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 Fri Jun 26 2020 - 23:30:03 PDT
