[gmx-users] Writing out individual coordinates

[Tsjerk Wassenaar]

Hey :)

Why not just use trjconv to write a .pdb file? C-alpha atoms is
offered as standard group, and the resulting file can be easily
processed with sed/python.

Cheers,

Tsjerk

On Thu, Apr 19, 2012 at 10:47 PM, Rodrigo Faccioli
<rodrigo_faccioli at uol.com.br> wrote:
> 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
>>
>> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands