Re: [AMBER] MMPBSA : SA Bomb in sa_arc : Allocation aborted error

From: Ray Luo <>
Date: Wed, 16 Jun 2010 11:08:35 -0700

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 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: Phones: (949) 824-9528, 9562

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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Received on Wed Jun 16 2010 - 11:30:03 PDT
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