577 2 2 0.000000 10.0000 0
	- 1578 1578 2 2 0.000000 10.0000 0
	- 1579 1579 2 2 0.000000 10.0000 0
	- 1580 1580 2 2 0.000000 10.0000 0
	- 1581 1581 2 2 0.000000 10.0000 0
	- 1582 1582 2 2 0.000000 10.0000 0
	- 1583 1583 2 2 0.000000 10.0000 0
	- 1584 1584 2 2 0.000000 10.0000 0
	- 1585 1585 2 2 0.000000 10.0000 0
	- 1586 1586 2 2 0.000000 10.0000 0
	- 1587 1587 2 2 0.000000 10.0000 0
	- 1588 1588 2 2 0.000000 10.0000 0
	- 1589 1589 2 2 0.000000 10.0000 0
	- 1590 1590 2 2 0.000000 10.0000 0
	- 1591 1591 2 2 0.000000 10.0000 0
	- 1592 1592 2 2 0.000000 10.0000 0
	- 1593 1593 2 2 0.000000 10.0000 0
	- 1594 1594 2 2 0.000000 10.0000 0
	- 1595 1595 2 2 0.000000 10.0000 0
	- 1596 1596 2 2 0.000000 10.0000 0
	- 1597 1597 2 2 0.000000 10.0000 0
	- 1598 1598 2 2 0.000000 10.0000 0
	- 1599 1599 2 2 0.000000 10.0000 0
	- 1600 1600 2 2 0.000000 10.0000 0
	- 1601 1601 2 2 0.000000 10.0000 0
	- 1602 1602 2 2 0.000000 10.0000 0
	- 1603 1603 2 2 0.000000 10.0000 0
	- 1604 1604 2 2 0.000000 10.0000 0
	- 1605 1605 2 2 0.000000 10.0000 0
	- 1606 1606 2 2 0.000000 10.0000 0
	- 1607 1607 2 2 0.000000 10.0000 0
	- 1608 1608 2 2 0.000000 10.0000 0
	- 1609 1609 2 2 0.000000 10.0000 0
	- 1610 1610 2 2 0.000000 10.0000 0
	- 1611 1611 2 2 0.000000 10.0000 0
	- 1612 1612 2 2 0.000000 10.0000 0
	- 1613 1613 2 2 0.000000 10.0000 0
	- 1614 1614 2 2 0.000000 10.0000 0
	- 1615 1615 2 2 0.000000 10.0000 0
	- 1616 1616 2 2 0.000000 10.0000 0
	- 1617 1617 2 2 0.000000 10.0000 0
	- 1618 1618 2 2 0.000000 10.0000 0
	- 1619 1619 2 2 0.000000 10.0000 0
	- 1620 1620 2 2 0.000000 10.0000 0
	- 1621 1621 2 2 0.000000 10.0000 0
	- 1622 1622 2 2 0.000000 10.0000 0
	- 1623 1623 2 2 0.000000 10.0000 0
	- 1624 1624 2 2 0.000000 10.0000 0
	- 1625 1625 2 2 0.000000 10.0000 0
	- 1626 1626 2 2 0.000000 10.0000 0
	- 1627 1627 2 2 0.000000 10.0000 0
	- 1628 1628 2 2 0.000000 10.0000 0
	- 1629 1629 2 2 0.000000 10.0000 0
	- 1630 1630 2 2 0.000000 10.0000 0
	- 1631 1631 2 2 0.000000 10.0000 0
	- 1632 1632 2 2 0.000000 10.0000 0
	- 1633 1633 2 2 0.000000 10.0000 0
	- 1634 1634 2 2 0.000000 10.0000 0
	- 1635 1635 2 2 0.000000 10.0000 0
	- 1636 1636 2 2 0.000000 10.0000 0
	- 1637 1637 2 2 0.000000 10.0000 0
	- 1638 1638 2 2 0.000000 10.0000 0
	- 1639 1639 2 2 0.000000 10.0000 0
	- 1640 1640 2 2 0.000000 10.0000 0
	- 1641 1641 2 2 0.000000 10.0000 0
	- 1642 1642 2 2 0.000000 10.0000 0
	- 1643 1643 2 2 0.000000 10.0000 0
	- 1644 1644 2 2 0.000000 10.0000 0
	- 1645 1645 2 2 0.000000 10.0000 0
	- 1646 1646 2 2 0.000000 10.0000 0
	- 1647 1647 2 2 0.000000 10.0000 0
	- 1648 1648 2 2 0.000000 10.0000 0
	- 1649 1649 2 2 0.000000 10.0000 0
	- 1650 1650 2 2 0.000000 10.0000 0
	- 1651 1651 2 2 0.000000 10.0000 0
	- 1652 1652 2 2 0.000000 10.0000 0
	- 1653 1653 2 2 0.000000 10.0000 0
	- 1654 1654 2 2 0.000000 10.0000 0
	- 1655 1655 2 2 0.000000 10.0000 0
	- 1656 1656 2 2 0.000000 10.0000 0
	- 1657 1657 2 2 0.000000 10.0000 0
	- 1658 1658 2 2 0.000000 10.0000 0
	- 1659 1659 2 2 0.000000 10.0000 0
	- 1660 1660 2 2 0.000000 10.0000 0
	- 1661 1661 2 2 0.000000 10.0000 0
	- 1662 1662 2 2 0.000000 10.0000 0
	- 1663 1663 2 2 0.000000 10.0000 0
	- 1664 1664 2 2 0.000000 10.0000 0
	- 1665 1665 2 2 0.000000 10.0000 0
	- 1666 1666 2 2 0.000000 10.0000 0
	- 1667 1667 2 2 0.000000 10.0000 0
	- 1668 1668 2 2 0.000000 10.0000 0
	- 1669 1669 2 2 0.000000 10.0000 0
	- 1670 1670 2 2 0.000000 10.0000 0
	- 1671 1671 2 2 0.000000 10.0000 0
	- 1672 1672 2 2 0.000000 10.0000 0
	- 1673 1673 2 2 0.000000 10.0000 0
	- 1674 1674 2 2 0.000000 10.0000 0
	- 1675 1675 2 2 0.000000 10.0000 0
	- 1676 1676 2 2 0.000000 10.0000 0
	- 1677 1677 2 2 0.000000 10.0000 0
	- 1678 1678 2 2 0.000000 10.0000 0
	- 1679 1679 2 2 0.000000 10.0000 0
	- 1680 1680 2 2 0.000000 10.0000 0
	- 1681 1681 3 3 0.000000 13.0000 0
	- 1682 1681 4 4 0.000000 50.0000 0
	- 1683 1681 4 4 0.000000 50.0000 0
	- 1684 1681 3 3 0.000000 13.0000 0
	- 1685 1681 4 4 0.000000 50.0000 0
	- 1686 1681 4 4 0.000000 50.0000 0
	- 1687 1681 3 3 0.000000 13.0000 0
	- 1688 1681 4 4 0.000000 50.0000 0
	- 1689 1681 4 4 0.000000 50.0000 0
	- 1690 1681 3 3 0.000000 13.0000 0
	- 1691 1681 4 4 0.000000 50.0000 0
	- 1692 1681 4 4 0.000000 50.0000 0
	- 1693 1681 3 3 0.000000 13.0000 0
	- 1694 1681 4 4 0.000000 50.0000 0
	- 1695 1681 4 4 0.000000 50.0000 0
	- 1696 1681 3 3 0.000000 13.0000 0
	- 1697 1681 4 4 0.000000 50.0000 0
	- 1698 1681 4 4 0.000000 50.0000 0
	- 1699 1681 3 3 0.000000 13.0000 0
	- 1700 1681 4 4 0.000000 50.0000 0
	- 1701 1681 4 4 0.000000 50.0000 0
	- 1702 1681 3 3 0.000000 13.0000 0
	- 1703 1681 4 4 0.000000 50.0000 0
	- 1704 1681 4 4 0.000000 50.0000 0
	- 1705 1681 3 3 0.000000 13.0000 0
	- 1706 1681 4 4 0.000000 50.0000 0
	- 1707 1681 4 4 0.000000 50.0000 0
	- 1708 1681 3 3 0.000000 13.0000 0
	- 1709 1681 4 4 0.000000 50.0000 0
	- 1710 1681 4 4 0.000000 50.0000 0
	- 1711 1681 3 3 0.000000 13.0000 0
	- 1712 1681 4 4 0.000000 50.0000 0
	- 1713 1681 4 4 0.000000 50.0000 0
	- 1714 1681 3 3 0.000000 13.0000 0
	- 1715 1681 4 4 0.000000 50.0000 0
	- 1716 1681 4 4 0.000000 50.0000 0
	-
	- 35 !NBOND: bonds
	- 1681 1682 1681 1683 1681 1684 1684 1685
	- 1684 1686 1684 1687 1687 1688 1687 1689
	- 1687 1690 1690 1691 1690 1692 1690 1693
	- 1693 1694 1693 1695 1693 1696 1696 1697
	- 1696 1698 1696 1699 1699 1700 1699 1701
	- 1699 1702 1702 1703 1702 1704 1702 1705
	- 1705 1706 1705 1707 1705 1708 1708 1709
	- 1708 1710 1708 1711 1711 1712 1711 1713
	- 1711 1714 1714 1715 1714 1716
	-
	- 66 !NTHETA: angles
	- 1681 1684 1687 1684 1687 1690 1687 1690 1693
	- 1690 1693 1696 1693 1696 1699 1696 1699 1702
	- 1699 1702 1705 1702 1705 1708 1705 1708 1711
	- 1708 1711 1714 1681 1684 1685 1681 1684 1686
	- 1682 1681 1684 1683 1681 1684 1684 1687 1688
	- 1684 1687 1689 1685 1684 1687 1686 1684 1687
	- 1687 1690 1691 1687 1690 1692 1688 1687 1690
	- 1689 1687 1690 1690 1693 1694 1690 1693 1695
	- 1691 1690 1693 1692 1690 1693 1693 1696 1697
	- 1693 1696 1698 1694 1693 1696 1695 1693 1696
	- 1696 1699 1700 1696 1699 1701 1697 1696 1699
	- 1698 1696 1699 1699 1702 1703 1699 1702 1704
	- 1700 1699 1702 1701 1699 1702 1702 1705 1706
	- 1702 1705 1707 1703 1702 1705 1704 1702 1705
	- 1705 1708 1709 1705 1708 1710 1706 1705 1708
	- 1707 1705 1708 1708 1711 1712 1708 1711 1713
	- 1709 1708 1711 1710 1708 1711 1711 1714 1715
	- 1711 1714 1716 1712 1711 1714 1713 1711 1714
	- 1682 1681 1683 1685 1684 1686 1688 1687 1689
	- 1691 1690 1692 1694 1693 1695 1697 1696 1698
	- 1700 1699 1701 1703 1702 1704 1706 1705 1707
	- 1709 1708 1710 1712 1711 1713 1715 1714 1716
	-
	- 9 !NPHI: dihedrals
	- 1681 1684 1687 1690 1684 1687 1690 1693
	- 1687 1690 1693 1696 1690 1693 1696 1699
	- 1693 1696 1699 1702 1696 1699 1702 1705
	- 1699 1702 1705 1708 1702 1705 1708 1711
	- 1705 1708 1711 1714
	-
	- 0 !NIMPHI: impropers
	-
	-
	- 0 !NDON: donors
	-
	-
	- 0 !NACC: acceptors
	-
	-
	- 0 !NNB
	-
	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 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/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg
	deleted file mode 100644
	index c1dcc4c18..000000000
	Binary files a/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt
	deleted file mode 100644
	index ee7bdac7e..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt
	+++ /dev/null
	@@ -1,105 +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
	- }
	-
	- # bond-type k r0
	-
	- write_once("Data Bond Coeffs") {
	- @bond:sidechain 30.0 1.2
	- @bond:bb 30.0 2.0 # "bb" shorthand for "backbone"
	- }
	-
	- # Although there's no need to define angular interactions (because this
	- # "molecule" only contains two atoms), we define the settings for angles
	- # or dihedrals which might be present later when we build a polymer.
	-
	- # angle-type k theta0
	-
	- write_once("Data Angle Coeffs") {
	- @angle:backbone 50.00 160
	- @angle:sidechain 50.00 120
	- @angle:RCR 50.00 120
	- }
	-
	- # dihedral-type K1 K2 K3 K4
	-
	- write_once("Data Dihedral Coeffs") {
	- @dihedral:backbn 1.411036 -0.271016 3.145034 0.0
	- }
	-
	- # 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:*
	- }
	-
	- # 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:*
	- }
	-
	-} # 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/CG_misc/translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt
	deleted file mode 100644
	index d7ab89dc3..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt
	+++ /dev/null
	@@ -1,35 +0,0 @@
	-import "monomer.lt"
	-
	-Polymer {
	-
	- # 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
	- }
	-
	- create_var { $mol } # Create a molecule ID number for this polymer
	-
	- # This causes monomer[0], monomer[1], ... to share the same molecule counter
	- # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks
	- # for a counter of that type in a parent molecule or earlier ancestor.
	-
	-} # Polymer
	-
	-
	-
	-# Angle, dihedral and improper interactions will be generated
	-# automatically according to the instructions in "monomer.lt"
	diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt
	deleted file mode 100644
	index 1073a58a1..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt
	deleted file mode 100644
	index 8057e3c6f..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt
	deleted file mode 100644
	index 41cc81900..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,53 +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
	- 0.0 36.0 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 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 bonded interactions. Delete them too.
	-# Note: In both cases the two molecule fragments will keep the same mol counter.
	diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt
	deleted file mode 100644
	index 79275a06b..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt
	deleted file mode 100644
	index dcccac941..000000000
	--- a/tools/moltemplate/examples/CG_misc/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/CG_misc/translocation/run.in.npt b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt
	deleted file mode 100644
	index 4a0f756a1..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt
	+++ /dev/null
	@@ -1,61 +0,0 @@
	-# -- Init Section --
	-
	-include system.in.init
	-
	-# -- Atom Definition Section --
	-
	-read_data system.data
	-
	-# -- Settings Section --
	-
	-include system.in.settings
	-
	-# -- Run Section --
	-
	-
	-timestep 1.0
	-dump 1 all custom 500 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 500 # time interval for printing out "thermo" data
	-
	-
	-velocity groupB zero angular
	-velocity groupB zero linear
	-# (I'm not sure if the two lines above are necessary, but they don't hurt.)
	-
	-# This next line is somewhat controversial. Feel free to delete this next line
	-
	-fix Ffreezestuff groupB rigid single force * off off off torque * off off off
	-
	-#(Neither Trung or Steve Plimpton use fix rigid for immobilizing objects, but
	-# I noticed that at NPT, it does a better job of maintaining the correct volume)
	-
	-# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the
	-# forces between immobilized atoms.
	-neigh_modify exclude group groupB groupB
	-
	-
	-# ------------------- NPT -----------------------
	-
	-# 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
	-compute pressMobile all pressure tempMobile
	-
	-thermo_style custom step c_tempMobile c_pressMobile temp press vol
	-
	-# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction
	-
	-fix fMoveStuff mobile npt temp 300 300 100 z 500 500 1000.0 dilate mobile
	-
	-fix_modify fMoveStuff temp tempMobile
	-
	-run 60000
	-
	-write_restart system_after_npt.rst
	diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
	deleted file mode 100644
	index 8ef52b1ed..000000000
	--- a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
	+++ /dev/null
	@@ -1,44 +0,0 @@
	-# -- Init Section --
	-
	-include system.in.init
	-
	-# -- Atom Definition Section --
	-
	-read_data system.data
	-
	-# -- Settings Section --
	-
	-include system.in.settings
	-
	-# -- Run Section --
	-
	-
	-timestep 1.0
	-dump 1 all custom 100 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 100 # 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
	-compute pressMobile all pressure tempMobile
	-
	-# Integrate the equations of motion:
	-fix fMoveStuff mobile nvt temp 300.0 300.0 100.0
	-fix_modify fMoveStuff temp tempMobile
	-
	-
	-run 200000
	-
	-write_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/README.TXT
	deleted file mode 100644
	index 31abcd66e..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT
	deleted file mode 100644
	index a52f73ff7..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh
	deleted file mode 100755
	index 45bd2d451..000000000
	--- a/tools/moltemplate/examples/CG_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_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh
	deleted file mode 100755
	index f2462426f..000000000
	--- a/tools/moltemplate/examples/CG_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-dihdedrals 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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualise.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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt
	deleted file mode 100644
	index e43026ba9..000000000
	--- a/tools/moltemplate/examples/CG_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) = 4eps_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt
	deleted file mode 100644
	index 54e2de437..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt
	deleted file mode 100644
	index 8266d2a89..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_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/CG_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 4.0piRR4.0eps(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 4.0pieps(R/r) (0.2term10 - 0.5h*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 = 4.0epspi(R/r) (0.2term10 - 0.5h*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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_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/CG_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
	-# 5.4epsilon and 6.0epsilon. 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 -AtermA - BtermB
	-
	-# 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 = (0.5sin(0.5(phi-phiA)conv_units)
	- expA * pow(cos(0.5(phi-phiA)conv_units), expA-1.0))
	- termB = (0.5sin(0.5(phi-phiB)conv_units)
	- expB * pow(cos(0.5(phi-phiB)conv_units), expB-1.0))
	- return -conv_units(AtermA + 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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt
	deleted file mode 100644
	index d70ea9b1f..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_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/CG_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
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	-1058 5.285 68.747688604 -1057.2880173
	-1059 5.29 74.2485588048 -1144.28722519
	-1060 5.295 80.2034084511 -1238.99729941
	-1061 5.3 86.6526140455 -1342.159288
	-1062 5.305 93.6404466809 -1454.59134086
	-1063 5.31 101.215478776 -1577.19736408
	-1064 5.315 109.431036641 -1710.97671817
	-1065 5.32 118.34570442 -1857.03509508
	-1066 5.325 128.023885682 -2016.59672751
	-1067 5.33 138.536429746 -2191.01810522
	-1068 5.335 149.961330771 -2381.80339751
	-1069 5.34 162.384508682 -2590.62180929
	-1070 5.345 175.900682252 -2819.32713038
	-1071 5.35 190.614346018 -3069.97977484
	-1072 5.355 206.640864322 -3344.87165027
	-1073 5.36 224.107697564 -3646.55424631
	-1074 5.365 243.155777879 -3977.87038879
	-1075 5.37 263.94105378 -4341.99017232
	-1076 5.375 286.636226144 -4742.45166023
	-1077 5.38 311.432700984 -5183.20703007
	-1078 5.385 338.542788186 -5668.67494529
	-1079 5.39 368.202179507 -6203.80005377
	-1080 5.395 400.672744018 -6794.12065257
	-1081 5.4 436.245684759 -7445.84572074
	-1082 5.405 475.24510682 -8165.94271045
	-1083 5.41 518.032054593 -8962.23770766
	-1084 5.415 565.009084574 -9843.52983097
	-1085 5.42 616.625450212 -10819.7220392
	-1086 5.425 673.382986997 -11901.9708721
	-1087 5.43 735.842799605 -13102.8580625
	-1088 5.435 804.63286882 -14436.5874481
	-1089 5.44 880.456714455 -15919.2111828
	-1090 5.445 964.103272175 -17568.8899241
	-1091 5.45 1056.45816742 -19406.1924747
	-1092 5.455 1158.5165993 -21454.4412936
	-1093 5.46 1271.39808224 -23740.1114163
	-1094 5.465 1396.36333377 -26293.2916416
	-1095 5.47 1534.83364542 -29148.2184174
	-1096 5.475 1688.41312989 -32343.8947285
	-1097 5.48 1858.91430495 -35924.8085125
	-1098 5.485 2048.38755344 -39941.7677902
	-1099 5.49 2259.15509234 -44452.8728701
	-1100 5.495 2493.85019506 -49524.6497873
	-1101 5.5 2755.46254268 -55233.3736945
	-1102 5.505 3047.39073711 -61666.616398
	-1103 5.51 3373.50319557 -68925.0588203
	-1104 5.515 3738.20886949 -77124.6171126
	-1105 5.52 4146.5394972 -86398.9407376
	-1106 5.525 4604.24542007 -96902.3524517
	-1107 5.53 5117.90737492 -108813.314199
	-1108 5.535 5695.06713732 -122338.52003
	-1109 5.54 6344.38044627 -137717.737992
	-1110 5.545 7075.79631164 -155229.548338
	-1111 5.55 7900.76761787 -175198.156456
	-1112 5.555 8832.49892104 -198001.497004
	-1113 5.56 9886.23853195 -224080.892415
	-1114 5.565 11079.6234321 -253952.586497
	-1115 5.57 12433.0873442 -288221.54474
	-1116 5.575 13970.3444496 -327598.000683
	-1117 5.58 15718.9639006 -372917.336362
	-1118 5.585 17711.0535455 -425164.019948
	-1119 5.59 19984.0753011 -485500.491894
	-1120 5.595 22581.8195717 -555302.100981
	-1121 5.6 25555.5722525 -636199.454754
	-1122 5.605 28965.5154724 -730129.879058
	-1123 5.61 32882.4127048 -839400.097247
	-1124 5.615 37389.6406876 -966762.764619
	-1125 5.62 42585.6453685 -1115510.15847
	-1126 5.625 48586.9176207 -1289589.16849
	-1127 5.63 55531.6077773 -1493742.80799
	-1128 5.635 63583.9274287 -1733684.84106
	-1129 5.64 72939.5241308 -2016315.88337
	-1130 5.645 83832.0618829 -2349991.60166
	-1131 5.65 96541.300368 -2744856.56324
	-1132 5.655 111403.042767 -3213261.07776
	-1133 5.66 128821.420452 -3770283.30061
	-1134 5.665 149284.109551 -4434385.29693
	-1135 5.67 173381.238005 -5228240.185
	-1136 5.675 201828.953692 -6179778.54971
	-1137 5.68 235498.900026 -7323516.93224
	-1138 5.685 275455.2056 -8702250.57742
	-1139 5.69 323001.06674 -10369218.4143
	-1140 5.695 379737.623748 -12390882.7371
	-1141 5.7 447638.654038 -14850512.384
	-1142 5.705 529145.697826 -17852820.7393
	-1143 5.71 627289.689791 -21529994.6762
	-1144 5.715 745847.124656 -26049566.1236
	-1145 5.72 889541.417924 -31624736.2614
	-1146 5.725 1064303.6889 -38527980.3963
	-1147 5.73 1277612.0471 -47109063.5591
	-1148 5.735 1538935.10642 -57819017.4811
	-1149 5.74 1860314.59485 -71242218.9505
	-1150 5.745 2257134.5845 -88139540.3817
	-1151 5.75 2749142.49547 -109506722.176
	-1152 5.755 3361811.73098 -136653799.897
	-1153 5.76 4128170.65016 -171313840.077
	-1154 5.765 5091272.07333 -215792744.495
	-1155 5.77 6307548.29223 -273176998.31
	-1156 5.775 7851398.52158 -347623759.363
	-1157 5.78 9821503.74726 -444768835.455
	-1158 5.785 12349580.5127 -572304762.479
	-1159 5.79 15612604.744 -740806327.342
	-1160 5.795 19850012.3018 -964919124.004
	-1161 5.8 25388097.1921 -1265085490.72
	-1162 5.805 32674911.255 -1670073366.45
	-1163 5.81 42330627.3386 -2220716617.13
	-1164 5.815 55220893.742 -2975502155.22
	-1165 5.82 72564721.5485 -4019002953.22
	-1166 5.825 96094798.4335 -5474746758.15
	-1167 5.83 128298297.388 -7525081897.32
	-1168 5.835 172782757.396 -10442221387.6
	-1169 5.84 234838762.891 -14637386017.7
	-1170 5.845 322316442.616 -20739670704.4
	-1171 5.85 447009526.718 -29724465089.5
	-1172 5.855 626872755.056 -43125823862.6
	-1173 5.86 889629660.718 -63393502739.0
	-1174 5.865 1278740106.83 -94503868935.1
	-1175 5.87 1863446791.23 -1.43025101229e+11
	-1176 5.875 2756012237.96 -2.20012469835e+11
	-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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_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/CG_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
	-40 0.195 8.50803294874e-07 -2.01969724788e-07
	-41 0.2 8.51826600486e-07 -2.07355135913e-07
	-42 0.205 8.52876872743e-07 -2.12756452745e-07
	-43 0.21 8.5395419223e-07 -2.18174099007e-07
	-44 0.215 8.55058641658e-07 -2.23608500394e-07
	-45 0.22 8.56190305871e-07 -2.29060084623e-07
	-46 0.225 8.57349271858e-07 -2.34529281482e-07
	-47 0.23 8.5853562876e-07 -2.40016522891e-07
	-48 0.235 8.59749467885e-07 -2.4552224295e-07
	-49 0.24 8.60990882715e-07 -2.51046877993e-07
	-50 0.245 8.62259968921e-07 -2.56590866647e-07
	-51 0.25 8.63556824372e-07 -2.62154649881e-07
	-52 0.255 8.64881549149e-07 -2.67738671065e-07
	-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
	-125 0.62 1.04676797537e-06 -7.64274544386e-07
	-126 0.625 1.0506107378e-06 -7.72841223537e-07
	-127 0.63 1.05449649623e-06 -7.81473080451e-07
	-128 0.635 1.05842557863e-06 -7.90170949513e-07
	-129 0.64 1.06239831715e-06 -7.98935673896e-07
	-130 0.645 1.06641504821e-06 -8.07768105686e-07
	-131 0.65 1.07047611249e-06 -8.1666910601e-07
	-132 0.655 1.074581855e-06 -8.25639545171e-07
	-133 0.66 1.07873262514e-06 -8.34680302772e-07
	-134 0.665 1.08292877671e-06 -8.43792267857e-07
	-135 0.67 1.08717066799e-06 -8.52976339042e-07
	-136 0.675 1.09145866179e-06 -8.62233424653e-07
	-137 0.68 1.09579312546e-06 -8.71564442867e-07
	-138 0.685 1.10017443099e-06 -8.80970321849e-07
	-139 0.69 1.10460295501e-06 -8.90451999898e-07
	-140 0.695 1.1090790789e-06 -9.0001042559e-07
	-141 0.7 1.11360318878e-06 -9.09646557926e-07
	-142 0.705 1.1181756756e-06 -9.19361366479e-07
	-143 0.71 1.1227969352e-06 -9.29155831544e-07
	-144 0.715 1.12746736833e-06 -9.39030944294e-07
	-145 0.72 1.13218738073e-06 -9.48987706931e-07
	-146 0.725 1.13695738317e-06 -9.59027132844e-07
	-147 0.73 1.14177779154e-06 -9.6915024677e-07
	-148 0.735 1.14664902685e-06 -9.79358084952e-07
	-149 0.74 1.15157151534e-06 -9.89651695304e-07
	-150 0.745 1.15654568852e-06 -1.00003213758e-06
	-151 0.75 1.16157198322e-06 -1.01050048352e-06
	-152 0.755 1.16665084166e-06 -1.02105781707e-06
	-153 0.76 1.17178271153e-06 -1.0317052345e-06
	-154 0.765 1.176968046e-06 -1.0424438446e-06
	-155 0.77 1.18220730383e-06 -1.05327476888e-06
	-156 0.775 1.18750094943e-06 -1.0641991417e-06
	-157 0.78 1.19284945291e-06 -1.07521811051e-06
	-158 0.785 1.19825329013e-06 -1.08633283599e-06
	-159 0.79 1.20371294282e-06 -1.09754449225e-06
	-160 0.795 1.20922889858e-06 -1.10885426703e-06
	-161 0.8 1.21480165102e-06 -1.12026336191e-06
	-162 0.805 1.22043169976e-06 -1.13177299243e-06
	-163 0.81 1.22611955055e-06 -1.14338438839e-06
	-164 0.815 1.23186571533e-06 -1.15509879397e-06
	-165 0.82 1.23767071227e-06 -1.16691746799e-06
	-166 0.825 1.24353506591e-06 -1.17884168407e-06
	-167 0.83 1.24945930716e-06 -1.19087273088e-06
	-168 0.835 1.25544397344e-06 -1.20301191233e-06
	-169 0.84 1.26148960871e-06 -1.21526054778e-06
	-170 0.845 1.26759676357e-06 -1.22761997229e-06
	-171 0.85 1.27376599533e-06 -1.2400915368e-06
	-172 0.855 1.27999786811e-06 -1.2526766084e-06
	-173 0.86 1.2862929529e-06 -1.26537657052e-06
	-174 0.865 1.29265182763e-06 -1.27819282318e-06
	-175 0.87 1.29907507731e-06 -1.29112678323e-06
	-176 0.875 1.30556329404e-06 -1.30417988457e-06
	-177 0.88 1.31211707714e-06 -1.31735357842e-06
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	-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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat
	deleted file mode 100644
	index d660fee30..000000000
	--- a/tools/moltemplate/examples/CG_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
	-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
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	-151 150.0 -5.19709125082 0.0281998053314
	-152 151.0 -5.22527672173 0.0281566017347
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	-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
	-202 201.0 -5.42696928781 -0.0534322755136
	-203 202.0 -5.37257284377 -0.055351918363
	-204 203.0 -5.316283293 -0.0572180396955
	-205 204.0 -5.25815548345 -0.059028008202
	-206 205.0 -5.19824682901 -0.0607793239895
	-207 206.0 -5.13661717604 -0.0624696227052
	-208 207.0 -5.0733286659 -0.0640966792879
	-209 208.0 -5.00844559393 -0.0656584113417
	-210 209.0 -4.94203426529 -0.0671528821253
	-211 210.0 -4.87416284794 -0.0685783031513
	-212 211.0 -4.80490122327 -0.0699330363936
	-213 212.0 -4.7343208347 -0.0712155960973
	-214 213.0 -4.66249453466 -0.0724246501921
	-215 214.0 -4.58949643037 -0.0735590213066
	-216 215.0 -4.51540172879 -0.0746176873849
	-217 216.0 -4.44028658118 -0.0755997819067
	-218 217.0 -4.3642279276 -0.0765045937139
	-219 218.0 -4.28730334182 -0.0773315664459
	-220 219.0 -4.20959087694 -0.0780802975905
	-221 220.0 -4.13116891218 -0.0787505371538
	-222 221.0 -4.0521160012 -0.0793421859574
	-223 222.0 -3.97251072229 -0.0798552935693
	-224 223.0 -3.89243153076 -0.0802900558785
	-225 224.0 -3.81195661404 -0.0806468123209
	-226 225.0 -3.73116374964 -0.0809260427693
	-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
	-233 232.0 -3.16309604794 -0.0807780007742
	-234 233.0 -3.08246641287 -0.0804698782381
	-235 234.0 -3.00217880976 -0.0800942039176
	-236 235.0 -2.92229997393 -0.079652625851
	-237 236.0 -2.84289494829 -0.0791468798106
	-238 237.0 -2.76402699866 -0.0785787832348
	-239 238.0 -2.68575753514 -0.0779502290223
	-240 239.0 -2.60814603984 -0.077263179207
	-241 240.0 -2.53125000097 -0.0765196585342
	-242 241.0 -2.4551248533 -0.0757217479546
	-243 242.0 -2.37982392531 -0.0748715780578
	-244 243.0 -2.30539839282 -0.073971322463
	-245 244.0 -2.23189723927 -0.0730231911866
	-246 245.0 -2.15936722267 -0.072029424007
	-247 246.0 -2.0878528491 -0.0709922838436
	-248 247.0 -2.01739635293 -0.0699140501714
	-249 248.0 -1.94803768347 -0.0687970124882
	-250 249.0 -1.87981449824 -0.0676434638537
	-251 250.0 -1.81276216256 -0.0664556945194
	-252 251.0 -1.74691375554 -0.0652359856651
	-253 252.0 -1.68230008218 -0.0639866032624
	-254 253.0 -1.61894969164 -0.0627097920793
	-255 254.0 -1.55688890134 -0.0614077698443
	-256 255.0 -1.49614182687 -0.0600827215855
	-257 256.0 -1.43673041741 -0.05873679416
	-258 257.0 -1.37867449659 -0.0573720909874
	-259 258.0 -1.32199180845 -0.0559906670036
	-260 259.0 -1.26669806833 -0.0545945238457
	-261 260.0 -1.21280701853 -0.0531856052829
	-262 261.0 -1.1603304883 -0.0517657929031
	-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
	-324 323.0 -0.560311056174 0.0303203258736
	-325 324.0 -0.59130230198 0.0316630167284
	-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
	-333 332.0 -0.887938493289 0.042513073745
	-334 333.0 -0.93112967973 0.0438687355968
	-335 334.0 -0.975674613021 0.0452203404434
	-336 335.0 -1.02156854218 0.0465664874361
	-337 336.0 -1.06880527714 0.0479056997168
	-338 337.0 -1.11737711415 0.0492364272675
	-339 338.0 -1.16727476416 0.0505570500574
	-340 339.0 -1.2184872845 0.051865881477
	-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/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min
	deleted file mode 100644
	index 321ba3c09..000000000
	--- a/tools/moltemplate/examples/CG_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt
	deleted file mode 100644
	index 7c0855cb8..000000000
	--- a/tools/moltemplate/examples/CG_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 read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT
	deleted file mode 100644
	index ecb9adad2..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
	deleted file mode 100755
	index 45bd2d451..000000000
	--- a/tools/moltemplate/examples/CG_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_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh
	deleted file mode 100755
	index f2462426f..000000000
	--- a/tools/moltemplate/examples/CG_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-dihdedrals 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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg
	deleted file mode 100644
	index c62a881b2..000000000
	Binary files a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg
	deleted file mode 100644
	index 38ef54396..000000000
	Binary files a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt
	deleted file mode 100644
	index e43026ba9..000000000
	--- a/tools/moltemplate/examples/CG_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) = 4eps_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt
	deleted file mode 100644
	index 54e2de437..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_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/CG_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 4.0piRR4.0eps(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 4.0pieps(R/r) (0.2term10 - 0.5h*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 = 4.0epspi(R/r) (0.2term10 - 0.5h*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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_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/CG_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
	-# 5.4epsilon and 6.0epsilon. 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 -AtermA - BtermB
	-
	-# 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 = (0.5sin(0.5(phi-phiA)conv_units)
	- expA * pow(cos(0.5(phi-phiA)conv_units), expA-1.0))
	- termB = (0.5sin(0.5(phi-phiB)conv_units)
	- expB * pow(cos(0.5(phi-phiB)conv_units), expB-1.0))
	- return -conv_units(AtermA + 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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt
	deleted file mode 100644
	index 1d37823b7..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles
	deleted file mode 100644
	index 7f95d7361..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles
	+++ /dev/null
	@@ -1,200 +0,0 @@
	-1 1 13 14 15
	-2 1 40 41 42
	-3 1 67 68 69
	-4 1 94 95 96
	-5 1 121 122 123
	-6 1 148 149 150
	-7 1 175 176 177
	-8 1 202 203 204
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type
	deleted file mode 100644
	index 6da6450d5..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type
	+++ /dev/null
	@@ -1 +0,0 @@
	- 1 @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/bond:1beadFrustrated/* @/bond:1beadFrustrated/*
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type.template
	deleted file mode 100644
	index aa72039fb..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type.template
	+++ /dev/null
	@@ -1 +0,0 @@
	- @/angle:1beadFrustrated/backbone @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/bond:1beadFrustrated/* @/bond:1beadFrustrated/*
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles.template
	deleted file mode 100644
	index 5848e6c2b..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles.template
	+++ /dev/null
	@@ -1,200 +0,0 @@
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms
	deleted file mode 100644
	index 4931bed87..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms
	+++ /dev/null
	@@ -1,224 +0,0 @@
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	-211 8 1 0.0 59.4 57.5 59.4
	-212 8 1 0.0 58.8 58.3 59.4
	-213 8 2 0.0 58.2 58.3 60.2
	-214 8 2 0.0 57.6 57.5 60.2
	-215 8 1 0.0 57.0 57.5 59.4
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	-223 15 4 0.0 40.0 40.0 0.0
	-224 16 4 0.0 40.0 40.0 40.0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms.template
	deleted file mode 100644
	index b21eea512..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms.template
	+++ /dev/null
	@@ -1,224 +0,0 @@
	-$/atom:proteins[0][0][0]/a1 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 17.6 21.7 20.0
	-$/atom:proteins[0][0][0]/a2 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 18.2 21.7 20.8
	-$/atom:proteins[0][0][0]/a3 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 18.8 22.5 20.8
	-$/atom:proteins[0][0][0]/a4 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 19.4 22.5 20.0
	-$/atom:proteins[0][0][0]/a5 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 20.0 21.7 20.0
	-$/atom:proteins[0][0][0]/a6 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 20.6 21.7 20.8
	-$/atom:proteins[0][0][0]/a7 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/N 0.0 21.2 22.5 20.8
	-$/atom:proteins[0][0][0]/a8 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/N 0.0 21.8 22.5 20.0
	-$/atom:proteins[0][0][0]/a9 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 22.4 21.7 20.0
	-$/atom:proteins[0][0][0]/a10 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 23.0 21.7 19.2
	-$/atom:proteins[0][0][0]/a11 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 23.0 20.7 19.2
	-$/atom:proteins[0][0][0]/a12 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 23.0 20.1 20.0
	-$/atom:proteins[0][0][0]/a13 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 23.8 19.5 20.0
	-$/atom:proteins[0][0][0]/a14 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 23.8 18.9 19.2
	-$/atom:proteins[0][0][0]/a15 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/N 0.0 23.0 18.3 19.2
	-$/atom:proteins[0][0][0]/a16 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/N 0.0 23.0 18.3 20.2
	-$/atom:proteins[0][0][0]/a17 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/N 0.0 22.4 17.5 20.2
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	-$/atom:proteins[0][0][0]/a20 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 20.6 18.3 20.2
	-$/atom:proteins[0][0][0]/a21 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 20.0 17.5 20.2
	-$/atom:proteins[0][0][0]/a22 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 19.4 17.5 19.4
	-$/atom:proteins[0][0][0]/a23 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/B 0.0 18.8 18.3 19.4
	-$/atom:proteins[0][0][0]/a24 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 18.2 18.3 20.2
	-$/atom:proteins[0][0][0]/a25 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 17.6 17.5 20.2
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	-$/atom:proteins[0][0][0]/a27 $/mol:proteins[0][0][0] @/atom:1beadFrustrated/L 0.0 16.4 18.3 19.4
	-$/atom:proteins[0][0][1]/a1 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 17.6 21.7 60.0
	-$/atom:proteins[0][0][1]/a2 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 18.2 21.7 60.8
	-$/atom:proteins[0][0][1]/a3 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 18.8 22.5 60.8
	-$/atom:proteins[0][0][1]/a4 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 19.4 22.5 60.0
	-$/atom:proteins[0][0][1]/a5 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 20.0 21.7 60.0
	-$/atom:proteins[0][0][1]/a6 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 20.6 21.7 60.8
	-$/atom:proteins[0][0][1]/a7 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/N 0.0 21.2 22.5 60.8
	-$/atom:proteins[0][0][1]/a8 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/N 0.0 21.8 22.5 60.0
	-$/atom:proteins[0][0][1]/a9 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 22.4 21.7 60.0
	-$/atom:proteins[0][0][1]/a10 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 23.0 21.7 59.2
	-$/atom:proteins[0][0][1]/a11 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 23.0 20.7 59.2
	-$/atom:proteins[0][0][1]/a12 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 23.0 20.1 60.0
	-$/atom:proteins[0][0][1]/a13 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 23.8 19.5 60.0
	-$/atom:proteins[0][0][1]/a14 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 23.8 18.9 59.2
	-$/atom:proteins[0][0][1]/a15 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/N 0.0 23.0 18.3 59.2
	-$/atom:proteins[0][0][1]/a16 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/N 0.0 23.0 18.3 60.2
	-$/atom:proteins[0][0][1]/a17 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/N 0.0 22.4 17.5 60.2
	-$/atom:proteins[0][0][1]/a18 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 21.8 17.5 59.4
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	-$/atom:proteins[0][0][1]/a22 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 19.4 17.5 59.4
	-$/atom:proteins[0][0][1]/a23 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 18.8 18.3 59.4
	-$/atom:proteins[0][0][1]/a24 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 18.2 18.3 60.2
	-$/atom:proteins[0][0][1]/a25 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 17.6 17.5 60.2
	-$/atom:proteins[0][0][1]/a26 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/B 0.0 17.0 17.5 59.4
	-$/atom:proteins[0][0][1]/a27 $/mol:proteins[0][0][1] @/atom:1beadFrustrated/L 0.0 16.4 18.3 59.4
	-$/atom:proteins[0][1][0]/a1 $/mol:proteins[0][1][0] @/atom:1beadFrustrated/L 0.0 17.6 61.7 20.0
	-$/atom:proteins[0][1][0]/a2 $/mol:proteins[0][1][0] @/atom:1beadFrustrated/B 0.0 18.2 61.7 20.8
	-$/atom:proteins[0][1][0]/a3 $/mol:proteins[0][1][0] @/atom:1beadFrustrated/L 0.0 18.8 62.5 20.8
	-$/atom:proteins[0][1][0]/a4 $/mol:proteins[0][1][0] @/atom:1beadFrustrated/B 0.0 19.4 62.5 20.0
	-$/atom:proteins[0][1][0]/a5 $/mol:proteins[0][1][0] @/atom:1beadFrustrated/L 0.0 20.0 61.7 20.0
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	-$/atom:proteins[1][1][1]/a19 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/B 0.0 61.2 58.3 59.4
	-$/atom:proteins[1][1][1]/a20 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/L 0.0 60.6 58.3 60.2
	-$/atom:proteins[1][1][1]/a21 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/L 0.0 60.0 57.5 60.2
	-$/atom:proteins[1][1][1]/a22 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/B 0.0 59.4 57.5 59.4
	-$/atom:proteins[1][1][1]/a23 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/B 0.0 58.8 58.3 59.4
	-$/atom:proteins[1][1][1]/a24 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/L 0.0 58.2 58.3 60.2
	-$/atom:proteins[1][1][1]/a25 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/L 0.0 57.6 57.5 60.2
	-$/atom:proteins[1][1][1]/a26 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/B 0.0 57.0 57.5 59.4
	-$/atom:proteins[1][1][1]/a27 $/mol:proteins[1][1][1] @/atom:1beadFrustrated/L 0.0 56.4 58.3 59.4
	-$/atom:chaperones[0][0][0]/C $/mol:chaperones[0][0][0] @/atom:Minichaperone/C 0.0 0.0 0.0 0.0
	-$/atom:chaperones[0][0][1]/C $/mol:chaperones[0][0][1] @/atom:Minichaperone/C 0.0 0.0 0.0 40.0
	-$/atom:chaperones[0][1][0]/C $/mol:chaperones[0][1][0] @/atom:Minichaperone/C 0.0 0.0 40.0 0.0
	-$/atom:chaperones[0][1][1]/C $/mol:chaperones[0][1][1] @/atom:Minichaperone/C 0.0 0.0 40.0 40.0
	-$/atom:chaperones[1][0][0]/C $/mol:chaperones[1][0][0] @/atom:Minichaperone/C 0.0 40.0 0.0 0.0
	-$/atom:chaperones[1][0][1]/C $/mol:chaperones[1][0][1] @/atom:Minichaperone/C 0.0 40.0 0.0 40.0
	-$/atom:chaperones[1][1][0]/C $/mol:chaperones[1][1][0] @/atom:Minichaperone/C 0.0 40.0 40.0 0.0
	-$/atom:chaperones[1][1][1]/C $/mol:chaperones[1][1][1] @/atom:Minichaperone/C 0.0 40.0 40.0 40.0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Bonds b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Bonds
	deleted file mode 100644
	index 8ed540e67..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Bonds
	+++ /dev/null
	@@ -1,208 +0,0 @@
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Bonds.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Bonds.template
	deleted file mode 100644
	index 21945c13c..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Bonds.template
	+++ /dev/null
	@@ -1,208 +0,0 @@
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Boundary b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Boundary
	deleted file mode 100644
	index 2fa8d12ee..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Boundary
	+++ /dev/null
	@@ -1,3 +0,0 @@
	- 0.0 80.0 xlo xhi
	- 0.0 80.0 ylo yhi
	- 0.0 80.0 zlo zhi
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Boundary.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Boundary.template
	deleted file mode 100644
	index 2fa8d12ee..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Boundary.template
	+++ /dev/null
	@@ -1,3 +0,0 @@
	- 0.0 80.0 xlo xhi
	- 0.0 80.0 ylo yhi
	- 0.0 80.0 zlo zhi
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Dihedrals b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Dihedrals
	deleted file mode 100644
	index fa3a978ba..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Dihedrals
	+++ /dev/null
	@@ -1,152 +0,0 @@
	-1 1 1 2 3 4
	-2 1 2 3 4 5
	-3 1 3 4 5 6
	-4 1 4 5 6 7
	-5 1 8 9 10 11
	-6 1 9 10 11 12
	-7 1 10 11 12 13
	-8 1 11 12 13 14
	-9 1 12 13 14 15
	-10 2 15 16 17 18
	-11 2 16 17 18 19
	-12 2 17 18 19 20
	-13 2 18 19 20 21
	-14 2 19 20 21 22
	-15 2 20 21 22 23
	-16 2 21 22 23 24
	-17 2 22 23 24 25
	-18 2 23 24 25 26
	-19 2 24 25 26 27
	-20 1 28 29 30 31
	-21 1 29 30 31 32
	-22 1 30 31 32 33
	-23 1 31 32 33 34
	-24 1 35 36 37 38
	-25 1 36 37 38 39
	-26 1 37 38 39 40
	-27 1 38 39 40 41
	-28 1 39 40 41 42
	-29 2 42 43 44 45
	-30 2 43 44 45 46
	-31 2 44 45 46 47
	-32 2 45 46 47 48
	-33 2 46 47 48 49
	-34 2 47 48 49 50
	-35 2 48 49 50 51
	-36 2 49 50 51 52
	-37 2 50 51 52 53
	-38 2 51 52 53 54
	-39 1 55 56 57 58
	-40 1 56 57 58 59
	-41 1 57 58 59 60
	-42 1 58 59 60 61
	-43 1 62 63 64 65
	-44 1 63 64 65 66
	-45 1 64 65 66 67
	-46 1 65 66 67 68
	-47 1 66 67 68 69
	-48 2 69 70 71 72
	-49 2 70 71 72 73
	-50 2 71 72 73 74
	-51 2 72 73 74 75
	-52 2 73 74 75 76
	-53 2 74 75 76 77
	-54 2 75 76 77 78
	-55 2 76 77 78 79
	-56 2 77 78 79 80
	-57 2 78 79 80 81
	-58 1 82 83 84 85
	-59 1 83 84 85 86
	-60 1 84 85 86 87
	-61 1 85 86 87 88
	-62 1 89 90 91 92
	-63 1 90 91 92 93
	-64 1 91 92 93 94
	-65 1 92 93 94 95
	-66 1 93 94 95 96
	-67 2 96 97 98 99
	-68 2 97 98 99 100
	-69 2 98 99 100 101
	-70 2 99 100 101 102
	-71 2 100 101 102 103
	-72 2 101 102 103 104
	-73 2 102 103 104 105
	-74 2 103 104 105 106
	-75 2 104 105 106 107
	-76 2 105 106 107 108
	-77 1 109 110 111 112
	-78 1 110 111 112 113
	-79 1 111 112 113 114
	-80 1 112 113 114 115
	-81 1 116 117 118 119
	-82 1 117 118 119 120
	-83 1 118 119 120 121
	-84 1 119 120 121 122
	-85 1 120 121 122 123
	-86 2 123 124 125 126
	-87 2 124 125 126 127
	-88 2 125 126 127 128
	-89 2 126 127 128 129
	-90 2 127 128 129 130
	-91 2 128 129 130 131
	-92 2 129 130 131 132
	-93 2 130 131 132 133
	-94 2 131 132 133 134
	-95 2 132 133 134 135
	-96 1 136 137 138 139
	-97 1 137 138 139 140
	-98 1 138 139 140 141
	-99 1 139 140 141 142
	-100 1 143 144 145 146
	-101 1 144 145 146 147
	-102 1 145 146 147 148
	-103 1 146 147 148 149
	-104 1 147 148 149 150
	-105 2 150 151 152 153
	-106 2 151 152 153 154
	-107 2 152 153 154 155
	-108 2 153 154 155 156
	-109 2 154 155 156 157
	-110 2 155 156 157 158
	-111 2 156 157 158 159
	-112 2 157 158 159 160
	-113 2 158 159 160 161
	-114 2 159 160 161 162
	-115 1 163 164 165 166
	-116 1 164 165 166 167
	-117 1 165 166 167 168
	-118 1 166 167 168 169
	-119 1 170 171 172 173
	-120 1 171 172 173 174
	-121 1 172 173 174 175
	-122 1 173 174 175 176
	-123 1 174 175 176 177
	-124 2 177 178 179 180
	-125 2 178 179 180 181
	-126 2 179 180 181 182
	-127 2 180 181 182 183
	-128 2 181 182 183 184
	-129 2 182 183 184 185
	-130 2 183 184 185 186
	-131 2 184 185 186 187
	-132 2 185 186 187 188
	-133 2 186 187 188 189
	-134 1 190 191 192 193
	-135 1 191 192 193 194
	-136 1 192 193 194 195
	-137 1 193 194 195 196
	-138 1 197 198 199 200
	-139 1 198 199 200 201
	-140 1 199 200 201 202
	-141 1 200 201 202 203
	-142 1 201 202 203 204
	-143 2 204 205 206 207
	-144 2 205 206 207 208
	-145 2 206 207 208 209
	-146 2 207 208 209 210
	-147 2 208 209 210 211
	-148 2 209 210 211 212
	-149 2 210 211 212 213
	-150 2 211 212 213 214
	-151 2 212 213 214 215
	-152 2 213 214 215 216
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Dihedrals.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Dihedrals.template
	deleted file mode 100644
	index de8425ae4..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Dihedrals.template
	+++ /dev/null
	@@ -1,152 +0,0 @@
	- $/dihedral:proteins[0][0][0]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a1 $/atom:proteins[0][0][0]/a2 $/atom:proteins[0][0][0]/a3 $/atom:proteins[0][0][0]/a4
	- $/dihedral:proteins[0][0][0]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a2 $/atom:proteins[0][0][0]/a3 $/atom:proteins[0][0][0]/a4 $/atom:proteins[0][0][0]/a5
	- $/dihedral:proteins[0][0][0]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a3 $/atom:proteins[0][0][0]/a4 $/atom:proteins[0][0][0]/a5 $/atom:proteins[0][0][0]/a6
	- $/dihedral:proteins[0][0][0]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a4 $/atom:proteins[0][0][0]/a5 $/atom:proteins[0][0][0]/a6 $/atom:proteins[0][0][0]/a7
	- $/dihedral:proteins[0][0][0]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a8 $/atom:proteins[0][0][0]/a9 $/atom:proteins[0][0][0]/a10 $/atom:proteins[0][0][0]/a11
	- $/dihedral:proteins[0][0][0]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a9 $/atom:proteins[0][0][0]/a10 $/atom:proteins[0][0][0]/a11 $/atom:proteins[0][0][0]/a12
	- $/dihedral:proteins[0][0][0]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a10 $/atom:proteins[0][0][0]/a11 $/atom:proteins[0][0][0]/a12 $/atom:proteins[0][0][0]/a13
	- $/dihedral:proteins[0][0][0]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a11 $/atom:proteins[0][0][0]/a12 $/atom:proteins[0][0][0]/a13 $/atom:proteins[0][0][0]/a14
	- $/dihedral:proteins[0][0][0]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][0]/a12 $/atom:proteins[0][0][0]/a13 $/atom:proteins[0][0][0]/a14 $/atom:proteins[0][0][0]/a15
	- $/dihedral:proteins[0][0][0]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a15 $/atom:proteins[0][0][0]/a16 $/atom:proteins[0][0][0]/a17 $/atom:proteins[0][0][0]/a18
	- $/dihedral:proteins[0][0][0]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a16 $/atom:proteins[0][0][0]/a17 $/atom:proteins[0][0][0]/a18 $/atom:proteins[0][0][0]/a19
	- $/dihedral:proteins[0][0][0]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a17 $/atom:proteins[0][0][0]/a18 $/atom:proteins[0][0][0]/a19 $/atom:proteins[0][0][0]/a20
	- $/dihedral:proteins[0][0][0]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a18 $/atom:proteins[0][0][0]/a19 $/atom:proteins[0][0][0]/a20 $/atom:proteins[0][0][0]/a21
	- $/dihedral:proteins[0][0][0]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a19 $/atom:proteins[0][0][0]/a20 $/atom:proteins[0][0][0]/a21 $/atom:proteins[0][0][0]/a22
	- $/dihedral:proteins[0][0][0]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a20 $/atom:proteins[0][0][0]/a21 $/atom:proteins[0][0][0]/a22 $/atom:proteins[0][0][0]/a23
	- $/dihedral:proteins[0][0][0]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a21 $/atom:proteins[0][0][0]/a22 $/atom:proteins[0][0][0]/a23 $/atom:proteins[0][0][0]/a24
	- $/dihedral:proteins[0][0][0]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a22 $/atom:proteins[0][0][0]/a23 $/atom:proteins[0][0][0]/a24 $/atom:proteins[0][0][0]/a25
	- $/dihedral:proteins[0][0][0]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a23 $/atom:proteins[0][0][0]/a24 $/atom:proteins[0][0][0]/a25 $/atom:proteins[0][0][0]/a26
	- $/dihedral:proteins[0][0][0]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][0]/a24 $/atom:proteins[0][0][0]/a25 $/atom:proteins[0][0][0]/a26 $/atom:proteins[0][0][0]/a27
	- $/dihedral:proteins[0][0][1]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a1 $/atom:proteins[0][0][1]/a2 $/atom:proteins[0][0][1]/a3 $/atom:proteins[0][0][1]/a4
	- $/dihedral:proteins[0][0][1]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a2 $/atom:proteins[0][0][1]/a3 $/atom:proteins[0][0][1]/a4 $/atom:proteins[0][0][1]/a5
	- $/dihedral:proteins[0][0][1]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a3 $/atom:proteins[0][0][1]/a4 $/atom:proteins[0][0][1]/a5 $/atom:proteins[0][0][1]/a6
	- $/dihedral:proteins[0][0][1]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a4 $/atom:proteins[0][0][1]/a5 $/atom:proteins[0][0][1]/a6 $/atom:proteins[0][0][1]/a7
	- $/dihedral:proteins[0][0][1]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a8 $/atom:proteins[0][0][1]/a9 $/atom:proteins[0][0][1]/a10 $/atom:proteins[0][0][1]/a11
	- $/dihedral:proteins[0][0][1]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a9 $/atom:proteins[0][0][1]/a10 $/atom:proteins[0][0][1]/a11 $/atom:proteins[0][0][1]/a12
	- $/dihedral:proteins[0][0][1]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a10 $/atom:proteins[0][0][1]/a11 $/atom:proteins[0][0][1]/a12 $/atom:proteins[0][0][1]/a13
	- $/dihedral:proteins[0][0][1]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a11 $/atom:proteins[0][0][1]/a12 $/atom:proteins[0][0][1]/a13 $/atom:proteins[0][0][1]/a14
	- $/dihedral:proteins[0][0][1]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][0][1]/a12 $/atom:proteins[0][0][1]/a13 $/atom:proteins[0][0][1]/a14 $/atom:proteins[0][0][1]/a15
	- $/dihedral:proteins[0][0][1]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a15 $/atom:proteins[0][0][1]/a16 $/atom:proteins[0][0][1]/a17 $/atom:proteins[0][0][1]/a18
	- $/dihedral:proteins[0][0][1]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a16 $/atom:proteins[0][0][1]/a17 $/atom:proteins[0][0][1]/a18 $/atom:proteins[0][0][1]/a19
	- $/dihedral:proteins[0][0][1]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a17 $/atom:proteins[0][0][1]/a18 $/atom:proteins[0][0][1]/a19 $/atom:proteins[0][0][1]/a20
	- $/dihedral:proteins[0][0][1]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a18 $/atom:proteins[0][0][1]/a19 $/atom:proteins[0][0][1]/a20 $/atom:proteins[0][0][1]/a21
	- $/dihedral:proteins[0][0][1]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a19 $/atom:proteins[0][0][1]/a20 $/atom:proteins[0][0][1]/a21 $/atom:proteins[0][0][1]/a22
	- $/dihedral:proteins[0][0][1]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a20 $/atom:proteins[0][0][1]/a21 $/atom:proteins[0][0][1]/a22 $/atom:proteins[0][0][1]/a23
	- $/dihedral:proteins[0][0][1]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a21 $/atom:proteins[0][0][1]/a22 $/atom:proteins[0][0][1]/a23 $/atom:proteins[0][0][1]/a24
	- $/dihedral:proteins[0][0][1]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a22 $/atom:proteins[0][0][1]/a23 $/atom:proteins[0][0][1]/a24 $/atom:proteins[0][0][1]/a25
	- $/dihedral:proteins[0][0][1]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a23 $/atom:proteins[0][0][1]/a24 $/atom:proteins[0][0][1]/a25 $/atom:proteins[0][0][1]/a26
	- $/dihedral:proteins[0][0][1]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][0][1]/a24 $/atom:proteins[0][0][1]/a25 $/atom:proteins[0][0][1]/a26 $/atom:proteins[0][0][1]/a27
	- $/dihedral:proteins[0][1][0]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a1 $/atom:proteins[0][1][0]/a2 $/atom:proteins[0][1][0]/a3 $/atom:proteins[0][1][0]/a4
	- $/dihedral:proteins[0][1][0]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a2 $/atom:proteins[0][1][0]/a3 $/atom:proteins[0][1][0]/a4 $/atom:proteins[0][1][0]/a5
	- $/dihedral:proteins[0][1][0]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a3 $/atom:proteins[0][1][0]/a4 $/atom:proteins[0][1][0]/a5 $/atom:proteins[0][1][0]/a6
	- $/dihedral:proteins[0][1][0]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a4 $/atom:proteins[0][1][0]/a5 $/atom:proteins[0][1][0]/a6 $/atom:proteins[0][1][0]/a7
	- $/dihedral:proteins[0][1][0]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a8 $/atom:proteins[0][1][0]/a9 $/atom:proteins[0][1][0]/a10 $/atom:proteins[0][1][0]/a11
	- $/dihedral:proteins[0][1][0]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a9 $/atom:proteins[0][1][0]/a10 $/atom:proteins[0][1][0]/a11 $/atom:proteins[0][1][0]/a12
	- $/dihedral:proteins[0][1][0]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a10 $/atom:proteins[0][1][0]/a11 $/atom:proteins[0][1][0]/a12 $/atom:proteins[0][1][0]/a13
	- $/dihedral:proteins[0][1][0]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a11 $/atom:proteins[0][1][0]/a12 $/atom:proteins[0][1][0]/a13 $/atom:proteins[0][1][0]/a14
