Re: [AMBER] PBSOL not equal to PBSUR + PBCAL?

From: Ray Luo <ray.luo.uci.edu>
Date: Thu, 18 Mar 2010 09:59:40 -0700

Jeffrey,

Can we take a look of your ".out" files?

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================



Jeffrey wrote:
> Dear AMBER users,
> I calculated the binding energy using pbsa by setting RADIOPT=1 and NPOPT=2 in which the nonpolar contribution (Gnp) was evaluated by:
> Gnp = Gdisp + CAVITY_SURFTEN*SASA + CAVITY_OFFET.
> But in the x_statistics.out file, the sum between the polar contribution (PBCAL) and the nonpolar contribution (PBSUR) is not equal to total solvation energy (PBSOL).
> Here is part of the output:
> -------------
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> PBSUR -5.92 0.29
> PBCAL 79.54 46.33
> PBSOL 113.89 46.91
> PBELE 66.83 20.17
> PBTOT 60.82 19.42
> -------
> where PBSUR + PBCAL = -5.92 + 79.54 = 73.26 != PBSOL (113.89).
>
> I am not sure whether I understand it correctly or not and request your comments.
>
> Many thanks.
> Jeffrey Yang
> ------
> DICP, CAS
>
>
>
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Received on Thu Mar 18 2010 - 10:30:03 PDT
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