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

[Swagata Patra]

Thank you Justin for your reply. I already analysed RMSD, RMSF, gyration
and no of H bonds using your tutorial.

Actually I had gone through some paper where they mention this thing (same
interaction pattern between docking result and simulation). That's why I
wanted to know.

So, are RMSD, RMSF, gyration and No. of H bonds enough to describe the
protein-ligand simulation.

On Tue, Jul 26, 2016 at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati