[gmx-users] Writing out individual coordinates
rodrigo_faccioli at uol.com.br
Thu Apr 19 22:47:58 CEST 2012
I believe BioPython project can help you. It load a PDB file and you have
methods which help you selecting atoms.
Please see ...
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
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:
>> 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 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
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