AMBER Archive (2004)

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

From: Ben Cossins (bcc_at_soton.ac.uk)
Date: Tue Dec 14 2004 - 07:41:08 CST

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.
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

On Friday 10 Dec 2004 21:36, Ray Luo wrote:
> Hi Dave and Ben,
>
> This correct. For small ligands, the default fillratio is too small and
> this causes pbsa generate garbage energies. This could be the reason the
> solvation energies fluctuate enormously.
>
> Best,
> Ray
>
> david.evans_at_ulsop.ac.uk wrote:
> >The comments in the code suggest that this error might occur when the
> >grid spacing is large.
> >So you could try increasing the fillratio. But I have no detailed
> >understanding of this program, and the developers will know better.
> >
> >Dave Evans
> >
> >---
> >School of Pharmacy
> >University of London
> >
> >---- Message from Ben Cossins <bcc_at_soton.ac.uk> at 2004-12-09
> >15:19:20 ------
> >
> >>Hey again,
> >> Sorry I should have said that the calculation does not fail but
> >
> >the ligand
> >
> >>solvation energies fluctuate enourmousely and have SD's of around
> >
> >1900.
> >
> >>Thanks
> >>Ben
> >>
> >>On Thursday 09 Dec 2004 14:58, Ben Cossins wrote:
> >>>Hey,
> >>> I have been using mm_p-bsa from amber 8 to calculate binding
> >
> >energies of
> >
> >>>ligand-receptor systems. I get an error from pbsa when it is
> >
> >calculating
> >
> >>>ligand solvation energy for some ligands and not for others.
> >>>The message is:-
> >>>
> >>>PB Warning in epsbnd(): No neighbor found for reentry boundary grid
> >>>
> >>>I have applied all bug fixes.
> >>>I have had a look at the code giving this error but dont instantly
> >
> >see what
> >
> >>>the error is for. I have seen that there has been a bug fix (bug
> >
> >fix4) a
> >
> >>>few lines above this.
> >>>
> >>>Can anyone offer me any advice.
> >>>
> >>>Thanks
> >>>
> >>>Ben
> >>
> >>--
> >>Benjamin Cossins
> >>Southampton University
> >>J. W. Essex group.
> >>---------------------------------------------------------------------
> >
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> >
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-- 
Benjamin Cossins
Southampton University
J. W. Essex group.
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