(unknown charset) Re:Re: [AMBER] PBSOL not equal to PBSUR + PBCAL?

From: (unknown charset) Jeffrey <jeffry20072008.yahoo.cn>
Date: Fri, 19 Mar 2010 09:41:51 +0800

 Thanks for the reply.
 All *.out files are attached. It is another run of the MMPBSA script, in which PBSOL is not equal to PBSUR + PBCAL.

Many thanks.

Jeffrey
>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 - 19:00:04 PDT
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