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
/usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
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>
app.file_setup()
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__
self.Query()
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.
Maryam
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Received on Sun Oct 02 2016 - 18:30:02 PDT
