AMBER Archive (2004)

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

From: david.evans_at_ulsop.ac.uk
Date: Thu Dec 09 2004 - 10:15:52 CST

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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