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 Thu Jun 25 2020 - 18:30:03 PDT
