Desmond to gromacs

[Dileepvijayan]

Hi, I was trying to use intermol to convert my Desmond cms file to gromacs. The cms file (linked) was created with the OPLS_2005 force field, water type TIP3P, using Maestro2016-4. It's a small protein-ligand complex and I removed all the water molecules before solvating.
link to the cms file: https://www.dropbox.com/s/9e2rktefrnvpese/desmond_setup_1-out.cms?dl=0 I kept getting this error:

--------------------Error message------------------ INFO 2017-05-16 12:29:02 Beginning InterMol conversion INFO 2017-05-16 12:29:02 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 "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/intermol/convert.py", line 807, in main()
File "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/intermol/convert.py", line 226, in main system, prefix = _load_desmond(cms_in=cms_in)
File "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/intermol/convert.py", line 589, in _load_desmond system = des.load(cms_file=cms_in)
File "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/intermol/desmond/desmond_parser.py", line 39, in load return parser.read()
File "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/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 "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/intermol/desmond/desmond_parser.py", line 903, in load_ffio_block self.sysDirectivetype
File "/data/vijayan/software/Python-2.7.6/lib/python2.7/site-packages/intermol/desmond/desmond_parser.py", line 793, in parse_constraints dHH = float(split[8]) IndexError: list index out of range -----------------End error message-----------------

[mrshirts]

Hi, Dileepvijayan- Try the master branch now. I think the commits that are in should fix it. Note that when I ran with --energy, the gromacs run crashed, but that appears to be because of bad initial coordinates, not a translation error. Let me know if there are still remaining errors after you look at the coordinates.

[Dileepvijayan]

Dear Dr Shirts

Thanks for the email.i will check with the initial coordinates. If that is wrong how come Desmond produce the results? I will check one more time and let you know about it. Thanks

Best regards

Dileep

On 24-May-2017 3:03 pm, "Michael Shirts" notifications@github.com wrote:

Hi, Dileepvijayan- Try the master branch now. I think the commits that are in should fix it. Note that when I ran with --energy, the gromacs run crashed, but that appears to be because of bad initial coordinates, not a translation error. Let me know if there are still remaining errors after you look at the coordinates.

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