[gmx-users] ERROR in cgenff_charmm2gmx.py

[Sergio Manzetti]

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 



Sergio Manzetti 

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[ 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 
340 West Campus Dr. 
Blacksburg, VA 24061 

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

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