added the "amberfrcmod2lt.sh script for converting user-supplied FRCM…

…OD files into moltemplate LT files that can be used with gaff.lt and gaff2.lt. Also corrected some some of the error messages in genpoly_lt.py

doc/doc_genpoly_lt.md

@@ -248,7 +248,7 @@ from the terminal) and a python library.  The former is documented below.
                    of the smallest rectangular box which encloses all of the
                    coordinates in the coordinate file.  The user must supply 3
                    comma-separated numbers (no spaces) which indicate how much
-                   extra room is needed in the x,y,z directions, at both ends.
+                   extra room is needed in the ±x, ±y, ±z directions.
 
     -polymer-directions polarities.txt
                    Change the order that coordinates are read from the file.

doc/moltemplate_manual_src/moltemplate_manual.tex

@@ -63,7 +63,7 @@ \subsubsection*{Warning:
   simulations.}
 However numerous examples and README files are available to
 demonstrate how to run these kinds of simulations.
-Downloading these examples is \textit{highly recommended}.
+Downloading these examples is highly recommended.
 (See section \ref{sec:installation}.)
 
 \section{Introduction}

moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberfrcmod2lt.sh

@@ -0,0 +1,188 @@
+#!/bin/sh
+
+SYNTAX_MSG=$(cat <<EOF
+Typical Usage:
+
+amberfrcmod2lt.sh DABPA_AC.frcmod GAFF > dabpa_ac_frcmod.lt
+
+(Then include the line "import dabpa_ac_frcmod.lt" at the beginning of the LT
+ describing the molecule(s) that needs this frcmod.  For example
+
+import "gaff.lt"
+import "dabpa_ac_frcmod.lt"
+DABPA inherits GAFF {
+  ...define molecule here...
+}  
+
+You may need to manually split the .frcmod file and run these scripts instead:
+amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...)
+(Be sure that all of these .py files are in your PATH as well.)
+
+EOF
+)
+
+if [ "$#" != "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 "# amberfrcmod2lt.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 "# You can do this afterwards using commands like \"set atom 70 charge -0.212\""
+echo "# For details, see http://lammps.sandia.gov/doc/set.html)"
+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
+
+
+#FRCMOD_FILE='gaff.dat'
+FRCMOD_FILE=$1
+
+# sections are separated by blank lines
+# some sections have comment lines at the beginning
+
+tail -n +2 < "$FRCMOD_FILE" | awk 'BEGIN{ignore=1} {if ((NF==1)&&($1=="MASS")) {ignore=0} else {if (NF==1) {ignore=1} if (!ignore) {if (NF>0) print $0}}}' > ${FRCMOD_FILE}.mass
+
+tail -n +2 < "$FRCMOD_FILE" | awk 'BEGIN{ignore=1} {if ((NF==1)&&($1=="BOND")) {ignore=0} else {if (NF==1) {ignore=1} if (!ignore) {if (NF>0) print $0}}}' > ${FRCMOD_FILE}.bond
+
+tail -n +2 < "$FRCMOD_FILE" | awk 'BEGIN{ignore=1} {if ((NF==1)&&($1=="ANGLE")) {ignore=0} else {if (NF==1) {ignore=1} if (!ignore) {if (NF>0) print $0}}}' > ${FRCMOD_FILE}.angle
+
+tail -n +2 < "$FRCMOD_FILE" | awk 'BEGIN{ignore=1} {if ((NF==1)&&($1=="DIHE")) {ignore=0} else {if (NF==1) {ignore=1} if (!ignore) {if (NF>0) print $0}}}' > ${FRCMOD_FILE}.dihedral
+
+tail -n +2 < "$FRCMOD_FILE" | awk 'BEGIN{ignore=1} {if ((NF==1)&&($1=="IMPROPER")) {ignore=0} else {if (NF==1) {ignore=1} if (!ignore) {if (NF>0) print $0}}}' > ${FRCMOD_FILE}.improper
+
+tail -n +2 < "$FRCMOD_FILE" | awk 'BEGIN{ignore=1} {if ((NF==1)&&($1=="NONBON")) {ignore=0} else {if (NF==1) {ignore=1} if (!ignore) {if (NF>0) print $0}}}' > ${FRCMOD_FILE}.pair
+
+
+./amberparm_mass_to_lt.py < "${FRCMOD_FILE}.mass" > "${FRCMOD_FILE}.mass.lt"
+./amberparm_pair_to_lt.py < "${FRCMOD_FILE}.pair" > "${FRCMOD_FILE}.pair.lt"
+./amberparm_bond_to_lt.py < "${FRCMOD_FILE}.bond" > "${FRCMOD_FILE}.bond.lt"
+./amberparm_angle_to_lt.py < "${FRCMOD_FILE}.angle" > "${FRCMOD_FILE}.angle.lt"
+./amberparm_dihedral_to_lt.py \
+     < "${FRCMOD_FILE}.dihedral" > "${FRCMOD_FILE}.dihedral.lt"
+./amberparm_improper_to_lt.py \
+     < "${FRCMOD_FILE}.improper" > "${FRCMOD_FILE}.improper.lt"
+
+
+
+echo "$2 {"
+echo ""
+echo "  # ----------------------------------------------------------------------"
+#echo "  # This file was automatically generated by \"common/amber/amberparm2lt.sh\""
+echo "  # The basic atom nomenclature and conventions are explained here:"
+echo "  #   http://ambermd.org/antechamber/gaff.pdf"
+echo "  # For reference, the original gaff.dat file and format documentation are here:"
+echo "  #   http://ambermd.org/AmberTools-get.html"
+echo "  #   http://ambermd.org/formats.html#parm.dat"
+echo "  # ----------------------------------------------------------------------"
+echo ""
+
+cat "$FRCMOD_FILE.mass.lt" \
+    "$FRCMOD_FILE.pair.lt" \
+    "$FRCMOD_FILE.bond.lt" \
+    "$FRCMOD_FILE.angle.lt" \
+    "$FRCMOD_FILE.dihedral.lt" \
+    "$FRCMOD_FILE.improper.lt"
+
+# Commenting out the following (should be already defined in main FF file.)
+#
+#AMBER_STYLES_INIT=$(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 ""

