Ben Cossins wrote:
>Hi Dave and Ray,
> Sorry for the delayed reply and thanks for your help. I am still having
>trouble. My ligands are not so small they are all over 85 atoms. I have
>increased the fillratio (by this a take it you mean the number of grid
>points/area) again and am still getting fluctuating solvation energies.
>
Ben,
fillratio is not grid points/area. This is a new keyword added to the
pbsa program. See Amber webpage.
Best,
Ray
>
>However they seem to fluctuate less as I increase the SCALE parameter. With
>6 grid points per angstrom it fluctates from about -2600 to -50 while the
>surface area values stay stable around 980. I am unable to work through the
>pbsa code and find what the problem is. Can you give me an idea of what i
>could try.
>
>sorry to bother you again
>
>Ben
>
>
>
--
====================================================
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 Dec 14 2004 - 16:53:00 PST
