From owner-chemistry@ccl.net Mon Aug 14 08:43:01 2006 From: "Reinaldo Pis Diez pis_diez.]-[.yahoo.com.ar" To: CCL Subject: CCL: Textbook on Semiempirical QM Message-Id: <-32386-060814081519-20719-K6On1L9veuAbMNKbMh3bNw]-[server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 14 Aug 2006 08:18:39 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [pis_diez++yahoo.com.ar] Dear Thomas, You'll find two chapters of different Reviews in Computational Chemistry volumes (http://chem.iupui.edu/~boyd/rccontents.html) very useful to teach SM-QM methods: 1) James J. P. Stewart, Semiempirical Molecular Orbital Methods, pp. 45-81 of RCC vol 1. 2) Michael C. Zerner, Semiempirical Molecular Orbital Methods, pp. 313-365 of RCC vol 2. As you can see they were written by people who were involve with SM > from the inside. Hope this helps. Regards, Reinaldo __________________________________________________ Preguntá. Respondé. Descubrí. Todo lo que querías saber, y lo que ni imaginabas, está en Yahoo! Respuestas (Beta). ¡Probalo ya! http://www.yahoo.com.ar/respuestas From owner-chemistry@ccl.net Mon Aug 14 15:49:00 2006 From: "XIN LIU xliu^^wistar.org" To: CCL Subject: CCL: thermodynamics of two sets of dependent binding sites Message-Id: <-32387-060814153120-4286-sncCotDT7cueaULQux8z+w[-]server.ccl.net> X-Original-From: "XIN LIU" Date: Mon, 14 Aug 2006 15:31:20 -0400 Sent to CCL by: "XIN LIU" [xliu * wistar.org] Dear CCL experts: I am dealing with a biological protein interaction system. Two binding sites have been discovered for protein A and protein B interaction. Site a1 on protein A binds to site b1 on protein B (with binding constatnt K1), and site a2 on protein A binds to site b2 on protein B (with binding constant K2). I am titrating protein A into protein B and the delta H (change of enthalpy for the system) of each titration is recorded. Now I have a curve of delta H (Y-axis) v.s. the used titrant protein A (X-axis). I was wondering anyone could give A thermodynamic equations, let's say delta H in in terms of K1, K2 and concentration of titrant etc. so that I can fit it onto the curve. it would be less complicated if the sites a1 and a2 were independent (e.g from two different proteins). However a1 and a2 exist in the same molecule. It's mostly like the drug design case where an organic linker is used to link two functionl group that both are able to bind two different sites on protein. People use this way to improve the binding affinity of the drug. Is there any way to deduce the function delta H = f([titratnt]) during the titrating? From owner-chemistry@ccl.net Mon Aug 14 16:24:00 2006 From: "Rajarshi Guha rguha]-[indiana.edu" To: CCL Subject: CCL: Visualizing MOPAC ESP data - command line program Message-Id: <-32388-060814122746-25945-8Hxaj6RkNhTbtqnaMziqjw[#]server.ccl.net> X-Original-From: "Rajarshi Guha" Date: Mon, 14 Aug 2006 12:27:45 -0400 Sent to CCL by: "Rajarshi Guha" [rguha[#]indiana.edu] Hi, does anybody know of a command line program (under Linux) that will visualize electrostatic potential surfaces generated by MOPAC - overlayed on the structure? Thanks, From owner-chemistry@ccl.net Mon Aug 14 16:59:01 2006 From: "Z. Rinkevicius rinkevic**theochem.kth.se" To: CCL Subject: CCL:G: Gaussian freq. calc. output Message-Id: <-32389-060814061304-11028-L6cr8GaA8ZLc+eYzBdCSXQ|*|server.ccl.net> X-Original-From: "Z. Rinkevicius" Date: Mon, 14 Aug 2006 06:13:03 -0400 Sent to CCL by: "Z. Rinkevicius" [rinkevic- -theochem.kth.se] Dear CCL users, I hope any one can clarify situation with Gaussian normal modes printout. I suspect normal modes are printed in mass-weighted form i.e. bohrs*amu**(1/2), or i am wrong? Thanking in advance, Dr. Z. Rinkevicius. From owner-chemistry@ccl.net Mon Aug 14 18:32:01 2006 From: "Tudor Oprea Toprea###salud.unm.edu" To: CCL Subject: CCL: unique opportunity - 20% discount for the EuroQSAR 2006 Message-Id: <-32390-060814154949-5389-D5Xbr2dKxWzVT9JZE8IaRg++server.ccl.net> X-Original-From: "Tudor Oprea" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Mon, 14 Aug 2006 13:07:13 -0600 Mime-Version: 1.0 Sent to CCL by: "Tudor Oprea" [Toprea() salud.unm.edu] ** High Priority ** Hi Everyone. As Chair of the QSAR and Modeling Society (www.qsar.org), I was asked to render assistance to the organizers of the EuroQSAR 2006. As some of you know, it is on a Cruise ship across the Mediterranean. http://www.euro-qsar2006.org/ The OPPORTUNITY that you all have is the following: register before close-of-business on August 19 on this website http://www.euro-qsar2006.org/application.php and pay until August 25, 2006 and receive a 20% discount on the ENTIRE congress package, which incldues the conference and accomodation fees. http://www.euro-qsar2006.org/costs.php Do not miss this unique opportunity to enjoy the beautiful Mediterranean, a relaxed atmosphere to discuss science and be a tourist (we stop in 5 different cities on 2 continents) This can be a most memorable event. Consider it, and apply today. Note that this offer is valid until August 19, 5 pm MST (you need to register by then). With thanks on behalf of the QSAR Society and the Organizing Committee, Tudor I. Oprea, MD PhD Professor and Chief, Division of Biocomputing Department of Biochemistry and Molecular Biology MSC11 6145 University of New Mexico School of Medicine Albuquerque, NM 87131, USA Vox: (505) 272-3694 Fax: (505) 272-0238 Email: toprea-x-salud.unm.edu Chair, QSAR and Modeling Society, http://www.qsar.org Division Website: http://hsc.unm.edu/som/biocomputing/ Company Website: http://www.sunsetmolecular.com Address for Rapid Delivery Services: Research Incubator Building--Suite 190 2703 Frontier NE Albuquerque, NM 87131-0001 Editor, "Chemoinformatics in Drug Discovery". ISBN: 3-527-30753-2. Available now from Wiley-VCH