[gmx-users] peptide ligand

Justin Lemkul jalemkul at vt.edu
Wed Oct 4 13:49:03 CEST 2017

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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