Re: [AMBER] MM PBSA - clarification

From: Ray Luo <rluo.uci.edu>
Date: Fri, 19 Apr 2019 21:35:12 +0800

Prasanth,

I suggest that you look at the overall correlation and rmsd of
relative affinities (delta delta G's) for all ligands instead of the
agreement of the delta G of a single ligand.

All the best,
Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Fri, Apr 19, 2019 at 9:12 PM Prasanth G, Research Scholar
<prasanthghanta.sssihl.edu.in> wrote:
>
> Dear all,
> I was interested in carrying out MM PBSA analysis of a protein with a set
> of ligands.
> My output file is as follows:
> |Input file:
> |--------------------------------------------------------------
> |Input file for running PB and GB
> |&general
> |   endframe=1000, verbose=2,
> |   full_traj=1,
> |   interval=5,
> |   netcdf=1,
> |   entropy=0,
> |/
> |&gb
> |  igb=5, saltcon=0.100,
> |/
> |&pb
> |  istrng=0.100,
> |  inp=1,
> |  radiopt=0,
> |/
>
> GB
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> DELTA G gas                -42.3091                2.3895
> 0.1690
> DELTA G solv                10.5381                1.0797
> 0.0763
>
> DELTA TOTAL                -31.7710                2.3820
> 0.1684
>
> PB
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> DELTA G gas                -42.3091                2.3895
> 0.1690
> DELTA G solv                24.9932                1.7929
> 0.1268
>
> DELTA TOTAL                -17.3158                2.7028
> 0.1911
>
> The difference between the PB and GB calculations seems to be high. Could
> someone please tell me, if this is normal and what this difference means.
> P.S: the calculation performed on the other ligand (with the same input
> files) yielded a better result. PB calculation being -5 less than GB
> calculation.
>
> --
> Regards,
> Prasanth.
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Received on Fri Apr 19 2019 - 07:00:02 PDT
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