ok, so I have a trick: Since ParmEd is pure Python, you can just add its
dir to PYTHONPATH
$ export PYTHONPATH=/home/haichit/programs/ParmEd-2.0.5:$PYTHONPATH
$ python -c 'import parmed as pmd; print(pmd)'
<module 'parmed' from
'/home/haichit/programs/ParmEd-2.0.5/parmed/__init__.py'>
Hai
On Fri, Mar 11, 2016 at 11:00 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
>>
>
>
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Received on Fri Mar 11 2016 - 11:30:03 PST
