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lammps/tools/moltemplate/src/oplsaa_moltemplate.py
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oplsaa_moltemplate.py
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#! /usr/bin/env python
#
# The purpose of this script is to create a moltemplate lt file for the oplsaa.
# forcefield. This will assist researchers in building complex simulations using
# this OPLS-UA and the OPLS-AA forcefields.
__author__="Jason Lambert"
# (some additional corrections by Miguel Gonzalez and Andrew Jewett)
__version__="0.20"
import sys
import os
from operator import itemgetter
g_program_name = __file__.split('/')[-1]
# First make a copy of the \"oplsaa.prm\" file
# (which can be downloaded from the TINKER web site).
# The lines in this file beginning with the word \"atoms\" should
# define the atoms which you plan to put in your simulation. All other
# lines beginning with the word \"atoms\" should be deleted.
# (Leave the other sections of this file alone.)
#""")
if sys.version > '3':
import io
else:
import cStringIO
try:
if sys.version < '2.7':
raise Exception('Error: Using python '+sys.version+'\n'+
' Alas, your version of python is too old.\n'
' You must upgrade to a newer version of python (2.7 or later).')
except Exception as err:
sys.stderr.write('\n\n'+str(err)+'\n')
sys.exit(-1)
#input data from file containing oplsaa force field parameters.
try:
f=open(sys.argv[1],"r")
except:
sys.stderr.write("Error: \n"
" You need to specify a file name as an input argument:\n"
" python oplsaa_moltemplate.py <forcefield file name>\n"
" (or the file name is specified incorrectly)\n")
sys.exit()
sys.stderr.write(g_program_name+", version "+__version__+"\n"
"Reading parameter file...\n")
#output lt file
g=open("oplsaa.lt","w")
lines = f.readlines()
# Ignore/Comment out lines before the "## Atom Type Definitions ##" section.
for i in range(0, len(lines)):
if (lines[i].find("## Atom Type Definitions ##") != -1):
break
else:
lines[i] = '# ' + lines[i]
# As of late 2014, there appear to be 906 atom types, but we don't assume this.
# First try to infer out how many atom types there were in the original
# oplsaa.prm file, or at least find an upper bound on the atom-type numbers.
# (Keep track of the maximum value of the first column in the "atom" section.)
max_atomType = 0
num_atomTypes = 0
for line in lines:
# skip over text after a # comment character
ic = line.find('#')
if ic != -1:
line = (line[:ic]).strip()
else:
line = line.strip()
# now look for lines beginning with the word "atom"
tokens = line.split()
if ((len(tokens)>2) and (tokens[0] == "atom")):
num_atomTypes += 1
if (int(tokens[1]) > max_atomType):
max_atomType = int(tokens[1])
if num_atomTypes > 25:
sys.stderr.write("\n"
"(Note: If your computer freezes while running "+g_program_name+",\n"
" it could be because you forgot to edit the .prm file.\n"
" The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n"
" types. If you run "+g_program_name+" on this file, it may freeze or\n"
" crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n"
" relevant to your problem. To do that, delete the lines from the .prm\n"
" file beginning with \"atom\" which you do not need.)\n\n")
#temporary storage file
atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key
#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms
atom=[[-10000,-10000] for i in range(0,max_atomType+1)]
#charge_by_type={} # lookup charge by atom type
#vdw_by_type={} # lookup epsilon & sigma paramters by atom type
charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom
vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma
#atom is declared this way so for sorting purposes.
