Gromacs topology parser

[subhamoymahajan]

If bond types are not specified under "[ bondtypes ]", and mentioned under molecule definitions in .top file, atom types (e.g., "cd") are not converted to integers leading to error in "gromacs/gromacs_parser.py line 805".

 File "convert.py", line 811, in <module>
    main()
  File "convert.py", line 223, in main
    system, prefix, gro_in, top_in = _load_gromacs(gromacs_files=args['gro_in'])
  File "convert.py", line 573, in _load_gromacs
    system = gmx.load(top_in, gro_in)
  File "/srv/home/smahajan29/softwares/InterMol/intermol/gromacs/gromacs_parser.py", line 38, in load
    return parser.read()
  File "/srv/home/smahajan29/softwares/InterMol/intermol/gromacs/gromacs_parser.py", line 419, in read
    self.create_moleculetype(top_moltype, mol_name, mol_count)
  File "/srv/home/smahajan29/softwares/InterMol/intermol/gromacs/gromacs_parser.py", line 727, in create_moleculetype
    self.create_bond(bond)
  File "/srv/home/smahajan29/softwares/InterMol/intermol/gromacs/gromacs_parser.py", line 805, in create_bond
    atoms = [int(n) for n in bond[:n_atoms]]
  File "/srv/home/smahajan29/softwares/InterMol/intermol/gromacs/gromacs_parser.py", line 805, in <listcomp>
    atoms = [int(n) for n in bond[:n_atoms]]
ValueError: invalid literal for int() with base 10: 'cd'

Currently modifying the topology file to defined bondtypes resolves the issue.