Desmond conversion

[tjgdamen]

When I try to convert a Desmond .cms file to any other format I get the following error:

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 "C:\ProgramData\PyMOL\lib\site-packages\intermol-0.1.0.dev0-py2.7.egg\intermol\desmond\desmond_parser.py", line 39, in load return parser.read() File "C:\ProgramData\PyMOL\lib\site-packages\intermol-0.1.0.dev0-py2.7.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 "C:\ProgramData\PyMOL\lib\site-packages\intermol-0.1.0.dev0-py2.7.egg\intermol\desmond\desmond_parser.py", line 903, in load_ffio_block self.sysDirectivetype File "C:\ProgramData\PyMOL\lib\site-packages\intermol-0.1.0.dev0-py2.7.egg\intermol\desmond\desmond_parser.py", line 576, in parse_bonds new_bond = self.create_forcetype(self.desmond_bonds[key], atoms, params) KeyError: 'INVALID'

I have read several topics with seem to have similar issues, but never found a solution for this error.

Thanks in advance for helping me out.

[mrshirts]

I can try to take a look, if you could send an example file that fails (the smaller, the better).

[tjgdamen]

Dear Dr. Michael Shirts,

Thanks a lot for your quick reply. Because of a National Holiday in The Netherlands last Friday I could only come back to you now; hopefully you are able to help me out.

Please find attached the .cms file created by Desmond and zipped with 7-zip to reduce its size. As an example I did a 1 ns MD simulation of pdb 5FNU. When I prepared the system, I removed all crystal waters before solvation in SPC waters. I used the Desmond version as is implemented in Maestro of Schrodinger Suite 2018-1.

When I try to convert the .cms file to gromacs (or any other format), I got the following error:

[cid:image001.png@01D3E08E.B4547C90]

BTW, I am running the convert.py script in the most recent Anaconda (python).

Thanks in advance for taking a deeper look at it and hopefully you can help me out!

Very kind regards,

Eddy

Eddy Damen, Ph.D. Group Leader Comp. Chem. & Drug Design

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Mercachem Kerkenbos 1013, 6546 BB Nijmegen P.O. Box 6747, 6503 GE Nijmegen The Netherlands phone: +31(0)24-3723307 fax: +31(0)24-3723305 e-mail: eddy.damen@mercachem.com

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From: Michael Shirts [mailto:notifications@github.com] Sent: donderdag 26 april 2018 22:31 To: shirtsgroup/InterMol InterMol@noreply.github.com Cc: Eddy Damen Eddy.Damen@Mercachem.Com; Author author@noreply.github.com Subject: Re: [shirtsgroup/InterMol] Desmond conversion (#344)

I can try to take a look, if you could send an example file that fails (the smaller, the better).

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[shansun7994]

I ran into the same problem. Do we have a solution now?

[mehdim390]

Dear all,

Any solution for this issue with Maestro (Schrodinger Suite 2018-1) ?

[mrshirts]

I apologize for the lack of response. We unfortunately don't have the manpower in the lab to bugfix this semester.

[Thuravi]

Dear Mr. Shirts,

Is there any updates on this? I am still facing the same error. It would be really helpful if you could reply regarding this issue. Thanks in advance.

Best, Santhosh