AMBER Archive (2004)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Dec 10 2004 - 15:36:53 CST

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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>
>
>>The AMBER Mail Reflector
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>.
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> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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