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, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
