I ended up being able to circumnavigate the problem by merely installing
it on another personal computer where everything went as it should. As
my need was merely to convert one parameter file to the GROMACS format,
the quick fix was good enough.
Now I just have to learn how to make a GROMACS binary. Thank you for all
of your help in this little adventure.
On 3/11/16 7:50 PM, Jason Swails wrote:
> On Thu, Mar 10, 2016 at 11:48 PM, Robert Molt <rwmolt07.gmail.com> wrote:
>
>> Good evening,
>>
>> That makes more sense. I installed it just fine for my user account.
>> However, I concede I am still screwing something up. After compiling OK,
>> I created my_script.py with contents
>>
>> #!/bin/python
>> import parmed as pmd
>>
>> amber = pmd.load_file('name_change_piggy.prmtop', '03_Equilibrate.mdcrd')
>> # Save a GROMACS topology and GRO file
>> amber.save('gromacs.top')
>> amber.save('gromacs.gro')
>>
>> I attempted to execute this via
>>
>> python my_script.py
>>
>> and get the error
>>
>> Traceback (most recent call last):
>> File "my_script.py", line 2, in <module>
>> import parmed as pmd
>> ImportError: No module named parmed
>>
> If "pip install" worked for ParmEd and you get this error above, the only
> thing I can think of is that your "pip" is linked to a different Python
> than `which python`. It doesn't make much sense...
>
> But this should all be fixed within the next month or so when AmberTools
> bundles the newest version of ParmEd. In the meantime, Hai's trick will
> work (it is just going to make Amber prmtop parsing take a little longer).
>
> All the best,
> Jason
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--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Fri Mar 11 2016 - 18:00:03 PST