	- $/dihedral:proteins[0][1][0]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][0]/a12 $/atom:proteins[0][1][0]/a13 $/atom:proteins[0][1][0]/a14 $/atom:proteins[0][1][0]/a15
	- $/dihedral:proteins[0][1][0]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a15 $/atom:proteins[0][1][0]/a16 $/atom:proteins[0][1][0]/a17 $/atom:proteins[0][1][0]/a18
	- $/dihedral:proteins[0][1][0]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a16 $/atom:proteins[0][1][0]/a17 $/atom:proteins[0][1][0]/a18 $/atom:proteins[0][1][0]/a19
	- $/dihedral:proteins[0][1][0]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a17 $/atom:proteins[0][1][0]/a18 $/atom:proteins[0][1][0]/a19 $/atom:proteins[0][1][0]/a20
	- $/dihedral:proteins[0][1][0]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a18 $/atom:proteins[0][1][0]/a19 $/atom:proteins[0][1][0]/a20 $/atom:proteins[0][1][0]/a21
	- $/dihedral:proteins[0][1][0]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a19 $/atom:proteins[0][1][0]/a20 $/atom:proteins[0][1][0]/a21 $/atom:proteins[0][1][0]/a22
	- $/dihedral:proteins[0][1][0]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a20 $/atom:proteins[0][1][0]/a21 $/atom:proteins[0][1][0]/a22 $/atom:proteins[0][1][0]/a23
	- $/dihedral:proteins[0][1][0]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a21 $/atom:proteins[0][1][0]/a22 $/atom:proteins[0][1][0]/a23 $/atom:proteins[0][1][0]/a24
	- $/dihedral:proteins[0][1][0]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a22 $/atom:proteins[0][1][0]/a23 $/atom:proteins[0][1][0]/a24 $/atom:proteins[0][1][0]/a25
	- $/dihedral:proteins[0][1][0]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a23 $/atom:proteins[0][1][0]/a24 $/atom:proteins[0][1][0]/a25 $/atom:proteins[0][1][0]/a26
	- $/dihedral:proteins[0][1][0]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][0]/a24 $/atom:proteins[0][1][0]/a25 $/atom:proteins[0][1][0]/a26 $/atom:proteins[0][1][0]/a27
	- $/dihedral:proteins[0][1][1]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a1 $/atom:proteins[0][1][1]/a2 $/atom:proteins[0][1][1]/a3 $/atom:proteins[0][1][1]/a4
	- $/dihedral:proteins[0][1][1]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a2 $/atom:proteins[0][1][1]/a3 $/atom:proteins[0][1][1]/a4 $/atom:proteins[0][1][1]/a5
	- $/dihedral:proteins[0][1][1]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a3 $/atom:proteins[0][1][1]/a4 $/atom:proteins[0][1][1]/a5 $/atom:proteins[0][1][1]/a6
	- $/dihedral:proteins[0][1][1]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a4 $/atom:proteins[0][1][1]/a5 $/atom:proteins[0][1][1]/a6 $/atom:proteins[0][1][1]/a7
	- $/dihedral:proteins[0][1][1]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a8 $/atom:proteins[0][1][1]/a9 $/atom:proteins[0][1][1]/a10 $/atom:proteins[0][1][1]/a11
	- $/dihedral:proteins[0][1][1]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a9 $/atom:proteins[0][1][1]/a10 $/atom:proteins[0][1][1]/a11 $/atom:proteins[0][1][1]/a12
	- $/dihedral:proteins[0][1][1]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a10 $/atom:proteins[0][1][1]/a11 $/atom:proteins[0][1][1]/a12 $/atom:proteins[0][1][1]/a13
	- $/dihedral:proteins[0][1][1]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a11 $/atom:proteins[0][1][1]/a12 $/atom:proteins[0][1][1]/a13 $/atom:proteins[0][1][1]/a14
	- $/dihedral:proteins[0][1][1]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[0][1][1]/a12 $/atom:proteins[0][1][1]/a13 $/atom:proteins[0][1][1]/a14 $/atom:proteins[0][1][1]/a15
	- $/dihedral:proteins[0][1][1]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a15 $/atom:proteins[0][1][1]/a16 $/atom:proteins[0][1][1]/a17 $/atom:proteins[0][1][1]/a18
	- $/dihedral:proteins[0][1][1]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a16 $/atom:proteins[0][1][1]/a17 $/atom:proteins[0][1][1]/a18 $/atom:proteins[0][1][1]/a19
	- $/dihedral:proteins[0][1][1]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a17 $/atom:proteins[0][1][1]/a18 $/atom:proteins[0][1][1]/a19 $/atom:proteins[0][1][1]/a20
	- $/dihedral:proteins[0][1][1]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a18 $/atom:proteins[0][1][1]/a19 $/atom:proteins[0][1][1]/a20 $/atom:proteins[0][1][1]/a21
	- $/dihedral:proteins[0][1][1]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a19 $/atom:proteins[0][1][1]/a20 $/atom:proteins[0][1][1]/a21 $/atom:proteins[0][1][1]/a22
	- $/dihedral:proteins[0][1][1]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a20 $/atom:proteins[0][1][1]/a21 $/atom:proteins[0][1][1]/a22 $/atom:proteins[0][1][1]/a23
	- $/dihedral:proteins[0][1][1]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a21 $/atom:proteins[0][1][1]/a22 $/atom:proteins[0][1][1]/a23 $/atom:proteins[0][1][1]/a24
	- $/dihedral:proteins[0][1][1]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a22 $/atom:proteins[0][1][1]/a23 $/atom:proteins[0][1][1]/a24 $/atom:proteins[0][1][1]/a25
	- $/dihedral:proteins[0][1][1]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a23 $/atom:proteins[0][1][1]/a24 $/atom:proteins[0][1][1]/a25 $/atom:proteins[0][1][1]/a26
	- $/dihedral:proteins[0][1][1]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[0][1][1]/a24 $/atom:proteins[0][1][1]/a25 $/atom:proteins[0][1][1]/a26 $/atom:proteins[0][1][1]/a27
	- $/dihedral:proteins[1][0][0]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a1 $/atom:proteins[1][0][0]/a2 $/atom:proteins[1][0][0]/a3 $/atom:proteins[1][0][0]/a4
	- $/dihedral:proteins[1][0][0]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a2 $/atom:proteins[1][0][0]/a3 $/atom:proteins[1][0][0]/a4 $/atom:proteins[1][0][0]/a5
	- $/dihedral:proteins[1][0][0]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a3 $/atom:proteins[1][0][0]/a4 $/atom:proteins[1][0][0]/a5 $/atom:proteins[1][0][0]/a6
	- $/dihedral:proteins[1][0][0]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a4 $/atom:proteins[1][0][0]/a5 $/atom:proteins[1][0][0]/a6 $/atom:proteins[1][0][0]/a7
	- $/dihedral:proteins[1][0][0]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a8 $/atom:proteins[1][0][0]/a9 $/atom:proteins[1][0][0]/a10 $/atom:proteins[1][0][0]/a11
	- $/dihedral:proteins[1][0][0]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a9 $/atom:proteins[1][0][0]/a10 $/atom:proteins[1][0][0]/a11 $/atom:proteins[1][0][0]/a12
	- $/dihedral:proteins[1][0][0]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a10 $/atom:proteins[1][0][0]/a11 $/atom:proteins[1][0][0]/a12 $/atom:proteins[1][0][0]/a13
	- $/dihedral:proteins[1][0][0]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a11 $/atom:proteins[1][0][0]/a12 $/atom:proteins[1][0][0]/a13 $/atom:proteins[1][0][0]/a14
	- $/dihedral:proteins[1][0][0]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][0]/a12 $/atom:proteins[1][0][0]/a13 $/atom:proteins[1][0][0]/a14 $/atom:proteins[1][0][0]/a15
	- $/dihedral:proteins[1][0][0]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a15 $/atom:proteins[1][0][0]/a16 $/atom:proteins[1][0][0]/a17 $/atom:proteins[1][0][0]/a18
	- $/dihedral:proteins[1][0][0]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a16 $/atom:proteins[1][0][0]/a17 $/atom:proteins[1][0][0]/a18 $/atom:proteins[1][0][0]/a19
	- $/dihedral:proteins[1][0][0]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a17 $/atom:proteins[1][0][0]/a18 $/atom:proteins[1][0][0]/a19 $/atom:proteins[1][0][0]/a20
	- $/dihedral:proteins[1][0][0]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a18 $/atom:proteins[1][0][0]/a19 $/atom:proteins[1][0][0]/a20 $/atom:proteins[1][0][0]/a21
	- $/dihedral:proteins[1][0][0]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a19 $/atom:proteins[1][0][0]/a20 $/atom:proteins[1][0][0]/a21 $/atom:proteins[1][0][0]/a22
	- $/dihedral:proteins[1][0][0]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a20 $/atom:proteins[1][0][0]/a21 $/atom:proteins[1][0][0]/a22 $/atom:proteins[1][0][0]/a23
	- $/dihedral:proteins[1][0][0]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a21 $/atom:proteins[1][0][0]/a22 $/atom:proteins[1][0][0]/a23 $/atom:proteins[1][0][0]/a24
	- $/dihedral:proteins[1][0][0]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a22 $/atom:proteins[1][0][0]/a23 $/atom:proteins[1][0][0]/a24 $/atom:proteins[1][0][0]/a25
	- $/dihedral:proteins[1][0][0]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a23 $/atom:proteins[1][0][0]/a24 $/atom:proteins[1][0][0]/a25 $/atom:proteins[1][0][0]/a26
	- $/dihedral:proteins[1][0][0]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][0]/a24 $/atom:proteins[1][0][0]/a25 $/atom:proteins[1][0][0]/a26 $/atom:proteins[1][0][0]/a27
	- $/dihedral:proteins[1][0][1]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a1 $/atom:proteins[1][0][1]/a2 $/atom:proteins[1][0][1]/a3 $/atom:proteins[1][0][1]/a4
	- $/dihedral:proteins[1][0][1]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a2 $/atom:proteins[1][0][1]/a3 $/atom:proteins[1][0][1]/a4 $/atom:proteins[1][0][1]/a5
	- $/dihedral:proteins[1][0][1]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a3 $/atom:proteins[1][0][1]/a4 $/atom:proteins[1][0][1]/a5 $/atom:proteins[1][0][1]/a6
	- $/dihedral:proteins[1][0][1]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a4 $/atom:proteins[1][0][1]/a5 $/atom:proteins[1][0][1]/a6 $/atom:proteins[1][0][1]/a7
	- $/dihedral:proteins[1][0][1]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a8 $/atom:proteins[1][0][1]/a9 $/atom:proteins[1][0][1]/a10 $/atom:proteins[1][0][1]/a11
	- $/dihedral:proteins[1][0][1]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a9 $/atom:proteins[1][0][1]/a10 $/atom:proteins[1][0][1]/a11 $/atom:proteins[1][0][1]/a12
	- $/dihedral:proteins[1][0][1]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a10 $/atom:proteins[1][0][1]/a11 $/atom:proteins[1][0][1]/a12 $/atom:proteins[1][0][1]/a13
	- $/dihedral:proteins[1][0][1]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a11 $/atom:proteins[1][0][1]/a12 $/atom:proteins[1][0][1]/a13 $/atom:proteins[1][0][1]/a14
	- $/dihedral:proteins[1][0][1]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][0][1]/a12 $/atom:proteins[1][0][1]/a13 $/atom:proteins[1][0][1]/a14 $/atom:proteins[1][0][1]/a15
	- $/dihedral:proteins[1][0][1]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a15 $/atom:proteins[1][0][1]/a16 $/atom:proteins[1][0][1]/a17 $/atom:proteins[1][0][1]/a18
	- $/dihedral:proteins[1][0][1]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a16 $/atom:proteins[1][0][1]/a17 $/atom:proteins[1][0][1]/a18 $/atom:proteins[1][0][1]/a19
	- $/dihedral:proteins[1][0][1]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a17 $/atom:proteins[1][0][1]/a18 $/atom:proteins[1][0][1]/a19 $/atom:proteins[1][0][1]/a20
	- $/dihedral:proteins[1][0][1]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a18 $/atom:proteins[1][0][1]/a19 $/atom:proteins[1][0][1]/a20 $/atom:proteins[1][0][1]/a21
	- $/dihedral:proteins[1][0][1]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a19 $/atom:proteins[1][0][1]/a20 $/atom:proteins[1][0][1]/a21 $/atom:proteins[1][0][1]/a22
	- $/dihedral:proteins[1][0][1]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a20 $/atom:proteins[1][0][1]/a21 $/atom:proteins[1][0][1]/a22 $/atom:proteins[1][0][1]/a23
	- $/dihedral:proteins[1][0][1]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a21 $/atom:proteins[1][0][1]/a22 $/atom:proteins[1][0][1]/a23 $/atom:proteins[1][0][1]/a24
	- $/dihedral:proteins[1][0][1]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a22 $/atom:proteins[1][0][1]/a23 $/atom:proteins[1][0][1]/a24 $/atom:proteins[1][0][1]/a25
	- $/dihedral:proteins[1][0][1]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a23 $/atom:proteins[1][0][1]/a24 $/atom:proteins[1][0][1]/a25 $/atom:proteins[1][0][1]/a26
	- $/dihedral:proteins[1][0][1]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][0][1]/a24 $/atom:proteins[1][0][1]/a25 $/atom:proteins[1][0][1]/a26 $/atom:proteins[1][0][1]/a27
	- $/dihedral:proteins[1][1][0]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a1 $/atom:proteins[1][1][0]/a2 $/atom:proteins[1][1][0]/a3 $/atom:proteins[1][1][0]/a4
	- $/dihedral:proteins[1][1][0]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a2 $/atom:proteins[1][1][0]/a3 $/atom:proteins[1][1][0]/a4 $/atom:proteins[1][1][0]/a5
	- $/dihedral:proteins[1][1][0]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a3 $/atom:proteins[1][1][0]/a4 $/atom:proteins[1][1][0]/a5 $/atom:proteins[1][1][0]/a6
	- $/dihedral:proteins[1][1][0]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a4 $/atom:proteins[1][1][0]/a5 $/atom:proteins[1][1][0]/a6 $/atom:proteins[1][1][0]/a7
	- $/dihedral:proteins[1][1][0]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a8 $/atom:proteins[1][1][0]/a9 $/atom:proteins[1][1][0]/a10 $/atom:proteins[1][1][0]/a11
	- $/dihedral:proteins[1][1][0]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a9 $/atom:proteins[1][1][0]/a10 $/atom:proteins[1][1][0]/a11 $/atom:proteins[1][1][0]/a12
	- $/dihedral:proteins[1][1][0]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a10 $/atom:proteins[1][1][0]/a11 $/atom:proteins[1][1][0]/a12 $/atom:proteins[1][1][0]/a13
	- $/dihedral:proteins[1][1][0]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a11 $/atom:proteins[1][1][0]/a12 $/atom:proteins[1][1][0]/a13 $/atom:proteins[1][1][0]/a14
	- $/dihedral:proteins[1][1][0]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][0]/a12 $/atom:proteins[1][1][0]/a13 $/atom:proteins[1][1][0]/a14 $/atom:proteins[1][1][0]/a15
	- $/dihedral:proteins[1][1][0]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a15 $/atom:proteins[1][1][0]/a16 $/atom:proteins[1][1][0]/a17 $/atom:proteins[1][1][0]/a18
	- $/dihedral:proteins[1][1][0]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a16 $/atom:proteins[1][1][0]/a17 $/atom:proteins[1][1][0]/a18 $/atom:proteins[1][1][0]/a19
	- $/dihedral:proteins[1][1][0]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a17 $/atom:proteins[1][1][0]/a18 $/atom:proteins[1][1][0]/a19 $/atom:proteins[1][1][0]/a20
	- $/dihedral:proteins[1][1][0]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a18 $/atom:proteins[1][1][0]/a19 $/atom:proteins[1][1][0]/a20 $/atom:proteins[1][1][0]/a21
	- $/dihedral:proteins[1][1][0]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a19 $/atom:proteins[1][1][0]/a20 $/atom:proteins[1][1][0]/a21 $/atom:proteins[1][1][0]/a22
	- $/dihedral:proteins[1][1][0]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a20 $/atom:proteins[1][1][0]/a21 $/atom:proteins[1][1][0]/a22 $/atom:proteins[1][1][0]/a23
	- $/dihedral:proteins[1][1][0]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a21 $/atom:proteins[1][1][0]/a22 $/atom:proteins[1][1][0]/a23 $/atom:proteins[1][1][0]/a24
	- $/dihedral:proteins[1][1][0]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a22 $/atom:proteins[1][1][0]/a23 $/atom:proteins[1][1][0]/a24 $/atom:proteins[1][1][0]/a25
	- $/dihedral:proteins[1][1][0]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a23 $/atom:proteins[1][1][0]/a24 $/atom:proteins[1][1][0]/a25 $/atom:proteins[1][1][0]/a26
	- $/dihedral:proteins[1][1][0]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][0]/a24 $/atom:proteins[1][1][0]/a25 $/atom:proteins[1][1][0]/a26 $/atom:proteins[1][1][0]/a27
	- $/dihedral:proteins[1][1][1]/d1 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a1 $/atom:proteins[1][1][1]/a2 $/atom:proteins[1][1][1]/a3 $/atom:proteins[1][1][1]/a4
	- $/dihedral:proteins[1][1][1]/d2 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a2 $/atom:proteins[1][1][1]/a3 $/atom:proteins[1][1][1]/a4 $/atom:proteins[1][1][1]/a5
	- $/dihedral:proteins[1][1][1]/d3 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a3 $/atom:proteins[1][1][1]/a4 $/atom:proteins[1][1][1]/a5 $/atom:proteins[1][1][1]/a6
	- $/dihedral:proteins[1][1][1]/d4 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a4 $/atom:proteins[1][1][1]/a5 $/atom:proteins[1][1][1]/a6 $/atom:proteins[1][1][1]/a7
	- $/dihedral:proteins[1][1][1]/d8 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a8 $/atom:proteins[1][1][1]/a9 $/atom:proteins[1][1][1]/a10 $/atom:proteins[1][1][1]/a11
	- $/dihedral:proteins[1][1][1]/d9 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a9 $/atom:proteins[1][1][1]/a10 $/atom:proteins[1][1][1]/a11 $/atom:proteins[1][1][1]/a12
	- $/dihedral:proteins[1][1][1]/d10 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a10 $/atom:proteins[1][1][1]/a11 $/atom:proteins[1][1][1]/a12 $/atom:proteins[1][1][1]/a13
	- $/dihedral:proteins[1][1][1]/d11 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a11 $/atom:proteins[1][1][1]/a12 $/atom:proteins[1][1][1]/a13 $/atom:proteins[1][1][1]/a14
	- $/dihedral:proteins[1][1][1]/d12 @/dihedral:1beadFrustrated/beta $/atom:proteins[1][1][1]/a12 $/atom:proteins[1][1][1]/a13 $/atom:proteins[1][1][1]/a14 $/atom:proteins[1][1][1]/a15
	- $/dihedral:proteins[1][1][1]/d15 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a15 $/atom:proteins[1][1][1]/a16 $/atom:proteins[1][1][1]/a17 $/atom:proteins[1][1][1]/a18
	- $/dihedral:proteins[1][1][1]/d16 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a16 $/atom:proteins[1][1][1]/a17 $/atom:proteins[1][1][1]/a18 $/atom:proteins[1][1][1]/a19
	- $/dihedral:proteins[1][1][1]/d17 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a17 $/atom:proteins[1][1][1]/a18 $/atom:proteins[1][1][1]/a19 $/atom:proteins[1][1][1]/a20
	- $/dihedral:proteins[1][1][1]/d18 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a18 $/atom:proteins[1][1][1]/a19 $/atom:proteins[1][1][1]/a20 $/atom:proteins[1][1][1]/a21
	- $/dihedral:proteins[1][1][1]/d19 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a19 $/atom:proteins[1][1][1]/a20 $/atom:proteins[1][1][1]/a21 $/atom:proteins[1][1][1]/a22
	- $/dihedral:proteins[1][1][1]/d20 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a20 $/atom:proteins[1][1][1]/a21 $/atom:proteins[1][1][1]/a22 $/atom:proteins[1][1][1]/a23
	- $/dihedral:proteins[1][1][1]/d21 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a21 $/atom:proteins[1][1][1]/a22 $/atom:proteins[1][1][1]/a23 $/atom:proteins[1][1][1]/a24
	- $/dihedral:proteins[1][1][1]/d22 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a22 $/atom:proteins[1][1][1]/a23 $/atom:proteins[1][1][1]/a24 $/atom:proteins[1][1][1]/a25
	- $/dihedral:proteins[1][1][1]/d23 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a23 $/atom:proteins[1][1][1]/a24 $/atom:proteins[1][1][1]/a25 $/atom:proteins[1][1][1]/a26
	- $/dihedral:proteins[1][1][1]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a24 $/atom:proteins[1][1][1]/a25 $/atom:proteins[1][1][1]/a26 $/atom:proteins[1][1][1]/a27
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses
	deleted file mode 100644
	index 6d05b1617..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses
	+++ /dev/null
	@@ -1,4 +0,0 @@
	- 1 1.0
	- 2 1.0
	- 3 1.0
	- 4 100.0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses.template
	deleted file mode 100644
	index b9b23fd56..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses.template
	+++ /dev/null
	@@ -1,4 +0,0 @@
	- @/atom:1beadFrustrated/B 1.0
	- @/atom:1beadFrustrated/L 1.0
	- @/atom:1beadFrustrated/N 1.0
	- @/atom:Minichaperone/C 100.0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init
	deleted file mode 100644
	index 1a2282f0a..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init
	+++ /dev/null
	@@ -1,21 +0,0 @@
	- # --- 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)
	- units lj
	- atom_style full
	- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0
	- 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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init.template
	deleted file mode 100644
	index 1a2282f0a..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init.template
	+++ /dev/null
	@@ -1,21 +0,0 @@
	- # --- 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)
	- units lj
	- atom_style full
	- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0
	- 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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings
	deleted file mode 100644
	index a3d5ac7c7..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings
	+++ /dev/null
	@@ -1,30 +0,0 @@
	- pair_coeff 1 1 lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
	- pair_coeff 1 2 lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
	- pair_coeff 1 3 lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
	- pair_coeff 2 2 lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
	- pair_coeff 2 3 lj/charmm/coul/charmm/inter 0.25 1.0 1 0
	- pair_coeff 3 3 lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
	- bond_coeff 1 harmonic 100.0 1.0
	- angle_coeff 1 harmonic 13.3333333333 105.0
	- # style file keyword
	- dihedral_coeff 2 table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
	- dihedral_coeff 1 table table_dihedral_frustrated.dat FRUSTRATED_BETA
	- # No need to specify dihedral interactions in the turn regions. (none exist)
	- # Optional: define the atoms in the "proteins" group
	- group proteins type 1
	- group proteins type 2
	- group proteins type 3
	- # 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 4 4 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 4
	- pair_coeff 4 1 table table_minichaperone_h=0.6.dat CH_H0.6
	- pair_coeff 4 2 table table_minichaperone_h=0.dat CH_H0
	- pair_coeff 4 3 table table_minichaperone_h=0.dat CH_H0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings.template
	deleted file mode 100644
	index 38a0070ac..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings.template
	+++ /dev/null
	@@ -1,30 +0,0 @@
	- pair_coeff @/atom:1beadFrustrated/B @/atom:1beadFrustrated/B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
	- pair_coeff @/atom:1beadFrustrated/B @/atom:1beadFrustrated/L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
	- pair_coeff @/atom:1beadFrustrated/B @/atom:1beadFrustrated/N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
	- pair_coeff @/atom:1beadFrustrated/L @/atom:1beadFrustrated/L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
	- pair_coeff @/atom:1beadFrustrated/L @/atom:1beadFrustrated/N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
	- pair_coeff @/atom:1beadFrustrated/N @/atom:1beadFrustrated/N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
	- bond_coeff @/bond:1beadFrustrated/backbone harmonic 100.0 1.0
	- angle_coeff @/angle:1beadFrustrated/backbone harmonic 13.3333333333 105.0
	- # style file keyword
	- dihedral_coeff @/dihedral:1beadFrustrated/alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
	- dihedral_coeff @/dihedral:1beadFrustrated/beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
	- # No need to specify dihedral interactions in the turn regions. (none exist)
	- # Optional: define the atoms in the "proteins" group
	- group proteins type @/atom:1beadFrustrated/B
	- group proteins type @/atom:1beadFrustrated/L
	- group proteins type @/atom:1beadFrustrated/N
	- # 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:Minichaperone/C @/atom:Minichaperone/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:Minichaperone/C
	- 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
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/ttree_assignments.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/ttree_assignments.txt
	deleted file mode 100644
	index e28394ee6..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/ttree_assignments.txt
	+++ /dev/null
	@@ -1,808 +0,0 @@
	-@/atom:Minichaperone/C 4
	-@/atom:1beadFrustrated/B 1
	-@/atom:1beadFrustrated/L 2
	-@/atom:1beadFrustrated/N 3
	-@/angle:1beadFrustrated/backbone 1
	-@/bond:1beadFrustrated/backbone 1
	-@/dihedral:1beadFrustrated/alpha 2
	-@/dihedral:1beadFrustrated/beta 1
	-$/atom:proteins[0][0][0]/a1 1
	-$/atom:proteins[0][0][0]/a2 2
	-$/atom:proteins[0][0][0]/a3 3
	-$/atom:proteins[0][0][0]/a4 4
	-$/atom:proteins[0][0][0]/a5 5
	-$/atom:proteins[0][0][0]/a6 6
	-$/atom:proteins[0][0][0]/a7 7
	-$/atom:proteins[0][0][0]/a8 8
	-$/atom:proteins[0][0][0]/a9 9
	-$/atom:proteins[0][0][0]/a10 10
	-$/atom:proteins[0][0][0]/a11 11
	-$/atom:proteins[0][0][0]/a12 12
	-$/atom:proteins[0][0][0]/a13 13
	-$/atom:proteins[0][0][0]/a14 14
	-$/atom:proteins[0][0][0]/a15 15
	-$/atom:proteins[0][0][0]/a16 16
	-$/atom:proteins[0][0][0]/a17 17
	-$/atom:proteins[0][0][0]/a18 18
	-$/atom:proteins[0][0][0]/a19 19
	-$/atom:proteins[0][0][0]/a20 20
	-$/atom:proteins[0][0][0]/a21 21
	-$/atom:proteins[0][0][0]/a22 22
	-$/atom:proteins[0][0][0]/a23 23
	-$/atom:proteins[0][0][0]/a24 24
	-$/atom:proteins[0][0][0]/a25 25
	-$/atom:proteins[0][0][0]/a26 26
	-$/atom:proteins[0][0][0]/a27 27
	-$/atom:proteins[0][0][1]/a1 28
	-$/atom:proteins[0][0][1]/a2 29
	-$/atom:proteins[0][0][1]/a3 30
	-$/atom:proteins[0][0][1]/a4 31
	-$/atom:proteins[0][0][1]/a5 32
	-$/atom:proteins[0][0][1]/a6 33
	-$/atom:proteins[0][0][1]/a7 34
	-$/atom:proteins[0][0][1]/a8 35
	-$/atom:proteins[0][0][1]/a9 36
	-$/atom:proteins[0][0][1]/a10 37
	-$/atom:proteins[0][0][1]/a11 38
	-$/atom:proteins[0][0][1]/a12 39
	-$/atom:proteins[0][0][1]/a13 40
	-$/atom:proteins[0][0][1]/a14 41
	-$/atom:proteins[0][0][1]/a15 42
	-$/atom:proteins[0][0][1]/a16 43
	-$/atom:proteins[0][0][1]/a17 44
	-$/atom:proteins[0][0][1]/a18 45
	-$/atom:proteins[0][0][1]/a19 46
	-$/atom:proteins[0][0][1]/a20 47
	-$/atom:proteins[0][0][1]/a21 48
	-$/atom:proteins[0][0][1]/a22 49
	-$/atom:proteins[0][0][1]/a23 50
	-$/atom:proteins[0][0][1]/a24 51
	-$/atom:proteins[0][0][1]/a25 52
	-$/atom:proteins[0][0][1]/a26 53
	-$/atom:proteins[0][0][1]/a27 54
	-$/atom:proteins[0][1][0]/a1 55
	-$/atom:proteins[0][1][0]/a2 56
	-$/atom:proteins[0][1][0]/a3 57
	-$/atom:proteins[0][1][0]/a4 58
	-$/atom:proteins[0][1][0]/a5 59
	-$/atom:proteins[0][1][0]/a6 60
	-$/atom:proteins[0][1][0]/a7 61
	-$/atom:proteins[0][1][0]/a8 62
	-$/atom:proteins[0][1][0]/a9 63
	-$/atom:proteins[0][1][0]/a10 64
	-$/atom:proteins[0][1][0]/a11 65
	-$/atom:proteins[0][1][0]/a12 66
	-$/atom:proteins[0][1][0]/a13 67
	-$/atom:proteins[0][1][0]/a14 68
	-$/atom:proteins[0][1][0]/a15 69
	-$/atom:proteins[0][1][0]/a16 70
	-$/atom:proteins[0][1][0]/a17 71
	-$/atom:proteins[0][1][0]/a18 72
	-$/atom:proteins[0][1][0]/a19 73
	-$/atom:proteins[0][1][0]/a20 74
	-$/atom:proteins[0][1][0]/a21 75
	-$/atom:proteins[0][1][0]/a22 76
	-$/atom:proteins[0][1][0]/a23 77
	-$/atom:proteins[0][1][0]/a24 78
	-$/atom:proteins[0][1][0]/a25 79
	-$/atom:proteins[0][1][0]/a26 80
	-$/atom:proteins[0][1][0]/a27 81
	-$/atom:proteins[0][1][1]/a1 82
	-$/atom:proteins[0][1][1]/a2 83
	-$/atom:proteins[0][1][1]/a3 84
	-$/atom:proteins[0][1][1]/a4 85
	-$/atom:proteins[0][1][1]/a5 86
	-$/atom:proteins[0][1][1]/a6 87
	-$/atom:proteins[0][1][1]/a7 88
	-$/atom:proteins[0][1][1]/a8 89
	-$/atom:proteins[0][1][1]/a9 90
	-$/atom:proteins[0][1][1]/a10 91
	-$/atom:proteins[0][1][1]/a11 92
	-$/atom:proteins[0][1][1]/a12 93
	-$/atom:proteins[0][1][1]/a13 94
	-$/atom:proteins[0][1][1]/a14 95
	-$/atom:proteins[0][1][1]/a15 96
	-$/atom:proteins[0][1][1]/a16 97
	-$/atom:proteins[0][1][1]/a17 98
	-$/atom:proteins[0][1][1]/a18 99
	-$/atom:proteins[0][1][1]/a19 100
	-$/atom:proteins[0][1][1]/a20 101
	-$/atom:proteins[0][1][1]/a21 102
	-$/atom:proteins[0][1][1]/a22 103
	-$/atom:proteins[0][1][1]/a23 104
	-$/atom:proteins[0][1][1]/a24 105
	-$/atom:proteins[0][1][1]/a25 106
	-$/atom:proteins[0][1][1]/a26 107
	-$/atom:proteins[0][1][1]/a27 108
	-$/atom:proteins[1][0][0]/a1 109
	-$/atom:proteins[1][0][0]/a2 110
	-$/atom:proteins[1][0][0]/a3 111
	-$/atom:proteins[1][0][0]/a4 112
	-$/atom:proteins[1][0][0]/a5 113
	-$/atom:proteins[1][0][0]/a6 114
	-$/atom:proteins[1][0][0]/a7 115
	-$/atom:proteins[1][0][0]/a8 116
	-$/atom:proteins[1][0][0]/a9 117
	-$/atom:proteins[1][0][0]/a10 118
	-$/atom:proteins[1][0][0]/a11 119
	-$/atom:proteins[1][0][0]/a12 120
	-$/atom:proteins[1][0][0]/a13 121
	-$/atom:proteins[1][0][0]/a14 122
	-$/atom:proteins[1][0][0]/a15 123
	-$/atom:proteins[1][0][0]/a16 124
	-$/atom:proteins[1][0][0]/a17 125
	-$/atom:proteins[1][0][0]/a18 126
	-$/atom:proteins[1][0][0]/a19 127
	-$/atom:proteins[1][0][0]/a20 128
	-$/atom:proteins[1][0][0]/a21 129
	-$/atom:proteins[1][0][0]/a22 130
	-$/atom:proteins[1][0][0]/a23 131
	-$/atom:proteins[1][0][0]/a24 132
	-$/atom:proteins[1][0][0]/a25 133
	-$/atom:proteins[1][0][0]/a26 134
	-$/atom:proteins[1][0][0]/a27 135
	-$/atom:proteins[1][0][1]/a1 136
	-$/atom:proteins[1][0][1]/a2 137
	-$/atom:proteins[1][0][1]/a3 138
	-$/atom:proteins[1][0][1]/a4 139
	-$/atom:proteins[1][0][1]/a5 140
	-$/atom:proteins[1][0][1]/a6 141
	-$/atom:proteins[1][0][1]/a7 142
	-$/atom:proteins[1][0][1]/a8 143
	-$/atom:proteins[1][0][1]/a9 144
	-$/atom:proteins[1][0][1]/a10 145
	-$/atom:proteins[1][0][1]/a11 146
	-$/atom:proteins[1][0][1]/a12 147
	-$/atom:proteins[1][0][1]/a13 148
	-$/atom:proteins[1][0][1]/a14 149
	-$/atom:proteins[1][0][1]/a15 150
	-$/atom:proteins[1][0][1]/a16 151
	-$/atom:proteins[1][0][1]/a17 152
	-$/atom:proteins[1][0][1]/a18 153
	-$/atom:proteins[1][0][1]/a19 154
	-$/atom:proteins[1][0][1]/a20 155
	-$/atom:proteins[1][0][1]/a21 156
	-$/atom:proteins[1][0][1]/a22 157
	-$/atom:proteins[1][0][1]/a23 158
	-$/atom:proteins[1][0][1]/a24 159
	-$/atom:proteins[1][0][1]/a25 160
	-$/atom:proteins[1][0][1]/a26 161
	-$/atom:proteins[1][0][1]/a27 162
	-$/atom:proteins[1][1][0]/a1 163
	-$/atom:proteins[1][1][0]/a2 164
	-$/atom:proteins[1][1][0]/a3 165
	-$/atom:proteins[1][1][0]/a4 166
	-$/atom:proteins[1][1][0]/a5 167
	-$/atom:proteins[1][1][0]/a6 168
	-$/atom:proteins[1][1][0]/a7 169
	-$/atom:proteins[1][1][0]/a8 170
	-$/atom:proteins[1][1][0]/a9 171
	-$/atom:proteins[1][1][0]/a10 172
	-$/atom:proteins[1][1][0]/a11 173
	-$/atom:proteins[1][1][0]/a12 174
	-$/atom:proteins[1][1][0]/a13 175
	-$/atom:proteins[1][1][0]/a14 176
	-$/atom:proteins[1][1][0]/a15 177
	-$/atom:proteins[1][1][0]/a16 178
	-$/atom:proteins[1][1][0]/a17 179
	-$/atom:proteins[1][1][0]/a18 180
	-$/atom:proteins[1][1][0]/a19 181
	-$/atom:proteins[1][1][0]/a20 182
	-$/atom:proteins[1][1][0]/a21 183
	-$/atom:proteins[1][1][0]/a22 184
	-$/atom:proteins[1][1][0]/a23 185
	-$/atom:proteins[1][1][0]/a24 186
	-$/atom:proteins[1][1][0]/a25 187
	-$/atom:proteins[1][1][0]/a26 188
	-$/atom:proteins[1][1][0]/a27 189
	-$/atom:proteins[1][1][1]/a1 190
	-$/atom:proteins[1][1][1]/a2 191
	-$/atom:proteins[1][1][1]/a3 192
	-$/atom:proteins[1][1][1]/a4 193
	-$/atom:proteins[1][1][1]/a5 194
	-$/atom:proteins[1][1][1]/a6 195
	-$/atom:proteins[1][1][1]/a7 196
	-$/atom:proteins[1][1][1]/a8 197
	-$/atom:proteins[1][1][1]/a9 198
	-$/atom:proteins[1][1][1]/a10 199
	-$/atom:proteins[1][1][1]/a11 200
	-$/atom:proteins[1][1][1]/a12 201
	-$/atom:proteins[1][1][1]/a13 202
	-$/atom:proteins[1][1][1]/a14 203
	-$/atom:proteins[1][1][1]/a15 204
	-$/atom:proteins[1][1][1]/a16 205
	-$/atom:proteins[1][1][1]/a17 206
	-$/atom:proteins[1][1][1]/a18 207
	-$/atom:proteins[1][1][1]/a19 208
	-$/atom:proteins[1][1][1]/a20 209
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	-$/angle:bytype55 55
	-$/angle:bytype56 56
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	-$/angle:bytype79 79
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	-$/angle:bytype87 87
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	-$/angle:bytype90 90
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	-$/angle:bytype94 94
	-$/angle:bytype95 95
	-$/angle:bytype96 96
	-$/angle:bytype97 97
	-$/angle:bytype98 98
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	-$/angle:bytype100 100
	-$/angle:bytype101 101
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	-$/angle:bytype104 104
	-$/angle:bytype105 105
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	-$/angle:bytype108 108
	-$/angle:bytype109 109
	-$/angle:bytype110 110
	-$/angle:bytype111 111
	-$/angle:bytype112 112
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	-$/angle:bytype115 115
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	-$/angle:bytype119 119
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	-$/angle:bytype121 121
	-$/angle:bytype122 122
	-$/angle:bytype123 123
	-$/angle:bytype124 124
	-$/angle:bytype125 125
	-$/angle:bytype126 126
	-$/angle:bytype127 127
	-$/angle:bytype128 128
	-$/angle:bytype129 129
	-$/angle:bytype130 130
	-$/angle:bytype131 131
	-$/angle:bytype132 132
	-$/angle:bytype133 133
	-$/angle:bytype134 134
	-$/angle:bytype135 135
	-$/angle:bytype136 136
	-$/angle:bytype137 137
	-$/angle:bytype138 138
	-$/angle:bytype139 139
	-$/angle:bytype140 140
	-$/angle:bytype141 141
	-$/angle:bytype142 142
	-$/angle:bytype143 143
	-$/angle:bytype144 144
	-$/angle:bytype145 145
	-$/angle:bytype146 146
	-$/angle:bytype147 147
	-$/angle:bytype148 148
	-$/angle:bytype149 149
	-$/angle:bytype150 150
	-$/angle:bytype151 151
	-$/angle:bytype152 152
	-$/angle:bytype153 153
	-$/angle:bytype154 154
	-$/angle:bytype155 155
	-$/angle:bytype156 156
	-$/angle:bytype157 157
	-$/angle:bytype158 158
	-$/angle:bytype159 159
	-$/angle:bytype160 160
	-$/angle:bytype161 161
	-$/angle:bytype162 162
	-$/angle:bytype163 163
	-$/angle:bytype164 164
	-$/angle:bytype165 165
	-$/angle:bytype166 166
	-$/angle:bytype167 167
	-$/angle:bytype168 168
	-$/angle:bytype169 169
	-$/angle:bytype170 170
	-$/angle:bytype171 171
	-$/angle:bytype172 172
	-$/angle:bytype173 173
	-$/angle:bytype174 174
	-$/angle:bytype175 175
	-$/angle:bytype176 176
	-$/angle:bytype177 177
	-$/angle:bytype178 178
	-$/angle:bytype179 179
	-$/angle:bytype180 180
	-$/angle:bytype181 181
	-$/angle:bytype182 182
	-$/angle:bytype183 183
	-$/angle:bytype184 184
	-$/angle:bytype185 185
	-$/angle:bytype186 186
	-$/angle:bytype187 187
	-$/angle:bytype188 188
	-$/angle:bytype189 189
	-$/angle:bytype190 190
	-$/angle:bytype191 191
	-$/angle:bytype192 192
	-$/angle:bytype193 193
	-$/angle:bytype194 194
	-$/angle:bytype195 195
	-$/angle:bytype196 196
	-$/angle:bytype197 197
	-$/angle:bytype198 198
	-$/angle:bytype199 199
	-$/angle:bytype200 200
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.data b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.data
	deleted file mode 100644
	index aadace600..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.data
	+++ /dev/null
	@@ -1,820 +0,0 @@
	-LAMMPS Description
	-
	- 224 atoms
	- 208 bonds
	- 200 angles
	- 152 dihedrals
	- 0 impropers
	-
	- 4 atom types
	- 1 bond types
	- 1 angle types
	- 2 dihedral types
	-
	- 0.0 80.0 xlo xhi
	- 0.0 80.0 ylo yhi
	- 0.0 80.0 zlo zhi
	-
	-Masses
	-
	- 1 1.0
	- 2 1.0
	- 3 1.0
	- 4 100.0
	-
	-Atoms
	-
	-1 1 2 0.0 17.6 21.7 20.0
	-2 1 1 0.0 18.2 21.7 20.8
	-3 1 2 0.0 18.8 22.5 20.8
	-4 1 1 0.0 19.4 22.5 20.0
	-5 1 2 0.0 20.0 21.7 20.0
	-6 1 1 0.0 20.6 21.7 20.8
	-7 1 3 0.0 21.2 22.5 20.8
	-8 1 3 0.0 21.8 22.5 20.0
	-9 1 1 0.0 22.4 21.7 20.0
	-10 1 2 0.0 23.0 21.7 19.2
	-11 1 1 0.0 23.0 20.7 19.2
	-12 1 2 0.0 23.0 20.1 20.0
	-13 1 1 0.0 23.8 19.5 20.0
	-14 1 2 0.0 23.8 18.9 19.2
	-15 1 3 0.0 23.0 18.3 19.2
	-16 1 3 0.0 23.0 18.3 20.2
	-17 1 3 0.0 22.4 17.5 20.2
	-18 1 1 0.0 21.8 17.5 19.4
	-19 1 1 0.0 21.2 18.3 19.4
	-20 1 2 0.0 20.6 18.3 20.2
	-21 1 2 0.0 20.0 17.5 20.2
	-22 1 1 0.0 19.4 17.5 19.4
	-23 1 1 0.0 18.8 18.3 19.4
	-24 1 2 0.0 18.2 18.3 20.2
	-25 1 2 0.0 17.6 17.5 20.2
	-26 1 1 0.0 17.0 17.5 19.4
	-27 1 2 0.0 16.4 18.3 19.4
	-28 2 2 0.0 17.6 21.7 60.0
	-29 2 1 0.0 18.2 21.7 60.8
	-30 2 2 0.0 18.8 22.5 60.8
	-31 2 1 0.0 19.4 22.5 60.0
	-32 2 2 0.0 20.0 21.7 60.0
	-33 2 1 0.0 20.6 21.7 60.8
	-34 2 3 0.0 21.2 22.5 60.8
	-35 2 3 0.0 21.8 22.5 60.0
	-36 2 1 0.0 22.4 21.7 60.0
	-37 2 2 0.0 23.0 21.7 59.2
	-38 2 1 0.0 23.0 20.7 59.2
	-39 2 2 0.0 23.0 20.1 60.0
	-40 2 1 0.0 23.8 19.5 60.0
	-41 2 2 0.0 23.8 18.9 59.2
	-42 2 3 0.0 23.0 18.3 59.2
	-43 2 3 0.0 23.0 18.3 60.2
	-44 2 3 0.0 22.4 17.5 60.2
	-45 2 1 0.0 21.8 17.5 59.4
	-46 2 1 0.0 21.2 18.3 59.4
	-47 2 2 0.0 20.6 18.3 60.2
	-48 2 2 0.0 20.0 17.5 60.2
	-49 2 1 0.0 19.4 17.5 59.4
	-50 2 1 0.0 18.8 18.3 59.4
	-51 2 2 0.0 18.2 18.3 60.2
	-52 2 2 0.0 17.6 17.5 60.2
	-53 2 1 0.0 17.0 17.5 59.4
	-54 2 2 0.0 16.4 18.3 59.4
	-55 3 2 0.0 17.6 61.7 20.0
	-56 3 1 0.0 18.2 61.7 20.8
	-57 3 2 0.0 18.8 62.5 20.8
	-58 3 1 0.0 19.4 62.5 20.0
	-59 3 2 0.0 20.0 61.7 20.0
	-60 3 1 0.0 20.6 61.7 20.8
	-61 3 3 0.0 21.2 62.5 20.8
	-62 3 3 0.0 21.8 62.5 20.0
	-63 3 1 0.0 22.4 61.7 20.0
	-64 3 2 0.0 23.0 61.7 19.2
	-65 3 1 0.0 23.0 60.7 19.2
	-66 3 2 0.0 23.0 60.1 20.0
	-67 3 1 0.0 23.8 59.5 20.0
	-68 3 2 0.0 23.8 58.9 19.2
	-69 3 3 0.0 23.0 58.3 19.2
	-70 3 3 0.0 23.0 58.3 20.2
	-71 3 3 0.0 22.4 57.5 20.2
	-72 3 1 0.0 21.8 57.5 19.4
	-73 3 1 0.0 21.2 58.3 19.4
	-74 3 2 0.0 20.6 58.3 20.2
	-75 3 2 0.0 20.0 57.5 20.2
	-76 3 1 0.0 19.4 57.5 19.4
	-77 3 1 0.0 18.8 58.3 19.4
	-78 3 2 0.0 18.2 58.3 20.2
	-79 3 2 0.0 17.6 57.5 20.2
	-80 3 1 0.0 17.0 57.5 19.4
	-81 3 2 0.0 16.4 58.3 19.4
	-82 4 2 0.0 17.6 61.7 60.0
	-83 4 1 0.0 18.2 61.7 60.8
	-84 4 2 0.0 18.8 62.5 60.8
	-85 4 1 0.0 19.4 62.5 60.0
	-86 4 2 0.0 20.0 61.7 60.0
	-87 4 1 0.0 20.6 61.7 60.8
	-88 4 3 0.0 21.2 62.5 60.8
	-89 4 3 0.0 21.8 62.5 60.0
	-90 4 1 0.0 22.4 61.7 60.0
	-91 4 2 0.0 23.0 61.7 59.2
	-92 4 1 0.0 23.0 60.7 59.2
	-93 4 2 0.0 23.0 60.1 60.0
	-94 4 1 0.0 23.8 59.5 60.0
	-95 4 2 0.0 23.8 58.9 59.2
	-96 4 3 0.0 23.0 58.3 59.2
	-97 4 3 0.0 23.0 58.3 60.2
	-98 4 3 0.0 22.4 57.5 60.2
	-99 4 1 0.0 21.8 57.5 59.4
	-100 4 1 0.0 21.2 58.3 59.4
	-101 4 2 0.0 20.6 58.3 60.2
	-102 4 2 0.0 20.0 57.5 60.2
	-103 4 1 0.0 19.4 57.5 59.4
	-104 4 1 0.0 18.8 58.3 59.4
	-105 4 2 0.0 18.2 58.3 60.2
	-106 4 2 0.0 17.6 57.5 60.2
	-107 4 1 0.0 17.0 57.5 59.4
	-108 4 2 0.0 16.4 58.3 59.4
	-109 5 2 0.0 57.6 21.7 20.0
	-110 5 1 0.0 58.2 21.7 20.8
	-111 5 2 0.0 58.8 22.5 20.8
	-112 5 1 0.0 59.4 22.5 20.0
	-113 5 2 0.0 60.0 21.7 20.0
	-114 5 1 0.0 60.6 21.7 20.8
	-115 5 3 0.0 61.2 22.5 20.8
	-116 5 3 0.0 61.8 22.5 20.0
	-117 5 1 0.0 62.4 21.7 20.0
	-118 5 2 0.0 63.0 21.7 19.2
	-119 5 1 0.0 63.0 20.7 19.2
	-120 5 2 0.0 63.0 20.1 20.0
	-121 5 1 0.0 63.8 19.5 20.0
	-122 5 2 0.0 63.8 18.9 19.2
	-123 5 3 0.0 63.0 18.3 19.2
	-124 5 3 0.0 63.0 18.3 20.2
	-125 5 3 0.0 62.4 17.5 20.2
	-126 5 1 0.0 61.8 17.5 19.4
	-127 5 1 0.0 61.2 18.3 19.4
	-128 5 2 0.0 60.6 18.3 20.2
	-129 5 2 0.0 60.0 17.5 20.2
	-130 5 1 0.0 59.4 17.5 19.4
	-131 5 1 0.0 58.8 18.3 19.4
	-132 5 2 0.0 58.2 18.3 20.2
	-133 5 2 0.0 57.6 17.5 20.2
	-134 5 1 0.0 57.0 17.5 19.4
	-135 5 2 0.0 56.4 18.3 19.4
	-136 6 2 0.0 57.6 21.7 60.0
	-137 6 1 0.0 58.2 21.7 60.8
	-138 6 2 0.0 58.8 22.5 60.8
	-139 6 1 0.0 59.4 22.5 60.0
	-140 6 2 0.0 60.0 21.7 60.0
	-141 6 1 0.0 60.6 21.7 60.8
	-142 6 3 0.0 61.2 22.5 60.8
	-143 6 3 0.0 61.8 22.5 60.0
	-144 6 1 0.0 62.4 21.7 60.0
	-145 6 2 0.0 63.0 21.7 59.2
	-146 6 1 0.0 63.0 20.7 59.2
	-147 6 2 0.0 63.0 20.1 60.0
	-148 6 1 0.0 63.8 19.5 60.0
	-149 6 2 0.0 63.8 18.9 59.2
	-150 6 3 0.0 63.0 18.3 59.2
	-151 6 3 0.0 63.0 18.3 60.2
	-152 6 3 0.0 62.4 17.5 60.2
	-153 6 1 0.0 61.8 17.5 59.4
	-154 6 1 0.0 61.2 18.3 59.4
	-155 6 2 0.0 60.6 18.3 60.2
	-156 6 2 0.0 60.0 17.5 60.2
	-157 6 1 0.0 59.4 17.5 59.4
	-158 6 1 0.0 58.8 18.3 59.4
	-159 6 2 0.0 58.2 18.3 60.2
	-160 6 2 0.0 57.6 17.5 60.2
	-161 6 1 0.0 57.0 17.5 59.4
	-162 6 2 0.0 56.4 18.3 59.4
	-163 7 2 0.0 57.6 61.7 20.0
	-164 7 1 0.0 58.2 61.7 20.8
	-165 7 2 0.0 58.8 62.5 20.8
	-166 7 1 0.0 59.4 62.5 20.0
	-167 7 2 0.0 60.0 61.7 20.0
	-168 7 1 0.0 60.6 61.7 20.8
	-169 7 3 0.0 61.2 62.5 20.8
	-170 7 3 0.0 61.8 62.5 20.0
	-171 7 1 0.0 62.4 61.7 20.0
	-172 7 2 0.0 63.0 61.7 19.2
	-173 7 1 0.0 63.0 60.7 19.2
	-174 7 2 0.0 63.0 60.1 20.0
	-175 7 1 0.0 63.8 59.5 20.0
	-176 7 2 0.0 63.8 58.9 19.2
	-177 7 3 0.0 63.0 58.3 19.2
	-178 7 3 0.0 63.0 58.3 20.2
	-179 7 3 0.0 62.4 57.5 20.2
	-180 7 1 0.0 61.8 57.5 19.4
	-181 7 1 0.0 61.2 58.3 19.4
	-182 7 2 0.0 60.6 58.3 20.2
	-183 7 2 0.0 60.0 57.5 20.2
	-184 7 1 0.0 59.4 57.5 19.4
	-185 7 1 0.0 58.8 58.3 19.4
	-186 7 2 0.0 58.2 58.3 20.2
	-187 7 2 0.0 57.6 57.5 20.2
	-188 7 1 0.0 57.0 57.5 19.4
	-189 7 2 0.0 56.4 58.3 19.4
	-190 8 2 0.0 57.6 61.7 60.0
	-191 8 1 0.0 58.2 61.7 60.8
	-192 8 2 0.0 58.8 62.5 60.8
	-193 8 1 0.0 59.4 62.5 60.0
	-194 8 2 0.0 60.0 61.7 60.0
	-195 8 1 0.0 60.6 61.7 60.8
	-196 8 3 0.0 61.2 62.5 60.8
	-197 8 3 0.0 61.8 62.5 60.0
	-198 8 1 0.0 62.4 61.7 60.0
	-199 8 2 0.0 63.0 61.7 59.2
	-200 8 1 0.0 63.0 60.7 59.2
	-201 8 2 0.0 63.0 60.1 60.0
	-202 8 1 0.0 63.8 59.5 60.0
	-203 8 2 0.0 63.8 58.9 59.2
	-204 8 3 0.0 63.0 58.3 59.2
	-205 8 3 0.0 63.0 58.3 60.2
	-206 8 3 0.0 62.4 57.5 60.2
	-207 8 1 0.0 61.8 57.5 59.4
	-208 8 1 0.0 61.2 58.3 59.4
	-209 8 2 0.0 60.6 58.3 60.2
	-210 8 2 0.0 60.0 57.5 60.2
	-211 8 1 0.0 59.4 57.5 59.4
	-212 8 1 0.0 58.8 58.3 59.4
	-213 8 2 0.0 58.2 58.3 60.2
	-214 8 2 0.0 57.6 57.5 60.2
	-215 8 1 0.0 57.0 57.5 59.4
	-216 8 2 0.0 56.4 58.3 59.4
	-217 9 4 0.0 0.0 0.0 0.0
	-218 10 4 0.0 0.0 0.0 40.0
	-219 11 4 0.0 0.0 40.0 0.0
	-220 12 4 0.0 0.0 40.0 40.0
	-221 13 4 0.0 40.0 0.0 0.0
	-222 14 4 0.0 40.0 0.0 40.0
	-223 15 4 0.0 40.0 40.0 0.0
	-224 16 4 0.0 40.0 40.0 40.0
	-
	-Bonds
	-
	-1 1 1 2
	-2 1 2 3
	-3 1 3 4
	-4 1 4 5
	-5 1 5 6
	-6 1 6 7
	-7 1 7 8
	-8 1 8 9
	-9 1 9 10
	-10 1 10 11
	-11 1 11 12
	-12 1 12 13
	-13 1 13 14
	-14 1 14 15
	-15 1 15 16
	-16 1 16 17
	-17 1 17 18
	-18 1 18 19
	-19 1 19 20
	-20 1 20 21
	-21 1 21 22
	-22 1 22 23
	-23 1 23 24
	-24 1 24 25
	-25 1 25 26
	-26 1 26 27
	-27 1 28 29
	-28 1 29 30
	-29 1 30 31
	-30 1 31 32
	-31 1 32 33
	-32 1 33 34
	-33 1 34 35
	-34 1 35 36
	-35 1 36 37
	-36 1 37 38
	-37 1 38 39
	-38 1 39 40
	-39 1 40 41
	-40 1 41 42
	-41 1 42 43
	-42 1 43 44
	-43 1 44 45
	-44 1 45 46
	-45 1 46 47
	-46 1 47 48
	-47 1 48 49
	-48 1 49 50
	-49 1 50 51
	-50 1 51 52
	-51 1 52 53
	-52 1 53 54
	-53 1 55 56
	-54 1 56 57
	-55 1 57 58
	-56 1 58 59
	-57 1 59 60
	-58 1 60 61
	-59 1 61 62
	-60 1 62 63
	-61 1 63 64
	-62 1 64 65
	-63 1 65 66
	-64 1 66 67
	-65 1 67 68
	-66 1 68 69
	-67 1 69 70
	-68 1 70 71
	-69 1 71 72
	-70 1 72 73
	-71 1 73 74
	-72 1 74 75
	-73 1 75 76
	-74 1 76 77
	-75 1 77 78
	-76 1 78 79
	-77 1 79 80
	-78 1 80 81
	-79 1 82 83
	-80 1 83 84
	-81 1 84 85
	-82 1 85 86
	-83 1 86 87
	-84 1 87 88
	-85 1 88 89
	-86 1 89 90
	-87 1 90 91
	-88 1 91 92
	-89 1 92 93
	-90 1 93 94
	-91 1 94 95
	-92 1 95 96
	-93 1 96 97
	-94 1 97 98
	-95 1 98 99
	-96 1 99 100
	-97 1 100 101
	-98 1 101 102
	-99 1 102 103
	-100 1 103 104
	-101 1 104 105
	-102 1 105 106
	-103 1 106 107
	-104 1 107 108
	-105 1 109 110
	-106 1 110 111
	-107 1 111 112
	-108 1 112 113
	-109 1 113 114
	-110 1 114 115
	-111 1 115 116
	-112 1 116 117
	-113 1 117 118
	-114 1 118 119
	-115 1 119 120
	-116 1 120 121
	-117 1 121 122
	-118 1 122 123
	-119 1 123 124
	-120 1 124 125
	-121 1 125 126
	-122 1 126 127
	-123 1 127 128
	-124 1 128 129
	-125 1 129 130
	-126 1 130 131
	-127 1 131 132
	-128 1 132 133
	-129 1 133 134
	-130 1 134 135
	-131 1 136 137
	-132 1 137 138
	-133 1 138 139
	-134 1 139 140
	-135 1 140 141
	-136 1 141 142
	-137 1 142 143
	-138 1 143 144
	-139 1 144 145
	-140 1 145 146
	-141 1 146 147
	-142 1 147 148
	-143 1 148 149
	-144 1 149 150
	-145 1 150 151
	-146 1 151 152
	-147 1 152 153
	-148 1 153 154
	-149 1 154 155
	-150 1 155 156
	-151 1 156 157
	-152 1 157 158
	-153 1 158 159
	-154 1 159 160
	-155 1 160 161
	-156 1 161 162
	-157 1 163 164
	-158 1 164 165
	-159 1 165 166
	-160 1 166 167
	-161 1 167 168
	-162 1 168 169
	-163 1 169 170
	-164 1 170 171
	-165 1 171 172
	-166 1 172 173
	-167 1 173 174
	-168 1 174 175
	-169 1 175 176
	-170 1 176 177
	-171 1 177 178
	-172 1 178 179
	-173 1 179 180
	-174 1 180 181
	-175 1 181 182
	-176 1 182 183
	-177 1 183 184
	-178 1 184 185
	-179 1 185 186
	-180 1 186 187
	-181 1 187 188
	-182 1 188 189
	-183 1 190 191
	-184 1 191 192
	-185 1 192 193
	-186 1 193 194
	-187 1 194 195
	-188 1 195 196
	-189 1 196 197
	-190 1 197 198
	-191 1 198 199
	-192 1 199 200
	-193 1 200 201
	-194 1 201 202
	-195 1 202 203
	-196 1 203 204
	-197 1 204 205
	-198 1 205 206
	-199 1 206 207
	-200 1 207 208
	-201 1 208 209
	-202 1 209 210
	-203 1 210 211
	-204 1 211 212
	-205 1 212 213
	-206 1 213 214
	-207 1 214 215
	-208 1 215 216
	-
	-Angles
	-
	-1 1 13 14 15
	-2 1 40 41 42
	-3 1 67 68 69
	-4 1 94 95 96
	-5 1 121 122 123
	-6 1 148 149 150
	-7 1 175 176 177
	-8 1 202 203 204
	-9 1 7 8 9
	-10 1 6 7 8
	-11 1 16 17 18
	-12 1 34 35 36
	-13 1 33 34 35
	-14 1 43 44 45
	-15 1 61 62 63
	-16 1 60 61 62
	-17 1 70 71 72
	-18 1 88 89 90
	-19 1 87 88 89
	-20 1 97 98 99
	-21 1 115 116 117
	-22 1 114 115 116
	-23 1 124 125 126
	-24 1 142 143 144
	-25 1 141 142 143
	-26 1 151 152 153
	-27 1 169 170 171
	-28 1 168 169 170
	-29 1 178 179 180
	-30 1 196 197 198
	-31 1 195 196 197
	-32 1 205 206 207
	-33 1 15 16 17
	-34 1 42 43 44
	-35 1 69 70 71
	-36 1 96 97 98
	-37 1 123 124 125
	-38 1 150 151 152
	-39 1 177 178 179
	-40 1 204 205 206
	-41 1 2 3 4
	-42 1 4 5 6
	-43 1 9 10 11
	-44 1 11 12 13
	-45 1 29 30 31
	-46 1 31 32 33
	-47 1 36 37 38
	-48 1 38 39 40
	-49 1 56 57 58
	-50 1 58 59 60
	-51 1 63 64 65
	-52 1 65 66 67
	-53 1 83 84 85
	-54 1 85 86 87
	-55 1 90 91 92
	-56 1 92 93 94
	-57 1 110 111 112
	-58 1 112 113 114
	-59 1 117 118 119
	-60 1 119 120 121
	-61 1 137 138 139
	-62 1 139 140 141
	-63 1 144 145 146
	-64 1 146 147 148
	-65 1 164 165 166
	-66 1 166 167 168
	-67 1 171 172 173
	-68 1 173 174 175
	-69 1 191 192 193
	-70 1 193 194 195
	-71 1 198 199 200
	-72 1 200 201 202
	-73 1 14 15 16
	-74 1 41 42 43
	-75 1 68 69 70
	-76 1 95 96 97
	-77 1 122 123 124
	-78 1 149 150 151
	-79 1 176 177 178
	-80 1 203 204 205
	-81 1 1 2 3
	-82 1 3 4 5
	-83 1 10 11 12
	-84 1 12 13 14
	-85 1 25 26 27
	-86 1 28 29 30
	-87 1 30 31 32
	-88 1 37 38 39
	-89 1 39 40 41
	-90 1 52 53 54
	-91 1 55 56 57
	-92 1 57 58 59
	-93 1 64 65 66
	-94 1 66 67 68
	-95 1 79 80 81
	-96 1 82 83 84
	-97 1 84 85 86
	-98 1 91 92 93
	-99 1 93 94 95
	-100 1 106 107 108
	-101 1 109 110 111
	-102 1 111 112 113
	-103 1 118 119 120
	-104 1 120 121 122
	-105 1 133 134 135
	-106 1 136 137 138
	-107 1 138 139 140
	-108 1 145 146 147
	-109 1 147 148 149
	-110 1 160 161 162
	-111 1 163 164 165
	-112 1 165 166 167
	-113 1 172 173 174
	-114 1 174 175 176
	-115 1 187 188 189
	-116 1 190 191 192
	-117 1 192 193 194
	-118 1 199 200 201
	-119 1 201 202 203
	-120 1 214 215 216
	-121 1 5 6 7
	-122 1 8 9 10
	-123 1 32 33 34
	-124 1 35 36 37
	-125 1 59 60 61
	-126 1 62 63 64
	-127 1 86 87 88
	-128 1 89 90 91
	-129 1 113 114 115
	-130 1 116 117 118
	-131 1 140 141 142
	-132 1 143 144 145
	-133 1 167 168 169
	-134 1 170 171 172
	-135 1 194 195 196
	-136 1 197 198 199
	-137 1 17 18 19
	-138 1 44 45 46
	-139 1 71 72 73
	-140 1 98 99 100
	-141 1 125 126 127
	-142 1 152 153 154
	-143 1 179 180 181
	-144 1 206 207 208
	-145 1 18 19 20
	-146 1 22 23 24
	-147 1 21 22 23
	-148 1 45 46 47
	-149 1 49 50 51
	-150 1 48 49 50
	-151 1 72 73 74
	-152 1 76 77 78
	-153 1 75 76 77
	-154 1 99 100 101
	-155 1 103 104 105
	-156 1 102 103 104
	-157 1 126 127 128
	-158 1 130 131 132
	-159 1 129 130 131
	-160 1 153 154 155
	-161 1 157 158 159
	-162 1 156 157 158
	-163 1 180 181 182
	-164 1 184 185 186
	-165 1 183 184 185
	-166 1 207 208 209
	-167 1 211 212 213
	-168 1 210 211 212
	-169 1 19 20 21
	-170 1 20 21 22
	-171 1 23 24 25
	-172 1 24 25 26
	-173 1 46 47 48
	-174 1 47 48 49
	-175 1 50 51 52
	-176 1 51 52 53
	-177 1 73 74 75
	-178 1 74 75 76
	-179 1 77 78 79
	-180 1 78 79 80
	-181 1 100 101 102
	-182 1 101 102 103
	-183 1 104 105 106
	-184 1 105 106 107
	-185 1 127 128 129
	-186 1 128 129 130
	-187 1 131 132 133
	-188 1 132 133 134
	-189 1 154 155 156
	-190 1 155 156 157
	-191 1 158 159 160
	-192 1 159 160 161
	-193 1 181 182 183
	-194 1 182 183 184
	-195 1 185 186 187
	-196 1 186 187 188
	-197 1 208 209 210
	-198 1 209 210 211
	-199 1 212 213 214
	-200 1 213 214 215
	-
	-Dihedrals
	-
	-1 1 1 2 3 4
	-2 1 2 3 4 5
	-3 1 3 4 5 6
	-4 1 4 5 6 7
	-5 1 8 9 10 11
	-6 1 9 10 11 12
	-7 1 10 11 12 13
	-8 1 11 12 13 14
	-9 1 12 13 14 15
	-10 2 15 16 17 18
	-11 2 16 17 18 19
	-12 2 17 18 19 20
	-13 2 18 19 20 21
	-14 2 19 20 21 22
	-15 2 20 21 22 23
	-16 2 21 22 23 24
	-17 2 22 23 24 25
	-18 2 23 24 25 26
	-19 2 24 25 26 27
	-20 1 28 29 30 31
	-21 1 29 30 31 32
	-22 1 30 31 32 33
	-23 1 31 32 33 34
	-24 1 35 36 37 38
	-25 1 36 37 38 39
	-26 1 37 38 39 40
	-27 1 38 39 40 41
	-28 1 39 40 41 42
	-29 2 42 43 44 45
	-30 2 43 44 45 46
	-31 2 44 45 46 47
	-32 2 45 46 47 48
	-33 2 46 47 48 49
	-34 2 47 48 49 50
	-35 2 48 49 50 51
	-36 2 49 50 51 52
	-37 2 50 51 52 53
	-38 2 51 52 53 54
	-39 1 55 56 57 58
	-40 1 56 57 58 59
	-41 1 57 58 59 60
	-42 1 58 59 60 61
	-43 1 62 63 64 65
	-44 1 63 64 65 66
	-45 1 64 65 66 67
	-46 1 65 66 67 68
	-47 1 66 67 68 69
	-48 2 69 70 71 72
	-49 2 70 71 72 73
	-50 2 71 72 73 74
	-51 2 72 73 74 75
	-52 2 73 74 75 76
	-53 2 74 75 76 77
	-54 2 75 76 77 78
	-55 2 76 77 78 79
	-56 2 77 78 79 80
	-57 2 78 79 80 81
	-58 1 82 83 84 85
	-59 1 83 84 85 86
	-60 1 84 85 86 87
	-61 1 85 86 87 88
	-62 1 89 90 91 92
	-63 1 90 91 92 93
	-64 1 91 92 93 94
	-65 1 92 93 94 95
	-66 1 93 94 95 96
	-67 2 96 97 98 99
	-68 2 97 98 99 100
	-69 2 98 99 100 101
	-70 2 99 100 101 102
	-71 2 100 101 102 103
	-72 2 101 102 103 104
	-73 2 102 103 104 105
	-74 2 103 104 105 106
	-75 2 104 105 106 107
	-76 2 105 106 107 108
	-77 1 109 110 111 112
	-78 1 110 111 112 113
	-79 1 111 112 113 114
	-80 1 112 113 114 115
	-81 1 116 117 118 119
	-82 1 117 118 119 120
	-83 1 118 119 120 121
	-84 1 119 120 121 122
	-85 1 120 121 122 123
	-86 2 123 124 125 126
	-87 2 124 125 126 127
	-88 2 125 126 127 128
	-89 2 126 127 128 129
	-90 2 127 128 129 130
	-91 2 128 129 130 131
	-92 2 129 130 131 132
	-93 2 130 131 132 133
	-94 2 131 132 133 134
	-95 2 132 133 134 135
	-96 1 136 137 138 139
	-97 1 137 138 139 140
	-98 1 138 139 140 141
	-99 1 139 140 141 142
	-100 1 143 144 145 146
	-101 1 144 145 146 147
	-102 1 145 146 147 148
	-103 1 146 147 148 149
	-104 1 147 148 149 150
	-105 2 150 151 152 153
	-106 2 151 152 153 154
	-107 2 152 153 154 155
	-108 2 153 154 155 156
	-109 2 154 155 156 157
	-110 2 155 156 157 158
	-111 2 156 157 158 159
	-112 2 157 158 159 160
	-113 2 158 159 160 161
	-114 2 159 160 161 162
	-115 1 163 164 165 166
	-116 1 164 165 166 167
	-117 1 165 166 167 168
	-118 1 166 167 168 169
	-119 1 170 171 172 173
	-120 1 171 172 173 174
	-121 1 172 173 174 175
	-122 1 173 174 175 176
	-123 1 174 175 176 177
	-124 2 177 178 179 180
	-125 2 178 179 180 181
	-126 2 179 180 181 182
	-127 2 180 181 182 183
	-128 2 181 182 183 184
	-129 2 182 183 184 185
	-130 2 183 184 185 186
	-131 2 184 185 186 187
	-132 2 185 186 187 188
	-133 2 186 187 188 189
	-134 1 190 191 192 193
	-135 1 191 192 193 194
	-136 1 192 193 194 195
	-137 1 193 194 195 196
	-138 1 197 198 199 200
	-139 1 198 199 200 201
	-140 1 199 200 201 202
	-141 1 200 201 202 203
	-142 1 201 202 203 204
	-143 2 204 205 206 207
	-144 2 205 206 207 208
	-145 2 206 207 208 209
	-146 2 207 208 209 210
	-147 2 208 209 210 211
	-148 2 209 210 211 212
	-149 2 210 211 212 213
	-150 2 211 212 213 214
	-151 2 212 213 214 215
	-152 2 213 214 215 216
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in
	deleted file mode 100644
	index 3bc8ede7b..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in
	+++ /dev/null
	@@ -1,41 +0,0 @@
	-
	-
	-# ----------------- Init Section -----------------
	-
	-include "system.in.init"
	-
	-
	-# ----------------- Atom Definition Section -----------------
	-
	-read_data "system.data"
	-
	-# ----------------- Settings Section -----------------
	-
	-include "system.in.settings"
	-
	-
	-# ----------------- Run Section -----------------
	-
	-# The lines above define the system you want to simulate.
	-# What you do next is up to you.
	-# Typically a user would minimize and equilibrate
	-# the system using commands similar to the following:
	-# ---- examples ----
	-#
	-# -- minimize --
	-# minimize 1.0e-5 1.0e-7 1000 10000
	-# (Note: Some fixes, for example "shake", interfere with the minimize command,
	-# You can use the "unfix" command to disable them before minimization.)
