From owner-chemistry@ccl.net Sun Apr 22 10:36:00 2007 From: "errol lewars elewars!A!trentu.ca" To: CCL Subject: CCL: MOLECULE Message-Id: <-34094-070422094946-24676-vtWbBYciVCbXBg/QELHZqA*o*server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 22 Apr 2007 09:50:32 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars[-]trentu.ca] 2007 April 22 In silico? If it's bigger than, say, H2, the easiest way is to use a graphical user interface (GUI). You put atoms and groups together on the screen, much like assembling a plastic model; the GUI generates the Cartesian (XYZ) coordinates which define the geometry. An older method, which may be very occasionally useful, is to use a Z-matrix, specifying how the atoms are arranged in a rectangular coordinate system; see e.g. the book by Hehre, Radom, Schleyer and Pople, or the book by Tim Clark. E. Lewars =========== neeraj misra misraneeraj[]gmail.com wrote: > WHAT IS THE EASIEST WAY TO BUILD A MOLECULE? From owner-chemistry@ccl.net Sun Apr 22 12:09:01 2007 From: "David A. Case case*scripps.edu" To: CCL Subject: CCL: Going from a Topology File to a .top File for an AMBER Forcefield Message-Id: <-34095-070420121559-19630-wHPpRNODsC1hbDXE7ovC9g++server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 20 Apr 2007 08:36:52 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case .. scripps.edu] On Thu, Apr 19, 2007, Jed Zaretzki zaretj .. rpi.edu wrote: > > I am looking for a tool which will go from a bare bones .pdb file to a .top > file. .pdb file should be considered a topology file. .top file can be > considered a detailed topology file with additional force field information > required to calculate partial charges upon the individual atoms of the > molecule (those partial charges are also in the file). I need this tool to > work for small molecules with at most 60 or 70 heavy atoms. I also need it > to work with an AMBER forcefield. This is exactly the description of antechamber, as far as I can see: http://amber.scripps.edu/antechamber ...good luck...dave case From owner-chemistry@ccl.net Sun Apr 22 14:42:01 2007 From: "William F. Coleman wcoleman-x-wellesley.edu" To: CCL Subject: CCL: MOLECULE Message-Id: <-34096-070422124658-10758-QMI+zUiA/P/SfMUQD4Z+tw^^^server.ccl.net> X-Original-From: "William F. Coleman" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 22 Apr 2007 12:08:48 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman]=[wellesley.edu] For small and medium-sized molecules I am a big fan of Discovery Studio Visualizer by Accelrys (http://www.accelrys.com/products/downloads/ds_visualizer/index.html), free to the community. It includes the drawing tools from the no longer available WebLab Viewer Pro from MSI, and does a very nice job of preparing molecules for submission to a variety of computational programs. For transition metal complexes I prefer GaussView, but if you do not have that the DS Visualizer can certainly do what you wish with a little work. Cheers, Flick _______________ William F. Coleman Professor and Chair, Department of Chemistry Wellesley College Wellesley, MA 02481 email: wcoleman(_)wellesley.edu web: www.wellesley.edu/Chemistry/colemanw.html voice: 781-283-3129 fax: 781-283-3642 Editor, JCE WebWare http://www.jce.divched.org/JCEDLib/WebWare/ From owner-chemistry@ccl.net Sun Apr 22 18:59:01 2007 From: "igor novak inovak ~~ csu.edu.au" To: CCL Subject: CCL: running g3 or cbs jobs at fixed geometry Message-Id: <-34097-070422182933-8453-1J0ATu9zCQCMGWp+EdaQ+g]*[server.ccl.net> X-Original-From: "igor novak" Date: Sun, 22 Apr 2007 18:29:29 -0400 Sent to CCL by: "igor novak" [inovak_+_csu.edu.au] Hi netters, does somebody know how to run a G3 or CBS type calculation without the first step which automatically optimizes the input geometry i.e. to run a G3 type calculation for a given, fixed geometry? Does somebody have complete sequence of steps? Thanks & regards I.Novak