From chemistry-request@server.ccl.net Wed Feb 12 04:11:16 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1C9BGx18659 for ; Wed, 12 Feb 2003 04:11:16 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 6F9DA88CABE; Wed, 12 Feb 2003 10:11:00 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 9411B88CAB7; Wed, 12 Feb 2003 10:10:58 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 12 Feb 03 10:10:58 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 12 Feb 03 10:10:49 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Deng, Jun" Date: Wed, 12 Feb 2003 10:10:36 +0100 Subject: CCL: orientation axis Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net, ewt@virgil.ruc.dk X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: X-Spam-Status: No, hits=-0.1 required=5.0 tests=DEAR_SOMEBODY,NOSPAM_INC,QUOTED_EMAIL_TEXT, SPAM_PHRASE_00_01 version=2.43 Jun Deng: > May I ask your opinion on calculating and displaying orientation > axis (or long axis??) given a molecule? Dear Jun Deng, you will find a discussion of orientation axes and molecular shape in the volume by Michl and Thulstrup: Josef Michl & Erik W. Thulstrup: "Spectroscopy With Polarized Light. Solute Alignment by Photoselection, in Liquid Crystals, Polymers, and Membranes", VCH Publishers, Inc., 1986 (ISBN 0-89573-346-3), 1995 (ISBN 1-56081-910-3). Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Feb 12 01:47:40 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1C6lex14963 for ; Wed, 12 Feb 2003 01:47:40 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h1C6ldj16272; Wed, 12 Feb 2003 01:47:39 -0500 (EST) Date: Wed, 12 Feb 2003 01:47:39 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net, mel@asdn.net cc: Jan Labanowski Subject: SELF-FORMATION THEORY and APPLICATION, Vilnus, Lithuania, Nov, 2003 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sixth International Conference and Exhibition SELF-FORMATION THEORY and APPLICATION Vilnius, Lithuania 26 - 28 November 2003 SCOPE Conference continues the series of Vilnius conferences on self-formation with international participation held every second year since 1983 with the last one held in 1992. It is expected to be the first conference on self-formation with European dimension. Self-formation concept covers an irreversible evolution of the artificial object followed by object complexity increasing. Although self-formation encompasses mathematical methods for the artificial object evolution approximation it also offers attractive technological possibilities in the microelectronics, photovoltaics and other semiconductor applications. Self-formation, predominating in living world, however still has little use in technological world for artificial objects formation processes without human or automatics intervention. Therefore Conference is designed to bring together fundamental and application driving research to open novel promising self-formation applications areas and generate critical mass of research resources to foster scientific excellence in the field. Present Conference foresees to cover following topics: . Self-formation of the artificial systems . Self-assembling of the artificial systems . Simulation of self-formation . Evolution with complexity increasing (self-organisation, synergetics, information, self-formation, genetics, etc) . Self-formation physics . Self-formation technology (photovoltaics, fuel cells) . Other applications (microelectronics, nanotechnology, molecular electronics, etc.) ORGANIZER Institute of Lithuanian Scientific Society. PROGRAMME COMMITTEE Prof. Ioannis Antoniou International Solvay Institutes, Belgium Habil. Dr. Antanas Cenys Semiconductors Physics Institute, Lithuania Dr. Vladas Algis Gapsys Confederation of Lithuanian Industrialists, Lithuania Prof. Hermann Haken Center of Synergetics, University of Stuttgart, Germany Habil. Dr. Stepas Janusonis Institute of Lithuanian Scientific Society, Lithuania Prof. Gregoire Nicolis Universite Libre de Bruxelles, Belgium Acad. Juras Pozela Semiconductors Physics Institute, Lithuania Prof. Laimutis Telksnys Institute of Mathematics and Informatics, Lithuania Dr. Juras Ulbikas Institute of Lithuanian Scientific Society, Lithuania VENUE The Conference will be held in Vilnius, the historical capital of Lithuania, founded in 1323. The city make boasts of the Old Town, which is an urban district of tremendous cultural and historic value from a national as well as an international point of view. Since 1994 the Old Town is on the UNESCO World Heritage list ( http://www.vilnius.lt ). PRE-REGISTRATION Intention to participate in the Conference or Exhibition could be made on-line or by request to organizers. On-line pre-registration is preferred. Registered persons will receive all news concerning Conference and in addition information about web site's updates. ABSTRACTS SUBMISSION: Please visit Conference home page for submission details and requirements for abstracts preparation. IMPORTANT DATES Deadline for pre-registration: 1 April Deadline for abstracts submission: 15 May Acceptance for abstracts: 15 June Call for papers: 1 July ADDRESS FOR CORRESPONDENCE Daiva Ulbikiene Institute of Lithuanian Scientific Society A.Gostauto 11 LT-2600 Vilnius Lithuania Telephone: (+370 5) 2617902 Fax: +370 5 2313762 E-mail: du@uj.pfi.lt WWW: http://www.self-formation.lt/ From chemistry-request@server.ccl.net Wed Feb 12 05:39:24 2003 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1CAdNx31816 for ; Wed, 12 Feb 2003 05:39:24 -0500 Received: from [10.4.21.43] (helo=uni-koeln.