AMBER Archive (2004)

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

From: Ben Cossins (bcc_at_soton.ac.uk)
Date: Fri Dec 10 2004 - 07:05:33 CST

Hi Dave and all,
  I have increased the SCALE parameter from 2 to 4. SCALE controls the
"Lattice spacing in no. of grids per Angstrom.". The Warning message has
gone now, however the corrected reaction field energy: still fluctuates far
more than I would expect and does for other Ligand-receptor systems (From
-22585.401762 to -73.254221). Does any one have any idea why this might be
happening. I am using the exact same settings as other calculations which
have turned out fine.

Thanks

Ben 

-- 
Benjamin Cossins
Southampton University
J. W. Essex group.

On Thursday 09 Dec 2004 16:15, 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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-- 
Benjamin Cossins
Southampton University
J. W. Essex group.
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