The "SA Bomb in sa_arc" message suggests that you do not have enough
memory to run the default high-resolution surface definition for PBSA,
please reset "arcres" to a larger number, the default is "arcres =
0.0625" (in A), try to use "arcres = 0.125" (in A) or even larger if the
message does not go away. A larger fillratio value wouldn't help here.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
Cristina Sisu wrote:
> Dear Amber users,
>
> I've been running some MMPBSA calculations and I encounter the following
> problem: my system seems to be exploding.
> I extracted snapshots from my trajectory of 1000ps and run the mmpbsa
> receptor-ligand binding free energy calculation. The system behaves
> normally until and including snapshot 127. After that everything
> explodes and I get the error:
>
>> SA Bomb in sa_arc(): Allocation aborted
>>
> I've tried using fill ratio 2.0, 3.0 but not change. I tried using
> different number of snapshots 150, 200, 250. Same problem.
> I've looked at the trajectory and it looks perfectly normal for the
> entire run of 1000 ps.
> If I use only 100 snapshots for the 1000ps trajectory, the systems
> behaves perfectly.
> I've split my trajectory in batches of 250 ps and extracted snapshots
> from them. Everything runs normal. However if I want to use all of them
> in one go. My systems is getting messy at the 128th snapshot.
>
> I've read the archive posts relating to the SA Bomb, but I could not
> come to any conclusion as to what is happening in my system.
>
> Any ideas would be highly appreciated.
>
>
> Cristina
>
>
>
>
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>
>
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Received on Wed Jun 16 2010 - 11:30:03 PDT
