Oliver Hucke wrote:
> Ray and Andreas,
>
> may I ask which version of sander you use for "cap simulations"?
> I would also be interested in the value of "cut".
>
> I am asking because I did get reasonable results with a cap and
> sander8 only with an infinite cutoff, which made the calculations very
> slow...
>
I meant sander8. There is no pb in previous versions of sander. If you
use sander8 and "igb=10", "cut" will not be used, just set it to zero in
case any memory allocation is invoked. A default _finite_ residue-based
cutoff (cutres) of 12 A, atom-based cutoff (cutnb) of 10 A will be used
for the pb simulation with cap.
Note that the current pb implementation does not support partial
solvation of a solute, i.e. cap on an active site of an enzyme only.
--
====================================================
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 Tue May 18 2004 - 23:53:01 PDT
