From chemistry-request@ccl.net Wed Jan 21 18:03:18 2004 Received: from ned.sims.nrc.ca (ned.SIMS.nrc.ca [132.246.109.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0LN3Gnj020364 for ; Wed, 21 Jan 2004 18:03:16 -0500 Received: from ned.sims.nrc.ca (localhost [127.0.0.1]) by ned.sims.nrc.ca (8.12.6/8.12.6/SuSE Linux 0.6) with ESMTP id i0LN4KRK030669; Wed, 21 Jan 2004 18:04:20 -0500 Received: from localhost (ps@localhost) by ned.sims.nrc.ca (8.12.6/8.12.6/Submit) with ESMTP id i0LN4KWL030666; Wed, 21 Jan 2004 18:04:20 -0500 Date: Wed, 21 Jan 2004 18:04:20 -0500 (EST) From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii..at..nrc.ca To: "Dr. Peter Burger" cc: chemistry..at..ccl.net Subject: Re: CCL:Analytical Overlap Integrals In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS - amavis-milter (http://www.amavis.org/) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 21 Jan 2004, Dr. Peter Burger wrote: > Dear CCLers > > I am looking for a reference to analytically solved overlap integrals > of STOs for up to d functions - spherical coordinates were preferred. > > Regards > > Peter > How many do you want? Off the top of my head: CCJ Roothaan JCP 19, 1445 (1951) RS Mulliken, CA Rieke, D. Orloff, H. Orloff, JCP 17, 1248 (1949) RR Sharma, PR A 13, 517 (1976) M McCourt, JW McIver Jr, J. Mol. Struct (Theochem) 163, 343 (1988) JD Talman, PRA 48, 243 (1993) W Hierse, P Oppeneer, JCP 99, 1278 (1993) W Hierse, P Oppeneer, Int J Quant Chem 52, 1249 (1994) ... and this excludes all the approaches published in the last 10 years (there have been several - e.g. by I.I. Guseinov, F.E. Harris, V. Magnasco, M. Yavuz, J. Fernandez-Rico, E.J. Weniger, and H. Safouhi - I am sure I missed a few names, too). These you can easily pick from your favorite literature search engine. For two-centre overlaps, my favorite is 1993 method by JD Talman - it is completely general, numerically very stable (particularly if some of the elementary integrals are taken by the method of H&O-1994), and reasonably fast. The original Talman's paper is for complex spherical harmonics. A slight modification for solid harmonics is described at: http://www.cobalt.chem.ucalgary.ca/ps/thesis/diss-technicals.ps Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii..at..nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From jkl@ccl.net Thu Jan 22 05:03:51 2004 -0500 Return-Path: Message-ID: <400F9FF5.3070704-.at.-zuegge.de> Date: Thu, 22 Jan 2004 10:03:33 +0000 Subject: Workshop: The Chemical Theatre of Biological Systems, May 24-28, Italy From: ccl We would like to inform you of our forthcoming workshop: The Chemical Theatre of Biological Systems May 24th-28th, 2004, Bozen, Italy. www.beilstein-institut.de/events The Beilstein workshops address contemporary issues in the chemical and related sciences by employing an interdisciplinary approach. Scientists > from a wide range of areas often outside chemistry are invited to present aspects of their work for discussion with the aim of not only to advance science, but also, to enhance interdisciplinary communication. One of the most current challenging problems of the natural and life sciences is the understanding and prediction of the biological chemistry of the cell, with particular reference to the role of organic compounds therein. These molecules are the products of highly refined in-vivo and in-vitro organic syntheses; they have complex biological functions making up the systems themselves as well as interacting with and perturbing them. It is our belief that advances can only realistically be achieved in an interdisciplinary environment, where the lines of thought of different scientific cultures are related sufficiently to each other that given the right circumstances, interactions can take place and new developments can follow. By