[gmx-users] protein ligand tutorial

[Tsjerk Wassenaar]

Hi,

Bound and "not hydrated" are completely different things. A ligand can be
partially exposed or may even be hydrated in a pocket. The difference
should be between ligand-environment1 interaction (solvent only) and
ligand-environment2 interaction (protein/solvent). So energygrps = Ligand
notLigand (or protein_solvent_ions) does make sense.

Cheers,

Tsjerk


On Mon, Jan 20, 2014 at 4:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.