AMBER Archive (2005)

Subject: Re: AMBER: error in pbsa calculation

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Apr 27 2005 - 12:03:33 CDT

Hi Mingche,

>
> Thanks for your answer! Yeah, it works now, but I have another
> problem. The pbsa calculation complained about " PB bomb in
> pb_reslist(): maxnbr too small". I modified the source code by
> increasing "cutres" from 11.0 to 15.0. Then it seems to fix the
> problem, but I am not sure whether the value I picked is reasonable.

This has been reported to the AMBER list before and your choice is fine.
It doesn't matter what cutoff you use as long as it runs.

>
> Another question about pbsa calculation is what kind of discrepancy it
> would be for the GB and PB (both delphi and pbsa) calculation? In my
> case (just testing on several snapshots), the energy difference
> between this two methods is up to ~80 kcal/mol. There must be
> something wrong. Could you suggest me a few papers of on pbsa?
>

I don't know about the difference between GB and PB. The two PB methods
should agree within 1%. Of course you'll see a larger absolute
difference for a larger system, but the correlation between the two PB
energies over all snapshots should be very very good. Otherwise, there
is a bug. Please let me know.

Best,
Ray 

-- 
====================================================
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_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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