Hi Jason,
Thank you very much.
Cheers !
Chanchal
On Fri, Nov 12, 2010 at 5:02 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 08:30:03 PST
