Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:

From: Ray Luo via AMBER <amber.ambermd.org> Date: Sat, 26 Aug 2023 22:43:22 -0700

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Fri, Aug 25, 2023 at 12:48 PM Kankana Bhattacharjee via AMBER
<amber.ambermd.org> wrote:
>
> Dear AMBER users,
>
> I am trying to reproduce the change in enthalpy of binding of
> protein-ligand complex using MMPBSA . In the paper,  Authors' used  amber12
> version  and cavity_surften, cavity_offset were set as  0.005420, -1.008
> respectively.
> Whereas, I am using amber22 version, in this case, default values of
> cavity_surften, cavity_offset are 0.0378, -0.5692 respectively. When my
> calculations were done using the default (cavity_surften, cavity_offset
> parameters), the result matched closely enough with the paper. But,
> when I explicitly
> mentioned the  cavity_surften, and cavity_offset parameters (based on the
> paper) in "mmpbsa.in" file,  I am getting positive enthalpy change of
> binding !! Could you kindly give suggestions regarding this?
>
> Your suggestions would be highly appreciated.
>
> Thanks and regards
> Kankana Bhattacharjee
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