AMBER: signal SIGSEGV(11)

From: Pankaj R. Daga <>
Date: Wed, 18 Apr 2007 10:25:55 -0500

Dear Amber community,


I am running optimization of one protein-ligand-DNA ternary complex with TIP3P water, in stepwise manner.

After minimizing solvent molecules in first step (which went fine), I am running full system minimization. While running the second minimization, there is sudden crash down of sander. The error I am getting is shown below. Could you please help me to understand, if this error is related to sander or mpi, and how to solve it?


MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank 1, Process 19180 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 1, Process 19180: Dumping core on signal SIGSEGV(11) into directory /work1/r1029/HDP_APR07
MPI: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11


Thanks for your help and support.



If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
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Received on Sun Apr 22 2007 - 06:07:12 PDT
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