CCL: How can I do cluster analysis or similarity analysis

 Sent to CCL by: Iain Moal [Iain.Moal#,#cancer.org.uk]
 Hi Yawen,
 Clustering analysis with AMBER can be found in section 6 of the AMBER tutorial
 B3: http://ambermd.org/tutorials/
 Alternatively, you can use the g_cluster, which comes packaged with the GROMACS.
 Iain Moal
 ________________________________________
 > From: owner-chemistry+iain.moal==cancer.org.uk_+_ccl.net
 [owner-chemistry+iain.moal==cancer.org.uk_+_ccl.net] On Behalf Of Yawen Li
 yl6c2!^!mail.missouri.edu [owner-chemistry_+_ccl.net]
 Sent: 28 September 2011 23:53
 To: Iain Moal
 Subject: CCL: How can I do cluster analysis or similarity analysis
 Sent to CCL by: "Yawen  Li" [yl6c2[*]mail.missouri.edu]
 Hi, all.
  I did a molecular dynamics simulation with AMBER, and I saved a thousand
 conformations during this run. I wish to do some cluster analysis, or similarity
 analysis on the conformations I saved. I think all the conformations can be
 groups into two main groups, because I see the structure changes from one
 conformation to the other in the MD simulation.
  Is there any free software that does this job?
 Thank you all for your attention, and I appreciate your help.
 Yawen Li
 Graduate Student
 Chemistry department
 University of Missouri - Columbia
 E-mail: yl6c2,mail.missouri.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txtNOTICE
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