Re: [AMBER] MMGBSA/MMPBSA Help

From: Ray Luo <rluo.uci.edu>
Date: Fri, 30 Oct 2020 07:42:37 -0700

Rashid,

Sorry for the delay in replying. Looks like our university gmail
server becomes hyperactive in moving most AMBER emails to Spam.

The reason for the difference is that GB does not support the membrane
option but you are using it by setting memopt=1 in PB.

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 Sat, Oct 3, 2020 at 4:35 AM Abdul-Rashid III Sampaco
<absampaco.up.edu.ph> wrote:
>
> Dear AMBER Community,
>
> I would like to ask for your help in making sense of my MMGBSA/MMPBSA
> results. I separately docked a short peptide onto two receptors. I also
> included calculations for an alanine scan on five of the peptide's amino
> acid residues.
>
> In my initial calculation, I used the following parameters:
>
> &general
>   startframe=1, endframe=100000, interval=100, verbose=1,
>   ligand_mask=":1761-1783", receptor_mask=":1-1760",
>   strip_mask=":WAT,PA,PC,PE,OL,K+,Cl-,CHL",
>   # entropy=1,
> /
> &gb
>   igb=2, saltcon=0.150,
> /
> &pb
>   istrng=0.100,
>   memopt=1,
>   inp=2, radiopt=0,
> /
> &alanine_scanning
> /
>
> However, MMPBSA results showed positive binding energy values. In another
> thread in this mailing list that featured a similar issue, it was suggested
> that inp=1 should be used instead of inp=2 to avoid obtaining positive
> values in MMPBSA. I reran my calculations using inp=1 and obtained the
> following results.
>
> receptor A:
> [image: image.png]
>
> receptor B:
> [image: image.png]
>
> Here are my questions:
>
> (1) There is a massive disparity between the MMGBSA and MMPBSA results on
> the potassium channel. Is this normal? Aren't the MMGBSA and MMPBSA results
> supposed to be fairly similar in magnitude since one is simply an
> approximation of another?
>
> (2) Are the results on different receptors comparable? Is it safe to say
> that according to the MMGBSA results, the peptide should prefer binding to
> receptor B rather than receptor A? But this is contradicted by the MMPBSA
> results.
>
> If these questions are deemed trivial, I will greatly appreciate being
> recommended the right papers to read.
>
> Best,
> Rashid
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Received on Fri Oct 30 2020 - 08:00:03 PDT