From owner-chemistry@ccl.net Thu Jun 21 01:26:00 2007 From: "Jon Lyon jtl3z .. virginia.edu" To: CCL Subject: CCL: values Message-Id: <-34534-070620214707-17663-VnuubneqKp0u71cLiWQJbA%a%server.ccl.net> X-Original-From: "Jon Lyon" Date: Wed, 20 Jun 2007 21:47:04 -0400 Sent to CCL by: "Jon Lyon" [jtl3z{=}virginia.edu] I have a quick question about computed numbers. I had heard or read at one point that if the computed value was more that 10% off from s(s+1) that a higher level calculation may be necessary. Can anyone confirm (reference)? Also, is this before of after annihilation. Can anyone explain to me the annihilation process? I am doing DFT calculations on metal complexes (which I know can be difficult to produce accurate results sometimes). Many thanks, Jon From owner-chemistry@ccl.net Thu Jun 21 04:41:00 2007 From: "Barbara Jagoda-Cwiklik barbara.cwiklik!=!uochb.cas.cz" To: CCL Subject: CCL: values Message-Id: <-34535-070621043759-5232-cGGj1xLM/NMeE68txuzLNg-x-server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 21 Jun 2007 10:37:50 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik+/-uochb.cas.cz] > Sent to CCL by: "Jon Lyon" [jtl3z{=}virginia.edu] > I have a quick question about computed numbers. I had heard or read > at one point that if the computed value was more that 10% off from s(s+1) that a higher level calculation may be necessary. Can anyone confirm (reference)? Also, is this before of after annihilation. Can anyone explain to me the annihilation process? I am doing DFT > calculations on metal complexes (which I know can be difficult to produce > accurate results sometimes). > > Many thanks, > Jon Hi Jon, For instance, one of the references is David C. Young "Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems". On page 227, you will find: "one rule of thumb, which was derived from the experience with organic molecule calculations, is that the spin contamination is negligible if..." (btw, I'd say that before annihilation) BUT the beginning of the sentence is definitely a kind of essential, I mean, it's only a rule. Another thing is that DFT suffers less from spin contamination than e.g. UMPn. And the paper on spin anihilation: J.J.W. McDouall and H.B. Schlegel, J. Chem. Phys. 90 (1989) 2363 Best regards, Basia -- Barbara Jagoda-Cwiklik, Ph.D Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Prague, Czech Republic e-mail: barbara.cwiklik~!~uochb.cas.cz From owner-chemistry@ccl.net Thu Jun 21 09:00:01 2007 From: "Matteo Masetti matteo : scfarm.unibo.it" To: CCL Subject: CCL:G: electrostatic potential sampling Message-Id: <-34536-070621084924-3571-d3jRwebDKMPwr3DYJMgDWQ!A!server.ccl.net> X-Original-From: "Matteo Masetti" Date: Thu, 21 Jun 2007 08:49:20 -0400 Sent to CCL by: "Matteo Masetti" [matteo=scfarm.unibo.it] Dear ccl users, a very basic question here. I've sampled the electrostatic potential for a molecule having a net charge of +1 by using the cubegen utility of the g03 suite. I'm a little bit confused to notice that no grid point sampled a negative potential. I can realize that the potential for a monopole decays more slowly with respect to that of higher order multipoles, nevertheless for me is quite surprising that it is able to overcome the local negative charge density, say, close to lone pairs. This is because cubegen also samples "inside" the molecule. Anyway if I compute for instance resp charges, according to the Merz-Sing-Kollmann sampling scheme (that is "outside" the molecule, but again no negative potential sampled), I get negative partial charges too (as i would expect, but... why?). Yes, I'm very confused, but I'm not able to match the two points. Any suggestions? Thanks a lot. From owner-chemistry@ccl.net Thu Jun 21 11:49:00 2007 From: "Barry Hardy barry.hardy*o*vtxmail.ch" To: CCL Subject: CCL: eCheminfo Autumn Meeting Program available Message-Id: <-34537-070621073234-23601-Dz/DSR6zbs1p1wuH+j+Abw ~ server.ccl.net> X-Original-From: "Barry Hardy" Date: Thu, 21 Jun 2007 07:32:31 -0400 Sent to CCL by: "Barry Hardy" [barry.hardy:-:vtxmail.ch] Schedule, Abstracts and Biographies for the eCheminfo Autumn Community of Practice meeting program at Bryn Mawr College, Philadelphia in October on "Latest Advances in Drug Discovery & Development" are now available through the eCheminfo website: http://echeminfo.colayer.net/COMTY_conferencesprog07 The meeting brochure may also be downloaded as a pdf: http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr07-web1.PDF Sponsors I would like to express our gratitude to the invaluable support of our Sponsors Merck Research Laboratories, Schering-Plough Research Institute, Johnson & Johnson PR&D, the Cambridge Crystallographic Data Centre (CCDC), SimBioSys and Tripos. Poster Session We will be running poster sessions in the evenings at the meeting with themes: knowledge management (Tuesday), drug design (Wednesday) and drug development and ADMET (Thursday). This option is available to all meeting attendees and we will include all approved abstracts received by 31 August on the formal program. Please send your abstract and biography of ca. 300-500 words each to eCheminfo (!-at-!) douglasconnect.com for approval. Invited Speakers: Stephen Burley (SGX Pharmaceuticals), Georgia McGaughey (Merck), Charles Lesburg (Schering-Plough), Rick Beger (FDA), Marc Nicklaus (NIH), Woody Sherman (Schrodinger), Daniel Cheney (Bristol Myers Squibb), Paul Labute (Chemical Computing Group), Ajay Jain (UCSF), Alan Cheng (Amgen), Tony Hopfinger (University of New Mexico), Anthony Klon (Pharmacopeia Drug Discovery), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer),Chaohong Sun (Abbott), Xavier Barril (University of Barcelona), Jose Duca(Schering-Plough), Terry Stouch (Lexicon Pharmaceuticals), Natasja Brooijmans(Wyeth), Gerard Kleywegt (University of Uppsala), Vladimir Poroikov (Russian Academy of Sciences), Christoph Helma (in silico toxicology), Ann Richard(EPA), Judy Madden (Liverpool John Moores University), Julian Tirado-Rives(Yale), Heather Carlson (University of Michigan), Joseph Tomaszewski (NCI), To: CCL Subject: CCL: The PDBbind database version 2007 is now released Message-Id: <-34538-070621143221-10026-wqbBvo1KvyyKDN6vxFYqyQ a server.ccl.net> X-Original-From: "Xueliang Fang" Date: Thu, 21 Jun 2007 14:32:17 -0400 Sent to CCL by: "Xueliang Fang" [xueliang]-[umich.edu] Dear researchers, Here we announce the release of the PDBbind database version 2007. The PDBbind database is created to provide a collection of binding affinity data exclusively for protein-ligand complexes in the Protein Data Bank. This version contains binding affinity data (Kd, Ki, & IC50) for over 3,100 protein-ligand complexes, which is the largest collection of this kind in the world. The PDBbind database is publicly accessible at http://www.pdbbind.org/. Registered users may browse, analyze or even download binding data on this web site. Other researchers are welcome to explore this web site through a demo account. Best regards, Xueliang Fang xueliang|,|umich.edu