From owner-chemistry %-% at %-% ccl.net Thu Sep 29 09:26:01 2011 From: "Iain Moal Iain.Moal.:.cancer.org.uk" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45552-110929023618-14286-Eb/uImp1s5tFeD/dUP9sFA]![server.ccl.net> X-Original-From: Iain Moal Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 29 Sep 2011 07:35:31 +0100 MIME-Version: 1.0 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 AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.