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

From: Ray Luo <rluo.uci.edu> Date: Thu, 25 Jun 2020 16:59:14 -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 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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