[gmx-users] ERROR in cgenff_charmm2gmx.py

[Justin Lemkul]

On 10/4/17 7:11 AM, Sergio Manzetti wrote:
> Hi Justin, can [ http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py | cgenff_charmm2gmx.py ] do full charges? I get an error:
> 
> Traceback (most recent call last):
> File "./charmm2gmx.py", line 47, in <module>
> import networkx as nx
> ImportError: No module named networkx
> 

That's a Python dependency. Install it.

-Justin

> 
> 
> Sergio Manzetti
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
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> 
> 
> 
> From: "sergio manzetti" <sergio.manzetti at fjordforsk.no>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Wednesday, October 4, 2017 1:07:20 PM
> Subject: Re: [gmx-users] Topolgen and topolbuild
> 
> Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated molecule?
> 
> 
> 
> Sergio Manzetti
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
> 
> 
> 
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Wednesday, October 4, 2017 12:41:50 PM
> Subject: Re: [gmx-users] Topolgen and topolbuild
> 
> On 10/4/17 6:09 AM, Sergio Manzetti wrote:
>> Hi Stephane. Thanks for that. I have tried it, however it generates a str file, and from there how to generate the GMX ITP is unknown.
>>
>> Is there a tutorial that shows how to generate ITP from STR?
> 
> Use our conversion script:
> 
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> 
> -Justin
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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