Re: [AMBER] controversy in PBSA and GBSA results

From: Ray Luo <rluo.uci.edu>
Date: Wed, 7 Oct 2020 10:35:08 -0700

Harut,

Here is my impression based on the initial inspection of your data.

For your first and fourth runs, the delta EGB's are 409 kcal/mol and
EPB's are 412 kcal/mol, which is highly consistent given the huge
complex energies in the order of 10,000 kcal/mol.

Looks like your nonpolar energy differences are even larger, ~-17
kcal/mol vs ~-21 kcal/mol. You are probably not using the same surface
tension coefficients between GB and PB runs.

For your second and third runs, the differences are larger, in the
50's kcal/mol, but your complex energies are also larger in the order
of 16000 kcal/mol.

Overall, I think your two runs are consistent within the previously
reported numerical uncertainties of MMPBSA and MMGBSA.

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 Wed, Oct 7, 2020 at 10:08 AM Ray Luo <rluo.uci.edu> wrote:
>
> Never mind. I got the old emails ...
>
> 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 Wed, Oct 7, 2020 at 10:06 AM Ray Luo <rluo.uci.edu> wrote:
> >
> > Hi Harut,
> >
> > Thanks a lot for sharing! By the way, what problem are you referring to again?
> >
> > 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 Wed, Oct 7, 2020 at 6:22 AM <h_sahakyan.mb.sci.am> wrote:
> > >
> > > Hi Ray
> > >
> > > I attached the final output files to this email. If it does not work you can download the files with the following links.
> > >
> > > https://drive.google.com/file/d/1K2MnlwWhcKk6WUxEG-OHWoe9YKXFZI16/view?usp=sharing (https://drive.google.com/file/d/1K2MnlwWhcKk6WUxEG-OHWoe9YKXFZI16/view?usp=sharing)
> > > https://drive.google.com/file/d/1hpMW5BYhMRN1H7RCwaJPvqMPEpo_RDR8/view?usp=sharing (https://drive.google.com/file/d/1hpMW5BYhMRN1H7RCwaJPvqMPEpo_RDR8/view?usp=sharing)
> > >
> > > Hope this helps.
> > >
> > > Best regards,
> > > Harut
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Oct 07 2020 - 11:00:02 PDT