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.
File "/home/ayesha/Documents/amber14/bin/MMPBSA.py", line 103, in <module>
app.file_setup()
File "/home/ayesha/Documents/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 "/home/ayesha/Documents/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 "/home/ayesha/Documents/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
self.Query()
File "/home/ayesha/Documents/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: /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 .
> Date: Wed, 30 Sep 2015 11:37:45 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> On Wed, Sep 30, 2015 at 10:46 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
> wrote:
>
> > hi,
> > I am using amber14 and Ambertool 14 when i type MMPBSA.py --clean or
> > MMPBSA.py --version it is generating error zsh: command not found:
> > MMPBSA.py.
> > and when i run the command ./MMPBSA.py it is again showing the same Error
> > Error: ptraj is needed for MMPBSA.
> >
> > ayesha.ayesha-Inspiron-3521[amber14] export
> > AMBERHOME=/home/ayesha/Desktop/amber14
> > ayesha.ayesha-Inspiron-3521[amber14] export
> > PATH="$/home/ayesha/Desktop/amber14/bin:$PATH"
> >
>
> Take out the first $ -- it is preventing $AMBERHOME/bin from being added
> to the PATH.
>
>
>
> > ayesha.ayesha-Inspiron-3521[amber14] cd bin
> >
> > ayesha.ayesha-Inspiron-3521[bin] MMPBSA.py --clean
> > zsh: command not found: MMPBSA.py
> > ayesha.ayesha-Inspiron-3521[bin] MMPBSA.py --version
> > zsh: command not found: MMPBSA.py
> >
>
> This is probably caused by the mistake above.
>
>
>
> >
> > ayesha.ayesha-Inspiron-3521[bin] ./MMPBSA.py
> >
> > Error: ptraj is needed for MMPBSA
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> > --clean to erase these files.
> >
>
> This error message hasn't been in any version of the MMPBSA.py source code
> that I could find except for a pre-release (that is still available on the
> Amber website, but there are no active links pointing to it) that was
> distributed through the tutorial webpage back in early 2010. It took me
> awhile to even find this version.
>
> Somehow, you replaced the MMPBSA.py distributed with AmberTools 14 or
> AmberTools 15 with the ancient (first) version distributed over 5 years ago
> (distributed as the file mmpbsa_py.tar.gz). This will definitely not
> work. Depending on how you replaced MMPBSA.py in AmberTools 14/15 with its
> ancient ancestor, this could be as simple as recompiling Amber. But if you
> extracted mmpbsa_py.tar.gz into $AMBERHOME/AmberTools/src (thereby
> overwriting the *new* version), then you've corrupted your source tree and
> you need to throw out your entire amber14 directory and recompile
> everything from scratch. And for safe measure, you should delete
> mmpbsa_py.tar.gz to prevent it from being used accidentally in the future.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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Received on Sun Oct 11 2015 - 07:30:03 PDT