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 18iuIT-0000Og-00; Wed, 12 Feb 2003 11:39:22 +0100 Message-ID: <3E4A2434.201@uni-koeln.de> Date: Wed, 12 Feb 2003 11:38:44 +0100 From: Christoph Steinbeck Reply-To: c.steinbeck@uni-koeln.de User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.2.1) Gecko/20021130 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Robert Sbaglia CC: chemistry@ccl.net Subject: Re: CCL:SMILES References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Robert Sbaglia wrote: > Hi, > > Was wondering if anyone had any tips for converting from SMILE format to > mol or mol2 format? Try our open-source java package "The Chemistry Development Kit (CDK)". The software is available from http://cdk.sf.net An article about the software library has just appeared in the ASAP section of the Journal of Chemical Information and Computer Sciences (http://pubs.acs.org/cgi-bin/asap.cgi/jcisd8/asap/pdf/ci025584y.pdf) Note that this is a chemoinformatics toolkit, not a ready-to-use file conversion application (although there is a demo file conversion app included in the tests section). Feel free to contact the developers mailing list cdk-devel@lists.sf.net with questions. Cheers, Christoph Steinbeck -- Dr. Christoph Steinbeck (e-mail: c.steinbeck@uni-koeln.de) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-5092 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Wed Feb 12 12:32:16 2003 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1CHWFx08095 for ; Wed, 12 Feb 2003 12:32:16 -0500 Received: from cornell.edu (sleepy.ccmr.cornell.edu [128.84.241.118]) by cornell.edu (8.9.3/8.9.3) with ESMTP id MAA02170; Wed, 12 Feb 2003 12:32:12 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3E4A851D.DE8C9328@cornell.edu> Date: Wed, 12 Feb 2003 12:32:13 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: Rudolf Herrmann , chemistry@ccl.net Subject: Re: CCL:convergence difficulties with GAMESS and PM3 method References: <3E4979F0.3A496822@cornell.edu> <200302121023.59920.rudolf.herrmann@physik.uni-augsburg.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Dr. Herrmann, Thanks for your suggestion. I implemented it, but I have encountered this error and I'm not sure what it means... Does it mean that GAMESS thinks my starting geometry is way off? It shouldn't be, I got the coordinates from a geometrically minimized starting point from another program/method... Do you have any suggestions as to how this might be corrected or what the problem is? I've inputed my initial coordinates using angstrom which I believe is the default. 35 34 22.430479963 -57.609487787 0.266971893 0.471095519 0.000000000 63.732671095 36 35 -3.262855183 -25.693335147 0.523318316 0.291702183 0.000000000 12.676958150 ---------------START SECOND ORDER SCF--------------- SOSCF IS SCALING ROTATION ANGLE MATRIX, SQCDF= 0.107134 SOSCF IS SCALING ROTATION ANGLE MATRIX, SQCDF= 0.107134 37 36 -66.720923114 -63.458067931 0.497892790 0.137064820 0.000000000 0.000000000 38 37 -71.201788754 -4.480865640 0.456986583 0.069737921 0.000000000 1.000000000 SOSCF ENCOUNTERS A SERIOUS PROBLEM IN -SONEWT- THE ROTATION ANGLE VECTOR HAS A HUGE NORM, SQCDF= 4.531E+00 REEXAMINE STARTING VECTORS, APPROPRIATENESS OF YOUR SCFTYP, ETC... EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Wed Feb 12 11:36:53 2003 4592280 WORDS OF DYNAMIC MEMORY USED STEP CPU TIME = 718.16 TOTAL CPU TIME = 771.9 ( 12.9 MIN) TOTAL WALL CLOCK TIME= 775.2 SECONDS, CPU UTILIZATION IS 99.57% *** ERROR TERMINATION *** IN COMPUTE PROCESS 0 STOP IN ABRT statement executed Thank you for your help. -Connie From chemistry-request@server.ccl.net Wed Feb 12 16:59:02 2003 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1CLx1x15241 for ; Wed, 12 Feb 2003 16:59:01 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.6/8.12.6) with ESMTP id h1CLwrTl014672; Wed, 12 Feb 2003 23:58:53 +0200 (EET) (envelope-from tamulis@mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.6/8.12.6/Submit) with ESMTP id h1CLwo0C014669; Wed, 12 Feb 2003 23:58:50 +0200 (EET) Date: Wed, 12 Feb 2003 23:58:50 +0200 (EET) From: Arvydas Tamulis To: CHEMISTRY@ccl.net cc: Stefano.Bellucci@lnf.infn.it, , , , , , , Subject: 6th Int. conf. "Self-Formation Theory and Application" Message-ID: <20030212234000.F14601-100000@mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I would like to introduce you 6th International conference "Self-Formation Theory and Application", to be hold in Vilnius, Lithuania, 26-28 November, 2003. Conference concerns also Molecular Electronics and Molecular Nano-Technology topics. More details at: http://www.self-formation.lt/ Best regards, Arvydas Tamulis ******************************************************************* Temporal address until 30 April 2003: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: 1 505 667-7278 Fax: 1 505 665-2659 e-mail: tamulis@cnls.lanl.gov *******************************************************************