From owner-chemistry@ccl.net Mon Aug 28 13:34:00 2006 From: "Bala Subramanian bala-x-igib.res.in" To: CCL Subject: CCL: most probable G:A base-pair Message-Id: <-32444-060828115653-22148-FODmIU5Hak10QmcKSfHBig/a\server.ccl.net> X-Original-From: "Bala Subramanian" Date: Mon, 28 Aug 2006 11:56:52 -0400 Sent to CCL by: "Bala Subramanian" [bala\a/igib.res.in] Dear CCL users, I have modelled a RNA duplex in which i have G:A mismatch. Since there are four possible base-pairs that are possible between hetero purines. I would like to know which is the most probable one in RNA. In my structure i have G:A N1-N1, carbonyl-amino hydrogen bonds. Although one straight way that i thought was to look in the RNA structures from PDB for the base-pairs existing for G:A mismatch, i would like to know whether there is any references where someone has worked on this issue. I also request someone to give some insight on how i should go about this. thank you in advance, C.Bala, Delhi-110007. From owner-chemistry@ccl.net Mon Aug 28 23:15:01 2006 From: "John Stone johns ~~ ks.uiuc.edu" To: CCL Subject: CCL: Announce: VMD 1.8.5 released Message-Id: <-32445-060828230912-25010-WP29zbg7pUH/vTYl1lkD1g|-|server.ccl.net> X-Original-From: John Stone Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 28 Aug 2006 21:31:39 -0500 Mime-Version: 1.0 Sent to CCL by: John Stone [johns~~ks.uiuc.edu] Hi, The latest version of the molecular visualization and analysis tool VMD is now available for download: http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.5/ The VMD 1.8.5 Release Notes, User Guide, and links to many tutorials developed by us and by others are available here: http://www.ks.uiuc.edu/Research/vmd/current/docs.html Key features of VMD 1.8.5: - Includes a new multiple sequence alignment bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids. - The MacOS X versions have been updated for MacOS X 10.4, and now support stereoscopic display and OpenGL programmable shading. - New collaboration plugins allow VMD users to chat, submit APBS and NAMD jobs to remote supercomputers and clusters, and exchange VMD views, all without the need to to install or run any additional software. - VMD includes new text commands and graphical interfaces for calculating radial distribution functions, IR spectral densities, and finding salt bridges. - New and updated structure building plugins provide text commands and graphical interfaces for structure building and editing, converting between all-atom and coarse grain simulation models, and calculating molecular dynamics force field parameters. Cheers, John Stone vmd%a%ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns%a%ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078