[gmx-users] protein topology

Justin Lemkul jalemkul at vt.edu
Wed Oct 28 12:29:54 CET 2015

On 10/28/15 3:03 AM, Nikhil wrote:
> thanks justin,
> now i got the idea
> but i have a basic question in case of protein-ligand simulation
> i got the system after docking.
> i made .gro files as per the tutorial (Protein-Ligand complex)
> but it is not coming in the location that i got after docking ,so how
> should i proceed to get the ligand in the correct position to do MD

Somehow you've changed the coordinates.  If you're following my tutorial 
exactly, that shouldn't happen.



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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