Thank you! This worked wonderfully!
On 3/11/16 2:11 PM, Hai Nguyen wrote:
> 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
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> --
>>> Dr. Robert Molt Jr.
>>> r.molt.chemical.physics.gmail.com
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>>
>>
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--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Fri Mar 11 2016 - 12:30:03 PST
