Your command is different from what I sent, so the log is different. But
yes, your install is successful.
So then I don't know why. I tried with your install command and then tested
$ python -c 'import parmed; print(parmed)'
<module 'parmed' from
'/home/haichit/.local/lib/python3.5/site-packages/parmed/__init__.py'>
Probably Jason will give you further debug. Good luck.
Hai
On Fri, Mar 11, 2016 at 8:32 AM, Robert Molt <rwmolt07.gmail.com> wrote:
> Perhaps herein lies the issue. When I do
>
> python setup.py install --user
>
> in the directory where I unpacked the tarball, my last few lines do not
> conclude an explicit statement of success. My last few lines are simply
>
> "copying build/scripts-2.7/parmed -> /N/u/rwmolt/Karst/.local/bin
> copying build/scripts-2.7/xparmed -> /N/u/rwmolt/Karst/.local/bin
> changing mode of /N/u/rwmolt/Karst/.local/bin/parmed to 755
> changing mode of /N/u/rwmolt/Karst/.local/bin/xparmed to 755
> running install_egg_info
> Removing
>
> /N/u/rwmolt/Karst/.local/lib/python2.7/site-packages/ParmEd-2.0.5-py2.7.egg-info
> Writing
>
> /N/u/rwmolt/Karst/.local/lib/python2.7/site-packages/ParmEd-2.0.5-py2.7.egg-info"
>
> as opposed to line 10 of the web link you gave being
>
> " Successfully installed ParmEd-2.3.2"
> Perhaps I am NOT successfully compiling; because I did not get an
> explicit error message, I assumed it was fine?
>
> On 3/11/16 1:21 AM, Hai Nguyen 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
> >>
> >> which is to say, it looks like it does not recognize the python command.
> >>
> >> Separately, it's obviously time I learned Python...if there is a quick
> >> fix, in the interim, it would nonetheless be appreciated.
> >
> > I don't think there is a quick fix unless you send your files to someone
> > having ParmEd.
> > But it's better to figure out why you can not import parmed.
> >
> > Did you see the message "Successfully installed ParmEd-2.3.2" (full log:
> > https://gist.github.com/hainm/151e36bb107462ad454d)
> >
> >
> >
> >> If I can
> >> manage to convert this amber topology to GROMACS form, I can use a type
> >> of trajectory analysis on DNA helices not suitable with the current form
> >> of Amber.
> >>
> > If you are more specific about "analysis on DNA helices", cpptraj
> > developers might have good answer for you.
> >
> > Hai
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 11 2016 - 08:30:02 PST
