Thank you Prof Luo,
Yes I am using the single-trajectory approach.
I have looked my mdout files as follows:
Initial production:
NSTEP = 1000 TIME(PS) = 227.000 TEMP(K) = 297.86 PRESS =
44.0
Etot = -278721.9198 EKtot = 73100.5391 EPtot =
-351822.4588
BOND = 4963.6198 ANGLE = 8911.3451 DIHED =
14084.5648
1-4 NB = 4086.6449 1-4 EEL = 41800.9648 VDWAALS =
38353.9534
EELEC = -464023.5516 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 30408.2418 VIRIAL = 29282.8995 VOLUME =
1184808.3971
Density =
1.0314
------------------------------------------------------------------------------
The final step :
NSTEP = 1000000 TIME(PS) = 80225.000 TEMP(K) = 300.51 PRESS =
-31.0
Etot = -278541.4335 EKtot = 73752.7891 EPtot =
-352294.2226
BOND = 4959.7447 ANGLE = 8790.5163 DIHED =
13994.7804
1-4 NB = 4100.5575 1-4 EEL = 42077.1414 VDWAALS =
38196.6976
EELEC = -464413.6606 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 30519.3848 VIRIAL = 31310.8016 VOLUME =
1183584.3968
Density =
1.0324
------------------------------------------------------------------------------
I also inspected the pdb files of the temporary of mmpbsa calculation, and
I found they are good.
Again, I would like to ask, how can I tackle the too high binding energy.
Thank you.
Nadaafiva
Pada tanggal Sab, 11 Apr 2020 pukul 08.43 Ray Luo <rluo.uci.edu> menulis:
> 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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Received on Sat Apr 11 2020 - 02:30:02 PDT
