[gmx-users] peptide ligand

‪farial tavakoli‬ ‪ farial.tavakoli at ymail.com
Wed Oct 4 14:30:06 CEST 2017

Dear Justin
Thank you so much for all of your help

      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 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

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