[gmx-users] How to check protein-ligand interaction pattern after completing simulaation.

[Justin Lemkul]

On 7/26/16 10:04 AM, Swagata Patra wrote:
> Hello Everyone,
>
> I am a very new Gromacs user. I have completed the protein-ligand
> simulation. I want to get the protein-ligand interaction using PyMol. I
> used editconf to convert the final .gro file to .pdb file. But when I am
> checking that .pdb file in pymol it is showing different interaction
> pattern from the interaction pattern that i got from docking study.
>
> So my question is, is it the right way to get the protein-ligand
> interaction pattern. If yes, then why  I am getting different interaction
> pattern in docking and simulation.
>

I would not expect a docking and MD result to be the same; MD includes solvation 
effects and dynamics whereas docking is in vacuo and largely rigid.

Moreover, simply looking at the final snapshot of the MD is not enough; you've 
got a whole trajectory worth of information and that's the whole point of MD. 
The final snapshot may not even be representative of what occurred during the MD.

Use the large suite of tools that GROMACS provides to get insight as to what 
happened during the MD and how it can help you answer whatever scientific 
question(s) you have.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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