AMBER Archive (2008)

Subject: Re: AMBER: Sander crashes >99999 atoms

From: David A. Case (
Date: Thu Jun 12 2008 - 20:25:31 CDT

On Thu, Jun 12, 2008, wrote:

> My system has 1060 residues (8730 atoms). The size of the system increased
> to >99999 atoms, when I added 10 A water. I am using amber 8 on a linux
> cluster amd64. When, I try to minimize, using 4 CPUs - I get the following
> error.

> forrtl: severe (174): SIGSEGV, segmentation fault occurred.

I doubt that this has anything directly to do with the number of atoms. We
run systems with more than 100000 atoms a lot.

Did you get any output? Does the segmentation fault occur immediately (i.e.
before the first energy step) or later? Does the job work in serial mode?

There is something odd about your system: a protein with 1000 residues would
ordinarily have about 16,000 atoms (not including the solvent). Is there
something unusual in your sequence that it has so few atoms?

Unfortunately, a segfault is not a very informative error message. But
usually some detective work can narrow down the possible/probably causes of
such a failure.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)