Dear SIr,
Thanks so much for your suggestions.
However, using the above input, the result is not improved.
Attached is the summary file for mmpbsa and mmgbsa binding energy.
Looking forward to hearing from you.
Best regards,
Nadaafiva
Pada tanggal Sab, 27 Jun 2020 pukul 22.21 Ray Luo <rluo.uci.edu> menulis:
> Nadaafiva,
>
> There are two differences in your mmpbsa and mmgbsa setups.
>
> 1) The radii are different. Please set radiopt=0 to use the values in
> the prmtop file as in the mmgbsa job.
>
> 2) The nonpolar term is also different. Please set
> "cavity_surften=0.005, cavity_offset=0.000" to be the same as in the
> mmgbsa job.
>
> Please use the latest AmberTools releases, as we have set the default
> input options to be consistent between the two calculations.
>
> 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, Jun 26, 2020 at 11:01 PM Nada Afiva <nadaafiva.gmail.com> wrote:
> >
> > Dear Sir,
> > Attached is the summary file in which mmgbsa is -19.1462, while mmpbsa is
> > 9.2735.
> > Thanks.
> >
> > Best regards,
> > Nadaafiva
> >
> >
> > Pada tanggal Jum, 26 Jun 2020 pukul 22.20 Ray Luo <rluo.uci.edu>
> menulis:
> >
> > > Hi Nadaafiva,
> > >
> > > Can you share the summary file with all the components, not just the
> > > total energy?
> > >
> > > 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 Thu, Jun 25, 2020 at 6:12 PM Nada Afiva <nadaafiva.gmail.com>
> wrote:
> > > >
> > > > Yes Sir, it improved, by still the mmpbsa energy was positive.
> > > > How the large difference occurred, and how to handle it.
> > > >
> > > >
> > > > best,
> > > > nadaafiva
> > > >
> > > > Pada tanggal Jum, 26 Jun 2020 pukul 07.00 Ray Luo <rluo.uci.edu>
> > > menulis:
> > > >
> > > > > Dear Nadaafiva,
> > > > >
> > > > > This is because your NP term is different between PB and GB runs.
> If
> > > > > you set inp=1, the numbers would agree better.
> > > > >
> > > > > 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 Thu, Jun 25, 2020 at 3:09 PM Nada Afiva <nadaafiva.gmail.com>
> > > wrote:
> > > > > >
> > > > > > Dear list,
> > > > > > I am performing MM-PBSA and MM-GBSA binding energy calculation
> using
> > > > > input
> > > > > > file below.
> > > > > > However, I got final MM-GBSA=-23.15 kcal/mol, while MM-PBSA
> =+11.43
> > > > > kcal/mol
> > > > > > I used single trajectory of MD, and obtained ligand and receptor
> > > > > topology
> > > > > > using Ante-MMPBSA.
> > > > > >
> > > > > > Here is the input file:
> > > > > >
> > > > > > Input file for running MMPBSA
> > > > > > |&general
> > > > > > | startframe=0, endframe=10000, keep_files=2, interval=100,
> > > > > > | verbose=2,
> > > > > > |/
> > > > > > |&gb
> > > > > > | igb=5, saltcon=0.1,
> > > > > > |/
> > > > > > |&pb
> > > > > > | istrng=0.1, exdi=80, indi=1.0,
> > > > > > inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
> > > > > > fillratio=4.00, scale=2.0
> > > > > > linit=1000, prbrad=1.4, radiopt=1,
> > > > > > |/
> > > > > >
> > > > > >
> > > > > > Thanks in advance.
> > > > > > Best regards,
> > > > > > nadaafiva
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Received on Sun Jun 28 2020 - 05:30:02 PDT
