From owner-chemistry@ccl.net Fri Aug 11 05:49:00 2006 From: "Jamie Platts platts|*|Cardiff.ac.uk" To: CCL Subject: CCL: pi interactions with functionals Message-Id: <-32369-060811051607-14806-81XUKCxNuLdgEzeRjkEwSw- -server.ccl.net> X-Original-From: "Jamie Platts" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 11 Aug 2006 09:22:19 +0100 Mime-Version: 1.0 Sent to CCL by: "Jamie Platts" [platts_+_Cardiff.ac.uk] Dear Rachel There have been a number of studies using DFT for pi-pi interactions recently. An early paper by Meijer and Sprik showed the local density approx (LDA) works surprisingly well for the benzene dimer: Meijer, E. J.; Sprik, M. J Chem Phys 1996, 105, 8684. Goddard et al suggested their X3LYP functional should work (Xu, X.; Goddard, W. A. Proc Natl Acad Sci USA 2004, 101, 2673) but Cerny and Hobza found it to fail for stacked DNA bases (Cerny, J.; Hobza, P. Phys Chem Chem Phys 2005, 7, 1624). Perez-Jorda (Perez*Jorda, J. M.; San-Fabian, E.; Perez*Jimenez, A. J. J Chem Phys 1999, 110, 1916) and Walsh (Walsh, T. R. Phys Chem Chem Phys 2005, 7, 443) have found Hartree*Fock plus Wilson*Levy correlation functional to work well. We showed that Becke's "half-and-half" functional works well for some model systems (M.P. Waller et al, J Comput Chem 27: 491*504, 2006), and have since used it to study some DNA oligomers (A. Robertazzi and J.A. Platts, J Phys Chem A, 2006 110, 3992) and complexes with cisplatin (A. Robertazzi and J.A. Platts, Chem. Eur. J., 2006, 12, 5747). Finally (that I'm aware of) Truhlar's group have proposed several functionals that work well for pi-stacking, hydrogen bonding, and metal-ligand bonding (Y. Zhao, N.E. Schultz, and D.G. Truhlar, J. Chem. Theory Comput. 2006, 2, 364 and Y. Zhao, N.E. Schultz, and D.G. Truhlar, J Chem Phys, 2005, 123, 161103). I'm sure there are others that I have missed, but hope this helps! Best regards, Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts{:}cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy >>> owner-chemistry{:}ccl.net 08/10/06 6:34 pm >>> Sent to CCL by: Rachel Crespo Otero [rachel-*-fq.uh.cu] Hello CCL members, I want to know about any density funcional that treat correctly pi interactions. I would appreciate some references. Best regards, Rachelhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Aug 11 10:39:00 2006 From: "Kumar Prashant prashantkbio##gmail.com" To: CCL Subject: CCL: RNA Modelling Message-Id: <-32370-060811060100-22506-ylS4OCx1pC8Po79X9csxag/./server.ccl.net> X-Original-From: "Kumar Prashant" Date: Fri, 11 Aug 2006 06:00:59 -0400 Sent to CCL by: "Kumar Prashant" [prashantkbio[*]gmail.com] Dear CCL members, I have some problem with the RNA structure prediction . First for the 2D structure prediction I tried Mfold and Kfold and the result from the both of them are different , I am in dielema which one is correct. And second I couldn't find any software which do some 3D modelling of RNA seq. Well Just before few days I started this work from my own interest . So please send me some suggestion regarding my this interest Prashant kumar From owner-chemistry@ccl.net Fri Aug 11 11:14:00 2006 From: "Atilio Anzellotti aanzellotti]^[vcu.edu" To: CCL Subject: CCL: volume calculation Message-Id: <-32371-060811092953-903-YEkwq8kAyWsiojjstlR87A^^^server.ccl.net> X-Original-From: "Atilio Anzellotti" Date: Fri, 11 Aug 2006 09:29:52 -0400 Sent to CCL by: "Atilio Anzellotti" [aanzellotti-.-vcu.edu] Dear Sir(s), I would like to know of any program that can easily calculate the volume of a molecule. Many Thanks. Atilio. From owner-chemistry@ccl.net Fri Aug 11 12:12:00 2006 From: "Michel Petitjean ptitjean|itodys.jussieu.fr" To: CCL Subject: CCL: volume calculation Message-Id: <-32372-060811120933-14901-gOj10RHV9tZ2TWi9MXu0wA _ server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 11 Aug 2006 18:09:24 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean++itodys.jussieu.fr] To: chemistry|ccl.net Subject: CCL: Re: volume calculation Sent to CCL by: "Atilio Anzellotti" [aanzellotti-.