	-# -- declare time step for normal MD --
	-# timestep 1.0
	-# -- run at constant pressure (Nose-Hoover)--
	-# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
	-# -- ALTERNATELY, run at constant volume (Nose-Hoover) --
	-# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
	-# -- ALTERNATELY, run at constant volume using Langevin dynamics. --
	-# -- (This is good for sparse CG polymers in implicit solvent.) --
	-fix fxlan all langevin 300.0 300.0 5000 48279
	-# -- Now, finally run the simulation --
	-# run 50000
	-# ---- (end of examples) ----
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.init b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.init
	deleted file mode 100644
	index 1a2282f0a..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.init
	+++ /dev/null
	@@ -1,21 +0,0 @@
	- # --- 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)
	- units lj
	- atom_style full
	- pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0
	- 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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.settings b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.settings
	deleted file mode 100644
	index aaa365fa5..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.settings
	+++ /dev/null
	@@ -1,30 +0,0 @@
	- pair_coeff 1 1 lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
	- pair_coeff 1 2 lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
	- pair_coeff 1 3 lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
	- pair_coeff 2 2 lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
	- pair_coeff 2 3 lj/charmm/coul/charmm/inter 0.25 1.0 1 0
	- pair_coeff 3 3 lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
	- bond_coeff 1 harmonic 100.0 1.0
	- angle_coeff 1 harmonic 13.3333333333 105.0
	- # style file keyword
	- dihedral_coeff 2 table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
	- dihedral_coeff 1 table table_dihedral_frustrated.dat FRUSTRATED_BETA
	- # No need to specify dihedral interactions in the turn regions. (none exist)
	- # Optional: define the atoms in the "proteins" group
	- group proteins type 1
	- group proteins type 2
	- group proteins type 3
	- # 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 4 4 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 4
	-pair_coeff 1 4 table table_minichaperone_h=0.6.dat CH_H0.6
	-pair_coeff 2 4 table table_minichaperone_h=0.dat CH_H0
	-pair_coeff 3 4 table table_minichaperone_h=0.dat CH_H0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt
	deleted file mode 100644
	index 8f8c37d08..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat
	deleted file mode 100644
	index d660fee30..000000000
	--- a/tools/moltemplate/examples/CG_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
	-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
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	-337 336.0 -1.1450815839 0.0513440218749
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	-341 340.0 -1.36176515529 0.0569651443923
	-342 341.0 -1.41941665773 0.0583350049463
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	-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
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/CG_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/CG_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
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	-981 8.0 0.0 0.0
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/CG_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/CG_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
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	-719 6.69 2.31145454526e-06 6.88573851497e-06
	-720 6.695 2.27729324613e-06 6.7790821789e-06
	-721 6.7 2.2436607404e-06 6.67421571025e-06
	-722 6.705 2.21054815986e-06 6.57110676157e-06
	-723 6.71 2.17794679649e-06 6.46972361177e-06
	-724 6.715 2.14584809929e-06 6.3700351531e-06
	-725 6.72 2.11424367135e-06 6.27201087853e-06
	-726 6.725 2.08312526676e-06 6.17562086942e-06
	-727 6.73 2.05248478781e-06 6.08083578334e-06
	-728 6.735 2.02231428205e-06 5.98762684229e-06
	-729 6.74 1.99260593955e-06 5.89596582112e-06
	-730 6.745 1.96335209014e-06 5.80582503618e-06
	-731 6.75 1.93454520075e-06 5.71717733423e-06
	-732 6.755 1.90617787275e-06 5.62999608165e-06
	-733 6.76 1.87824283942e-06 5.54425515378e-06
	-734 6.765 1.85073296341e-06 5.4599289246e-06
	-735 6.77 1.82364123426e-06 5.37699225653e-06
	-736 6.775 1.79696076603e-06 5.29542049053e-06
	-737 6.78 1.77068479486e-06 5.21518943638e-06
	-738 6.785 1.74480667672e-06 5.13627536317e-06
	-739 6.79 1.71931988509e-06 5.05865498999e-06
	-740 6.795 1.69421800875e-06 4.98230547687e-06
	-741 6.8 1.66949474959e-06 4.90720441581e-06
	-742 6.805 1.6451439205e-06 4.83332982211e-06
	-743 6.81 1.62115944323e-06 4.76066012583e-06
	-744 6.815 1.59753534637e-06 4.68917416347e-06
	-745 6.82 1.57426576334e-06 4.61885116973e-06
	-746 6.825 1.55134493038e-06 4.54967076962e-06
	-747 6.83 1.52876718466e-06 4.48161297055e-06
	-748 6.835 1.50652696239e-06 4.41465815471e-06
	-749 6.84 1.48461879691e-06 4.3487870716e-06
	-750 6.845 1.46303731695e-06 4.28398083065e-06
	-751 6.85 1.44177724478e-06 4.22022089406e-06
	-752 6.855 1.42083339451e-06 4.15748906981e-06
	-753 6.86 1.40020067034e-06 4.09576750471e-06
	-754 6.865 1.37987406492e-06 4.03503867774e-06
	-755 6.87 1.35984865768e-06 3.97528539342e-06
	-756 6.875 1.34011961322e-06 3.91649077535e-06
	-757 6.88 1.32068217977e-06 3.85863825993e-06
	-758 6.885 1.30153168756e-06 3.80171159016e-06
	-759 6.89 1.2826635474e-06 3.74569480958e-06
	-760 6.895 1.26407324911e-06 3.69057225636e-06
	-761 6.9 1.2457563601e-06 3.63632855747e-06
	-762 6.905 1.22770852394e-06 3.58294862303e-06
	-763 6.91 1.20992545896e-06 3.53041764074e-06
	-764 6.915 1.19240295686e-06 3.47872107044e-06
	-765 6.92 1.17513688137e-06 3.42784463875e-06
	-766 6.925 1.15812316694e-06 3.37777433388e-06
	-767 6.93 1.14135781743e-06 3.32849640049e-06
	-768 6.935 1.12483690484e-06 3.27999733473e-06
	-769 6.94 1.10855656808e-06 3.23226387928e-06
	-770 6.945 1.09251301173e-06 3.18528301858e-06
	-771 6.95 1.07670250488e-06 3.13904197413e-06
	-772 6.955 1.06112137989e-06 3.09352819987e-06
	-773 6.96 1.0457660313e-06 3.0487293777e-06
	-774 6.965 1.03063291469e-06 3.00463341302e-06
	-775 6.97 1.01571854555e-06 2.96122843043e-06
	-776 6.975 1.0010194982e-06 2.9185027695e-06
	-777 6.98 9.86532404745e-07 2.87644498061e-06
	-778 6.985 9.72253954022e-07 2.83504382088e-06
	-779 6.99 9.58180890566e-07 2.79428825018e-06
	-780 6.995 9.44310013618e-07 2.75416742728e-06
	-781 7.0 9.30638176135e-07 2.71467070595e-06
	-782 7.005 9.17162283824e-07 2.6757876313e-06
	-783 7.01 9.03879294199e-07 2.63750793605e-06
	-784 7.015 8.90786215647e-07 2.59982153697e-06
	-785 7.02 8.77880106517e-07 2.56271853136e-06
	-786 7.025 8.6515807423e-07 2.5261891936e-06
	-787 7.03 8.52617274397e-07 2.49022397175e-06
	-788 7.035 8.40254909964e-07 2.4548134843e-06
	-789 7.04 8.28068230364e-07 2.41994851684e-06
	-790 7.045 8.16054530689e-07 2.38562001899e-06
	-791 7.05 8.04211150882e-07 2.35181910119e-06
	-792 7.055 7.92535474938e-07 2.3185370317e-06
	-793 7.06 7.81024930121e-07 2.28576523364e-06
	-794 7.065 7.696769862e-07 2.25349528197e-06
	-795 7.07 7.58489154692e-07 2.22171890072e-06
	-796 7.075 7.47458988133e-07 2.19042796013e-06
	-797 7.08 7.36584079342e-07 2.15961447389e-06
	-798 7.085 7.2586206072e-07 2.12927059646e-06
	-799 7.09 7.15290603549e-07 2.09938862041e-06
	-800 7.095 7.04867417307e-07 2.06996097384e-06
	-801 7.1 6.94590249e-07 2.04098021782e-06
	-802 7.105 6.84456882499e-07 2.01243904392e-06
	-803 7.11 6.74465137898e-07 1.98433027176e-06
	-804 7.115 6.64612870877e-07 1.9566468466e-06
	-805 7.12 6.5489797208e-07 1.92938183703e-06
	-806 7.125 6.45318366505e-07 1.90252843264e-06
	-807 7.13 6.35872012904e-07 1.87607994179e-06
	-808 7.135 6.26556903196e-07 1.85002978938e-06
	-809 7.14 6.17371061887e-07 1.8243715147e-06
	-810 7.145 6.08312545506e-07 1.7990987693e-06
	-811 7.15 5.99379442048e-07 1.77420531491e-06
	-812 7.155 5.90569870428e-07 1.74968502142e-06
	-813 7.16 5.81881979945e-07 1.72553186483e-06
	-814 7.165 5.73313949757e-07 1.70173992537e-06
	-815 7.17 5.64863988364e-07 1.67830338549e-06
	-816 7.175 5.56530333103e-07 1.65521652804e-06
	-817 7.18 5.4831124965e-07 1.63247373439e-06
	-818 7.185 5.40205031528e-07 1.61006948263e-06
	-819 7.19 5.32209999637e-07 1.58799834581e-06
	-820 7.195 5.24324501773e-07 1.56625499017e-06
	-821 7.2 5.16546912175e-07 1.54483417343e-06
	-822 7.205 5.08875631066e-07 1.52373074317e-06
	-823 7.21 5.01309084211e-07 1.50293963511e-06
	-824 7.215 4.93845722479e-07 1.48245587157e-06
	-825 7.22 4.86484021414e-07 1.46227455985e-06
	-826 7.225 4.79222480814e-07 1.44239089069e-06
	-827 7.23 4.72059624319e-07 1.42280013677e-06
	-828 7.235 4.64993999004e-07 1.4034976512e-06
	-829 7.24 4.58024174978e-07 1.38447886607e-06
	-830 7.245 4.51148744997e-07 1.36573929102e-06
	-831 7.25 4.44366324079e-07 1.34727451183e-06
	-832 7.255 4.37675549122e-07 1.32908018904e-06
	-833 7.26 4.31075078542e-07 1.31115205663e-06
	-834 7.265 4.24563591899e-07 1.29348592063e-06
	-835 7.27 4.1813978955e-07 1.2760776579e-06
	-836 7.275 4.11802392291e-07 1.25892321479e-06
	-837 7.28 4.05550141016e-07 1.24201860594e-06
	-838 7.285 3.99381796376e-07 1.22535991301e-06
	-839 7.29 3.9329613845e-07 1.20894328352e-06
	-840 7.295 3.87291966418e-07 1.19276492962e-06
	-841 7.3 3.81368098239e-07 1.17682112698e-06
	-842 7.305 3.75523370336e-07 1.16110821364e-06
	-843 7.31 3.69756637291e-07 1.14562258888e-06
	-844 7.315 3.64066771537e-07 1.13036071214e-06
	-845 7.32 3.58452663062e-07 1.11531910195e-06
	-846 7.325 3.52913219116e-07 1.10049433488e-06
	-847 7.33 3.47447363922e-07 1.0858830445e-06
	-848 7.335 3.42054038397e-07 1.07148192036e-06
	-849 7.34 3.3673219987e-07 1.05728770703e-06
	-850 7.345 3.31480821814e-07 1.04329720308e-06
	-851 7.35 3.26298893574e-07 1.02950726017e-06
	-852 7.355 3.21185420107e-07 1.01591478207e-06
	-853 7.36 3.16139421723e-07 1.00251672378e-06
	-854 7.365 3.1115993383e-07 9.89310090577e-07
	-855 7.37 3.06246006687e-07 9.76291937184e-07
	-856 7.375 3.01396705156e-07 9.63459366859e-07
	-857 7.38 2.96611108464e-07 9.50809530558e-07
	-858 7.385 2.91888309966e-07 9.38339626099e-07
	-859 7.39 2.87227416913e-07 9.26046897331e-07
	-860 7.395 2.82627550221e-07 9.13928633336e-07
	-861 7.4 2.78087844251e-07 9.01982167635e-07
	-862 7.405 2.73607446588e-07 8.90204877406e-07
	-863 7.41 2.6918551782e-07 8.78594182731e-07
	-864 7.415 2.64821231333e-07 8.67147545837e-07
	-865 7.42 2.60513773095e-07 8.55862470371e-07
	-866 7.425 2.56262341455e-07 8.44736500673e-07
	-867 7.43 2.5206614694e-07 8.33767221072e-07
	-868 7.435 2.47924412057e-07 8.22952255188e-07
	-869 7.44 2.43836371097e-07 8.12289265255e-07
	-870 7.445 2.39801269946e-07 8.01775951447e-07
	-871 7.45 2.35818365896e-07 7.91410051224e-07
	-872 7.455 2.31886927457e-07 7.81189338689e-07
	-873 7.46 2.28006234181e-07 7.7111162395e-07
	-874 7.465 2.2417557648e-07 7.61174752504e-07
	-875 7.47 2.20394255452e-07 7.51376604623e-07
	-876 7.475 2.16661582706e-07 7.41715094759e-07
	-877 7.48 2.12976880196e-07 7.32188170953e-07
	-878 7.485 2.09339480053e-07 7.22793814262e-07
	-879 7.49 2.05748724421e-07 7.13530038185e-07
	-880 7.495 2.02203965296e-07 7.04394888118e-07
	-881 7.5 1.9870456437e-07 6.95386440797e-07
	-882 7.505 1.95249892873e-07 6.86502803769e-07
	-883 7.51 1.91839331421e-07 6.77742114863e-07
	-884 7.515 1.88472269866e-07 6.69102541673e-07
	-885 7.52 1.85148107151e-07 6.60582281052e-07
	-886 7.525 1.8186625116e-07 6.52179558612e-07
	-887 7.53 1.7862611858e-07 6.43892628236e-07
	-888 7.535 1.75427134757e-07 6.35719771598e-07
	-889 7.54 1.72268733561e-07 6.27659297689e-07
	-890 7.545 1.6915035725e-07 6.19709542357e-07
	-891 7.55 1.66071456337e-07 6.11868867849e-07
	-892 7.555 1.63031489458e-07 6.04135662368e-07
	-893 7.56 1.60029923244e-07 5.96508339628e-07
	-894 7.565 1.57066232194e-07 5.88985338432e-07
	-895 7.57 1.54139898552e-07 5.81565122242e-07
	-896 7.575 1.51250412185e-07 5.74246178766e-07
	-897 7.58 1.48397270459e-07 5.6702701955e-07
	-898 7.585 1.45579978125e-07 5.59906179576e-07
	-899 7.59 1.42798047202e-07 5.52882216872e-07
	-900 7.595 1.40050996861e-07 5.4595371212e-07
	-901 7.6 1.37338353314e-07 5.39119268281e-07
	-902 7.605 1.34659649703e-07 5.32377510221e-07
	-903 7.61 1.32014425993e-07 5.25727084341e-07
	-904 7.615 1.29402228861e-07 5.19166658223e-07
	-905 7.62 1.26822611598e-07 5.12694920274e-07
	-906 7.625 1.24275133998e-07 5.06310579376e-07
	-907 7.63 1.21759362262e-07 5.0001236455e-07
	-908 7.635 1.19274868896e-07 4.93799024619e-07
	-909 7.64 1.16821232612e-07 4.87669327877e-07
	-910 7.645 1.14398038233e-07 4.8162206177e-07
	-911 7.65 1.120048766e-07 4.75656032572e-07
	-912 7.655 1.09641344473e-07 4.69770065082e-07
	-913 7.66 1.07307044442e-07 4.63963002309e-07
	-914 7.665 1.05001584841e-07 4.58233705177e-07
	-915 7.67 1.02724579651e-07 4.52581052224e-07
	-916 7.675 1.0047564842e-07 4.47003939317e-07
	-917 7.68 9.82544161708e-08 4.41501279361e-07
	-918 7.685 9.60605133226e-08 4.36072002025e-07
	-919 7.69 9.38935756035e-08 4.30715053459e-07
	-920 7.695 9.17532439703e-08 4.25429396028e-07
	-921 7.7 8.96391645283e-08 4.20214008047e-07
	-922 7.705 8.75509884516e-08 4.15067883513e-07
	-923 7.71 8.54883719059e-08 4.09990031857e-07
	-924 7.715 8.34509759714e-08 4.04979477684e-07
	-925 7.72 8.14384665682e-08 4.00035260529e-07
	-926 7.725 7.94505143815e-08 3.95156434615e-07
	-927 7.73 7.74867947896e-08 3.90342068606e-07
	-928 7.735 7.55469877916e-08 3.85591245382e-07
	-929 7.74 7.36307779372e-08 3.80903061797e-07
	-930 7.745 7.17378542573e-08 3.76276628463e-07
	-931 7.75 6.9867910196e-08 3.71711069515e-07
	-932 7.755 6.80206435432e-08 3.67205522401e-07
	-933 7.76 6.61957563687e-08 3.62759137662e-07
	-934 7.765 6.43929549576e-08 3.5837107872e-07
	-935 7.77 6.26119497457e-08 3.54040521671e-07
	-936 7.775 6.08524552575e-08 3.49766655078e-07
	-937 7.78 5.91141900435e-08 3.45548679773e-07
	-938 7.785 5.73968766201e-08 3.41385808656e-07
	-939 7.79 5.57002414093e-08 3.37277266505e-07
	-940 7.795 5.402401468e-08 3.33222289779e-07
	-941 7.8 5.23679304898e-08 3.29220126433e-07
	-942 7.805 5.07317266285e-08 3.25270035737e-07
	-943 7.81 4.91151445613e-08 3.21371288087e-07
	-944 7.815 4.75179293742e-08 3.17523164833e-07
	-945 7.82 4.59398297194e-08 3.13724958102e-07
	-946 7.825 4.43805977617e-08 3.09975970624e-07
	-947 7.83 4.28399891263e-08 3.06275515564e-07
	-948 7.835 4.13177628469e-08 3.02622916355e-07
	-949 7.84 3.98136813144e-08 2.99017506534e-07
	-950 7.845 3.83275102273e-08 2.95458629582e-07
	-951 7.85 3.68590185422e-08 2.91945638765e-07
	-952 7.855 3.54079784251e-08 2.8847789698e-07
	-953 7.86 3.39741652039e-08 2.85054776599e-07
	-954 7.865 3.25573573211e-08 2.81675659322e-07
	-955 7.87 3.11573362879e-08 2.78339936025e-07
	-956 7.875 2.97738866382e-08 2.7504700662e-07
	-957 7.88 2.84067958844e-08 2.71796279909e-07
	-958 7.885 2.70558544725e-08 2.68587173443e-07
	-959 7.89 2.57208557397e-08 2.65419113385e-07
	-960 7.895 2.44015958707e-08 2.62291534374e-07
	-961 7.9 2.30978738564e-08 2.59203879393e-07
	-962 7.905 2.18094914519e-08 2.56155599635e-07
	-963 7.91 2.05362531363e-08 2.53146154374e-07
	-964 7.915 1.92779660724e-08 2.50175010842e-07
	-965 7.92 1.8034440067e-08 2.47241644098e-07
	-966 7.925 1.68054875325e-08 2.44345536912e-07
	-967 7.93 1.55909234484e-08 2.41486179638e-07
	-968 7.935 1.43905653237e-08 2.38663070101e-07
	-969 7.94 1.32042331597e-08 2.35875713474e-07
	-970 7.945 1.20317494138e-08 2.33123622171e-07
	-971 7.95 1.08729389636e-08 2.30406315726e-07
	-972 7.955 9.72762907123e-09 2.27723320689e-07
	-973 7.96 8.59564934896e-09 2.2507417051e-07
	-974 7.965 7.47683172465e-09 2.2245840544e-07
	-975 7.97 6.37101040818e-09 2.19875572416e-07
	-976 7.975 5.27802185823e-09 2.17325224966e-07
	-977 7.98 4.19770474957e-09 2.148069231e-07
	-978 7.985 3.12989994095e-09 2.12320233213e-07
	-979 7.99 2.07445044336e-09 2.09864727985e-07
	-980 7.995 1.03120138888e-09 2.07439986287e-07
	-981 8.0 0.0 0.0
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min
	deleted file mode 100644
	index e2d4a5cce..000000000
	--- a/tools/moltemplate/examples/CG_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt
	deleted file mode 100644
	index 523a16575..000000000
	--- a/tools/moltemplate/examples/CG_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 read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README.TXT
	deleted file mode 100644
	index 77af3de15..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_run.sh
	deleted file mode 100755
	index 99338c770..000000000
	--- a/tools/moltemplate/examples/CG_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_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_short_sim.in.nvt # production run
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh
	deleted file mode 100755
	index f2462426f..000000000
	--- a/tools/moltemplate/examples/CG_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-dihdedrals 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/CG_protein_folding_examples/1bead+chaperone/frustrated/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_visualise.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/CG_protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt
	deleted file mode 100644
	index 074b55c73..000000000
	--- a/tools/moltemplate/examples/CG_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) = 4eps_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/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt
	deleted file mode 100644
	index 54e2de437..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_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/CG_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
	-# 5.4epsilon and 6.0epsilon. 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 -AtermA - BtermB
	-
	-# 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 = (0.5sin(0.5(phi-phiA)conv_units)
	- expA * pow(cos(0.5(phi-phiA)conv_units), expA-1.0))
	- termB = (0.5sin(0.5(phi-phiB)conv_units)
	- expB * pow(cos(0.5(phi-phiB)conv_units), expB-1.0))
	- return -conv_units(AtermA + 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/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt
	deleted file mode 100644
	index a27595559..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat
	deleted file mode 100644
	index d660fee30..000000000
	--- a/tools/moltemplate/examples/CG_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
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	-171 170.0 -5.64698076513 0.0114143131467
	-172 171.0 -5.65759052241 0.00979534879707
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	-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
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	-197 196.0 -5.29239542138 -0.0404630575223
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	-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
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	-211 210.0 -4.54935211328 -0.0640351946902
	-212 211.0 -4.4846815919 -0.0652948446678
	-213 212.0 -4.41878466581 -0.0664877739558
	-214 213.0 -4.35172872155 -0.0676126754981
	-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
	-222 221.0 -3.78198120223 -0.0740549990687
	-223 222.0 -3.70768097086 -0.0745332827669
	-224 223.0 -3.63293896573 -0.0749385839297
	-225 224.0 -3.5578280347 -0.0752711944755
	-226 225.0 -3.48242066643 -0.075531540416
	-227 226.0 -3.4067888579 -0.0757201784978
	-228 227.0 -3.33100398548 -0.0758377925383
	-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
	-235 234.0 -2.80203355622 -0.0747545911191
	-236 235.0 -2.72747997572 -0.0743424509249
	-237 236.0 -2.65336861841 -0.073870421164
	-238 237.0 -2.57975853208 -0.0733401976859
	-239 238.0 -2.50670703279 -0.0727535470871
	-240 239.0 -2.4342696372 -0.0721123005638
	-241 240.0 -2.36250000104 -0.0714183476691
	-242 241.0 -2.29144986396 -0.0706736299971
	-243 242.0 -2.22116900065 -0.0698801348102
	-244 243.0 -2.15170517837 -0.0690398886302
	-245 244.0 -2.0831041209 -0.0681549508121
	-246 245.0 -2.01540947892 -0.067227407119
	-247 246.0 -1.94866280684 -0.0662593633171
	-248 247.0 -1.88290354594 -0.0652529388105
	-249 248.0 -1.81816901389 -0.0642102603325
	-250 249.0 -1.7544944006 -0.0631334557138
	-251 250.0 -1.69191277013 -0.0620246477436
	-252 251.0 -1.6304550688 -0.0608859481423
	-253 252.0 -1.57015013921 -0.059719451663
	-254 253.0 -1.51102474011 -0.0585272303374
	-255 254.0 -1.45310357187 -0.0573113278834
	-256 255.0 -1.39640930762 -0.0560737542899
	-257 256.0 -1.34096262951 -0.054816480593
	-258 257.0 -1.28678227024 -0.0535414338587
	-259 258.0 -1.23388505944 -0.0522504923856
	-260 259.0 -1.18228597475 -0.0509454811405
	-261 260.0 -1.13199819729 -0.0496281674395
	-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
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/run.in.min
	deleted file mode 100644
	index fce9843aa..000000000
	--- a/tools/moltemplate/examples/CG_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt
	deleted file mode 100644
	index 2974c12e8..000000000
	--- a/tools/moltemplate/examples/CG_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 the read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT
	deleted file mode 100644
	index 5da41b9a8..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh
	deleted file mode 100755
	index 45bd2d451..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh
	deleted file mode 100755
	index f2462426f..000000000
	--- a/tools/moltemplate/examples/CG_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-dihdedrals 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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualise.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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg
	deleted file mode 100644
	index a0da344db..000000000
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	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt
	deleted file mode 100644
	index 0dc1f5dd0..000000000
	--- a/tools/moltemplate/examples/CG_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) = 4eps_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt
	deleted file mode 100644
	index cbc8fe217..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt
	deleted file mode 100644
	index 8266d2a89..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_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/CG_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 4.0piRR4.0eps(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 4.0pieps(R/r) (0.2term10 - 0.5h*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 = 4.0epspi(R/r) (0.2term10 - 0.5h*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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt
	deleted file mode 100644
	index d8781c26f..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_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/CG_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
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	-1124 5.615 37389.6406876 -966762.764619
	-1125 5.62 42585.6453685 -1115510.15847
	-1126 5.625 48586.9176207 -1289589.16849
	-1127 5.63 55531.6077773 -1493742.80799
	-1128 5.635 63583.9274287 -1733684.84106
	-1129 5.64 72939.5241308 -2016315.88337
	-1130 5.645 83832.0618829 -2349991.60166
	-1131 5.65 96541.300368 -2744856.56324
	-1132 5.655 111403.042767 -3213261.07776
	-1133 5.66 128821.420452 -3770283.30061
	-1134 5.665 149284.109551 -4434385.29693
	-1135 5.67 173381.238005 -5228240.185
	-1136 5.675 201828.953692 -6179778.54971
	-1137 5.68 235498.900026 -7323516.93224
	-1138 5.685 275455.2056 -8702250.57742
	-1139 5.69 323001.06674 -10369218.4143
	-1140 5.695 379737.623748 -12390882.7371
	-1141 5.7 447638.654038 -14850512.384
	-1142 5.705 529145.697826 -17852820.7393
	-1143 5.71 627289.689791 -21529994.6762
	-1144 5.715 745847.124656 -26049566.1236
	-1145 5.72 889541.417924 -31624736.2614
	-1146 5.725 1064303.6889 -38527980.3963
	-1147 5.73 1277612.0471 -47109063.5591
	-1148 5.735 1538935.10642 -57819017.4811
	-1149 5.74 1860314.59485 -71242218.9505
	-1150 5.745 2257134.5845 -88139540.3817
	-1151 5.75 2749142.49547 -109506722.176
	-1152 5.755 3361811.73098 -136653799.897
	-1153 5.76 4128170.65016 -171313840.077
	-1154 5.765 5091272.07333 -215792744.495
	-1155 5.77 6307548.29223 -273176998.31
	-1156 5.775 7851398.52158 -347623759.363
	-1157 5.78 9821503.74726 -444768835.455
	-1158 5.785 12349580.5127 -572304762.479
	-1159 5.79 15612604.744 -740806327.342
	-1160 5.795 19850012.3018 -964919124.004
	-1161 5.8 25388097.1921 -1265085490.72
	-1162 5.805 32674911.255 -1670073366.45
	-1163 5.81 42330627.3386 -2220716617.13
	-1164 5.815 55220893.742 -2975502155.22
	-1165 5.82 72564721.5485 -4019002953.22
	-1166 5.825 96094798.4335 -5474746758.15
	-1167 5.83 128298297.388 -7525081897.32
	-1168 5.835 172782757.396 -10442221387.6
	-1169 5.84 234838762.891 -14637386017.7
	-1170 5.845 322316442.616 -20739670704.4
	-1171 5.85 447009526.718 -29724465089.5
	-1172 5.855 626872755.056 -43125823862.6
	-1173 5.86 889629660.718 -63393502739.0
	-1174 5.865 1278740106.83 -94503868935.1
	-1175 5.87 1863446791.23 -1.43025101229e+11
	-1176 5.875 2756012237.96 -2.20012469835e+11
	-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/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_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/CG_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
	-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
	-40 0.195 8.50803294874e-07 -2.01969724788e-07
	-41 0.2 8.51826600486e-07 -2.07355135913e-07
	-42 0.205 8.52876872743e-07 -2.12756452745e-07
	-43 0.21 8.5395419223e-07 -2.18174099007e-07
	-44 0.215 8.55058641658e-07 -2.23608500394e-07
	-45 0.22 8.56190305871e-07 -2.29060084623e-07
	-46 0.225 8.57349271858e-07 -2.34529281482e-07
	-47 0.23 8.5853562876e-07 -2.40016522891e-07
	-48 0.235 8.59749467885e-07 -2.4552224295e-07
	-49 0.24 8.60990882715e-07 -2.51046877993e-07
	-50 0.245 8.62259968921e-07 -2.56590866647e-07
	-51 0.25 8.63556824372e-07 -2.62154649881e-07
	-52 0.255 8.64881549149e-07 -2.67738671065e-07
	-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
	-125 0.62 1.04676797537e-06 -7.64274544386e-07
	-126 0.625 1.0506107378e-06 -7.72841223537e-07
	-127 0.63 1.05449649623e-06 -7.81473080451e-07
	-128 0.635 1.05842557863e-06 -7.90170949513e-07
	-129 0.64 1.06239831715e-06 -7.98935673896e-07
	-130 0.645 1.06641504821e-06 -8.07768105686e-07
	-131 0.65 1.07047611249e-06 -8.1666910601e-07
	-132 0.655 1.074581855e-06 -8.25639545171e-07
	-133 0.66 1.07873262514e-06 -8.34680302772e-07
	-134 0.665 1.08292877671e-06 -8.43792267857e-07
	-135 0.67 1.08717066799e-06 -8.52976339042e-07
	-136 0.675 1.09145866179e-06 -8.62233424653e-07
	-137 0.68 1.09579312546e-06 -8.71564442867e-07
	-138 0.685 1.10017443099e-06 -8.80970321849e-07
	-139 0.69 1.10460295501e-06 -8.90451999898e-07
	-140 0.695 1.1090790789e-06 -9.0001042559e-07
	-141 0.7 1.11360318878e-06 -9.09646557926e-07
	-142 0.705 1.1181756756e-06 -9.19361366479e-07
	-143 0.71 1.1227969352e-06 -9.29155831544e-07
	-144 0.715 1.12746736833e-06 -9.39030944294e-07
	-145 0.72 1.13218738073e-06 -9.48987706931e-07
	-146 0.725 1.13695738317e-06 -9.59027132844e-07
	-147 0.73 1.14177779154e-06 -9.6915024677e-07
	-148 0.735 1.14664902685e-06 -9.79358084952e-07
	-149 0.74 1.15157151534e-06 -9.89651695304e-07
	-150 0.745 1.15654568852e-06 -1.00003213758e-06
	-151 0.75 1.16157198322e-06 -1.01050048352e-06
	-152 0.755 1.16665084166e-06 -1.02105781707e-06
	-153 0.76 1.17178271153e-06 -1.0317052345e-06
	-154 0.765 1.176968046e-06 -1.0424438446e-06
	-155 0.77 1.18220730383e-06 -1.05327476888e-06
	-156 0.775 1.18750094943e-06 -1.0641991417e-06
	-157 0.78 1.19284945291e-06 -1.07521811051e-06
	-158 0.785 1.19825329013e-06 -1.08633283599e-06
	-159 0.79 1.20371294282e-06 -1.09754449225e-06
	-160 0.795 1.20922889858e-06 -1.10885426703e-06
	-161 0.8 1.21480165102e-06 -1.12026336191e-06
	-162 0.805 1.22043169976e-06 -1.13177299243e-06
	-163 0.81 1.22611955055e-06 -1.14338438839e-06
	-164 0.815 1.23186571533e-06 -1.15509879397e-06
	-165 0.82 1.23767071227e-06 -1.16691746799e-06
	-166 0.825 1.24353506591e-06 -1.17884168407e-06
	-167 0.83 1.24945930716e-06 -1.19087273088e-06
	-168 0.835 1.25544397344e-06 -1.20301191233e-06
	-169 0.84 1.26148960871e-06 -1.21526054778e-06
	-170 0.845 1.26759676357e-06 -1.22761997229e-06
	-171 0.85 1.27376599533e-06 -1.2400915368e-06
	-172 0.855 1.27999786811e-06 -1.2526766084e-06
	-173 0.86 1.2862929529e-06 -1.26537657052e-06
	-174 0.865 1.29265182763e-06 -1.27819282318e-06
	-175 0.87 1.29907507731e-06 -1.29112678323e-06
	-176 0.875 1.30556329404e-06 -1.30417988457e-06
	-177 0.88 1.31211707714e-06 -1.31735357842e-06
	-178 0.885 1.31873703325e-06 -1.33064933354e-06
	-179 0.89 1.32542377639e-06 -1.34406863648e-06
	-180 0.895 1.33217792804e-06 -1.35761299185e-06
	-181 0.9 1.33900011726e-06 -1.37128392257e-06
	-182 0.905 1.34589098079e-06 -1.38508297012e-06
	-183 0.91 1.35285116309e-06 -1.39901169482e-06
	-184 0.915 1.3598813165e-06 -1.41307167609e-06
	-185 0.92 1.36698210128e-06 -1.42726451271e-06
	-186 0.925 1.37415418575e-06 -1.44159182311e-06
	-187 0.93 1.38139824636e-06 -1.45605524565e-06
	-188 0.935 1.38871496782e-06 -1.47065643891e-06
	-189 0.94 1.39610504317e-06 -1.48539708196e-06
	-190 0.945 1.40356917389e-06 -1.50027887466e-06
	-191 0.95 1.41110807003e-06 -1.51530353796e-06
	-192 0.955 1.41872245029e-06 -1.5304728142e-06
	-193 0.96 1.42641304213e-06 -1.54578846742e-06
	-194 0.965 1.4341805819e-06 -1.56125228366e-06
	-195 0.97 1.44202581492e-06 -1.57686607128e-06
	-196 0.975 1.44994949562e-06 -1.59263166129e-06
	-197 0.98 1.45795238763e-06 -1.60855090765e-06
	-198 0.985 1.46603526391e-06 -1.62462568762e-06
	-199 0.99 1.47419890689e-06 -1.64085790209e-06
	-200 0.995 1.48244410853e-06 -1.65724947591e-06
	-201 1.0 1.4907716705e-06 -1.67380235825e-06
	-202 1.005 1.49918240425e-06 -1.69051852294e-06
	-203 1.01 1.50767713119e-06 -1.70739996882e-06
	-204 1.015 1.51625668278e-06 -1.72444872011e-06
	-205 1.02 1.52492190065e-06 -1.74166682675e-06
	-206 1.025 1.53367363676e-06 -1.75905636483e-06
	-207 1.03 1.54251275352e-06 -1.77661943691e-06
	-208 1.035 1.5514401239e-06 -1.7943581724e-06
	-209 1.04 1.56045663161e-06 -1.81227472801e-06
	-210 1.045 1.56956317119e-06 -1.83037128807e-06
	-211 1.05 1.57876064818e-06 -1.84865006497e-06
	-212 1.055 1.58804997927e-06 -1.86711329958e-06
	-213 1.06 1.59743209239e-06 -1.88576326162e-06
	-214 1.065 1.60690792693e-06 -1.90460225011e-06
	-215 1.07 1.61647843382e-06 -1.92363259378e-06
	-216 1.075 1.62614457572e-06 -1.94285665153e-06
	-217 1.08 1.63590732717e-06 -1.9622768128e-06
	-218 1.085 1.64576767472e-06 -1.98189549811e-06
	-219 1.09 1.65572661711e-06 -2.00171515944e-06
	-220 1.095 1.66578516541e-06 -2.02173828072e-06
	-221 1.1 1.67594434321e-06 -2.04196737828e-06
	-222 1.105 1.68620518674e-06 -2.06240500133e-06
	-223 1.11 1.69656874507e-06 -2.08305373245e-06
	-224 1.115 1.70703608027e-06 -2.10391618807e-06
	-225 1.12 1.71760826757e-06 -2.12499501897e-06
	-226 1.125 1.72828639555e-06 -2.14629291076e-06
	-227 1.13 1.73907156631e-06 -2.16781258443e-06
	-228 1.135 1.74996489563e-06 -2.18955679685e-06
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	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min
	deleted file mode 100644
	index fce9843aa..000000000
	--- a/tools/moltemplate/examples/CG_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt
	deleted file mode 100644
	index 5fb8d71b3..000000000
	--- a/tools/moltemplate/examples/CG_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 read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT
	deleted file mode 100644
	index b2770e3e3..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh
	deleted file mode 100755
	index 45bd2d451..000000000
	--- a/tools/moltemplate/examples/CG_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_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh
	deleted file mode 100755
	index cb3196cf8..000000000
	--- a/tools/moltemplate/examples/CG_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-dihdedrals 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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_visualise.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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt
	deleted file mode 100644
	index 0dc1f5dd0..000000000
	--- a/tools/moltemplate/examples/CG_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) = 4eps_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt
	deleted file mode 100644
	index cbc8fe217..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt
	deleted file mode 100644
	index 5ebe6efb8..000000000
	--- a/tools/moltemplate/examples/CG_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/CG_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min
	deleted file mode 100644
	index fce9843aa..000000000
	--- a/tools/moltemplate/examples/CG_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt
	deleted file mode 100644
	index a831a97b4..000000000
	--- a/tools/moltemplate/examples/CG_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 read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-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_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README.TXT
	deleted file mode 100644
	index 0078be171..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README.TXT
	+++ /dev/null
	@@ -1,44 +0,0 @@
	-# -------- REQUIREMENTS: ---------
	-# 1) This example requires the "CLASS2" package. (Use "make yes-CLASS2")
	-# 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/CG_protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_run.sh
	deleted file mode 100755
	index 45bd2d451..000000000
	--- a/tools/moltemplate/examples/CG_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_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/CG_protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_setup.sh
	deleted file mode 100755
	index cb3196cf8..000000000
	--- a/tools/moltemplate/examples/CG_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-dihdedrals 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/CG_protein_folding_examples/1beadProtSci2010/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_visualise.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/CG_protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg
	deleted file mode 100644
	index b4d919f9e..000000000
	Binary files a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg
	deleted file mode 100644
	index cd65146ff..000000000
	Binary files a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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/CG_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/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt
	deleted file mode 100644
	index 3ee6ee4e8..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt
	+++ /dev/null
	@@ -1,276 +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 class2
	- 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
	- }
	-
	-
	-
	- # 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
	-
	- }
	-
	-
	- # 2-body (non-bonded) interactions:
	- #
	- # Uij(r) = 4eps_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
	- }
	-
	- # angleType atomtypes1 2 3 bondtypes1 2
	-
	- write_once("Data Angles By Type") {
	- @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
	- }
	-
	-
	-
	-
	-
	- # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60)
	- # (scratchwork: 1.2cos(x+60) = -1.2cos(x+60-180) = -1.2*cos(x-120))
	- # and 1.2cos(3x) = -1.2cos(3x-180)
	- # and 0.2cos(x) = -0.2cos(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
	- }
	-
	-
	- # 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:* * * *
	- @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 * * *
	- }
	-
	-} # 1beadProtSci2010 (namespace)
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh
	deleted file mode 100755
	index b534e7bf5..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh
	+++ /dev/null
	@@ -1,7 +0,0 @@
	-# run moltemplate this way
	-
	-moltemplate.sh -overlay-dihdedrals system.lt
	-
	-# This will generate various files with names ending in .in and *.data
	-# which are needed by LAMMPS.
	-
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
	deleted file mode 100644
	index fcc6188f7..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,25 +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
	-}
	-
	-
	-
	-
	-# ------------ Note: -------------
	-#
	-# If you want to try the version using "CHARMM" dihedrals, import this instead:
	-#
	-# import "versions_with_comments/1beadProtSci2010_charmm.lt"
	-#
	-# (The two versions should behave identically. However by overlaying
	-# dihedral interactions on top of eachother, charmm allows you to construct
	-# a Fourier series with an arbitrary number of terms. Class2 stops at 3.
	-# This is useful if one day you want to use a more complex dihedral potential.)
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010.lt
	deleted file mode 100644
	index a0e305f84..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/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 ~= 0.52^(1/6) + 0.4sqrt(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 ~= 0.52^(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) = 4eps_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: 1.2cos(x+60) = -1.2cos(x+60-180) = -1.2*cos(x-120))
	- # and 1.2cos(3x) = -1.2cos(3x-180)
	- # and 0.2cos(x) = -0.2cos(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/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010_charmm.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010_charmm.lt
	deleted file mode 100644
	index dad5ff548..000000000
	--- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010_charmm.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 ~= 0.52^(1/6) + 0.4sqrt(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 ~= 0.52^(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) = 4eps_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 2012-8-08, only dihedral_style table or charmm can use this formula.
	- # (dihedral_style class2 is bugged).
	- # 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 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/CG_protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/run.in.min
	deleted file mode 100644
	index fce9843aa..000000000
	--- a/tools/moltemplate/examples/CG_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_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/run.in.nvt
	deleted file mode 100644
	index 925aa2b69..000000000
	--- a/tools/moltemplate/examples/CG_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 read_restart command in this file below.)
	-# read_restart system_after_min.rst
	-
	-read_data system.data
	-
	-# -- Settings Section --
	-
	-include system.in.settings
	-
	-# -- Run Section --
	-
	-
	-timestep 0.008
	-dump 1 all custom 250 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 250 #(time interval for printing out "thermo" data)
	-
	-restart 10000000 restart_nvt
	-
	-run 1000000
	-
	-write_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT
	deleted file mode 100644
	index 33eeddda6..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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/CG_solvent/cyclododecane+watMW/README_run.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh
	deleted file mode 100755
	index 9617e16d4..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh
	+++ /dev/null
	@@ -1,25 +0,0 @@
	-# This is just an example.
	-#
	-# Note: The 3 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
	-# created earlier with moltemplate.sh:
	-# system.in.init, system.in.settings, system.data, system.in.sw
	-
	-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.npt # equilibrate the pressure
	-#"$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL)
	-
	-# 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.npt # equilibrate the pressure
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL)
	-
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh
	deleted file mode 100755
	index cb4d90898..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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/CG_solvent/cyclododecane+watMW/README_visualise.txt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualise.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/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg
	deleted file mode 100644
	index 5123dc7f6..000000000
	Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg
	deleted file mode 100644
	index 4003ac5f0..000000000
	Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg
	deleted file mode 100644
	index f1dd1467c..000000000
	Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg
	deleted file mode 100644
	index 6591b236a..000000000
	Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg
	deleted file mode 100644
	index 9b4ca06fb..000000000
	Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index 97a19f0ff..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,3669 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 2496 !NATOM
	- 1 1 1 1 0.000000 18.0200 0
	- 2 2 1 1 0.000000 18.0200 0
	- 3 3 1 1 0.000000 18.0200 0
	- 4 4 1 1 0.000000 18.0200 0
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	- 2295 1776 2 2 0.000000 14.1707 0
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	- 2298 1776 2 2 0.000000 14.1707 0
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	- 2300 1776 2 2 0.000000 14.1707 0
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	- 2302 1776 2 2 0.000000 14.1707 0
	- 2303 1776 2 2 0.000000 14.1707 0
	- 2304 1776 2 2 0.000000 14.1707 0
	- 2305 1777 2 2 0.000000 14.1707 0
	- 2306 1777 2 2 0.000000 14.1707 0
	- 2307 1777 2 2 0.000000 14.1707 0
	- 2308 1777 2 2 0.000000 14.1707 0
	- 2309 1777 2 2 0.000000 14.1707 0
	- 2310 1777 2 2 0.000000 14.1707 0
	- 2311 1777 2 2 0.000000 14.1707 0
	- 2312 1777 2 2 0.000000 14.1707 0
	- 2313 1777 2 2 0.000000 14.1707 0
	- 2314 1777 2 2 0.000000 14.1707 0
	- 2315 1777 2 2 0.000000 14.1707 0
	- 2316 1777 2 2 0.000000 14.1707 0
	- 2317 1778 2 2 0.000000 14.1707 0
	- 2318 1778 2 2 0.000000 14.1707 0
	- 2319 1778 2 2 0.000000 14.1707 0
	- 2320 1778 2 2 0.000000 14.1707 0
	- 2321 1778 2 2 0.000000 14.1707 0
	- 2322 1778 2 2 0.000000 14.1707 0
	- 2323 1778 2 2 0.000000 14.1707 0
	- 2324 1778 2 2 0.000000 14.1707 0
	- 2325 1778 2 2 0.000000 14.1707 0
	- 2326 1778 2 2 0.000000 14.1707 0
	- 2327 1778 2 2 0.000000 14.1707 0
	- 2328 1778 2 2 0.000000 14.1707 0
	- 2329 1779 2 2 0.000000 14.1707 0
	- 2330 1779 2 2 0.000000 14.1707 0
	- 2331 1779 2 2 0.000000 14.1707 0
	- 2332 1779 2 2 0.000000 14.1707 0
	- 2333 1779 2 2 0.000000 14.1707 0
	- 2334 1779 2 2 0.000000 14.1707 0
	- 2335 1779 2 2 0.000000 14.1707 0
	- 2336 1779 2 2 0.000000 14.1707 0
	- 2337 1779 2 2 0.000000 14.1707 0
	- 2338 1779 2 2 0.000000 14.1707 0
	- 2339 1779 2 2 0.000000 14.1707 0
	- 2340 1779 2 2 0.000000 14.1707 0
	- 2341 1780 2 2 0.000000 14.1707 0
	- 2342 1780 2 2 0.000000 14.1707 0
	- 2343 1780 2 2 0.000000 14.1707 0
	- 2344 1780 2 2 0.000000 14.1707 0
	- 2345 1780 2 2 0.000000 14.1707 0
	- 2346 1780 2 2 0.000000 14.1707 0
	- 2347 1780 2 2 0.000000 14.1707 0
	- 2348 1780 2 2 0.000000 14.1707 0
	- 2349 1780 2 2 0.000000 14.1707 0
	- 2350 1780 2 2 0.000000 14.1707 0
	- 2351 1780 2 2 0.000000 14.1707 0
	- 2352 1780 2 2 0.000000 14.1707 0
	- 2353 1781 2 2 0.000000 14.1707 0
	- 2354 1781 2 2 0.000000 14.1707 0
	- 2355 1781 2 2 0.000000 14.1707 0
	- 2356 1781 2 2 0.000000 14.1707 0
	- 2357 1781 2 2 0.000000 14.1707 0
	- 2358 1781 2 2 0.000000 14.1707 0
	- 2359 1781 2 2 0.000000 14.1707 0
	- 2360 1781 2 2 0.000000 14.1707 0
	- 2361 1781 2 2 0.000000 14.1707 0
	- 2362 1781 2 2 0.000000 14.1707 0
	- 2363 1781 2 2 0.000000 14.1707 0
	- 2364 1781 2 2 0.000000 14.1707 0
	- 2365 1782 2 2 0.000000 14.1707 0
	- 2366 1782 2 2 0.000000 14.1707 0
	- 2367 1782 2 2 0.000000 14.1707 0
	- 2368 1782 2 2 0.000000 14.1707 0
	- 2369 1782 2 2 0.000000 14.1707 0
	- 2370 1782 2 2 0.000000 14.1707 0
	- 2371 1782 2 2 0.000000 14.1707 0
	- 2372 1782 2 2 0.000000 14.1707 0
	- 2373 1782 2 2 0.000000 14.1707 0
	- 2374 1782 2 2 0.000000 14.1707 0
	- 2375 1782 2 2 0.000000 14.1707 0
	- 2376 1782 2 2 0.000000 14.1707 0
	- 2377 1783 2 2 0.000000 14.1707 0
	- 2378 1783 2 2 0.000000 14.1707 0
	- 2379 1783 2 2 0.000000 14.1707 0
	- 2380 1783 2 2 0.000000 14.1707 0
	- 2381 1783 2 2 0.000000 14.1707 0
	- 2382 1783 2 2 0.000000 14.1707 0
	- 2383 1783 2 2 0.000000 14.1707 0
	- 2384 1783 2 2 0.000000 14.1707 0
	- 2385 1783 2 2 0.000000 14.1707 0
	- 2386 1783 2 2 0.000000 14.1707 0
	- 2387 1783 2 2 0.000000 14.1707 0
	- 2388 1783 2 2 0.000000 14.1707 0
	- 2389 1784 2 2 0.000000 14.1707 0
	- 2390 1784 2 2 0.000000 14.1707 0
	- 2391 1784 2 2 0.000000 14.1707 0
	- 2392 1784 2 2 0.000000 14.1707 0
	- 2393 1784 2 2 0.000000 14.1707 0
	- 2394 1784 2 2 0.000000 14.1707 0
	- 2395 1784 2 2 0.000000 14.1707 0
	- 2396 1784 2 2 0.000000 14.1707 0
	- 2397 1784 2 2 0.000000 14.1707 0
	- 2398 1784 2 2 0.000000 14.1707 0
	- 2399 1784 2 2 0.000000 14.1707 0
	- 2400 1784 2 2 0.000000 14.1707 0
	- 2401 1785 2 2 0.000000 14.1707 0
	- 2402 1785 2 2 0.000000 14.1707 0
	- 2403 1785 2 2 0.000000 14.1707 0
	- 2404 1785 2 2 0.000000 14.1707 0
	- 2405 1785 2 2 0.000000 14.1707 0
	- 2406 1785 2 2 0.000000 14.1707 0
	- 2407 1785 2 2 0.000000 14.1707 0
	- 2408 1785 2 2 0.000000 14.1707 0
	- 2409 1785 2 2 0.000000 14.1707 0
	- 2410 1785 2 2 0.000000 14.1707 0
	- 2411 1785 2 2 0.000000 14.1707 0
	- 2412 1785 2 2 0.000000 14.1707 0
	- 2413 1786 2 2 0.000000 14.1707 0
	- 2414 1786 2 2 0.000000 14.1707 0
	- 2415 1786 2 2 0.000000 14.1707 0
	- 2416 1786 2 2 0.000000 14.1707 0
	- 2417 1786 2 2 0.000000 14.1707 0
	- 2418 1786 2 2 0.000000 14.1707 0
	- 2419 1786 2 2 0.000000 14.1707 0
	- 2420 1786 2 2 0.000000 14.1707 0
	- 2421 1786 2 2 0.000000 14.1707 0
	- 2422 1786 2 2 0.000000 14.1707 0
	- 2423 1786 2 2 0.000000 14.1707 0
	- 2424 1786 2 2 0.000000 14.1707 0
	- 2425 1787 2 2 0.000000 14.1707 0
	- 2426 1787 2 2 0.000000 14.1707 0
	- 2427 1787 2 2 0.000000 14.1707 0
	- 2428 1787 2 2 0.000000 14.1707 0
	- 2429 1787 2 2 0.000000 14.1707 0
	- 2430 1787 2 2 0.000000 14.1707 0
	- 2431 1787 2 2 0.000000 14.1707 0
	- 2432 1787 2 2 0.000000 14.1707 0
	- 2433 1787 2 2 0.000000 14.1707 0
	- 2434 1787 2 2 0.000000 14.1707 0
	- 2435 1787 2 2 0.000000 14.1707 0
	- 2436 1787 2 2 0.000000 14.1707 0
	- 2437 1788 2 2 0.000000 14.1707 0
	- 2438 1788 2 2 0.000000 14.1707 0
	- 2439 1788 2 2 0.000000 14.1707 0
	- 2440 1788 2 2 0.000000 14.1707 0
	- 2441 1788 2 2 0.000000 14.1707 0
	- 2442 1788 2 2 0.000000 14.1707 0
	- 2443 1788 2 2 0.000000 14.1707 0
	- 2444 1788 2 2 0.000000 14.1707 0
	- 2445 1788 2 2 0.000000 14.1707 0
	- 2446 1788 2 2 0.000000 14.1707 0
	- 2447 1788 2 2 0.000000 14.1707 0
	- 2448 1788 2 2 0.000000 14.1707 0
	- 2449 1789 2 2 0.000000 14.1707 0
	- 2450 1789 2 2 0.000000 14.1707 0
	- 2451 1789 2 2 0.000000 14.1707 0
	- 2452 1789 2 2 0.000000 14.1707 0
	- 2453 1789 2 2 0.000000 14.1707 0
	- 2454 1789 2 2 0.000000 14.1707 0
	- 2455 1789 2 2 0.000000 14.1707 0
	- 2456 1789 2 2 0.000000 14.1707 0
	- 2457 1789 2 2 0.000000 14.1707 0
	- 2458 1789 2 2 0.000000 14.1707 0
	- 2459 1789 2 2 0.000000 14.1707 0
	- 2460 1789 2 2 0.000000 14.1707 0
	- 2461 1790 2 2 0.000000 14.1707 0
	- 2462 1790 2 2 0.000000 14.1707 0
	- 2463 1790 2 2 0.000000 14.1707 0
	- 2464 1790 2 2 0.000000 14.1707 0
	- 2465 1790 2 2 0.000000 14.1707 0
	- 2466 1790 2 2 0.000000 14.1707 0
	- 2467 1790 2 2 0.000000 14.1707 0
	- 2468 1790 2 2 0.000000 14.1707 0
	- 2469 1790 2 2 0.000000 14.1707 0
	- 2470 1790 2 2 0.000000 14.1707 0
	- 2471 1790 2 2 0.000000 14.1707 0
	- 2472 1790 2 2 0.000000 14.1707 0
	- 2473 1791 2 2 0.000000 14.1707 0
	- 2474 1791 2 2 0.000000 14.1707 0
	- 2475 1791 2 2 0.000000 14.1707 0
	- 2476 1791 2 2 0.000000 14.1707 0
	- 2477 1791 2 2 0.000000 14.1707 0
	- 2478 1791 2 2 0.000000 14.1707 0
	- 2479 1791 2 2 0.000000 14.1707 0
	- 2480 1791 2 2 0.000000 14.1707 0
	- 2481 1791 2 2 0.000000 14.1707 0
	- 2482 1791 2 2 0.000000 14.1707 0
	- 2483 1791 2 2 0.000000 14.1707 0
	- 2484 1791 2 2 0.000000 14.1707 0
	- 2485 1792 2 2 0.000000 14.1707 0
	- 2486 1792 2 2 0.000000 14.1707 0
	- 2487 1792 2 2 0.000000 14.1707 0
	- 2488 1792 2 2 0.000000 14.1707 0
	- 2489 1792 2 2 0.000000 14.1707 0
	- 2490 1792 2 2 0.000000 14.1707 0
	- 2491 1792 2 2 0.000000 14.1707 0
	- 2492 1792 2 2 0.000000 14.1707 0
	- 2493 1792 2 2 0.000000 14.1707 0
	- 2494 1792 2 2 0.000000 14.1707 0
	- 2495 1792 2 2 0.000000 14.1707 0
	- 2496 1792 2 2 0.000000 14.1707 0
	-
	- 768 !NBOND: bonds
	- 1729 1730 1729 1740 1730 1731 1731 1732
	- 1732 1733 1733 1734 1734 1735 1735 1736
	- 1736 1737 1737 1738 1738 1739 1739 1740
	- 1741 1742 1741 1752 1742 1743 1743 1744
	- 1744 1745 1745 1746 1746 1747 1747 1748
	- 1748 1749 1749 1750 1750 1751 1751 1752
	- 1753 1754 1753 1764 1754 1755 1755 1756
	- 1756 1757 1757 1758 1758 1759 1759 1760
	- 1760 1761 1761 1762 1762 1763 1763 1764
	- 1765 1766 1765 1776 1766 1767 1767 1768
	- 1768 1769 1769 1770 1770 1771 1771 1772
	- 1772 1773 1773 1774 1774 1775 1775 1776
	- 1777 1778 1777 1788 1778 1779 1779 1780
	- 1780 1781 1781 1782 1782 1783 1783 1784
	- 1784 1785 1785 1786 1786 1787 1787 1788
	- 1789 1790 1789 1800 1790 1791 1791 1792
	- 1792 1793 1793 1794 1794 1795 1795 1796
	- 1796 1797 1797 1798 1798 1799 1799 1800
	- 1801 1802 1801 1812 1802 1803 1803 1804
	- 1804 1805 1805 1806 1806 1807 1807 1808
	- 1808 1809 1809 1810 1810 1811 1811 1812
	- 1813 1814 1813 1824 1814 1815 1815 1816
	- 1816 1817 1817 1818 1818 1819 1819 1820
	- 1820 1821 1821 1822 1822 1823 1823 1824
	- 1825 1826 1825 1836 1826 1827 1827 1828
	- 1828 1829 1829 1830 1830 1831 1831 1832
	- 1832 1833 1833 1834 1834 1835 1835 1836
	- 1837 1838 1837 1848 1838 1839 1839 1840
	- 1840 1841 1841 1842 1842 1843 1843 1844
	- 1844 1845 1845 1846 1846 1847 1847 1848
	- 1849 1850 1849 1860 1850 1851 1851 1852
	- 1852 1853 1853 1854 1854 1855 1855 1856
	- 1856 1857 1857 1858 1858 1859 1859 1860
	- 1861 1862 1861 1872 1862 1863 1863 1864
	- 1864 1865 1865 1866 1866 1867 1867 1868
	- 1868 1869 1869 1870 1870 1871 1871 1872
	- 1873 1874 1873 1884 1874 1875 1875 1876
	- 1876 1877 1877 1878 1878 1879 1879 1880
	- 1880 1881 1881 1882 1882 1883 1883 1884
	- 1885 1886 1885 1896 1886 1887 1887 1888
	- 1888 1889 1889 1890 1890 1891 1891 1892
	- 1892 1893 1893 1894 1894 1895 1895 1896
	- 1897 1898 1897 1908 1898 1899 1899 1900
	- 1900 1901 1901 1902 1902 1903 1903 1904
	- 1904 1905 1905 1906 1906 1907 1907 1908
	- 1909 1910 1909 1920 1910 1911 1911 1912
	- 1912 1913 1913 1914 1914 1915 1915 1916
	- 1916 1917 1917 1918 1918 1919 1919 1920
	- 1921 1922 1921 1932 1922 1923 1923 1924
	- 1924 1925 1925 1926 1926 1927 1927 1928
	- 1928 1929 1929 1930 1930 1931 1931 1932
	- 1933 1934 1933 1944 1934 1935 1935 1936
	- 1936 1937 1937 1938 1938 1939 1939 1940
	- 1940 1941 1941 1942 1942 1943 1943 1944
	- 1945 1946 1945 1956 1946 1947 1947 1948
	- 1948 1949 1949 1950 1950 1951 1951 1952
	- 1952 1953 1953 1954 1954 1955 1955 1956
	- 1957 1958 1957 1968 1958 1959 1959 1960
	- 1960 1961 1961 1962 1962 1963 1963 1964
	- 1964 1965 1965 1966 1966 1967 1967 1968
	- 1969 1970 1969 1980 1970 1971 1971 1972
	- 1972 1973 1973 1974 1974 1975 1975 1976
	- 1976 1977 1977 1978 1978 1979 1979 1980
	- 1981 1982 1981 1992 1982 1983 1983 1984
	- 1984 1985 1985 1986 1986 1987 1987 1988
	- 1988 1989 1989 1990 1990 1991 1991 1992
	- 1993 1994 1993 2004 1994 1995 1995 1996
	- 1996 1997 1997 1998 1998 1999 1999 2000
	- 2000 2001 2001 2002 2002 2003 2003 2004
	- 2005 2006 2005 2016 2006 2007 2007 2008
	- 2008 2009 2009 2010 2010 2011 2011 2012
	- 2012 2013 2013 2014 2014 2015 2015 2016
	- 2017 2018 2017 2028 2018 2019 2019 2020
	- 2020 2021 2021 2022 2022 2023 2023 2024
	- 2024 2025 2025 2026 2026 2027 2027 2028
	- 2029 2030 2029 2040 2030 2031 2031 2032
	- 2032 2033 2033 2034 2034 2035 2035 2036
	- 2036 2037 2037 2038 2038 2039 2039 2040
	- 2041 2042 2041 2052 2042 2043 2043 2044
	- 2044 2045 2045 2046 2046 2047 2047 2048
	- 2048 2049 2049 2050 2050 2051 2051 2052
	- 2053 2054 2053 2064 2054 2055 2055 2056
	- 2056 2057 2057 2058 2058 2059 2059 2060
	- 2060 2061 2061 2062 2062 2063 2063 2064
	- 2065 2066 2065 2076 2066 2067 2067 2068
	- 2068 2069 2069 2070 2070 2071 2071 2072
	- 2072 2073 2073 2074 2074 2075 2075 2076
	- 2077 2078 2077 2088 2078 2079 2079 2080
	- 2080 2081 2081 2082 2082 2083 2083 2084
	- 2084 2085 2085 2086 2086 2087 2087 2088
	- 2089 2090 2089 2100 2090 2091 2091 2092
	- 2092 2093 2093 2094 2094 2095 2095 2096
	- 2096 2097 2097 2098 2098 2099 2099 2100
	- 2101 2102 2101 2112 2102 2103 2103 2104
	- 2104 2105 2105 2106 2106 2107 2107 2108
	- 2108 2109 2109 2110 2110 2111 2111 2112
	- 2113 2114 2113 2124 2114 2115 2115 2116
	- 2116 2117 2117 2118 2118 2119 2119 2120
	- 2120 2121 2121 2122 2122 2123 2123 2124
	- 2125 2126 2125 2136 2126 2127 2127 2128
	- 2128 2129 2129 2130 2130 2131 2131 2132
	- 2132 2133 2133 2134 2134 2135 2135 2136
	- 2137 2138 2137 2148 2138 2139 2139 2140
	- 2140 2141 2141 2142 2142 2143 2143 2144
	- 2144 2145 2145 2146 2146 2147 2147 2148
	- 2149 2150 2149 2160 2150 2151 2151 2152
	- 2152 2153 2153 2154 2154 2155 2155 2156
	- 2156 2157 2157 2158 2158 2159 2159 2160
	- 2161 2162 2161 2172 2162 2163 2163 2164
	- 2164 2165 2165 2166 2166 2167 2167 2168
	- 2168 2169 2169 2170 2170 2171 2171 2172
	- 2173 2174 2173 2184 2174 2175 2175 2176
	- 2176 2177 2177 2178 2178 2179 2179 2180
	- 2180 2181 2181 2182 2182 2183 2183 2184
	- 2185 2186 2185 2196 2186 2187 2187 2188
	- 2188 2189 2189 2190 2190 2191 2191 2192
	- 2192 2193 2193 2194 2194 2195 2195 2196
	- 2197 2198 2197 2208 2198 2199 2199 2200
	- 2200 2201 2201 2202 2202 2203 2203 2204
	- 2204 2205 2205 2206 2206 2207 2207 2208
	- 2209 2210 2209 2220 2210 2211 2211 2212
	- 2212 2213 2213 2214 2214 2215 2215 2216
	- 2216 2217 2217 2218 2218 2219 2219 2220
	- 2221 2222 2221 2232 2222 2223 2223 2224
	- 2224 2225 2225 2226 2226 2227 2227 2228
	- 2228 2229 2229 2230 2230 2231 2231 2232
	- 2233 2234 2233 2244 2234 2235 2235 2236
	- 2236 2237 2237 2238 2238 2239 2239 2240
	- 2240 2241 2241 2242 2242 2243 2243 2244
	- 2245 2246 2245 2256 2246 2247 2247 2248
	- 2248 2249 2249 2250 2250 2251 2251 2252
	- 2252 2253 2253 2254 2254 2255 2255 2256
	- 2257 2258 2257 2268 2258 2259 2259 2260
	- 2260 2261 2261 2262 2262 2263 2263 2264
	- 2264 2265 2265 2266 2266 2267 2267 2268
	- 2269 2270 2269 2280 2270 2271 2271 2272
	- 2272 2273 2273 2274 2274 2275 2275 2276
	- 2276 2277 2277 2278 2278 2279 2279 2280
	- 2281 2282 2281 2292 2282 2283 2283 2284
	- 2284 2285 2285 2286 2286 2287 2287 2288
	- 2288 2289 2289 2290 2290 2291 2291 2292
	- 2293 2294 2293 2304 2294 2295 2295 2296
	- 2296 2297 2297 2298 2298 2299 2299 2300
	- 2300 2301 2301 2302 2302 2303 2303 2304
	- 2305 2306 2305 2316 2306 2307 2307 2308
	- 2308 2309 2309 2310 2310 2311 2311 2312
	- 2312 2313 2313 2314 2314 2315 2315 2316
	- 2317 2318 2317 2328 2318 2319 2319 2320
	- 2320 2321 2321 2322 2322 2323 2323 2324
	- 2324 2325 2325 2326 2326 2327 2327 2328
	- 2329 2330 2329 2340 2330 2331 2331 2332
	- 2332 2333 2333 2334 2334 2335 2335 2336
	- 2336 2337 2337 2338 2338 2339 2339 2340
	- 2341 2342 2341 2352 2342 2343 2343 2344
	- 2344 2345 2345 2346 2346 2347 2347 2348
	- 2348 2349 2349 2350 2350 2351 2351 2352
	- 2353 2354 2353 2364 2354 2355 2355 2356
	- 2356 2357 2357 2358 2358 2359 2359 2360
	- 2360 2361 2361 2362 2362 2363 2363 2364
	- 2365 2366 2365 2376 2366 2367 2367 2368
	- 2368 2369 2369 2370 2370 2371 2371 2372
	- 2372 2373 2373 2374 2374 2375 2375 2376
	- 2377 2378 2377 2388 2378 2379 2379 2380
	- 2380 2381 2381 2382 2382 2383 2383 2384
	- 2384 2385 2385 2386 2386 2387 2387 2388
	- 2389 2390 2389 2400 2390 2391 2391 2392
	- 2392 2393 2393 2394 2394 2395 2395 2396
	- 2396 2397 2397 2398 2398 2399 2399 2400
	- 2401 2402 2401 2412 2402 2403 2403 2404
	- 2404 2405 2405 2406 2406 2407 2407 2408
	- 2408 2409 2409 2410 2410 2411 2411 2412
	- 2413 2414 2413 2424 2414 2415 2415 2416
	- 2416 2417 2417 2418 2418 2419 2419 2420
	- 2420 2421 2421 2422 2422 2423 2423 2424
	- 2425 2426 2425 2436 2426 2427 2427 2428
	- 2428 2429 2429 2430 2430 2431 2431 2432
	- 2432 2433 2433 2434 2434 2435 2435 2436
	- 2437 2438 2437 2448 2438 2439 2439 2440
	- 2440 2441 2441 2442 2442 2443 2443 2444
	- 2444 2445 2445 2446 2446 2447 2447 2448
	- 2449 2450 2449 2460 2450 2451 2451 2452
	- 2452 2453 2453 2454 2454 2455 2455 2456
	- 2456 2457 2457 2458 2458 2459 2459 2460
	- 2461 2462 2461 2472 2462 2463 2463 2464
	- 2464 2465 2465 2466 2466 2467 2467 2468
	- 2468 2469 2469 2470 2470 2471 2471 2472
	- 2473 2474 2473 2484 2474 2475 2475 2476
	- 2476 2477 2477 2478 2478 2479 2479 2480
	- 2480 2481 2481 2482 2482 2483 2483 2484
	- 2485 2486 2485 2496 2486 2487 2487 2488
	- 2488 2489 2489 2490 2490 2491 2491 2492
	- 2492 2493 2493 2494 2494 2495 2495 2496
	-
	- 768 !NTHETA: angles
	- 1729 1730 1731 1729 1740 1739 1730 1729 1740
	- 1730 1731 1732 1731 1732 1733 1732 1733 1734
	- 1733 1734 1735 1734 1735 1736 1735 1736 1737
	- 1736 1737 1738 1737 1738 1739 1738 1739 1740
	- 1741 1742 1743 1741 1752 1751 1742 1741 1752
	- 1742 1743 1744 1743 1744 1745 1744 1745 1746
	- 1745 1746 1747 1746 1747 1748 1747 1748 1749
	- 1748 1749 1750 1749 1750 1751 1750 1751 1752
	- 1753 1754 1755 1753 1764 1763 1754 1753 1764
	- 1754 1755 1756 1755 1756 1757 1756 1757 1758
	- 1757 1758 1759 1758 1759 1760 1759 1760 1761
	- 1760 1761 1762 1761 1762 1763 1762 1763 1764
	- 1765 1766 1767 1765 1776 1775 1766 1765 1776
	- 1766 1767 1768 1767 1768 1769 1768 1769 1770
	- 1769 1770 1771 1770 1771 1772 1771 1772 1773
	- 1772 1773 1774 1773 1774 1775 1774 1775 1776
	- 1777 1778 1779 1777 1788 1787 1778 1777 1788
	- 1778 1779 1780 1779 1780 1781 1780 1781 1782
	- 1781 1782 1783 1782 1783 1784 1783 1784 1785
	- 1784 1785 1786 1785 1786 1787 1786 1787 1788
	- 1789 1790 1791 1789 1800 1799 1790 1789 1800
	- 1790 1791 1792 1791 1792 1793 1792 1793 1794
	- 1793 1794 1795 1794 1795 1796 1795 1796 1797
	- 1796 1797 1798 1797 1798 1799 1798 1799 1800
	- 1801 1802 1803 1801 1812 1811 1802 1801 1812
	- 1802 1803 1804 1803 1804 1805 1804 1805 1806
	- 1805 1806 1807 1806 1807 1808 1807 1808 1809
	- 1808 1809 1810 1809 1810 1811 1810 1811 1812
	- 1813 1814 1815 1813 1824 1823 1814 1813 1824
	- 1814 1815 1816 1815 1816 1817 1816 1817 1818
	- 1817 1818 1819 1818 1819 1820 1819 1820 1821
	- 1820 1821 1822 1821 1822 1823 1822 1823 1824
	- 1825 1826 1827 1825 1836 1835 1826 1825 1836
	- 1826 1827 1828 1827 1828 1829 1828 1829 1830
	- 1829 1830 1831 1830 1831 1832 1831 1832 1833
	- 1832 1833 1834 1833 1834 1835 1834 1835 1836
	- 1837 1838 1839 1837 1848 1847 1838 1837 1848
	- 1838 1839 1840 1839 1840 1841 1840 1841 1842
	- 1841 1842 1843 1842 1843 1844 1843 1844 1845
	- 1844 1845 1846 1845 1846 1847 1846 1847 1848
	- 1849 1850 1851 1849 1860 1859 1850 1849 1860
	- 1850 1851 1852 1851 1852 1853 1852 1853 1854
	- 1853 1854 1855 1854 1855 1856 1855 1856 1857
	- 1856 1857 1858 1857 1858 1859 1858 1859 1860
	- 1861 1862 1863 1861 1872 1871 1862 1861 1872
	- 1862 1863 1864 1863 1864 1865 1864 1865 1866
	- 1865 1866 1867 1866 1867 1868 1867 1868 1869
	- 1868 1869 1870 1869 1870 1871 1870 1871 1872
	- 1873 1874 1875 1873 1884 1883 1874 1873 1884
	- 1874 1875 1876 1875 1876 1877 1876 1877 1878
	- 1877 1878 1879 1878 1879 1880 1879 1880 1881
	- 1880 1881 1882 1881 1882 1883 1882 1883 1884
	- 1885 1886 1887 1885 1896 1895 1886 1885 1896
	- 1886 1887 1888 1887 1888 1889 1888 1889 1890
	- 1889 1890 1891 1890 1891 1892 1891 1892 1893
	- 1892 1893 1894 1893 1894 1895 1894 1895 1896
	- 1897 1898 1899 1897 1908 1907 1898 1897 1908
	- 1898 1899 1900 1899 1900 1901 1900 1901 1902
	- 1901 1902 1903 1902 1903 1904 1903 1904 1905
	- 1904 1905 1906 1905 1906 1907 1906 1907 1908
	- 1909 1910 1911 1909 1920 1919 1910 1909 1920
	- 1910 1911 1912 1911 1912 1913 1912 1913 1914
	- 1913 1914 1915 1914 1915 1916 1915 1916 1917
	- 1916 1917 1918 1917 1918 1919 1918 1919 1920
	- 1921 1922 1923 1921 1932 1931 1922 1921 1932
	- 1922 1923 1924 1923 1924 1925 1924 1925 1926
	- 1925 1926 1927 1926 1927 1928 1927 1928 1929
	- 1928 1929 1930 1929 1930 1931 1930 1931 1932
	- 1933 1934 1935 1933 1944 1943 1934 1933 1944
	- 1934 1935 1936 1935 1936 1937 1936 1937 1938
	- 1937 1938 1939 1938 1939 1940 1939 1940 1941
	- 1940 1941 1942 1941 1942 1943 1942 1943 1944
	- 1945 1946 1947 1945 1956 1955 1946 1945 1956
	- 1946 1947 1948 1947 1948 1949 1948 1949 1950
	- 1949 1950 1951 1950 1951 1952 1951 1952 1953
	- 1952 1953 1954 1953 1954 1955 1954 1955 1956
	- 1957 1958 1959 1957 1968 1967 1958 1957 1968
	- 1958 1959 1960 1959 1960 1961 1960 1961 1962
	- 1961 1962 1963 1962 1963 1964 1963 1964 1965
	- 1964 1965 1966 1965 1966 1967 1966 1967 1968
	- 1969 1970 1971 1969 1980 1979 1970 1969 1980
	- 1970 1971 1972 1971 1972 1973 1972 1973 1974
	- 1973 1974 1975 1974 1975 1976 1975 1976 1977
	- 1976 1977 1978 1977 1978 1979 1978 1979 1980
	- 1981 1982 1983 1981 1992 1991 1982 1981 1992
	- 1982 1983 1984 1983 1984 1985 1984 1985 1986
	- 1985 1986 1987 1986 1987 1988 1987 1988 1989
	- 1988 1989 1990 1989 1990 1991 1990 1991 1992
	- 1993 1994 1995 1993 2004 2003 1994 1993 2004
	- 1994 1995 1996 1995 1996 1997 1996 1997 1998
	- 1997 1998 1999 1998 1999 2000 1999 2000 2001
	- 2000 2001 2002 2001 2002 2003 2002 2003 2004
	- 2005 2006 2007 2005 2016 2015 2006 2005 2016
	- 2006 2007 2008 2007 2008 2009 2008 2009 2010
	- 2009 2010 2011 2010 2011 2012 2011 2012 2013
	- 2012 2013 2014 2013 2014 2015 2014 2015 2016
	- 2017 2018 2019 2017 2028 2027 2018 2017 2028
	- 2018 2019 2020 2019 2020 2021 2020 2021 2022
	- 2021 2022 2023 2022 2023 2024 2023 2024 2025
	- 2024 2025 2026 2025 2026 2027 2026 2027 2028
	- 2029 2030 2031 2029 2040 2039 2030 2029 2040
	- 2030 2031 2032 2031 2032 2033 2032 2033 2034
	- 2033 2034 2035 2034 2035 2036 2035 2036 2037
	- 2036 2037 2038 2037 2038 2039 2038 2039 2040
	- 2041 2042 2043 2041 2052 2051 2042 2041 2052
	- 2042 2043 2044 2043 2044 2045 2044 2045 2046
	- 2045 2046 2047 2046 2047 2048 2047 2048 2049
	- 2048 2049 2050 2049 2050 2051 2050 2051 2052
	- 2053 2054 2055 2053 2064 2063 2054 2053 2064
	- 2054 2055 2056 2055 2056 2057 2056 2057 2058
	- 2057 2058 2059 2058 2059 2060 2059 2060 2061
	- 2060 2061 2062 2061 2062 2063 2062 2063 2064
	- 2065 2066 2067 2065 2076 2075 2066 2065 2076
	- 2066 2067 2068 2067 2068 2069 2068 2069 2070
	- 2069 2070 2071 2070 2071 2072 2071 2072 2073
	- 2072 2073 2074 2073 2074 2075 2074 2075 2076
	- 2077 2078 2079 2077 2088 2087 2078 2077 2088
	- 2078 2079 2080 2079 2080 2081 2080 2081 2082
	- 2081 2082 2083 2082 2083 2084 2083 2084 2085
	- 2084 2085 2086 2085 2086 2087 2086 2087 2088
	- 2089 2090 2091 2089 2100 2099 2090 2089 2100
	- 2090 2091 2092 2091 2092 2093 2092 2093 2094
	- 2093 2094 2095 2094 2095 2096 2095 2096 2097
	- 2096 2097 2098 2097 2098 2099 2098 2099 2100
	- 2101 2102 2103 2101 2112 2111 2102 2101 2112
	- 2102 2103 2104 2103 2104 2105 2104 2105 2106
	- 2105 2106 2107 2106 2107 2108 2107 2108 2109
	- 2108 2109 2110 2109 2110 2111 2110 2111 2112
	- 2113 2114 2115 2113 2124 2123 2114 2113 2124
	- 2114 2115 2116 2115 2116 2117 2116 2117 2118
	- 2117 2118 2119 2118 2119 2120 2119 2120 2121
	- 2120 2121 2122 2121 2122 2123 2122 2123 2124
	- 2125 2126 2127 2125 2136 2135 2126 2125 2136
	- 2126 2127 2128 2127 2128 2129 2128 2129 2130
	- 2129 2130 2131 2130 2131 2132 2131 2132 2133
	- 2132 2133 2134 2133 2134 2135 2134 2135 2136
	- 2137 2138 2139 2137 2148 2147 2138 2137 2148
	- 2138 2139 2140 2139 2140 2141 2140 2141 2142
	- 2141 2142 2143 2142 2143 2144 2143 2144 2145
	- 2144 2145 2146 2145 2146 2147 2146 2147 2148
	- 2149 2150 2151 2149 2160 2159 2150 2149 2160
	- 2150 2151 2152 2151 2152 2153 2152 2153 2154
	- 2153 2154 2155 2154 2155 2156 2155 2156 2157
	- 2156 2157 2158 2157 2158 2159 2158 2159 2160
	- 2161 2162 2163 2161 2172 2171 2162 2161 2172
	- 2162 2163 2164 2163 2164 2165 2164 2165 2166
	- 2165 2166 2167 2166 2167 2168 2167 2168 2169
	- 2168 2169 2170 2169 2170 2171 2170 2171 2172
	- 2173 2174 2175 2173 2184 2183 2174 2173 2184
	- 2174 2175 2176 2175 2176 2177 2176 2177 2178
	- 2177 2178 2179 2178 2179 2180 2179 2180 2181
	- 2180 2181 2182 2181 2182 2183 2182 2183 2184
	- 2185 2186 2187 2185 2196 2195 2186 2185 2196
	- 2186 2187 2188 2187 2188 2189 2188 2189 2190
	- 2189 2190 2191 2190 2191 2192 2191 2192 2193
	- 2192 2193 2194 2193 2194 2195 2194 2195 2196
	- 2197 2198 2199 2197 2208 2207 2198 2197 2208
	- 2198 2199 2200 2199 2200 2201 2200 2201 2202
	- 2201 2202 2203 2202 2203 2204 2203 2204 2205
	- 2204 2205 2206 2205 2206 2207 2206 2207 2208
	- 2209 2210 2211 2209 2220 2219 2210 2209 2220
	- 2210 2211 2212 2211 2212 2213 2212 2213 2214
	- 2213 2214 2215 2214 2215 2216 2215 2216 2217
	- 2216 2217 2218 2217 2218 2219 2218 2219 2220
	- 2221 2222 2223 2221 2232 2231 2222 2221 2232
	- 2222 2223 2224 2223 2224 2225 2224 2225 2226
	- 2225 2226 2227 2226 2227 2228 2227 2228 2229
	- 2228 2229 2230 2229 2230 2231 2230 2231 2232
	- 2233 2234 2235 2233 2244 2243 2234 2233 2244
	- 2234 2235 2236 2235 2236 2237 2236 2237 2238
	- 2237 2238 2239 2238 2239 2240 2239 2240 2241
	- 2240 2241 2242 2241 2242 2243 2242 2243 2244
	- 2245 2246 2247 2245 2256 2255 2246 2245 2256
	- 2246 2247 2248 2247 2248 2249 2248 2249 2250
	- 2249 2250 2251 2250 2251 2252 2251 2252 2253
	- 2252 2253 2254 2253 2254 2255 2254 2255 2256
	- 2257 2258 2259 2257 2268 2267 2258 2257 2268
	- 2258 2259 2260 2259 2260 2261 2260 2261 2262
	- 2261 2262 2263 2262 2263 2264 2263 2264 2265
	- 2264 2265 2266 2265 2266 2267 2266 2267 2268
	- 2269 2270 2271 2269 2280 2279 2270 2269 2280
	- 2270 2271 2272 2271 2272 2273 2272 2273 2274
	- 2273 2274 2275 2274 2275 2276 2275 2276 2277
	- 2276 2277 2278 2277 2278 2279 2278 2279 2280
	- 2281 2282 2283 2281 2292 2291 2282 2281 2292
	- 2282 2283 2284 2283 2284 2285 2284 2285 2286
	- 2285 2286 2287 2286 2287 2288 2287 2288 2289
	- 2288 2289 2290 2289 2290 2291 2290 2291 2292
	- 2293 2294 2295 2293 2304 2303 2294 2293 2304
	- 2294 2295 2296 2295 2296 2297 2296 2297 2298
	- 2297 2298 2299 2298 2299 2300 2299 2300 2301
	- 2300 2301 2302 2301 2302 2303 2302 2303 2304
	- 2305 2306 2307 2305 2316 2315 2306 2305 2316
	- 2306 2307 2308 2307 2308 2309 2308 2309 2310
	- 2309 2310 2311 2310 2311 2312 2311 2312 2313
	- 2312 2313 2314 2313 2314 2315 2314 2315 2316
	- 2317 2318 2319 2317 2328 2327 2318 2317 2328
	- 2318 2319 2320 2319 2320 2321 2320 2321 2322
	- 2321 2322 2323 2322 2323 2324 2323 2324 2325
	- 2324 2325 2326 2325 2326 2327 2326 2327 2328
	- 2329 2330 2331 2329 2340 2339 2330 2329 2340
	- 2330 2331 2332 2331 2332 2333 2332 2333 2334
	- 2333 2334 2335 2334 2335 2336 2335 2336 2337
	- 2336 2337 2338 2337 2338 2339 2338 2339 2340
	- 2341 2342 2343 2341 2352 2351 2342 2341 2352
	- 2342 2343 2344 2343 2344 2345 2344 2345 2346
	- 2345 2346 2347 2346 2347 2348 2347 2348 2349
	- 2348 2349 2350 2349 2350 2351 2350 2351 2352
	- 2353 2354 2355 2353 2364 2363 2354 2353 2364
	- 2354 2355 2356 2355 2356 2357 2356 2357 2358
	- 2357 2358 2359 2358 2359 2360 2359 2360 2361
	- 2360 2361 2362 2361 2362 2363 2362 2363 2364
	- 2365 2366 2367 2365 2376 2375 2366 2365 2376
	- 2366 2367 2368 2367 2368 2369 2368 2369 2370
	- 2369 2370 2371 2370 2371 2372 2371 2372 2373
	- 2372 2373 2374 2373 2374 2375 2374 2375 2376
	- 2377 2378 2379 2377 2388 2387 2378 2377 2388
	- 2378 2379 2380 2379 2380 2381 2380 2381 2382
	- 2381 2382 2383 2382 2383 2384 2383 2384 2385
	- 2384 2385 2386 2385 2386 2387 2386 2387 2388
	- 2389 2390 2391 2389 2400 2399 2390 2389 2400
	- 2390 2391 2392 2391 2392 2393 2392 2393 2394
	- 2393 2394 2395 2394 2395 2396 2395 2396 2397
	- 2396 2397 2398 2397 2398 2399 2398 2399 2400
	- 2401 2402 2403 2401 2412 2411 2402 2401 2412
	- 2402 2403 2404 2403 2404 2405 2404 2405 2406
	- 2405 2406 2407 2406 2407 2408 2407 2408 2409
	- 2408 2409 2410 2409 2410 2411 2410 2411 2412
	- 2413 2414 2415 2413 2424 2423 2414 2413 2424
	- 2414 2415 2416 2415 2416 2417 2416 2417 2418
	- 2417 2418 2419 2418 2419 2420 2419 2420 2421
	- 2420 2421 2422 2421 2422 2423 2422 2423 2424
	- 2425 2426 2427 2425 2436 2435 2426 2425 2436
	- 2426 2427 2428 2427 2428 2429 2428 2429 2430
	- 2429 2430 2431 2430 2431 2432 2431 2432 2433
	- 2432 2433 2434 2433 2434 2435 2434 2435 2436
	- 2437 2438 2439 2437 2448 2447 2438 2437 2448
	- 2438 2439 2440 2439 2440 2441 2440 2441 2442
	- 2441 2442 2443 2442 2443 2444 2443 2444 2445
	- 2444 2445 2446 2445 2446 2447 2446 2447 2448
	- 2449 2450 2451 2449 2460 2459 2450 2449 2460
	- 2450 2451 2452 2451 2452 2453 2452 2453 2454
	- 2453 2454 2455 2454 2455 2456 2455 2456 2457
	- 2456 2457 2458 2457 2458 2459 2458 2459 2460
	- 2461 2462 2463 2461 2472 2471 2462 2461 2472
	- 2462 2463 2464 2463 2464 2465 2464 2465 2466
	- 2465 2466 2467 2466 2467 2468 2467 2468 2469
	- 2468 2469 2470 2469 2470 2471 2470 2471 2472
	- 2473 2474 2475 2473 2484 2483 2474 2473 2484
	- 2474 2475 2476 2475 2476 2477 2476 2477 2478
	- 2477 2478 2479 2478 2479 2480 2479 2480 2481
	- 2480 2481 2482 2481 2482 2483 2482 2483 2484
	- 2485 2486 2487 2485 2496 2495 2486 2485 2496
	- 2486 2487 2488 2487 2488 2489 2488 2489 2490
	- 2489 2490 2491 2490 2491 2492 2491 2492 2493
	- 2492 2493 2494 2493 2494 2495 2494 2495 2496
	-
	- 768 !NPHI: dihedrals
	- 1729 1730 1731 1732 1738 1739 1740 1729
	- 1730 1729 1740 1739 1730 1731 1732 1733
	- 1740 1729 1730 1731 1731 1732 1733 1734
	- 1732 1733 1734 1735 1733 1734 1735 1736
	- 1734 1735 1736 1737 1735 1736 1737 1738
	- 1736 1737 1738 1739 1737 1738 1739 1740
	- 1741 1742 1743 1744 1750 1751 1752 1741
	- 1742 1741 1752 1751 1742 1743 1744 1745
	- 1752 1741 1742 1743 1743 1744 1745 1746
	- 1744 1745 1746 1747 1745 1746 1747 1748
	- 1746 1747 1748 1749 1747 1748 1749 1750
	- 1748 1749 1750 1751 1749 1750 1751 1752
	- 1753 1754 1755 1756 1762 1763 1764 1753
	- 1754 1753 1764 1763 1754 1755 1756 1757
	- 1764 1753 1754 1755 1755 1756 1757 1758
	- 1756 1757 1758 1759 1757 1758 1759 1760
	- 1758 1759 1760 1761 1759 1760 1761 1762
	- 1760 1761 1762 1763 1761 1762 1763 1764
	- 1765 1766 1767 1768 1774 1775 1776 1765
	- 1766 1765 1776 1775 1766 1767 1768 1769
	- 1776 1765 1766 1767 1767 1768 1769 1770
	- 1768 1769 1770 1771 1769 1770 1771 1772
	- 1770 1771 1772 1773 1771 1772 1773 1774
	- 1772 1773 1774 1775 1773 1774 1775 1776
	- 1777 1778 1779 1780 1786 1787 1788 1777
	- 1778 1777 1788 1787 1778 1779 1780 1781
	- 1788 1777 1778 1779 1779 1780 1781 1782
	- 1780 1781 1782 1783 1781 1782 1783 1784
	- 1782 1783 1784 1785 1783 1784 1785 1786
	- 1784 1785 1786 1787 1785 1786 1787 1788
	- 1789 1790 1791 1792 1798 1799 1800 1789
	- 1790 1789 1800 1799 1790 1791 1792 1793
	- 1800 1789 1790 1791 1791 1792 1793 1794
	- 1792 1793 1794 1795 1793 1794 1795 1796
	- 1794 1795 1796 1797 1795 1796 1797 1798
	- 1796 1797 1798 1799 1797 1798 1799 1800
	- 1801 1802 1803 1804 1810 1811 1812 1801
	- 1802 1801 1812 1811 1802 1803 1804 1805
	- 1812 1801 1802 1803 1803 1804 1805 1806
	- 1804 1805 1806 1807 1805 1806 1807 1808
	- 1806 1807 1808 1809 1807 1808 1809 1810
	- 1808 1809 1810 1811 1809 1810 1811 1812
	- 1813 1814 1815 1816 1822 1823 1824 1813
	- 1814 1813 1824 1823 1814 1815 1816 1817
	- 1824 1813 1814 1815 1815 1816 1817 1818
	- 1816 1817 1818 1819 1817 1818 1819 1820
	- 1818 1819 1820 1821 1819 1820 1821 1822
	- 1820 1821 1822 1823 1821 1822 1823 1824
	- 1825 1826 1827 1828 1834 1835 1836 1825
	- 1826 1825 1836 1835 1826 1827 1828 1829
	- 1836 1825 1826 1827 1827 1828 1829 1830
	- 1828 1829 1830 1831 1829 1830 1831 1832
	- 1830 1831 1832 1833 1831 1832 1833 1834
	- 1832 1833 1834 1835 1833 1834 1835 1836
	- 1837 1838 1839 1840 1846 1847 1848 1837
	- 1838 1837 1848 1847 1838 1839 1840 1841
	- 1848 1837 1838 1839 1839 1840 1841 1842
	- 1840 1841 1842 1843 1841 1842 1843 1844
	- 1842 1843 1844 1845 1843 1844 1845 1846
	- 1844 1845 1846 1847 1845 1846 1847 1848
	- 1849 1850 1851 1852 1858 1859 1860 1849
	- 1850 1849 1860 1859 1850 1851 1852 1853
	- 1860 1849 1850 1851 1851 1852 1853 1854
	- 1852 1853 1854 1855 1853 1854 1855 1856
	- 1854 1855 1856 1857 1855 1856 1857 1858
	- 1856 1857 1858 1859 1857 1858 1859 1860
	- 1861 1862 1863 1864 1870 1871 1872 1861
	- 1862 1861 1872 1871 1862 1863 1864 1865
	- 1872 1861 1862 1863 1863 1864 1865 1866
	- 1864 1865 1866 1867 1865 1866 1867 1868
	- 1866 1867 1868 1869 1867 1868 1869 1870
	- 1868 1869 1870 1871 1869 1870 1871 1872
	- 1873 1874 1875 1876 1882 1883 1884 1873
	- 1874 1873 1884 1883 1874 1875 1876 1877
	- 1884 1873 1874 1875 1875 1876 1877 1878
	- 1876 1877 1878 1879 1877 1878 1879 1880
	- 1878 1879 1880 1881 1879 1880 1881 1882
	- 1880 1881 1882 1883 1881 1882 1883 1884
	- 1885 1886 1887 1888 1894 1895 1896 1885
	- 1886 1885 1896 1895 1886 1887 1888 1889
	- 1896 1885 1886 1887 1887 1888 1889 1890
	- 1888 1889 1890 1891 1889 1890 1891 1892
	- 1890 1891 1892 1893 1891 1892 1893 1894
	- 1892 1893 1894 1895 1893 1894 1895 1896
	- 1897 1898 1899 1900 1906 1907 1908 1897
	- 1898 1897 1908 1907 1898 1899 1900 1901
	- 1908 1897 1898 1899 1899 1900 1901 1902
	- 1900 1901 1902 1903 1901 1902 1903 1904
	- 1902 1903 1904 1905 1903 1904 1905 1906
	- 1904 1905 1906 1907 1905 1906 1907 1908
	- 1909 1910 1911 1912 1918 1919 1920 1909
	- 1910 1909 1920 1919 1910 1911 1912 1913
	- 1920 1909 1910 1911 1911 1912 1913 1914
	- 1912 1913 1914 1915 1913 1914 1915 1916
	- 1914 1915 1916 1917 1915 1916 1917 1918
	- 1916 1917 1918 1919 1917 1918 1919 1920
	- 1921 1922 1923 1924 1930 1931 1932 1921
	- 1922 1921 1932 1931 1922 1923 1924 1925
	- 1932 1921 1922 1923 1923 1924 1925 1926
	- 1924 1925 1926 1927 1925 1926 1927 1928
	- 1926 1927 1928 1929 1927 1928 1929 1930
	- 1928 1929 1930 1931 1929 1930 1931 1932
	- 1933 1934 1935 1936 1942 1943 1944 1933
	- 1934 1933 1944 1943 1934 1935 1936 1937
	- 1944 1933 1934 1935 1935 1936 1937 1938
	- 1936 1937 1938 1939 1937 1938 1939 1940
	- 1938 1939 1940 1941 1939 1940 1941 1942
	- 1940 1941 1942 1943 1941 1942 1943 1944
	- 1945 1946 1947 1948 1954 1955 1956 1945
	- 1946 1945 1956 1955 1946 1947 1948 1949
	- 1956 1945 1946 1947 1947 1948 1949 1950
	- 1948 1949 1950 1951 1949 1950 1951 1952
	- 1950 1951 1952 1953 1951 1952 1953 1954
	- 1952 1953 1954 1955 1953 1954 1955 1956
	- 1957 1958 1959 1960 1966 1967 1968 1957
	- 1958 1957 1968 1967 1958 1959 1960 1961
	- 1968 1957 1958 1959 1959 1960 1961 1962
	- 1960 1961 1962 1963 1961 1962 1963 1964
	- 1962 1963 1964 1965 1963 1964 1965 1966
	- 1964 1965 1966 1967 1965 1966 1967 1968
	- 1969 1970 1971 1972 1978 1979 1980 1969
	- 1970 1969 1980 1979 1970 1971 1972 1973
	- 1980 1969 1970 1971 1971 1972 1973 1974
	- 1972 1973 1974 1975 1973 1974 1975 1976
	- 1974 1975 1976 1977 1975 1976 1977 1978
	- 1976 1977 1978 1979 1977 1978 1979 1980
	- 1981 1982 1983 1984 1990 1991 1992 1981
	- 1982 1981 1992 1991 1982 1983 1984 1985
	- 1992 1981 1982 1983 1983 1984 1985 1986
	- 1984 1985 1986 1987 1985 1986 1987 1988
	- 1986 1987 1988 1989 1987 1988 1989 1990
	- 1988 1989 1990 1991 1989 1990 1991 1992
	- 1993 1994 1995 1996 2002 2003 2004 1993
	- 1994 1993 2004 2003 1994 1995 1996 1997
	- 2004 1993 1994 1995 1995 1996 1997 1998
	- 1996 1997 1998 1999 1997 1998 1999 2000
	- 1998 1999 2000 2001 1999 2000 2001 2002
	- 2000 2001 2002 2003 2001 2002 2003 2004
	- 2005 2006 2007 2008 2014 2015 2016 2005
	- 2006 2005 2016 2015 2006 2007 2008 2009
	- 2016 2005 2006 2007 2007 2008 2009 2010
	- 2008 2009 2010 2011 2009 2010 2011 2012
	- 2010 2011 2012 2013 2011 2012 2013 2014
	- 2012 2013 2014 2015 2013 2014 2015 2016
	- 2017 2018 2019 2020 2026 2027 2028 2017
	- 2018 2017 2028 2027 2018 2019 2020 2021
	- 2028 2017 2018 2019 2019 2020 2021 2022
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	- 2022 2023 2024 2025 2023 2024 2025 2026
	- 2024 2025 2026 2027 2025 2026 2027 2028
	- 2029 2030 2031 2032 2038 2039 2040 2029
	- 2030 2029 2040 2039 2030 2031 2032 2033
	- 2040 2029 2030 2031 2031 2032 2033 2034
	- 2032 2033 2034 2035 2033 2034 2035 2036
	- 2034 2035 2036 2037 2035 2036 2037 2038
	- 2036 2037 2038 2039 2037 2038 2039 2040
	- 2041 2042 2043 2044 2050 2051 2052 2041
	- 2042 2041 2052 2051 2042 2043 2044 2045
	- 2052 2041 2042 2043 2043 2044 2045 2046
	- 2044 2045 2046 2047 2045 2046 2047 2048
	- 2046 2047 2048 2049 2047 2048 2049 2050
	- 2048 2049 2050 2051 2049 2050 2051 2052
	- 2053 2054 2055 2056 2062 2063 2064 2053
	- 2054 2053 2064 2063 2054 2055 2056 2057
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	-
	- 0 !NIMPHI: impropers
	-
	-
	- 0 !NDON: donors
	-
	-
	- 0 !NACC: acceptors
	-
	-
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 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/CG_solvent/cyclododecane+watMW/images/watMW.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg
	deleted file mode 100644
	index 0ac8c2c01..000000000
	Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh
	deleted file mode 100755
	index 97b9f577d..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt
	deleted file mode 100644
	index ceaa1c69d..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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 $atom:C1
	- }
	-
	-} # Cyclododecane
	-
	-
	-# coordinates in the "Data Atoms" section generated by this python code:
	-# from math import *
	-# bond_length=1.54
	-# N=12
	-# R=(Nbond_length)/(2pi)
	-# for i in range(0,N):
	-# print('$atom:C'+str(i+1)+' $mol:... @atom:TraPPE/CH2 0.0 0.00000 '+
	-# str(round(Rcos(i2pi/N),5))+' '+str(round(Rsin(i2pi/N),5)))
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt
	deleted file mode 100644
	index 4a7063491..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt
	deleted file mode 100644
	index 34bdfead7..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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/CG_solvent/cyclododecane+watMW/run.in.min b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.min
	deleted file mode 100644
	index 218c1229c..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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 500 traj_min.lammpstrj id mol type x y z ix iy iz
	-
	-minimize 1.0e-5 1.0e-7 500 2000
	-
	-write_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
	deleted file mode 100644
	index 936867ef1..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-# run.in.npt
	-#
	-# -- Usage --
	-#
	-# lmp_g++ -i run.in.npt
	-# (assuming lmp_g++ 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 --
	-
	-# Here I just read the raw coordinate data generated by moltemplate.sh.
	-# (If I were more careful, I would minimize the system before the run command.)
	-
	-read_data system.data
	-
	-# -- Settings Section --
	-
	-include system.in.settings
	-
	-# -- Run Section --
	-
	-
	-timestep 2.0 # <- can be increased to 5.0 or 10.0 if careful
	-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_restart system_after_npt.rst
	diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
	deleted file mode 100644
	index 535d089b7..000000000
	--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-# -- init section --
	-include system.in.init
	-
	-# -- atom definition section --
	-
	-# I assume you have already finished these steps:
	-#read_data system.data
	-#read_restart system_after_min.rst
	-
	-read_restart system_after_npt.rst
	-
	-
	-# -- 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
	-
	-
	-#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_restart system_after_nvt.rst
	-
	-
	diff --git a/tools/moltemplate/examples/README.TXT b/tools/moltemplate/examples/README.TXT
	deleted file mode 100644
	index 0ecddbbbd..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 run the other scripts. These files have not been optimized.)
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README.TXT b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README.TXT
	deleted file mode 100644
	index 2d94bc36e..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README.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:
	-Execute the commands in:
	-
	-step 1)
	-README_run_ltemplify.sh
	-
	-and then
	-
	-step 2)
	-README_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 "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
	-(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...).
	- -----------
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh
	deleted file mode 100755
	index d7606aa56..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh
	+++ /dev/null
	@@ -1,9 +0,0 @@
	-
	-LAMMPS_BINARY="lmp_ubuntu" # change this if your binary has a different name
	-
	-# To verify that the files created by ltemplify.py and moltemplate.sh are
	-# valid LAMMPS files, you can start a short simulation with them this way:
	-$LAMMPS_BINARY -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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh
	deleted file mode 100755
	index 5b0a31421..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh
	+++ /dev/null
	@@ -1,11 +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
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh
	deleted file mode 100755
	index e79e9f40b..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-# After you have used ltemplify to generate the LT files you will need,
	-# use thhe following command to generate the LAMMPS input script and data file
	-# (and other auxilliary files) that LAMMPS will need:
	-
	-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).
	-
	-# 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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualise.txt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualise.txt
	deleted file mode 100644
	index 3b9be3e9c..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualise.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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data
	deleted file mode 100644
	index 1f18ff4ae..000000000
	--- a/tools/moltemplate/examples/all_atom_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
	-20 2 1 0.000000 11.173 7.969 7.164
	-21 2 1 0.000000 11.173 7.969 4.328
	-22 2 1 0.000000 12.031 8.827 5.037
	-23 2 1 0.000000 12.031 8.827 6.455
	-24 2 1 0.000000 12.345 10.000 7.164
	-25 2 1 0.000000 12.345 10.000 8.582
	-26 2 1 0.000000 12.031 11.173 9.291
	-27 2 1 0.000000 12.031 11.173 10.709
	-28 2 1 0.000000 11.173 12.031 11.418
	-29 2 1 0.000000 11.173 12.031 8.582
	-30 2 1 0.000000 10.000 12.345 9.291
	-31 2 1 0.000000 10.000 12.345 10.709
	-32 2 1 0.000000 8.827 12.031 11.418
	-33 2 1 0.000000 8.827 12.031 8.582
	-34 2 1 0.000000 7.969 11.173 9.291
	-35 2 1 0.000000 7.969 11.173 10.709
	-36 2 1 0.000000 7.655 10.000 11.418
	-37 2 1 0.000000 7.655 10.000 8.582
	-38 2 1 0.000000 7.969 8.827 9.291
	-39 2 1 0.000000 7.969 8.827 10.709
	-40 2 1 0.000000 8.827 7.969 11.418
	-41 2 1 0.000000 8.827 7.969 8.582
	-42 2 1 0.000000 10.000 7.655 9.291
	-43 2 1 0.000000 10.000 7.655 10.709
	-44 2 1 0.000000 11.173 7.969 11.418
	-45 2 1 0.000000 11.173 7.969 8.582
	-46 2 1 0.000000 12.031 8.827 9.291
	-47 2 1 0.000000 12.031 8.827 10.709
	-48 2 1 0.000000 12.345 10.000 11.418
	-49 2 1 0.000000 12.345 10.000 12.836
	-50 2 1 0.000000 12.031 11.173 13.545
	-51 2 1 0.000000 12.031 11.173 14.963
	-52 2 1 0.000000 11.173 12.031 15.672
	-53 2 1 0.000000 11.173 12.031 12.836
	-54 2 1 0.000000 10.000 12.345 13.545
	-55 2 1 0.000000 10.000 12.345 14.963
	-56 2 1 0.000000 8.827 12.031 15.672
	-57 2 1 0.000000 8.827 12.031 12.836
	-58 2 1 0.000000 7.969 11.173 13.545
	-59 2 1 0.000000 7.969 11.173 14.963
	-60 2 1 0.000000 7.655 10.000 15.672
	-61 2 1 0.000000 7.655 10.000 12.836
	-62 2 1 0.000000 7.969 8.827 13.545
	-63 2 1 0.000000 7.969 8.827 14.963
	-64 2 1 0.000000 8.827 7.969 15.672
	-65 2 1 0.000000 8.827 7.969 12.836
	-66 2 1 0.000000 10.000 7.655 13.545
	-67 2 1 0.000000 10.000 7.655 14.963
	-68 2 1 0.000000 11.173 7.969 15.672
	-69 2 1 0.000000 11.173 7.969 12.836
	-70 2 1 0.000000 12.031 8.827 13.545
	-71 2 1 0.000000 12.031 8.827 14.963
	-72 2 1 0.000000 12.345 10.000 15.672
	-73 1 9 -0.18 -3.365 0.678 1.133
	-74 1 4 0.09 -2.854 1.624 1.417
	-75 1 4 0.09 -4.302 0.58 1.719
	-76 1 9 -0.09 -1.647 -0.716 0.047
	-77 1 4 0.09 -1.451 -1.802 -0.11
	-78 1 10 -0.18 -2.425 -0.518 1.369
	-79 1 5 0.09 -1.756 -0.365 2.24
	-80 1 5 0.09 -3.037 -1.427 1.561
	-81 1 11 -0.09 -3.628 0.67 -0.366
	-82 1 4 0.09 -3.892 1.592 -0.905
	-83 1 10 -0.18 -4.015 -0.644 -0.985
	-84 1 5 0.09 -4.264 -1.466 -0.292
	-85 1 5 0.09 -4.56 -0.575 -1.945
	-86 1 12 -0.09 -2.584 -0.196 -1.019
	-87 1 4 0.09 -2.203 0.152 -1.987
	-88 1 8 0.28 1.737 0.629 -0.049
	-89 1 16 -0.71 1.009 1.811 -0.085
	-90 1 7 0.34 -0.238 1.412 -0.066
	-91 1 3 0.12 -1.102 2.079 -0.079
	-92 1 14 -0.05 -0.385 0.043 -0.026
	-93 1 15 -0.74 3.524 -0.923 0.002
	-94 1 7 0.5 2.59 -1.876 0.037
	-95 1 3 0.13 2.97 -2.901 0.072
	-96 1 15 -0.75 1.258 -1.76 0.035
	-97 1 8 0.43 0.895 -0.468 -0.01
	-98 1 6 0.46 3.123 0.37 -0.042
	-99 1 13 -0.77 4.058 1.336 -0.077
	-100 1 2 0.38 5.012 1.052 -0.068
	-101 1 2 0.38 3.805 2.299 -0.107
	-
	-
	-Bond Coeffs
	-
	- 1 2.0 1.4
	- 2 2.0 1.4 # comments can appear
	- 3 2.0 1.4 # at the end of lines
	- 4 2.0 1.4 # in each data file section
	- 5 2.0 1.1
	- 6 2.0 1.4
	- 7 2.0 1.4
	- 8 2.0 1.4
	- 9 2.0 1.4
	- 10 2.0 1.4
	- 11 2.0 1.4
	- 12 2.0 1.4
	- 13 2.0 1.4
	- 14 2.0 1.4
	- 15 2.0 1.4
	- 16 2.0 1.1
	- 17 2.0 1.4
	- 18 2.0 1.4
	- 19 2.0 1.1
	- 20 2.0 1.4
	- 21 2.0 1.4
	- 22 2.0 1.1
	- 23 2.0 1.1
	- 24 2.0 1.1
	-
	-Bonds
	-
	-1 1 1 2 # descriptive comments can
	-2 1 1 22 # appear at the end of lines
	-3 1 2 3 # in each data file section
	-4 1 2 5 # (removed from this file)
	-5 1 3 24
	-6 1 3 4
	-7 1 4 7
	-8 1 4 29
	-9 1 5 6
	-10 1 6 7
	-11 1 6 9
	-12 1 7 8
	-13 1 8 33
	-14 1 8 11
	-15 1 9 10
	-16 1 10 13
	-17 1 10 11
	-18 1 11 12
	-19 1 12 15
	-20 1 12 37
	-21 1 13 14
	-22 1 14 17
	-23 1 14 15
	-24 1 15 16
	-25 1 16 19
	-26 1 16 41
	-27 1 17 18
	-28 1 18 21
	-29 1 18 19
	-30 1 19 20
	-31 1 20 23
	-32 1 20 45
	-33 1 21 22
	-34 1 22 23
	-35 1 23 24
	-36 1 24 25
	-37 1 25 26
	-38 1 25 46
	-39 1 26 27
	-40 1 26 29
	-41 1 27 48
	-42 1 27 28
	-43 1 28 31
	-44 1 28 53
	-45 1 29 30
	-46 1 30 31
	-47 1 30 33
	-48 1 31 32
	-49 1 32 57
	-50 1 32 35
	-51 1 33 34
	-52 1 34 37
	-53 1 34 35
	-54 1 35 36
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	-56 1 36 61
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	-60 1 39 40
	-61 1 40 43
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	-64 1 42 45
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	-112 14 81 86
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	-129 11 97 96
	-130 9 97 88
	-131 3 98 99
	-132 2 98 88
	-133 24 99 100
	-134 24 99 101
	-
	-
	-Angle Coeffs
	-
	- 1 0 120.0 0 2.0
	- 2 0 120.0 0 2.0 # comments can appear
	- 3 0 120.0 0 2.0 # at the end of lines
	- 4 0 120.0 0 2.0 # in each data file section
	- 5 0 120.0 0 2.0
	- 6 0 120.0 0 2.0
	- 7 0 120.0 0 2.0
	- 8 0 120.0 0 2.0
	- 9 0 120.0 0 2.0
	- 10 0 120.0 0 2.0
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	- 13 0 120.0 0 2.0
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	- 16 0 120.0 0 2.0
	- 17 0 120.0 0 2.0
	- 18 0 120.0 0 2.0
	- 19 0 60.0 0 2.0
	- 20 0 120.0 0 2.0
	- 21 0 60.0 0 2.0
	- 22 0 120.0 0 2.0
	- 23 0 120.0 0 2.0
	- 24 0 120.0 0 2.0
	- 25 0 120.0 0 2.0
	- 26 0 120.0 0 2.0
	- 27 0 120.0 0 2.0
	- 28 0 120.0 0 2.0
	- 29 0 120.0 0 2.0
	- 30 0 60.0 0 2.0
	- 31 0 120.0 0 2.0
	- 32 0 90.0 0 2.0
	- 33 0 120.0 0 2.0
	- 34 0 120.0 0 2.0
	- 35 0 120.0 0 2.0
	- 36 0 120.0 0 2.0
	- 37 0 120.0 0 2.0
	- 38 0 120.0 0 2.0
	- 39 0 120.0 0 2.0
	- 40 0 120.0 0 2.0
	- 41 0 120.0 0 2.0
	- 42 0 120.0 0 2.0
	- 43 0 120.0 0 2.0
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	- 46 0 120.0 0 2.0
	- 47 0 120.0 0 2.0
	- 48 0 120.0 0 2.0
	- 49 0 120.0 0 2.0
	- 50 0 120.0 0 2.0
	-
	-Angles
	-
	-1 1 2 1 22
	-2 1 1 2 3 # comments can appear
	-3 1 1 2 5 # at the end of lines
	-4 1 3 2 5 # in each data file section
	-5 1 2 3 24
	-6 1 2 3 4
	-7 1 4 3 24
	-8 1 3 4 7
	-9 1 3 4 29
	-10 1 7 4 29
	-11 1 2 5 6
	-12 1 5 6 7
	-13 1 5 6 9
	-14 1 7 6 9
	-15 1 4 7 6
	-16 1 4 7 8
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	-19 1 7 8 11
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	-22 1 9 10 13
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	-28 1 11 12 15
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	-31 1 10 13 14
	-32 1 13 14 17
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	-35 1 12 15 14
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	-37 1 14 15 16
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	-41 1 14 17 18
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	-210 37 78 73 75
	-211 37 78 73 74
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	-213 46 79 78 80
	-214 20 81 86 87
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	-217 22 81 83 84
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	-220 17 81 73 74
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	-251 10 99 98 88
	-252 40 100 99 101
	-
	-Dihedral Coeffs
	-
	- 1 0.0 2 180 1
	- 2 0.0 2 180 1 # comments can appear
	- 3 0.0 2 180 1 # at the end of lines
	- 4 0.0 2 180 1 # in each data file section
	- 5 0.0 2 180 1
	- 6 0.0 2 180 1
	- 7 0.0 2 180 1
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	- 22 0.0 2 180 1
	- 23 0.0 1 180 1
	- 24 0.0 1 180 1
	- 25 0.0 3 180 1
	- 26 0.0 2 180 1
	- 27 0.0 2 180 1
	- 28 0.0 2 180 1
	- 29 0.0 2 180 1
	- 30 0.0 6 180 1
	- 31 0.0 3 180 1
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	- 34 0.0 3 180 1
	- 35 0.0 3 180 1
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	- 55 0.0 3 180 1
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	- 78 0.0 2 180 1
	-
	-Dihedrals
	-
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	-2 1 22 1 2 5
	-3 1 2 1 22 21
	-4 1 2 1 22 23
	-5 1 1 2 3 24
	-6 1 1 2 3 4
	-7 1 5 2 3 24
	-8 1 5 2 3 4
	-9 1 1 2 5 6
	-10 1 3 2 5 6
	-11 1 2 3 24 23
	-12 1 2 3 24 25
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	-14 1 4 3 24 25
	-15 1 2 3 4 7
	-16 1 2 3 4 29
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	-24 1 3 4 29 30
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	-27 1 2 5 6 7
	-28 1 2 5 6 9
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	-31 1 9 6 7 4
	-32 1 9 6 7 8
	-33 1 5 6 9 10
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	-35 1 4 7 8 33
	-36 1 4 7 8 11
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	-39 1 7 8 33 30
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	-43 1 7 8 11 10
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	-47 1 6 9 10 13
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	-49 1 9 10 13 14
	-50 1 11 10 13 14
	-51 1 9 10 11 8
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	-54 1 13 10 11 12
	-55 1 8 11 12 15
	-56 1 8 11 12 37
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	-60 1 11 12 15 16
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	-64 1 11 12 37 38
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	-450 66 93 98 99 101
	-451 19 93 98 88 97
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	-457 6 96 94 93 98
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in
	deleted file mode 100644
	index 64eef828d..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg b/tools/moltemplate/examples/all_atom_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/all_atom_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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg b/tools/moltemplate/examples/all_atom_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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg
	deleted file mode 100644
	index 628371b0d..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg
	deleted file mode 100644
	index 3489773ad..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_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/all_atom_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/all_atom_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
	- 1 1 1 1 0.000000 10.0000 0
	- 2 1 1 1 0.000000 10.0000 0
	- 3 1 1 1 0.000000 10.0000 0
	- 4 1 1 1 0.000000 10.0000 0
	- 5 1 1 1 0.000000 10.0000 0
	- 6 1 1 1 0.000000 10.0000 0
	- 7 1 1 1 0.000000 10.0000 0
	- 8 1 1 1 0.000000 10.0000 0
	- 9 1 1 1 0.000000 10.0000 0
	- 10 1 1 1 0.000000 10.0000 0
	- 11 1 1 1 0.000000 10.0000 0
	- 12 1 1 1 0.000000 10.0000 0
	- 13 1 1 1 0.000000 10.0000 0
	- 14 1 1 1 0.000000 10.0000 0
	- 15 1 1 1 0.000000 10.0000 0
	- 16 1 1 1 0.000000 10.0000 0
	- 17 1 1 1 0.000000 10.0000 0
	- 18 1 1 1 0.000000 10.0000 0
	- 19 1 1 1 0.000000 10.0000 0
	- 20 1 1 1 0.000000 10.0000 0
	- 21 1 1 1 0.000000 10.0000 0
	- 22 1 1 1 0.000000 10.0000 0
	- 23 1 1 1 0.000000 10.0000 0
	- 24 1 1 1 0.000000 10.0000 0
	- 25 1 1 1 0.000000 10.0000 0
	- 26 1 1 1 0.000000 10.0000 0
	- 27 1 1 1 0.000000 10.0000 0
	- 28 1 1 1 0.000000 10.0000 0
	- 29 1 1 1 0.000000 10.0000 0
	- 30 1 1 1 0.000000 10.0000 0
	- 31 1 1 1 0.000000 10.0000 0
	- 32 1 1 1 0.000000 10.0000 0
	- 33 1 1 1 0.000000 10.0000 0
	- 34 1 1 1 0.000000 10.0000 0
	- 35 1 1 1 0.000000 10.0000 0
	- 36 1 1 1 0.000000 10.0000 0
	- 37 1 1 1 0.000000 10.0000 0
	- 38 1 1 1 0.000000 10.0000 0
	- 39 1 1 1 0.000000 10.0000 0
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	- 76 2 9 9 -0.090000 10.0000 0
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	- 88 2 8 8 0.280000 10.0000 0
	- 89 2 16 16 -0.710000 10.0000 0
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	- 92 2 14 14 -0.050000 10.0000 0
	- 93 2 15 15 -0.740000 10.0000 0
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	- 102 3 9 9 -0.180000 10.0000 0
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	- 104 3 4 4 0.090000 10.0000 0
	- 105 3 9 9 -0.090000 10.0000 0
	- 106 3 4 4 0.090000 10.0000 0
	- 107 3 10 10 -0.180000 10.0000 0
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	- 109 3 5 5 0.090000 10.0000 0
	- 110 3 11 11 -0.090000 10.0000 0
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	- 114 3 5 5 0.090000 10.0000 0
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	- 127 3 6 6 0.460000 10.0000 0
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	- 130 3 2 2 0.380000 10.0000 0
	-
	- 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
	- 18 19 19 20 20 23 20 45
	- 21 22 22 23 23 24 24 25
	- 25 26 25 46 26 27 26 29
	- 27 48 27 28 28 31 28 53
	- 29 30 30 31 30 33 31 32
	- 32 57 32 35 33 34 34 37
	- 34 35 35 36 36 39 36 61
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	- 40 43 40 65 41 42 42 45
	- 42 43 43 44 44 47 44 69
	- 45 46 46 47 47 48 48 49
	- 49 50 49 70 50 51 50 53
	- 51 72 51 52 52 55 53 54
	- 54 55 54 57 55 56 56 59
	- 57 58 58 61 58 59 59 60
	- 60 63 61 62 62 65 62 63
	- 63 64 64 67 65 66 66 69
	- 66 67 67 68 68 71 69 70
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	- 73 75 73 78 76 78 76 77
	- 76 92 76 86 78 79 78 80
	- 81 86 81 83 81 82 83 86
	- 83 84 83 85 86 87 88 89
	- 88 97 88 98 89 90 90 91
	- 90 92 92 97 93 98 93 94
	- 94 95 94 96 96 97 98 99
	- 99 100 99 101 102 110 102 103
	- 102 104 102 107 105 107 105 106
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	- 110 115 110 112 110 111 112 115
	- 112 113 112 114 115 116 117 118
	- 117 126 117 127 118 119 119 120
	- 119 121 121 126 122 127 122 123
	- 123 124 123 125 125 126 127 128
	- 128 129 128 130
	-
	- 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
	- 5 6 9 7 6 9 4 7 6
	- 4 7 8 6 7 8 7 8 33
	- 7 8 11 11 8 33 6 9 10
	- 9 10 13 9 10 11 11 10 13
	- 8 11 10 8 11 12 10 11 12
	- 11 12 15 11 12 37 15 12 37
	- 10 13 14 13 14 17 13 14 15
	- 15 14 17 12 15 14 12 15 16
	- 14 15 16 15 16 19 15 16 41
	- 19 16 41 14 17 18 17 18 21
	- 17 18 19 19 18 21 16 19 18
	- 16 19 20 18 19 20 19 20 23
	- 19 20 45 23 20 45 18 21 22
	- 1 22 21 1 22 23 21 22 23
	- 20 23 22 20 23 24 22 23 24
	- 3 24 23 3 24 25 23 24 25
	- 24 25 26 24 25 46 26 25 46
	- 25 26 27 25 26 29 27 26 29
	- 26 27 48 26 27 28 28 27 48
	- 27 28 31 27 28 53 31 28 53
	- 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
	- 16 41 38 16 41 42 38 41 42
	- 41 42 45 41 42 43 43 42 45
	- 40 43 42 40 43 44 42 43 44
	- 43 44 47 43 44 69 47 44 69
	- 20 45 42 20 45 46 42 45 46
	- 25 46 45 25 46 47 45 46 47
	- 44 47 46 44 47 48 46 47 48
	- 27 48 47 27 48 49 47 48 49
	- 48 49 50 48 49 70 50 49 70
	- 49 50 51 49 50 53 51 50 53
	- 50 51 72 50 51 52 52 51 72
	- 51 52 55 28 53 50 28 53 54
	- 50 53 54 53 54 55 53 54 57
	- 55 54 57 52 55 54 52 55 56
	- 54 55 56 55 56 59 32 57 54
	- 32 57 58 54 57 58 57 58 61
	- 57 58 59 59 58 61 56 59 58
	- 56 59 60 58 59 60 59 60 63
	- 36 61 58 36 61 62 58 61 62
	- 61 62 65 61 62 63 63 62 65
	- 60 63 62 60 63 64 62 63 64
	- 63 64 67 40 65 62 40 65 66
	- 62 65 66 65 66 69 65 66 67
	- 67 66 69 64 67 66 64 67 68
	- 66 67 68 67 68 71 44 69 66
	- 44 69 70 66 69 70 49 70 69
	- 49 70 71 69 70 71 68 71 70
	- 68 71 72 70 71 72 51 72 71
	- 73 81 82 73 81 83 73 81 86
	- 73 78 80 73 78 79 74 73 75
	- 76 92 90 76 92 97 76 86 87
	- 76 86 83 76 86 81 76 78 80
	- 76 78 79 73 78 76 77 76 92
	- 78 76 92 77 76 78 75 73 78
	- 74 73 78 78 73 81 79 78 80
	- 81 86 87 81 86 83 81 83 85
	- 81 83 84 81 83 86 75 73 81
	- 74 73 81 83 86 87 82 81 83
	- 84 83 85 85 83 86 84 83 86
	- 82 81 86 83 81 86 86 76 92
	- 77 76 86 78 76 86 88 98 93
	- 88 89 90 89 88 97 89 90 91
	- 88 97 92 92 97 96 89 90 92
	- 91 90 92 93 94 96 93 94 95
	- 94 93 98 95 94 96 88 97 96
	- 94 96 97 90 92 97 98 99 101
	- 98 99 100 97 88 98 89 88 98
	- 93 98 99 88 98 99 100 99 101
	- 102 110 111 102 110 112 102 110 115
	- 102 107 109 102 107 108 103 102 104
	- 105 121 119 105 121 126 105 115 116
	- 105 115 112 105 115 110 105 107 109
	- 105 107 108 102 107 105 106 105 121
	- 107 105 121 106 105 107 104 102 107
	- 103 102 107 107 102 110 108 107 109
	- 110 115 116 110 115 112 110 112 114
	- 110 112 113 110 112 115 104 102 110
	- 103 102 110 112 115 116 111 110 112
	- 113 112 114 114 112 115 113 112 115
	- 111 110 115 112 110 115 115 105 121
	- 106 105 115 107 105 115 117 127 122
	- 117 118 119 118 117 126 118 119 120
	- 117 126 121 121 126 125 118 119 121
	- 120 119 121 122 123 125 122 123 124
	- 123 122 127 124 123 125 117 126 125
	- 123 125 126 119 121 126 127 128 130
	- 127 128 129 126 117 127 118 117 127
	- 122 127 128 117 127 128 129 128 130
	-
	- 554 !NPHI: dihedrals
	- 22 1 2 3 22 1 2 5
	- 2 1 22 21 2 1 22 23
	- 1 2 3 24 1 2 3 4
	- 5 2 3 24 5 2 3 4
	- 1 2 5 6 3 2 5 6
	- 2 3 24 23 2 3 24 25
	- 4 3 24 23 4 3 24 25
	- 2 3 4 7 2 3 4 29
	- 24 3 4 7 24 3 4 29
	- 3 4 7 6 3 4 7 8
	- 29 4 7 6 29 4 7 8
	- 3 4 29 26 3 4 29 30
	- 7 4 29 26 7 4 29 30
	- 2 5 6 7 2 5 6 9
	- 5 6 7 4 5 6 7 8
	- 9 6 7 4 9 6 7 8
	- 5 6 9 10 7 6 9 10
	- 4 7 8 33 4 7 8 11
	- 6 7 8 33 6 7 8 11
	- 7 8 33 30 7 8 33 34
	- 11 8 33 30 11 8 33 34
	- 7 8 11 10 7 8 11 12
	- 33 8 11 10 33 8 11 12
	- 6 9 10 13 6 9 10 11
	- 9 10 13 14 11 10 13 14
	- 9 10 11 8 9 10 11 12
	- 13 10 11 8 13 10 11 12
	- 8 11 12 15 8 11 12 37
	- 10 11 12 15 10 11 12 37
	- 11 12 15 14 11 12 15 16
	- 37 12 15 14 37 12 15 16
	- 11 12 37 34 11 12 37 38
	- 15 12 37 34 15 12 37 38
	- 10 13 14 17 10 13 14 15
	- 13 14 17 18 15 14 17 18
	- 13 14 15 12 13 14 15 16
	- 17 14 15 12 17 14 15 16
	- 12 15 16 19 12 15 16 41
	- 14 15 16 19 14 15 16 41
	- 15 16 19 18 15 16 19 20
	- 41 16 19 18 41 16 19 20
	- 15 16 41 38 15 16 41 42
	- 19 16 41 38 19 16 41 42
	- 14 17 18 21 14 17 18 19
	- 17 18 21 22 19 18 21 22
	- 17 18 19 16 17 18 19 20
	- 21 18 19 16 21 18 19 20
	- 16 19 20 23 16 19 20 45
	- 18 19 20 23 18 19 20 45
	- 19 20 23 22 19 20 23 24
	- 45 20 23 22 45 20 23 24
	- 19 20 45 42 19 20 45 46
	- 23 20 45 42 23 20 45 46
	- 18 21 22 1 18 21 22 23
	- 1 22 23 20 1 22 23 24
	- 21 22 23 20 21 22 23 24
	- 20 23 24 3 20 23 24 25
	- 22 23 24 3 22 23 24 25
	- 3 24 25 26 3 24 25 46
	- 23 24 25 26 23 24 25 46
	- 24 25 26 27 24 25 26 29
	- 46 25 26 27 46 25 26 29
	- 24 25 46 45 24 25 46 47
	- 26 25 46 45 26 25 46 47
	- 25 26 27 48 25 26 27 28
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	- 25 26 29 4 25 26 29 30
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	- 28 27 48 47 28 27 48 49
	- 26 27 28 31 26 27 28 53
	- 48 27 28 31 48 27 28 53
	- 27 28 31 30 27 28 31 32
	- 53 28 31 30 53 28 31 32
	- 27 28 53 50 27 28 53 54
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	- 4 29 30 31 4 29 30 33
	- 26 29 30 31 26 29 30 33
	- 29 30 31 28 29 30 31 32
	- 33 30 31 28 33 30 31 32
	- 29 30 33 8 29 30 33 34
	- 31 30 33 8 31 30 33 34
	- 28 31 32 57 28 31 32 35
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	- 33 34 37 12 33 34 37 38
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	- 33 34 35 32 33 34 35 36
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	- 12 37 38 41 12 37 38 39
	- 34 37 38 41 34 37 38 39
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	- 65 40 43 42 65 40 43 44
	- 39 40 65 62 39 40 65 66
	- 43 40 65 62 43 40 65 66
	- 16 41 42 45 16 41 42 43
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	- 45 42 43 40 45 42 43 44
	- 40 43 44 47 40 43 44 69
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	- 43 44 47 46 43 44 47 48
	- 69 44 47 46 69 44 47 48
	- 43 44 69 66 43 44 69 70
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	- 50 51 72 71 52 51 72 71
	- 50 51 52 55 72 51 52 55
	- 51 52 55 54 51 52 55 56
	- 28 53 54 55 28 53 54 57
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	- 32 57 58 61 32 57 58 59
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	- 57 58 61 36 57 58 61 62
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	- 65 62 63 60 65 62 63 64
	- 60 63 64 67 62 63 64 67
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	- 65 66 67 64 65 66 67 68
	- 69 66 67 64 69 66 67 68
	- 64 67 68 71 66 67 68 71
	- 67 68 71 70 67 68 71 72
	- 44 69 70 49 44 69 70 71
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	- 49 70 71 68 49 70 71 72
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	- 68 71 72 51 70 71 72 51
	- 73 81 86 76 73 81 86 83
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	- 73 81 83 84 73 81 83 85
	- 86 76 78 73 77 76 78 73
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	- 74 73 78 79 74 73 78 80
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	- 84 83 86 76 85 83 86 76
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	- 78 76 86 87 78 76 92 97
	- 78 76 92 90 78 73 81 86
	- 78 73 81 83 78 73 81 82
	- 86 76 78 79 92 76 78 79
	- 81 73 78 79 86 76 78 80
	- 92 76 78 80 81 73 78 80
	- 92 76 86 81 84 83 86 81
	- 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 96 102 110 115 105
	- 102 110 115 112 102 110 115 116
	- 102 110 112 115 102 110 112 113
	- 102 110 112 114 115 105 107 102
	- 106 105 107 102 121 105 107 102
	- 103 102 107 105 103 102 107 108
	- 103 102 107 109 103 102 110 115
	- 103 102 110 112 103 102 110 111
	- 104 102 107 105 104 102 107 108
	- 104 102 107 109 104 102 110 115
	- 104 102 110 112 104 102 110 111
	- 105 121 126 125 105 121 126 117
	- 120 119 121 105 118 119 121 105
	- 112 110 115 105 111 110 115 105
	- 110 112 115 105 113 112 115 105
	- 114 112 115 105 110 102 107 105
	- 106 105 115 110 106 105 115 112
	- 106 105 115 116 106 105 107 108
	- 106 105 107 109 106 105 121 126
	- 106 105 121 119 107 105 115 110
	- 107 105 115 112 107 105 115 116
	- 107 105 121 126 107 105 121 119
	- 107 102 110 115 107 102 110 112
	- 107 102 110 111 115 105 107 108
	- 121 105 107 108 110 102 107 108
	- 115 105 107 109 121 105 107 109
	- 110 102 107 109 121 105 115 110
	- 113 112 115 110 114 112 115 110
	- 110 112 115 116 111 110 115 112
	- 111 110 115 116 111 110 112 115
	- 111 110 112 113 111 110 112 114
	- 121 105 115 112 112 110 115 116
	- 115 110 112 113 113 112 115 116
	- 115 110 112 114 114 112 115 116
	- 115 105 121 126 115 105 121 119
	- 121 105 115 116 117 127 128 129
	- 117 127 128 130 123 122 127 117
	- 119 121 126 117 123 125 126 117
	- 117 118 119 121 117 118 119 120
	- 118 119 121 126 118 117 127 128
	- 118 117 127 122 118 117 126 121
	- 118 117 126 125 119 121 126 125
	- 127 117 118 119 126 117 118 119
	- 120 119 121 126 123 125 126 121
	- 127 117 126 121 122 127 128 129
	- 122 127 128 130 126 117 127 122
	- 122 123 125 126 123 122 127 128
	- 127 122 123 124 124 123 125 126
	- 127 117 126 125 127 122 123 125
	-
	- 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
	-
	- 1 0 !NGRP
	- 0 0 0
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf b/tools/moltemplate/examples/all_atom_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/all_atom_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
	- REMARKS VMD generated structure x-plor psf file
	-
	- 101 !NATOM
	- 1 2 1 1 0.000000 10.0000 0
	- 2 2 1 1 0.000000 10.0000 0
	- 3 2 1 1 0.000000 10.0000 0
	- 4 2 1 1 0.000000 10.0000 0
	- 5 2 1 1 0.000000 10.0000 0
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	- 9 2 1 1 0.000000 10.0000 0
	- 10 2 1 1 0.000000 10.0000 0
	- 11 2 1 1 0.000000 10.0000 0
	- 12 2 1 1 0.000000 10.0000 0
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	- 15 2 1 1 0.000000 10.0000 0
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	- 17 2 1 1 0.000000 10.0000 0
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	- 20 2 1 1 0.000000 10.0000 0
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	- 59 2 1 1 0.000000 10.0000 0
	- 60 2 1 1 0.000000 10.0000 0
	- 61 2 1 1 0.000000 10.0000 0
	- 62 2 1 1 0.000000 10.0000 0
	- 63 2 1 1 0.000000 10.0000 0
	- 64 2 1 1 0.000000 10.0000 0
	- 65 2 1 1 0.000000 10.0000 0
	- 66 2 1 1 0.000000 10.0000 0
	- 67 2 1 1 0.000000 10.0000 0
	- 68 2 1 1 0.000000 10.0000 0
	- 69 2 1 1 0.000000 10.0000 0
	- 70 2 1 1 0.000000 10.0000 0
	- 71 2 1 1 0.000000 10.0000 0
	- 72 2 1 1 0.000000 10.0000 0
	- 73 1 9 9 -0.180000 10.0000 0
	- 74 1 4 4 0.090000 10.0000 0
	- 75 1 4 4 0.090000 10.0000 0
	- 76 1 9 9 -0.090000 10.0000 0
	- 77 1 4 4 0.090000 10.0000 0
	- 78 1 10 10 -0.180000 10.0000 0
	- 79 1 5 5 0.090000 10.0000 0
	- 80 1 5 5 0.090000 10.0000 0
	- 81 1 11 11 -0.090000 10.0000 0
	- 82 1 4 4 0.090000 10.0000 0
	- 83 1 10 10 -0.180000 10.0000 0
	- 84 1 5 5 0.090000 10.0000 0
	- 85 1 5 5 0.090000 10.0000 0
	- 86 1 12 12 -0.090000 10.0000 0
	- 87 1 4 4 0.090000 10.0000 0
	- 88 1 8 8 0.280000 10.0000 0
	- 89 1 16 16 -0.710000 10.0000 0
	- 90 1 7 7 0.340000 10.0000 0
	- 91 1 3 3 0.120000 10.0000 0
	- 92 1 14 14 -0.050000 10.0000 0
	- 93 1 15 15 -0.740000 10.0000 0
	- 94 1 7 7 0.500000 10.0000 0
	- 95 1 3 3 0.130000 10.0000 0
	- 96 1 15 15 -0.750000 10.0000 0
	- 97 1 8 8 0.430000 10.0000 0
	- 98 1 6 6 0.460000 10.0000 0
	- 99 1 13 13 -0.770000 10.0000 0
	- 100 1 2 2 0.380000 10.0000 0
	- 101 1 2 2 0.380000 10.0000 0
	-
	- 134 !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
	- 18 19 19 20 20 23 20 45
	- 21 22 22 23 23 24 24 25
	- 25 26 25 46 26 27 26 29
	- 27 48 27 28 28 31 28 53
	- 29 30 30 31 30 33 31 32
	- 32 57 32 35 33 34 34 37
	- 34 35 35 36 36 39 36 61
	- 37 38 38 41 38 39 39 40
	- 40 43 40 65 41 42 42 45
	- 42 43 43 44 44 47 44 69
	- 45 46 46 47 47 48 48 49
	- 49 50 49 70 50 51 50 53
	- 51 72 51 52 52 55 53 54
	- 54 55 54 57 55 56 56 59
	- 57 58 58 61 58 59 59 60
	- 60 63 61 62 62 65 62 63
	- 63 64 64 67 65 66 66 69
	- 66 67 67 68 68 71 69 70
	- 70 71 71 72 73 81 73 74
	- 73 75 73 78 76 78 76 77
	- 76 92 76 86 78 79 78 80
	- 81 86 81 83 81 82 83 86
	- 83 84 83 85 86 87 88 89
	- 88 97 88 98 89 90 90 91
	- 90 92 92 97 93 98 93 94
	- 94 95 94 96 96 97 98 99
	- 99 100 99 101
	-
	- 252 !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
	- 5 6 9 7 6 9 4 7 6
	- 4 7 8 6 7 8 7 8 33
	- 7 8 11 11 8 33 6 9 10
	- 9 10 13 9 10 11 11 10 13
	- 8 11 10 8 11 12 10 11 12
	- 11 12 15 11 12 37 15 12 37
	- 10 13 14 13 14 17 13 14 15
	- 15 14 17 12 15 14 12 15 16
	- 14 15 16 15 16 19 15 16 41
	- 19 16 41 14 17 18 17 18 21
	- 17 18 19 19 18 21 16 19 18
	- 16 19 20 18 19 20 19 20 23
	- 19 20 45 23 20 45 18 21 22
	- 1 22 21 1 22 23 21 22 23
	- 20 23 22 20 23 24 22 23 24
	- 3 24 23 3 24 25 23 24 25
	- 24 25 26 24 25 46 26 25 46
	- 25 26 27 25 26 29 27 26 29
	- 26 27 48 26 27 28 28 27 48
	- 27 28 31 27 28 53 31 28 53
	- 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
	- 16 41 38 16 41 42 38 41 42
	- 41 42 45 41 42 43 43 42 45
	- 40 43 42 40 43 44 42 43 44
	- 43 44 47 43 44 69 47 44 69
	- 20 45 42 20 45 46 42 45 46
	- 25 46 45 25 46 47 45 46 47
	- 44 47 46 44 47 48 46 47 48
	- 27 48 47 27 48 49 47 48 49
	- 48 49 50 48 49 70 50 49 70
	- 49 50 51 49 50 53 51 50 53
	- 50 51 72 50 51 52 52 51 72
	- 51 52 55 28 53 50 28 53 54
	- 50 53 54 53 54 55 53 54 57
	- 55 54 57 52 55 54 52 55 56
	- 54 55 56 55 56 59 32 57 54
	- 32 57 58 54 57 58 57 58 61
	- 57 58 59 59 58 61 56 59 58
	- 56 59 60 58 59 60 59 60 63
	- 36 61 58 36 61 62 58 61 62
	- 61 62 65 61 62 63 63 62 65
	- 60 63 62 60 63 64 62 63 64
	- 63 64 67 40 65 62 40 65 66
	- 62 65 66 65 66 69 65 66 67
	- 67 66 69 64 67 66 64 67 68
	- 66 67 68 67 68 71 44 69 66
	- 44 69 70 66 69 70 49 70 69
	- 49 70 71 69 70 71 68 71 70
	- 68 71 72 70 71 72 51 72 71
	- 73 81 82 73 81 83 73 81 86
	- 73 78 80 73 78 79 74 73 75
	- 76 92 90 76 92 97 76 86 87
	- 76 86 83 76 86 81 76 78 80
	- 76 78 79 73 78 76 77 76 92
	- 78 76 92 77 76 78 75 73 78
	- 74 73 78 78 73 81 79 78 80
	- 81 86 87 81 86 83 81 83 85
	- 81 83 84 81 83 86 75 73 81
	- 74 73 81 83 86 87 82 81 83
	- 84 83 85 85 83 86 84 83 86
	- 82 81 86 83 81 86 86 76 92
	- 77 76 86 78 76 86 88 98 93
	- 88 89 90 89 88 97 89 90 91
	- 88 97 92 92 97 96 89 90 92
	- 91 90 92 93 94 96 93 94 95
	- 94 93 98 95 94 96 88 97 96
	- 94 96 97 90 92 97 98 99 101
	- 98 99 100 97 88 98 89 88 98
	- 93 98 99 88 98 99 100 99 101
	-
	- 457 !NPHI: dihedrals
	- 22 1 2 3 22 1 2 5
	- 2 1 22 21 2 1 22 23
	- 1 2 3 24 1 2 3 4
	- 5 2 3 24 5 2 3 4
	- 1 2 5 6 3 2 5 6
	- 2 3 24 23 2 3 24 25
	- 4 3 24 23 4 3 24 25
	- 2 3 4 7 2 3 4 29
	- 24 3 4 7 24 3 4 29
	- 3 4 7 6 3 4 7 8
	- 29 4 7 6 29 4 7 8
	- 3 4 29 26 3 4 29 30
	- 7 4 29 26 7 4 29 30
	- 2 5 6 7 2 5 6 9
	- 5 6 7 4 5 6 7 8
	- 9 6 7 4 9 6 7 8
	- 5 6 9 10 7 6 9 10
	- 4 7 8 33 4 7 8 11
	- 6 7 8 33 6 7 8 11
	- 7 8 33 30 7 8 33 34
	- 11 8 33 30 11 8 33 34
	- 7 8 11 10 7 8 11 12
	- 33 8 11 10 33 8 11 12
	- 6 9 10 13 6 9 10 11
	- 9 10 13 14 11 10 13 14
	- 9 10 11 8 9 10 11 12
	- 13 10 11 8 13 10 11 12
	- 8 11 12 15 8 11 12 37
	- 10 11 12 15 10 11 12 37
	- 11 12 15 14 11 12 15 16
	- 37 12 15 14 37 12 15 16
	- 11 12 37 34 11 12 37 38
	- 15 12 37 34 15 12 37 38
	- 10 13 14 17 10 13 14 15
	- 13 14 17 18 15 14 17 18
	- 13 14 15 12 13 14 15 16
	- 17 14 15 12 17 14 15 16
	- 12 15 16 19 12 15 16 41
	- 14 15 16 19 14 15 16 41
	- 15 16 19 18 15 16 19 20
	- 41 16 19 18 41 16 19 20
	- 15 16 41 38 15 16 41 42
	- 19 16 41 38 19 16 41 42
	- 14 17 18 21 14 17 18 19
	- 17 18 21 22 19 18 21 22
	- 17 18 19 16 17 18 19 20
	- 21 18 19 16 21 18 19 20
	- 16 19 20 23 16 19 20 45
	- 18 19 20 23 18 19 20 45
	- 19 20 23 22 19 20 23 24
	- 45 20 23 22 45 20 23 24
	- 19 20 45 42 19 20 45 46
	- 23 20 45 42 23 20 45 46
	- 18 21 22 1 18 21 22 23
	- 1 22 23 20 1 22 23 24
	- 21 22 23 20 21 22 23 24
	- 20 23 24 3 20 23 24 25
	- 22 23 24 3 22 23 24 25
	- 3 24 25 26 3 24 25 46
	- 23 24 25 26 23 24 25 46
	- 24 25 26 27 24 25 26 29
	- 46 25 26 27 46 25 26 29
	- 24 25 46 45 24 25 46 47
	- 26 25 46 45 26 25 46 47
	- 25 26 27 48 25 26 27 28
	- 29 26 27 48 29 26 27 28
	- 25 26 29 4 25 26 29 30
	- 27 26 29 4 27 26 29 30
	- 26 27 48 47 26 27 48 49
	- 28 27 48 47 28 27 48 49
	- 26 27 28 31 26 27 28 53
	- 48 27 28 31 48 27 28 53
	- 27 28 31 30 27 28 31 32
	- 53 28 31 30 53 28 31 32
	- 27 28 53 50 27 28 53 54
	- 31 28 53 50 31 28 53 54
	- 4 29 30 31 4 29 30 33
	- 26 29 30 31 26 29 30 33
	- 29 30 31 28 29 30 31 32
	- 33 30 31 28 33 30 31 32
	- 29 30 33 8 29 30 33 34
	- 31 30 33 8 31 30 33 34
	- 28 31 32 57 28 31 32 35
	- 30 31 32 57 30 31 32 35
	- 31 32 57 54 31 32 57 58
	- 35 32 57 54 35 32 57 58
	- 31 32 35 34 31 32 35 36
	- 57 32 35 34 57 32 35 36
	- 8 33 34 37 8 33 34 35
	- 30 33 34 37 30 33 34 35
	- 33 34 37 12 33 34 37 38
	- 35 34 37 12 35 34 37 38
	- 33 34 35 32 33 34 35 36
	- 37 34 35 32 37 34 35 36
	- 32 35 36 39 32 35 36 61
	- 34 35 36 39 34 35 36 61
	- 35 36 39 38 35 36 39 40
	- 61 36 39 38 61 36 39 40
	- 35 36 61 58 35 36 61 62
	- 39 36 61 58 39 36 61 62
	- 12 37 38 41 12 37 38 39
	- 34 37 38 41 34 37 38 39
	- 37 38 41 16 37 38 41 42
	- 39 38 41 16 39 38 41 42
	- 37 38 39 36 37 38 39 40
	- 41 38 39 36 41 38 39 40
	- 36 39 40 43 36 39 40 65
	- 38 39 40 43 38 39 40 65
	- 39 40 43 42 39 40 43 44
	- 65 40 43 42 65 40 43 44
	- 39 40 65 62 39 40 65 66
	- 43 40 65 62 43 40 65 66
	- 16 41 42 45 16 41 42 43
	- 38 41 42 45 38 41 42 43
	- 41 42 45 20 41 42 45 46
	- 43 42 45 20 43 42 45 46
	- 41 42 43 40 41 42 43 44
	- 45 42 43 40 45 42 43 44
	- 40 43 44 47 40 43 44 69
	- 42 43 44 47 42 43 44 69
	- 43 44 47 46 43 44 47 48
	- 69 44 47 46 69 44 47 48
	- 43 44 69 66 43 44 69 70
	- 47 44 69 66 47 44 69 70
	- 20 45 46 25 20 45 46 47
	- 42 45 46 25 42 45 46 47
	- 25 46 47 44 25 46 47 48
	- 45 46 47 44 45 46 47 48
	- 44 47 48 27 44 47 48 49
	- 46 47 48 27 46 47 48 49
	- 27 48 49 50 27 48 49 70
	- 47 48 49 50 47 48 49 70
	- 48 49 50 51 48 49 50 53
	- 70 49 50 51 70 49 50 53
	- 48 49 70 69 48 49 70 71
	- 50 49 70 69 50 49 70 71
	- 49 50 51 72 49 50 51 52
	- 53 50 51 72 53 50 51 52
	- 49 50 53 28 49 50 53 54
	- 51 50 53 28 51 50 53 54
	- 50 51 72 71 52 51 72 71
	- 50 51 52 55 72 51 52 55
	- 51 52 55 54 51 52 55 56
	- 28 53 54 55 28 53 54 57
	- 50 53 54 55 50 53 54 57
	- 53 54 55 52 53 54 55 56
	- 57 54 55 52 57 54 55 56
	- 53 54 57 32 53 54 57 58
	- 55 54 57 32 55 54 57 58
	- 52 55 56 59 54 55 56 59
	- 55 56 59 58 55 56 59 60
	- 32 57 58 61 32 57 58 59
	- 54 57 58 61 54 57 58 59
	- 57 58 61 36 57 58 61 62
	- 59 58 61 36 59 58 61 62
	- 57 58 59 56 57 58 59 60
	- 61 58 59 56 61 58 59 60
	- 56 59 60 63 58 59 60 63
	- 59 60 63 62 59 60 63 64
	- 36 61 62 65 36 61 62 63
	- 58 61 62 65 58 61 62 63
	- 61 62 65 40 61 62 65 66
	- 63 62 65 40 63 62 65 66
	- 61 62 63 60 61 62 63 64
	- 65 62 63 60 65 62 63 64
	- 60 63 64 67 62 63 64 67
	- 63 64 67 66 63 64 67 68
	- 40 65 66 69 40 65 66 67
	- 62 65 66 69 62 65 66 67
	- 65 66 69 44 65 66 69 70
	- 67 66 69 44 67 66 69 70
	- 65 66 67 64 65 66 67 68
	- 69 66 67 64 69 66 67 68
	- 64 67 68 71 66 67 68 71
	- 67 68 71 70 67 68 71 72
	- 44 69 70 49 44 69 70 71
	- 66 69 70 49 66 69 70 71
	- 49 70 71 68 49 70 71 72
	- 69 70 71 68 69 70 71 72
	- 68 71 72 51 70 71 72 51
	- 73 81 86 76 73 81 86 83
	- 73 81 86 87 73 81 83 86
	- 73 81 83 84 73 81 83 85
	- 86 76 78 73 77 76 78 73
	- 92 76 78 73 74 73 78 76
	- 74 73 78 79 74 73 78 80
	- 74 73 81 86 74 73 81 83
	- 74 73 81 82 75 73 78 76
	- 75 73 78 79 75 73 78 80
	- 75 73 81 86 75 73 81 83
	- 75 73 81 82 76 92 97 96
	- 76 92 97 88 91 90 92 76
	- 89 90 92 76 83 81 86 76
	- 82 81 86 76 81 83 86 76
	- 84 83 86 76 85 83 86 76
	- 81 73 78 76 77 76 86 81
	- 77 76 86 83 77 76 86 87
	- 77 76 78 79 77 76 78 80
	- 77 76 92 97 77 76 92 90
	- 78 76 86 81 78 76 86 83
	- 78 76 86 87 78 76 92 97
	- 78 76 92 90 78 73 81 86
	- 78 73 81 83 78 73 81 82
	- 86 76 78 79 92 76 78 79
	- 81 73 78 79 86 76 78 80
	- 92 76 78 80 81 73 78 80
	- 92 76 86 81 84 83 86 81
	- 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/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt
	deleted file mode 100644
	index 5c1d2d417..000000000
	--- a/tools/moltemplate/examples/all_atom_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_restart system_after_nvt.rst
	-
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt
	deleted file mode 100644
	index 70fdb7548..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/heteropolymer_melt_attempt1/README.TXT b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README.TXT
	deleted file mode 100644
	index 1a077178e..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README.TXT
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-This is a very crude attempt to create a polymer melt
	-consisting of 150 copies of the same polymer.
	-
	-THE FORCE FIELD PARAMETERS AND CONFORMATION FOR THIS SYSTEM ARE COMPLETELY WRONG
	-
	-The purpose of this example is to demonstrate one way to create a
	-large number of randomly generated polymers, and to use
	-an NPT simulation to pack them all into a small box.
	-(Smaller than their initial outstretched length.)
	-
	-Each polymer is a random heteropolymer of length 200 monomers.
	-This polymer is a polymoer of PVDF and PCTFE monomers
	-selected randomly in a 1:3 ratio.
	-Again, this is not a realistic simulation of PVDV or PCTFE polymers,
	-
	-Furthermore, even after the simulation is done, the arrangement of the
	-polymers in the box is not characteristic of a truly random polymer melt.
	-
	-
	----- A note on size ---
	-
	-This is a large system with nearly 200000 atoms.
	-It takes several minutes to compile this example
	-and (currently requiring at least 4.0 Gb of memory).
	-(I'm working on reducing that requirement. -Andrew 2012-9-12)
	-
	------------------------
	-
	-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/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh
	deleted file mode 100755
	index e8e13dec7..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh
	+++ /dev/null
	@@ -1,19 +0,0 @@
	-# This is just an example.
	-#
	-# Note: The "run.in.nvt" file is a LAMMPS input script which attempts to read
	-# the input scripts and data files you created with 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.nvt
	-
	-# Alternately, if you have MPI installed, try something like this:
	-
	-#NUMPROCS=4
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt
	diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_setup.sh
	deleted file mode 100755
	index acc5fbbaa..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/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/all_atom_examples/heteropolymer_melt_attempt1/README_visualise.txt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_visualise.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.)
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	diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/monomers.lt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/monomers.lt
	deleted file mode 100644
	index af043b39e..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/monomers.lt
	+++ /dev/null
	@@ -1,125 +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. --
	- # ----------------------------------------------------------------------
	-
	-
	-MonomerTypes {
	-
	-
	- PVDF {
	- # atom-id mol-id atom-type charge x y z
	-
	- write("Data Atoms") {
	- $atom:C1 $mol:... @atom:../C 0.0 -1.000 0.4000 0.00000
	- $atom:H1 $mol:... @atom:../RH 0.0 -1.000 1.000 1.000
	- $atom:H2 $mol:... @atom:../RH 0.0 -1.000 1.000 -1.000
	- $atom:C2 $mol:... @atom:../C 0.0 1.000 -0.4000 0.00000
	- $atom:F1 $mol:... @atom:../RF 0.0 1.000 -1.000 1.000
	- $atom:F2 $mol:... @atom:../RF 0.0 1.000 -1.000 -1.000
	- }
	-
	- # bond-id bond-type atom-id1 atom-id2
	-
	- write("Data Bonds") {
	- $bond:C1R1 @bond:../sidechain $atom:C1 $atom:H1
	- $bond:C1R2 @bond:../sidechain $atom:C1 $atom:H2
	- $bond:C2R1 @bond:../sidechain $atom:C2 $atom:F1
	- $bond:C2R2 @bond:../sidechain $atom:C2 $atom:F2
	- $bond:C12 @bond:../bb $atom:C1 $atom:C2
	- }
	- } # PVDF
	-
	-
	- PCTFE {
	- # atom-id mol-id atom-type charge x y z
	-
	- write("Data Atoms") {
	- $atom:C1 $mol:... @atom:../C 0.0 -1.000 0.4000 0.00000
	- $atom:F1 $mol:... @atom:../RF 0.0 -1.000 1.000 1.000
	- $atom:F2 $mol:... @atom:../RF 0.0 -1.000 1.000 -1.000
	- $atom:C2 $mol:... @atom:../C 0.0 1.000 -0.4000 0.00000
	- $atom:F3 $mol:... @atom:../RF 0.0 1.000 -1.000 1.000
	- $atom:CL $mol:... @atom:../RCl 0.0 1.000 -1.000 -1.000
	- }
	-
	- # bond-id bond-type atom-id1 atom-id2
	-
	- write("Data Bonds") {
	- $bond:C1R1 @bond:../sidechain $atom:C1 $atom:F1
	- $bond:C1R2 @bond:../sidechain $atom:C1 $atom:F2
	- $bond:C2R1 @bond:../sidechain $atom:C2 $atom:F3
	- $bond:C2R2 @bond:../sidechain $atom:C2 $atom:CL
	- $bond:C12 @bond:../bb $atom:C1 $atom:C2
	- }
	- } # PCTFE
	-
	-
	- # atom-type mass
	-
	- write_once("Data Masses") {
	- @atom:C 12.0
	- @atom:RH 1.0
	- @atom:RF 19.0
	- @atom:RCl 35.453
	- }
	-
	-
	- # atom-type atom-type epsilon sigma
	-
	- write_once("In Settings") {
	- pair_coeff @atom:C @atom:C 0.20 2.0
	- pair_coeff @atom:RH @atom:RH 0.20 1.0
	- pair_coeff @atom:RF @atom:RF 0.40 2.0
	- pair_coeff @atom:RCl @atom:RCl 0.40 2.0
	- }
	-
	-
	- # bond-type k r0
	-
	- write_once("Data Bond Coeffs") {
	- @bond:sidechain 30.0 1.2
	- @bond:bb 30.0 2.0 # "bb" shorthand for "backbone"
	- }
	-
	- # Although there's no need to define angular interactions (because this
	- # "molecule" only contains two atoms), we define the settings for angles
	- # or dihedrals which might be present later when we build a polymer.
	-
	- # angle-type k theta0
	-
	- write_once("Data Angle Coeffs") {
	- @angle:backbone 50.00 160
	- @angle:sidechain 50.00 120
	- @angle:RCR 50.00 120
	- }
	-
	- # dihedral-type K1 K2 K3 K4
	-
	- write_once("Data Dihedral Coeffs") {
	- @dihedral:backbn 1.411036 -0.271016 3.145034 0.0
	- }
	-
	- # 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:C @atom:C @atom:C @bond:* @bond:*
	- @angle:sidechain @atom:C @atom:C @atom:R* @bond:* @bond:*
	- @angle:RCR @atom:R* @atom:C @atom:R* @bond:* @bond:*
	- }
	-
	- # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3
	-
	- write_once("Data Dihedrals By Type") {
	- @dihedral:backbn @atom:C @atom:C @atom:C @atom:C @bond:* @bond:* @bond:*
	- }
	-
	-} # MonomerTypes
	diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/polymer.lt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/polymer.lt
	deleted file mode 100644
	index 27d1c16b0..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/polymer.lt
	+++ /dev/null
	@@ -1,231 +0,0 @@
	-import "monomers.lt"
	-
	-using namespace MonomerTypes
	-
	-Polymer200 {
	-
	- # Make a chain of monomers with random composition:
	-
	- monomers = new random([PVDF,PCTFE], [0.25,0.75]) [200].move(4.0, 0, 0)
	-
	- # Now, link the monomers together this way:
	- write("Data Bonds") {
	- $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/C2 $atom:monomers[1]/C1
	- $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/C2 $atom:monomers[2]/C1
	- $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/C2 $atom:monomers[3]/C1
	- $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/C2 $atom:monomers[4]/C1
	- $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/C2 $atom:monomers[5]/C1
	- $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/C2 $atom:monomers[6]/C1
	- $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/C2 $atom:monomers[7]/C1
	- $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/C2 $atom:monomers[8]/C1
	- $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/C2 $atom:monomers[9]/C1
	- $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/C2 $atom:monomers[10]/C1
	- $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/C2 $atom:monomers[11]/C1
	- $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/C2 $atom:monomers[12]/C1
	- $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/C2 $atom:monomers[13]/C1
	- $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/C2 $atom:monomers[14]/C1
	- $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/C2 $atom:monomers[15]/C1
	- $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/C2 $atom:monomers[16]/C1
	- $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/C2 $atom:monomers[17]/C1
	- $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/C2 $atom:monomers[18]/C1
	- $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/C2 $atom:monomers[19]/C1
	- $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/C2 $atom:monomers[20]/C1
	- $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/C2 $atom:monomers[21]/C1
	- $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/C2 $atom:monomers[22]/C1
	- $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/C2 $atom:monomers[23]/C1
	- $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/C2 $atom:monomers[24]/C1
	- $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/C2 $atom:monomers[25]/C1
	- $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/C2 $atom:monomers[26]/C1
	- $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/C2 $atom:monomers[27]/C1
	- $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/C2 $atom:monomers[28]/C1
	- $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/C2 $atom:monomers[29]/C1
	- $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/C2 $atom:monomers[30]/C1
	- $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/C2 $atom:monomers[31]/C1
	- $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/C2 $atom:monomers[32]/C1
	- $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/C2 $atom:monomers[33]/C1
	- $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/C2 $atom:monomers[34]/C1
	- $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/C2 $atom:monomers[35]/C1
	- $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/C2 $atom:monomers[36]/C1
	- $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/C2 $atom:monomers[37]/C1
	- $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/C2 $atom:monomers[38]/C1
	- $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/C2 $atom:monomers[39]/C1
	- $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/C2 $atom:monomers[40]/C1
	- $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/C2 $atom:monomers[41]/C1
	- $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/C2 $atom:monomers[42]/C1
	- $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/C2 $atom:monomers[43]/C1
	- $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/C2 $atom:monomers[44]/C1
	- $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/C2 $atom:monomers[45]/C1
	- $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/C2 $atom:monomers[46]/C1
	- $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/C2 $atom:monomers[47]/C1
	- $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/C2 $atom:monomers[48]/C1
	- $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/C2 $atom:monomers[49]/C1
	- $bond:bb50 @bond:MonomerTypes/bb $atom:monomers[49]/C2 $atom:monomers[50]/C1
	- $bond:bb51 @bond:MonomerTypes/bb $atom:monomers[50]/C2 $atom:monomers[51]/C1
	- $bond:bb52 @bond:MonomerTypes/bb $atom:monomers[51]/C2 $atom:monomers[52]/C1
	- $bond:bb53 @bond:MonomerTypes/bb $atom:monomers[52]/C2 $atom:monomers[53]/C1
	- $bond:bb54 @bond:MonomerTypes/bb $atom:monomers[53]/C2 $atom:monomers[54]/C1
	- $bond:bb55 @bond:MonomerTypes/bb $atom:monomers[54]/C2 $atom:monomers[55]/C1
	- $bond:bb56 @bond:MonomerTypes/bb $atom:monomers[55]/C2 $atom:monomers[56]/C1
	- $bond:bb57 @bond:MonomerTypes/bb $atom:monomers[56]/C2 $atom:monomers[57]/C1
	- $bond:bb58 @bond:MonomerTypes/bb $atom:monomers[57]/C2 $atom:monomers[58]/C1
	- $bond:bb59 @bond:MonomerTypes/bb $atom:monomers[58]/C2 $atom:monomers[59]/C1
	- $bond:bb60 @bond:MonomerTypes/bb $atom:monomers[59]/C2 $atom:monomers[60]/C1
	- $bond:bb61 @bond:MonomerTypes/bb $atom:monomers[60]/C2 $atom:monomers[61]/C1
	- $bond:bb62 @bond:MonomerTypes/bb $atom:monomers[61]/C2 $atom:monomers[62]/C1
	- $bond:bb63 @bond:MonomerTypes/bb $atom:monomers[62]/C2 $atom:monomers[63]/C1
	- $bond:bb64 @bond:MonomerTypes/bb $atom:monomers[63]/C2 $atom:monomers[64]/C1
	- $bond:bb65 @bond:MonomerTypes/bb $atom:monomers[64]/C2 $atom:monomers[65]/C1
	- $bond:bb66 @bond:MonomerTypes/bb $atom:monomers[65]/C2 $atom:monomers[66]/C1
	- $bond:bb67 @bond:MonomerTypes/bb $atom:monomers[66]/C2 $atom:monomers[67]/C1
	- $bond:bb68 @bond:MonomerTypes/bb $atom:monomers[67]/C2 $atom:monomers[68]/C1
	- $bond:bb69 @bond:MonomerTypes/bb $atom:monomers[68]/C2 $atom:monomers[69]/C1
	- $bond:bb70 @bond:MonomerTypes/bb $atom:monomers[69]/C2 $atom:monomers[70]/C1
	- $bond:bb71 @bond:MonomerTypes/bb $atom:monomers[70]/C2 $atom:monomers[71]/C1
	- $bond:bb72 @bond:MonomerTypes/bb $atom:monomers[71]/C2 $atom:monomers[72]/C1
	- $bond:bb73 @bond:MonomerTypes/bb $atom:monomers[72]/C2 $atom:monomers[73]/C1
	- $bond:bb74 @bond:MonomerTypes/bb $atom:monomers[73]/C2 $atom:monomers[74]/C1
	- $bond:bb75 @bond:MonomerTypes/bb $atom:monomers[74]/C2 $atom:monomers[75]/C1
	- $bond:bb76 @bond:MonomerTypes/bb $atom:monomers[75]/C2 $atom:monomers[76]/C1
	- $bond:bb77 @bond:MonomerTypes/bb $atom:monomers[76]/C2 $atom:monomers[77]/C1
	- $bond:bb78 @bond:MonomerTypes/bb $atom:monomers[77]/C2 $atom:monomers[78]/C1
	- $bond:bb79 @bond:MonomerTypes/bb $atom:monomers[78]/C2 $atom:monomers[79]/C1
	- $bond:bb80 @bond:MonomerTypes/bb $atom:monomers[79]/C2 $atom:monomers[80]/C1
	- $bond:bb81 @bond:MonomerTypes/bb $atom:monomers[80]/C2 $atom:monomers[81]/C1
	- $bond:bb82 @bond:MonomerTypes/bb $atom:monomers[81]/C2 $atom:monomers[82]/C1
	- $bond:bb83 @bond:MonomerTypes/bb $atom:monomers[82]/C2 $atom:monomers[83]/C1
	- $bond:bb84 @bond:MonomerTypes/bb $atom:monomers[83]/C2 $atom:monomers[84]/C1
	- $bond:bb85 @bond:MonomerTypes/bb $atom:monomers[84]/C2 $atom:monomers[85]/C1
	- $bond:bb86 @bond:MonomerTypes/bb $atom:monomers[85]/C2 $atom:monomers[86]/C1
	- $bond:bb87 @bond:MonomerTypes/bb $atom:monomers[86]/C2 $atom:monomers[87]/C1
	- $bond:bb88 @bond:MonomerTypes/bb $atom:monomers[87]/C2 $atom:monomers[88]/C1
	- $bond:bb89 @bond:MonomerTypes/bb $atom:monomers[88]/C2 $atom:monomers[89]/C1
	- $bond:bb90 @bond:MonomerTypes/bb $atom:monomers[89]/C2 $atom:monomers[90]/C1
	- $bond:bb91 @bond:MonomerTypes/bb $atom:monomers[90]/C2 $atom:monomers[91]/C1
	- $bond:bb92 @bond:MonomerTypes/bb $atom:monomers[91]/C2 $atom:monomers[92]/C1
	- $bond:bb93 @bond:MonomerTypes/bb $atom:monomers[92]/C2 $atom:monomers[93]/C1
	- $bond:bb94 @bond:MonomerTypes/bb $atom:monomers[93]/C2 $atom:monomers[94]/C1
	- $bond:bb95 @bond:MonomerTypes/bb $atom:monomers[94]/C2 $atom:monomers[95]/C1
	- $bond:bb96 @bond:MonomerTypes/bb $atom:monomers[95]/C2 $atom:monomers[96]/C1
	- $bond:bb97 @bond:MonomerTypes/bb $atom:monomers[96]/C2 $atom:monomers[97]/C1
	- $bond:bb98 @bond:MonomerTypes/bb $atom:monomers[97]/C2 $atom:monomers[98]/C1
	- $bond:bb99 @bond:MonomerTypes/bb $atom:monomers[98]/C2 $atom:monomers[99]/C1
	- $bond:bb100 @bond:MonomerTypes/bb $atom:monomers[99]/C2 $atom:monomers[100]/C1
	- $bond:bb101 @bond:MonomerTypes/bb $atom:monomers[100]/C2 $atom:monomers[101]/C1
	- $bond:bb102 @bond:MonomerTypes/bb $atom:monomers[101]/C2 $atom:monomers[102]/C1
	- $bond:bb103 @bond:MonomerTypes/bb $atom:monomers[102]/C2 $atom:monomers[103]/C1
	- $bond:bb104 @bond:MonomerTypes/bb $atom:monomers[103]/C2 $atom:monomers[104]/C1
	- $bond:bb105 @bond:MonomerTypes/bb $atom:monomers[104]/C2 $atom:monomers[105]/C1
	- $bond:bb106 @bond:MonomerTypes/bb $atom:monomers[105]/C2 $atom:monomers[106]/C1
	- $bond:bb107 @bond:MonomerTypes/bb $atom:monomers[106]/C2 $atom:monomers[107]/C1
	- $bond:bb108 @bond:MonomerTypes/bb $atom:monomers[107]/C2 $atom:monomers[108]/C1
	- $bond:bb109 @bond:MonomerTypes/bb $atom:monomers[108]/C2 $atom:monomers[109]/C1
	- $bond:bb110 @bond:MonomerTypes/bb $atom:monomers[109]/C2 $atom:monomers[110]/C1
	- $bond:bb111 @bond:MonomerTypes/bb $atom:monomers[110]/C2 $atom:monomers[111]/C1
	- $bond:bb112 @bond:MonomerTypes/bb $atom:monomers[111]/C2 $atom:monomers[112]/C1
	- $bond:bb113 @bond:MonomerTypes/bb $atom:monomers[112]/C2 $atom:monomers[113]/C1
	- $bond:bb114 @bond:MonomerTypes/bb $atom:monomers[113]/C2 $atom:monomers[114]/C1
	- $bond:bb115 @bond:MonomerTypes/bb $atom:monomers[114]/C2 $atom:monomers[115]/C1
	- $bond:bb116 @bond:MonomerTypes/bb $atom:monomers[115]/C2 $atom:monomers[116]/C1
	- $bond:bb117 @bond:MonomerTypes/bb $atom:monomers[116]/C2 $atom:monomers[117]/C1
	- $bond:bb118 @bond:MonomerTypes/bb $atom:monomers[117]/C2 $atom:monomers[118]/C1
	- $bond:bb119 @bond:MonomerTypes/bb $atom:monomers[118]/C2 $atom:monomers[119]/C1
	- $bond:bb120 @bond:MonomerTypes/bb $atom:monomers[119]/C2 $atom:monomers[120]/C1
	- $bond:bb121 @bond:MonomerTypes/bb $atom:monomers[120]/C2 $atom:monomers[121]/C1
	- $bond:bb122 @bond:MonomerTypes/bb $atom:monomers[121]/C2 $atom:monomers[122]/C1
	- $bond:bb123 @bond:MonomerTypes/bb $atom:monomers[122]/C2 $atom:monomers[123]/C1
	- $bond:bb124 @bond:MonomerTypes/bb $atom:monomers[123]/C2 $atom:monomers[124]/C1
	- $bond:bb125 @bond:MonomerTypes/bb $atom:monomers[124]/C2 $atom:monomers[125]/C1
	- $bond:bb126 @bond:MonomerTypes/bb $atom:monomers[125]/C2 $atom:monomers[126]/C1
	- $bond:bb127 @bond:MonomerTypes/bb $atom:monomers[126]/C2 $atom:monomers[127]/C1
	- $bond:bb128 @bond:MonomerTypes/bb $atom:monomers[127]/C2 $atom:monomers[128]/C1
	- $bond:bb129 @bond:MonomerTypes/bb $atom:monomers[128]/C2 $atom:monomers[129]/C1
	- $bond:bb130 @bond:MonomerTypes/bb $atom:monomers[129]/C2 $atom:monomers[130]/C1
	- $bond:bb131 @bond:MonomerTypes/bb $atom:monomers[130]/C2 $atom:monomers[131]/C1
	- $bond:bb132 @bond:MonomerTypes/bb $atom:monomers[131]/C2 $atom:monomers[132]/C1
	- $bond:bb133 @bond:MonomerTypes/bb $atom:monomers[132]/C2 $atom:monomers[133]/C1
	- $bond:bb134 @bond:MonomerTypes/bb $atom:monomers[133]/C2 $atom:monomers[134]/C1
	- $bond:bb135 @bond:MonomerTypes/bb $atom:monomers[134]/C2 $atom:monomers[135]/C1
	- $bond:bb136 @bond:MonomerTypes/bb $atom:monomers[135]/C2 $atom:monomers[136]/C1
	- $bond:bb137 @bond:MonomerTypes/bb $atom:monomers[136]/C2 $atom:monomers[137]/C1
	- $bond:bb138 @bond:MonomerTypes/bb $atom:monomers[137]/C2 $atom:monomers[138]/C1
	- $bond:bb139 @bond:MonomerTypes/bb $atom:monomers[138]/C2 $atom:monomers[139]/C1
	- $bond:bb140 @bond:MonomerTypes/bb $atom:monomers[139]/C2 $atom:monomers[140]/C1
	- $bond:bb141 @bond:MonomerTypes/bb $atom:monomers[140]/C2 $atom:monomers[141]/C1
	- $bond:bb142 @bond:MonomerTypes/bb $atom:monomers[141]/C2 $atom:monomers[142]/C1
	- $bond:bb143 @bond:MonomerTypes/bb $atom:monomers[142]/C2 $atom:monomers[143]/C1
	- $bond:bb144 @bond:MonomerTypes/bb $atom:monomers[143]/C2 $atom:monomers[144]/C1
	- $bond:bb145 @bond:MonomerTypes/bb $atom:monomers[144]/C2 $atom:monomers[145]/C1
	- $bond:bb146 @bond:MonomerTypes/bb $atom:monomers[145]/C2 $atom:monomers[146]/C1
	- $bond:bb147 @bond:MonomerTypes/bb $atom:monomers[146]/C2 $atom:monomers[147]/C1
	- $bond:bb148 @bond:MonomerTypes/bb $atom:monomers[147]/C2 $atom:monomers[148]/C1
	- $bond:bb149 @bond:MonomerTypes/bb $atom:monomers[148]/C2 $atom:monomers[149]/C1
	- $bond:bb150 @bond:MonomerTypes/bb $atom:monomers[149]/C2 $atom:monomers[150]/C1
	- $bond:bb151 @bond:MonomerTypes/bb $atom:monomers[150]/C2 $atom:monomers[151]/C1
	- $bond:bb152 @bond:MonomerTypes/bb $atom:monomers[151]/C2 $atom:monomers[152]/C1
	- $bond:bb153 @bond:MonomerTypes/bb $atom:monomers[152]/C2 $atom:monomers[153]/C1
	- $bond:bb154 @bond:MonomerTypes/bb $atom:monomers[153]/C2 $atom:monomers[154]/C1
	- $bond:bb155 @bond:MonomerTypes/bb $atom:monomers[154]/C2 $atom:monomers[155]/C1
	- $bond:bb156 @bond:MonomerTypes/bb $atom:monomers[155]/C2 $atom:monomers[156]/C1
	- $bond:bb157 @bond:MonomerTypes/bb $atom:monomers[156]/C2 $atom:monomers[157]/C1
	- $bond:bb158 @bond:MonomerTypes/bb $atom:monomers[157]/C2 $atom:monomers[158]/C1
	- $bond:bb159 @bond:MonomerTypes/bb $atom:monomers[158]/C2 $atom:monomers[159]/C1
	- $bond:bb160 @bond:MonomerTypes/bb $atom:monomers[159]/C2 $atom:monomers[160]/C1
	- $bond:bb161 @bond:MonomerTypes/bb $atom:monomers[160]/C2 $atom:monomers[161]/C1
	- $bond:bb162 @bond:MonomerTypes/bb $atom:monomers[161]/C2 $atom:monomers[162]/C1
	- $bond:bb163 @bond:MonomerTypes/bb $atom:monomers[162]/C2 $atom:monomers[163]/C1
	- $bond:bb164 @bond:MonomerTypes/bb $atom:monomers[163]/C2 $atom:monomers[164]/C1
	- $bond:bb165 @bond:MonomerTypes/bb $atom:monomers[164]/C2 $atom:monomers[165]/C1
	- $bond:bb166 @bond:MonomerTypes/bb $atom:monomers[165]/C2 $atom:monomers[166]/C1
	- $bond:bb167 @bond:MonomerTypes/bb $atom:monomers[166]/C2 $atom:monomers[167]/C1
	- $bond:bb168 @bond:MonomerTypes/bb $atom:monomers[167]/C2 $atom:monomers[168]/C1
	- $bond:bb169 @bond:MonomerTypes/bb $atom:monomers[168]/C2 $atom:monomers[169]/C1
	- $bond:bb170 @bond:MonomerTypes/bb $atom:monomers[169]/C2 $atom:monomers[170]/C1
	- $bond:bb171 @bond:MonomerTypes/bb $atom:monomers[170]/C2 $atom:monomers[171]/C1
	- $bond:bb172 @bond:MonomerTypes/bb $atom:monomers[171]/C2 $atom:monomers[172]/C1
	- $bond:bb173 @bond:MonomerTypes/bb $atom:monomers[172]/C2 $atom:monomers[173]/C1
	- $bond:bb174 @bond:MonomerTypes/bb $atom:monomers[173]/C2 $atom:monomers[174]/C1
	- $bond:bb175 @bond:MonomerTypes/bb $atom:monomers[174]/C2 $atom:monomers[175]/C1
	- $bond:bb176 @bond:MonomerTypes/bb $atom:monomers[175]/C2 $atom:monomers[176]/C1
	- $bond:bb177 @bond:MonomerTypes/bb $atom:monomers[176]/C2 $atom:monomers[177]/C1
	- $bond:bb178 @bond:MonomerTypes/bb $atom:monomers[177]/C2 $atom:monomers[178]/C1
	- $bond:bb179 @bond:MonomerTypes/bb $atom:monomers[178]/C2 $atom:monomers[179]/C1
	- $bond:bb180 @bond:MonomerTypes/bb $atom:monomers[179]/C2 $atom:monomers[180]/C1
	- $bond:bb181 @bond:MonomerTypes/bb $atom:monomers[180]/C2 $atom:monomers[181]/C1
	- $bond:bb182 @bond:MonomerTypes/bb $atom:monomers[181]/C2 $atom:monomers[182]/C1
	- $bond:bb183 @bond:MonomerTypes/bb $atom:monomers[182]/C2 $atom:monomers[183]/C1
	- $bond:bb184 @bond:MonomerTypes/bb $atom:monomers[183]/C2 $atom:monomers[184]/C1
	- $bond:bb185 @bond:MonomerTypes/bb $atom:monomers[184]/C2 $atom:monomers[185]/C1
	- $bond:bb186 @bond:MonomerTypes/bb $atom:monomers[185]/C2 $atom:monomers[186]/C1
	- $bond:bb187 @bond:MonomerTypes/bb $atom:monomers[186]/C2 $atom:monomers[187]/C1
	- $bond:bb188 @bond:MonomerTypes/bb $atom:monomers[187]/C2 $atom:monomers[188]/C1
	- $bond:bb189 @bond:MonomerTypes/bb $atom:monomers[188]/C2 $atom:monomers[189]/C1
	- $bond:bb190 @bond:MonomerTypes/bb $atom:monomers[189]/C2 $atom:monomers[190]/C1
	- $bond:bb191 @bond:MonomerTypes/bb $atom:monomers[190]/C2 $atom:monomers[191]/C1
	- $bond:bb192 @bond:MonomerTypes/bb $atom:monomers[191]/C2 $atom:monomers[192]/C1
	- $bond:bb193 @bond:MonomerTypes/bb $atom:monomers[192]/C2 $atom:monomers[193]/C1
	- $bond:bb194 @bond:MonomerTypes/bb $atom:monomers[193]/C2 $atom:monomers[194]/C1
	- $bond:bb195 @bond:MonomerTypes/bb $atom:monomers[194]/C2 $atom:monomers[195]/C1
	- $bond:bb196 @bond:MonomerTypes/bb $atom:monomers[195]/C2 $atom:monomers[196]/C1
	- $bond:bb197 @bond:MonomerTypes/bb $atom:monomers[196]/C2 $atom:monomers[197]/C1
	- $bond:bb198 @bond:MonomerTypes/bb $atom:monomers[197]/C2 $atom:monomers[198]/C1
	- $bond:bb199 @bond:MonomerTypes/bb $atom:monomers[198]/C2 $atom:monomers[199]/C1
	- }
	-
	-
	- # These lines of moltemplate script above were generated in python:
	- #
	- # for i in range(0,199):
	- # print('$bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers['
	- # +str(i)+']/C2 $atom:monomers['+str(i+1)+']/C1')
	-
	-
	- # Finally, create a molecule ID number for this large polymer object
	-
	- create_var { $mol }
	-
	-} # Polymer200
	-
	-
	-
	-# Angle, dihedral and improper interactions will be generated
	-# automatically according to the instructions in "monomer.lt"
	diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/system.lt
	deleted file mode 100644
	index 7fced4143..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,44 +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") {
	- 0.0 840.0 xlo xhi
	- 0.0 840.0 ylo yhi
	- 0.0 840.0 zlo zhi
	-}
	-
	-
	-import "polymer.lt"
	-
	-# Create 150 long polymers
	-
	-polymers = new Polymer200.rot(4,0,1,1).move(-360, 0,-360)
	- [15].move(0, 56, 0).rot(96, 0,1,0)
	- [10].move(0, 0, 80)
	-
	-
	-
	-
	-
	-# If you only want one polymer, try this instead:
	-# polymer = new Polymer200
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.npt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.npt
	deleted file mode 100644
	index 8d8b09afd..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.npt
	+++ /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 1.0
	-dump 1 all custom 2000 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 100 # time interval for printing out "thermo" data
	-
	-# ------------------- NPT -----------------------
	-
	-fix fxlan all langevin 500.0 500.0 120 48279
	-fix fxnph all nph iso 900.0 900.0 1000
	-
	-# Temperature = 500 degrees, Pressure = 900 atm
	-
	-run 100000
	diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.nvt
	deleted file mode 100644
	index e58a94675..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.nvt
	+++ /dev/null
	@@ -1,31 +0,0 @@
	-# -- Init Section --
	-
	-include system.in.init
	-
	-# -- Atom Definition Section --
	-
	-#read_data system.data
	-# (You must run the npt simulation first.)
	-read_restart system_after_npt.rst
	-
	-# -- Settings Section --
	-
	-include system.in.settings
	-
	-# -- Run Section --
	-
	-
	-timestep 2.0
	-dump 1 all custom 2000 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 100 # time interval for printing out "thermo" data
	-
	-fix 1 all nvt temp 500.0 500.0 100.0
	-
	-# Temperature = 500 degrees
	-
	-run 100000
	-
	-write_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT
	deleted file mode 100644
	index 3dda0a7c0..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT
	+++ /dev/null
	@@ -1,35 +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)
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh
	deleted file mode 100755
	index acc5fbbaa..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/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/all_atom_examples/nanotube+water/README_visualise.txt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualise.txt
	deleted file mode 100644
	index 206db9903..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualise.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/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index 64f874dce..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,3195 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 2454 !NATOM
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	- 1914 810 3 3 0.423800 1.0080 0
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	- 1917 811 3 3 0.423800 1.0080 0
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	- 1920 812 3 3 0.423800 1.0080 0
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	- 1923 813 3 3 0.423800 1.0080 0
	- 1924 814 2 2 -0.847600 15.9994 0
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	- 1926 814 3 3 0.423800 1.0080 0
	- 1927 815 2 2 -0.847600 15.9994 0
	- 1928 815 3 3 0.423800 1.0080 0
	- 1929 815 3 3 0.423800 1.0080 0
	- 1930 816 2 2 -0.847600 15.9994 0
	- 1931 816 3 3 0.423800 1.0080 0
	- 1932 816 3 3 0.423800 1.0080 0
	- 1933 817 2 2 -0.847600 15.9994 0
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	- 1935 817 3 3 0.423800 1.0080 0
	- 1936 818 2 2 -0.847600 15.9994 0
	- 1937 818 3 3 0.423800 1.0080 0
	- 1938 818 3 3 0.423800 1.0080 0
	- 1939 819 2 2 -0.847600 15.9994 0
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	- 1941 819 3 3 0.423800 1.0080 0
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	- 1944 820 3 3 0.423800 1.0080 0
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	- 2358 958 3 3 0.423800 1.0080 0
	- 2359 959 2 2 -0.847600 15.9994 0
	- 2360 959 3 3 0.423800 1.0080 0
	- 2361 959 3 3 0.423800 1.0080 0
	- 2362 960 2 2 -0.847600 15.9994 0
	- 2363 960 3 3 0.423800 1.0080 0
	- 2364 960 3 3 0.423800 1.0080 0
	- 2365 961 2 2 -0.847600 15.9994 0
	- 2366 961 3 3 0.423800 1.0080 0
	- 2367 961 3 3 0.423800 1.0080 0
	- 2368 962 2 2 -0.847600 15.9994 0
	- 2369 962 3 3 0.423800 1.0080 0
	- 2370 962 3 3 0.423800 1.0080 0
	- 2371 963 2 2 -0.847600 15.9994 0
	- 2372 963 3 3 0.423800 1.0080 0
	- 2373 963 3 3 0.423800 1.0080 0
	- 2374 964 2 2 -0.847600 15.9994 0
	- 2375 964 3 3 0.423800 1.0080 0
	- 2376 964 3 3 0.423800 1.0080 0
	- 2377 965 2 2 -0.847600 15.9994 0
	- 2378 965 3 3 0.423800 1.0080 0
	- 2379 965 3 3 0.423800 1.0080 0
	- 2380 966 2 2 -0.847600 15.9994 0
	- 2381 966 3 3 0.423800 1.0080 0
	- 2382 966 3 3 0.423800 1.0080 0
	- 2383 967 2 2 -0.847600 15.9994 0
	- 2384 967 3 3 0.423800 1.0080 0
	- 2385 967 3 3 0.423800 1.0080 0
	- 2386 968 2 2 -0.847600 15.9994 0
	- 2387 968 3 3 0.423800 1.0080 0
	- 2388 968 3 3 0.423800 1.0080 0
	- 2389 969 2 2 -0.847600 15.9994 0
	- 2390 969 3 3 0.423800 1.0080 0
	- 2391 969 3 3 0.423800 1.0080 0
	- 2392 970 2 2 -0.847600 15.9994 0
	- 2393 970 3 3 0.423800 1.0080 0
	- 2394 970 3 3 0.423800 1.0080 0
	- 2395 971 2 2 -0.847600 15.9994 0
	- 2396 971 3 3 0.423800 1.0080 0
	- 2397 971 3 3 0.423800 1.0080 0
	- 2398 972 2 2 -0.847600 15.9994 0
	- 2399 972 3 3 0.423800 1.0080 0
	- 2400 972 3 3 0.423800 1.0080 0
	- 2401 973 2 2 -0.847600 15.9994 0
	- 2402 973 3 3 0.423800 1.0080 0
	- 2403 973 3 3 0.423800 1.0080 0
	- 2404 974 2 2 -0.847600 15.9994 0
	- 2405 974 3 3 0.423800 1.0080 0
	- 2406 974 3 3 0.423800 1.0080 0
	- 2407 975 2 2 -0.847600 15.9994 0
	- 2408 975 3 3 0.423800 1.0080 0
	- 2409 975 3 3 0.423800 1.0080 0
	- 2410 976 2 2 -0.847600 15.9994 0
	- 2411 976 3 3 0.423800 1.0080 0
	- 2412 976 3 3 0.423800 1.0080 0
	- 2413 977 2 2 -0.847600 15.9994 0
	- 2414 977 3 3 0.423800 1.0080 0
	- 2415 977 3 3 0.423800 1.0080 0
	- 2416 978 2 2 -0.847600 15.9994 0
	- 2417 978 3 3 0.423800 1.0080 0
	- 2418 978 3 3 0.423800 1.0080 0
	- 2419 979 2 2 -0.847600 15.9994 0
	- 2420 979 3 3 0.423800 1.0080 0
	- 2421 979 3 3 0.423800 1.0080 0
	- 2422 980 2 2 -0.847600 15.9994 0
	- 2423 980 3 3 0.423800 1.0080 0
	- 2424 980 3 3 0.423800 1.0080 0
	- 2425 981 2 2 -0.847600 15.9994 0
	- 2426 981 3 3 0.423800 1.0080 0
	- 2427 981 3 3 0.423800 1.0080 0
	- 2428 982 2 2 -0.847600 15.9994 0
	- 2429 982 3 3 0.423800 1.0080 0
	- 2430 982 3 3 0.423800 1.0080 0
	- 2431 983 2 2 -0.847600 15.9994 0
	- 2432 983 3 3 0.423800 1.0080 0
	- 2433 983 3 3 0.423800 1.0080 0
	- 2434 984 2 2 -0.847600 15.9994 0
	- 2435 984 3 3 0.423800 1.0080 0
	- 2436 984 3 3 0.423800 1.0080 0
	- 2437 985 2 2 -0.847600 15.9994 0
	- 2438 985 3 3 0.423800 1.0080 0
	- 2439 985 3 3 0.423800 1.0080 0
	- 2440 986 2 2 -0.847600 15.9994 0
	- 2441 986 3 3 0.423800 1.0080 0
	- 2442 986 3 3 0.423800 1.0080 0
	- 2443 987 2 2 -0.847600 15.9994 0
	- 2444 987 3 3 0.423800 1.0080 0
	- 2445 987 3 3 0.423800 1.0080 0
	- 2446 988 2 2 -0.847600 15.9994 0
	- 2447 988 3 3 0.423800 1.0080 0
	- 2448 988 3 3 0.423800 1.0080 0
	- 2449 989 2 2 -0.847600 15.9994 0
	- 2450 989 3 3 0.423800 1.0080 0
	- 2451 989 3 3 0.423800 1.0080 0
	- 2452 990 2 2 -0.847600 15.9994 0
	- 2453 990 3 3 0.423800 1.0080 0
	- 2454 990 3 3 0.423800 1.0080 0
	-
	- 972 !NBOND: bonds
	- 997 998 997 999 1000 1001 1000 1002
	- 1003 1004 1003 1005 1006 1007 1006 1008
	- 1009 1010 1009 1011 1012 1013 1012 1014
	- 1015 1016 1015 1017 1018 1019 1018 1020
	- 1021 1022 1021 1023 1024 1025 1024 1026
	- 1027 1028 1027 1029 1030 1031 1030 1032
	- 1033 1034 1033 1035 1036 1037 1036 1038
	- 1039 1040 1039 1041 1042 1043 1042 1044
	- 1045 1046 1045 1047 1048 1049 1048 1050
	- 1051 1052 1051 1053 1054 1055 1054 1056
	- 1057 1058 1057 1059 1060 1061 1060 1062
	- 1063 1064 1063 1065 1066 1067 1066 1068
	- 1069 1070 1069 1071 1072 1073 1072 1074
	- 1075 1076 1075 1077 1078 1079 1078 1080
	- 1081 1082 1081 1083 1084 1085 1084 1086
	- 1087 1088 1087 1089 1090 1091 1090 1092
	- 1093 1094 1093 1095 1096 1097 1096 1098
	- 1099 1100 1099 1101 1102 1103 1102 1104
	- 1105 1106 1105 1107 1108 1109 1108 1110
	- 1111 1112 1111 1113 1114 1115 1114 1116
	- 1117 1118 1117 1119 1120 1121 1120 1122
	- 1123 1124 1123 1125 1126 1127 1126 1128
	- 1129 1130 1129 1131 1132 1133 1132 1134
	- 1135 1136 1135 1137 1138 1139 1138 1140
	- 1141 1142 1141 1143 1144 1145 1144 1146
	- 1147 1148 1147 1149 1150 1151 1150 1152
	- 1153 1154 1153 1155 1156 1157 1156 1158
	- 1159 1160 1159 1161 1162 1163 1162 1164
	- 1165 1166 1165 1167 1168 1169 1168 1170
	- 1171 1172 1171 1173 1174 1175 1174 1176
	- 1177 1178 1177 1179 1180 1181 1180 1182
	- 1183 1184 1183 1185 1186 1187 1186 1188
	- 1189 1190 1189 1191 1192 1193 1192 1194
	- 1195 1196 1195 1197 1198 1199 1198 1200
	- 1201 1202 1201 1203 1204 1205 1204 1206
	- 1207 1208 1207 1209 1210 1211 1210 1212
	- 1213 1214 1213 1215 1216 1217 1216 1218
	- 1219 1220 1219 1221 1222 1223 1222 1224
	- 1225 1226 1225 1227 1228 1229 1228 1230
	- 1231 1232 1231 1233 1234 1235 1234 1236
	- 1237 1238 1237 1239 1240 1241 1240 1242
	- 1243 1244 1243 1245 1246 1247 1246 1248
	- 1249 1250 1249 1251 1252 1253 1252 1254
	- 1255 1256 1255 1257 1258 1259 1258 1260
	- 1261 1262 1261 1263 1264 1265 1264 1266
	- 1267 1268 1267 1269 1270 1271 1270 1272
	- 1273 1274 1273 1275 1276 1277 1276 1278
	- 1279 1280 1279 1281 1282 1283 1282 1284
	- 1285 1286 1285 1287 1288 1289 1288 1290
	- 1291 1292 1291 1293 1294 1295 1294 1296
	- 1297 1298 1297 1299 1300 1301 1300 1302
	- 1303 1304 1303 1305 1306 1307 1306 1308
	- 1309 1310 1309 1311 1312 1313 1312 1314
	- 1315 1316 1315 1317 1318 1319 1318 1320
	- 1321 1322 1321 1323 1324 1325 1324 1326
	- 1327 1328 1327 1329 1330 1331 1330 1332
	- 1333 1334 1333 1335 1336 1337 1336 1338
	- 1339 1340 1339 1341 1342 1343 1342 1344
	- 1345 1346 1345 1347 1348 1349 1348 1350
	- 1351 1352 1351 1353 1354 1355 1354 1356
	- 1357 1358 1357 1359 1360 1361 1360 1362
	- 1363 1364 1363 1365 1366 1367 1366 1368
	- 1369 1370 1369 1371 1372 1373 1372 1374
	- 1375 1376 1375 1377 1378 1379 1378 1380
	- 1381 1382 1381 1383 1384 1385 1384 1386
	- 1387 1388 1387 1389 1390 1391 1390 1392
	- 1393 1394 1393 1395 1396 1397 1396 1398
	- 1399 1400 1399 1401 1402 1403 1402 1404
	- 1405 1406 1405 1407 1408 1409 1408 1410
	- 1411 1412 1411 1413 1414 1415 1414 1416
	- 1417 1418 1417 1419 1420 1421 1420 1422
	- 1423 1424 1423 1425 1426 1427 1426 1428
	- 1429 1430 1429 1431 1432 1433 1432 1434
	- 1435 1436 1435 1437 1438 1439 1438 1440
	- 1441 1442 1441 1443 1444 1445 1444 1446
	- 1447 1448 1447 1449 1450 1451 1450 1452
	- 1453 1454 1453 1455 1456 1457 1456 1458
	- 1459 1460 1459 1461 1462 1463 1462 1464
	- 1465 1466 1465 1467 1468 1469 1468 1470
	- 1471 1472 1471 1473 1474 1475 1474 1476
	- 1477 1478 1477 1479 1480 1481 1480 1482
	- 1483 1484 1483 1485 1486 1487 1486 1488
	- 1489 1490 1489 1491 1492 1493 1492 1494
	- 1495 1496 1495 1497 1498 1499 1498 1500
	- 1501 1502 1501 1503 1504 1505 1504 1506
	- 1507 1508 1507 1509 1510 1511 1510 1512
	- 1513 1514 1513 1515 1516 1517 1516 1518
	- 1519 1520 1519 1521 1522 1523 1522 1524
	- 1525 1526 1525 1527 1528 1529 1528 1530
	- 1531 1532 1531 1533 1534 1535 1534 1536
	- 1537 1538 1537 1539 1540 1541 1540 1542
	- 1543 1544 1543 1545 1546 1547 1546 1548
	- 1549 1550 1549 1551 1552 1553 1552 1554
	- 1555 1556 1555 1557 1558 1559 1558 1560
	- 1561 1562 1561 1563 1564 1565 1564 1566
	- 1567 1568 1567 1569 1570 1571 1570 1572
	- 1573 1574 1573 1575 1576 1577 1576 1578
	- 1579 1580 1579 1581 1582 1583 1582 1584
	- 1585 1586 1585 1587 1588 1589 1588 1590
	- 1591 1592 1591 1593 1594 1595 1594 1596
	- 1597 1598 1597 1599 1600 1601 1600 1602
	- 1603 1604 1603 1605 1606 1607 1606 1608
	- 1609 1610 1609 1611 1612 1613 1612 1614
	- 1615 1616 1615 1617 1618 1619 1618 1620
	- 1621 1622 1621 1623 1624 1625 1624 1626
	- 1627 1628 1627 1629 1630 1631 1630 1632
	- 1633 1634 1633 1635 1636 1637 1636 1638
	- 1639 1640 1639 1641 1642 1643 1642 1644
	- 1645 1646 1645 1647 1648 1649 1648 1650
	- 1651 1652 1651 1653 1654 1655 1654 1656
	- 1657 1658 1657 1659 1660 1661 1660 1662
	- 1663 1664 1663 1665 1666 1667 1666 1668
	- 1669 1670 1669 1671 1672 1673 1672 1674
	- 1675 1676 1675 1677 1678 1679 1678 1680
	- 1681 1682 1681 1683 1684 1685 1684 1686
	- 1687 1688 1687 1689 1690 1691 1690 1692
	- 1693 1694 1693 1695 1696 1697 1696 1698
	- 1699 1700 1699 1701 1702 1703 1702 1704
	- 1705 1706 1705 1707 1708 1709 1708 1710
	- 1711 1712 1711 1713 1714 1715 1714 1716
	- 1717 1718 1717 1719 1720 1721 1720 1722
	- 1723 1724 1723 1725 1726 1727 1726 1728
	- 1729 1730 1729 1731 1732 1733 1732 1734
	- 1735 1736 1735 1737 1738 1739 1738 1740
	- 1741 1742 1741 1743 1744 1745 1744 1746
	- 1747 1748 1747 1749 1750 1751 1750 1752
	- 1753 1754 1753 1755 1756 1757 1756 1758
	- 1759 1760 1759 1761 1762 1763 1762 1764
	- 1765 1766 1765 1767 1768 1769 1768 1770
	- 1771 1772 1771 1773 1774 1775 1774 1776
	- 1777 1778 1777 1779 1780 1781 1780 1782
	- 1783 1784 1783 1785 1786 1787 1786 1788
	- 1789 1790 1789 1791 1792 1793 1792 1794
	- 1795 1796 1795 1797 1798 1799 1798 1800
	- 1801 1802 1801 1803 1804 1805 1804 1806
	- 1807 1808 1807 1809 1810 1811 1810 1812
	- 1813 1814 1813 1815 1816 1817 1816 1818
	- 1819 1820 1819 1821 1822 1823 1822 1824
	- 1825 1826 1825 1827 1828 1829 1828 1830
	- 1831 1832 1831 1833 1834 1835 1834 1836
	- 1837 1838 1837 1839 1840 1841 1840 1842
	- 1843 1844 1843 1845 1846 1847 1846 1848
	- 1849 1850 1849 1851 1852 1853 1852 1854
	- 1855 1856 1855 1857 1858 1859 1858 1860
	- 1861 1862 1861 1863 1864 1865 1864 1866
	- 1867 1868 1867 1869 1870 1871 1870 1872
	- 1873 1874 1873 1875 1876 1877 1876 1878
	- 1879 1880 1879 1881 1882 1883 1882 1884
	- 1885 1886 1885 1887 1888 1889 1888 1890
	- 1891 1892 1891 1893 1894 1895 1894 1896
	- 1897 1898 1897 1899 1900 1901 1900 1902
	- 1903 1904 1903 1905 1906 1907 1906 1908
	- 1909 1910 1909 1911 1912 1913 1912 1914
	- 1915 1916 1915 1917 1918 1919 1918 1920
	- 1921 1922 1921 1923 1924 1925 1924 1926
	- 1927 1928 1927 1929 1930 1931 1930 1932
	- 1933 1934 1933 1935 1936 1937 1936 1938
	- 1939 1940 1939 1941 1942 1943 1942 1944
	- 1945 1946 1945 1947 1948 1949 1948 1950
	- 1951 1952 1951 1953 1954 1955 1954 1956
	- 1957 1958 1957 1959 1960 1961 1960 1962
	- 1963 1964 1963 1965 1966 1967 1966 1968
	- 1969 1970 1969 1971 1972 1973 1972 1974
	- 1975 1976 1975 1977 1978 1979 1978 1980
	- 1981 1982 1981 1983 1984 1985 1984 1986
	- 1987 1988 1987 1989 1990 1991 1990 1992
	- 1993 1994 1993 1995 1996 1997 1996 1998
	- 1999 2000 1999 2001 2002 2003 2002 2004
	- 2005 2006 2005 2007 2008 2009 2008 2010
	- 2011 2012 2011 2013 2014 2015 2014 2016
	- 2017 2018 2017 2019 2020 2021 2020 2022
	- 2023 2024 2023 2025 2026 2027 2026 2028
	- 2029 2030 2029 2031 2032 2033 2032 2034
	- 2035 2036 2035 2037 2038 2039 2038 2040
	- 2041 2042 2041 2043 2044 2045 2044 2046
	- 2047 2048 2047 2049 2050 2051 2050 2052
	- 2053 2054 2053 2055 2056 2057 2056 2058
	- 2059 2060 2059 2061 2062 2063 2062 2064
	- 2065 2066 2065 2067 2068 2069 2068 2070
	- 2071 2072 2071 2073 2074 2075 2074 2076
	- 2077 2078 2077 2079 2080 2081 2080 2082
	- 2083 2084 2083 2085 2086 2087 2086 2088
	- 2089 2090 2089 2091 2092 2093 2092 2094
	- 2095 2096 2095 2097 2098 2099 2098 2100
	- 2101 2102 2101 2103 2104 2105 2104 2106
	- 2107 2108 2107 2109 2110 2111 2110 2112
	- 2113 2114 2113 2115 2116 2117 2116 2118
	- 2119 2120 2119 2121 2122 2123 2122 2124
	- 2125 2126 2125 2127 2128 2129 2128 2130
	- 2131 2132 2131 2133 2134 2135 2134 2136
	- 2137 2138 2137 2139 2140 2141 2140 2142
	- 2143 2144 2143 2145 2146 2147 2146 2148
	- 2149 2150 2149 2151 2152 2153 2152 2154
	- 2155 2156 2155 2157 2158 2159 2158 2160
	- 2161 2162 2161 2163 2164 2165 2164 2166
	- 2167 2168 2167 2169 2170 2171 2170 2172
	- 2173 2174 2173 2175 2176 2177 2176 2178
	- 2179 2180 2179 2181 2182 2183 2182 2184
	- 2185 2186 2185 2187 2188 2189 2188 2190
	- 2191 2192 2191 2193 2194 2195 2194 2196
	- 2197 2198 2197 2199 2200 2201 2200 2202
	- 2203 2204 2203 2205 2206 2207 2206 2208
	- 2209 2210 2209 2211 2212 2213 2212 2214
	- 2215 2216 2215 2217 2218 2219 2218 2220
	- 2221 2222 2221 2223 2224 2225 2224 2226
	- 2227 2228 2227 2229 2230 2231 2230 2232
	- 2233 2234 2233 2235 2236 2237 2236 2238
	- 2239 2240 2239 2241 2242 2243 2242 2244
	- 2245 2246 2245 2247 2248 2249 2248 2250
	- 2251 2252 2251 2253 2254 2255 2254 2256
	- 2257 2258 2257 2259 2260 2261 2260 2262
	- 2263 2264 2263 2265 2266 2267 2266 2268
	- 2269 2270 2269 2271 2272 2273 2272 2274
	- 2275 2276 2275 2277 2278 2279 2278 2280
	- 2281 2282 2281 2283 2284 2285 2284 2286
	- 2287 2288 2287 2289 2290 2291 2290 2292
	- 2293 2294 2293 2295 2296 2297 2296 2298
	- 2299 2300 2299 2301 2302 2303 2302 2304
	- 2305 2306 2305 2307 2308 2309 2308 2310
	- 2311 2312 2311 2313 2314 2315 2314 2316
	- 2317 2318 2317 2319 2320 2321 2320 2322
	- 2323 2324 2323 2325 2326 2327 2326 2328
	- 2329 2330 2329 2331 2332 2333 2332 2334
	- 2335 2336 2335 2337 2338 2339 2338 2340
	- 2341 2342 2341 2343 2344 2345 2344 2346
	- 2347 2348 2347 2349 2350 2351 2350 2352
	- 2353 2354 2353 2355 2356 2357 2356 2358
	- 2359 2360 2359 2361 2362 2363 2362 2364
	- 2365 2366 2365 2367 2368 2369 2368 2370
	- 2371 2372 2371 2373 2374 2375 2374 2376
	- 2377 2378 2377 2379 2380 2381 2380 2382
	- 2383 2384 2383 2385 2386 2387 2386 2388
	- 2389 2390 2389 2391 2392 2393 2392 2394
	- 2395 2396 2395 2397 2398 2399 2398 2400
	- 2401 2402 2401 2403 2404 2405 2404 2406
	- 2407 2408 2407 2409 2410 2411 2410 2412
	- 2413 2414 2413 2415 2416 2417 2416 2418
	- 2419 2420 2419 2421 2422 2423 2422 2424
	- 2425 2426 2425 2427 2428 2429 2428 2430
	- 2431 2432 2431 2433 2434 2435 2434 2436
	- 2437 2438 2437 2439 2440 2441 2440 2442
	- 2443 2444 2443 2445 2446 2447 2446 2448
	- 2449 2450 2449 2451 2452 2453 2452 2454
	-
	- 486 !NTHETA: angles
	- 998 997 999 1001 1000 1002 1004 1003 1005
	- 1007 1006 1008 1010 1009 1011 1013 1012 1014
	- 1016 1015 1017 1019 1018 1020 1022 1021 1023
	- 1025 1024 1026 1028 1027 1029 1031 1030 1032
	- 1034 1033 1035 1037 1036 1038 1040 1039 1041
	- 1043 1042 1044 1046 1045 1047 1049 1048 1050
	- 1052 1051 1053 1055 1054 1056 1058 1057 1059
	- 1061 1060 1062 1064 1063 1065 1067 1066 1068
	- 1070 1069 1071 1073 1072 1074 1076 1075 1077
	- 1079 1078 1080 1082 1081 1083 1085 1084 1086
	- 1088 1087 1089 1091 1090 1092 1094 1093 1095
	- 1097 1096 1098 1100 1099 1101 1103 1102 1104
	- 1106 1105 1107 1109 1108 1110 1112 1111 1113
	- 1115 1114 1116 1118 1117 1119 1121 1120 1122
	- 1124 1123 1125 1127 1126 1128 1130 1129 1131
	- 1133 1132 1134 1136 1135 1137 1139 1138 1140
	- 1142 1141 1143 1145 1144 1146 1148 1147 1149
	- 1151 1150 1152 1154 1153 1155 1157 1156 1158
	- 1160 1159 1161 1163 1162 1164 1166 1165 1167
	- 1169 1168 1170 1172 1171 1173 1175 1174 1176
	- 1178 1177 1179 1181 1180 1182 1184 1183 1185
	- 1187 1186 1188 1190 1189 1191 1193 1192 1194
	- 1196 1195 1197 1199 1198 1200 1202 1201 1203
	- 1205 1204 1206 1208 1207 1209 1211 1210 1212
	- 1214 1213 1215 1217 1216 1218 1220 1219 1221
	- 1223 1222 1224 1226 1225 1227 1229 1228 1230
	- 1232 1231 1233 1235 1234 1236 1238 1237 1239
	- 1241 1240 1242 1244 1243 1245 1247 1246 1248
	- 1250 1249 1251 1253 1252 1254 1256 1255 1257
	- 1259 1258 1260 1262 1261 1263 1265 1264 1266
	- 1268 1267 1269 1271 1270 1272 1274 1273 1275
	- 1277 1276 1278 1280 1279 1281 1283 1282 1284
	- 1286 1285 1287 1289 1288 1290 1292 1291 1293
	- 1295 1294 1296 1298 1297 1299 1301 1300 1302
	- 1304 1303 1305 1307 1306 1308 1310 1309 1311
	- 1313 1312 1314 1316 1315 1317 1319 1318 1320
	- 1322 1321 1323 1325 1324 1326 1328 1327 1329
	- 1331 1330 1332 1334 1333 1335 1337 1336 1338
	- 1340 1339 1341 1343 1342 1344 1346 1345 1347
	- 1349 1348 1350 1352 1351 1353 1355 1354 1356
	- 1358 1357 1359 1361 1360 1362 1364 1363 1365
	- 1367 1366 1368 1370 1369 1371 1373 1372 1374
	- 1376 1375 1377 1379 1378 1380 1382 1381 1383
	- 1385 1384 1386 1388 1387 1389 1391 1390 1392
	- 1394 1393 1395 1397 1396 1398 1400 1399 1401
	- 1403 1402 1404 1406 1405 1407 1409 1408 1410
	- 1412 1411 1413 1415 1414 1416 1418 1417 1419
	- 1421 1420 1422 1424 1423 1425 1427 1426 1428
	- 1430 1429 1431 1433 1432 1434 1436 1435 1437
	- 1439 1438 1440 1442 1441 1443 1445 1444 1446
	- 1448 1447 1449 1451 1450 1452 1454 1453 1455
	- 1457 1456 1458 1460 1459 1461 1463 1462 1464
	- 1466 1465 1467 1469 1468 1470 1472 1471 1473
	- 1475 1474 1476 1478 1477 1479 1481 1480 1482
	- 1484 1483 1485 1487 1486 1488 1490 1489 1491
	- 1493 1492 1494 1496 1495 1497 1499 1498 1500
	- 1502 1501 1503 1505 1504 1506 1508 1507 1509
	- 1511 1510 1512 1514 1513 1515 1517 1516 1518
	- 1520 1519 1521 1523 1522 1524 1526 1525 1527
	- 1529 1528 1530 1532 1531 1533 1535 1534 1536
	- 1538 1537 1539 1541 1540 1542 1544 1543 1545
	- 1547 1546 1548 1550 1549 1551 1553 1552 1554
	- 1556 1555 1557 1559 1558 1560 1562 1561 1563
	- 1565 1564 1566 1568 1567 1569 1571 1570 1572
	- 1574 1573 1575 1577 1576 1578 1580 1579 1581
	- 1583 1582 1584 1586 1585 1587 1589 1588 1590
	- 1592 1591 1593 1595 1594 1596 1598 1597 1599
	- 1601 1600 1602 1604 1603 1605 1607 1606 1608
	- 1610 1609 1611 1613 1612 1614 1616 1615 1617
	- 1619 1618 1620 1622 1621 1623 1625 1624 1626
	- 1628 1627 1629 1631 1630 1632 1634 1633 1635
	- 1637 1636 1638 1640 1639 1641 1643 1642 1644
	- 1646 1645 1647 1649 1648 1650 1652 1651 1653
	- 1655 1654 1656 1658 1657 1659 1661 1660 1662
	- 1664 1663 1665 1667 1666 1668 1670 1669 1671
	- 1673 1672 1674 1676 1675 1677 1679 1678 1680
	- 1682 1681 1683 1685 1684 1686 1688 1687 1689
	- 1691 1690 1692 1694 1693 1695 1697 1696 1698
	- 1700 1699 1701 1703 1702 1704 1706 1705 1707
	- 1709 1708 1710 1712 1711 1713 1715 1714 1716
	- 1718 1717 1719 1721 1720 1722 1724 1723 1725
	- 1727 1726 1728 1730 1729 1731 1733 1732 1734
	- 1736 1735 1737 1739 1738 1740 1742 1741 1743
	- 1745 1744 1746 1748 1747 1749 1751 1750 1752
	- 1754 1753 1755 1757 1756 1758 1760 1759 1761
	- 1763 1762 1764 1766 1765 1767 1769 1768 1770
	- 1772 1771 1773 1775 1774 1776 1778 1777 1779
	- 1781 1780 1782 1784 1783 1785 1787 1786 1788
	- 1790 1789 1791 1793 1792 1794 1796 1795 1797
	- 1799 1798 1800 1802 1801 1803 1805 1804 1806
	- 1808 1807 1809 1811 1810 1812 1814 1813 1815
	- 1817 1816 1818 1820 1819 1821 1823 1822 1824
	- 1826 1825 1827 1829 1828 1830 1832 1831 1833
	- 1835 1834 1836 1838 1837 1839 1841 1840 1842
	- 1844 1843 1845 1847 1846 1848 1850 1849 1851
	- 1853 1852 1854 1856 1855 1857 1859 1858 1860
	- 1862 1861 1863 1865 1864 1866 1868 1867 1869
	- 1871 1870 1872 1874 1873 1875 1877 1876 1878
	- 1880 1879 1881 1883 1882 1884 1886 1885 1887
	- 1889 1888 1890 1892 1891 1893 1895 1894 1896
	- 1898 1897 1899 1901 1900 1902 1904 1903 1905
	- 1907 1906 1908 1910 1909 1911 1913 1912 1914
	- 1916 1915 1917 1919 1918 1920 1922 1921 1923
	- 1925 1924 1926 1928 1927 1929 1931 1930 1932
	- 1934 1933 1935 1937 1936 1938 1940 1939 1941
	- 1943 1942 1944 1946 1945 1947 1949 1948 1950
	- 1952 1951 1953 1955 1954 1956 1958 1957 1959
	- 1961 1960 1962 1964 1963 1965 1967 1966 1968
	- 1970 1969 1971 1973 1972 1974 1976 1975 1977
	- 1979 1978 1980 1982 1981 1983 1985 1984 1986
	- 1988 1987 1989 1991 1990 1992 1994 1993 1995
	- 1997 1996 1998 2000 1999 2001 2003 2002 2004
	- 2006 2005 2007 2009 2008 2010 2012 2011 2013
	- 2015 2014 2016 2018 2017 2019 2021 2020 2022
	- 2024 2023 2025 2027 2026 2028 2030 2029 2031
	- 2033 2032 2034 2036 2035 2037 2039 2038 2040
	- 2042 2041 2043 2045 2044 2046 2048 2047 2049
	- 2051 2050 2052 2054 2053 2055 2057 2056 2058
	- 2060 2059 2061 2063 2062 2064 2066 2065 2067
	- 2069 2068 2070 2072 2071 2073 2075 2074 2076
	- 2078 2077 2079 2081 2080 2082 2084 2083 2085
	- 2087 2086 2088 2090 2089 2091 2093 2092 2094
	- 2096 2095 2097 2099 2098 2100 2102 2101 2103
	- 2105 2104 2106 2108 2107 2109 2111 2110 2112
	- 2114 2113 2115 2117 2116 2118 2120 2119 2121
	- 2123 2122 2124 2126 2125 2127 2129 2128 2130
	- 2132 2131 2133 2135 2134 2136 2138 2137 2139
	- 2141 2140 2142 2144 2143 2145 2147 2146 2148
	- 2150 2149 2151 2153 2152 2154 2156 2155 2157
	- 2159 2158 2160 2162 2161 2163 2165 2164 2166
	- 2168 2167 2169 2171 2170 2172 2174 2173 2175
	- 2177 2176 2178 2180 2179 2181 2183 2182 2184
	- 2186 2185 2187 2189 2188 2190 2192 2191 2193
	- 2195 2194 2196 2198 2197 2199 2201 2200 2202
	- 2204 2203 2205 2207 2206 2208 2210 2209 2211
	- 2213 2212 2214 2216 2215 2217 2219 2218 2220
	- 2222 2221 2223 2225 2224 2226 2228 2227 2229
	- 2231 2230 2232 2234 2233 2235 2237 2236 2238
	- 2240 2239 2241 2243 2242 2244 2246 2245 2247
	- 2249 2248 2250 2252 2251 2253 2255 2254 2256
	- 2258 2257 2259 2261 2260 2262 2264 2263 2265
	- 2267 2266 2268 2270 2269 2271 2273 2272 2274
	- 2276 2275 2277 2279 2278 2280 2282 2281 2283
	- 2285 2284 2286 2288 2287 2289 2291 2290 2292
	- 2294 2293 2295 2297 2296 2298 2300 2299 2301
	- 2303 2302 2304 2306 2305 2307 2309 2308 2310
	- 2312 2311 2313 2315 2314 2316 2318 2317 2319
	- 2321 2320 2322 2324 2323 2325 2327 2326 2328
	- 2330 2329 2331 2333 2332 2334 2336 2335 2337
	- 2339 2338 2340 2342 2341 2343 2345 2344 2346
	- 2348 2347 2349 2351 2350 2352 2354 2353 2355
	- 2357 2356 2358 2360 2359 2361 2363 2362 2364
	- 2366 2365 2367 2369 2368 2370 2372 2371 2373
	- 2375 2374 2376 2378 2377 2379 2381 2380 2382
	- 2384 2383 2385 2387 2386 2388 2390 2389 2391
	- 2393 2392 2394 2396 2395 2397 2399 2398 2400
	- 2402 2401 2403 2405 2404 2406 2408 2407 2409
	- 2411 2410 2412 2414 2413 2415 2417 2416 2418
	- 2420 2419 2421 2423 2422 2424 2426 2425 2427
	- 2429 2428 2430 2432 2431 2433 2435 2434 2436
	- 2438 2437 2439 2441 2440 2442 2444 2443 2445
	- 2447 2446 2448 2450 2449 2451 2453 2452 2454
	-
	- 0 !NPHI: dihedrals
	-
	-
	- 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
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 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/all_atom_examples/nanotube+water/images/graphene_unit_cell.jpg b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/graphene_unit_cell.jpg
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	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh
	deleted file mode 100644
	index 8b16c87e3..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh
	+++ /dev/null
	@@ -1,27 +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 "common" directory.
