AMBER: Error at Equilibration....

From: Sandeep Kaushik <>
Date: Mon, 2 Apr 2007 12:44:17 +0530

I am using parallel version of sander on Gmac5, with mpich.
I have just finished minimizing my protein which is solvated.
And when i tried putting it for equilibration i get following error.

mpirun -np 4 sander.MPI -O -i -o equi1.out -c Min1.rst -p -r Equi1.rst -x equi.mdcrd &

mpiexec_bicg5quad.local: mpd_uncaught_except_tb handling:
  exceptions.IOError: [Errno 9] Bad file descriptor
    /Users/deb/mpich2-install/bin/mpirun 1035 handle_stdin_input
        sys.stdin.flush() # probably does nothing
    /Users/deb/mpich2-install/bin/ 527 handle_active_streams
    /Users/deb/mpich2-install/bin/mpirun 493 mpiexec
        rv = streamHandler.handle_active_streams(timeout=1.0)
    /Users/deb/mpich2-install/bin/mpirun 1393 ?

[2] Exit 1 mpirun -np 4 sander.MPI -O -i
equi1.out -c Min1.rst -p ...

Please tell me what is wrong and what could be the solution.
I haven't attached the equilbn input file coz this error appeared to be more
technical to me rather than input error.

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Received on Wed Apr 04 2007 - 06:07:20 PDT
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