Re: [AMBER] segmentation fault

From: case <>
Date: Thu, 22 Jul 2010 09:53:22 -0400

On Thu, Jul 22, 2010, Jagdeesh C wrote:
> I upgraded and installed everything again (amber 10). Then I ran the file
> you had provided earlier >Run.dhfr.min_prcg (attached)

> /usr/local/amber10/test/dhfr# ./Run.dhfr.min_prcg
> Segmentation fault
> ./Run.dhfr.min_prcg: Program error

OK..this looks like an Amber10 bug, which I can reproduce in Amber10, but
which works in Amber11. The implementation of xmin inside sander has changed
a lot in going from Amber10 to Amber11 -- moving from a fortran version to
the same C version that is used in NAB. So, it's not clear that it will
be very easy to find and fix the problem in Amber10. For the moment, you
should either upgrade to Amber11, or use the NAB interface to run xmin

Or, if you have a little expertise: compile a debugging version of sander,
run the dhfr.min_prcg test case, and find the location of the error. It may
be that the fix to Amber10 will be obvious. We'll keep this bug on file,
and maybe someone on the list will be able to recommend a fix as well.


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Received on Thu Jul 22 2010 - 07:00:08 PDT
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