Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies

From: Ray Luo <rluo.uci.edu> Date: Fri, 26 Jun 2020 08:19:35 -0700

--
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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