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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> >
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Received on Fri Apr 10 2020 - 19:00:03 PDT