raising the curtain on the Chemical Theatre of Biological Systems and through the performances of players invited from the areas of chemical, biological and information sciences, our aim is that this workshop, supported by the active participation of the audience, will afford new insights into contemporary scientific issues. The workshop will take place in the historic Hotel Schloss Korb. The setting and the limited number of participants (ca. 50-60), provide a very convivial atmosphere for the ready exchange of thoughts and ideas. Please find further general information, the scientific program and the registration form on our web site: http://www.beilstein-institut.de/events Places at the workshop are limited and will be allocated on a first-come basis. We have an excellent line-up of speakers including: Chris Adami, California Institute of Technology Alexander Alanine, F. Hoffman-La Roche Ltd. Virginia Cornish, Columbia University Athel Cornish-Bowden, CNRS Marseille Ernesto Freire, Johns Hopkins University Johann Gasteiger, University of Erlangen-N|rnberg Richard Goldstein, National Institute for Medical Research Douglas Kell, UMIST Hugo Kubinyi, University of Heidelberg Steven Ley, University of Cambridge Alex MacDonald, F. Hoffman-La Roche Ltd. Gerald Maggiora, University of Arizona Alan Mark, University of Groningen Keith Russell, AstraZeneca Gisbert Schneider, University of Frankfurt Thomas Schneider, National Cancer Institute Holger Wallmeier, Aventis Nicholas Westwood, University of St. Andrews Peter Willett, University of Sheffield Contact address: ----------------------------------------- Dr. Martin G. Hicks Beilstein-Institut Trakehner Str. 7-9 60487 Frankfurt am Main Tel: +49 (0)69 716732 20 Fax: +49 (0)69 716732 19 mhicks-.at.-beilstein-institut.de ----------------------------------------- From jkl@ccl.net Thu Jan 22 15:51:09 2004 -0500 Return-Path: Message-ID: <001401c3e129$172475c0$0e0e10ac@quimanche> From: "Ramiro Arratia" To: chemistry~at~ccl.net Subject: Comp Chem/Molec Spect Workshop in Chile, October 19-22 Date: Thu, 22 Jan 2004 17:48:27 -0300 I would like to announce the 4th version of the Workshop of Computational Chemistry and Molecular Spectroscopy to be held during October 19-22 in Punta de Tralca, Chile. Punta de Tralca is a beatiful beach located about 80 miles west from Santiago, and next to Isla Negra (where is Neruda's musseum). Aproximate Fees: USD 340 (academics) USD 200 (students) These prices may vary according to variations in currency exhange. It covers breaskfast, lunch, dinner, accomodations, tour and Proceedings. For more information, please contact Ramiro Arratia-Perez Director, Depto. de Ciencias Quimicas Facultad de Ecologia y Recursos Naturales Universidad Andres Bello Republica 275, Santiago Fono: (562)-661-8232 Fax: (562)-661-5679 Fax: (562)-661-8269 From chemistry-request@ccl.net Thu Jan 22 10:19:37 2004 Received: from mail.metronet.co.uk (mail.metronet.co.uk [213.162.97.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MFJWjs017712 for ; Thu, 22 Jan 2004 10:19:36 -0500 Received: from christian (unknown [213.162.106.11]) by mail.metronet.co.uk (MetroNet Mail) with ESMTP id 4D05240D551 for ; Thu, 22 Jan 2004 15:20:44 +0000 (GMT) From: "David Livingstone" Organization: ChemQuest To: chemistry(at)ccl.net Date: Thu, 22 Jan 2004 15:21:19 +0100 MIME-Version: 1.0 Subject: CCL: Great Conference in Edinburgh - March 21-24 2004 Reply-To: Davel(at)chemquest.uk.com Message-ID: <400FEA6F.32312.FE99EF@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.12a) Content-type: text/html; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Spam-Status: No, hits=0.9 required=7.0 tests=HTML_70_80, HTML_FONTCOLOR_GREEN,HTML_MESSAGE,HTML_TITLE_EMPTY,MIME_HTML_ONLY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net
Dear All,

