can you try ambertools 16?
http://ambermd.org/AmberTools16-get.html
Hai
On Sun, Oct 2, 2016 at 9:01 PM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> 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
