Re: [AMBER] Regarding MMPBSA calculation:

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Thu, 28 Mar 2024 22:36:35 -0700

Kankana,

Indeed inp=2 tends to make delta G dramatically more positive. However,
inp=1 tends to make delta G dramatically more negative, and MMPBSA free
energies are overall far more negative than alchemical free energies. In
general, you need to compare with the experimental values, not with each
other.

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 Thu, Mar 28, 2024 at 9:50 PM Kankana Bhattacharjee via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER users,
>
> I have performed MMPBSA calculation of a protein-ligand complex. And, I
> have checked the keyword "inp=1" and "inp=2". But, when I have used inp=2,
> then delta_G value increased and magnitude decreased substantially. I have
> got delta_G value of -2.93 kcal/mol while using inp=2. I am not able to
> figure it out. Also, importantly, vdW energy contribution is more for my
> system. I have to consider dispersion term for my MMPBSA calculation.
> Kindly help me with this regarding the obtained delta_G value while used
> inp=2.
>
> Thanks and regards
> Kankana Bhattacharjee
> Ph.D. Scholar
> Department of Chemistry
> Ashoka University
> Sonipat, Haryana
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Received on Thu Mar 28 2024 - 23:00:02 PDT
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