Re: [AMBER] controversy in PBSA and GBSA results

From: Ray Luo <rluo.uci.edu> Date: Wed, 30 Sep 2020 15:57:45 -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 Wed, Sep 30, 2020 at 4:44 AM <h_sahakyan.mb.sci.am> wrote:
>
> Dear All,
>
> I used MM-PBSA/GBSA methods to calculate the binding free energy between two subunits of a protein. The binding energies were -101 and -94 kcal/mol for GBSA and PBSA respectively. However, in the presents of a ligand (between two subunits), binding energies were -124/-67 (GBSA/PBSA). As you can see, according to GBSA the ligand makes the interaction stronger and vice versa according to the PBSA calculation. What can be the reason for this controversy?
>
> I used MMPBSA.py with following input:
>
> pbsa_gbsa
> &general
>  startframe=1, interval=50, endframe=5000,
>  verbose=2, keep_files=0, netcdf=0,
>  strip_mask = ":WAT,Cl-,Na+,K+,",
>  ligand_mask = ":1-437,867,869",
>  receptor_mask = ":438-865,866,868,870",
> /
> &gb
> saltcon=0.150,
> /
> &pb
> inp=1 # I tried inp=2 it gives more weird results, generally with positive energy values
> istrng=0.150
> /
> Best wishes,
> Harutyun
> Senior Assistant at Laboratory of
> Computational Modeling of Biological Processes,
> Institute of Molecular Biology, NAS RA
> 7 Hasratyan St, Yerevan, Armenia
> Tel: +374 93 323990
> E-mail: h_sahakyan.mb.sci.am (mailto:h_sahakyan.mb.sci.am)
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