From owner-chemistry@ccl.net Mon Oct 14 13:04:00 2013 From: "Fran ois Zielinski francois.zielinski(a)manchester.ac.uk" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49236-131014130328-22903-Zwp8GtzijRESxhKzGsIoLw*server.ccl.net> X-Original-From: "Fran ois Zielinski" Date: Mon, 14 Oct 2013 13:03:27 -0400 Sent to CCL by: "Fran ois Zielinski" [francois.zielinski+/-manchester.ac.uk] Dear CCLers, My current concern is monitoring a dihedral angle evolution from MD runs (DL_POLY HISTORY file, but it can be converted). PyMOL looks like a possible way of extracting it, or with R scripts perhaps... However, is there some dedicated tool that enables that sort of analysis? Indeed, a single dihedral stays simple at the moment, but I foresee the need for some more complex operations. Best Regards, Franois From owner-chemistry@ccl.net Mon Oct 14 13:38:01 2013 From: "Mezei, Mihaly mihaly.mezei(0)mssm.edu" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49237-131014131942-7136-ZhcOyNEMt7ZcUhuppo7I5w---server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 14 Oct 2013 17:19:18 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei]_[mssm.edu] > My current concern is monitoring a dihedral angle evolution from MD runs (DL_POLY HISTORY file, but it can be converted). PyMOL looks like a possible way of extracting it, or with R scripts perhaps... However, is there some dedicated tool that enables that sort of analysis? Indeed, a single dihedral stays simple at the moment, but I foresee the need for some more complex operations. You can try my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) - it can give dial plots (a la Beveridge) of any angle from your MD run (Amber, Charmm or MMC trajectories only). Mihaly Mezei Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://www.mssm.edu/departments-and-institutes/structural-and-chemical-biology From owner-chemistry@ccl.net Mon Oct 14 14:48:00 2013 From: "Elaine Meng meng.{}.cgl.ucsf.edu" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49238-131014141751-18212-VoP6GyFL90BNUTMsL2JyWQ{}server.ccl.net> X-Original-From: "Elaine Meng" Date: Mon, 14 Oct 2013 14:17:49 -0400 Sent to CCL by: "Elaine Meng" [meng**cgl.ucsf.edu] Hi Francois, There are probably many solutions, and perhaps a nongraphical one would be most efficient... however, depending on your trajectory file formats, you may be able to display the trajectory in Chimera, plot various various measurements (including dihedrals) versus frame, and "dump values" from the plots into text files. The Chimera tool is "MD Movie," see documentation including "Startup and Input" and "Plotting": http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html Chimera is free to download (Mac, Windows, Linux) for any noncommercial use. http://www.rbvi.ucsf.edu/chimera/index.html Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco