From chemistry-request@server.ccl.net Thu Mar 13 08:53:49 2003 Received: from typhoeus.chem.york.ac.uk ([144.32.72.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2DDrn507737 for ; Thu, 13 Mar 2003 08:53:49 -0500 Received: from ysbl.york.ac.uk (rasher [144.32.20.17]) by typhoeus.chem.york.ac.uk (8.12.8/8.12.8) with ESMTP id h2DDrkxZ029253 for ; Thu, 13 Mar 2003 13:53:47 GMT Sender: greaves@typhoeus.chem.york.ac.uk Message-ID: <3E708D6A.FDD84C09@ysbl.york.ac.uk> Date: Thu, 13 Mar 2003 13:53:46 +0000 From: Richard Greaves Reply-To: greaves@ysbl.york.ac.uk Organization: York Structural Biology Laboratory X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Using PCM for single point SCF on larger systems Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I'm trying run single point SCF calculations on an atomic systems of between 70 and 100 atoms. Has anyone out there got experience of using PCM on large systems? What dimensions are optimal in GAMESS for such runs - i.e. what should I set MXSP and MXTS to? Richard Greaves, University of York, UK. From chemistry-request@server.ccl.net Thu Mar 13 19:54:13 2003 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2E0sC527863 for ; Thu, 13 Mar 2003 19:54:12 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout4.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2E0s1Lv006692 for ; Thu, 13 Mar 2003 16:54:02 -0800 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2E0s1wa001247 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 13 Mar 2003 16:54:01 -0800 Message-ID: <3E71283C.1010402@u.washington.edu> Date: Thu, 13 Mar 2003 16:54:20 -0800 From: Carsten Detering Organization: University of Washington User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: LUDI for RNA Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi everybody, I would like to know if someone has tried to use LUDI with other molecules than proteins, and if that works at all. Thanks for helpful comments, Carsten -- ~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665 ~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Mar 12 15:58:57 2003 Received: from alchemy.chem.utoronto.ca ([142.150.224.224]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2CKwv503664 for ; Wed, 12 Mar 2003 15:58:57 -0500 Received: from chem.utoronto.ca (zigoto [142.150.226.11]) by alchemy.chem.utoronto.ca (8.11.6/8.11.6) with ESMTP id h2CKwqF28956 for ; Wed, 12 Mar 2003 15:58:52 -0500 Message-ID: <3E6F9F8C.4000600@chem.utoronto.ca> Date: Wed, 12 Mar 2003 15:58:52 -0500 From: Jeremy Schofield Reply-To: jmschofi@chem.utoronto.ca Organization: Department of Chemistry, University of Toronto User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: Canadian Computational Chemistry Conf Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit First Announcement and Call for Abstracts 5th Canadian Computational Chemistry Conference (CCCC5) http://www.chem.utoronto.ca/symposium/cccc5/ We are pleased to announce that the 5th annual Canadian Computational Chemistry Conference will be held in Toronto, Canada on July 27-30, 2003. The meeting is intended to foster the excellence of computational chemistry in Canada. One of the principal goals of the conference is to highlight the impact of computational chemistry in academia, industry and society. As in the previous incarnations of this meeting, a program covering major new directions in research and applications of the computational discipline has been put together, with a special emphasis on computational chemistry applied to biophysics and material science. For this purpose, we have prepared a program of speakers actively involved in developing new methods and applications of high performance computing in chemistry and related areas. The meeting will be held on the campus of the University of Toronto, with inexpensive rooms available on campus and in nearby hotels at special rates. Toronto is an exciting, diverse city with many attractions, ranging from excellent museums to fine dining. Since Toronto is the largest urban centre in Canada, travel to and from the city is easy and relatively inexpensive. The costs of the meeting are modest (all figures in Canadian dollars): Students/Post-docs: $100 (early) - $130 (after June 1) All others: $300 (early) - $330 (after June 1) Included in the prices above are registration, Banquet and Reception. This edition of the conference targets a number of areas in which computational chemistry has a large impact, including applications in material science, computational studies of rough energy landscapes, soluble and membrane proteins, advances in structure-based drug design, self-assembly, membranes, and transport, in-silico adme/tox in drug discovery, and the development of new methods in quantum chemistry. A number of outstanding researchers have been invited for the fifth edition of this meeting, including: Tucker Carrington (UdeM) Emily Carter (UCLA) Gerbrand Ceder (MIT) G.M. Crippen (Michigan) Gabriel Cruciani (ADME Perugia) Julian Gale (Imperial College of Science, Technology and Medicine) Angel Garcia (LANL) Shekhar Garde (Rensselaer) Phillip Geissler (MIT) P. Grutenhuis (Deltagen) Hannes Jonsson (Iceland) Leslie Kuhn (Michigan State) Glen Martyna (Indiana) Andrew McCammon (UCSD) Gilles Peslherbe (Concordia) Enrico Purísima (BRI Montréal) D. Reichman (Harvard) Pierre-Nicolas Roy (Alberta) Klaus Schulten (UIUC) Michiel Sprik (Cambridge University) Peter Tieleman (Calgary) Each session of the meeting will consist of a combination of a number of invited lectures complemented by several oral presentations selected from submitted abstracts. In