AMBER Archive (2004)

Subject: Re: AMBER: pbsa error in mm_pbsa amber 8

From: Ray Luo (
Date: Wed Dec 15 2004 - 00:17:01 CST

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.

fillratio is not grid points/area. This is a new keyword added to the
pbsa program. See Amber webpage.


>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

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:
Home page:

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