Getting an average pdb, whether from the rst files or snapshots from your
.mdcrd is just a matter of aligning all the structures, and then taking the
average of each position. I know ptraj has an alignment command, not sure
about the averaging. VMD can also align. Worst case scenario you can
average with your own little script.
~Aron
On Fri, Dec 21, 2012 at 7:26 AM, edu troche <eduardo.troche.uvigo.es> wrote:
> Hi Amber users,
> I have a doubt about ambpdb and its functionality when generating an
> average pdb from a simulation. Because of time machine restrictions, I had
> to perform a MD simulation in fragments. I know that I can join the .mdcrd
> parts together with a simple ptraj script. Is there a way that I can do the
> same with with the .rst individual files, so that I can create afterwards
> an average pdb file from the whole simulation?
>
> Thanks in advance ,
>
> Eduardo Troche Pesqueira <http://webs.uvigo.es/webqo3/people/eduardo.html>
> Tel. 986812309
> Edificio E, Andar 3º, Laboratorio1
> Facultade de Químicas
> Departamenteo de Química Orgánica
> Lagoas-Marcosende
> Universidade de Vigo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 21 2012 - 08:00:02 PST
