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 - 08:30:02 PDT
