[gmx-users] protein-ligand complex

[Mahboobeh Eslami]

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?
I'm sorry if my question has problem grammar
I am sorry for asking so many questions.
thanks a lot





On Friday, January 17, 2014 11:04 AM, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
 
dear justin
I sincerely thank you
Can I use flexible receptor in docking process and then do the MD simulation? In this case, will the coordinates of the protein  in MD simulation be changed?
best wishes for you





On Thursday, January 16, 2014 11:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 



On 1/16/14, 9:51 AM, Mahboobeh Eslami wrote:
> hi GMX user please help me
>
> i want to simulated a protein-ligand complex. This complex has previously
> been studied
 experimentally. I  draw and opt this ligand by Gaussian
> software. i get the native protein of RCSB. i dock my ligand in the active
> site of the protein and select the best pose. This pose was almost close to
> the experimental structure, but not much. i run 10ns simulation but the
> simulation results were not close to the experimental results, especially
> conformation of the ligand in the active site of the protein.
>

You have two potential problems, either the ligand topology or its initial pose. 
  Run a simulation of the experimental complex, and if the ligand's position 
deviates similarly, then your topology is of poor quality.  If it is reasonable, 
then your docked pose is of insufficient quality ("almost close...but not much" 
does not inspire confidence).

-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
University of Maryland, Baltimore
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Baltimore, MD 21201

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


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