Re: AMBER: signal SIGSEGV(11)

From: Chris Moth <>
Date: Wed, 18 Apr 2007 15:22:58 -0500

There is a chance you might find it helpful to set maxcyc to 1300 so
that you can get final output, and take a look (visualize) the
structure. Though the energies may look reasonable, looking at the
structure, relative to start structure, could be informative.
Especially look around the atoms that are listed in the output file
often. What is going on near CG atom 4880? H1 atom 6532?

If you strongly suspect the minimization algorithm is essentially
failing, then perhaps setting input for "always use steepest descent"
(ntmin=2) would get you to an coordinate set, from which conjugate
gradient performs better.

I'm not predicting either of the above will be successful :) - but they
are quick things I might "try" to move ahead if I were stuck.


Pankaj R. Daga wrote:
> Hi Dr. Case and Dr. Ross,
> Thank you very much for your inputs. I have tried to run same job with
> single processor. But I am still facing the same error.
> The protein I am dealing with is a homology model of enzyme and it is
> a ternary complex of enzyme-DNA-ligand. The ternary system is solvated
> in TIP3PBOX. My aim is to run MD simulation on optimized system.
> Hence, I started with stepwise minimization.
> First step minimization went well but when I submitted the output file
> from first step minimization for the next step, sander minimizes the
> molecule for few steps (1300 out of 5000). Then I face this error.
> This error is reprodicible. I am attaching the input file and output
> file here.
> ************************************************
> MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank
> 0, Process 17288 received signal SIGSEGV(11)
> MPI: --------stack traceback-------
> sh: line 1: idb: command not found
> MPI: -----stack traceback ends-----
> MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank
> 0, Process 17288: Dumping core on signal SIGSEGV(11) into directory
> /work1/r1029/HDP_APR07
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> MPI: aborting job
> MPI: Received signal 11

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Received on Sun Apr 22 2007 - 06:07:17 PDT
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