Hi
MMPBSA calculations are also sensitive to internal dielectric (indi value).
You might want to look at what suits your system.
Look at this paper
https://pubs.acs.org/doi/abs/10.1021/ci100275a to decide
what might be suitable for your system.
Best Regards
Elvis
On Sun, 28 Jun 2020 at 17:37, Nada Afiva <nadaafiva.gmail.com> wrote:
> 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 - 05:30:03 PDT
