[gmx-users] protein-ligand complex

Justin Lemkul jalemkul at vt.edu
Fri Jan 17 14:03:22 CET 2014

On 1/17/14, 2:34 AM, Mahboobeh Eslami wrote:
> dear justin
> I sincerely thank you
> Can I use flexible receptor in docking process and then do the MD simulation? In

You can do whatever you think makes sense.  Fully rigid docking, in my opinion, 
has limited use.  It's fast, but not realistic.

> this case, will the coordinates of the protein  in MD simulation be changed?

Coordinates always change during MD, that's the point :)



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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