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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Received on Thu Mar 10 2016 - 22:30:02 PST
