Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/tools/moltemplate/common/amber/amberparm2lt.sh
4a1807d39739lammm-master-deprecated

Last Change
Raw File

amberparm2lt.sh
View Options

#!/bin/sh
SYNTAX_MSG=$(cat <<EOF
Typical Usage:
amberparm2lt.sh gaff.dat GAFF > gaff.lt
You can also try:
amberparm2lt.sh parm94.dat "AMBERFF94 inherits GAFF" > amberff94.lt
(However, this later usage may not work.
You may need to manually split the .dat file and run these scripts instead:
amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...)
Be sure that all of these .py files are in your PATH as well.)
EOF
)
if [ "$#" != "2" ]; then
echo "${SYNTAX_MSG}" >&2
echo "" >&2
echo "Error: This script requires two arguments," >&2
echo " 1) the name of the amber parm file to be converted (eg \"gaff.dat\")" >&2
echo " 2) the name of the moltemplate object to be created (eg \"GAFF\")" >&2
echo " (This may include the \"inherits\" keyword and parent classes.)" >&2
exit 1
fi
MOLTEMPLATE_USAGE_MSG=$(cat <<EOF
# Background information and usage explanation:
# This file contanis a list of atom types and rules for generating bonded
# interactions between these atoms (hopefully) according to AMBER conventions.
# By using the atom types shown below in your own molecules, bonds and angular
# interactions will be automatically generated.
# AMBER (GAFF) force-field parameters will also be assigned to each angle
# interaction (according to these atom types).
# One way to apply the GAFF force field to a particular type of molecule, is
# to use the "inherits" keyword when you define that molecule. For example:
# import("gaff.lt")
# MoleculeType inherits GAFF {
# write_once("Data Atoms") {
# \$atom:C1 \$mol:... @atom:cx 0.0 4.183 3.194 13.285
# \$atom:C2 \$mol:... @atom:cx 0.0 4.291 4.618 13.382
# : : :
# }
# }
#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.)
EOF
)
# (Note that the full name of the atom type in this example is "@atom:/GAFF/cx"
# You can always refer to atom types this way as well. Using "inherits GAFF"
# allows you to use more conventient "@atom:cx" shorthand notation instead.)
echo "####################################################################"
echo "# To use this, LAMMPS currently must be compiled with the USER-MISC package."
echo "# (Type \"make yes-user-misc\" into the shell before compiling LAMMPS.)"
echo "####################################################################"
echo "# This moltemplate (LT) file was generated automatically using"
echo "# amberparm2lt.sh $1 $2"
echo "####################################################################"
echo "$MOLTEMPLATE_USAGE_MSG"
echo "####################################################################"
echo "# Moltemplate can not assign atom charge. You must assign atomic"
echo "# charges yourself. (Moltemplate is only a simple text manipulation tool.)"
echo "####################################################################"
echo ""
echo ""
if ! which ./amberparm_mass_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_mass_to_lt.py\" not found.\n" >&2
echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
exit 2
fi
if ! which ./amberparm_pair_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_pair_to_lt.py\" not found.\n" >&2
echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
exit 2
fi
if ! which ./amberparm_bond_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_bond_to_lt.py\" not found.\n" >&2
echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
exit 2
fi
if ! which ./amberparm_angle_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_angle_to_lt.py\" not found.\n" >&2
echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
exit 2
fi
if ! which ./amberparm_dihedral_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_dihedral_to_lt.py\" not found.\n" >&2
echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
exit 2
fi
if ! which ./amberparm_improper_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_improper_to_lt.py\" not found. (Update your PATH?)\n" >&2
echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2
exit 2
fi
#PARM_FILE='gaff.dat'
PARM_FILE=$1
# sections are separated by blank lines
# some sections have comment lines at the beginning
# The 1st section is the mass (note: skip the first line)
tail -n +2 < "$PARM_FILE" | \
awk -v n=1 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
> "${PARM_FILE}.mass"
# The 2nd section has the list of 2-body bond force-field params
awk -v n=2 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
| tail -n +2 \
> "${PARM_FILE}.bond"
# The 3rd section has the list of 3-body angle force-field params
awk -v n=3 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.angle"
# The 4th section has the list of 4-body dihedral force-field params
awk -v n=4 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.dihedral"
# The 5th section has the list of 4-body improper force-field params
awk -v n=5 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.improper"
# The 6th section has the hbond-parameters (no-longer used. ignore)
awk -v n=6 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.hbond"
# The 7th "section" is just a blank line. (skip that)
# The 8th section has the list of non-bonded ("pair") force-field parameters
awk -v n=8 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
| tail -n +2 \
> "${PARM_FILE}.pair"
./amberparm_mass_to_lt.py < "${PARM_FILE}.mass" > "${PARM_FILE}.mass.lt"
./amberparm_pair_to_lt.py < "${PARM_FILE}.pair" > "${PARM_FILE}.pair.lt"
./amberparm_bond_to_lt.py < "${PARM_FILE}.bond" > "${PARM_FILE}.bond.lt"
./amberparm_angle_to_lt.py < "${PARM_FILE}.angle" > "${PARM_FILE}.angle.lt"
./amberparm_dihedral_to_lt.py \
< "${PARM_FILE}.dihedral" > "${PARM_FILE}.dihedral.lt"
./amberparm_improper_to_lt.py \
< "${PARM_FILE}.improper" > "${PARM_FILE}.improper.lt"
echo "$2 {"
echo ""
echo " # ----------------------------------------------------------------------"
#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\""
echo " # The basic atom nomenclature and conventions are explained here:"
echo " # http://ambermd.org/antechamber/gaff.pdf"
echo " # For reference, the original gaff.dat file and format documenation are here:"
echo " # http://ambermd.org/AmberTools-get.html"
echo " # http://ambermd.org/formats.html#parm.dat"
echo " # ----------------------------------------------------------------------"
echo ""
cat "$PARM_FILE.mass.lt" \
"$PARM_FILE.pair.lt" \
"$PARM_FILE.bond.lt" \
"$PARM_FILE.angle.lt" \
"$PARM_FILE.dihedral.lt" \
"$PARM_FILE.improper.lt"
AMBER_STYLES_INIT=$(cat <<EOF
write_once("In Init") {
# Default styles and settings for AMBER based force-fields:
units real
atom_style full
bond_style hybrid harmonic
angle_style hybrid harmonic
dihedral_style hybrid fourier
improper_style hybrid cvff
pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
kspace_style pppm 0.0001
# NOTE: If you do not want to use long-range coulombic forces,
# comment out the two lines above and uncomment this line:
# pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
pair_modify mix arithmetic
special_bonds amber
}
EOF
)
echo "$AMBER_STYLES_INIT"
echo ""
echo "}"
echo ""
echo ""
c4science · Help