Thanks Ray!
On Fri, Oct 30, 2020 at 10:46 PM Ray Luo <rluo.uci.edu> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Nov 01 2020 - 21:30:02 PST