-vcu.edu] > Dear Sir(s), > > I would like to know of any program that can easily calculate the volume of a molecule. > > Many Thanks. > > Atilio. ASV does that (free): http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Michel Petitjean, Email: petitjean|itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean|ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html From owner-chemistry@ccl.net Fri Aug 11 13:28:00 2006 From: "Igor Filippov Contr igorf{=}helix.nih.gov" To: CCL Subject: CCL: volume calculation Message-Id: <-32373-060811131809-8752-tPxz/Rzf5XEdC2jGLI5gEw[a]server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 11 Aug 2006 11:51:18 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf(-)helix.nih.gov] You can use Scitegic Pipeline Pilot to calculate that and many other properties. Cheers, Igor On Fri, 2006-08-11 at 11:14 -0400, Atilio Anzellotti aanzellotti]^ [vcu.edu wrote: > Sent to CCL by: "Atilio Anzellotti" [aanzellotti-.-vcu.edu] > Dear Sir(s), > > I would like to know of any program that can easily calculate the volume of a molecule. > > Many Thanks. > > Atilio. From owner-chemistry@ccl.net Fri Aug 11 16:35:00 2006 From: "Negi, Surendra S. ssnegi**utmb.edu" To: CCL Subject: CCL: volume calculation Message-Id: <-32374-060811122411-28749-eKs0HrPPeKh2L1eJ1ZBKBA]~[server.ccl.net> X-Original-From: "Negi, Surendra S." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Fri, 11 Aug 2006 10:36:05 -0500 MIME-Version: 1.0 Sent to CCL by: "Negi, Surendra S." [ssnegi]*[utmb.edu] check this website http://www.csb.yale.edu/userguides/graphics/msp/vol_area.html -----Original Message----- > From: Atilio Anzellotti aanzellotti]^[vcu.edu [mailto:owner-chemistry^^^ccl.net] Sent: Fri 8/11/2006 10:16 AM To: Negi, Surendra S. Cc: Subject: CCL: volume calculation Sent to CCL by: "Atilio Anzellotti" [aanzellotti-.-vcu.edu] Dear Sir(s), I would like to know of any program that can easily calculate the volume of a molecule. Many Thanks. Atilio.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Aug 11 17:10:00 2006 From: "Thomas Steinbrecher thomas.steinbrecher[A]physchem.uni-freiburg.de" To: CCL Subject: CCL: Textbook on Semiempirical QM Message-Id: <-32375-060811135317-30596-9Sgg2X4IGwvJqWm9f7XmDA(_)server.ccl.net> X-Original-From: "Thomas Steinbrecher" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Fri, 11 Aug 2006 18:49:08 +0200 MIME-Version: 1.0 Sent to CCL by: "Thomas Steinbrecher" [thomas.steinbrecher]|[physchem.uni-freiburg.de] Dear CCLers, this question has likely been asked before and I assume there is no single 'good' answer. Nevertheless I would be happy to hear your suggestions for a textbook that describes semi-empirical quantum chemistry methods well. The level of treatment should be on the advanced grad student/PostDoc level and go into detail of the methods themselves with references to some applications. I know all of this information can be found in research papers, but these are often presented in a very concise manner, so I hope there is a more exhaustive in-detail treatment of the subject matter out there. Kind Regards, Thomas Dr. Thomas Steinbrecher Institut für physikalische Chemie Albertstr. 23a 79108 Freiburg From owner-chemistry@ccl.net Fri Aug 11 17:44:00 2006 From: "Elaine Meng meng__cgl.ucsf.edu" To: CCL Subject: CCL: volume calculation Message-Id: <-32376-060811172853-9110-IyYvZceRebjWImuKK6BqgQ=-=server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 11 Aug 2006 17:28:52 -0400 Sent to CCL by: "Elaine Meng" [meng^-^cgl.ucsf.edu] You can calculate the volume enclosed in a molecular surface with Chimera. Show the surface on your structure (Actions... Surface... show) and then use the Measure Volume tool (Tools... Volume Data... Measure Volume) on that surface. This surface is the molecular surface by the Richards definition (the solvent-excluded surface), not the solvent-accessible surface. If you want to get fancy, the probe size, vertex density, etc. are adjustable. Chimera home page: http://www.cgl.ucsf.edu/chimera/index.html man page for Measure Volume tool: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html Hope this helps, Elaine ---- Elaine C. Meng, Ph.D. meng,+,cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Fri Aug 11 22:48:01 2006 From: "Bingxing Wang wangbx,dicp.ac.cn" To: CCL Subject: CCL:G: about pmp2 method Message-Id: <-32377-060811111800-6137-YViMCDtad6ODvhgJynbLOQ%%server.ccl.net> X-Original-From: "Bingxing Wang" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Fri, 11 Aug 2006 22:35:17 +0800 Mime-Version: 1.0 Sent to CCL by: "Bingxing Wang" [wangbx[#]dicp.ac.cn] Dear cclers: in some articles, there is a method named pmp2 or pmp3. in order to find what it is, i really get the amost original paper. but i still don't know how to calculate with this method in G03. who can tell me how to do it in detail? please give an example. thank you. With best regards, Sincerely yours, Bingxing Wang 2006-08-11