Re: [AMBER] Coulomb energy in MMPBSA

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Fri, 1 Sep 2023 09:22:45 -0700

Richard,

The 14EEL is scaled by a factor as specified in the prmtop file. If
you want to reproduce the number, you'll need to use the same scaling
factor in the prmtop file.

This is supposed to be force field specific. However I don't think
Amber can use different scaling factors simultaneously if there are
several force fields with different scaling factors in one prmtop
file.

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, Sep 1, 2023 at 5:40 AM Richard Kullmann via AMBER
<amber.ambermd.org> wrote:
>
> Dear Amber users,
>
> In order to understand results I obtained from MMPBSA calculations, I
> tried to calculate the Coulomb energy myself. I can confirm the EEL term
> for complex-receptor-ligand. However, I am struggling when it comes to
> the internal EEL energies. When I sum over all pairwise interactions
> (excluding 1-2 and 1-3; I don't treat 1-4 special since I use GLYCAM), I
> am not able to reproduce the EEL results. Is there something else I
> might be missing?
>
> Best regards,
>
> Richard
>
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Received on Fri Sep 01 2023 - 09:30:02 PDT
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