CCL: How can I do cluster analysis or similarity analysis

 Sent to CCL by: Marcin =?iso-8859-2?Q?Kr=F3l?= [mykrol.:.cyf-kr.edu.pl]
 Hi Yawen
 If you did the simulation in AMBER you can use ptraj program from the
 AMBER suite. Have a look at 'cluster' command in ptraj, described in
 detail in AmberTools manual (http://ambermd.org/doc11/AmberTools.pdf)
 Best
 marcin
 >
 > 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.edu>
 >
 >