[gmx-users] protein-ligand complex

[Mahboobeh Eslami]

dear justin
I thank you for your friendly guide
Can I assume some of torsion steady and don't change them for getting results better of docking  ? can i reduce rotatable bonds for my ligand in docking process then do MD simulation? 
if i reduce rotatable bonds, i will get much better results of docking.
Your sincerely





On Friday, January 17, 2014 7:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 


On 1/17/14, 10:23 AM, Mahboobeh Eslami wrote:
> 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?

Yes.


-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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Baltimore, MD 21201

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

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