AMBER Archive (2006)

Subject: Re: AMBER: amber9: SA Bomb in sa_arc

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Oct 25 2006 - 04:14:08 CDT

Giulio,

Could you sent me (not the list) a tarball of your files so I can test
it with your input?

All the best,
Ray

Giulio Rastelli wrote:

> Dear Ray,
> the reason why I set fillration to 4 is that for some small ligands
> the PBSA calc fails. However, I reset fillratio to 2, compiled pbsa
> again, and run PBSA
> again with scale=4, and aain I have the same error. I am running amber9
> on a linux network opteron quadriprocessor with 32Gb central memory.
> Is PBSA in amber9 so demanding in terms of memory? I have been using
> fillratio=4
> with amber8 and never had problems with scale=4, or even scale=5.
> I guess that the PBSA code was rewritten in amber9, but can't find
> any documentation on this.
> All the best,
> Giulio
> Ray Luo wrote:
>
>> Guilio,
>>
>> You're running out of memory. Please don't use fillratio =4 for such
>> a large system. Reduce fillratio to 2 to see whether your memory is
>> enough.
>>
>> Best,
>> Ray
>>
>> Giulio Rastelli wrote:
>>
>>> Dear developers,
>>> I am using amber9 to run mm_pbsa calculation on a protein-ligand
>>> complex.
>>> Using a SCALE parameter of 2 (grid space 0.5), PBSA works fine.
>>> When I try to increase the SCALE parameter to 4 (grid space 0.25)
>>> I have this error:
>>> SA surface: setting up working radii
>>> SA surface: found nonzero radii 5172
>>> Number of SA srf points exposed 52227
>>> SA Bomb in sa_arc(): Allocation aborted 0 0
>>> 1 0 0
>>>
>>> I am using a fillratio equal to 4.
>>> Looking at the amber9 code is_init.f, it seems to me that the maxarc
>>> and/or maxarcdot have to be redimensioned to higher values.
>>> Before doing that, I would prefer receiving a feedback from
>>> the developers.
>>> Thank you very much in advance
>>> Giulio
>>>
>>> part of MM_PBSA input:
>>> ______________________________
>>> @PB
>>> PROC 2
>>> REFE 0
>>> INDI 1.0
>>> EXDI 80.0
>>> SCALE 4
>>> LINIT 1000
>>> PRBRAD 1.4
>>> #
>>> RADIOPT 0
>>> NPOPT 1
>>> CAVITY_SURFTEN 0.0072
>>> CAVITY_OFFSET 0.00
>>> ______________________________
>>
>>
>>
>>
>
> 

-- 
====================================================
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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