>2. The "SURFTEN" and "SURFOFF" parameters in PB section.
>I have seen a few different settings of these two parameters in others' papers, such as 0.00542 and 0.092, 0.00542 and 0.92, 0.005 and 0, I wonder which setting is appropriate on earth while delphi is used.
>
>
It should be pointed out that the surface tension parameters
(SURFTEN/SURFOFF) depend on what radii set is used to compute the
SURFACE area of a molecule. It is the molecule's nonpolar solvation
energy that is to be reproduced, i.e. "SURFTEN * SURFACE + SURFOFF" is
the same for the molecule even if SURFTEN and SURFOFF are different.
So it is not a surprise that there are different SURFTEN values because
different radii sets are used to compute the molecule's SURFACE area.
Your first cited parameter set 0.00542/0.92 was originally for the PARSE
radii set. I think the offset of 0.092 in your second cited parameter
set is a typo. Your third cited parameter set 0.005/0.86 (not ZERO) are
for the RADIOPT=1 set in PBSA program.
>3. "RADIOPT".
>The example says that a value of 0 uses the cavity radii from the prmtop file, and a value of 1 sets up optimized cavity radii at the pbsa initialization phase. I wonder which one is better for the case of protein-protein interaction.
>
>
You may want to do your own research to find out. The calculations are
very fast.
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.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
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Received on Fri Dec 02 2005 - 06:53:01 PST
