and when i configure MMPBSA.py it show the following warning
ayesha.ayesha-Inspiron-3521[bin] ./MMPBSA.py [ 7:27PM]
/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)
InputError: No input file was provided!
Enter `MMPBSA.py --help` for help
how can i resolve this problem?
> From: ayesha_comsian.hotmail.com
> To: amber.ambermd.org
> Date: Sun, 11 Oct 2015 19:23:49 +0500
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Oct 11 2015 - 08:00:03 PDT
