Hi Chanchal,
On Fri, Nov 12, 2010 at 10:50 AM, Chanchal <chanchal.kar.gmail.com> wrote:
> Hi,
> I want to estimate the absolute binding free energy of a protein-steroid
> complex using the MM-PBSA method. I am using iAPBS for the solution to the
> PB equation. My question is, does the nonpolar term include the dispersion
> term? Does the MM-PBSA method (using iAPBS) calculate nonpolar term using
> the equation:
> G_{np} = \gamma * SASA + b where \gamma = 0.00549 kcal.mol^{-1}\AA^{-2} and
> b = 0.92 kcal/mol ?
>
iAPBS does not use an offset, to my understanding. It's easy enough to
subtract this after-the-fact. However, the non-polar solvation energy does
have this form, and the default gamma value is 0.00542 kcal/mol/A^2, but
it's converted to kJ/mol/A^2 for use in APBS, I believe.
Hope this helps,
Jason
> Thanks
> Chanchal
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Nov 12 2010 - 08:30:02 PST
