From: Joshua Adelman (jla65_at_pitt.edu)
Date: Thu Apr 29 2010 - 18:06:38 CDT
Hi Basak,
You can probably use the gromacs tools:
http://manual.gromacs.org/current/online/g_cluster.html
There are other tools like MSMbuilder that has clustering functionality (built partially on gromacs tools):
https://simtk.org/home/msmbuilder
For both of the above, you will need to convert the dcd file to either trr or xtc format. The former is possible using catdcd.
You could also use something like kmeans in matlab in combination with the matdcd tools. There are probably many other options that others can suggest.
Good luck.
Josh
On Apr 29, 2010, at 6:51 PM, Basak Isin wrote:
> Hello,
> I would like to cluster different conformations of a protein focusing on certain residues and their side chains. Is there any available softwares/algorithms that would perform this?
> Thanks much.
> Basak
>
>
-- Dr. Joshua L. Adelman Postdoctoral Researcher - Grabe Lab Department of Biological Sciences University of Pittsburgh, Pittsburgh, PA
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:43 CST