[gmx-users] g_cluster analysis for structure refirement

James Starlight jmsstarlight at gmail.com
Fri Jul 25 09:53:43 CEST 2014

Dear Gromacs users!

I'd like to use g_cluster utility to cluster a big set of models produced
by Modeller as the result of the refirement of some parts of my protein. In
this case all structures differs only in the conformation of 1 longest loop
(~ 30 amino acids including 2 disulphide bridges) so I need to cluster all
models based on the RMSD in this region.   As the result I'd like to obtain
projection of all set of conformers onto the plane of some coordinates
 correspond to some selected structural criteriums (for instance percent of
the occurence of secondary structure elements  in the refined (loop)
region; and/or some geometrical criteriums like distance between pair of
residues, occurence of the salt-bridges in this region etc. As the result
I'd like to visualize data and chose most representative structures from
each cluster for further MD simulation. Could such processing be performed
by g_cluster taking into account that I have gromacs-like trr consisted of
my conformers ? On what cluster algoritms and parameters  should I pay a
lot of attention?

Many thanks for suggestion,


More information about the gromacs.org_gmx-users mailing list