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

From: Ray Luo via AMBER <amber.ambermd.org> Date: Sun, 27 Aug 2023 16:12:51 -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 Sun, Aug 27, 2023 at 12:15 PM Kankana Bhattacharjee <
kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
> Hello,
>
> I am sharing the "mmpbsa.in
> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
> and "Final-mmpbsa.dat", "energy.dat" files herewith.
>
> Thanks & Regards
> Kankana Bhattacharjee
>
> ---------- Forwarded message ---------
> From: Ray Luo <rluo.uci.edu>
> Date: Sun, Aug 27, 2023 at 11:13 AM
> Subject: Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:
> To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>,
> AMBER Mailing List <amber.ambermd.org>
>
>
> Dear Bhattacharjee,
>
> Can you share your "mmpbsa.in
> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
> and also the result output files?
>
> All the best,
> Ray
>
> All the best,
> Ray
> --
> 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
> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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