Hi Robert,
Last year I wanted to play around with some of the different clustering algorithms in Gromacs.
I used the VMD plugin Topotool where you load your amber format .prmtop and .rst files in VMD, then use the TkConsole:
“package require topotools”; “topo writegmxtop mayflies.top”.
I need to underline that this is a quick and dirty trick (underlining ‘dirty’)! The obtained .top file is truncated and only suitable for analysis purposes!
From there you can use make_ndx to obtain an .ndx file and then grompp to get the .tpr file (note that you need to provide a .mdp file here).
I would, however, recommend you to stick with ParmEd. It is really powerful and the time spend to familiarise yourself with it (and python) now, will most likely be returned severalfold later on.
Also, I would recommend you to explain what sort of DNA analysis you would like to perform.
cpptraj has an ever growing list of analysis available and if that particular analysis is not implemented it could go on the wishlist and maybe help others later on :-)
All the best,
Sarah
> On 11 Mar 2016, at 07:21, Hai Nguyen <nhai.qn.gmail.com> 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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Received on Fri Mar 11 2016 - 04:00:02 PST