	-# Set MOLTEMPLATE_PATH to point to the "common" directory.
	-#
	-# -----------------------------------------------------------
	-#
	-# To run moltemplate, use:
	-
	-moltemplate.sh system.lt
	-
	-# This will generate:system.data, system.in, system.in.init, system.in.settings
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
	deleted file mode 100644
	index 6a177c59f..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-# You can use the definitions in this file to
	-# create graphene, graphite, or nanotubes.
	-
	-
	-
	-Graphene {
	-
	- 2AtomCellAlignX {
	-
	- # The 2AtomCellAlignX "molecule" is a minimal basis cell
	- # for any hexagonal arrangement of atoms in 2-dimensions.
	- # The distance between these two atoms is equal to "l", where "l" is
	- # the length of each side of a hexegon, which I set to 1.420 Angstroms.
	- #
	- # l = length of each hexagonal side = 1.42 Angstroms
	- # L = length of each hexagon = 2*l = 2.84 Angstroms
	- # W = width of each hexagon = 2lsqrt(3)/2 = 2.4595121467478056 Angstroms
	- #
	- # The Lattice-cell vectors for graphene (graphite) are
	- # (2.4595121467478, 0, 0) (aligned with X axis)
	- # (1.2297560733739, 2.13, 0) (2.13 = 1.5*l)
	- # ( 0 1.00, 3.35) (3.35 = distance between layers of
	- # graphene sheets in graphite.)
	-
	-
	- # 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
	- }
	-
	- } # 2AtomCellAlignX
	-
	-
	-
	-
	- # Notice that the two atoms in the unit-cell above lie in the XY plane.
	- # (Their z-coord is zero). It's also handy to have a version of this
	- # object which lies in the XZ plan, so we make this below.
	-
	- 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0)
	-
	-
	-
	-
	- # Define properties of the Carbon-Hydrogen graphene atom
	- write_once("Data Masses") {
	- @atom:C 12.0
	- }
	-
	- write_once("In Init") {
	- pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
	- }
	-
	- write_once("In Settings") {
	- # Define a group consisting of only carbon atoms in graphene molecules
	- group Cgraphene type @atom:C
	-
	- # i j epsilon sigma
	- pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 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)
	- }
	-
	-} # Graphene
	-
	-
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt
	deleted file mode 100644
	index 25aa34103..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt
	+++ /dev/null
	@@ -1,34 +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 = 2lsqrt(3)/2 = 2.4595121467478 Angstroms
	-
	-Wall {
	- unitcells = new Graphene/2AtomCellAlignX [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)
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
	deleted file mode 100644
	index 2b982b341..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
	+++ /dev/null
	@@ -1,26 +0,0 @@
	-import "graphene.lt"
	-
	-# ------------------ nanotube ---------------
	-
	-# Now use this to build a simple ("zigzag") nanotube where the long-axis of
	-# each hexagon (of length L=2*l), 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 satisfies Rtan((2pi)/(4*N)) = W/4
	-# --> R = (W/4) / tan((2pi)/(4N)) = 5.457193512764 Angstroms (when N=14)
	-#
	-# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms.
	-
	-
	-nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0)
	- [14].rot(25.7142857,0,0,1) # = 360.0/14
	- [12].rot(12.8571429,0,0,1).move(0, 0, 2.13)
	-
	- # Note: The length is 12 hexegons, the circumference
	- # is 14 hexegons, and 2.13 Angstroms is the distance
	- # between nearest carbon neighbors multiplied by 1.5.
	-
	-# Move it to the location of the graphene sheet with the hole in it
	-
	-nanotube[][].move(0, 0, 33.42)
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt
	deleted file mode 100644
	index 3bb7bca40..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/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 200.0 1.0
	- angle_coeff @angle:HOH harmonic 200.0 109.47
	- 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/all_atom_examples/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt
	deleted file mode 100644
	index ea1fdfe48..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,37 +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
	- 0.0 80.00 zlo zhi
	-}
	-
	-# ---------------------------------------------
	-
	-
	-
	-write_once("In Init") {
	- # -- override any earlier pair_style settings: --
	- pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 &
	- lj/charmm/coul/charmm 9.0 10.0
	-}
	-
	-
	-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/charmm/coul/long 0.114 3.28
	- pair_coeff @atom:Graphene/C @atom:SPCE/H lj/charmm/coul/long 0.0 3.28
	-}
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt
	deleted file mode 100644
	index 73553da11..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt
	+++ /dev/null
	@@ -1,19 +0,0 @@
	-import "spce.lt"
	-
	-# --------------- water ------------------
	-
	-# Create a rectangular box of water
	-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/all_atom_examples/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
	deleted file mode 100644
	index ff9fe17cc..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-# 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 -------------------------------
	-
	-
	-timestep 1.0
	-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 1000 # time interval for printing out "thermo" data
	-
	-
	-velocity Cgraphene zero angular
	-velocity Cgraphene zero linear
	-# (I'm not sure if the two lines above are necessary, but they don't hurt.)
	-
	-# This next line is somewhat controversial. Feel free to delete this next line
	-
	-fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off
	-
	-#(Neither Trung or Steve Plimpton use fix rigid for immobilizing objects, but
	-# I noticed that at NPT, it does a better job of maintaining the correct volume)
	-
	-# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the
	-# forces between immobilized atoms.
	-neigh_modify exclude group Cgraphene Cgraphene
	-
	-
	-# ------------------- NPT -----------------------
	-
	-# Only the Cgraphene atoms are immobile.
	-
	-group mobile subtract all Cgraphene
	-
	-# The next two lines recalculate the temperature
	-# using only the mobile degrees of freedom:
	-
	-compute tempMobile mobile temp
	-compute pressMobile all pressure tempMobile
	-
	-thermo_style custom step c_tempMobile c_pressMobile temp press vol
	-
	-# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction
	-
	-fix fMoveStuff mobile npt temp 300 300 100 z 100 100 1000.0 dilate mobile
	-
	-fix_modify fMoveStuff temp tempMobile
	-
	-run 100000
	-
	-write_restart system_after_npt.rst
	diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
	deleted file mode 100644
	index d4c767869..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-# ----------------------------- Initialization Section --------------------
	-
	-include system.in.init
	-
	-# ----------------------------- Atom Definition Section -------------------
	-
	-read_data system.data
	-
	-# ----------------------------- Settings Section --------------------------
	-
	-include system.in.settings
	-
	-# ----------------------------- Run Section -------------------------------
	-
	-timestep 1.0
	-dump 1 all custom 2500 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 2500 # 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 Cgraphene Cgraphene
	-
	-# Only the Cgraphene atoms are immobile.
	-group mobile subtract all Cgraphene
	-
	-# The next two lines recalculate the temperature
	-# using only the mobile degrees of freedom:
	-
	-compute tempMobile mobile temp
	-compute pressMobile all pressure tempMobile
	-
	-# Integrate the equations of motion:
	-fix fMoveStuff mobile nvt temp 300.0 300.0 100.0
	-fix_modify fMoveStuff temp tempMobile
	-
	-# Alternately, here's how to use fix langevin
	-# fix fMoveStuff mobile nve
	-# fix fLangevin mobile langevin 300.0 300.0 120 48279
	-
	-restart 1000000 restart_nvt
	-run 10000000
	-
	-write_restart system_after_nvt.rst
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT
	deleted file mode 100644
	index 0e58ef44c..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
	deleted file mode 100755
	index bf2be9f95..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
	+++ /dev/null
	@@ -1,31 +0,0 @@
	-# You would probably run lammps this way:
	-#
	-# lmp_ubuntu -i run.in.nvt
	-
	-# The "run.in.nvt" file is a LAMMPS input scripts which refers
	-# 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:
	-
	-"$LAMMPS_COMMAND" -i run.in.min # minimize
	-"$LAMMPS_COMMAND" -i run.in.npt # pressure equilibration
	-"$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
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt
	diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh
	deleted file mode 100755
	index 5d2be2133..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt
	deleted file mode 100644
	index 8063d535f..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index 8ebdc4dc8..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,1124 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 780 !NATOM
	- 1 1 1 1 -0.847600 15.9994 0
	- 2 1 2 2 0.423800 1.0080 0
	- 3 1 2 2 0.423800 1.0080 0
	- 4 2 1 1 -0.847600 15.9994 0
	- 5 2 2 2 0.423800 1.0080 0
	- 6 2 2 2 0.423800 1.0080 0
	- 7 3 1 1 -0.847600 15.9994 0
	- 8 3 2 2 0.423800 1.0080 0
	- 9 3 2 2 0.423800 1.0080 0
	- 10 4 1 1 -0.847600 15.9994 0
	- 11 4 2 2 0.423800 1.0080 0
	- 12 4 2 2 0.423800 1.0080 0
	- 13 5 1 1 -0.847600 15.9994 0
	- 14 5 2 2 0.423800 1.0080 0
	- 15 5 2 2 0.423800 1.0080 0
	- 16 6 1 1 -0.847600 15.9994 0
	- 17 6 2 2 0.423800 1.0080 0
	- 18 6 2 2 0.423800 1.0080 0
	- 19 7 1 1 -0.847600 15.9994 0
	- 20 7 2 2 0.423800 1.0080 0
	- 21 7 2 2 0.423800 1.0080 0
	- 22 8 1 1 -0.847600 15.9994 0
	- 23 8 2 2 0.423800 1.0080 0
	- 24 8 2 2 0.423800 1.0080 0
	- 25 9 1 1 -0.847600 15.9994 0
	- 26 9 2 2 0.423800 1.0080 0
	- 27 9 2 2 0.423800 1.0080 0
	- 28 10 1 1 -0.847600 15.9994 0
	- 29 10 2 2 0.423800 1.0080 0
	- 30 10 2 2 0.423800 1.0080 0
	- 31 11 1 1 -0.847600 15.9994 0
	- 32 11 2 2 0.423800 1.0080 0
	- 33 11 2 2 0.423800 1.0080 0
	- 34 12 1 1 -0.847600 15.9994 0
	- 35 12 2 2 0.423800 1.0080 0
	- 36 12 2 2 0.423800 1.0080 0
	- 37 13 1 1 -0.847600 15.9994 0
	- 38 13 2 2 0.423800 1.0080 0
	- 39 13 2 2 0.423800 1.0080 0
	- 40 14 1 1 -0.847600 15.9994 0
	- 41 14 2 2 0.423800 1.0080 0
	- 42 14 2 2 0.423800 1.0080 0
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	- 533 178 2 2 0.423800 1.0080 0
	- 534 178 2 2 0.423800 1.0080 0
	- 535 179 1 1 -0.847600 15.9994 0
	- 536 179 2 2 0.423800 1.0080 0
	- 537 179 2 2 0.423800 1.0080 0
	- 538 180 1 1 -0.847600 15.9994 0
	- 539 180 2 2 0.423800 1.0080 0
	- 540 180 2 2 0.423800 1.0080 0
	- 541 181 1 1 -0.847600 15.9994 0
	- 542 181 2 2 0.423800 1.0080 0
	- 543 181 2 2 0.423800 1.0080 0
	- 544 182 1 1 -0.847600 15.9994 0
	- 545 182 2 2 0.423800 1.0080 0
	- 546 182 2 2 0.423800 1.0080 0
	- 547 183 1 1 -0.847600 15.9994 0
	- 548 183 2 2 0.423800 1.0080 0
	- 549 183 2 2 0.423800 1.0080 0
	- 550 184 1 1 -0.847600 15.9994 0
	- 551 184 2 2 0.423800 1.0080 0
	- 552 184 2 2 0.423800 1.0080 0
	- 553 185 1 1 -0.847600 15.9994 0
	- 554 185 2 2 0.423800 1.0080 0
	- 555 185 2 2 0.423800 1.0080 0
	- 556 186 1 1 -0.847600 15.9994 0
	- 557 186 2 2 0.423800 1.0080 0
	- 558 186 2 2 0.423800 1.0080 0
	- 559 187 1 1 -0.847600 15.9994 0
	- 560 187 2 2 0.423800 1.0080 0
	- 561 187 2 2 0.423800 1.0080 0
	- 562 188 1 1 -0.847600 15.9994 0
	- 563 188 2 2 0.423800 1.0080 0
	- 564 188 2 2 0.423800 1.0080 0
	- 565 189 1 1 -0.847600 15.9994 0
	- 566 189 2 2 0.423800 1.0080 0
	- 567 189 2 2 0.423800 1.0080 0
	- 568 190 1 1 -0.847600 15.9994 0
	- 569 190 2 2 0.423800 1.0080 0
	- 570 190 2 2 0.423800 1.0080 0
	- 571 191 1 1 -0.847600 15.9994 0
	- 572 191 2 2 0.423800 1.0080 0
	- 573 191 2 2 0.423800 1.0080 0
	- 574 192 1 1 -0.847600 15.9994 0
	- 575 192 2 2 0.423800 1.0080 0
	- 576 192 2 2 0.423800 1.0080 0
	- 577 193 1 1 -0.847600 15.9994 0
	- 578 193 2 2 0.423800 1.0080 0
	- 579 193 2 2 0.423800 1.0080 0
	- 580 194 1 1 -0.847600 15.9994 0
	- 581 194 2 2 0.423800 1.0080 0
	- 582 194 2 2 0.423800 1.0080 0
	- 583 195 1 1 -0.847600 15.9994 0
	- 584 195 2 2 0.423800 1.0080 0
	- 585 195 2 2 0.423800 1.0080 0
	- 586 196 1 1 -0.847600 15.9994 0
	- 587 196 2 2 0.423800 1.0080 0
	- 588 196 2 2 0.423800 1.0080 0
	- 589 197 1 1 -0.847600 15.9994 0
	- 590 197 2 2 0.423800 1.0080 0
	- 591 197 2 2 0.423800 1.0080 0
	- 592 198 1 1 -0.847600 15.9994 0
	- 593 198 2 2 0.423800 1.0080 0
	- 594 198 2 2 0.423800 1.0080 0
	- 595 199 1 1 -0.847600 15.9994 0
	- 596 199 2 2 0.423800 1.0080 0
	- 597 199 2 2 0.423800 1.0080 0
	- 598 200 1 1 -0.847600 15.9994 0
	- 599 200 2 2 0.423800 1.0080 0
	- 600 200 2 2 0.423800 1.0080 0
	- 601 201 1 1 -0.847600 15.9994 0
	- 602 201 2 2 0.423800 1.0080 0
	- 603 201 2 2 0.423800 1.0080 0
	- 604 202 1 1 -0.847600 15.9994 0
	- 605 202 2 2 0.423800 1.0080 0
	- 606 202 2 2 0.423800 1.0080 0
	- 607 203 1 1 -0.847600 15.9994 0
	- 608 203 2 2 0.423800 1.0080 0
	- 609 203 2 2 0.423800 1.0080 0
	- 610 204 1 1 -0.847600 15.9994 0
	- 611 204 2 2 0.423800 1.0080 0
	- 612 204 2 2 0.423800 1.0080 0
	- 613 205 1 1 -0.847600 15.9994 0
	- 614 205 2 2 0.423800 1.0080 0
	- 615 205 2 2 0.423800 1.0080 0
	- 616 206 1 1 -0.847600 15.9994 0
	- 617 206 2 2 0.423800 1.0080 0
	- 618 206 2 2 0.423800 1.0080 0
	- 619 207 1 1 -0.847600 15.9994 0
	- 620 207 2 2 0.423800 1.0080 0
	- 621 207 2 2 0.423800 1.0080 0
	- 622 208 1 1 -0.847600 15.9994 0
	- 623 208 2 2 0.423800 1.0080 0
	- 624 208 2 2 0.423800 1.0080 0
	- 625 209 1 1 -0.847600 15.9994 0
	- 626 209 2 2 0.423800 1.0080 0
	- 627 209 2 2 0.423800 1.0080 0
	- 628 210 1 1 -0.847600 15.9994 0
	- 629 210 2 2 0.423800 1.0080 0
	- 630 210 2 2 0.423800 1.0080 0
	- 631 211 1 1 -0.847600 15.9994 0
	- 632 211 2 2 0.423800 1.0080 0
	- 633 211 2 2 0.423800 1.0080 0
	- 634 212 1 1 -0.847600 15.9994 0
	- 635 212 2 2 0.423800 1.0080 0
	- 636 212 2 2 0.423800 1.0080 0
	- 637 213 1 1 -0.847600 15.9994 0
	- 638 213 2 2 0.423800 1.0080 0
	- 639 213 2 2 0.423800 1.0080 0
	- 640 214 1 1 -0.847600 15.9994 0
	- 641 214 2 2 0.423800 1.0080 0
	- 642 214 2 2 0.423800 1.0080 0
	- 643 215 1 1 -0.847600 15.9994 0
	- 644 215 2 2 0.423800 1.0080 0
	- 645 215 2 2 0.423800 1.0080 0
	- 646 216 1 1 -0.847600 15.9994 0
	- 647 216 2 2 0.423800 1.0080 0
	- 648 216 2 2 0.423800 1.0080 0
	- 649 217 1 1 -0.847600 15.9994 0
	- 650 217 2 2 0.423800 1.0080 0
	- 651 217 2 2 0.423800 1.0080 0
	- 652 218 1 1 -0.847600 15.9994 0
	- 653 218 2 2 0.423800 1.0080 0
	- 654 218 2 2 0.423800 1.0080 0
	- 655 219 1 1 -0.847600 15.9994 0
	- 656 219 2 2 0.423800 1.0080 0
	- 657 219 2 2 0.423800 1.0080 0
	- 658 220 1 1 -0.847600 15.9994 0
	- 659 220 2 2 0.423800 1.0080 0
	- 660 220 2 2 0.423800 1.0080 0
	- 661 221 1 1 -0.847600 15.9994 0
	- 662 221 2 2 0.423800 1.0080 0
	- 663 221 2 2 0.423800 1.0080 0
	- 664 222 1 1 -0.847600 15.9994 0
	- 665 222 2 2 0.423800 1.0080 0
	- 666 222 2 2 0.423800 1.0080 0
	- 667 223 1 1 -0.847600 15.9994 0
	- 668 223 2 2 0.423800 1.0080 0
	- 669 223 2 2 0.423800 1.0080 0
	- 670 224 1 1 -0.847600 15.9994 0
	- 671 224 2 2 0.423800 1.0080 0
	- 672 224 2 2 0.423800 1.0080 0
	- 673 225 1 1 -0.847600 15.9994 0
	- 674 225 2 2 0.423800 1.0080 0
	- 675 225 2 2 0.423800 1.0080 0
	- 676 226 1 1 -0.847600 15.9994 0
	- 677 226 2 2 0.423800 1.0080 0
	- 678 226 2 2 0.423800 1.0080 0
	- 679 227 1 1 -0.847600 15.9994 0
	- 680 227 2 2 0.423800 1.0080 0
	- 681 227 2 2 0.423800 1.0080 0
	- 682 228 1 1 -0.847600 15.9994 0
	- 683 228 2 2 0.423800 1.0080 0
	- 684 228 2 2 0.423800 1.0080 0
	- 685 229 1 1 -0.847600 15.9994 0
	- 686 229 2 2 0.423800 1.0080 0
	- 687 229 2 2 0.423800 1.0080 0
	- 688 230 1 1 -0.847600 15.9994 0
	- 689 230 2 2 0.423800 1.0080 0
	- 690 230 2 2 0.423800 1.0080 0
	- 691 231 1 1 -0.847600 15.9994 0
	- 692 231 2 2 0.423800 1.0080 0
	- 693 231 2 2 0.423800 1.0080 0
	- 694 232 1 1 -0.847600 15.9994 0
	- 695 232 2 2 0.423800 1.0080 0
	- 696 232 2 2 0.423800 1.0080 0
	- 697 233 1 1 -0.847600 15.9994 0
	- 698 233 2 2 0.423800 1.0080 0
	- 699 233 2 2 0.423800 1.0080 0
	- 700 234 1 1 -0.847600 15.9994 0
	- 701 234 2 2 0.423800 1.0080 0
	- 702 234 2 2 0.423800 1.0080 0
	- 703 235 1 1 -0.847600 15.9994 0
	- 704 235 2 2 0.423800 1.0080 0
	- 705 235 2 2 0.423800 1.0080 0
	- 706 236 1 1 -0.847600 15.9994 0
	- 707 236 2 2 0.423800 1.0080 0
	- 708 236 2 2 0.423800 1.0080 0
	- 709 237 1 1 -0.847600 15.9994 0
	- 710 237 2 2 0.423800 1.0080 0
	- 711 237 2 2 0.423800 1.0080 0
	- 712 238 1 1 -0.847600 15.9994 0
	- 713 238 2 2 0.423800 1.0080 0
	- 714 238 2 2 0.423800 1.0080 0
	- 715 239 1 1 -0.847600 15.9994 0
	- 716 239 2 2 0.423800 1.0080 0
	- 717 239 2 2 0.423800 1.0080 0
	- 718 240 1 1 -0.847600 15.9994 0
	- 719 240 2 2 0.423800 1.0080 0
	- 720 240 2 2 0.423800 1.0080 0
	- 721 241 1 1 -0.847600 15.9994 0
	- 722 241 2 2 0.423800 1.0080 0
	- 723 241 2 2 0.423800 1.0080 0
	- 724 242 1 1 -0.847600 15.9994 0
	- 725 242 2 2 0.423800 1.0080 0
	- 726 242 2 2 0.423800 1.0080 0
	- 727 243 1 1 -0.847600 15.9994 0
	- 728 243 2 2 0.423800 1.0080 0
	- 729 243 2 2 0.423800 1.0080 0
	- 730 244 1 1 -0.847600 15.9994 0
	- 731 244 2 2 0.423800 1.0080 0
	- 732 244 2 2 0.423800 1.0080 0
	- 733 245 1 1 -0.847600 15.9994 0
	- 734 245 2 2 0.423800 1.0080 0
	- 735 245 2 2 0.423800 1.0080 0
	- 736 246 1 1 -0.847600 15.9994 0
	- 737 246 2 2 0.423800 1.0080 0
	- 738 246 2 2 0.423800 1.0080 0
	- 739 247 1 1 -0.847600 15.9994 0
	- 740 247 2 2 0.423800 1.0080 0
	- 741 247 2 2 0.423800 1.0080 0
	- 742 248 1 1 -0.847600 15.9994 0
	- 743 248 2 2 0.423800 1.0080 0
	- 744 248 2 2 0.423800 1.0080 0
	- 745 249 1 1 -0.847600 15.9994 0
	- 746 249 2 2 0.423800 1.0080 0
	- 747 249 2 2 0.423800 1.0080 0
	- 748 250 1 1 -0.847600 15.9994 0
	- 749 250 2 2 0.423800 1.0080 0
	- 750 250 2 2 0.423800 1.0080 0
	- 751 251 1 1 -0.847600 15.9994 0
	- 752 251 2 2 0.423800 1.0080 0
	- 753 251 2 2 0.423800 1.0080 0
	- 754 252 1 1 -0.847600 15.9994 0
	- 755 252 2 2 0.423800 1.0080 0
	- 756 252 2 2 0.423800 1.0080 0
	- 757 253 1 1 -0.847600 15.9994 0
	- 758 253 2 2 0.423800 1.0080 0
	- 759 253 2 2 0.423800 1.0080 0
	- 760 254 1 1 -0.847600 15.9994 0
	- 761 254 2 2 0.423800 1.0080 0
	- 762 254 2 2 0.423800 1.0080 0
	- 763 255 1 1 -0.847600 15.9994 0
	- 764 255 2 2 0.423800 1.0080 0
	- 765 255 2 2 0.423800 1.0080 0
	- 766 256 1 1 -0.847600 15.9994 0
	- 767 256 2 2 0.423800 1.0080 0
	- 768 256 2 2 0.423800 1.0080 0
	- 769 257 1 1 -0.847600 15.9994 0
	- 770 257 2 2 0.423800 1.0080 0
	- 771 257 2 2 0.423800 1.0080 0
	- 772 258 1 1 -0.847600 15.9994 0
	- 773 258 2 2 0.423800 1.0080 0
	- 774 258 2 2 0.423800 1.0080 0
	- 775 259 1 1 -0.847600 15.9994 0
	- 776 259 2 2 0.423800 1.0080 0
	- 777 259 2 2 0.423800 1.0080 0
	- 778 260 1 1 -0.847600 15.9994 0
	- 779 260 2 2 0.423800 1.0080 0
	- 780 260 2 2 0.423800 1.0080 0
	-
	- 520 !NBOND: bonds
	- 1 2 1 3 4 5 4 6
	- 7 8 7 9 10 11 10 12
	- 13 14 13 15 16 17 16 18
	- 19 20 19 21 22 23 22 24
	- 25 26 25 27 28 29 28 30
	- 31 32 31 33 34 35 34 36
	- 37 38 37 39 40 41 40 42
	- 43 44 43 45 46 47 46 48
	- 49 50 49 51 52 53 52 54
	- 55 56 55 57 58 59 58 60
	- 61 62 61 63 64 65 64 66
	- 67 68 67 69 70 71 70 72
	- 73 74 73 75 76 77 76 78
	- 79 80 79 81 82 83 82 84
	- 85 86 85 87 88 89 88 90
	- 91 92 91 93 94 95 94 96
	- 97 98 97 99 100 101 100 102
	- 103 104 103 105 106 107 106 108
	- 109 110 109 111 112 113 112 114
	- 115 116 115 117 118 119 118 120
	- 121 122 121 123 124 125 124 126
	- 127 128 127 129 130 131 130 132
	- 133 134 133 135 136 137 136 138
	- 139 140 139 141 142 143 142 144
	- 145 146 145 147 148 149 148 150
	- 151 152 151 153 154 155 154 156
	- 157 158 157 159 160 161 160 162
	- 163 164 163 165 166 167 166 168
	- 169 170 169 171 172 173 172 174
	- 175 176 175 177 178 179 178 180
	- 181 182 181 183 184 185 184 186
	- 187 188 187 189 190 191 190 192
	- 193 194 193 195 196 197 196 198
	- 199 200 199 201 202 203 202 204
	- 205 206 205 207 208 209 208 210
	- 211 212 211 213 214 215 214 216
	- 217 218 217 219 220 221 220 222
	- 223 224 223 225 226 227 226 228
	- 229 230 229 231 232 233 232 234
	- 235 236 235 237 238 239 238 240
	- 241 242 241 243 244 245 244 246
	- 247 248 247 249 250 251 250 252
	- 253 254 253 255 256 257 256 258
	- 259 260 259 261 262 263 262 264
	- 265 266 265 267 268 269 268 270
	- 271 272 271 273 274 275 274 276
	- 277 278 277 279 280 281 280 282
	- 283 284 283 285 286 287 286 288
	- 289 290 289 291 292 293 292 294
	- 295 296 295 297 298 299 298 300
	- 301 302 301 303 304 305 304 306
	- 307 308 307 309 310 311 310 312
	- 313 314 313 315 316 317 316 318
	- 319 320 319 321 322 323 322 324
	- 325 326 325 327 328 329 328 330
	- 331 332 331 333 334 335 334 336
	- 337 338 337 339 340 341 340 342
	- 343 344 343 345 346 347 346 348
	- 349 350 349 351 352 353 352 354
	- 355 356 355 357 358 359 358 360
	- 361 362 361 363 364 365 364 366
	- 367 368 367 369 370 371 370 372
	- 373 374 373 375 376 377 376 378
	- 379 380 379 381 382 383 382 384
	- 385 386 385 387 388 389 388 390
	- 391 392 391 393 394 395 394 396
	- 397 398 397 399 400 401 400 402
	- 403 404 403 405 406 407 406 408
	- 409 410 409 411 412 413 412 414
	- 415 416 415 417 418 419 418 420
	- 421 422 421 423 424 425 424 426
	- 427 428 427 429 430 431 430 432
	- 433 434 433 435 436 437 436 438
	- 439 440 439 441 442 443 442 444
	- 445 446 445 447 448 449 448 450
	- 451 452 451 453 454 455 454 456
	- 457 458 457 459 460 461 460 462
	- 463 464 463 465 466 467 466 468
	- 469 470 469 471 472 473 472 474
	- 475 476 475 477 478 479 478 480
	- 481 482 481 483 484 485 484 486
	- 487 488 487 489 490 491 490 492
	- 493 494 493 495 496 497 496 498
	- 499 500 499 501 502 503 502 504
	- 505 506 505 507 508 509 508 510
	- 511 512 511 513 514 515 514 516
	- 517 518 517 519 520 521 520 522
	- 523 524 523 525 526 527 526 528
	- 529 530 529 531 532 533 532 534
	- 535 536 535 537 538 539 538 540
	- 541 542 541 543 544 545 544 546
	- 547 548 547 549 550 551 550 552
	- 553 554 553 555 556 557 556 558
	- 559 560 559 561 562 563 562 564
	- 565 566 565 567 568 569 568 570
	- 571 572 571 573 574 575 574 576
	- 577 578 577 579 580 581 580 582
	- 583 584 583 585 586 587 586 588
	- 589 590 589 591 592 593 592 594
	- 595 596 595 597 598 599 598 600
	- 601 602 601 603 604 605 604 606
	- 607 608 607 609 610 611 610 612
	- 613 614 613 615 616 617 616 618
	- 619 620 619 621 622 623 622 624
	- 625 626 625 627 628 629 628 630
	- 631 632 631 633 634 635 634 636
	- 637 638 637 639 640 641 640 642
	- 643 644 643 645 646 647 646 648
	- 649 650 649 651 652 653 652 654
	- 655 656 655 657 658 659 658 660
	- 661 662 661 663 664 665 664 666
	- 667 668 667 669 670 671 670 672
	- 673 674 673 675 676 677 676 678
	- 679 680 679 681 682 683 682 684
	- 685 686 685 687 688 689 688 690
	- 691 692 691 693 694 695 694 696
	- 697 698 697 699 700 701 700 702
	- 703 704 703 705 706 707 706 708
	- 709 710 709 711 712 713 712 714
	- 715 716 715 717 718 719 718 720
	- 721 722 721 723 724 725 724 726
	- 727 728 727 729 730 731 730 732
	- 733 734 733 735 736 737 736 738
	- 739 740 739 741 742 743 742 744
	- 745 746 745 747 748 749 748 750
	- 751 752 751 753 754 755 754 756
	- 757 758 757 759 760 761 760 762
	- 763 764 763 765 766 767 766 768
	- 769 770 769 771 772 773 772 774
	- 775 776 775 777 778 779 778 780
	-
	- 260 !NTHETA: angles
	- 2 1 3 5 4 6 8 7 9
	- 11 10 12 14 13 15 17 16 18
	- 20 19 21 23 22 24 26 25 27
	- 29 28 30 32 31 33 35 34 36
	- 38 37 39 41 40 42 44 43 45
	- 47 46 48 50 49 51 53 52 54
	- 56 55 57 59 58 60 62 61 63
	- 65 64 66 68 67 69 71 70 72
	- 74 73 75 77 76 78 80 79 81
	- 83 82 84 86 85 87 89 88 90
	- 92 91 93 95 94 96 98 97 99
	- 101 100 102 104 103 105 107 106 108
	- 110 109 111 113 112 114 116 115 117
	- 119 118 120 122 121 123 125 124 126
	- 128 127 129 131 130 132 134 133 135
	- 137 136 138 140 139 141 143 142 144
	- 146 145 147 149 148 150 152 151 153
	- 155 154 156 158 157 159 161 160 162
	- 164 163 165 167 166 168 170 169 171
	- 173 172 174 176 175 177 179 178 180
	- 182 181 183 185 184 186 188 187 189
	- 191 190 192 194 193 195 197 196 198
	- 200 199 201 203 202 204 206 205 207
	- 209 208 210 212 211 213 215 214 216
	- 218 217 219 221 220 222 224 223 225
	- 227 226 228 230 229 231 233 232 234
	- 236 235 237 239 238 240 242 241 243
	- 245 244 246 248 247 249 251 250 252
	- 254 253 255 257 256 258 260 259 261
	- 263 262 264 266 265 267 269 268 270
	- 272 271 273 275 274 276 278 277 279
	- 281 280 282 284 283 285 287 286 288
	- 290 289 291 293 292 294 296 295 297
	- 299 298 300 302 301 303 305 304 306
	- 308 307 309 311 310 312 314 313 315
	- 317 316 318 320 319 321 323 322 324
	- 326 325 327 329 328 330 332 331 333
	- 335 334 336 338 337 339 341 340 342
	- 344 343 345 347 346 348 350 349 351
	- 353 352 354 356 355 357 359 358 360
	- 362 361 363 365 364 366 368 367 369
	- 371 370 372 374 373 375 377 376 378
	- 380 379 381 383 382 384 386 385 387
	- 389 388 390 392 391 393 395 394 396
	- 398 397 399 401 400 402 404 403 405
	- 407 406 408 410 409 411 413 412 414
	- 416 415 417 419 418 420 422 421 423
	- 425 424 426 428 427 429 431 430 432
	- 434 433 435 437 436 438 440 439 441
	- 443 442 444 446 445 447 449 448 450
	- 452 451 453 455 454 456 458 457 459
	- 461 460 462 464 463 465 467 466 468
	- 470 469 471 473 472 474 476 475 477
	- 479 478 480 482 481 483 485 484 486
	- 488 487 489 491 490 492 494 493 495
	- 497 496 498 500 499 501 503 502 504
	- 506 505 507 509 508 510 512 511 513
	- 515 514 516 518 517 519 521 520 522
	- 524 523 525 527 526 528 530 529 531
	- 533 532 534 536 535 537 539 538 540
	- 542 541 543 545 544 546 548 547 549
	- 551 550 552 554 553 555 557 556 558
	- 560 559 561 563 562 564 566 565 567
	- 569 568 570 572 571 573 575 574 576
	- 578 577 579 581 580 582 584 583 585
	- 587 586 588 590 589 591 593 592 594
	- 596 595 597 599 598 600 602 601 603
	- 605 604 606 608 607 609 611 610 612
	- 614 613 615 617 616 618 620 619 621
	- 623 622 624 626 625 627 629 628 630
	- 632 631 633 635 634 636 638 637 639
	- 641 640 642 644 643 645 647 646 648
	- 650 649 651 653 652 654 656 655 657
	- 659 658 660 662 661 663 665 664 666
	- 668 667 669 671 670 672 674 673 675
	- 677 676 678 680 679 681 683 682 684
	- 686 685 687 689 688 690 692 691 693
	- 695 694 696 698 697 699 701 700 702
	- 704 703 705 707 706 708 710 709 711
	- 713 712 714 716 715 717 719 718 720
	- 722 721 723 725 724 726 728 727 729
	- 731 730 732 734 733 735 737 736 738
	- 740 739 741 743 742 744 746 745 747
	- 749 748 750 752 751 753 755 754 756
	- 758 757 759 761 760 762 764 763 765
	- 767 766 768 770 769 771 773 772 774
	- 776 775 777 779 778 780
	-
	- 0 !NPHI: dihedrals
	-
	-
	- 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
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh
	deleted file mode 100755
	index 4ebc7b17a..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
	deleted file mode 100644
	index 0ed5103cb..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
	deleted file mode 100644
	index 3bb7bca40..000000000
	--- a/tools/moltemplate/examples/all_atom_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 200.0 1.0
	- angle_coeff @angle:HOH harmonic 200.0 109.47
	- 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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
	deleted file mode 100644
	index 274d8aeb1..000000000
	--- a/tools/moltemplate/examples/all_atom_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/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.min b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.min
	deleted file mode 100644
	index ea100b01e..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.min
	+++ /dev/null
	@@ -1,18 +0,0 @@
	-##################################################
	-# Box of water
	-##################################################
	-#
	-# define the system being simulated:
	-
	-include "system.in"
	-
	-dump 1 all custom 100 traj_min.lammpstrj id mol type x y z ix iy iz
	-
	-# fSHAKE was defined in system.in.settings. It is incompatible with "minimize".
	-unfix fSHAKE
	-minimize 1.0e-4 1.0e-6 500 2000
	-
	-# (For a system with ~6000 atoms, this takes 1-4 minutes on a i7 720 processor.)
	-# Alternate (faster) minimizer settings (about 10 sec):
	-
	-write_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
	deleted file mode 100644
	index 7cee108bc..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
	+++ /dev/null
	@@ -1,33 +0,0 @@
	-##################################################
	-# Box of water
	-##################################################
	-#
	-# define the system being simulated:
	-
	-# -- init section --
	-include system.in.init
	-
	-# -- atom definition section --
	-
	-#read_data system.data
	-read_restart system_after_min.rst
	-
	-# -- settings section --
	-include system.in.settings
	-
	-# -- run section --
	-
	-# Note: It is possible to use a 2.0 timestep with SPCE water,
	-# if you start from a reasonable starting structure.
	-# However during equilibration I often set it to 1.0 to be safe.
	-timestep 1.0
	-
	-dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz
	-fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0
	-
	-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
	-thermo 100
	-
	-run 10000
	-
	-write_restart system_after_npt.rst
	diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
	deleted file mode 100644
	index b4c7088db..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-##################################################
	-# Box of water
	-##################################################
	-#
	-# define the system being simulated:
	-
	-# -- init section --
	-include system.in.init
	-
	-# -- atom definition section --
	-
	-#read_data system.data
	-#read_restart system_after_min.rst
	-read_restart system_after_npt.rst
	-
	-# -- 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
	-#dump 1 all dcd 100 traj_nvt.dcd
	-#dump_modify unwrap yes
	-fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
	-
	-thermo_style custom step temp pe etotal press vol epair ebond eangle
	-thermo 500 # time interval for printing out "thermo" data
	-#thermo_modify flush yes
	-
	-restart 100000 restart_nvt
	-
	-run 1000000
	-
	-write_restart system_after_nvt.rst
	-
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh
	deleted file mode 100755
	index 85bb1278f..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh
	+++ /dev/null
	@@ -1,25 +0,0 @@
	-# This is just an example.
