[gmx-users] Query on Protein-ligand interaction energy calculation

[Justin Lemkul]

On 1/24/16 4:24 AM, David van der Spoel wrote:
> On 23/01/16 18:53, abhinav kv wrote:
>> Hi..
>>
>> Is it possible to break down the "Potential Energy" term of the
>> gromacs steepest
>> descent energy minimization output into its individual components of
>> protein-ligand interaction energy without running a free energy
>> simulation...?
> Try defining energy groups in the mdp file.
>
>> I would also be very useful if you could please elaborate on breaking down
>> the internal terms using gmx convert-tpr and mdrun -rerun and use of g_bar
>> on energy.edr to obtain these values.
> Not possible as far as I know.

One can quantify the internal terms and intramolecular nonbonded terms by 
extracting the coordinates for the molecule of interest with trjconv, making a 
matching .tpr with convert-tpr, and doing a single-point energy evaluation on 
the coordinate file.  What use that has, I don't know, but it can be done.

-Justin

>>
>>
>>
>> Regards,
>>
>> Abhinav.
>>
>
>

-- 
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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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