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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 11 2016 - 17:00:04 PST
