[AMBER] MMPBSA.py TrajError: Could not find number of frames in MMPBSA.mdcrd

From: maryam azimzadehirani <maryamai1988.gmail.com>
Date: Mon, 3 Oct 2016 09:01:24 +0800

Dear All,
I am trying to run MMPB/GBSA calculation. I keep getting this error:
It seems that the frames can not be found in the trajecotry. I usually save
the trajectories in netcdf format. Does that cause this issue?
Thank you for your help

Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
Preparing trajectories for simulation...
Usage: /usr/local/packages/amber12/amber12/bin/cpptraj [-p <Top1>, -p
<Top2>, ...] [-i <Input>] [-debug <N>]
       /usr/local/packages/amber12/amber12/bin/cpptraj <Top1> <Input>
       Additional options:
         --help, -help: print usage information and exit.
         -V, --version: print version information and exit.
             --defines: print list of defines used in compilation.
  File "/usr/local/packages/amber14/bin/MMPBSA.py", line 95, in <module>
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/main.py", line
156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/make_trajs.py",
line 59, in make_trajectories
    traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/make_trajs.py",
line 467, in __init__
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/make_trajs.py",
line 609, in Query
    raise TrajError('Could not find number of frames in ' + traj)
TrajError: Could not find number of frames in MMPBSA.mdcrd
Exiting. All files have been retained.

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Received on Sun Oct 02 2016 - 18:30:02 PDT
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