AMBER Archive (2006)

Subject: Re: AMBER: Q: results from PB solver in example no.3

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Jan 04 2006 - 20:45:28 CST

Hi Masaki,

> Q1) The final result stored in "ras_raf_II_wt_statistics.out", I found
> that values of PBTOT (-66.2) and GBTOT (-51.4) are quite different. Is
> the difference between the two methods common? Are they should be
> closer in theory?

No. In general they are different. To make sure your pb and gb
calculations are comparable. You first need to set radiopt=0 for pb so
both pb and gb use the same radi set.

> Q2) If one or another is better, which value we should take? PBTOT or
> GBTOT?

Please read original mmpbsa papers on this to see whether you can
reproduce their computational results in either pb or gb with their
_identical parameters_. If you can, you can answer the question by
working out your own systems and comparing with experiment.

> Q3) When I introduced ZAP, I got -96.1 for PBTOT which is far
> different from the above two values. What do you think?

ZAP is a different numerical pb solver that uses a very different
molecular surface to define protein low dielectric region. If you want
to use ZAP, you need to figure out the best parameters through your own
research, i.e. different radi set and so on, to see whether you can get
good results.

> Request ) Did anyone calculate PBTOT by using Delphi starting from the
> same input file in the directory? If you did not yet and have Delphi
> in your hand, could you possibly calculate it? The value of PBTOT
> (-66.2) in the directory was given from AMBER's PB solver. I want to
> know what value a world standard software gave?

We have performed extensive comparison between amber/pbsa and delphi for
over 800 proteins/protein domains and found them to be highly
consistent, within 1% of each other when scale=4 in delphi (scale=2 is
good enough for pbsa).

All the 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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