	-#
	-# Note: The 3 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
	-# created earlier with moltemplate.sh:
	-# 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.npt # equilibrate the pressure
	-#"$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL)
	-
	-# 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.npt # equilibrate the pressure
	-#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL)
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh
	deleted file mode 100755
	index 3a0821269..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/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/all_atom_examples/waterSPCE+Na+Cl/README_visualise.txt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualise.txt
	deleted file mode 100644
	index 019afc144..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualise.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/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg
	deleted file mode 100644
	index 5261bedc2..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg
	deleted file mode 100644
	index 78c4056f8..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf
	deleted file mode 100644
	index d255bf368..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf
	+++ /dev/null
	@@ -1,4257 +0,0 @@
	-PSF
	-
	- 1 !NTITLE
	- REMARKS VMD generated structure x-plor psf file
	-
	- 3016 !NATOM
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	- 2766 922 4 4 0.423800 1.0080 0
	- 2767 923 3 3 -0.847600 15.9994 0
	- 2768 923 4 4 0.423800 1.0080 0
	- 2769 923 4 4 0.423800 1.0080 0
	- 2770 924 3 3 -0.847600 15.9994 0
	- 2771 924 4 4 0.423800 1.0080 0
	- 2772 924 4 4 0.423800 1.0080 0
	- 2773 925 3 3 -0.847600 15.9994 0
	- 2774 925 4 4 0.423800 1.0080 0
	- 2775 925 4 4 0.423800 1.0080 0
	- 2776 926 3 3 -0.847600 15.9994 0
	- 2777 926 4 4 0.423800 1.0080 0
	- 2778 926 4 4 0.423800 1.0080 0
	- 2779 927 3 3 -0.847600 15.9994 0
	- 2780 927 4 4 0.423800 1.0080 0
	- 2781 927 4 4 0.423800 1.0080 0
	- 2782 928 3 3 -0.847600 15.9994 0
	- 2783 928 4 4 0.423800 1.0080 0
	- 2784 928 4 4 0.423800 1.0080 0
	- 2785 929 3 3 -0.847600 15.9994 0
	- 2786 929 4 4 0.423800 1.0080 0
	- 2787 929 4 4 0.423800 1.0080 0
	- 2788 930 3 3 -0.847600 15.9994 0
	- 2789 930 4 4 0.423800 1.0080 0
	- 2790 930 4 4 0.423800 1.0080 0
	- 2791 931 3 3 -0.847600 15.9994 0
	- 2792 931 4 4 0.423800 1.0080 0
	- 2793 931 4 4 0.423800 1.0080 0
	- 2794 932 3 3 -0.847600 15.9994 0
	- 2795 932 4 4 0.423800 1.0080 0
	- 2796 932 4 4 0.423800 1.0080 0
	- 2797 933 3 3 -0.847600 15.9994 0
	- 2798 933 4 4 0.423800 1.0080 0
	- 2799 933 4 4 0.423800 1.0080 0
	- 2800 934 3 3 -0.847600 15.9994 0
	- 2801 934 4 4 0.423800 1.0080 0
	- 2802 934 4 4 0.423800 1.0080 0
	- 2803 935 3 3 -0.847600 15.9994 0
	- 2804 935 4 4 0.423800 1.0080 0
	- 2805 935 4 4 0.423800 1.0080 0
	- 2806 936 3 3 -0.847600 15.9994 0
	- 2807 936 4 4 0.423800 1.0080 0
	- 2808 936 4 4 0.423800 1.0080 0
	- 2809 937 3 3 -0.847600 15.9994 0
	- 2810 937 4 4 0.423800 1.0080 0
	- 2811 937 4 4 0.423800 1.0080 0
	- 2812 938 3 3 -0.847600 15.9994 0
	- 2813 938 4 4 0.423800 1.0080 0
	- 2814 938 4 4 0.423800 1.0080 0
	- 2815 939 3 3 -0.847600 15.9994 0
	- 2816 939 4 4 0.423800 1.0080 0
	- 2817 939 4 4 0.423800 1.0080 0
	- 2818 940 3 3 -0.847600 15.9994 0
	- 2819 940 4 4 0.423800 1.0080 0
	- 2820 940 4 4 0.423800 1.0080 0
	- 2821 941 3 3 -0.847600 15.9994 0
	- 2822 941 4 4 0.423800 1.0080 0
	- 2823 941 4 4 0.423800 1.0080 0
	- 2824 942 3 3 -0.847600 15.9994 0
	- 2825 942 4 4 0.423800 1.0080 0
	- 2826 942 4 4 0.423800 1.0080 0
	- 2827 943 3 3 -0.847600 15.9994 0
	- 2828 943 4 4 0.423800 1.0080 0
	- 2829 943 4 4 0.423800 1.0080 0
	- 2830 944 3 3 -0.847600 15.9994 0
	- 2831 944 4 4 0.423800 1.0080 0
	- 2832 944 4 4 0.423800 1.0080 0
	- 2833 945 3 3 -0.847600 15.9994 0
	- 2834 945 4 4 0.423800 1.0080 0
	- 2835 945 4 4 0.423800 1.0080 0
	- 2836 946 3 3 -0.847600 15.9994 0
	- 2837 946 4 4 0.423800 1.0080 0
	- 2838 946 4 4 0.423800 1.0080 0
	- 2839 947 3 3 -0.847600 15.9994 0
	- 2840 947 4 4 0.423800 1.0080 0
	- 2841 947 4 4 0.423800 1.0080 0
	- 2842 948 3 3 -0.847600 15.9994 0
	- 2843 948 4 4 0.423800 1.0080 0
	- 2844 948 4 4 0.423800 1.0080 0
	- 2845 949 3 3 -0.847600 15.9994 0
	- 2846 949 4 4 0.423800 1.0080 0
	- 2847 949 4 4 0.423800 1.0080 0
	- 2848 950 3 3 -0.847600 15.9994 0
	- 2849 950 4 4 0.423800 1.0080 0
	- 2850 950 4 4 0.423800 1.0080 0
	- 2851 951 3 3 -0.847600 15.9994 0
	- 2852 951 4 4 0.423800 1.0080 0
	- 2853 951 4 4 0.423800 1.0080 0
	- 2854 952 3 3 -0.847600 15.9994 0
	- 2855 952 4 4 0.423800 1.0080 0
	- 2856 952 4 4 0.423800 1.0080 0
	- 2857 953 3 3 -0.847600 15.9994 0
	- 2858 953 4 4 0.423800 1.0080 0
	- 2859 953 4 4 0.423800 1.0080 0
	- 2860 954 3 3 -0.847600 15.9994 0
	- 2861 954 4 4 0.423800 1.0080 0
	- 2862 954 4 4 0.423800 1.0080 0
	- 2863 955 3 3 -0.847600 15.9994 0
	- 2864 955 4 4 0.423800 1.0080 0
	- 2865 955 4 4 0.423800 1.0080 0
	- 2866 956 3 3 -0.847600 15.9994 0
	- 2867 956 4 4 0.423800 1.0080 0
	- 2868 956 4 4 0.423800 1.0080 0
	- 2869 957 3 3 -0.847600 15.9994 0
	- 2870 957 4 4 0.423800 1.0080 0
	- 2871 957 4 4 0.423800 1.0080 0
	- 2872 958 3 3 -0.847600 15.9994 0
	- 2873 958 4 4 0.423800 1.0080 0
	- 2874 958 4 4 0.423800 1.0080 0
	- 2875 959 3 3 -0.847600 15.9994 0
	- 2876 959 4 4 0.423800 1.0080 0
	- 2877 959 4 4 0.423800 1.0080 0
	- 2878 960 3 3 -0.847600 15.9994 0
	- 2879 960 4 4 0.423800 1.0080 0
	- 2880 960 4 4 0.423800 1.0080 0
	- 2881 961 3 3 -0.847600 15.9994 0
	- 2882 961 4 4 0.423800 1.0080 0
	- 2883 961 4 4 0.423800 1.0080 0
	- 2884 962 3 3 -0.847600 15.9994 0
	- 2885 962 4 4 0.423800 1.0080 0
	- 2886 962 4 4 0.423800 1.0080 0
	- 2887 963 3 3 -0.847600 15.9994 0
	- 2888 963 4 4 0.423800 1.0080 0
	- 2889 963 4 4 0.423800 1.0080 0
	- 2890 964 3 3 -0.847600 15.9994 0
	- 2891 964 4 4 0.423800 1.0080 0
	- 2892 964 4 4 0.423800 1.0080 0
	- 2893 965 3 3 -0.847600 15.9994 0
	- 2894 965 4 4 0.423800 1.0080 0
	- 2895 965 4 4 0.423800 1.0080 0
	- 2896 966 3 3 -0.847600 15.9994 0
	- 2897 966 4 4 0.423800 1.0080 0
	- 2898 966 4 4 0.423800 1.0080 0
	- 2899 967 3 3 -0.847600 15.9994 0
	- 2900 967 4 4 0.423800 1.0080 0
	- 2901 967 4 4 0.423800 1.0080 0
	- 2902 968 3 3 -0.847600 15.9994 0
	- 2903 968 4 4 0.423800 1.0080 0
	- 2904 968 4 4 0.423800 1.0080 0
	- 2905 969 3 3 -0.847600 15.9994 0
	- 2906 969 4 4 0.423800 1.0080 0
	- 2907 969 4 4 0.423800 1.0080 0
	- 2908 970 3 3 -0.847600 15.9994 0
	- 2909 970 4 4 0.423800 1.0080 0
	- 2910 970 4 4 0.423800 1.0080 0
	- 2911 971 3 3 -0.847600 15.9994 0
	- 2912 971 4 4 0.423800 1.0080 0
	- 2913 971 4 4 0.423800 1.0080 0
	- 2914 972 3 3 -0.847600 15.9994 0
	- 2915 972 4 4 0.423800 1.0080 0
	- 2916 972 4 4 0.423800 1.0080 0
	- 2917 973 3 3 -0.847600 15.9994 0
	- 2918 973 4 4 0.423800 1.0080 0
	- 2919 973 4 4 0.423800 1.0080 0
	- 2920 974 3 3 -0.847600 15.9994 0
	- 2921 974 4 4 0.423800 1.0080 0
	- 2922 974 4 4 0.423800 1.0080 0
	- 2923 975 3 3 -0.847600 15.9994 0
	- 2924 975 4 4 0.423800 1.0080 0
	- 2925 975 4 4 0.423800 1.0080 0
	- 2926 976 3 3 -0.847600 15.9994 0
	- 2927 976 4 4 0.423800 1.0080 0
	- 2928 976 4 4 0.423800 1.0080 0
	- 2929 977 3 3 -0.847600 15.9994 0
	- 2930 977 4 4 0.423800 1.0080 0
	- 2931 977 4 4 0.423800 1.0080 0
	- 2932 978 3 3 -0.847600 15.9994 0
	- 2933 978 4 4 0.423800 1.0080 0
	- 2934 978 4 4 0.423800 1.0080 0
	- 2935 979 3 3 -0.847600 15.9994 0
	- 2936 979 4 4 0.423800 1.0080 0
	- 2937 979 4 4 0.423800 1.0080 0
	- 2938 980 3 3 -0.847600 15.9994 0
	- 2939 980 4 4 0.423800 1.0080 0
	- 2940 980 4 4 0.423800 1.0080 0
	- 2941 981 3 3 -0.847600 15.9994 0
	- 2942 981 4 4 0.423800 1.0080 0
	- 2943 981 4 4 0.423800 1.0080 0
	- 2944 982 3 3 -0.847600 15.9994 0
	- 2945 982 4 4 0.423800 1.0080 0
	- 2946 982 4 4 0.423800 1.0080 0
	- 2947 983 3 3 -0.847600 15.9994 0
	- 2948 983 4 4 0.423800 1.0080 0
	- 2949 983 4 4 0.423800 1.0080 0
	- 2950 984 3 3 -0.847600 15.9994 0
	- 2951 984 4 4 0.423800 1.0080 0
	- 2952 984 4 4 0.423800 1.0080 0
	- 2953 985 3 3 -0.847600 15.9994 0
	- 2954 985 4 4 0.423800 1.0080 0
	- 2955 985 4 4 0.423800 1.0080 0
	- 2956 986 3 3 -0.847600 15.9994 0
	- 2957 986 4 4 0.423800 1.0080 0
	- 2958 986 4 4 0.423800 1.0080 0
	- 2959 987 3 3 -0.847600 15.9994 0
	- 2960 987 4 4 0.423800 1.0080 0
	- 2961 987 4 4 0.423800 1.0080 0
	- 2962 988 3 3 -0.847600 15.9994 0
	- 2963 988 4 4 0.423800 1.0080 0
	- 2964 988 4 4 0.423800 1.0080 0
	- 2965 989 3 3 -0.847600 15.9994 0
	- 2966 989 4 4 0.423800 1.0080 0
	- 2967 989 4 4 0.423800 1.0080 0
	- 2968 990 3 3 -0.847600 15.9994 0
	- 2969 990 4 4 0.423800 1.0080 0
	- 2970 990 4 4 0.423800 1.0080 0
	- 2971 991 3 3 -0.847600 15.9994 0
	- 2972 991 4 4 0.423800 1.0080 0
	- 2973 991 4 4 0.423800 1.0080 0
	- 2974 992 3 3 -0.847600 15.9994 0
	- 2975 992 4 4 0.423800 1.0080 0
	- 2976 992 4 4 0.423800 1.0080 0
	- 2977 993 3 3 -0.847600 15.9994 0
	- 2978 993 4 4 0.423800 1.0080 0
	- 2979 993 4 4 0.423800 1.0080 0
	- 2980 994 3 3 -0.847600 15.9994 0
	- 2981 994 4 4 0.423800 1.0080 0
	- 2982 994 4 4 0.423800 1.0080 0
	- 2983 995 3 3 -0.847600 15.9994 0
	- 2984 995 4 4 0.423800 1.0080 0
	- 2985 995 4 4 0.423800 1.0080 0
	- 2986 996 3 3 -0.847600 15.9994 0
	- 2987 996 4 4 0.423800 1.0080 0
	- 2988 996 4 4 0.423800 1.0080 0
	- 2989 997 3 3 -0.847600 15.9994 0
	- 2990 997 4 4 0.423800 1.0080 0
	- 2991 997 4 4 0.423800 1.0080 0
	- 2992 998 3 3 -0.847600 15.9994 0
	- 2993 998 4 4 0.423800 1.0080 0
	- 2994 998 4 4 0.423800 1.0080 0
	- 2995 999 3 3 -0.847600 15.9994 0
	- 2996 999 4 4 0.423800 1.0080 0
	- 2997 999 4 4 0.423800 1.0080 0
	- 2998 1000 3 3 -0.847600 15.9994 0
	- 2999 1000 4 4 0.423800 1.0080 0
	- 3000 1000 4 4 0.423800 1.0080 0
	- 3001 1001 1 1 1.000000 22.9898 0
	- 3002 1002 1 1 1.000000 22.9898 0
	- 3003 1003 1 1 1.000000 22.9898 0
	- 3004 1004 1 1 1.000000 22.9898 0
	- 3005 1005 1 1 1.000000 22.9898 0
	- 3006 1006 1 1 1.000000 22.9898 0
	- 3007 1007 1 1 1.000000 22.9898 0
	- 3008 1008 1 1 1.000000 22.9898 0
	- 3009 1009 2 2 -1.000000 35.4530 0
	- 3010 1010 2 2 -1.000000 35.4530 0
	- 3011 1011 2 2 -1.000000 35.4530 0
	- 3012 1012 2 2 -1.000000 35.4530 0
	- 3013 1013 2 2 -1.000000 35.4530 0
	- 3014 1014 2 2 -1.000000 35.4530 0
	- 3015 1015 2 2 -1.000000 35.4530 0
	- 3016 1016 2 2 -1.000000 35.4530 0
	-
	- 2000 !NBOND: bonds
	- 1 2 1 3 4 5 4 6
	- 7 8 7 9 10 11 10 12
	- 13 14 13 15 16 17 16 18
	- 19 20 19 21 22 23 22 24
	- 25 26 25 27 28 29 28 30
	- 31 32 31 33 34 35 34 36
	- 37 38 37 39 40 41 40 42
	- 43 44 43 45 46 47 46 48
	- 49 50 49 51 52 53 52 54
	- 55 56 55 57 58 59 58 60
	- 61 62 61 63 64 65 64 66
	- 67 68 67 69 70 71 70 72
	- 73 74 73 75 76 77 76 78
	- 79 80 79 81 82 83 82 84
	- 85 86 85 87 88 89 88 90
	- 91 92 91 93 94 95 94 96
	- 97 98 97 99 100 101 100 102
	- 103 104 103 105 106 107 106 108
	- 109 110 109 111 112 113 112 114
	- 115 116 115 117 118 119 118 120
	- 121 122 121 123 124 125 124 126
	- 127 128 127 129 130 131 130 132
	- 133 134 133 135 136 137 136 138
	- 139 140 139 141 142 143 142 144
	- 145 146 145 147 148 149 148 150
	- 151 152 151 153 154 155 154 156
	- 157 158 157 159 160 161 160 162
	- 163 164 163 165 166 167 166 168
	- 169 170 169 171 172 173 172 174
	- 175 176 175 177 178 179 178 180
	- 181 182 181 183 184 185 184 186
	- 187 188 187 189 190 191 190 192
	- 193 194 193 195 196 197 196 198
	- 199 200 199 201 202 203 202 204
	- 205 206 205 207 208 209 208 210
	- 211 212 211 213 214 215 214 216
	- 217 218 217 219 220 221 220 222
	- 223 224 223 225 226 227 226 228
	- 229 230 229 231 232 233 232 234
	- 235 236 235 237 238 239 238 240
	- 241 242 241 243 244 245 244 246
	- 247 248 247 249 250 251 250 252
	- 253 254 253 255 256 257 256 258
	- 259 260 259 261 262 263 262 264
	- 265 266 265 267 268 269 268 270
	- 271 272 271 273 274 275 274 276
	- 277 278 277 279 280 281 280 282
	- 283 284 283 285 286 287 286 288
	- 289 290 289 291 292 293 292 294
	- 295 296 295 297 298 299 298 300
	- 301 302 301 303 304 305 304 306
	- 307 308 307 309 310 311 310 312
	- 313 314 313 315 316 317 316 318
	- 319 320 319 321 322 323 322 324
	- 325 326 325 327 328 329 328 330
	- 331 332 331 333 334 335 334 336
	- 337 338 337 339 340 341 340 342
	- 343 344 343 345 346 347 346 348
	- 349 350 349 351 352 353 352 354
	- 355 356 355 357 358 359 358 360
	- 361 362 361 363 364 365 364 366
	- 367 368 367 369 370 371 370 372
	- 373 374 373 375 376 377 376 378
	- 379 380 379 381 382 383 382 384
	- 385 386 385 387 388 389 388 390
	- 391 392 391 393 394 395 394 396
	- 397 398 397 399 400 401 400 402
	- 403 404 403 405 406 407 406 408
	- 409 410 409 411 412 413 412 414
	- 415 416 415 417 418 419 418 420
	- 421 422 421 423 424 425 424 426
	- 427 428 427 429 430 431 430 432
	- 433 434 433 435 436 437 436 438
	- 439 440 439 441 442 443 442 444
	- 445 446 445 447 448 449 448 450
	- 451 452 451 453 454 455 454 456
	- 457 458 457 459 460 461 460 462
	- 463 464 463 465 466 467 466 468
	- 469 470 469 471 472 473 472 474
	- 475 476 475 477 478 479 478 480
	- 481 482 481 483 484 485 484 486
	- 487 488 487 489 490 491 490 492
	- 493 494 493 495 496 497 496 498
	- 499 500 499 501 502 503 502 504
	- 505 506 505 507 508 509 508 510
	- 511 512 511 513 514 515 514 516
	- 517 518 517 519 520 521 520 522
	- 523 524 523 525 526 527 526 528
	- 529 530 529 531 532 533 532 534
	- 535 536 535 537 538 539 538 540
	- 541 542 541 543 544 545 544 546
	- 547 548 547 549 550 551 550 552
	- 553 554 553 555 556 557 556 558
	- 559 560 559 561 562 563 562 564
	- 565 566 565 567 568 569 568 570
	- 571 572 571 573 574 575 574 576
	- 577 578 577 579 580 581 580 582
	- 583 584 583 585 586 587 586 588
	- 589 590 589 591 592 593 592 594
	- 595 596 595 597 598 599 598 600
	- 601 602 601 603 604 605 604 606
	- 607 608 607 609 610 611 610 612
	- 613 614 613 615 616 617 616 618
	- 619 620 619 621 622 623 622 624
	- 625 626 625 627 628 629 628 630
	- 631 632 631 633 634 635 634 636
	- 637 638 637 639 640 641 640 642
	- 643 644 643 645 646 647 646 648
	- 649 650 649 651 652 653 652 654
	- 655 656 655 657 658 659 658 660
	- 661 662 661 663 664 665 664 666
	- 667 668 667 669 670 671 670 672
	- 673 674 673 675 676 677 676 678
	- 679 680 679 681 682 683 682 684
	- 685 686 685 687 688 689 688 690
	- 691 692 691 693 694 695 694 696
	- 697 698 697 699 700 701 700 702
	- 703 704 703 705 706 707 706 708
	- 709 710 709 711 712 713 712 714
	- 715 716 715 717 718 719 718 720
	- 721 722 721 723 724 725 724 726
	- 727 728 727 729 730 731 730 732
	- 733 734 733 735 736 737 736 738
	- 739 740 739 741 742 743 742 744
	- 745 746 745 747 748 749 748 750
	- 751 752 751 753 754 755 754 756
	- 757 758 757 759 760 761 760 762
	- 763 764 763 765 766 767 766 768
	- 769 770 769 771 772 773 772 774
	- 775 776 775 777 778 779 778 780
	- 781 782 781 783 784 785 784 786
	- 787 788 787 789 790 791 790 792
	- 793 794 793 795 796 797 796 798
	- 799 800 799 801 802 803 802 804
	- 805 806 805 807 808 809 808 810
	- 811 812 811 813 814 815 814 816
	- 817 818 817 819 820 821 820 822
	- 823 824 823 825 826 827 826 828
	- 829 830 829 831 832 833 832 834
	- 835 836 835 837 838 839 838 840
	- 841 842 841 843 844 845 844 846
	- 847 848 847 849 850 851 850 852
	- 853 854 853 855 856 857 856 858
	- 859 860 859 861 862 863 862 864
	- 865 866 865 867 868 869 868 870
	- 871 872 871 873 874 875 874 876
	- 877 878 877 879 880 881 880 882
	- 883 884 883 885 886 887 886 888
	- 889 890 889 891 892 893 892 894
	- 895 896 895 897 898 899 898 900
	- 901 902 901 903 904 905 904 906
	- 907 908 907 909 910 911 910 912
	- 913 914 913 915 916 917 916 918
	- 919 920 919 921 922 923 922 924
	- 925 926 925 927 928 929 928 930
	- 931 932 931 933 934 935 934 936
	- 937 938 937 939 940 941 940 942
	- 943 944 943 945 946 947 946 948
	- 949 950 949 951 952 953 952 954
	- 955 956 955 957 958 959 958 960
	- 961 962 961 963 964 965 964 966
	- 967 968 967 969 970 971 970 972
	- 973 974 973 975 976 977 976 978
	- 979 980 979 981 982 983 982 984
	- 985 986 985 987 988 989 988 990
	- 991 992 991 993 994 995 994 996
	- 997 998 997 999 1000 1001 1000 1002
	- 1003 1004 1003 1005 1006 1007 1006 1008
	- 1009 1010 1009 1011 1012 1013 1012 1014
	- 1015 1016 1015 1017 1018 1019 1018 1020
	- 1021 1022 1021 1023 1024 1025 1024 1026
	- 1027 1028 1027 1029 1030 1031 1030 1032
	- 1033 1034 1033 1035 1036 1037 1036 1038
	- 1039 1040 1039 1041 1042 1043 1042 1044
	- 1045 1046 1045 1047 1048 1049 1048 1050
	- 1051 1052 1051 1053 1054 1055 1054 1056
	- 1057 1058 1057 1059 1060 1061 1060 1062
	- 1063 1064 1063 1065 1066 1067 1066 1068
	- 1069 1070 1069 1071 1072 1073 1072 1074
	- 1075 1076 1075 1077 1078 1079 1078 1080
	- 1081 1082 1081 1083 1084 1085 1084 1086
	- 1087 1088 1087 1089 1090 1091 1090 1092
	- 1093 1094 1093 1095 1096 1097 1096 1098
	- 1099 1100 1099 1101 1102 1103 1102 1104
	- 1105 1106 1105 1107 1108 1109 1108 1110
	- 1111 1112 1111 1113 1114 1115 1114 1116
	- 1117 1118 1117 1119 1120 1121 1120 1122
	- 1123 1124 1123 1125 1126 1127 1126 1128
	- 1129 1130 1129 1131 1132 1133 1132 1134
	- 1135 1136 1135 1137 1138 1139 1138 1140
	- 1141 1142 1141 1143 1144 1145 1144 1146
	- 1147 1148 1147 1149 1150 1151 1150 1152
	- 1153 1154 1153 1155 1156 1157 1156 1158
	- 1159 1160 1159 1161 1162 1163 1162 1164
	- 1165 1166 1165 1167 1168 1169 1168 1170
	- 1171 1172 1171 1173 1174 1175 1174 1176
	- 1177 1178 1177 1179 1180 1181 1180 1182
	- 1183 1184 1183 1185 1186 1187 1186 1188
	- 1189 1190 1189 1191 1192 1193 1192 1194
	- 1195 1196 1195 1197 1198 1199 1198 1200
	- 1201 1202 1201 1203 1204 1205 1204 1206
	- 1207 1208 1207 1209 1210 1211 1210 1212
	- 1213 1214 1213 1215 1216 1217 1216 1218
	- 1219 1220 1219 1221 1222 1223 1222 1224
	- 1225 1226 1225 1227 1228 1229 1228 1230
	- 1231 1232 1231 1233 1234 1235 1234 1236
	- 1237 1238 1237 1239 1240 1241 1240 1242
	- 1243 1244 1243 1245 1246 1247 1246 1248
	- 1249 1250 1249 1251 1252 1253 1252 1254
	- 1255 1256 1255 1257 1258 1259 1258 1260
	- 1261 1262 1261 1263 1264 1265 1264 1266
	- 1267 1268 1267 1269 1270 1271 1270 1272
	- 1273 1274 1273 1275 1276 1277 1276 1278
	- 1279 1280 1279 1281 1282 1283 1282 1284
	- 1285 1286 1285 1287 1288 1289 1288 1290
	- 1291 1292 1291 1293 1294 1295 1294 1296
	- 1297 1298 1297 1299 1300 1301 1300 1302
	- 1303 1304 1303 1305 1306 1307 1306 1308
	- 1309 1310 1309 1311 1312 1313 1312 1314
	- 1315 1316 1315 1317 1318 1319 1318 1320
	- 1321 1322 1321 1323 1324 1325 1324 1326
	- 1327 1328 1327 1329 1330 1331 1330 1332
	- 1333 1334 1333 1335 1336 1337 1336 1338
	- 1339 1340 1339 1341 1342 1343 1342 1344
	- 1345 1346 1345 1347 1348 1349 1348 1350
	- 1351 1352 1351 1353 1354 1355 1354 1356
	- 1357 1358 1357 1359 1360 1361 1360 1362
	- 1363 1364 1363 1365 1366 1367 1366 1368
	- 1369 1370 1369 1371 1372 1373 1372 1374
	- 1375 1376 1375 1377 1378 1379 1378 1380
	- 1381 1382 1381 1383 1384 1385 1384 1386
	- 1387 1388 1387 1389 1390 1391 1390 1392
	- 1393 1394 1393 1395 1396 1397 1396 1398
	- 1399 1400 1399 1401 1402 1403 1402 1404
	- 1405 1406 1405 1407 1408 1409 1408 1410
	- 1411 1412 1411 1413 1414 1415 1414 1416
	- 1417 1418 1417 1419 1420 1421 1420 1422
	- 1423 1424 1423 1425 1426 1427 1426 1428
	- 1429 1430 1429 1431 1432 1433 1432 1434
	- 1435 1436 1435 1437 1438 1439 1438 1440
	- 1441 1442 1441 1443 1444 1445 1444 1446
	- 1447 1448 1447 1449 1450 1451 1450 1452
	- 1453 1454 1453 1455 1456 1457 1456 1458
	- 1459 1460 1459 1461 1462 1463 1462 1464
	- 1465 1466 1465 1467 1468 1469 1468 1470
	- 1471 1472 1471 1473 1474 1475 1474 1476
	- 1477 1478 1477 1479 1480 1481 1480 1482
	- 1483 1484 1483 1485 1486 1487 1486 1488
	- 1489 1490 1489 1491 1492 1493 1492 1494
	- 1495 1496 1495 1497 1498 1499 1498 1500
	- 1501 1502 1501 1503 1504 1505 1504 1506
	- 1507 1508 1507 1509 1510 1511 1510 1512
	- 1513 1514 1513 1515 1516 1517 1516 1518
	- 1519 1520 1519 1521 1522 1523 1522 1524
	- 1525 1526 1525 1527 1528 1529 1528 1530
	- 1531 1532 1531 1533 1534 1535 1534 1536
	- 1537 1538 1537 1539 1540 1541 1540 1542
	- 1543 1544 1543 1545 1546 1547 1546 1548
	- 1549 1550 1549 1551 1552 1553 1552 1554
	- 1555 1556 1555 1557 1558 1559 1558 1560
	- 1561 1562 1561 1563 1564 1565 1564 1566
	- 1567 1568 1567 1569 1570 1571 1570 1572
	- 1573 1574 1573 1575 1576 1577 1576 1578
	- 1579 1580 1579 1581 1582 1583 1582 1584
	- 1585 1586 1585 1587 1588 1589 1588 1590
	- 1591 1592 1591 1593 1594 1595 1594 1596
	- 1597 1598 1597 1599 1600 1601 1600 1602
	- 1603 1604 1603 1605 1606 1607 1606 1608
	- 1609 1610 1609 1611 1612 1613 1612 1614
	- 1615 1616 1615 1617 1618 1619 1618 1620
	- 1621 1622 1621 1623 1624 1625 1624 1626
	- 1627 1628 1627 1629 1630 1631 1630 1632
	- 1633 1634 1633 1635 1636 1637 1636 1638
	- 1639 1640 1639 1641 1642 1643 1642 1644
	- 1645 1646 1645 1647 1648 1649 1648 1650
	- 1651 1652 1651 1653 1654 1655 1654 1656
	- 1657 1658 1657 1659 1660 1661 1660 1662
	- 1663 1664 1663 1665 1666 1667 1666 1668
	- 1669 1670 1669 1671 1672 1673 1672 1674
	- 1675 1676 1675 1677 1678 1679 1678 1680
	- 1681 1682 1681 1683 1684 1685 1684 1686
	- 1687 1688 1687 1689 1690 1691 1690 1692
	- 1693 1694 1693 1695 1696 1697 1696 1698
	- 1699 1700 1699 1701 1702 1703 1702 1704
	- 1705 1706 1705 1707 1708 1709 1708 1710
	- 1711 1712 1711 1713 1714 1715 1714 1716
	- 1717 1718 1717 1719 1720 1721 1720 1722
	- 1723 1724 1723 1725 1726 1727 1726 1728
	- 1729 1730 1729 1731 1732 1733 1732 1734
	- 1735 1736 1735 1737 1738 1739 1738 1740
	- 1741 1742 1741 1743 1744 1745 1744 1746
	- 1747 1748 1747 1749 1750 1751 1750 1752
	- 1753 1754 1753 1755 1756 1757 1756 1758
	- 1759 1760 1759 1761 1762 1763 1762 1764
	- 1765 1766 1765 1767 1768 1769 1768 1770
	- 1771 1772 1771 1773 1774 1775 1774 1776
	- 1777 1778 1777 1779 1780 1781 1780 1782
	- 1783 1784 1783 1785 1786 1787 1786 1788
	- 1789 1790 1789 1791 1792 1793 1792 1794
	- 1795 1796 1795 1797 1798 1799 1798 1800
	- 1801 1802 1801 1803 1804 1805 1804 1806
	- 1807 1808 1807 1809 1810 1811 1810 1812
	- 1813 1814 1813 1815 1816 1817 1816 1818
	- 1819 1820 1819 1821 1822 1823 1822 1824
	- 1825 1826 1825 1827 1828 1829 1828 1830
	- 1831 1832 1831 1833 1834 1835 1834 1836
	- 1837 1838 1837 1839 1840 1841 1840 1842
	- 1843 1844 1843 1845 1846 1847 1846 1848
	- 1849 1850 1849 1851 1852 1853 1852 1854
	- 1855 1856 1855 1857 1858 1859 1858 1860
	- 1861 1862 1861 1863 1864 1865 1864 1866
	- 1867 1868 1867 1869 1870 1871 1870 1872
	- 1873 1874 1873 1875 1876 1877 1876 1878
	- 1879 1880 1879 1881 1882 1883 1882 1884
	- 1885 1886 1885 1887 1888 1889 1888 1890
	- 1891 1892 1891 1893 1894 1895 1894 1896
	- 1897 1898 1897 1899 1900 1901 1900 1902
	- 1903 1904 1903 1905 1906 1907 1906 1908
	- 1909 1910 1909 1911 1912 1913 1912 1914
	- 1915 1916 1915 1917 1918 1919 1918 1920
	- 1921 1922 1921 1923 1924 1925 1924 1926
	- 1927 1928 1927 1929 1930 1931 1930 1932
	- 1933 1934 1933 1935 1936 1937 1936 1938
	- 1939 1940 1939 1941 1942 1943 1942 1944
	- 1945 1946 1945 1947 1948 1949 1948 1950
	- 1951 1952 1951 1953 1954 1955 1954 1956
	- 1957 1958 1957 1959 1960 1961 1960 1962
	- 1963 1964 1963 1965 1966 1967 1966 1968
	- 1969 1970 1969 1971 1972 1973 1972 1974
	- 1975 1976 1975 1977 1978 1979 1978 1980
	- 1981 1982 1981 1983 1984 1985 1984 1986
	- 1987 1988 1987 1989 1990 1991 1990 1992
	- 1993 1994 1993 1995 1996 1997 1996 1998
	- 1999 2000 1999 2001 2002 2003 2002 2004
	- 2005 2006 2005 2007 2008 2009 2008 2010
	- 2011 2012 2011 2013 2014 2015 2014 2016
	- 2017 2018 2017 2019 2020 2021 2020 2022
	- 2023 2024 2023 2025 2026 2027 2026 2028
	- 2029 2030 2029 2031 2032 2033 2032 2034
	- 2035 2036 2035 2037 2038 2039 2038 2040
	- 2041 2042 2041 2043 2044 2045 2044 2046
	- 2047 2048 2047 2049 2050 2051 2050 2052
	- 2053 2054 2053 2055 2056 2057 2056 2058
	- 2059 2060 2059 2061 2062 2063 2062 2064
	- 2065 2066 2065 2067 2068 2069 2068 2070
	- 2071 2072 2071 2073 2074 2075 2074 2076
	- 2077 2078 2077 2079 2080 2081 2080 2082
	- 2083 2084 2083 2085 2086 2087 2086 2088
	- 2089 2090 2089 2091 2092 2093 2092 2094
	- 2095 2096 2095 2097 2098 2099 2098 2100
	- 2101 2102 2101 2103 2104 2105 2104 2106
	- 2107 2108 2107 2109 2110 2111 2110 2112
	- 2113 2114 2113 2115 2116 2117 2116 2118
	- 2119 2120 2119 2121 2122 2123 2122 2124
	- 2125 2126 2125 2127 2128 2129 2128 2130
	- 2131 2132 2131 2133 2134 2135 2134 2136
	- 2137 2138 2137 2139 2140 2141 2140 2142
	- 2143 2144 2143 2145 2146 2147 2146 2148
	- 2149 2150 2149 2151 2152 2153 2152 2154
	- 2155 2156 2155 2157 2158 2159 2158 2160
	- 2161 2162 2161 2163 2164 2165 2164 2166
	- 2167 2168 2167 2169 2170 2171 2170 2172
	- 2173 2174 2173 2175 2176 2177 2176 2178
	- 2179 2180 2179 2181 2182 2183 2182 2184
	- 2185 2186 2185 2187 2188 2189 2188 2190
	- 2191 2192 2191 2193 2194 2195 2194 2196
	- 2197 2198 2197 2199 2200 2201 2200 2202
	- 2203 2204 2203 2205 2206 2207 2206 2208
	- 2209 2210 2209 2211 2212 2213 2212 2214
	- 2215 2216 2215 2217 2218 2219 2218 2220
	- 2221 2222 2221 2223 2224 2225 2224 2226
	- 2227 2228 2227 2229 2230 2231 2230 2232
	- 2233 2234 2233 2235 2236 2237 2236 2238
	- 2239 2240 2239 2241 2242 2243 2242 2244
	- 2245 2246 2245 2247 2248 2249 2248 2250
	- 2251 2252 2251 2253 2254 2255 2254 2256
	- 2257 2258 2257 2259 2260 2261 2260 2262
	- 2263 2264 2263 2265 2266 2267 2266 2268
	- 2269 2270 2269 2271 2272 2273 2272 2274
	- 2275 2276 2275 2277 2278 2279 2278 2280
	- 2281 2282 2281 2283 2284 2285 2284 2286
	- 2287 2288 2287 2289 2290 2291 2290 2292
	- 2293 2294 2293 2295 2296 2297 2296 2298
	- 2299 2300 2299 2301 2302 2303 2302 2304
	- 2305 2306 2305 2307 2308 2309 2308 2310
	- 2311 2312 2311 2313 2314 2315 2314 2316
	- 2317 2318 2317 2319 2320 2321 2320 2322
	- 2323 2324 2323 2325 2326 2327 2326 2328
	- 2329 2330 2329 2331 2332 2333 2332 2334
	- 2335 2336 2335 2337 2338 2339 2338 2340
	- 2341 2342 2341 2343 2344 2345 2344 2346
	- 2347 2348 2347 2349 2350 2351 2350 2352
	- 2353 2354 2353 2355 2356 2357 2356 2358
	- 2359 2360 2359 2361 2362 2363 2362 2364
	- 2365 2366 2365 2367 2368 2369 2368 2370
	- 2371 2372 2371 2373 2374 2375 2374 2376
	- 2377 2378 2377 2379 2380 2381 2380 2382
	- 2383 2384 2383 2385 2386 2387 2386 2388
	- 2389 2390 2389 2391 2392 2393 2392 2394
	- 2395 2396 2395 2397 2398 2399 2398 2400
	- 2401 2402 2401 2403 2404 2405 2404 2406
	- 2407 2408 2407 2409 2410 2411 2410 2412
	- 2413 2414 2413 2415 2416 2417 2416 2418
	- 2419 2420 2419 2421 2422 2423 2422 2424
	- 2425 2426 2425 2427 2428 2429 2428 2430
	- 2431 2432 2431 2433 2434 2435 2434 2436
	- 2437 2438 2437 2439 2440 2441 2440 2442
	- 2443 2444 2443 2445 2446 2447 2446 2448
	- 2449 2450 2449 2451 2452 2453 2452 2454
	- 2455 2456 2455 2457 2458 2459 2458 2460
	- 2461 2462 2461 2463 2464 2465 2464 2466
	- 2467 2468 2467 2469 2470 2471 2470 2472
	- 2473 2474 2473 2475 2476 2477 2476 2478
	- 2479 2480 2479 2481 2482 2483 2482 2484
	- 2485 2486 2485 2487 2488 2489 2488 2490
	- 2491 2492 2491 2493 2494 2495 2494 2496
	- 2497 2498 2497 2499 2500 2501 2500 2502
	- 2503 2504 2503 2505 2506 2507 2506 2508
	- 2509 2510 2509 2511 2512 2513 2512 2514
	- 2515 2516 2515 2517 2518 2519 2518 2520
	- 2521 2522 2521 2523 2524 2525 2524 2526
	- 2527 2528 2527 2529 2530 2531 2530 2532
	- 2533 2534 2533 2535 2536 2537 2536 2538
	- 2539 2540 2539 2541 2542 2543 2542 2544
	- 2545 2546 2545 2547 2548 2549 2548 2550
	- 2551 2552 2551 2553 2554 2555 2554 2556
	- 2557 2558 2557 2559 2560 2561 2560 2562
	- 2563 2564 2563 2565 2566 2567 2566 2568
	- 2569 2570 2569 2571 2572 2573 2572 2574
	- 2575 2576 2575 2577 2578 2579 2578 2580
	- 2581 2582 2581 2583 2584 2585 2584 2586
	- 2587 2588 2587 2589 2590 2591 2590 2592
	- 2593 2594 2593 2595 2596 2597 2596 2598
	- 2599 2600 2599 2601 2602 2603 2602 2604
	- 2605 2606 2605 2607 2608 2609 2608 2610
	- 2611 2612 2611 2613 2614 2615 2614 2616
	- 2617 2618 2617 2619 2620 2621 2620 2622
	- 2623 2624 2623 2625 2626 2627 2626 2628
	- 2629 2630 2629 2631 2632 2633 2632 2634
	- 2635 2636 2635 2637 2638 2639 2638 2640
	- 2641 2642 2641 2643 2644 2645 2644 2646
	- 2647 2648 2647 2649 2650 2651 2650 2652
	- 2653 2654 2653 2655 2656 2657 2656 2658
	- 2659 2660 2659 2661 2662 2663 2662 2664
	- 2665 2666 2665 2667 2668 2669 2668 2670
	- 2671 2672 2671 2673 2674 2675 2674 2676
	- 2677 2678 2677 2679 2680 2681 2680 2682
	- 2683 2684 2683 2685 2686 2687 2686 2688
	- 2689 2690 2689 2691 2692 2693 2692 2694
	- 2695 2696 2695 2697 2698 2699 2698 2700
	- 2701 2702 2701 2703 2704 2705 2704 2706
	- 2707 2708 2707 2709 2710 2711 2710 2712
	- 2713 2714 2713 2715 2716 2717 2716 2718
	- 2719 2720 2719 2721 2722 2723 2722 2724
	- 2725 2726 2725 2727 2728 2729 2728 2730
	- 2731 2732 2731 2733 2734 2735 2734 2736
	- 2737 2738 2737 2739 2740 2741 2740 2742
	- 2743 2744 2743 2745 2746 2747 2746 2748
	- 2749 2750 2749 2751 2752 2753 2752 2754
	- 2755 2756 2755 2757 2758 2759 2758 2760
	- 2761 2762 2761 2763 2764 2765 2764 2766
	- 2767 2768 2767 2769 2770 2771 2770 2772
	- 2773 2774 2773 2775 2776 2777 2776 2778
	- 2779 2780 2779 2781 2782 2783 2782 2784
	- 2785 2786 2785 2787 2788 2789 2788 2790
	- 2791 2792 2791 2793 2794 2795 2794 2796
	- 2797 2798 2797 2799 2800 2801 2800 2802
	- 2803 2804 2803 2805 2806 2807 2806 2808
	- 2809 2810 2809 2811 2812 2813 2812 2814
	- 2815 2816 2815 2817 2818 2819 2818 2820
	- 2821 2822 2821 2823 2824 2825 2824 2826
	- 2827 2828 2827 2829 2830 2831 2830 2832
	- 2833 2834 2833 2835 2836 2837 2836 2838
	- 2839 2840 2839 2841 2842 2843 2842 2844
	- 2845 2846 2845 2847 2848 2849 2848 2850
	- 2851 2852 2851 2853 2854 2855 2854 2856
	- 2857 2858 2857 2859 2860 2861 2860 2862
	- 2863 2864 2863 2865 2866 2867 2866 2868
	- 2869 2870 2869 2871 2872 2873 2872 2874
	- 2875 2876 2875 2877 2878 2879 2878 2880
	- 2881 2882 2881 2883 2884 2885 2884 2886
	- 2887 2888 2887 2889 2890 2891 2890 2892
	- 2893 2894 2893 2895 2896 2897 2896 2898
	- 2899 2900 2899 2901 2902 2903 2902 2904
	- 2905 2906 2905 2907 2908 2909 2908 2910
	- 2911 2912 2911 2913 2914 2915 2914 2916
	- 2917 2918 2917 2919 2920 2921 2920 2922
	- 2923 2924 2923 2925 2926 2927 2926 2928
	- 2929 2930 2929 2931 2932 2933 2932 2934
	- 2935 2936 2935 2937 2938 2939 2938 2940
	- 2941 2942 2941 2943 2944 2945 2944 2946
	- 2947 2948 2947 2949 2950 2951 2950 2952
	- 2953 2954 2953 2955 2956 2957 2956 2958
	- 2959 2960 2959 2961 2962 2963 2962 2964
	- 2965 2966 2965 2967 2968 2969 2968 2970
	- 2971 2972 2971 2973 2974 2975 2974 2976
	- 2977 2978 2977 2979 2980 2981 2980 2982
	- 2983 2984 2983 2985 2986 2987 2986 2988
	- 2989 2990 2989 2991 2992 2993 2992 2994
	- 2995 2996 2995 2997 2998 2999 2998 3000
	-
	- 1000 !NTHETA: angles
	- 2 1 3 5 4 6 8 7 9
	- 11 10 12 14 13 15 17 16 18
	- 20 19 21 23 22 24 26 25 27
	- 29 28 30 32 31 33 35 34 36
	- 38 37 39 41 40 42 44 43 45
	- 47 46 48 50 49 51 53 52 54
	- 56 55 57 59 58 60 62 61 63
	- 65 64 66 68 67 69 71 70 72
	- 74 73 75 77 76 78 80 79 81
	- 83 82 84 86 85 87 89 88 90
	- 92 91 93 95 94 96 98 97 99
	- 101 100 102 104 103 105 107 106 108
	- 110 109 111 113 112 114 116 115 117
	- 119 118 120 122 121 123 125 124 126
	- 128 127 129 131 130 132 134 133 135
	- 137 136 138 140 139 141 143 142 144
	- 146 145 147 149 148 150 152 151 153
	- 155 154 156 158 157 159 161 160 162
	- 164 163 165 167 166 168 170 169 171
	- 173 172 174 176 175 177 179 178 180
	- 182 181 183 185 184 186 188 187 189
	- 191 190 192 194 193 195 197 196 198
	- 200 199 201 203 202 204 206 205 207
	- 209 208 210 212 211 213 215 214 216
	- 218 217 219 221 220 222 224 223 225
	- 227 226 228 230 229 231 233 232 234
	- 236 235 237 239 238 240 242 241 243
	- 245 244 246 248 247 249 251 250 252
	- 254 253 255 257 256 258 260 259 261
	- 263 262 264 266 265 267 269 268 270
	- 272 271 273 275 274 276 278 277 279
	- 281 280 282 284 283 285 287 286 288
	- 290 289 291 293 292 294 296 295 297
	- 299 298 300 302 301 303 305 304 306
	- 308 307 309 311 310 312 314 313 315
	- 317 316 318 320 319 321 323 322 324
	- 326 325 327 329 328 330 332 331 333
	- 335 334 336 338 337 339 341 340 342
	- 344 343 345 347 346 348 350 349 351
	- 353 352 354 356 355 357 359 358 360
	- 362 361 363 365 364 366 368 367 369
	- 371 370 372 374 373 375 377 376 378
	- 380 379 381 383 382 384 386 385 387
	- 389 388 390 392 391 393 395 394 396
	- 398 397 399 401 400 402 404 403 405
	- 407 406 408 410 409 411 413 412 414
	- 416 415 417 419 418 420 422 421 423
	- 425 424 426 428 427 429 431 430 432
	- 434 433 435 437 436 438 440 439 441
	- 443 442 444 446 445 447 449 448 450
	- 452 451 453 455 454 456 458 457 459
	- 461 460 462 464 463 465 467 466 468
	- 470 469 471 473 472 474 476 475 477
	- 479 478 480 482 481 483 485 484 486
	- 488 487 489 491 490 492 494 493 495
	- 497 496 498 500 499 501 503 502 504
	- 506 505 507 509 508 510 512 511 513
	- 515 514 516 518 517 519 521 520 522
	- 524 523 525 527 526 528 530 529 531
	- 533 532 534 536 535 537 539 538 540
	- 542 541 543 545 544 546 548 547 549
	- 551 550 552 554 553 555 557 556 558
	- 560 559 561 563 562 564 566 565 567
	- 569 568 570 572 571 573 575 574 576
	- 578 577 579 581 580 582 584 583 585
	- 587 586 588 590 589 591 593 592 594
	- 596 595 597 599 598 600 602 601 603
	- 605 604 606 608 607 609 611 610 612
	- 614 613 615 617 616 618 620 619 621
	- 623 622 624 626 625 627 629 628 630
	- 632 631 633 635 634 636 638 637 639
	- 641 640 642 644 643 645 647 646 648
	- 650 649 651 653 652 654 656 655 657
	- 659 658 660 662 661 663 665 664 666
	- 668 667 669 671 670 672 674 673 675
	- 677 676 678 680 679 681 683 682 684
	- 686 685 687 689 688 690 692 691 693
	- 695 694 696 698 697 699 701 700 702
	- 704 703 705 707 706 708 710 709 711
	- 713 712 714 716 715 717 719 718 720
	- 722 721 723 725 724 726 728 727 729
	- 731 730 732 734 733 735 737 736 738
	- 740 739 741 743 742 744 746 745 747
	- 749 748 750 752 751 753 755 754 756
	- 758 757 759 761 760 762 764 763 765
	- 767 766 768 770 769 771 773 772 774
	- 776 775 777 779 778 780 782 781 783
	- 785 784 786 788 787 789 791 790 792
	- 794 793 795 797 796 798 800 799 801
	- 803 802 804 806 805 807 809 808 810
	- 812 811 813 815 814 816 818 817 819
	- 821 820 822 824 823 825 827 826 828
	- 830 829 831 833 832 834 836 835 837
	- 839 838 840 842 841 843 845 844 846
	- 848 847 849 851 850 852 854 853 855
	- 857 856 858 860 859 861 863 862 864
	- 866 865 867 869 868 870 872 871 873
	- 875 874 876 878 877 879 881 880 882
	- 884 883 885 887 886 888 890 889 891
	- 893 892 894 896 895 897 899 898 900
	- 902 901 903 905 904 906 908 907 909
	- 911 910 912 914 913 915 917 916 918
	- 920 919 921 923 922 924 926 925 927
	- 929 928 930 932 931 933 935 934 936
	- 938 937 939 941 940 942 944 943 945
	- 947 946 948 950 949 951 953 952 954
	- 956 955 957 959 958 960 962 961 963
	- 965 964 966 968 967 969 971 970 972
	- 974 973 975 977 976 978 980 979 981
	- 983 982 984 986 985 987 989 988 990
	- 992 991 993 995 994 996 998 997 999
	- 1001 1000 1002 1004 1003 1005 1007 1006 1008
	- 1010 1009 1011 1013 1012 1014 1016 1015 1017
	- 1019 1018 1020 1022 1021 1023 1025 1024 1026
	- 1028 1027 1029 1031 1030 1032 1034 1033 1035
	- 1037 1036 1038 1040 1039 1041 1043 1042 1044
	- 1046 1045 1047 1049 1048 1050 1052 1051 1053
	- 1055 1054 1056 1058 1057 1059 1061 1060 1062
	- 1064 1063 1065 1067 1066 1068 1070 1069 1071
	- 1073 1072 1074 1076 1075 1077 1079 1078 1080
	- 1082 1081 1083 1085 1084 1086 1088 1087 1089
	- 1091 1090 1092 1094 1093 1095 1097 1096 1098
	- 1100 1099 1101 1103 1102 1104 1106 1105 1107
	- 1109 1108 1110 1112 1111 1113 1115 1114 1116
	- 1118 1117 1119 1121 1120 1122 1124 1123 1125
	- 1127 1126 1128 1130 1129 1131 1133 1132 1134
	- 1136 1135 1137 1139 1138 1140 1142 1141 1143
	- 1145 1144 1146 1148 1147 1149 1151 1150 1152
	- 1154 1153 1155 1157 1156 1158 1160 1159 1161
	- 1163 1162 1164 1166 1165 1167 1169 1168 1170
	- 1172 1171 1173 1175 1174 1176 1178 1177 1179
	- 1181 1180 1182 1184 1183 1185 1187 1186 1188
	- 1190 1189 1191 1193 1192 1194 1196 1195 1197
	- 1199 1198 1200 1202 1201 1203 1205 1204 1206
	- 1208 1207 1209 1211 1210 1212 1214 1213 1215
	- 1217 1216 1218 1220 1219 1221 1223 1222 1224
	- 1226 1225 1227 1229 1228 1230 1232 1231 1233
	- 1235 1234 1236 1238 1237 1239 1241 1240 1242
	- 1244 1243 1245 1247 1246 1248 1250 1249 1251
	- 1253 1252 1254 1256 1255 1257 1259 1258 1260
	- 1262 1261 1263 1265 1264 1266 1268 1267 1269
	- 1271 1270 1272 1274 1273 1275 1277 1276 1278
	- 1280 1279 1281 1283 1282 1284 1286 1285 1287
	- 1289 1288 1290 1292 1291 1293 1295 1294 1296
	- 1298 1297 1299 1301 1300 1302 1304 1303 1305
	- 1307 1306 1308 1310 1309 1311 1313 1312 1314
	- 1316 1315 1317 1319 1318 1320 1322 1321 1323
	- 1325 1324 1326 1328 1327 1329 1331 1330 1332
	- 1334 1333 1335 1337 1336 1338 1340 1339 1341
	- 1343 1342 1344 1346 1345 1347 1349 1348 1350
	- 1352 1351 1353 1355 1354 1356 1358 1357 1359
	- 1361 1360 1362 1364 1363 1365 1367 1366 1368
	- 1370 1369 1371 1373 1372 1374 1376 1375 1377
	- 1379 1378 1380 1382 1381 1383 1385 1384 1386
	- 1388 1387 1389 1391 1390 1392 1394 1393 1395
	- 1397 1396 1398 1400 1399 1401 1403 1402 1404
	- 1406 1405 1407 1409 1408 1410 1412 1411 1413
	- 1415 1414 1416 1418 1417 1419 1421 1420 1422
	- 1424 1423 1425 1427 1426 1428 1430 1429 1431
	- 1433 1432 1434 1436 1435 1437 1439 1438 1440
	- 1442 1441 1443 1445 1444 1446 1448 1447 1449
	- 1451 1450 1452 1454 1453 1455 1457 1456 1458
	- 1460 1459 1461 1463 1462 1464 1466 1465 1467
	- 1469 1468 1470 1472 1471 1473 1475 1474 1476
	- 1478 1477 1479 1481 1480 1482 1484 1483 1485
	- 1487 1486 1488 1490 1489 1491 1493 1492 1494
	- 1496 1495 1497 1499 1498 1500 1502 1501 1503
	- 1505 1504 1506 1508 1507 1509 1511 1510 1512
	- 1514 1513 1515 1517 1516 1518 1520 1519 1521
	- 1523 1522 1524 1526 1525 1527 1529 1528 1530
	- 1532 1531 1533 1535 1534 1536 1538 1537 1539
	- 1541 1540 1542 1544 1543 1545 1547 1546 1548
	- 1550 1549 1551 1553 1552 1554 1556 1555 1557
	- 1559 1558 1560 1562 1561 1563 1565 1564 1566
	- 1568 1567 1569 1571 1570 1572 1574 1573 1575
	- 1577 1576 1578 1580 1579 1581 1583 1582 1584
	- 1586 1585 1587 1589 1588 1590 1592 1591 1593
	- 1595 1594 1596 1598 1597 1599 1601 1600 1602
	- 1604 1603 1605 1607 1606 1608 1610 1609 1611
	- 1613 1612 1614 1616 1615 1617 1619 1618 1620
	- 1622 1621 1623 1625 1624 1626 1628 1627 1629
	- 1631 1630 1632 1634 1633 1635 1637 1636 1638
	- 1640 1639 1641 1643 1642 1644 1646 1645 1647
	- 1649 1648 1650 1652 1651 1653 1655 1654 1656
	- 1658 1657 1659 1661 1660 1662 1664 1663 1665
	- 1667 1666 1668 1670 1669 1671 1673 1672 1674
	- 1676 1675 1677 1679 1678 1680 1682 1681 1683
	- 1685 1684 1686 1688 1687 1689 1691 1690 1692
	- 1694 1693 1695 1697 1696 1698 1700 1699 1701
	- 1703 1702 1704 1706 1705 1707 1709 1708 1710
	- 1712 1711 1713 1715 1714 1716 1718 1717 1719
	- 1721 1720 1722 1724 1723 1725 1727 1726 1728
	- 1730 1729 1731 1733 1732 1734 1736 1735 1737
	- 1739 1738 1740 1742 1741 1743 1745 1744 1746
	- 1748 1747 1749 1751 1750 1752 1754 1753 1755
	- 1757 1756 1758 1760 1759 1761 1763 1762 1764
	- 1766 1765 1767 1769 1768 1770 1772 1771 1773
	- 1775 1774 1776 1778 1777 1779 1781 1780 1782
	- 1784 1783 1785 1787 1786 1788 1790 1789 1791
	- 1793 1792 1794 1796 1795 1797 1799 1798 1800
	- 1802 1801 1803 1805 1804 1806 1808 1807 1809
	- 1811 1810 1812 1814 1813 1815 1817 1816 1818
	- 1820 1819 1821 1823 1822 1824 1826 1825 1827
	- 1829 1828 1830 1832 1831 1833 1835 1834 1836
	- 1838 1837 1839 1841 1840 1842 1844 1843 1845
	- 1847 1846 1848 1850 1849 1851 1853 1852 1854
	- 1856 1855 1857 1859 1858 1860 1862 1861 1863
	- 1865 1864 1866 1868 1867 1869 1871 1870 1872
	- 1874 1873 1875 1877 1876 1878 1880 1879 1881
	- 1883 1882 1884 1886 1885 1887 1889 1888 1890
	- 1892 1891 1893 1895 1894 1896 1898 1897 1899
	- 1901 1900 1902 1904 1903 1905 1907 1906 1908
	- 1910 1909 1911 1913 1912 1914 1916 1915 1917
	- 1919 1918 1920 1922 1921 1923 1925 1924 1926
	- 1928 1927 1929 1931 1930 1932 1934 1933 1935
	- 1937 1936 1938 1940 1939 1941 1943 1942 1944
	- 1946 1945 1947 1949 1948 1950 1952 1951 1953
	- 1955 1954 1956 1958 1957 1959 1961 1960 1962
	- 1964 1963 1965 1967 1966 1968 1970 1969 1971
	- 1973 1972 1974 1976 1975 1977 1979 1978 1980
	- 1982 1981 1983 1985 1984 1986 1988 1987 1989
	- 1991 1990 1992 1994 1993 1995 1997 1996 1998
	- 2000 1999 2001 2003 2002 2004 2006 2005 2007
	- 2009 2008 2010 2012 2011 2013 2015 2014 2016
	- 2018 2017 2019 2021 2020 2022 2024 2023 2025
	- 2027 2026 2028 2030 2029 2031 2033 2032 2034
	- 2036 2035 2037 2039 2038 2040 2042 2041 2043
	- 2045 2044 2046 2048 2047 2049 2051 2050 2052
	- 2054 2053 2055 2057 2056 2058 2060 2059 2061
	- 2063 2062 2064 2066 2065 2067 2069 2068 2070
	- 2072 2071 2073 2075 2074 2076 2078 2077 2079
	- 2081 2080 2082 2084 2083 2085 2087 2086 2088
	- 2090 2089 2091 2093 2092 2094 2096 2095 2097
	- 2099 2098 2100 2102 2101 2103 2105 2104 2106
	- 2108 2107 2109 2111 2110 2112 2114 2113 2115
	- 2117 2116 2118 2120 2119 2121 2123 2122 2124
	- 2126 2125 2127 2129 2128 2130 2132 2131 2133
	- 2135 2134 2136 2138 2137 2139 2141 2140 2142
	- 2144 2143 2145 2147 2146 2148 2150 2149 2151
	- 2153 2152 2154 2156 2155 2157 2159 2158 2160
	- 2162 2161 2163 2165 2164 2166 2168 2167 2169
	- 2171 2170 2172 2174 2173 2175 2177 2176 2178
	- 2180 2179 2181 2183 2182 2184 2186 2185 2187
	- 2189 2188 2190 2192 2191 2193 2195 2194 2196
	- 2198 2197 2199 2201 2200 2202 2204 2203 2205
	- 2207 2206 2208 2210 2209 2211 2213 2212 2214
	- 2216 2215 2217 2219 2218 2220 2222 2221 2223
	- 2225 2224 2226 2228 2227 2229 2231 2230 2232
	- 2234 2233 2235 2237 2236 2238 2240 2239 2241
	- 2243 2242 2244 2246 2245 2247 2249 2248 2250
	- 2252 2251 2253 2255 2254 2256 2258 2257 2259
	- 2261 2260 2262 2264 2263 2265 2267 2266 2268
	- 2270 2269 2271 2273 2272 2274 2276 2275 2277
	- 2279 2278 2280 2282 2281 2283 2285 2284 2286
	- 2288 2287 2289 2291 2290 2292 2294 2293 2295
	- 2297 2296 2298 2300 2299 2301 2303 2302 2304
	- 2306 2305 2307 2309 2308 2310 2312 2311 2313
	- 2315 2314 2316 2318 2317 2319 2321 2320 2322
	- 2324 2323 2325 2327 2326 2328 2330 2329 2331
	- 2333 2332 2334 2336 2335 2337 2339 2338 2340
	- 2342 2341 2343 2345 2344 2346 2348 2347 2349
	- 2351 2350 2352 2354 2353 2355 2357 2356 2358
	- 2360 2359 2361 2363 2362 2364 2366 2365 2367
	- 2369 2368 2370 2372 2371 2373 2375 2374 2376
	- 2378 2377 2379 2381 2380 2382 2384 2383 2385
	- 2387 2386 2388 2390 2389 2391 2393 2392 2394
	- 2396 2395 2397 2399 2398 2400 2402 2401 2403
	- 2405 2404 2406 2408 2407 2409 2411 2410 2412
	- 2414 2413 2415 2417 2416 2418 2420 2419 2421
	- 2423 2422 2424 2426 2425 2427 2429 2428 2430
	- 2432 2431 2433 2435 2434 2436 2438 2437 2439
	- 2441 2440 2442 2444 2443 2445 2447 2446 2448
	- 2450 2449 2451 2453 2452 2454 2456 2455 2457
	- 2459 2458 2460 2462 2461 2463 2465 2464 2466
	- 2468 2467 2469 2471 2470 2472 2474 2473 2475
	- 2477 2476 2478 2480 2479 2481 2483 2482 2484
	- 2486 2485 2487 2489 2488 2490 2492 2491 2493
	- 2495 2494 2496 2498 2497 2499 2501 2500 2502
	- 2504 2503 2505 2507 2506 2508 2510 2509 2511
	- 2513 2512 2514 2516 2515 2517 2519 2518 2520
	- 2522 2521 2523 2525 2524 2526 2528 2527 2529
	- 2531 2530 2532 2534 2533 2535 2537 2536 2538
	- 2540 2539 2541 2543 2542 2544 2546 2545 2547
	- 2549 2548 2550 2552 2551 2553 2555 2554 2556
	- 2558 2557 2559 2561 2560 2562 2564 2563 2565
	- 2567 2566 2568 2570 2569 2571 2573 2572 2574
	- 2576 2575 2577 2579 2578 2580 2582 2581 2583
	- 2585 2584 2586 2588 2587 2589 2591 2590 2592
	- 2594 2593 2595 2597 2596 2598 2600 2599 2601
	- 2603 2602 2604 2606 2605 2607 2609 2608 2610
	- 2612 2611 2613 2615 2614 2616 2618 2617 2619
	- 2621 2620 2622 2624 2623 2625 2627 2626 2628
	- 2630 2629 2631 2633 2632 2634 2636 2635 2637
	- 2639 2638 2640 2642 2641 2643 2645 2644 2646
	- 2648 2647 2649 2651 2650 2652 2654 2653 2655
	- 2657 2656 2658 2660 2659 2661 2663 2662 2664
	- 2666 2665 2667 2669 2668 2670 2672 2671 2673
	- 2675 2674 2676 2678 2677 2679 2681 2680 2682
	- 2684 2683 2685 2687 2686 2688 2690 2689 2691
	- 2693 2692 2694 2696 2695 2697 2699 2698 2700
	- 2702 2701 2703 2705 2704 2706 2708 2707 2709
	- 2711 2710 2712 2714 2713 2715 2717 2716 2718
	- 2720 2719 2721 2723 2722 2724 2726 2725 2727
	- 2729 2728 2730 2732 2731 2733 2735 2734 2736
	- 2738 2737 2739 2741 2740 2742 2744 2743 2745
	- 2747 2746 2748 2750 2749 2751 2753 2752 2754
	- 2756 2755 2757 2759 2758 2760 2762 2761 2763
	- 2765 2764 2766 2768 2767 2769 2771 2770 2772
	- 2774 2773 2775 2777 2776 2778 2780 2779 2781
	- 2783 2782 2784 2786 2785 2787 2789 2788 2790
	- 2792 2791 2793 2795 2794 2796 2798 2797 2799
	- 2801 2800 2802 2804 2803 2805 2807 2806 2808
	- 2810 2809 2811 2813 2812 2814 2816 2815 2817
	- 2819 2818 2820 2822 2821 2823 2825 2824 2826
	- 2828 2827 2829 2831 2830 2832 2834 2833 2835
	- 2837 2836 2838 2840 2839 2841 2843 2842 2844
	- 2846 2845 2847 2849 2848 2850 2852 2851 2853
	- 2855 2854 2856 2858 2857 2859 2861 2860 2862
	- 2864 2863 2865 2867 2866 2868 2870 2869 2871
	- 2873 2872 2874 2876 2875 2877 2879 2878 2880
	- 2882 2881 2883 2885 2884 2886 2888 2887 2889
	- 2891 2890 2892 2894 2893 2895 2897 2896 2898
	- 2900 2899 2901 2903 2902 2904 2906 2905 2907
	- 2909 2908 2910 2912 2911 2913 2915 2914 2916
	- 2918 2917 2919 2921 2920 2922 2924 2923 2925
	- 2927 2926 2928 2930 2929 2931 2933 2932 2934
	- 2936 2935 2937 2939 2938 2940 2942 2941 2943
	- 2945 2944 2946 2948 2947 2949 2951 2950 2952
	- 2954 2953 2955 2957 2956 2958 2960 2959 2961
	- 2963 2962 2964 2966 2965 2967 2969 2968 2970
	- 2972 2971 2973 2975 2974 2976 2978 2977 2979
	- 2981 2980 2982 2984 2983 2985 2987 2986 2988
	- 2990 2989 2991 2993 2992 2994 2996 2995 2997
	- 2999 2998 3000
	-
	- 0 !NPHI: dihedrals
	-
	-
	- 0 !NIMPHI: impropers
	-
	-
	- 0 !NDON: donors
	-
	-
	- 0 !NACC: acceptors
	-
	-
	- 0 !NNB
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	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 0 0 0 0 0 0 0 0
	- 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/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg
	deleted file mode 100644
	index 60aaf90b9..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
	deleted file mode 100644
	index 2c34754c4..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg
	deleted file mode 100644
	index 220a71727..000000000
	Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg and /dev/null differ
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt
	deleted file mode 100644
	index 5de99b2af..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt
	+++ /dev/null
	@@ -1,58 +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 {
	- write_once("In Settings") {
	- pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.212
	- }
	-
	- 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 ions type @atom:NaIon/Na @atom:ClIon/Cl
	-}
	-
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
	deleted file mode 100644
	index 3bb7bca40..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/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 200.0 1.0
	- angle_coeff @angle:HOH harmonic 200.0 109.47
	- 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/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt
	deleted file mode 100644
	index a0f4d5a96..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-import "ions.lt" # <- This defines the ions "NaIon" and "ClIon".
	-
	-import "spce.lt" # <- This defines the SPCE water molecule. This file is
	- # located in the "common" directory. You can either copy it
	- # here, or (preferably), you can define a MOLTEMPLATE_PATH
	- # environment variable and point it to "common".
	- # (as explained in the installation section of the manual).
	-
	-
	-# 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, 0.01)
	- [10].move(3.45, 0.01, 0.01)
	-
	-# 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(5,5,5)
	-cl[][][*].move(12,12,12)
	-
	-# (The (5,5,5) and (12,12,12) 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/all_atom_examples/waterSPCE+Na+Cl/run.in.min b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.min
	deleted file mode 100644
	index 992bcd22e..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.min
	+++ /dev/null
	@@ -1,26 +0,0 @@
	-# ------------------------------- Initialization Section --------------------
	-
	-include system.in.init
	-
	-# ------------------------------- Atom Definition Section -------------------
	-
	-read_data system.data
	-
	-# ------------------------------- Settings Section --------------------------
	-
	-include system.in.settings
	-
	-# ------------------------------- Run Section -------------------------------
	-
	-dump 1 all custom 20 traj_min.lammpstrj id mol type x y z ix iy iz
	-
	-# fSHAKE was defined in system.in.settings. It is incompatible with "minimize".
	-unfix fSHAKE
	-minimize 1.0e-5 1.0e-7 100000 400000
	-
	-# (For a system with ~6000 atoms, this takes 1-4 minutes on a i7 720 processor.)
	-# Alternate (faster) minimizer settings (about 10 sec):
	-# minimize 1.0e-4 1.0e-6 500 2000
	-
	-
	-write_restart system_after_min.rst
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
	deleted file mode 100644
	index dff24722b..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-# ------------------------------- Initialization Section --------------------
	-
	-include system.in.init
	-
	-# ------------------------------- Atom Definition Section -------------------
	-
	-# I probably should minimize the system first,
	-# but it turns out to not be necessary in this case.
	-# Instead I just read the raw atom coordinates generated by moltemplate.
	-read_data system.data
	-
	-# ------------------------------- Settings Section --------------------------
	-
	-include system.in.settings
	-
	-# ------------------------------- Run Section -------------------------------
	-
	-
	-timestep 2.0
	-dump 1 all custom 100 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 50000
	-
	-write_restart system_after_npt.rst
	diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
	deleted file mode 100644
	index c42223a16..000000000
	--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
	+++ /dev/null
	@@ -1,33 +0,0 @@
	-# ------------------------------- Initialization Section --------------------
	-
	-include system.in.init
	-
	-# ------------------------------- Atom Definition Section -------------------
	-
	-#read_data system.data
	-#read_restart system_after_min.rst
	-read_restart system_after_npt.rst
	-
	-# ------------------------------- 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
	-#thermo_modify flush yes
	-
	-
	-restart 100000 restart_nvt
	-
	-run 1000000
	-
	-write_restart system_after_nvt.rst
	-
	-
	diff --git a/tools/moltemplate/moltemplate_manual.pdf b/tools/moltemplate/moltemplate_manual.pdf
	deleted file mode 100644
	index 6d0d66754..000000000
	--- a/tools/moltemplate/moltemplate_manual.pdf
	+++ /dev/null
	@@ -1,9291 +0,0 @@
	-%PDF-1.4
	-%ÐÔÅØ
	-1 0 obj
	-<< /S /GoTo /D (section.1) >>
	-endobj
	-4 0 obj
	-(Introduction)
	-endobj
	-5 0 obj
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	-endobj
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	-endobj
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	-endobj
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	-endobj
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	-(Introductory tutorial)
	-endobj
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	-endobj
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	-endobj
	-56 0 obj
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	-endobj
	-57 0 obj
	-<< /S /GoTo /D (subsection.5.1) >>
	-endobj
	-60 0 obj
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	-endobj
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	-endobj
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	-endobj
	-89 0 obj
	-<< /S /GoTo /D (subsection.5.4) >>
	-endobj
	-92 0 obj
	-(``Data'' and ``In'')
	-endobj
	-93 0 obj
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	-endobj
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	-endobj
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	-endobj
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	-endobj
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	-(Building a simple polymer)
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	-endobj
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	-endobj
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	-endobj
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	-endobj
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	-trailer
	-<< /Size 1001
	-/Root 999 0 R
	-/Info 1000 0 R
	-/ID [<BD3B56AAEB55B2B24B1E8DDB7274543D> <BD3B56AAEB55B2B24B1E8DDB7274543D>] >>
	-startxref
	-745139
	-%%EOF
	diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py
	deleted file mode 100755
	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 100755
	index 663d66a0a..000000000
	--- a/tools/moltemplate/src/ltemplify.py
	+++ /dev/null
	@@ -1,2034 +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 .ttree 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.ttree
	-
	-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.ttree").
