[gmx-users] protein ligand tutorial

[Justin Lemkul]

On 1/20/14, 9:12 AM, Albert wrote:
> Hello:
>
> I noticed that in the tutorial ligand Gromacs tutorial, there is a setting in
> .mdp file like:
>
> energygrps:  protein ligand
>
> in order to claculate the interactions between protein/ligand by g_lie.
>
> I am just wondering, would it be better to include the solvent to evalutate the
> protein ligand interactions and create energy group like:
>
> energygrps: protein_water_ions ligand ?
>

That wouldn't make much sense, because you're considering the protein, water, 
and ions to be some sort of solvent that may have very different interactions 
with water.  The LIE assumption is that the binding energy can be calculated as 
the difference between bound (not hydrated) and free (hydrated).  If you have a 
bound state where the ligand still interacts with water, I think the LIE 
approximation will fail.

-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
20 Penn St.
Baltimore, MD 21201

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

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