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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Received on Fri Nov 11 2005 - 17:53:01 PST
