Re: [AMBER-Developers] SANDER in Amber12 fails to read Amber11 generated files on some local machines ...

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 22 Nov 2013 14:24:28 -0800

All tests passed on that machine … As for pmemd, this is also what I
suggested Tom to try next …

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Nov 22, 2013 at 11:58 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, 2013-11-22 at 11:31 -0800, Ray Luo, Ph.D. wrote:
> > Hi All,
> >
> > We have a user reporting that sander/sander.mpi work well with Amber12
> > generated prmtop/inpcrd files, but not with Amber11 generated files.
> > Portion of his email is enclosed below. I'm also attaching the diff file
> > between the two prmtop files, which only contains the GB-specific
> > ATOMIC_NUMBER and SCEE/SCNB sections. The absence of these sections
> should
> > all be taken care of by the new sander.
> >
> > The symptom of the failure is that the system temperature rises very
> > quickly to thousands of degrees when using the Amber11 generated files as
> > shown in the attached output file. More interestingly, the failure is
> > machine dependent. It only occurs on certain local machines. What could
> be
> > the cause?
>
> Do the tests pass on all of the machines?  Does the same thing happen
> with pmemd?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Nov 22 2013 - 14:30:02 PST
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