Re: [AMBER] Inconsistent results of MMPBSA.py with option inp=1 and inp=2

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 4 Apr 2014 09:29:49 -0700

Tong,

Yes, this is normal. inp=2 considers van der Waals effect explicitly
in the binding and this leads to smaller absolute values in binding
free energies.

For example, you can check delta delta G's between inp=1 and inp=2 to
see which one gives results more consistent with experiment.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Apr 4, 2014 at 7:57 AM, tong <tongzhu9110.gmail.com> wrote:
> Dear everyone,
>
> I am using MMPBSA.py to compute the binding affinity of a protein-ligand
> system. My input file is:
>
>
> input file for running PB and GB
> &general
>  endframe=20, keep_files=2,
> /
> &gb
>   igb=2,saltcon=0.100
> /
> &pb
>   istrng=0.100,
> /
>
>
> However, the calculated results are very strange, with the deltaG=
> 4.73kal/mol:
>
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err.
> of Mean
> -------------------------------------------------------------------------------
> VDWAALS                    -39.1172                3.1360
> 0.7012
> EEL                        -64.1091                4.9433
> 1.1054
> EPB                         83.7146                6.2319
> 1.3935
> ENPOLAR                    -29.2044                0.8518
> 0.1905
> EDISPER                     53.4513                1.2155
> 0.2718
>
> DELTA G gas               -103.2263                5.7924
> 1.2952
> DELTA G solv               107.9616                6.5209
> 1.4581
>
> DELTA TOTAL                  4.7353                5.7145
> 1.2778
>
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> Then I add a option in the &pb session of the input file: inp=1, (the
> default is inp=2), then the results is much better:
>
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err.
> of Mean
> -------------------------------------------------------------------------------
> VDWAALS                    -39.1172                3.1360
> 0.7012
> EEL                        -64.1091                4.9433
> 1.1054
> EPB                         83.7146                6.2319
> 1.3935
> ENPOLAR                     -3.9779                0.1122
> 0.0251
> EDISPER                      0.0000                0.0000
> 0.0000
>
> DELTA G gas               -103.2263                5.7924
> 1.2952
> DELTA G solv                79.7368                6.1816
> 1.3822
>
> DELTA TOTAL                -23.4895                5.3000
> 1.1851
>
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
>
> I checked the manual, and found that inp=1 or inp=2 just mean that
> MMPBSA.py using different methods to calculate the non-polar term of
> solvation energy. So, is the large difference between these results are
> normal? Or did I make some thing wrong?
>
> Please help me to figure it out!
>
> Thank you so much!
>
> Tong
>
>
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Received on Fri Apr 04 2014 - 10:00:02 PDT