[gmx-users] protein-ligand complex
mahboobeh.eslami at yahoo.com
Fri Jan 17 15:57:54 CET 2014
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?
On Friday, January 17, 2014 4:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 1/17/14, 3:15 AM, Mahboobeh Eslami wrote:
> dear justin
> i have another question
> Can the increasing of MD simulation time improve docking results? can the
> increasing of MD simulation time create the experimental conformation of the
> ligand in the active site of the protein or close to it?
Possibly, but the original point stands - if the initial pose is very poor or
the topology incorrect, more running time usually just means more wasted time.
You need to establish whether or not your starting conditions are reasonable.
Justin A. Lemkul, Ph.D.
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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