Hi Ray,
I didn't use Delphi. I used pb program in Amber8. I find a problem. I check the
values of "corrected reaction filed energy". Its mean is not equal to
the "PBCAL". Why is that?
Thank you!
Wei
ÒýÓÃ Ray Luo <rluo.uci.edu>:
> Hi Wei,
>
> Could you email me your files so I can take a look why your pbsa output
> disagrees with your Delphi output? Please email me the files only for
> the snapshot where you see the largest difference.
>
> Best,
> Ray
>
> Wei Chen wrote:
>
> >Hi, Ray,
> >
> >Thank you for your reply!
> >
> >Did you mean bugfix.49? It supposed to be fix by my administor. But I
> checked
> >the pb_force.f file. It doesn't. I am wondering how I can "temporarily
> force
> >the net charges of neutral systems zero within rounding error". Actually,
> my
> >proteins have a net charge '+1'.
> >
> >The radii for pb and gb are used as the same as those in the "Example"
> fold.
> >
> >Regards,
> >
> >Wei Chen
> >
> >
> >Quoting Ray Luo <rluo.uci.edu>:
> >
> >
> >
> >>Did you patch bugfix.48 for pbsa? Are you sure you have used the same
> >>radii for pb and gb?
> >>
> >>Wei Chen wrote:
> >>
> >>
> >>
> >>>Hello, all Amber users,
> >>>
> >>>I am using mm_pbsa in Amber8 to calculate binding free energy of
> two-protein
> >>>binding. When I used PB or GB to calculate polar solvation energy, I got
> >>>
> >>>
> >>very
> >>
> >>
> >>>different values. The free energies (not including entropy) are
> >>>
> >>>
> >>93.28+/-90.46
> >>
> >>
> >>>kcal/mol with PB and -37.43+/-5.54 kcal/mol with GB. First of all, the
> mean
> >>>value with PB is positive, which doesn't make any sense. And the standard
> >>>deviation with PB is so large that it is the same order as the mean
> value.
> >>>
> >>>
> >>The
> >>
> >>
> >>>value with GB seems to be more acceptable. However, I think that GB is an
> >>>approximation to PB. So anybody can help me to understand the results?
> >>>
> >>>Thanks!
> >>>
> >>>Wei Chen
> >>>
> >>>--
> >>>
> >>>-----------------------------------------------------------------------
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> >>>
> >>>
> >>>
> >>>
> >>>
> >>--
> >>====================================================
> >>Ray Luo, Ph.D.
> >>Department of Molecular Biology and Biochemistry
> >>University of California, Irvine, CA 92697-3900
> >>Office: (949)824-9528 Lab: (949)824-9562
> >>Fax: (949)824-8551 e-mail: rluo.uci.edu
> >>Home page: http://rayl0.bio.uci.edu/rayl/
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>
> --
> ====================================================
> Ray Luo, Ph.D.
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
> Office: (949)824-9528 Lab: (949)824-9562
> Fax: (949)824-8551 e-mail: rluo.uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
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Received on Sun Nov 13 2005 - 05:53:01 PST
