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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Received on Fri Apr 10 2020 - 18:00:02 PDT