moltemplate/genpoly_lt.py

@@ -132,7 +132,7 @@ def ParseArgs(self, argv):
             elif argv[i].lower() == '-bond':
                 if i + 3 >= len(argv):
                     raise InputError(
-                        'Error: ' + argv[i] + ' flag should be followed by 4 strings.\n')
+                        'Error: ' + argv[i] + ' flag should be followed by 3 strings.\n')
                 # self.bonds_name.append(argv[i+1])
                 self.bonds_type.append(argv[i + 1])
                 self.bonds_atoms.append((argv[i + 2],
@@ -142,7 +142,7 @@ def ParseArgs(self, argv):
             elif argv[i].lower() == '-angle':
                 if i + 7 >= len(argv):
                     raise InputError(
-                        'Error: ' + argv[i] + ' flag should be followed by 5 strings and 3 integers.\n')
+                        'Error: ' + argv[i] + ' flag should be followed by 4 strings and 3 integers.\n')
                 # self.angles_name.append(argv[i+1])
                 self.angles_type.append(argv[i + 1])
                 self.angles_atoms.append((argv[i + 2],
@@ -160,7 +160,7 @@ def ParseArgs(self, argv):
             elif argv[i].lower() == '-dihedral':
                 if i + 9 >= len(argv):
                     raise InputError(
-                        'Error: ' + argv[i] + ' flag should be followed by 6 strings and 4 integers.\n')
+                        'Error: ' + argv[i] + ' flag should be followed by 5 strings and 4 integers.\n')
                 # self.dihedrals_name.append(argv[i+1])
                 self.dihedrals_type.append(argv[i + 1])
                 self.dihedrals_atoms.append((argv[i + 2],
@@ -181,7 +181,7 @@ def ParseArgs(self, argv):
             elif argv[i].lower() == '-improper':
                 if i + 9 >= len(argv):
                     raise InputError(
-                        'Error: ' + argv[i] + ' flag should be followed by 6 strings and 4 integers.\n')
+                        'Error: ' + argv[i] + ' flag should be followed by 5 strings and 4 integers.\n')
                 # self.impropers_name.append(argv[i+1])
                 self.impropers_type.append(argv[i + 1])
                 self.impropers_atoms.append((argv[i + 2],

moltemplate/scripts/moltemplate.sh

@@ -6,8 +6,8 @@
 # Copyright (c) 2013
 
 G_PROGRAM_NAME="moltemplate.sh"
-G_VERSION="2.16.5"
-G_DATE="2020-3-25"
+G_VERSION="2.17.0"
+G_DATE="2020-4-03"
 
 echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
 echo "" >&2

setup.py

@@ -45,9 +45,9 @@
 
   url='https://github.com/jewettaij/moltemplate',
 
-  download_url='https://github.com/jewettaij/moltemplate/archive/v2.16.5.zip',
+  download_url='https://github.com/jewettaij/moltemplate/archive/v2.17.0.zip',
 
-  version='2.16.5',
+  version='2.17.0',
 
   keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder',
             'ESPResSo'],