	-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 StringToInterval(sel_str, slice_delim='*'):
	- i_slice = sel_str.find(slice_delim)
	-
	- if i_slice == -1:
	- if sel_str.isdigit():
	- a = int(sel_str)
	- b = int(sel_str)
	- else:
	- a = sel_str
	- b = sel_str
	-
	- else:
	- a = sel_str[:i_slice]
	- b = sel_str[i_slice+len(slice_delim):]
	-
	- if (((len(a)>0) and (not a.isdigit())) or
	- ((len(b)>0) and (not b.isdigit()))):
	- raise InputError('Error: invalid selection string \"'+
	- sel_str+'\"\n')
	- if (len(a) > 0):
	- a = int(a)
	- else:
	- a = None
	-
	- if (len(b) > 0):
	- b = int(b)
	- else:
	- b = None
	-
	- return a,b
	-
	-
	-# Selections are simply lists of 2-tuples (pairs)
	-
	-def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '):
	-
	- """
	- This function converts a string such as "14 6 912" into
	- a list of tuples, for example: [(1,4), (6,6), (9,12)]
	- 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()
	- (a,b) = StringToInterval(token, slice_delim)
	- selection_list.append((a, b))
	-
	- 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 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 = 'lemplify.py'
	- g_version_str = '0.3'
	- g_date_str = '2012-12-11'
	- 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_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
	-
	-
	- # To process the selections, we need to know the atom style:
	- atom_style_undefined = True
	-
	- i_atomid = None
	- i_atomtype = None
	- i_molid = 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_data_masses = []
	- l_data_bond_coeffs = []
	- l_data_angle_coeffs = []
	- l_data_dihedral_coeffs = []
	- l_data_improper_coeffs = []
	- l_data_pair_coeffs = []
	- l_data_atoms = []
	- l_data_velocities = []
	- l_data_bonds = []
	- l_data_angles = []
	- l_data_dihedrals = []
	- l_data_impropers = []
	-
	- # class2 force fields
	- 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
	-
	-
	- argv = 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] == '-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)
	- 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() == '-$atoms')
	- ):
	- if i+1 >= len(argv):
	- raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n'
	- ' (or strings). These identify the group of atoms you want to\n'
	- ' to include in the template you are creating.\n')
	- atomid_selection += LammpsSelectToIntervals(argv[i+1])
	- min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection)
	- del(argv[i:i+2])
	- elif ((argv[i].lower() == '-type') or
	- #(argv[i].lower() == '-t') or
	- (argv[i].lower() == '-atomtype') or
	- (argv[i].lower() == '-atom-type')
	- #(argv[i].lower() == '-atomtypes') or
	- #(argv[i].lower() == '-atom-types') or
	- #(argv[i].lower() == '-@atom') or
	- #(argv[i].lower() == '-@atoms') or
	- #(argv[i].lower() == '-@atomtype') or
	- #(argv[i].lower() == '-@atomtypes')
	- ):
	- if i+1 >= len(argv):
	- raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n'
	- ' (or strings). These identify the group of atom types you want to\n'
	- ' to include in the template you are creating.\n')
	- atomtype_selection += LammpsSelectToIntervals(argv[i+1])
	- min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection)
	- del(argv[i:i+2])
	- elif ((argv[i].lower() == '-mol') or
	- #(argv[i].lower() == '-m') or
	- (argv[i].lower() == '-molid') or
	- #(argv[i].lower() == '-molids') or
	- (argv[i].lower() == '-mol-id') or
	- #(argv[i].lower() == '-mol-ids') or
	- #(argv[i].lower() == '-molecule') or
	- (argv[i].lower() == '-moleculeid') or
	- (argv[i].lower() == '-molecule-id')
	- #(argv[i].lower() == '-molecules') or
	- #(argv[i].lower() == '-molecule-ids') or
	- #(argv[i].lower() == '-$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
	-
	- if atom_style_undefined:
	- # The default atom_style is "full"
	- column_names = AtomStyle2ColNames('full')
	- i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
	-
	- #---------------------------------------------------------
	- #-- 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)
	-
	- 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',
	- 'impoper_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(' processing \"'+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(' processing \"'+line.strip()+'\"\n')
	- atoms_already_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) <= 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
	- (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_atomtype] = '@atom:type'+tokens[i_atomtype]
	- if i_molid:
	- tokens[i_molid] = '$mol:id'+tokens[i_molid]
	- l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n'))
	- needed_atomids.add(atomid)
	- needed_atomtypes.add(int(atomtype))
	-
	- for atomtype in needed_atomtypes:
	- if type(atomtype) is int:
	- if ((min_needed_atomtype == None) or
	- (min_needed_atomtype > atomtype)):
	- min_needed_atomtype = atomtype
	- if ((max_needed_atomtype == None) or
	- (max_needed_atomtype < atomtype)):
	- max_needed_atomtype = atomtype
	-
	-
	- elif (line.strip() == 'Masses'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- atomtype = Intify(tokens[0])
	- if BelongsToSel(atomtype, atomtype_selection):
	- #tokens[0] = '@atom:type'+tokens[0]
	- l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n'))
	- elif (line.strip() == 'Velocities'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- atomid = Intify(tokens[0])
	- atomtype = None
	- if atomid in atomid2type:
	- atomtype = atomid2type[atomid]
	- moldid = None
	- if atomid in atomid2mol:
	- molid = atomid2mol[atomid]
	- if (BelongsToSel(atomid, atomid_selection) and
	- BelongsToSel(atomtype, atomtype_selection) and
	- BelongsToSel(molid, molid_selection)):
	- tokens[0] = '$atom:id'+tokens[0]
	- l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n'))
	-
	- # non-point-like-particles:
	- elif (line.strip() == 'Ellipsoids'):
	- sys.stderr.write(' processing \"'+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] = '$atom:id'+tokens[0]
	- l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n'))
	- elif (line.strip() == 'Lines'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- atomid = Intify(tokens[0])
	- atomtype = None
	- if atomid in atomid2type:
	- atomtype = atomid2type[atomid]
	- moldid = None
	- if atomid in atomid2mol:
	- molid = atomid2mol[atomid]
	- if (BelongsToSel(atomid, atomid_selection) and
	- BelongsToSel(atomtype, atomtype_selection) and
	- BelongsToSel(molid, molid_selection)):
	- tokens[0] = '$atom:id'+tokens[0]
	- l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n'))
	- elif (line.strip() == 'Triangles'):
	- sys.stderr.write(' processing \"'+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] = '$atom:id'+tokens[0]
	- l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n'))
	-
	- elif (line.strip() == 'Bonds'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- if (len(tokens) < 4):
	- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
	- ' Nonsensical line in Bonds section:\n'
	- ' \"'+line.strip()+'\"\n')
	- #tokens[0] = '$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] = '$atom:id'+tokens[2+n]
	- some_in_selection = True
	- else:
	- in_selections = False
	- if in_selections:
	- l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n'))
	- elif some_in_selection:
	- sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n')
	- sys.stderr.write(' (between atom ids: ')
	-
	- for n in range(0,2):
	- sys.stderr.write(str(atomids[n])+' ')
	- sys.stderr.write(')\n'
	- ' The atoms you selected are bonded\n'
	- ' to other atoms you didn\'t select.\n'
	- ' Are you sure you selected the correct atoms?\n')
	- no_warnings = False
	-
	-
	-
	- elif (line.strip() == 'Angles'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line == '':
	- break
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- if (len(tokens) < 5):
	- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
	- ' Nonsensical line in Angles section:\n'
	- ' \"'+line.strip()+'\"\n')
	- #tokens[0] = '$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] = '$atom:id'+tokens[2+n]
	- some_in_selection = True
	- else:
	- in_selections = False
	- if in_selections:
	- l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n'))
	- elif some_in_selection:
	- sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n')
	- sys.stderr.write(' (between atom ids: ')
	- for n in range(0,3):
	- sys.stderr.write(str(atomids[n])+' ')
	- sys.stderr.write(')\n'
	- ' The atoms you selected participate in 3-body \"Angle\"\n'
	- ' interactions with other atoms you didn\'t select.\n'
	- ' (They will be ignored.)\n'
	- ' Are you sure you selected the correct atoms?\n')
	- no_warnings = False
	-
	-
	- elif (line.strip() == 'Dihedrals'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- if (len(tokens) < 6):
	- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
	- ' Nonsensical line in Dihedrals section:\n'
	- ' \"'+line.strip()+'\"\n')
	- #tokens[0] = '$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] = '$atom:id'+tokens[2+n]
	- some_in_selection = True
	- else:
	- in_selections = False
	- if in_selections:
	- l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n'))
	- elif some_in_selection:
	- sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n')
	- sys.stderr.write(' (between atom ids: ')
	- for n in range(0,4):
	- sys.stderr.write(str(atomids[n])+' ')
	- sys.stderr.write(')\n'
	- ' The atoms you selected participate in 4-body \"Dihedral\"\n'
	- ' interactions with other atoms you didn\'t select.\n'
	- ' (They will be ignored.)\n'
	- ' Are you sure you selected the correct atoms?\n')
	- no_warnings = False
	-
	-
	- elif (line.strip() == 'Impropers'):
	- sys.stderr.write(' processing \"'+line.strip()+'\"\n')
	- while lex:
	- line = lex.ReadLine()
	- if line.strip() in data_file_header_names:
	- lex.push_raw_text(line) # <- Save line for later
	- break
	- tokens = line.strip().split()
	- if len(tokens) > 0:
	- if (len(tokens) < 6):
	- raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
	- ' Nonsensical line in Impropers section:\n'
	- ' \"'+line.strip()+'\"\n')
	- #tokens[0] = '$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]
	- 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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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 2012-7, 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 (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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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(' processing \"'+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'))
	-
	- else:
	- sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n')
	-
	- sys.stderr.write('\n\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:
	- tokens[0] = '@atom:type'+str(atomtype)
	- 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 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 104 2010 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 410 1020 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)
	- 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]
	- 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 104 2010 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 410 1020 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)
	- 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)
	- 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)
	- 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:
	- if 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
	- 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 = i_b = Intify(bondtype_str)
	-
	- 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:
	- assert(i_a == i_b)
	- if (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)
	- 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
	-
	- # delete in_angle_coeffs for angletypes we don't care about anymore:
	- for angletype in needed_angletypes:
	- if 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
	- 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:
	- assert(i_a == i_b)
	- if (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)
	- 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
	-
	- # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore:
	- for dihedraltype in needed_dihedraltypes:
	- if 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
	- 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:
	- assert(i_a == i_b)
	- if (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)
	- 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
	-
	- # delete in_improper_coeffs for impropertypes we don't care about anymore:
	- for impropertype in needed_impropertypes:
	- if 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
	- 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:
	- assert(i_a == i_b)
	- if (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])
	-
	-
	-
	-
	-
	-
	-
	-
	- 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 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 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 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 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 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### 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
	-
	- # 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))
	-
	- 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 mol_name != '':
	- sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n')
	-
	- if non_empty_output and no_warnings:
	- sys.stderr.write('WARNING: The '+g_program_name+' script has not been rigorously tested.\n'
	- ' Exotic (manybody) pair styles (and other force-field styles\n'
	- ' with unusual syntax) are not understood by '+g_program_name+'\n'
	- ' (although they are supported by moltemplate). Please look over\n'
	- ' the resulting LT file and check for errors. Convert any remaining\n'
	- ' atom, bond, angle, dihedral, or improper id or type numbers to the\n'
	- ' corresponding variables. Feel free to report any bugs you find.\n'
	- ' (-Andrew Jewett 2012-12-11)\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 100755
	index b5c7328b2..000000000
	--- a/tools/moltemplate/src/lttree.py
	+++ /dev/null
	@@ -1,736 +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('+__file__+'):\n'
	- 'Unrecogized 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('+__file__+'):\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 = 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 \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)
	- 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 = 'lttree.py'
	- g_date_str = '2012-12-15'
	- g_version_str = '0.7'
	-
	- ####### 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 newever 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')
	-
	- # Step 11: Now write the variable bindings/assignments table.
	- # 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 100755
	index e97dcef6e..000000000
	--- a/tools/moltemplate/src/lttree_check.py
	+++ /dev/null
	@@ -1,2099 +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 newever 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() == '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() == '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 $atom:id2\n'+
	- '----------------------------------------------------\n'+
	- g_no_check_msg)
	-
	-
	- elif filename == 'Data Angles':
	- table = TableFromTemplate(command.tmpl_list,
	- [[' ', '\t', '\r'], '\n'],
	- [True, False])
	- for i in range(0, len(table)):
	- syntax_err = False
	- assert(hasattr(table[i], '__len__'))
	- if len(table[i]) > 0:
	- if ((len(table[i]) > 1) and
	- isinstance(table[i][0], TextBlock) and
	- (len(table[i][0].text) > 0) and
	- (table[i][0].text == '#')):
	- pass
	- else:
	- if len(table[i]) < 5:
	- syntax_err = True
	- table_entry = table[i][0]
	- if (not ((isinstance(table_entry, VarRef)) and
	- (table_entry.prefix in ('$','${')) and
	- (ExtractCatName(table_entry.descr_str) == 'angle'))):
	- syntax_err = True
	- if len(table[i]) > 1:
	- table_entry = table[i][1]
	- if (not ((isinstance(table_entry, VarRef)) and
	- (table_entry.prefix in ('@', '@{')) and
	- (table_entry.nptr.cat_name == 'angle') and
	- (table_entry.nptr.cat_node == root_node))):
	- syntax_err = True
	- if len(table[i]) > 2:
	- table_entry = table[i][2]
	- if (not ((isinstance(table_entry, VarRef)) and
	- (table_entry.prefix in ('$','${')) and
	- (ExtractCatName(table_entry.descr_str) == 'atom'))):
	- syntax_err = True
	- if len(table[i]) > 3:
	- table_entry = table[i][3]
	- if (not ((isinstance(table_entry, VarRef)) and
	- (table_entry.prefix in ('$','${')) and
	- (ExtractCatName(table_entry.descr_str) == 'atom'))):
	- syntax_err = True
	- if len(table[i]) > 4:
	- table_entry = table[i][4]
	- if (not ((isinstance(table_entry, VarRef)) and
	- (table_entry.prefix in ('$','${')) 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 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:
	- 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('+__file__+'):\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 = 'lttree_check.py'
	- g_version_str = '0.72'
	- g_date_str = '2012-12-15'
	- 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...')
	- AssignVarPtrs(static_tree_root,
	- search_instance_commands=False)
	- AssignVarPtrs(static_tree_root,
	- 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))):
	- 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_missing_coeffs.py b/tools/moltemplate/src/lttree_missing_coeffs.py
	deleted file mode 100644
	index 93221707a..000000000
	--- a/tools/moltemplate/src/lttree_missing_coeffs.py
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-if __name__ == "__main__":
	-
	- try:
	-
	- # Data structures to store the class definitionss and instances
	- static_tree_root = StaticObj('', None) # The root of the static tree
	- # has name ''
	-
	- # Parsing, and compiling is a multi-pass process.
	-
	- # Step 1: Read in the StaticObj (class) defintions, 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)
	-
	- #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()
	-
	- # 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...')
	- AssignVarPtrs(static_tree_root, search_instance_commands=False)
	- AssignVarPtrs(static_tree_root, 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')
	diff --git a/tools/moltemplate/src/lttree_postprocess.py b/tools/moltemplate/src/lttree_postprocess.py
	deleted file mode 100755
	index bb040c98a..000000000
	--- a/tools/moltemplate/src/lttree_postprocess.py
	+++ /dev/null
	@@ -1,326 +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 = 'lttree_postprocess.py'
	-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"
	-
	-
	-g_program_name = 'lttree_postprocess.py'
	-g_version_str = '0.4'
	-g_date_str = '2012-12-12'
	-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:MoleculeType2:N 2
	- # :
	- # $/atom:molecule1141:C2 13578
	- # $/atom:molecule1142:N1 13579
	- #
	- # We only care about instance variables (which use the '$' prefix)
	- # Lines in this file with a different prefix ('@') which don't
	- # contain '$' should be ignored.
	- i_prefix = tokens[0].find('$')
	- 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)
	-
	- 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 b36935417..000000000
	--- a/tools/moltemplate/src/lttree_styles.py
	+++ /dev/null
	@@ -1,235 +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_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_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 'atomâID' in column_names: # (â is the character used in the manual)
	- i_atomid = column_names.index('atomâID')
	- 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 'atomâtype' in column_names: # (â hyphen character used in manual)
	- i_atomtype = column_names.index('atomâtype')
	- 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 'moleculeâID' in column_names: # (â hyphen character used in manual)
	- i_molid = column_names.index('moleculeâID')
	- 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')
	- 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 82c3f1ffc..000000000
	--- a/tools/moltemplate/src/moltemplate.sh
	+++ /dev/null
	@@ -1,1412 +0,0 @@
	-#!/bin/sh
	-
	-# 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.
	-
	-G_PROGRAM_NAME="moltemplate.sh"
	-G_VERSION="1.01"
	-G_DATE="2012-12-15"
	-
	-echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
	-echo "" >&2
	-
	-
	-# First, determine the directory in which this shell script is located.
	-# (The python script files should also be located here as well.)
	-SCRIPT_DIR=$(dirname $0)
	-
	-
	-# Check for python:
	-# I prefer python over python3 because python3 requires
	-# more memory. Just use regular python when available.
	-if which python > /dev/null; then
	- PYTHON_COMMAND='python'
	-elif which python3 > /dev/null; then
	- PYTHON_COMMAND='python3'
	-else
	- echo "Error: $G_PROGRAM_NAME requires python or python3" >&2
	- exit 1
	-fi
	-
	-
	-IMOLPATH=""
	-if [ -n "${MOLTEMPLATE_PATH}" ]; then
	- IMOLPATH="-importpath ${MOLTEMPLATE_PATH}"
	-fi
	-
	-# command that invokes lttree.py
	-LTTREE_COMMAND="$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 ${IMOLPATH}"
	-
	-# command that invokes nbody_by_type.py
	-NBODY_COMMAND="$PYTHON_COMMAND ${SCRIPT_DIR}/nbody_by_type.py"
	-
	-# command that invokes nbody_fix_ttree_assignments.py
	-NBODY_FIX_COMMAND="$PYTHON_COMMAND ${SCRIPT_DIR}/nbody_fix_ttree_assignments.py"
	-
	-# command that invokes ttree_render.py
	-TTREE_RENDER="$PYTHON_COMMAND ${SCRIPT_DIR}/ttree_render.py"
	-
	-
	-# What is the name of the .LT file we are reading?
	-for LAST_ARG; do true; done
	-# (I copied this code from a web page:
	-# http://stackoverflow.com/questions/1853946/getting-the-last-argument-passed-to-a-shell-script)
	-
	-# Check to see if this string ends in .lt or .LT
	-# If so, then set the base name of the output files
	-# to equal the base name of the .LT file being read.
	-# (Being careful here.
	-# Sometimes the last argument is not the .lt or .LT file.
	-# Sometimes that file appears earlier in the argument list.
	-# I want to supply a default value.)
	-#
	-# Note, in bash you can use:
	-# if [ "${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:
	-LTFILE="$LAST_ARG"
	-LTFILE_DIR=`dirname "$LTFILE"`
	-LTFILE_BASE=`basename "$LTFILE" .lt`
	-LTFILE_NO_EXT="${LTFILE_DIR}/${LTFILE_BASE}"
	-OUT_FILE_BASE="system"
	-if [ "$LTFILE_NO_EXT" != "$LTFILE" ]; then
	- OUT_FILE_BASE="$LTFILE_BASE"
	-else
	- LTFILE_BASE=`basename "$LAST_ARG" .LT`
	- LTFILE_NO_EXT="${LTFILE_DIR}/${LTFILE_BASE}"
	- if [ "$LTFILE_NO_EXT" != "$LTFILE" ]; then
	- OUT_FILE_BASE="$LTFILE_BASE"
	- fi
	-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"
	-
	-
	-# -----------------------------------------------------------
	-# 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_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_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"
	-
	-# 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
	-$data_bond_coeffs
	-$data_angle_coeffs
	-$data_dihedral_coeffs
	-$data_improper_coeffs
	-$data_atoms
	-$data_velocities
	-$data_bonds
	-$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
	-$data_angles_by_type
	-$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.
	-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 "$tmp_atom_coords"
	-
	-# Optional files containing atom coordinates:
	-PDB_FILE=""
	-XYZ_FILE=""
	-# REMOVE_DUPLICATE variables:
	-# ...If true (default), then any duplicate entries in the lists of bonds
	-# bonds, angles, dihedrals, or impropers in the LAMMPS DATA file
	-# are removed, giving priority to the most recent entry in the list.
	-# (This might not be necessary, but I want to be careful.)
	-REMOVE_DUPLICATE_BONDS="true"
	-REMOVE_DUPLICATE_ANGLES="true"
	-REMOVE_DUPLICATE_DIHEDRALS="true"
	-REMOVE_DUPLICATE_IMPROPERS="true"
	-
	-
	-ARGC=0
	-for A in "$@"; do
	- ARGC=$((ARGC+1))
	- eval ARGV${ARGC}=\"$A\"
	-done
	-
	-TTREE_ARGS=""
	-
	-i=0
	-while [ "$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 [ "$A" = "-overlay-dihdedrals" ]; then
	- # In that case, do not remove duplicate dihedral interactions
	- unset REMOVE_DUPLICATE_DIHEDRALS
	- elif [ "$A" = "-overlay-impropers" ]; then
	- # In that case, do not remove duplicate improper interactions
	- unset REMOVE_DUPLICATE_IMPROPERS
	- elif [ "$A" = "-xyz" ]; then
	- if [ "$i" -eq "$ARGC" ]; then
	- echo "$SYNTAX_MSG" >&2
	- exit 2
	- fi
	- # "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
	- 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 3
	- fi
	- #echo " (extracting coordinates from \"$XYZ_FILE\")" >&2
	- 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 "$SYNTAX_MSG" >&2
	- exit 2
	- fi
	- i=$((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 \"$PDB_FILE\"." >&2
	- echo " (File is empty or does not exist.)" >&2
	- exit 3
	- fi
	- #echo " (extracting coordinates from \"$PDB_FILE\")" >&2
	- if grep -q '^ATOM \\|^HETATM' "$PDB_FILE"; then
	- # Extract the coords from the "ATOM" records in the PDB file
	- pdbsort.py < "$PDB_FILE" \| awk '/^ATOM \|^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"
	- else
	- echo "$SYNTAX_MSG" >&2
	- echo "-----------------------" >&2
	- echo "" >&2
	- echo "Error: File \"$PDB_FILE\" is not a valid PDB file." >&2
	- exit 4
	- 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 $BOXSIZE_Bsin($GAMMA$PI/180.0)}"`
	- BOXSIZE_XY=`awk "BEGIN{print $BOXSIZE_Bcos($GAMMA$PI/180.0)}"`
	- BOXSIZE_XZ=`awk "BEGIN{print $BOXSIZE_Ccos($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-(cgcb))/sg}"`
	- BOXSIZE_Z=`awk "BEGIN{print sqrt(($BOXSIZE_C2)-(($BOXSIZE_XZ2)+($BOXSIZE_YZ**2)))}"`
	- else
	- BOXSIZE_X=$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=$BOXSIZE_Z
	-
	- #else: If the arguments are not understood in this script, then
	- # pass them on to "lttree.py"
	- else
	- if [ -z "$TTREE_ARGS" ]; then
	- TTREE_ARGS="\"$A\""
	- else
	- TTREE_ARGS="${TTREE_ARGS} \"$A\""
	- fi
	- fi
	-done
	-
	-
	-
	-
	-
	-
	-
	-
	-# --------------------------------------------------------------------
	-# --- Now run ttree/lttree to generate the file fragments we need. ---
	-# ------ (Afterwards, we will paste these fragments together.) -----
	-# --------------------------------------------------------------------
	-
	-
	-
	-
	-
	-# If checking is not disabled, then first check for common spelling errors.
	-
	-if [ -n "$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 $TTREE_ARGS; then
	- exit 1
	-fi
	-
	-# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
	-# > Traceback (most recent call last):
	-# > File "./lttree.py", line...
	-# .-.
	-# (0.0)
	-# '=.\|m\|.='
	-# .='`"``=.
	-#
	-# Hopefully this does not happen.
	-# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
	-
	-echo "" >&2
	-
	-
	-if [ -s "${data_atoms}" ]; then
	- remove_duplicate_atoms.py < "${data_atoms}" > "${data_atoms}.tmp"
	- mv -f "${data_atoms}.tmp" "${data_atoms}"
	- remove_duplicate_atoms.py < "${data_atoms}".template > "${data_atoms}.tmp"
	- mv -f "${data_atoms}.tmp" "${data_atoms}".template
	- renumber_DATA_first_column.py < ${data_atoms} > "${data_atoms}.tmp"
	- mv -f "${data_atoms}.tmp" "${data_atoms}"
	-else
	- echo "Error: There are no atoms in your system." >&2
	- echo "" >&2
	- echo " Make sure that the object(s) you created are indeed molecules." >&2
	- echo " (Molecule objects must contain at least one" >&2
	- echo " write(\"${data_atoms}\") command.)" >&2
	- echo "" >&2
	- echo " (This error often occurs if you instantiated an object" >&2
	- echo " which you thought was a molecule, but it is actually" >&2
	- echo " only a namespace, a force-field name or category" >&2
	- echo " containing the definitions of other molecules.)" >&2
	- echo "" >&2
	- exit 1
	-fi
	-
	-
	-
	-
	-# ---------------- Interactions By Type -----------------
	-# At the time of writing, bonded-interactions-by-atom-type were not
	-# understood by LAMMPS. These features require auxilliary python scripts.
	-# These data sections must be processed before everything else (because
	-# they effect the other data sections, and the ttree_assignments.txt file.)
	-# -------------------------------------------------------
	-if [ -s "$data_angles_by_type" ]; then
	- echo "\nGenerating 3-body angle interactions by atom/bond type" >&2
	- #-- Generate a file containing the list of interactions on separate lines --
	- if ! $NBODY_COMMAND Angles \
	- -atoms "${data_atoms}.template" \
	- -bonds "${data_bonds}.template" \
	- -nbodybytype "${data_angles_by_type}.template" \
	- -prefix '$/angle:bytype' > gen_Angles.template.tmp; then
	- exit 1
	- fi
	-
	- # ---- cleanup: ----
	- # ---- Re-build the "${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 ! $NBODY_FIX_COMMAND '/angle' gen_Angles.template.tmp \
	- < ttree_assignments.txt \
	- > ttree_assignments.tmp; then
	- exit 1
	- fi
	-
	- echo "(Rendering ttree_assignments.tmp file after angles added.)" >&2
	-
	- # ---- Re-build (render) the "$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 ! $TTREE_RENDER ttree_assignments.tmp \
	- < "${data_angles}.template" \
	- > "$data_angles"; then
	- exit 1
	- fi
	-
	- mv -f ttree_assignments.tmp ttree_assignments.txt
	- rm -f gen_Angles.template.tmp new_Angles.template.tmp
	-fi
	-
	-
	-
	-if [ -s "$data_dihedrals_by_type" ]; then
	- echo "\nGenerating 4-body dihedral interactions by atom/bond type" >&2
	- #-- Generate a file containing the list of interactions on separate lines --
	- if ! $NBODY_COMMAND Dihedrals \
	- -atoms "${data_atoms}.template" \
	- -bonds "${data_bonds}.template" \
	- -nbodybytype "${data_dihedrals_by_type}.template" \
	- -prefix '$/dihedral:bytype' > gen_Dihedrals.template.tmp; then
	- exit 1
	- fi
	- # ---- cleanup: ----
	- # ---- Re-build the "${data_dihedrals}.template" file ----
	- # Instert these lines into the "${data_dihedrals}.template" file which includes
	- # the newly generated interactions. (Note: these are in .template format)
	-
	- cp -f gen_Dihedrals.template.tmp new_Dihedrals.template.tmp
	- if [ -s "${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 ! $NBODY_FIX_COMMAND '/dihedral' gen_Dihedrals.template.tmp \
	- < ttree_assignments.txt \
	- > ttree_assignments.tmp; then
	- exit 1
	- fi
	-
	- echo "(Rendering ttree_assignments.tmp file after dihedral added.)" >&2
	-
	- # ---- Re-build (render) the "$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 ! $TTREE_RENDER ttree_assignments.tmp \
	- < "${data_dihedrals}.template" \
	- > "$data_dihedrals"; then
	- exit 1
	- fi
	-
	- mv -f ttree_assignments.tmp ttree_assignments.txt
	- rm -f gen_Dihedrals.template.tmp new_Dihedrals.template.tmp
	-fi
	-
	-
	-
	-if [ -s "$data_impropers_by_type" ]; then
	- echo "Generating 4-body impropers interactions by atom/bond type" >&2
	- #-- Generate a file containing the list of interactions on separate lines --
	- if ! $NBODY_COMMAND Impropers \
	- -atoms "${data_atoms}.template" \
	- -bonds "${data_bonds}.template" \
	- -nbodybytype "${data_impropers_by_type}.template" \
	- -prefix '$/improper:bytype' > gen_Impropers.template.tmp; then
	- exit 1
	- fi
	- # ---- cleanup: ----
	- # ---- Re-build the "${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 ! $NBODY_FIX_COMMAND '/improper' gen_Impropers.template.tmp \
	- < ttree_assignments.txt \
	- > ttree_assignments.tmp; then
	- exit 1
	- fi
	-
	- echo "(Rendering ttree_assignments.tmp file after impropers added.)" >&2
	-
	- # ---- Re-build (render) the "$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 ! $TTREE_RENDER ttree_assignments.tmp \
	- < "${data_impropers}.template" \
	- > "$data_impropers"; then
	- exit 1
	- fi
	-
	- mv -f ttree_assignments.tmp ttree_assignments.txt
	- rm -f gen_Impropers.template.tmp new_Impropers.template.tmp
	-fi
	-
	-
	-
	-if [ -n "$LTTREE_POSTPROCESS_COMMAND" ]; then
	- echo "" >&2
	- if ! eval $LTTREE_POSTPROCESS_COMMAND $TTREE_ARGS; then
	- exit 1
	- fi
	- echo "" >&2
	-fi
	-
	-
	-# -------------------------------------------------------
	-# If present, then remove duplicate bonds, angles, dihedrals, and impropers
	-# (unless overridden by the user).
	-# -------------------------------------------------------
	-
	-
	-if [ -s "${data_masses}" ]; then
	- remove_duplicate_atoms.py < "${data_masses}" > "${data_masses}.tmp"
	- mv -f "${data_masses}.tmp" "${data_masses}"
	-fi
	-
	-
	-
	-if [ -s "${data_bonds}" ]; then
	- if [ ! -z $REMOVE_DUPLICATE_BONDS ]; then
	- remove_duplicates_nbody.py 2 < "${data_bonds}" > "${data_bonds}.tmp"
	- mv "${data_bonds}.tmp" "${data_bonds}"
	- remove_duplicates_nbody.py 2 < "${data_bonds}".template > "${data_bonds}.tmp"
	- mv "${data_bonds}.tmp" "${data_bonds}".template
	- fi
	- renumber_DATA_first_column.py < ${data_bonds} > "${data_bonds}.tmp"
	- mv -f "${data_bonds}.tmp" "${data_bonds}"
	-fi
	-
	-
	-if [ -s "${data_angles}" ]; then
	- if [ ! -z $REMOVE_DUPLICATE_ANGLES ]; then
	- remove_duplicates_nbody.py 3 < "${data_angles}" > "${data_angles}.tmp"
	- mv "${data_angles}.tmp" "${data_angles}"
	- remove_duplicates_nbody.py 3 < "${data_angles}".template > "${data_angles}.tmp"
	- mv "${data_angles}.tmp" "${data_angles}".template
	- fi
	- renumber_DATA_first_column.py < ${data_angles} > "${data_angles}.tmp"
	- mv -f "${data_angles}.tmp" "${data_angles}"
	-fi
	-
	-
	-if [ -s "${data_dihedrals}" ]; then
	- if [ ! -z $REMOVE_DUPLICATE_DIHEDRALS ]; then
	- remove_duplicates_nbody.py 4 < "${data_dihedrals}" > "${data_dihedrals}.tmp"
	- mv "${data_dihedrals}.tmp" "${data_dihedrals}"
	- remove_duplicates_nbody.py 4 < "${data_dihedrals}".template > "${data_dihedrals}.tmp"
	- mv "${data_dihedrals}.tmp" "${data_dihedrals}".template
	- fi
	- renumber_DATA_first_column.py < ${data_dihedrals} > "${data_dihedrals}.tmp"
	- mv -f "${data_dihedrals}.tmp" "${data_dihedrals}"
	-fi
	-
	-
	-if [ -s "${data_impropers}" ]; then
	- if [ ! -z $REMOVE_DUPLICATE_IMPROPERS ]; then
	- remove_duplicates_nbody.py 4 < "${data_impropers}" > "${data_impropers}.tmp"
	- mv "${data_impropers}.tmp" "${data_impropers}"
	- remove_duplicates_nbody.py 4 < "${data_impropers}".template > "${data_impropers}.tmp"
	- mv "${data_impropers}.tmp" "${data_impropers}".template
	- fi
	- renumber_DATA_first_column.py < ${data_impropers} > "${data_impropers}.tmp"
	- mv -f "${data_impropers}.tmp" "${data_impropers}"
	-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=`awk '{if ($3=="xlo") {xlo=$1}} END{print xlo}' < "$data_boundary"`
	- BOXSIZE_MAXX=`awk '{if ($4=="xhi") {xhi=$2}} END{print xhi}' < "$data_boundary"`
	-
	- BOXSIZE_MINY=`awk '{if ($3=="ylo") {ylo=$1}} END{print ylo}' < "$data_boundary"`
	- BOXSIZE_MAXY=`awk '{if ($4=="yhi") {yhi=$2}} END{print yhi}' < "$data_boundary"`
	-
	- BOXSIZE_MINZ=`awk '{if ($3=="zlo") {zlo=$1}} END{print zlo}' < "$data_boundary"`
	- BOXSIZE_MAXZ=`awk '{if ($4=="zhi") {zhi=$2}} END{print zhi}' < "$data_boundary"`
	-
	- if [ -z "$BOXSIZE_MINX" ] \|\| [ -z "$BOXSIZE_MAXX" ]; then
	- echo "Error: Problem with box boundary format (\"xlo xhi\") in \"$data_boundary\"" >&2
	- exit 7
	- fi
	- if [ -z "$BOXSIZE_MINY" ] \|\| [ -z "$BOXSIZE_MAXY" ]; then
	- echo "Error: Problem with box boundary format (\"ylo yhi\") in \"$data_boundary\"" >&2
	- exit 8
	- fi
	- if [ -z "$BOXSIZE_MINZ" ] \|\| [ -z "$BOXSIZE_MAXZ" ]; then
	- echo "Error: Problem with box boundary format (\"zlo zhi\") in \"$data_boundary\"" >&2
	- exit 9
	- 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 10
	- 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 $1-0.5marginwidth}"`
	- BOXSIZE_MAXX=`echo $MINMAX_BOUNDS \| awk "{margin=0.1; width=$2-$1; print $2+0.5marginwidth}"`
	- BOXSIZE_MINY=`echo $MINMAX_BOUNDS \| awk "{margin=0.1; width=$4-$3; print $3-0.5marginwidth}"`
	- BOXSIZE_MAXY=`echo $MINMAX_BOUNDS \| awk "{margin=0.1; width=$4-$3; print $4+0.5marginwidth}"`
	- BOXSIZE_MINZ=`echo $MINMAX_BOUNDS \| awk "{margin=0.1; width=$6-$5; print $5-0.5marginwidth}"`
	- BOXSIZE_MAXZ=`echo $MINMAX_BOUNDS \| awk "{margin=0.1; width=$6-$5; print $6+0.5marginwidth}"`
	- else
	- # By default, choose some reasonably large box:
	- BOXSIZE_MINX="-100.0"
	- BOXSIZE_MAXX="100.0"
	- BOXSIZE_MINY="-100.0"
	- BOXSIZE_MAXY="100.0"
	- BOXSIZE_MINZ="-100.0"
	- BOXSIZE_MAXZ="100.0"
	- # ...and print message scolding the user for being lazy
	- echo "----------------------------------------------------------------------" >&2
	- echo "---- WARNING: Unable to determine periodic boundary conditions. ----" >&2
	- echo "---- (A default cube of volume=(200.0)^3 was used. ----" >&2
	- echo "---- This is probably not what you want!) ----" >&2
	- echo "---- It is recommended that you specify your periodic boundary ----" >&2
	- echo "---- by adding a write_once(\"Boundary\") command to your .lt file. ----" >&2
	- echo "---- For example: ----" >&2
	- #echo "----------------------------------------------------------------------" >&2
	- echo "---- ----" >&2
	- echo "---- write_once(\"Boundary\") { ----" >&2
	- echo "---- 2.51 46.79 xlo xhi ----" >&2
	- echo "---- -4.38 35.824 ylo yhi ----" >&2
	- echo "---- 0.3601 42.95 zlo zhi ----" >&2
	- echo "---- } ----" >&2
	- echo "----------------------------------------------------------------------" >&2
	- fi
	-fi
	-
	-
	-
	-
	-if [ -z "$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"
	-else
	- 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 "$data_atoms" ]; then
	- echo "Atoms" >> "$OUT_FILE_DATA"
	- if [ -s "$tmp_atom_coords" ]; then
	- echo "# (Note: x,y,z coordinates may overlap and can be modified later.)" >> "$OUT_FILE_DATA"
	- else
	- echo "" >> "$OUT_FILE_DATA"
	- fi
	- cat "$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
	- 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 "" >> $OUT_FILE_INPUT_SCRIPT
	- NATOMS=`awk '/^\\\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
	- NATOMCRDS=`awk '{if (NF>=3) natom+=1} END{print(natom)}' < "$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 ($NATOMS)" >&2
	- exit 6
	- fi
	-else
	- rm -f "$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="
	-"
	-for file in $MOLTEMPLATE_TEMP_FILES; do
	- #echo "file=\"$file\""
	- rm -f "output_ttree/$file" >/dev/null 2>&1 \|\| true
	- mv "$file" output_ttree/ >/dev/null 2>&1 \|\| true
	-done
	-IFS=$OIFS
	-
	-
	-
	-
	-
	-# ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################
	-
	-
	-N_data_prefix=`expr length "$data_prefix"`
	-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`
	- # 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
	-
	-
	-
	-N_in_prefix=`expr length "$in_prefix"`
	-ls "${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`
	- # 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
	- echo "" >> $OUT_FILE_INPUT_SCRIPT
	- cat "$file_name" >> $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 \"$file_name\"" >&2
	- postprocess_input_script.py input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp
	- echo "" >&2
	- mv "$file_name".tmp "$file_name"
	- cat "$file_name" >> input_scripts_so_far.tmp
	- fi
	-done
	-
	-
	-ls "${in_prefix}"* 2> /dev/null \| while read file_name; do
	- echo "postprocessing file \"$file_name\"" >&2
	- postprocess_input_script.py input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp
	- 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 "# -- 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
	-
	diff --git a/tools/moltemplate/src/nbody_Angles.py b/tools/moltemplate/src/nbody_Angles.py
	deleted file mode 100644
	index df2bb0185..000000000
	--- a/tools/moltemplate/src/nbody_Angles.py
	+++ /dev/null
	@@ -1,41 +0,0 @@
	-from nbody_graph_search import Ugraph
	-
	-# 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):
	- """
	- 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 3-body angle
	- interaction between atoms 1, 2, 3 AND 3, 2, 1. This is the same triplet
	- of atoms, and the angle between them is the same.)
	-
	- """
	- # 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_Dihedrals.py b/tools/moltemplate/src/nbody_Dihedrals.py
	deleted file mode 100644
	index d3243b0d4..000000000
	--- a/tools/moltemplate/src/nbody_Dihedrals.py
	+++ /dev/null
	@@ -1,44 +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.
	- 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 dihedral-
	- angle interaction between atoms 1, 2, 3, 4 AND 4, 3, 2, 1. The dihedral-
	- angle is not altered when the order of atoms is reversed, so we arbitrarily
	- choose whichever order causes the first atom to have the lower atomID.)
	-
	- """
	-
	- # 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 fdc2c9b7a..000000000
	--- a/tools/moltemplate/src/nbody_Impropers.py
	+++ /dev/null
	@@ -1,41 +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)])
	-# (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 defined as the angle between planes formed by atoms 1,2,3 & 2,3,4.
	- This is not effected by 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]
	- if atom1 <= atom2:
	- #return ((atom0,atom1,atom2,atom3), match[1]) same thing as:
	- return match
	- else:
	- return ((atom0,atom2,atom1,atom3), match[1])
	diff --git a/tools/moltemplate/src/nbody_by_type.py b/tools/moltemplate/src/nbody_by_type.py
	deleted file mode 100755
	index 79a1175b2..000000000
	--- a/tools/moltemplate/src/nbody_by_type.py
	+++ /dev/null
	@@ -1,582 +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
	-
	-
	-
	-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()
	-
	-
	- g = __import__(src_bond_pattern) #defines g.bond_pattern, g.canonical_order
	-
	-
	- 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 = 'nbody_by_type.py'
	- g_date_str = '2012-8-14'
	- g_version_str = '0.10'
	-
	- ####### 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.)
	-
	- # 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][0] == '-':
	- raise InputError('Error('+__file__+'):\n'
	- 'Unrecogized 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'
	-
	- elif len(argv) == 2:
	- section_name = argv[1]
	- 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('+__file__+'):\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')
	-
	-
	- # ------------ Done parsing argument list ----------
	-
	- section_name_bytype = section_name + ' By Type'
	-
	- 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 431172d9b..000000000
	--- a/tools/moltemplate/src/nbody_by_type_lib.py
	+++ /dev/null
	@@ -1,312 +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
	-from collections import defaultdict, OrderedDict
	-from ttree_lex import MatchesPattern, MatchesAll, InputError
	-#import gc
	-
	-
	-def GenInteractions_int(G_system,
	- g_bond_pattern,
	- typepattern_to_coefftype,
	- 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_coefftype".
	-
	- 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_coefftype", 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_coefftype 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(' Looking up atom and bond types...')
	-
	- # Now test each match to see if the types of atoms and bonds involved match
	- # any of the type-patterns in the "typepattern_to_coefftype" argument.
	- # If so, store them in the out_topo list
	-
	- #coefftype_to_atomids = defaultdict(list)
	- #abids_to_coefftypes = defaultdict(list)
	- coefftype_to_atomids = OrderedDict()
	- abids_to_coefftypes = OrderedDict()
	-
	- count = 0
	-
	- for typepattern, coefftype in typepattern_to_coefftype:
	- if report_progress:
	- sys.stderr.write(' Checking (atom-types,bond-types) against \n '+str(typepattern)+'-->'+coefftype+'\n')
	- 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(' done\n (found '+
	- str(count)+' non-redundant matches)\n')
	-
	- return coefftype_to_atomids
	-
	-
	-
	-
	-
	-
	-
	-
	-def GenInteractions_str(bond_pairs,
	- g_bond_pattern,
	- typepattern_to_coefftype,
	- 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_coefftype,
	- canonical_order,
	- atomtypes_int2str,
	- bondtypes_int2str,
	- report_progress)
	- coefftype_to_atomids_str = OrderedDict()
	- for coefftype, atomidss_int in coefftype_to_atomids_int.items():
	- 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 100755
	index 53c8cb69c..000000000
	--- a/tools/moltemplate/src/nbody_fix_ttree_assignments.py
	+++ /dev/null
	@@ -1,147 +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 $0}' \
	- < ttree_assignments.txt >> ttree_assignments_new.txt
	-
	-I wrote this python script (instead of using awk) just to handle quoted stings
	-(and strings with other fancy characters and escape sequences).
	-
	-"""
	-
	-import sys
	-from ttree_lex import SplitQuotedString, EscCharStrToChar, SafelyEncodeString, InputError
	-
	-try:
	- if (len(sys.argv) != 3):
	- raise InputError('Error running \"'+__file__+'\"\n'
	- ' Wrong number of arguments.\n'
	- ' (This is likely a programmer error.\n'
	- ' This script was not intended to be run by end users.)\n')
	-
	- cat_name = sys.argv[1]
	- f = open(sys.argv[2])
	- lines_generated = f.readlines()
	- f.close()
	-
	- # Selections are simply lists of 2-tuples (pairs)
	- #f = open('ttree_assignments.txt','r')
	- #lines_bindings = f.readlines()
	- #f.close()
	- lines_bindings = sys.stdin.readlines()
	-
	- # Figure out which lines in the 'ttree_assignments.txt' file
	- # contain the variables of the type you are looking for.
	- # Make note of the relevant line numbers
	- i_preexisting_begin = -1
	- i_preexisting_end = -1
	- in_section = False
	- possible_cat_names = set(['$'+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 b82449a20..000000000
	--- a/tools/moltemplate/src/nbody_graph_search.py
	+++ /dev/null
	@@ -1,974 +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):
	- 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):
	- 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/pdbsort.py b/tools/moltemplate/src/pdbsort.py
	deleted file mode 100755
	index c3c98a47f..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) <= (other.chainID, other.seqNum, other.iCode)
	-
	- def __lt__(self, other):
	- return (self.chainID, self.seqNum, self.iCode) < (other.chainID, other.seqNum, other.iCode)
	-
	- 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) == (other.chainID, other.seqNum, other.iCode)
	-
	- 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 = 0.1
	-g_date_str = 2012-5-06
	-
	-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 100755
	index 85a3b3e85..000000000
	--- a/tools/moltemplate/src/postprocess_input_script.py
	+++ /dev/null
	@@ -1,144 +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.
	-
	- Right now, the only thing this script does is swap the I and J integers in
	- "pair_coeff I J ..." commands. Later changes may be added.
	-
	-"""
	-
	-import sys
	-lines_orig = []
	-in_stream = sys.stdin
	-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 ((tokens[5] == 'i') and (tokens[3][0:6]=='hbond/')):
	- tokens[5] = 'j'
	- sys.stderr.write(' (and replaced \"i\" with \"j\")\n')
	- elif ((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 (tokens[4] == 'i'):
	- tokens[4] = 'j'
	- sys.stderr.write(' (and replaced \"i\" with \"j\")\n')
	- elif (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/remove_duplicate_atoms.py b/tools/moltemplate/src/remove_duplicate_atoms.py
	deleted file mode 100755
	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 100755
	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 100755
	index daecc4c85..000000000
	--- a/tools/moltemplate/src/renumber_DATA_first_column.py
	+++ /dev/null
	@@ -1,66 +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
	-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')
	- if '#' in line_orig:
	- ic = line.find('#')
	- line = line_orig[:ic]
	-
	- 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:])])
	- 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/ttree.py b/tools/moltemplate/src/ttree.py
	deleted file mode 100755
	index 6984142b7..000000000
	--- a/tools/moltemplate/src/ttree.py
	+++ /dev/null
	@@ -1,4719 +0,0 @@
	-#!/usr/bin/env python
	-
	-# Authors: 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.
	-
	-"""
	-ttree Ttree is a simple program for recursively composing and generating
	- large redundant text files from small template files.
	-
	- 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.
	-
	- ttree was designed to be useful for generating input files for
	- molecular simulation software like LAMMPS or NAMD.
	-
	-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 *
	-
	-
	-# -- ordereddict.py --
	-# For users who are not able to upgrade to python 2.7 or higher,
	-# I included a copy of "ordereddict.py" (MIT license)
	-# by Raymond Hettinger (v1.1, rev345), downloaded from these sources:
	-# https://projects.coin-or.org/CoinBazaar/browser/projects/PyCoinInstall/trunk/tpl/ordereddict.py
	-# http://pypi.python.org/pypi/ordereddict
	-# http://code.activestate.com/recipes/576693/
	-# If you are using python 2.7 (or 3) or higher, you can
	-# delete "odereddict.py"
	-
	-if sys.version < '2.7':
	- from ordereddict import OrderedDict
	-elif sys.version < '2.6':
	- raise InputError('Error: Alas, you must upgrade to a newever version of python.')
	-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 = '2012-12-15'
	-g_version_str = '0.73'
	-
	-
	-
	-
	-
	-
	-
	-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 storea 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)."""
	-
	- 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):
	- 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).
	-
	- """
	-
	- 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.
	-
	- """
	- def __init__(self,
	- name = None,
	- class_ref = None,
	- srcloc = None):
	- Command.__init__(self, srcloc)
	- self.name = name
	- #if class_ref is None:
	- # self.class_ref = ClassReference()
	- #else:
	- self.class_ref = class_ref
	-
	- def __str__(self):
	- return 'InstantiateCommand('+self.name+')'
	-
	- def __copy__(self):
	- return InstantiateCommand(self.name, self.class_ref, self.srcloc)
	-
	-
	-class DeleteCommand(Command):
	- 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.)
	-
	- """
	-
	- 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):
	- 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):
	- 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):
	- 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):
	- 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):
	- 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):
	- 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):
	- 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):
	- 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):
	- 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 MOME
	-#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).
	-#
	-# """
	-#
	-# 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):
	- 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:
	- """
	- for child in node.children:
	- if child.name == name:
	- return child
	-
	- # The object-oriented inheritance stuff appears here.
	- # If you don't care about OOP or inheritance,
	- # then comment out the loop that follows:
	-
	- if isinstance(node, StaticObj):
	- #CONTINUEHERE: DEBUG THIS FEATURE AND EXTEND NAMESPACES TO INSTOBJS
	- # Search recursively over the "children" (ie attributes or members)
	- # belonging to any OOP ancestors of this node.
	- for class_parent in node.class_parents:
	- for child in class_parent.children:
	- child = FindChild(name, class_parent, dbg_loc)
	- if child != None:
	- return child
	- for namespace_node in node.namespaces:
	- for child in namespace_node.children:
	- child = FindChild(name, namespace_node, dbg_loc)
	- if child != None:
	- return child
	-
	- # 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 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):
	- 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):
	- 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__'+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.append(StaticObj(new_leaf_name, parent_node))
	- elif isinstance(parent_node, InstanceObj):
	- parent_node.children.append(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[-1]
	- 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.append(StaticObj(new_leaf_name, parent_node))
	- elif isinstance(parent_node, InstanceObj):
	- parent_node.children.append(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[-1]
	-
	-
	- 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):
	- def __init__(self, n0 = 1, nincr = 1):
	- 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).
	-
	- """
	-
	- def __init__(self,
	- name = '',
	- bindings = None,
	- counter = None,
	- manual_assignments = None,
	- reserved_values = None,
	- num_user_vars = 0):
	-
	- self.name = name
	-
	- if bindings is None:
	- self.bindings = OrderedDict()
	- else:
	- self.bindings = bindings
	-
	- if counter is None:
	- self.counter = SimpleCounter(1,1)
	- 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
	-
	- # The next member is for a feature ("query()") which
	- # has not yet been implemented. Commenting it out:
	- #
	- # num_user_vars This variable keeps track of: how many variables
	- # belonging to a particular category have been created
	- # and assigned to values. We restrict this to variables
	- # which are not automatically generated (like query()
	- # variables).
	- # self.num_user_vars = num_user_vars
	-
	-
	-
	-
	-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" (branches in the tree. -Not- OOP class children. 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.
	-
	- 5) var_bindings
	- A list of variable bindings which point to it.
	- This is useful to keep track of in case this object gets modified
	- or deleted
	-
	- """
	-
	- 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 = [] # 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):
	- 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).
	- """
	-
	- #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 == 'create_vars')):
	- 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') or
	- (cmd_token == 'create_vars')):
	- 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 ((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':
	- # 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]=='$')):
	- raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
	- ' Error near '+ErrorLeader(entry.srcloc.infile,
	- entry.srcloc.lineno)+'\n'
	- ' Illegal variable: \"'+entry.prefix+entry.descr_str+entry.suffix+'\"\n'
	- ' All variables in a \"write_once()\" statement must be statically\n'
	- ' defined, and hence they must begin with a \'@\' prefix character.\n'
	- ' (not a \'$\' character).\n'
	- ' Suggestion: Use the \"write()\" command instead.\n')
	-
	-
	-
	- if cmd_token == 'write':
	- commands = self.instance_commands
	- elif cmd_token == 'write_once':
	- commands = self.commands
	- elif ((cmd_token == 'create_var') or
	- (cmd_token == 'create_vars')):
	- 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.
	-
	- 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 = None
	- for child in self.children:
	- if child.name == child_name:
	- break
	- # If found, we refer to it as "child".
	- # If not, then we create a new StaticObj named "child".
	- if (child is None) or (child.name != child_name):
	- child = StaticObj(child_name, self)
	- self.children.append(child)
	- assert(child in self.children)
	- # 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()
	- 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 class\'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
	-
	- # 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 preceeded by a class name.')
	- class_names = []
	- weights = []
	- if class_name_str == 'random':
	- class_names, weights = 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 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:
	- digits = [0 for d in range(0, D)]
	- table_filled = False
	- pushed_commands = []
	- while (not table_filled):
	- instance_name = base_name
	- for d in range(0, D):
	- i = digits[d]
	- instance_name += '['+str(i)+']'
	-
	- # Does the user want us to select
	- # a class at random?
	- if len(class_names) > 0:
	- 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
	-
	-
	- pass
	-
	-
	- else:
	- if len(class_names) > 0:
	- 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.
	- # (IE. check if it present in the list of children.)
	- for i in range(0, len(self.children)):
	- if self.children[i].name == child_name:
	- if self.children[i].IsDeleted():
	- del self.children[i]
	- 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.append(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')
	- # CONTINUEHERE: 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", "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()
	-
	-
	-
	- @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:
	- 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 preceeded 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')
	-
	- tot_weight = sum(weights)
	- if (tot_weight <= 0.0):
	- if (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)
	-
	-
	- 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:
	- 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 += '('
	- for i in range(0,len(self.children)):
	- if i+1 < len(self.children):
	- out_str += str(self.children[i])+', '
	- else:
	- out_str += str(self.children[i])+')'
	- 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.)
	-
	- """
	-
	- 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)
	-
	- ##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 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
	-
	-
	- 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 true if self.parent == self
	- # for this node (or for any ancestor node).
	- node = self
	- while node.parent != None:
	- if node.parent == node:
	- return True
	- node = node.parent
	- return False
	-
	-
	-
	-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."""
	-
	- 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 = OrderedDict() # 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.)
	-
	- # always equal self.statobj.categories.
	- # It may seem redundant to make a
	- # new member to store the same data,
	- # but I do it because then the two
	- # types of trees (StaticObjs, InstanceObjs) have
	- # the same member names (although different
	- # connectivity). This way I can write
	- # simple functions (eg FindCatNode())
	- # which can traverse through either
	- # type of tree.
	-
	- self.commands = [] # An ordered list of commands that should be carried out
	- # during instantiation
	-
	- self.commands_push = [] # Stackable commands to carry out during instantiation
	- self.commands_pop = [] # Stackable commands to carry out during instantiation
	-
	-
	- self.srcloc_begin = None # Keep track of location in user files
	- self.srcloc_end = None # (useful for error message reporting)
	-
	-
	-
	-
	- 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())): # (make sure not "deleted")
	- 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):
	- if len(self.children) > 0:
	- out_str = self.name + '('
	- for i in range(0,len(self.children)):
	- if i+1 < len(self.children):
	- out_str += str(self.children[i])+', '
	- else:
	- out_str += str(self.children[i])+')'
	- else:
	- out_str = self.name
	-
	- return out_str
	-
	-
	-
	- def Dealloc(self):
	- InstanceObjBasic.Dealloc(self)
	- # Trying to remove pointers and variables.
	- # Hope I'm doing it correctly
	- #sys.stderr.write(self.name+'.Dealloc() invoked.\n')
	- N = len(self.commands)-1
	- for i in range(0, len(self.commands)):
	- del self.commands[N-i]
	- N = len(self.children)-1
	- for i in range(0, len(self.children)):
	- child = self.children[N-i]
	- child.Dealloc()
	- del self.children[N-i]
	-
	-
	-
	- #def __del__(self):
	- # sys.stderr.write(self.name+'.__del__() invoked.\n')
	-
	-
	- def DeleteSelf(self):
	- # Modification: 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
	- # Commenting out:
	- #assert(parent != None)
	- #i = 0
	- #while i < len(parent.children):
	- # if command.instobj == parent.children[i]:
	- # del parent.children[i]
	- # else:
	- # i += 1
	-
	- self.Dealloc()
	- InstanceObjBasic.DeleteSelf(self)
	-
	-
	-
	-
	- 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.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.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.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 len(instobj_list) == 0:
	- if isinstance(mod_command.command, DeleteCommand):
	- # It's possible that some nodes we want to delete have
	- # not yet been created yet. Deal with these later.
	- # (See InvokeAllDeletes().)
	- self.commands.append(mod_command.__copy__())
	- else:
	- 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:
	- if isinstance(mod_command.command, DeleteCommand):
	- # We need the instance tree to be fully defined after
	- # this function is called, so carry out the deletion now
	- instobj.DeleteSelf()
	- else:
	- 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
	-
	- # Not needed:
	- #if isinstance(command, DeleteCommand):
	- # self.DeleteSelf()
	- # return # (Note: we do not append this command to self.commands)
	-
	- # 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
	-
	- child = InstanceObj(command.name, self)
	- 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.append(child)
	- 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):
	- # To save memory don't generate any commands
	- # for trivial (leaf) nodes
	- assert(len(self.children) == 0)
	- 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)
	-
	- i_child = 0
	- for command in self.commands:
	- if isinstance(command, InstantiateCommand):
	- child = self.children[i_child]
	- child.BuildCommandList(command_list)
	- i_child += 1
	- 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 AssignVarPtrs(context_node, search_instance_commands = False):
	- """
	- 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.)
	- Also check to see the nodes in the tree that are refered to by the
	- descriptor exist, and, if so, assign pointers to these nodes.
	- If not, then (in some cases), create new node whose names match the
	- variable descriptor names (and assign pointers to them).
	- Also figure out the category node and name which specify the type of
	- variable. These three pieces of information
	- This node (it's name and location in the tree) essentially identifies the
	- variable, (like a variable name) but it does not store anything.
	- Also: 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.
	- """
	-
	- #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):
	-
	- 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
	- ((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)
	-
	-
	-
	- # Recursively invoke AssignVarPtrs() on all (non-leaf) child nodes:
	- for child in context_node.children:
	- AssignVarPtrs(child, search_instance_commands)
	-
	-
	-
	-
	-
	-def AssignVarOrderByFile(context_node, 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.
	-
	- """
	-
	- if search_instance_commands:
	- assert(isinstance(context_node, StaticObj))
	- commands = context_node.instance_commands_push + \
	- context_node.instance_commands + \
	- context_node.instance_commands_pop
	- else:
	- commands = context_node.commands
	- for command in commands:
	- if isinstance(command, WriteFileCommand):
	- tmpl_list = command.tmpl_list
	- for var_ref in tmpl_list:
	- if isinstance(var_ref, VarRef):
	- if (((var_ref.prefix == '@') and
	- isinstance(context_node, StaticObj)) or
	- ((var_ref.prefix == '$') and
	- isinstance(context_node, InstanceObjBasic))):
	- #if ((var_ref.prefix == '@') or
	- # (not search_instance_commands)):
	- if ((var_ref.binding.order is None) or
	- (var_ref.binding.order > var_ref.srcloc.order)):
	- var_ref.binding.order = var_ref.srcloc.order
	-
	- for child in context_node.children:
	- AssignVarOrderByFile(child, search_instance_commands)
	-
	-
	-
	-
	-def AssignVarOrderByCommand(command_list, prefix_filter):
	- """
	- For each category in context_node, and each variable in that category,
	- set the order of each variable according to the position of the
	- write(), write_once(), or other command that created it.
	- Only variables with the correct prefix ('$' 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 AutoAssignVals(cat_node,
	- sort_variables,
	- reserved_values = None,
	- ignore_prior_values = False):
	- """
	- This function automatically assigns 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()):
	-
	- # 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:
	- AutoAssignVals(child,
	- sort_variables,
	- reserved_values,
	- ignore_prior_values)
	-
	-
	-
	-
	-
	-
	-
	-
	-def InvokeAllDeletes(node,
	- null_list_warning=False,
	- null_list_error=True):
	- """ This is a short simple function to carry out any remaining delete
	- statements which have not yet been processed. """
	-
	- i_child = 0
	- i = 0
	- while i < len(node.commands):
	- command = node.commands[i]
	- if isinstance(command, ModCommand):
	- mod_command = command
	- if isinstance(mod_command.command, DeleteCommand):
	- instobj_list = node.LookupMultiDescrStr(mod_command.multi_descr_str,
	- mod_command.command.srcloc,
	- null_list_warning,
	- null_list_error)
	- for instobj in instobj_list:
	- instobj.DeleteSelf()
	- del node.commands[i]
	- else:
	- assert(False)
	- elif isinstance(command, DeleteCommand):
	- node.DeleteSelf()
	- del node.commands[i]
	- elif isinstance(command, InstantiateCommand):
	- child = node.children[i_child]
	- InvokeAllDeletes(child,
	- null_list_warning,
	- null_list_error)
	- i_child += 1
	- i += 1
	- else:
	- i += 1
	-
	-
	-
	-# 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 preceeded 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'
	- ' '+var_ref.prefix+var_ref.descr_str+var_ref.suffix+'\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 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 commands.
	-
	- """
	- 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 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:
	- WriteVarBindingsFile(child)
	-
	-
	-
	-def CustomizeBindings(bindings,
	- g_objectdefs,
	- g_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,
	- g_objectdefs,
	- dbg_loc)
	- elif prefix == '$':
	- var_binding = LookupVar(var_descr_str,
	- g_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
	-
	-
	-
	-
	-##############################################################
	-##################### 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'
	- ' \"'+bindings_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):
	- 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'
	- 'Unrecogized 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) defintions, 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...')
	- # Here we assign pointers for variables in "write_once(){text}" templates:
	- AssignVarPtrs(static_tree_root, search_instance_commands=False)
	- # Here we assign pointers for variables in "write(){text}" templates:
	- AssignVarPtrs(static_tree_root, 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: Now scan through all the (instance) variables within the templates
	- # and replace the (instance) variable references to pointers
	- # to nodes in the InstanceObj tree:
	- sys.stderr.write(' done\nlooking up $variables...')
	- AssignVarPtrs(instance_tree_root, search_instance_commands=False)
	- #sys.stderr.write('done\n garbage collection...')
	- #gc.collect()
	-
	- # Step 6: Now carry out all of the "delete" commands (deferred earlier).
	- # (These were deferred because the instance tree must be complete before any
	- # references to target nodes (with non-trivial paths) can be understood.)
	- InvokeAllDeletes(instance_tree_root,
	- null_list_warning=False,
	- null_list_error=True)
	- sys.stderr.write(' done\n')
	- #sys.stderr.write('instance_v = ' + str(instance_tree_root) + '\n')
	- #gc.collect()
	-
	- # Step 7: The commands must be carried out in a specific order.
	- # (for example, the "write()" and "new" commands).
	- # Search through the tree, and append commands to a command list.
	- # Then re-order the list in the order the commands should have
	- # been executed in. (We don't carry out the commands yet,
	- # we just store them and sort them.)
	- class_parents_in_use = set([])
	- static_tree_root.BuildCommandList(static_commands)
	- instance_tree_root.BuildCommandList(instance_commands)
	- #sys.stderr.write('static_commands = '+str(static_commands)+'\n')
	- #sys.stderr.write('instance_commands = '+str(instance_commands)+'\n')
	-
	- # Step 8: We are about to assign numbers to the variables.
	- # We need to decide the order in which to assign them.
	- # By default static variables (@) are assigned in the order
	- # they appear in the file.
	- # And, by default instance variables ($)
	- # 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=False)
	- AssignVarOrderByFile(static_tree_root, search_instance_commands=True)
	- AssignVarOrderByCommand(instance_commands, '$')
	-
	- # Step 9: Assign the variables.
	- # (If the user requested any customized variable bindings,
	- # load those now.)
	- if len(settings.user_bindings_x) > 0:
	- 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:
	- 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)
	-
	- 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 f5f5af13a..000000000
	--- a/tools/moltemplate/src/ttree_lex.py
	+++ /dev/null
	@@ -1,2074 +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 >= 0:
	- 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).
	-
	- """
	- 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.
	-
	- "order"
	- Later on, during development, the "order" member was added. Why:
	- If you want to know whether block of text comes before or after a
	- different block of text, unfortunately you can not just compare the
	- corresponding line numbers of the files they come from because the
	- files may differ, and multiple short blocks of text may occupy the
	- same line. Consequently, "OSrcLoc" also maintains an internal
	- counter which keeps track of how many OSrcLoc() objects have been
	- created so far. (This can be useful if the user requests that
	- variables and commands be assigned in a non-standard order.)
	- The "order" member is assigned to this counter.
	- Most of the time, the "order" member can be ignored.
	-
	- """
	-
	- count = 0
	-
	- def __init__(self, infile='', lineno=-1):
	- self.infile = infile
	- self.lineno = lineno
	- OSrcLoc.count += 1
	- self.order = OSrcLoc.count
	-
	- 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."""
	- 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."""
	- def __init__(self,
	- prefix = '', # '$' or '${'
	- descr_str = '', # <- descriptor string: "cpath/category:lpath"
	- suffix = '', # '}'
	- srcloc = None,# location in file where defined
	- binding = None,# a pointer to a tuple storing the value
	- nptr = None):# <- see class VarNPtr
	-
	- self.prefix = prefix #Any text before the descriptor string goes here
	- self.suffix = suffix #Any text after the descriptor string goes here
	- self.descr_str = descr_str
	- if srcloc == None: # <- Location in text file where variable appears
	- self.srcloc = OSrcLoc()
	- else:
	- self.srcloc = srcloc
	-
	- self.binding = binding
	-
	- if nptr == None:
	- self.nptr = VarNPtr()
	- else:
	- self.nptr = nptr
	-
	- def __lt__(self, x):
	- return self.order < x.order
	-
	- #def __repr__(self):
	- # return repr((self.prefix + self.descr_str + self.suffix, srcloc))
	-
	-
	-class VarNPtr(object):
	- """
	- Every time a variable appears in a template, it has has a "descritpor".
	- For example, consider the variable
	- "$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.
	- It must be inferred/determined.)
	- (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.
	-
	- """
	- 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.
	-
	- """
	- def __init__(self,
	- full_name = '',
	- nptr = None,
	- value = None,
	- refs = None,
	- order = None,
	- 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 preceeding 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 preceeded 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+='./$@&%^!*~`-_+:;?<>[]' #Allow these chars
	- #
	- # Ommisions:
	- # Note: I left out quotes, whitespace, comment chars ('#'), and escape
	- # characters ('\\') because they are also dealt with separately.
	- # Those characters should not overlap with settings.lex.wordchars.
	- #
	- # Enabling unicode support requires that we override this choice
	- # by specifying "lex.wordterminators" instead of "wordchars".
	- #
	- # lex.wordterminators should be the (printable) set inverse of lex.wordchars
	- # I'm not sure which ascii characters are NOT included in the string above
	- # (We need to figure that out, and put them in settings.lex.wordterminators)
	- # To figure that out, uncomment the 8 lines below:
	- #
	- #self.wordterminators=''
	- #for i in range(0,256):
	- # c = chr(i)
	- # if c not in self.wordchars:
	- # self.wordterminators += c
	- #sys.stderr.write('-------- wordterminators = --------\n')
	- #sys.stderr.write(self.wordterminators+'\n')
	- #sys.stderr.write('-----------------------------------\n')
	- #
	- # Here is the result:
	- self.wordterminators = '(),={\|}' + \
	- self.whitespace + \
	- self.quotes + \
	- self.escape + \
	- self.commenters
	- # Note:
	- # self.whitespace = ' \t\r\f\n'
	- # self.quotes = '\'"'
	- # self.escape = '\\'
	- # self.commenters = '#'
	-
	- self.source_triggers=set(['include','import'])
	- self.source_triggers_x=set(['import'])
	-
	-
	-
	-
	- def GetSrcLoc(self):
	- return OSrcLoc(self.infile, self.lineno)
	-
	-
	- def ReadTemplate(self,
	- simplify_output=False,
	- terminators='}',
	- other_esc_chars='{',
	- keep_terminal_char = True):
	- """
	- ReadTemplate() reads a block of text (between terminators)
	- and divides it into variables (tokens following a '$' 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 "${var}", is used to denote a
	- bracketed variable, and does not cause ReadTemplate() to stop reading)
	- OR if they are part of a two-character escape sequence
	- (for example, '}' in "\}" does not cause terminate parsing).
	- In that case, the text is considered normal text. (However the
	- '\' character is also stripped out. It is also stripped out if it
	- preceeds any characters in "other_esc_chars", which is
	- the second argument. Otherwise it is left in the text block.)
	-
	- """
	- #print(' ReadTemplate('+terminators+') invoked at '+self.error_leader())
	-
	- # The main loop of the parser reads only one variable at time.
	- # The following variables keep track of where we are in the template.
	- reading_var=False # Are we currently reading in the name of a variable?
	-
	- prev_char_delim=False #True iff we just read a var_delim character like '$'
	- 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, 10.0sin(30), 10.0cos(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(0,10.0sin(30),10.0cos(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.
	-
	- """
	- 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 near or before '+self.error_leader()+'\n'
	- 'Invalid expression: \"'+expr_str+'\"')
	- expr_str += token
	- paren_depth = expr_str.count(left_paren) - expr_str.count(right_paren)
	- if (paren_depth != 0):
	- raise InputError('Error near or before '+self.error_leader()+'\n'
	- 'Invalid expression: \"'+expr_str+'\"')
	- 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 d5b1944b7..000000000
	--- a/tools/moltemplate/src/ttree_matrix_stack.py
	+++ /dev/null
	@@ -1,618 +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.
	-
	-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('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_xaxis_x + axis_yaxis_y + axis_z*axis_z)
	- X = axis_x / r
	- Y = axis_y / r
	- Z = axis_z / r
	-
	- #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] = XX(1-c) + c
	- dest[1][1] = YY(1-c) + c
	- dest[2][2] = ZZ(1-c) + c
	-
	- dest[0][1] = XY(1-c) - Z*s
	- dest[0][2] = XZ(1-c) + Y*s
	-
	- dest[1][0] = YX(1-c) + Z*s
	- dest[2][0] = ZX(1-c) - Y*s
	-
	- dest[1][2] = YZ(1-c) - X*s
	- dest[2][1] = ZY(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)
	-
	-
	diff --git a/tools/moltemplate/src/ttree_render.py b/tools/moltemplate/src/ttree_render.py
	deleted file mode 100755
	index 11f3406ab..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 \"'+__file__+'\"\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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