#atom contains the following data upon allocation
#atom[][0]=atom_id( Important for partial charges and non_bonded interactions)
#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers)
#atom[][2]=atom_mass
#atom[][3]=partial charge
#atom[][4]=non_bonding sigma
#atom[][5]=non_bonding epsilon
#atom[][6]=atom comment
bond=[]
#bond contains the following data
#bond[0]=atom 1 ffid
#bond[1]=atom 2 ffid
#bond[2]=bond spring constant(OPLS-aa compatible)
#bond[3]=equilibrium bond distance(Angstrom)
angle=[]
#angle contains the following data
#angle[0]=atom 1 ffid
#angle[1]=atom 2 ffid
#angle[2]=atom 3 ffid
#angle[3]=spring constant
#angle[4]=equilibrium angle (degrees)
dihedral=[]
#dihedral contains the following data
#dihedral[0]=atom 1 ffid
#dihedral[1]=atom 2 ffid
#dihedral[2]=atom 3 ffid
#dihedral[3]=atom 4 ffid
#dihedral[4]=v1
#dihedral[5]=v2
#dihedral[6]=v3
#dihedral[7]=v4
improper=[]
#improper[0]=atom 1 ffid
#improper[1]=atom 2 ffid(central atom)
#improper[2]=atom 3 ffid
#improper[3]=atom 4 ffid
#improper[4]=spring coefficient
#improper[5]=equilibrium angle
#This section gets all the parameters from the force field file
for line in lines:
# skip over text after a # comment character
ic = line.find('#')
if ic != -1:
line = (line[:ic]).strip()
else:
line = line.strip()
if line.find("atom") == 0:
line=line.split()
atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]),
0.0,0.0,0.0," ".join(line[3:-2])]
elif line.find("vdw") == 0:
line=line.split()
#vdw_temp.append([float(line[1]),float(line[2]),float(line[3])])
if (int(line[1]) <= max_atomType):
vdw_by_type[int(line[1])] = (float(line[2]),float(line[3]))
elif line.find("bond") == 0:
line=line.split()
bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])])
elif line.find("angle") == 0:
line=line.split()
angle.append([int(line[1]),int(line[2]),int(line[3]),
float(line[4]),float(line[5])])
elif line.find("torsion") == 0:
line=line.split()
dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]),
float(line[5]),float(line[8]), float(line[11]), 0.0])
elif line.find("charge") == 0:
line=line.split()
#charge_temp.append([int(line[1]),float(line[2])])
if (int(line[1]) <= max_atomType):
charge_by_type[int(line[1])] = float(line[2])
elif line.find("imptors") == 0:
line=line.split()
improper.append([int(line[1]), int(line[2]),
int(line[3]), int(line[4]), float(line[5]), float(line[6])])
#if len(atom) > 600:
# sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n"
# " (You were supposed to edit out the atoms you don't need.\n"
# " Not doing this may crash your computer.)\n"
# "\n"
# " Proceed? (Y/N): ")
# reply = sys.stdin.readline()
# if find(reply.strip().lower(), 'y') != 0:
# exit(0)
#adding the charge and Lennard Jones parameters to
#to each atom type.
#----------------------------------------------#
for i in range(0,len(atom)):
atom_type_num = atom[i][0]
#q = charge_by_type.get(atomTypeNum)
#if q:
# atom[i][3] = q
if atom_type_num != -10000:
q = charge_by_type[atom_type_num]
atom[i][3] = q
for i in range(0,len(atom)):
atom_type_num = atom[i][0]
#vdw_params = vdw_by_type.get(atomTypeNum)
#if vdw_params:
# atom[i][4] = vdw_params[0]
# atom[i][5] = vdw_params[1]
if atom_type_num != -10000:
vdw_params = vdw_by_type[atom_type_num]
atom[i][4] = vdw_params[0]
atom[i][5] = vdw_params[1]
del(charge_by_type)
del(vdw_by_type)
#----------------------------------------------------------#
#begin writing content to lt file
g.write("# NOTE: This file was created automatically using:\n"
"# "+g_program_name+" \""+sys.argv[1]+"\"\n\n\n")
g.write("OPLSAA {\n\n" )
#write out the atom masses
#----------------------------------------------------------#
g.write(" write_once(\"Data Masses\"){\n")#checked with gaff
for i,x in enumerate(atom):
if x[0] != -10000:
g.write(" @atom:{} {} #{} partial charge={}\n".format(
x[0],x[2],x[6],x[3]))
g.write(" } #(end of atom masses)\n\n")
#----------------------------------------------------------#
#write out the pair coefficients
#----------------------------------------------------------#
g.write(" write_once(\"In Settings\"){\n")#checked with gaff
for i,x in enumerate(atom):
if x[0] != -10000:
g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4]))
g.write(" } #(end of pair coeffs)\n\n")
g.write(" write_once(\"In Charges\"){\n")#checked with gaff
for i,x in enumerate(atom):
if x[0] != -10000:
g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3]))
g.write(" } #(end of atom charges)\n\n")
