Hi,
Have all patches been applied? What is the output of './update_amber
--version'? Also, do all test cases pass for MMPBSA.py and cpptraj?
-Dan
On Mon, Dec 14, 2015 at 2:22 PM, Marc Zhang <marczhang_md.zoho.com> wrote:
> Dear AMBER user group
>
>
>
> I have a problem with MMPBSA.py, when I run my calculation on our local
> cluster.
>
>
>
> Could some expert help me figure out where the problem is and how I should
> address it?
>
>
>
> Thank you very much for your help!
>
>
>
> Here is the error message I received.
>
> ----------------------------------------------------------------------------
> ----------------
>
> Loading and checking parameter files for compatibility...
>
> mmpbsa_py_energy found! Using /pdc/vol/amber/14/amber14/bin/mmpbsa_py_energy
>
> cpptraj found! Using /pdc/vol/amber/14/amber14/bin/cpptraj
>
> Preparing trajectories for simulation...
>
> File "/pdc/vol/amber/14/amber14/bin/MMPBSA.py.MPI", line 103, in <module>
>
> app.file_setup()
>
> File
> "/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
> line 156, in file_setup
>
> self.mpi_size, str(external_progs['cpptraj']), self.pre)
>
> File
> "/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/make_traj
> s.py", line 59, in make_trajectorie
>
> s
>
> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
>
> File
> "/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/make_traj
> s.py", line 467, in __init__
>
> self.Query()
>
> File
> "/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/make_traj
> s.py", line 611, in Query
>
> raise RuntimeError('Unexpected output from cpptraj. Has format '
>
> RuntimeError: Unexpected output from cpptraj. Has format changed?
>
> Error occured on rank 0.
>
> Exiting. All files have been retained.
>
> Rank 0 [Mon Dec 14 21:58:14 2015] [c0-0c0s11n2] application called
> MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> _pmiu_daemon(SIGCHLD): [NID 00046] [c0-0c0s11n2] [Mon Dec 14 21:58:14 2015]
> PE RANK 0 exit signal Aborted
>
> ----------------------------------------------------------------------------
> -----------------------------
>
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Dec 15 2015 - 09:00:07 PST
