Re: AMBER: mm_pbsa

From: Ray Luo <rluo.uci.edu>
Date: Tue, 08 Nov 2005 21:26:52 -0800

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
>
>--
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>.
>
>
>

-- 
====================================================
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/
====================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 09 2005 - 21:53:00 PST
Custom Search