The problem now is solved. I also needed to “clean” the environmental variable PYTHONPATH because (as pointed by Dr. Case) I have other versions of miniconda installed in my system and MMPBSA.py tried to find python libraries in a wrong location (the one in which I have Python 2.7 from miniconda). Concerning the errors with the python 2.7 version, I can´t reproduce them right now, but it seems that they were also related with mismatch between miniconda versions installed in my system. Thank you very much for your help.
Best
> El 10 may 2018, a las 22:24, Hai Nguyen <nhai.qn.gmail.com> escribió:
>
> On Thu, May 10, 2018 at 3:11 PM, David A Case <david.case.rutgers.edu <mailto: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 Fri May 11 2018 - 00:30:01 PDT
