[gmx-users] protein ligand simulation

Justin Lemkul jalemkul at vt.edu
Tue Apr 19 15:08:47 CEST 2016

On 4/19/16 9:03 AM, bharat gupta wrote:
> Dear Gmx users,
> I am performing a protein-ligand simulation using gromacs latest tutorial
> for 5.0.x version. As per the tutorial, I included the coordinates of the
> ligand in the complex.gro file (also updated total no. of atoms after
> adding ligand atoms) and updated the topology file (topol.top) by including
> its name under the molecules sections and also included its ligand.itp
> file. But, I am not able to find the ligand group while making an index
> file for it. Please let me know where am I going wrong ?

Well the ligand can't suddenly disappear, but in the absence of your actual 
commands and the screen output of make_ndx, there's nothing anyone can conclude 
about what the issue is.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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