Sent to CCL by: Jose Duarte [duarte ~ molgen.mpg.de]maxcluster does a very good job and very fast rmsd calculations. It also can do clustering using a few methods. I'm not sure though of the input formats, we have used it only with PDB files here.
See http://www.sbg.bio.ic.ac.uk/~maxcluster/index.html Jose -- Jose M. Duarte Max Planck Institue for Molecular Genetics Berlin Antje Wolf antje.wolf(-)scai.fraunhofer.de wrote:
Sent to CCL by: "Antje Wolf" [antje.wolf]~[scai.fraunhofer.de] Hi, I am looking for a (free) tool for calculating the RMSD between two molecule conformations, preferably a script or command line tool as I want to use it in batch mode. It would be great if this tool also includes the possibility to do a clustering. Perhaps, someone has a good suggestion. Thanks in advance, Antje>