On Thu, May 10, 2018, Jose Manuel Granadino Roldán wrote:
>
> I have installed AmberTools18 downloading the install_ambertools.sh
> file and typing afterwards: bash install_ambertools.sh —prefix
> /programas/ -v 3. I am trying -v 3 because -v 2 gave me plenty of
> errors with parmed, MMPBSA.py y ante-MMPBSA.py. Now I am able to
> run parmed and ante-MMPBSA.py without any problem but when I try to
> execute MMPBSA.py I get the following error:
>
> File "/programas//amber18/bin/MMPBSA.py", line 71
> except CommandlineError, e:
> ^
> SyntaxError: invalid syntax
>
(I think Dan's answer is wrong here): what you are seeing is indeed
a syntax error in python3:
https://stackoverflow.com/questions/2535760/python-try-except-comma-vs-as-in-except
Here's what I think is happening: Hai (cc-ed here) fixed the MMPBSA.py
script just a few days ago (after the release of AmberTools18), but this
fix has not yet been posted as an update, and not made it into the
released binary version.
There are two lines like the above (at lines 71 and 91) that would need
to be changed: try editing those lines and see if everything else
works.
It would be nice to know more about the problems you had with python v2.
I recognize that you said "plenty of errors", but telling us even the
first one or two might help others who would have similar problems.
Amber should be using its own (miniconda) version of python: do you have
anaconda or miniconda installed any where else on your system?
...thx...dac
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Received on Thu May 10 2018 - 12:30:01 PDT
