[gmx-users] g_mmpbsa

[Justin Lemkul]

On 8/16/15 12:38 PM, elham tazikeh wrote:
> Dear GMX Users
> is there anyone to help me in g_mmpbsa using for binding free energy
> calculation
> i have questions about *.mdp files as polar.mdp or....
> for instance: what is the value of pdie in  protein-ligand combinations
> i really appriciate for any help
>

Their documentation seems quite comprehensive:

http://rashmikumari.github.io/g_mmpbsa/Polar-solvation-input-parameters.html

pdie is the internal dielectric of the solute (protein) hence (p)(die) = pdie.

-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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