Justin Lemkul has a set of outstanding tutorials. Have a look:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
Helped me when I was figuring out how to run GROMACS.
HTH,
Jason
On Fri, Mar 11, 2016 at 8:33 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
>
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Received on Fri Mar 11 2016 - 18:00:10 PST
