From chemistry-request@ccl.net Thu Jul 3 13:04:22 2003 Received: from web15213.mail.bjs.yahoo.com (web15213.mail.bjs.yahoo.com [202.3.77.143]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h63Gqwqe006033 for ; Thu, 3 Jul 2003 12:53:02 -0400 Message-ID: <20030703164342.10007.qmail.-at-.web15213.mail.bjs.yahoo.com> Received: from [168.160.11.10] by web15213.mail.bjs.yahoo.com via HTTP; Fri, 04 Jul 2003 00:43:42 CST Date: Fri, 4 Jul 2003 00:43:42 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: About Parabolic fields in CoMFA To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I don't find what I need in the manual of QSAR about the parabolic fields. Anyone here could tell how to set the parameters, e.g., cutoff values, etc., for parabolic fields. Another questions, if it's reasonable to combine the parabolic fields of CoMFA with the hydrophobic of CoMSIA in one PLS analysis? I mean, if it's possible to derive one QSAR model using two 3D-QSAR methods, i.e., CoMFA and CoMSIA? Any comments and suggestions will be very welcome! Thanks in advance! Regards, Jinsong _________________________________________________________ Do You Yahoo!? 9zDZ5gSJSC;'74@,;x5w2i@-?*a!D; http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.tech.yahoo.com/zhuanti/laji/index.html From chemistry-request@ccl.net Thu Jul 3 09:32:51 2003 Received: from mail.cybermesa.com (mail.cybermesa.com [198.59.109.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h63DWoqe030882 for ; Thu, 3 Jul 2003 09:32:51 -0400 Received: from dave (qwest98-dsl3.cybermesa.com [216.84.163.98]) by mail.cybermesa.com (8.11.6/8.11.6) with SMTP id h63DWnH24646 for ; Thu, 3 Jul 2003 07:32:49 -0600 (MDT) From: "David Miller" To: Subject: CCL: extended queries in ChemTK Date: Thu, 3 Jul 2003 07:33:59 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 ChemTK version 2.5 evaluation is now available for download > from http://www.chemtk.com New features include: - Logical expression shorthand, allowing queries such as: cLogP < 2.0 && Target != "kinase" MolWeight <= 500 && ( slq c1ccccc1 || slq n1ccccc1 ) - Filter new (unseen) molecule data into existing scaffold classes - R tables can be stored persistently in ChemTK (*.ctk) files - Export of similarity-screening results to ChemTK or text files - Columns can be added to, and deleted from, the Class View grid Visit http://www.chemtk.com to download the ChemTK product sheet, documentation, and release notes, and to learn more about the inexpensive licensing terms. Best regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller.-at-.sageinformatics.com From chemistry-request@ccl.net Thu Jul 3 06:58:25 2003 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h63AwPqe027720 for ; Thu, 3 Jul 2003 06:58:25 -0400 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Thu, 3 Jul 2003 11:58:24 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.7+Sun/8.9.3) id h63AwND19813; Thu, 3 Jul 2003 11:58:23 +0100 (BST) Message-Id: <200307031058.h63AwND19813.-at-.socrates-a.ucl.ac.uk> Subject: CCL:re DFT and small basis sets To: chemistry.-at-.ccl.net (CCL) Date: Thu, 3 Jul 2003 11:58:23 +0100 (BST) Cc: T.vanMourik.-at-.ucl.ac.uk (Tanja van Mourik) In-Reply-To: <3F02ECDD.D642E01A.-at-.trentu.ca> from "elewars" at Jul 02, 2003 10:31:57 AM From: Tanja van Mourik X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All, Lynch, Zhao and Truhlar advocate including diffuse functions on non-hydrogenic atoms when calculating reaction energies, barrier heights and conformational energies with DFT, see: J Phys Chem A 107 (9): 1384-1388 (2003). So I would recommend using 6-31+G* rather than 6-31G* as the smallest basis set for yielding accurate results. Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik.-at-.ucl.ac.uk London WC1H 0AJ, UK home: tanja_van_mourik.-at-.btopenworld.com http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== > > Re "Has anyone ever published a discussion of the accuracy of DFT at > small basis sets?" > > I'm not sure just what you consider small (most workers now would likely > say that > 6-31G* is small), but DFT calculations are known to be saturated by > basis > functions more quickly than are ab initio calculations. Here are three > refs: > > 1) "Once the double split-valence level is reached, further improvement > in basis > set quality offers little in the way of structutal or energetic > improvement." G. > N. Merrill, S. Gronert, and S. R. Kass. J Phys Chem, 1997, _101_, 204. > > 2) "Our results also show that B3LYP calculations converge rapidly with > > increasing basis set size and that the cost-to-benefit- ratio is optimal > at the > 6-31G* basis set level. 6-31G* will be the basis set of choice in B3LYP > calculations on much larger molecules [than C4H6O2]." P. J. Stephens, F. > J. > Devlin, C. F. Chablowski, and M. J. Frisch, J Phys Chem, 1994, _98_, > 11623, and > refs therein. > > 3) In defiance of tradition, the unequivocally small 3-21G(*) set has > been used > to optimize carbene geometries: H. M. Muchall, N. H. Werstiuk, and B. > Chodhurry, > Can J Chem, 1998, _76_, 221. > > (You my also find some useful info in E. Lewars, "Computational > Chemistry", > Kluwer, 2003; section 7.3.2.2). > > E. Lewars > ======== > > Ed Brothers wrote: > > > Folks: > > Has anyone ever published a discussion of the accuracy of DFT at > > small basis sets? > > > > Ed. > > Merz group. > > Penn State. > > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY.-at-.ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >