amberparm2lt.sh
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Created: Sat, Jan 4, 10:16

amberparm2lt.sh
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	#!/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 ""

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