Re: AMBER: pbsa error in mm_pbsa amber 8

From: <>
Date: Thu, 9 Dec 2004 16:15:52 +0000

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 <> 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
>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
>> 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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Received on Thu Dec 09 2004 - 16:53:00 PST
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