Re: [AMBER] Very low MMPBSA result

From: Ray Luo <rluo.uci.edu>
Date: Fri, 10 Apr 2020 18:42:27 -0700

Nadaafiva,

Are you using the single-trajectory approach?

The solvated original MD trajectories are probably fine. However,
please take a look of your mdout file to see whether you see super
large bond energies and fluctuations.

The solvent-ion/free files are those directly used by mmpbsa. You can
use the keep_files option to keep all temporary files. Visualize those
for your defined receptor and ligand to see if anything is unusual.

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, Apr 10, 2020 at 5:56 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> Dear Prof. Luo,
> I have inspected my structure at last time of the simulation.
> I found out that nothing is error with the structure.
> But since the ligand contain phosphate group, is it possible that the
> phosphate group is a source of high bond term?
> And if so, what should I do?
> Thank you.
>
> nadaafiva
>
> Pada tanggal Sab, 11 Apr 2020 pukul 05.38 Ray Luo <rluo.uci.edu> menulis:
>
> > Nadaafiva,
> >
> > I think there is something wrong with your calculation as the bond
> > term is very large.
> >
> > You may want to visualize your solvent/ion-free inpcrd/prmtop files to
> > see if there is anything wrong with your definitions of ligand and
> > receptor.
> >
> > 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, Apr 10, 2020 at 2:20 PM Nada Afiva <nadaafiva.gmail.com> wrote:
> > >
> > > Dear Amber list,
> > > I would like to ask you why the MMPBSA result calculation is very low.
> > > The protein consisted of 3 chains.
> > > Here is the result:
> > >
> > > Differences (Complex - Receptor - Ligand):
> > > Energy Component            Average              Std. Dev.   Std. Err. of
> > > Mean
> > >
> > -------------------------------------------------------------------------------
> > > BOND                     -1513.5105              991.7405
> > > 49.5252
> > > ANGLE                      -75.0126               35.0680
> > >  1.7512
> > > DIHED                      -16.8837                3.6245
> > >  0.1810
> > > VDWAALS                    -23.7054                5.0137
> > >  0.2504
> > > EEL                        -96.9434               13.9892
> > >  0.6986
> > > 1-4 VDW                      0.1667                0.0543
> > >  0.0027
> > > 1-4 EEL                      4.8667                0.3734
> > >  0.0186
> > > EPB                        116.8118               11.7134
> > >  0.5849
> > > ENPOLAR                     -3.8042                0.1633
> > >  0.0082
> > > EDISPER                      0.0000                0.0000
> > >  0.0000
> > >
> > > DELTA G gas              -1721.0221             1009.5413
> > > 50.4141
> > > DELTA G solv               113.0076               11.6352
> > >  0.5810
> > >
> > > DELTA TOTAL              -1608.0146             1010.1913
> > > 50.4465
> > >
> > > Here the input:
> > > |Input file for running MMPBSA
> > > |&general
> > > |   startframe=20000, endframe=40000, keep_files=2, interval=50,
> > > |   verbose=2,
> > > |/
> > > |&gb
> > > |   igb=5, saltcon=0.100
> > > |/
> > > |&pb
> > > |   istrng=0.100, fillratio=4.00, inp=1,
> > >
> > >
> > > Thank you.
> > > Nadaafiva
> > > _______________________________________________
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> >
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Received on Fri Apr 10 2020 - 19:00:03 PDT