Issue when converting from Desmond input to LAMMPS output

[dadrion]

Hello, I am reaching out about an issue that I am having with converting from the MD output from a Desmond calculation (.cms format) to the trajectory output from LAMMPS (.lammpstrj format), which I want to use for some post processing. I am getting the following error:

Traceback (most recent call last):
  File "/Users/lopezlab/Downloads/InterMol/intermol/convert.py", line 811, in <module>
    main()
  File "/Users/lopezlab/Downloads/InterMol/intermol/convert.py", line 226, in main
    system, prefix = _load_desmond(cms_in=cms_in)
  File "/Users/lopezlab/Downloads/InterMol/intermol/convert.py", line 589, in _load_desmond
    system = des.load(cms_file=cms_in)
  File "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/intermol/desmond/desmond_parser.py", line 40, in load
    return parser.read()
  File "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/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 "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/intermol/desmond/desmond_parser.py", line 925, in load_ffio_block
    self.sysDirective[type](*params)
  File "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/intermol/desmond/desmond_parser.py", line 579, in parse_bonds
    new_bond = self.create_forcetype(self.desmond_bonds[key], atoms, params)

I have tried using the --energy option when running also just to test if this would help, but it did not. I am happy to answer any follow up questions. I have also attached my .cms file in text format for reference. Thanks! cyp_dmso_nvt-out.txt

[ctk3b]

Hi @dadrion - could you post the full traceback? I don't see an error

[dadrion]

@ctk3b my apologies, I seem to have left out the error part, here is all of the output that I get after the command line

INFO 2022-03-02 16:29:38 Beginning InterMol conversion

INFO 2022-03-02 16:29:38 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 "/Users/lopezlab/Downloads/InterMol/intermol/convert.py", line 811, in <module>
    main()
  File "/Users/lopezlab/Downloads/InterMol/intermol/convert.py", line 226, in main
    system, prefix = _load_desmond(cms_in=cms_in)
  File "/Users/lopezlab/Downloads/InterMol/intermol/convert.py", line 589, in _load_desmond
    system = des.load(cms_file=cms_in)
  File "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/intermol/desmond/desmond_parser.py", line 40, in load
    return parser.read()
  File "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/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 "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/intermol/desmond/desmond_parser.py", line 925, in load_ffio_block
    self.sysDirective[type](*params)
  File "/Users/lopezlab/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/intermol/desmond/desmond_parser.py", line 579, in parse_bonds
    new_bond = self.create_forcetype(self.desmond_bonds[key], atoms, params)
KeyError: 'INVALID'

[ctk3b]

I'm not very familiar with the .cms format anymore but the error message is telling you that the bond type INVALID is not supported. We only support HARM and HARM_CONSTRAINTED

Looking at your .cms file, there appear to be a bunch of bond types labeled INVALID or INVALID_CONSTRAINED