Re: AMBER: Problem with running Sander

From: Lili Peng <>
Date: Tue, 10 Jul 2007 15:58:22 -0700

Hi Dr. Case,

By test case do you mean the tutorial? I was running the simulation with
the NMA tutorial. But I actually called SDSC, and they were able to help me
resolve the problem. Basically the problem had to do something with that
the tutorial was written for a single user, and with my case I was running
it on different nodes. All I had to do was to replaced the "sander" with
the executable file "sander1.cpu" and the program was executed successfully.

Thanks for your response,

On 7/10/07, David A. Case <> wrote:
> On Tue, Jul 10, 2007, Lili Peng wrote:
> >
> > I tried running the AMBER advanced tutorial A2 with the NMA file, and I
> > receive the same error message. I've tried Googling the error but
> nothing
> > relevant came up. I'm not sure what MPI I'm using. I'm running AMBER 9
> on
> > a Linux machine via ssh to the SDSC Teragrid machine, and I don't know
> if
> > the MPI can be changed through that.
> Again: this message has nothing to do with Amber: it doesn't depend on
> on what molecule or system you are running.
> Now that we know you are trying to run on SDSC Tergrid, people on the list
> may know more about how to help you. If not, contact the support people
> at SDSC.
> I note that you did not reply to my earlier question: "Can you run the
> test
> cases?" It's always good to check this out, since we know that the test
> cases
> should work, and we can rule out user error in creating the input files.
> ...dac
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Received on Wed Jul 11 2007 - 06:07:53 PDT
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