[gmx-users] protein-ligand complex

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Fri Jan 17 16:23:13 CET 2014

dear justin
Some articles mentioned that the  protein simulation in water before docking can improve the docking results. Do you think that this is true?
Thank you for your helpful answers

On Friday, January 17, 2014 6:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 1/17/14, 9:54 AM, Mahboobeh Eslami wrote:
> dear justin
> thanks a lot
> if i use flexible receptor in docking process, must i  change  the coordinates
> of the protein as initial configuration  in the MD simulation?

No, that doesn't make any sense and only serves to add another variable into an 
already unclear situation.



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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