On Thu, May 10, 2018 at 3:11 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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.
>
>
Alternatively 2to3 program (bundled in python 3) can be used:
2to3 -w /programas//amber18/bin/MMPBSA.py
Hai
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 - 13:30:02 PDT
