Re: clustering of trajectory

From: Nicholas M Glykos (
Date: Tue Jul 05 2011 - 09:57:50 CDT

Hi Bala,

> Someone please suggest me any tool to cluster conformations based on
> dihedral angle.

Carma[1] can do dihedral PCA and then use the trajectory's projection on
the top three eigenvectors to perform a rudimentary cluster analysis. If
three principal components are not enough [see the Altis, Otten, Nguyen,
Hegger & Stock (2008) paper], or you want to assign each and every frame
to a cluster, have a look at the second link shown below.




          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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