Thank you Jason. You were right. It is working now.
On Mon, Oct 3, 2016 at 11:00 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sun, Oct 2, 2016 at 8:53 PM, maryam azimzadehirani <
> maryamai1988.gmail.com> wrote:
>
> > Hi,
> > I did try the mask and I am still getting the same error. To make sure I
> > ran a new short simulation and ran the analysis and I get this error:
> >
> > 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
> >
>
> MMPBSA.py is using cpptraj and mmpbsa_py_energy from Amber 12 it seems.
>
>
>
> > 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.
> >
>
> This error output suggests that MMPBSA.py is feeding incorrect
> command-line arguments to cpptraj.
>
>
> > File "/usr/local/packages/amber14/bin/MMPBSA.py", line 95, in <module>
> > app.file_setup()
> >
>
> These traceback messages show that MMPBSA.py from Amber 14 is being used.
>
> This is likely your problem. cpptraj has probably changed between Amber 12
> and Amber 14, and MMPBSA.py uses features not present in earlier versions.
>
> In general, you can't mix-and-match different components of different
> AmberTools installations. You need to clean up your path to make sure that
> MMPBSA.py is finding the right AmberTools components (in particular, make
> sure AMBERHOME points to your latest Amber installation).
>
> I also recommend updating to the latest version of AmberTools.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Mon Oct 03 2016 - 20:30:02 PDT
