From: Thakur, Abhishek <axt651.miami.edu>
Date: Fri, 8 Jul 2016 16:57:16 +0000


I am trying to do MMPBSA calculation using script

mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp receptor.prmtop -lp peptide.prmtop -y *.crd

But I am getting an error which I am unable to solve it

Error: *.crd matches no files.
  File "/nethome/axt651/apps/amber14/bin/MMPBSA.py.MPI", line 103, in <module>
  File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 59, in make_trajectories
    traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
  File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
  File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 602, in Query
    raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /nethome/axt651/apps/amber14/bin/cpptraj failed when querying *.crd
Error occured on rank 0.
Exiting. All files have been retained.
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.

I have cross checked MMPBSA.py.MPI is correctly installed in amber home directory
Kindly help me out.

thanking you,

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Received on Fri Jul 08 2016 - 10:00:02 PDT
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