On Sun, Oct 11, 2015 at 10:23 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> hi all,
>
> After getting suggestions from you I have upgraded my AmberTools from
>
>
> AmberTools 14 to AmberTools15. But even after doing that I'm getting
>
> another error message different from the earlier. I have copied both the
>
> error messages. it would be great if you would have suggestions regarding
>
>
> further proceedings.
>
> ayesha.ayesha-Inspiron-3521[amber14] $AMBERHOME/bin/MMPBSA.py -O -i
> mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp
> ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y ras-raf_top_mdcrd.mdcrd
> /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9
> warnings.warn(_msg, ModuleDeprecationWarning)
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/ayesha/Documents/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /home/ayesha/Documents/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> Error: ras-raf_top_mdcrd.mdcrd matches no files.
>
It says this file does not exist.
> TrajError: /home/ayesha/Documents/amber14/bin/cpptraj failed when querying
> ras-raf_top_mdcrd.mdcrd
>
>
Exiting. All files have been retained.
>
> kindly guide me in this matter .
>
The error seems to suggest that the trajectory you are trying to analyze
does not exist. Obviously MMPBSA.py cannot read a trajectory file that is
not there (or is misspelled).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Oct 11 2015 - 08:30:03 PDT
