[gmx-users] peptide ligand

[‪farial tavakoli‬ ‪]

Dear Justin
Thank you so much for all of your help
best 
Farial


      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Wednesday, 4 October 2017, 15:19:38
 Subject: Re: [gmx-users] peptide ligand
   


On 10/3/17 1:51 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Because in tuturial , energygroups = protein JZ4So I think ,I have to seperate my ligand and Protein in .mdp files and determine H bonds?
> 

It has nothing to do with the .mdp file. If you want to analyze hydrogen bonds, 
then you can create an .ndx file later for use with gmx hbond.

-Justin

-- 
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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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