Have you checked the sander output files? They should be called
_MMPBSA_complex_gb.mdout and _MMPBSA_complex_pb.mdout for the complex, with
corresponding names for the receptor and ligand. Those files might give some
insight into the problem, also. Are you running this calculation on a local
computer, or a cluster? Have you applied all the bugfixes for MMPBSA.py and
downloaded the most recent version from the tutorial website (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/)?
-Bill
On Mon, Mar 7, 2011 at 8:33 AM, hari krishna <haricoolguy111.gmail.com>wrote:
> Please guess something to resolve from this problem
>
>
> I am using the following command to rum MMPBSA analysis:
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> complex_sol.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop
> -y prodn.mdcrd
>
> *
> Following is the output I am getting:*
>
> ptraj found! Using /home/ppilab/AMBER10/exe/ptraj
> sander found! Using /home/ppilab/AMBER10/exe/sander
> Assuming /home/ppilab/AMBER10/exe/sander is part of
> amber9 or amber10. Using old PB input file.
> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
> Bondi radii (mbondi)
>
> Preparing trajectories with ptraj...
> 50 frames were read in and processed by ptraj for use in calculation.
>
> Starting calculations...
>
> Starting gb calculation...
>
> calculating ligand contribution...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> calculating receptor contribution...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> calculating complex contribution...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> Starting pb calculation...
>
> calculating ligand contribution...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> calculating receptor contribution...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> calculating complex contribution...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> Calculations complete. Writing output file(s)...
>
> Error: No potential terms in sander output! Check output files.
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Mar 07 2011 - 06:00:08 PST
