[gmx-users] Writing out individual coordinates

[Rodrigo Faccioli]

I believe BioPython project can help you. It load a PDB file and you have
methods which help you selecting atoms.

Please see [1]...

[1] http://biopython.org/wiki/Main_Page

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Thu, Apr 19, 2012 at 5:25 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> patrick wintrode wrote:
>
>> Hi.
>>
>> For each alpha carbon in my protein, I want to write out the x, y and z
>> coordinates as separate time series.
>>
>> If I use g_traj with the flags -oxt -x (or y orz) and -n along with an
>> index file selecting the appropriate alpha carbon, will that do the trick?
>> Does anyone know of a less cumbersome way of doing this?
>>
>>
> You don't necessarily have to do each alpha carbon separately (though you
> could script all of it, which is relatively easy).  If you use the default
> C-alpha group, all of the chosen x/y/z coordinates are printed in order of
> the atom number, which can then be parsed with something like awk or perl.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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