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
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--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Fri Mar 11 2016 - 06:00:05 PST
