[AMBER] MMPBSA.py.MPI compling issue

From: Marc Zhang <marczhang_md.zoho.com>
Date: Mon, 14 Dec 2015 22:22:14 +0100

Dear AMBER user group


I have a problem with MMPBSA.py, when I run my calculation on our local


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>


line 156, in file_setup

    self.mpi_size, str(external_progs['cpptraj']), self.pre)

s.py", line 59, in make_trajectorie


    traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)

s.py", line 467, in __init__


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



AMBER mailing list
Received on Mon Dec 14 2015 - 13:30:04 PST
Custom Search