GROMACS格式的文件转成LAMMPS格式的工具GRO2LAM - 计算化学公社

INFO 2022-12-19 00:35:43 Converting dihedral1_vacuum
INFO 2022-12-19 00:35:43 Converting dihedral2_vacuum
INFO 2022-12-19 00:35:43 Converting dihedral3_vacuum
INFO 2022-12-19 00:35:43 Converting dihedral4_vacuum
INFO 2022-12-19 00:35:43 Converting dihedral5_vacuum
INFO 2022-12-19 00:35:43 Converting dihedral9_vacuum
Traceback (most recent call last):
File "test_all.py", line 96, in <module>
testing_function(args['compute_energies'], args['output_dir'])
File "test_all.py", line 24, in test_gromacs_unit
output_dir=output_dir)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/tests/testing_tools.py", line 90, in convert_one_to_all
output_dir=output_dir)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/tests/testing_tools.py", line 219, in _convert_from_engine
diff = convert.main(flags)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/convert.py", line 223, in main
system, prefix, gro_in, top_in = _load_gromacs(gromacs_files=args['gro_in'])
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/convert.py", line 573, in _load_gromacs
system = gmx.load(top_in, gro_in)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 38, in load
return parser.read()
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 416, in read
self.process_file(self.top_filename)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1142, in process_file
self.process_line(top_filename, '{0} {1}'.format(append, line))
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1281, in process_line
self.process_dihedraltype(line)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1487, in process_dihedraltype
self.gromacs_dihedral_types, self.canonical_dihedral)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1509, in process_forcetype
kwds = self.create_kwds_from_entries(fields, gromacs_force_type, offset=n_atoms+1)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 347, in create_kwds_from_entries
entries, force_class, offset=offset)
File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/forces/forcefunctions.py", line 139, in create_kwds_from_entries
kwds[p] = float(entries[offset+i]) * u[i]
IndexError: list index out of range

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