addition, an important component of the conference will be two poster sessions covering all aspects of computational chemistry. Abstracts from all sectors including industry, academia and government are welcome. We strongly encourage you and any interested colleague to visit the conference web page, submit an abstract, and attend this informal, "Gordon Conference" style meeting. For submission of poster abstracts please go to our website (http://www.chem.utoronto.ca/symposium/cccc5/) and follow the instructions for electronic submission. We hope to see you there! The Organizing Committee: -------------------------------------------------- Jeremy Schofield, Department of Chemistry, University of Toronto http://www.chem.utoronto.ca/staff/JMS/schofield_j.html John S. Tse, Steacie Institute for Molecular Science, National Research Council of Canada http://www.sims.nrc.ca/sims/theory_e.html Sanjay Srivastava, Chemistry Department, AstraZeneca R&D Montreal http://www.astrazeneca-montreal.com Régis Pomès, Structural Biology & Biochemistry, Hospital for Sick Children, Toronto http://www.sickkids.on.ca/research/custom/profiles/p From chemistry-request@server.ccl.net Thu Mar 13 12:42:43 2003 Received: from mail.cm.utexas.edu ([146.6.135.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2DHgh516319 for ; Thu, 13 Mar 2003 12:42:43 -0500 Received: from 127.0.0.1 (localhost [127.0.0.1]) by dummy.domain.name (Postfix) with SMTP id 2C59E1A75C for ; Thu, 13 Mar 2003 11:42:43 -0600 (CST) Received: from mail.cm.utexas.edu (localhost [127.0.0.1]) by mail.cm.utexas.edu (Postfix) with SMTP id EF6881A6DB for ; Thu, 13 Mar 2003 11:42:42 -0600 (CST) Received: from 146.6.144.166 (SquirrelMail authenticated user smwilliams) by mail.cm.utexas.edu with HTTP; Thu, 13 Mar 2003 11:42:42 -0600 (CST) Message-ID: <4979.146.6.144.166.1047577362.squirrel@mail.cm.utexas.edu> Date: Thu, 13 Mar 2003 11:42:42 -0600 (CST) Subject: Ab inito/DFT calculations on non-unity multiplicity metal complexes From: "Sheldon M. Williams" To: X-Priority: 3 Importance: Normal Reply-To: smwilliams@mail.cm.utexas.edu X-Mailer: SquirrelMail (version 1.2.10) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2DHgh516320 Hello, I have been having problems with SCF convergence and running out of memory trying to perform ab inito geometry optimization calculations on Cu(II) and Fe(III) ion complexes with crown ethers. I run MMFF conformational searches with the ion constrained near the center of the crown ether ring to get close to the global minimum, as I get poor configurations with low level calculations if I do not contrain these metal ions. I then do a PM3 geometry optimization, if possible. After this I have attempted both ROHF/ and UOHF/3-21G*, 6-31G*, and LACVP* geometry optimizations with SCF cycles set to up to 5000, but the calculation always runs out of memory. I'm performing the calculations with Spartan PC 2002 on a 2.0GHz P4 with 1.0GB of SDRAM. Trying to perform a DFT calculation directly from the MMFF or semi-emperical geometry has worse SCF convergence and memory problems. It appears to be a problem of the multiplicities of these complexes as Ag(I) and Cu(I) work. Almost all papers on ab initio or DFT calculations on transition metal-ligand complexes use the oxidation state with singlet multiplicity. I haven't gotten any useful info from support at wavefunction. I would be grateful if you could suggest what the problem might be or direct me somewhere I could find help? Thank you for your time and attention, Sheldon M. Williams Ph.D. Candidate, Analytical Chemistry Jennifer Brodbelt Lab Chem & Biochem Department 1 University Station A5300 University of Texas at Austin Austin, TX 78712 Phone:(512)471-0041 FAX: (512)471-8696 E-mail: smwilliams@mail.cm.utexas.edu From chemistry-request@server.ccl.net Thu Mar 13 18:43:01 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2DNh1526052 for ; Thu, 13 Mar 2003 18:43:01 -0500 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.12.8/8.12.8) with ESMTP id h2DNgoDt187892; Thu, 13 Mar 2003 15:42:56 -0800 Date: Thu, 13 Mar 2003 15:42:50 -0800 (PST) From: Roy Jensen To: chemistry@ccl.net Subject: O2(a-X) splitting In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) All I was looking at the splitting between the a-1-delta and X-3-sigma states of oxygen using the UQCISD/6-311++G(d,p) level of theory. The calculated singlet-triplet spacing is 47 % higher than the experimentally observed value (11618 vs 7918 cm-1, respectively). I am sure there is a ready explanation for this; however, I am drawing a blank...any insights would be greatly appreciated! Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------ From chemistry-request@server.ccl.net Thu Mar 13 22:02:40 2003 Received: from sina.com ([202.106.187.156]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2E32a530494 for ; Thu, 13 Mar 2003 22:02:37 -0500 Message-Id: <200303140302.h2E32a530494@server.ccl.net> Received: (qmail 42356 invoked from network); 14 Mar 2003 02:46:26 -0000 Received: from unknown (HELO njuitccwx) (202.119.32.27) by 202.106.187.156 with SMTP; 14 Mar 2003 02:46:26 -0000 Date: Fri, 14 Mar 2003 10:56:59 +0800 From: wxin To: "chemistry@ccl.net" Subject: symmetry in G98 X-mailer: FoxMail 3.11 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCL-lister, When I use Gaussian98 to do CASSCF calculation I found that the program can not identify the symmetry of some orbitals. Does anyone can give me some advice on this problem? Thank you. Xin Wang Institute of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Nanjing University Nanjing, 210093 P. R. China