Dear Sir,
Using your suggestions, the result is now much improved.
I got mmpbsa -30.23, while mmgbsa -19.15.
Thanks so much for Elvin Martis and your helps.
I used AmberTools16.
Thanks.
Best regards,
Nadaafiva
Pada tanggal Min, 28 Jun 2020 pukul 23.31 Ray Luo <rluo.uci.edu> menulis:
> Nadaafiva,
>
> The observed difference about 25 kcal/mol is bigger than what we have
> been seeing.
>
> For the complex the numbers are -10025 versus -11113. This is almost
> 10%. Which version of AmberTools are you using?
>
> 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 Sun, Jun 28, 2020 at 5:12 AM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
> >
> > 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 - 15:30:03 PDT
