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.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
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Received on Sun Oct 29 2006 - 06:07:08 PST
