shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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Error in converting cms to Gromacs topology #372

Open Moh-Pou opened 3 years ago

Moh-Pou commented 3 years ago

Dear InterMol developers,

I get an error when converting the cms file to Gromacs, and I would appreciate it if you could help me resolve the issue.

This is a link to the cms file: https://drive.google.com/file/d/1kqiS1MXduum09GpD3jtezi36n2qtRz1a/view?usp=sharing

This is the command that I use: python convert.py --des_in ~/Downloads/desmond_setup_SAH-out.cms --gromacs --odir ~/Downloads/

This is the error message:

INFO 2020-11-18 21:43:38 Beginning InterMol conversion

INFO 2020-11-18 21:43:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1

Traceback (most recent call last): File "convert.py", line 811, in main() File "convert.py", line 226, in main system, prefix = _load_desmond(cms_in=cms_in) File "convert.py", line 589, in _load_desmond system = des.load(cms_file=cms_in) File "/anaconda3/lib/python3.7/site-packages/intermol-0.1.0-py3.7.egg/intermol/desmond/desmond_parser.py", line 40, in load return parser.read() File "/anaconda3/lib/python3.7/site-packages/intermol-0.1.0-py3.7.egg/intermol/desmond/desmond_parser.py", line 1170, in read self.load_ffio_block(molname, self.ffio_blockpos[i], self.fmct_blockpos[i+1]-1) File "/anaconda3/lib/python3.7/site-packages/intermol-0.1.0-py3.7.egg/intermol/desmond/desmond_parser.py", line 925, in load_ffio_block self.sysDirectivetype File "/anaconda3/lib/python3.7/site-packages/intermol-0.1.0-py3.7.egg/intermol/desmond/desmond_parser.py", line 579, in parse_bonds new_bond = self.create_forcetype(self.desmond_bonds[key], atoms, params) KeyError: 'INVALID'

Thuravi commented 2 years ago

Dear Mr. Pourmousa,

I am currently facing the same issue. Is there any update regarding this? Could you able to solve this issue?

Best Santhosh