AMBER Archive (2004)

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

From: Ben Cossins (
Date: Wed Dec 15 2004 - 06:04:50 CST

Hi Dave and Ray,
  Thanks for the replies. I have added "fillratio=4" to the pbsa input
creation script. I still seem to be getting the same problems. Not sure
why. If anyone has any other ideas then please help.



On Wednesday 15 Dec 2004 06:17, Ray Luo wrote:
> 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

Benjamin Cossins
Southampton University
J. W. Essex group.
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