Re: [AMBER] MMPBSA, signal SIGSEGV failure

From: Ray Luo <>
Date: Thu, 25 Feb 2021 09:09:36 -0800


This is rare. I suppose this is from a serial run? There is not enough
information for us to see what's going on. Are you able to see any
snapshot completed at all? Could you share your input file and the PB
output file where you see the error message?

All the best,
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Thu, Feb 25, 2021 at 8:17 AM Matthew Guberman-Pfeffer
<> wrote:
> Dear Amber community,
> I ran a series of MMGB- and MMPBSA calculations, but one of them came back with “Program received signal SIGSEGV: Segmentation fault - invalid memory reference.” The stage of the calculation where this happened was (to the best that I can tell):
> Beginning PB calculations with /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/bin/sander
>   calculating complex contribution…
> The GB calculation seems to have finished normally.
> What could be going wrong, or how can I figure that out? I’m a bit confused why this particular calculation is having an issue, because the other calculations that finished normally were essentially the same structure, just different point mutants.
> Best,
> Matthew
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Received on Thu Feb 25 2021 - 09:30:02 PST
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