#-----------------------------------------------------------#
# This part of the code creates a lookup dictionary
# that allows you to find every type of atom by its
# force field id. force field id is the id number
# relevant to bonds, angles, dihedrals, and impropers.
# This greatly increases the speed of angle, bond, dihedral
# and improper assignment.
#------------------------------------------------------------#
atom=sorted(atom,key=itemgetter(1))
atom_ffid=0
for x in atom:
if x[1]==atom_ffid:
atom_lookup[x[1]].append(x[0])
elif x[1]>atom_ffid:
atom_lookup[x[1]]=[x[0]]
atom_ffid=x[1]
atom_lookup[0]=["*"]
#-------------------------------------------------------------#
#writing out the bond coefficients and bond parameters#
#-------------------------------------------------------------#
# First check if the atoms in system can potentially form bonds
might_have_bonds = False
for x in bond:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
might_have_bonds = True
if might_have_bonds:
h=open("temp.txt","w+")
g.write(" write_once(\"In Settings\") {\n")
index1=0
for x in bond:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
#g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3]))
# Miguel Gonzales corrected this line to:
g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3]))
h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z))
g.write(" } #(end of bond_coeffs)\n\n")
h.seek(0,0)
g.write(" write_once(\"Data Bonds By Type\") {\n")
for line in h.readlines():
g.write(line)
g.write(" } #(end of bonds by type)\n\n")
del(bond)
h.close()
#-----------------------------------------------------------#
#writing out angle coefficients and angles by type.---------#
#-----------------------------------------------------------#
# First check if the atoms in system can potentially form angle interactions
might_have_angles = False
for x in angle:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
for u in atom_lookup.get(x[2],[]):
might_have_angles = True
if might_have_angles:
h=open("temp.txt","w+")
g.write(" write_once(\"Data Angles By Type\"){\n")
for x in angle:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
for u in atom_lookup.get(x[2],[]):
#print(y,z,u,x)
#h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4]))
# Miguel Gonzales corrected this line:
h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4]))
g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u))
g.write(" } #(end of angles by type)\n\n")
h.seek(0,0)
g.write(" write_once(\"In Settings\" ){\n")
for line in h.readlines():
g.write(line)
g.write(" } #(end of angle_coeffs)\n\n")
del(angle)
h.close()
#----------------------------------------------------------#
#writing dihedrals by type and dihedral coefficients-------#
#----------------------------------------------------------#
# First check if the atoms in system can potentially form dihedral interactions
might_have_dihedrals = False
for x in dihedral:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
for u in atom_lookup.get(x[2],[]):
for v in atom_lookup.get(x[3],[]):
might_have_dihedrals = True
if might_have_dihedrals:
h=open("temp.txt","w+")
g.write(" write_once(\"Data Dihedrals By Type\") {\n")
#print(atom_lookup)
for x in dihedral:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
for u in atom_lookup.get(x[2],[]):
for v in atom_lookup.get(x[3],[]):
if x[0]!=0 and x[3]!=0:
g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format(y,z,u,v,x[4],x[5],x[6],x[7]))
elif x[0]==0 and x[3]!=0:
g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(
y,z,u,v))
h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format(z,u,v,x[4],x[5],x[6],x[7]))
elif x[0]==0 and x[3]==0:
g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
#h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7]))
h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7]))
del(dihedral)
g.write(" } #(end of Dihedrals by type)\n\n")
h.seek(0,0)
g.write(" write_once(\"In Settings\") {\n")
for line in h.readlines():
g.write(line)
g.write(" } #(end of dihedral_coeffs)\n\n")
h.close()
#-----------------------------------------------------------------------#
#----writing out improper coefficients and impropers by type------------#
#-----------------------------------------------------------------------#
# First check if the atoms in system can potentially form improper interactions
might_have_impropers = False
for x in improper:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
for u in atom_lookup.get(x[2],[]):
for v in atom_lookup.get(x[3],[]):
might_have_impropers = True
if might_have_impropers:
h=open("temp.txt","w+")
g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n")
for x in improper:
for y in atom_lookup.get(x[0],[]):
for z in atom_lookup.get(x[1],[]):
for u in atom_lookup.get(x[2],[]):
for v in atom_lookup.get(x[3],[]):
# Notation: let I,J,K,L denote the atom types ("biotypes")
# listed in the order they appear in the "oplsaa.prm" file.
# (I think J and L are represented by "u" and "v" in the code here.)
# It looks like the "oplsaa.prm" file distributed with tinker
# treats the third atom ("K") as the central atom.
# After checking the code, it appears that the improper angle is
# calculated as the angle between the I,J,K and the J,K,L planes
if x[0]==0 and x[1]==0 and x[3]==0:
g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180))
else:
g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v))
h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180))
g.write(" } #(end of impropers by type)\n\n")
h.seek(0,0)
g.write(" write_once(\"In Settings\") {\n")
for line in h.readlines():
g.write(line)
g.write(" } #(end of improp_coeffs)\n\n")
h.close()
#-----------------------------------------------------------------------#
#This section writes out the input parameters required for an opls-aa simulation
# lammps.
g.write(" write_once(\"In Init\") {\n")
g.write(" units real\n")
g.write(" atom_style full\n")
g.write(" bond_style hybrid harmonic\n")
g.write(" angle_style hybrid harmonic\n")
g.write(" dihedral_style hybrid opls\n")
g.write(" improper_style hybrid harmonic\n")
#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n")
g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n")
g.write(" pair_modify mix geometric\n")
g.write(" special_bonds lj/coul 0.0 0.0 0.5\n")
g.write(" kspace_style pppm 0.0001\n")
g.write(" } #end of init parameters\n\n")
g.write("} # OPLSAA\n")
f.close()
g.close()
os.remove("temp.txt")
sys.stderr.write("...finished.\n")
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