Thank you; I appreciate this. I wrote my own code for analysis, but
would very much like an independent metric to judge if my code is correct.
On 3/11/16 8:51 PM, Jason Swails wrote:
> Justin Lemkul has a set of outstanding tutorials. Have a look:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
>
> Helped me when I was figuring out how to run GROMACS.
>
> HTH,
> Jason
>
> On Fri, Mar 11, 2016 at 8:33 PM, Robert Molt <rwmolt07.gmail.com> wrote:
>
>> I ended up being able to circumnavigate the problem by merely installing
>> it on another personal computer where everything went as it should. As
>> my need was merely to convert one parameter file to the GROMACS format,
>> the quick fix was good enough.
>>
>> Now I just have to learn how to make a GROMACS binary. Thank you for all
>> of your help in this little adventure.
>>
>> On 3/11/16 7:50 PM, Jason Swails 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
>>>>
>>> If "pip install" worked for ParmEd and you get this error above, the
>> only
>>> thing I can think of is that your "pip" is linked to a different Python
>>> than `which python`. It doesn't make much sense...
>>>
>>> But this should all be fixed within the next month or so when AmberTools
>>> bundles the newest version of ParmEd. In the meantime, Hai's trick will
>>> work (it is just going to make Amber prmtop parsing take a little
>> longer).
>>> All the best,
>>> Jason
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Dr. Robert Molt Jr.
>> r.molt.chemical.physics.gmail.com
>>
>>
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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 - 19:00:04 PST
