[gmx-users] Protein-Ligand

Justin Lemkul jalemkul at vt.edu
Mon Aug 3 19:32:27 CEST 2015

On 8/3/15 1:29 PM, su wrote:
> Hello
> I am confused about my MD results.According to Justin's tutorial of protein-ligand MD, i performed short 1ns md on my protein-ligand system. After completion, when i opened up the md.gro and md.xtc in VMD, it is only showing up protein.Ligand is absent from box. When i tried to view hydrogen bond interactions, it gave fatal error that no topol.trr is found. I have also prepared movie.pdb and viewed it in pymol, but in that also ligand is not showing. Can anyone please tell me if this is a common error? do i need to insert the ligand file manually? or shall i provide PBC. I can attach the files if required.

I answered this already:




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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