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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Received on Wed Sep 30 2015 - 09:00:03 PDT
