Fix the atom types names in a acpype generated itp file for Gromacs.Input: *_GMX.itp *_NEW.pdb eg: NAD_H_GMX.itp NAD_H_NEW.pdbto run: python itpsort2.py NAD_H_GMX.itp NAD_H_NEW.pdb

itpsort2.py

import os
import sys
from shutil import copyfile
"""
Fix the atom types names in a acpype generated itp file for Gromacs.
Input: *_GMX.itp *_NEW.pdb  eg: NAD_H_GMX.itp NAD_H_NEW.pdb
to run: python itpsort2.py NAD_H_GMX.itp NAD_H_NEW.pdb
"""
file  =  sys.argv[1] #"NAD_H_GMX.itp"
pdb = sys.argv[2] # "NAD_H_NEW.pdb"
copyfile(file, file + "backup")

lines  = open(file , "r").readlines()
pdb = open(pdb, "r").readlines()
#comment everything before atom type
comment = 1
change_atom_type = 0
out_lines = []
for line in lines:
    #just comment everything before moleculetype section
    if "[ moleculetype ]" in line:
        comment = 0 #we don't anymore when we reach molecule section
    if comment:
        line = ";" + line

    #changing atom type
    if line[10:11] == "":
        change_atom_type = 0
    if change_atom_type:
        index = int(line.split()[0])
        atom_type = pdb[index].split()[-1].strip()
        line = line[:8] + "  " + atom_type + line[11:]
    if ";   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type" in line:
        change_atom_type = 1 #we have reached the atoms section

    out_lines.append(line)

with open(file, "w") as out:
    out.writelines(out_lines)
    out.close()