AMBER Archive (2006)

Subject: Re: AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ?

From: Ray Luo (
Date: Thu Jul 13 2006 - 16:21:30 CDT

I think I my last reply didn't go through ...

Hi Changge,

The repulsive enthalpy is extremely small, so they are omitted. However,
the cavity free energy originates from the repulsive van der Waals term,
so their contribution is still in the solvation free energy.

All the best,

Changge Ji wrote:

>In amber 8, Gnp = SURFTEN * SASA + SURFOFF.
>In amber9 , a new nonpolar solvation model with an explicit treatment of dispersion interaction was included .
> Gnp = G(disp) + G(cavity) .
>In Gaussian03, Gnp = G(Cavitation) + G (Dispersion) + G (Repulsion)
>In amber9, the dispersion interaction and cavatitation energy were treated explicitly .
> But where is the repulsion energy, was it compressed into the cavatitation energy against experiment ?


==================================================== Ray Luo, Ph.D. Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 Office: (949)824-9528 Lab: (949)824-9562 Fax: (949)824-8551 e-mail: Home page: ====================================================

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