Desmond to GMX

[billy-noonan]

Hi All,

I have a system consisting of a protein-ligand complex in 150 mM NaCl solvent. When I run MD on this system using Desmond, everything runs smoothly. When I try to use convert.py using InterMol to generate GROMACS files with:

mkdir gmx

python ~/InterMol-master/intermol/convert.py --des_in 1_MD_gmx.cms --gromacs --odir gmx --energy

I receive the following error, which I presume has something to do with the .cms file:

File "/vcp2/student/billy/InterMol-master/intermol/convert.py", line 811, in <module>
    main()
  File "/vcp2/student/billy/InterMol-master/intermol/convert.py", line 226, in main
    system, prefix = _load_desmond(cms_in=cms_in)
  File "/vcp2/student/billy/InterMol-master/intermol/convert.py", line 589, in _load_desmond
    system = des.load(cms_file=cms_in)
  File "/vcp2/student/billy/anaconda3/lib/python3.6/site-packages/intermol-0.1.0.dev0-py3.6.egg/intermol/desmond/desmond_parser.py", line 39, in load
    return parser.read()
  File "/vcp2/student/billy/anaconda3/lib/python3.6/site-packages/intermol-0.1.0.dev0-py3.6.egg/intermol/desmond/desmond_parser.py", line 1079, in read
    with open(self.cms_file, 'r') as fl:

When I use a system consisting of a cyclic peptide in chloroform, I don't get this error...

Please advise?

Cheers,

Billy

[ctk3b]

Hi Billy, looks like the last bit of the traceback got chopped off. Could you post the full error message? Also if possible, can you share the input files? That makes it significantly easier for us to debug.

[billy-noonan]

Hi ctk3b,

I am unable to send you the .cms file for the entire system, however I did try this with the protein alone in solvent, and received the same error.

When running the following command:

python ~/InterMol-master/intermol/convert.py --des_in protein_MD.cms --gromacs --odir gmx --energy

I get the same error:

^CFailed to import the site module Traceback (most recent call last): File "/vcp2/student/billy/anaconda3/lib/python3.6/site.py", line 544, in main() File "/vcp2/student/billy/anaconda3/lib/python3.6/site.py", line 537, in main execsitecustomize() File "/vcp2/student/billy/anaconda3/lib/python3.6/site.py", line 481, in execsitecustomize import sitecustomize File "", line 961, in _find_and_load File "", line 946, in _find_and_load_unlocked File "", line 885, in _find_spec File "", line 1157, in find_spec File "", line 1129, in _get_spec File "", line 1245, in find_spec File "", line 1285, in _fill_cache KeyboardInterrupt billy@eta:~/Documents/SPSB/sim015/protein_MD> mkdir gmx billy@eta:~/Documents/SPSB/sim015/protein_MD> python ~/InterMol-master/intermol/convert.py --des_in protein_MD.cms --gromacs --odir gmx --energy INFO 2017-11-01 17:04:52 Beginning InterMol conversion

INFO 2017-11-01 17:04:52 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 "/vcp2/student/billy/InterMol-master/intermol/convert.py", line 811, in main() File "/vcp2/student/billy/InterMol-master/intermol/convert.py", line 226, in main system, prefix = _load_desmond(cms_in=cms_in) File "/vcp2/student/billy/InterMol-master/intermol/convert.py", line 589, in _load_desmond system = des.load(cms_file=cms_in) File "/vcp2/student/billy/anaconda3/lib/python3.6/site-packages/intermol-0.1.0.dev0-py3.6.egg/intermol/desmond/desmond_parser.py", line 39, in load return parser.read() File "/vcp2/student/billy/anaconda3/lib/python3.6/site-packages/intermol-0.1.0.dev0-py3.6.egg/intermol/desmond/desmond_parser.py", line 1141, in read self.load_ffio_block(molname, self.ffio_blockpos[i], self.fmct_blockpos[i+1]-1) File "/vcp2/student/billy/anaconda3/lib/python3.6/site-packages/intermol-0.1.0.dev0-py3.6.egg/intermol/desmond/desmond_parser.py", line 903, in load_ffio_block self.sysDirectivetype File "/vcp2/student/billy/anaconda3/lib/python3.6/site-packages/intermol-0.1.0.dev0-py3.6.egg/intermol/desmond/desmond_parser.py", line 576, in parse_bonds new_bond = self.create_forcetype(self.desmond_bonds[key], atoms, params) KeyError: 'INVALID'

If you send me an e-mail, I'll send you the .cms file attached.

Thanks again for the help!

Cheers,

Billy

[fgentile89]

Hi, I got the same problem while converting cms to Amber:

python InterMol/intermol/convert.py --des_in desmond_md_job.cms --amber

It is a protein-ligand system, solvated and with 0.15M of NaCl created with Maestro. What do you think the problem could be?

[camposgavy]

When you encounter KeyError: 'INVALID', you have "INVALID" as a keyword in your .cms file. Please review the input and ensure it is in the correct format.