[gmx-users] peptide ligand

Justin Lemkul jalemkul at vt.edu
Wed Oct 4 13:48:32 CEST 2017

On 10/3/17 1:46 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; } Oh I am sorry. Yes  I am trying to run md on my protein peptide complex. At first you advice me to use pdb2gmx to generate a topology for my complex and  I did. Then  according to the protein ligand complex tuturial in gromacs, I defined newbox and solvate After adding ions, I need to do energy minimization and use .mdp file which I should specify energygrouos , But my protein and ligand are not sepearate from each other. I just eant to know isnt there any problem if protein and ligand are merged and not separated?

The use of energygrps may or may not even be useful. It's not necessary for 
actually doing the simulation and you can always look at it later with mdrun -rerun.



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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