There is a great meeting coming up in Edinburgh covering all aspects of Drug Discovery and Development. This is a multi-track meeting and since there is a good deal of "in silico", it may be worthwhile considering to put on your agenda!

Feel free to pass on to your colleagues.

http://www.soci.org/SCI/SCIpharm/html/prog.jsp

Regards,

            David L.
--
D.J. Livingstone                ChemQuest
                       Delamere House, 1 Royal Crescent,
                       Sandown. Isle of Wight UK PO36 8LZ

Phone & Fax: +44 (0)1983 401793
e-mail davel(at)chemquest.uk.com     www.chemquest.uk.com
------------------------------------------------------------------
From chemistry-request@ccl.net Thu Jan 22 08:30:49 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MDUljs011179 for ; Thu, 22 Jan 2004 08:30:48 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HRW00FKW89XOH(at)mailserver.unimi.it> for chemistry(at)ccl.net; Thu, 22 Jan 2004 14:32:22 +0100 (MET) Received: from villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0HRW00L0Z89T49(at)smtp.unimi.it> for chemistry(at)ccl.net; Thu, 22 Jan 2004 14:32:18 +0100 (MET) Date: Thu, 22 Jan 2004 14:38:02 +0100 From: Giulio Vistoli Subject: CCL: Vega on line To: CCL Message-id: <001101c3e0ec$f53ec0a0$424f959f@villa> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net dear CCLers, VEGA On-line (VEGAWE, http://galaxy.farma.unimi.it/vegawe) is a server-based service for all Internet users that want use the VEGA features without install it on their computer. VEGAWE can convert several file formats, add hydrogen atoms, assign atom types and atomic charges. It has got some interesting features: 1)It can be used with some Web server. At this time it was tested with Internet Information Service by Microsoft. 2)No script interpreter required. VEGA WE is a small application written in C allowing fast Web server responses with a low resource consumption. 3) No files can be directly uploaded to the server in order to prevent DoS attacks. 4)All user operations are logged and the logging level can be changed in order to obtain more exhaustive information. 5)The interface can be customized in easy way with an initialization scripts. 6)Support for PocketPC devices trough specific pages with low-detailed graphic and automatic detection for handled/desktop PC. 7)VEGA WE/On-line can be obtained free of charges contacting directly the Authors. Best regards Giulio Vistoli & Alessandro Pedretti _________________________ Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli(at)unimi.it http://www.ddl.unimi.it From chemistry-request@ccl.net Thu Jan 22 09:00:09 2004 Received: from mail9.messagelabs.com (mail9.messagelabs.com [194.205.110.133]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i0ME02js012805 for ; Thu, 22 Jan 2004 09:00:03 -0500 X-VirusChecked: Checked X-Env-Sender: Daniel.Tackley*at*avecia.com X-Msg-Ref: server-22.tower-9.messagelabs.com!1074780162!1305397 X-StarScan-Version: 5.1.15; banners=-,-,- Received: (qmail 21076 invoked from network); 22 Jan 2004 14:02:42 -0000 Received: from unknown (HELO wwwhx980.avecia.com) (217.205.231.98) by server-22.tower-9.messagelabs.com with SMTP; 22 Jan 2004 14:02:42 -0000 Received: from wwwhx109.avecia.com by wwwhx980.avecia.com via smtpd (for mail9.messagelabs.com [194.205.110.133]) with ESMTP; Thu, 22 Jan 2004 13:58:35 +0000 Received: from [10.156.1.180] (unverified) by wwwhx109.avecia.com (Content Technologies SMTPRS 4.2.10) with ESMTP id for ; Thu, 22 Jan 2004 13:58:35 +0000 Received: from avecia.com by [10.156.1.180] via smtpd (for wwwhx109.avecia.com [10.156.1.109]) with ESMTP; Thu, 22 Jan 2004 14:01:30 +0000 Received: by UKHX48 with Internet Mail Service (5.5.2653.19) id ; Thu, 22 Jan 2004 14:01:27 -0000 Message-ID: <67DFB9481700D111900E00805F59F86104C0472D@UKHX14> From: Tackley Daniel R To: "Comp Chem Mailing List (E-mail)" Subject: Gaussian 98 Cube File Error Date: Thu, 22 Jan 2004 14:01:26 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Has anyone else seen / solved this problem: I want to visualise some electron density differences between ground and excited state molecules calculated using G98W. To do this I need to create two cube files which I can then subtract. The problem I am getting is that in many cases, the structure in the cube file is offset from the points describing the density. Also, the density doesn't seem to be centred within the box defined by the cube dimensions and on visualising, spills out of the box, thereby wrapping round to the other side of the box. Result - a complete mess. There seems to be spurious density points all over the place and the cubes cannot be subtracted due to the offset structures. This seems to be the case when either the molecule is greater than a certain size (which is not very big) or when the number of points to evaluate in each dimension are greater than a certain number (again not very big). It also makes no difference whether the CUBE keyword is used or the post-processing cubegen program is. I have tried contacting Gaussian multiple times with no respose. Any ideas anyone? Thanks, Daniel Tackley -- Dr Daniel Tackley Computational Chemistry Group Avecia Ltd Manchester UK Tel: +44 (0)161 721 2541 Email: daniel.tackley*at*avecia.com From chemistry-request@ccl.net Thu Jan 22 12:22:50 2004 Received: from bohr.quimica.ufpr.br ([200.17.215.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MHMmjs025837 for ; Thu, 22 Jan 2004 12:22:49 -0500 Received: from laplace.quimica.ufpr.br ([200.17.215.88] helo=quimica.ufpr.br) by bohr.quimica.ufpr.br with esmtp (Exim 3.36 #1 (Debian)) id 1AjiYw-0001nz-00 for ; Thu, 22 Jan 2004 15:24:14 -0200 Message-ID: <4010073D.1060308*at*quimica.ufpr.br> Date: Thu, 22 Jan 2004 15:24:13 -0200 From: Eduardo User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:1.4) Gecko/20031105 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Chemistry@Ccl. Net" Subject: Ionic Radius of Sn(II) Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Sirs and Madams Could you please point me any reference so that I can find the ionic radius of Sn(II)? Sn(IV) is easilly findable, but Sn(II) is something not spread. Thanks a lot in advance yours Eduardo -- Eduardo Lemos de Sa - edulsa*at*quimica.ufpr.br Dep. Quimica - Universidade Federal do Parana Curitiba - PR - Brazil Box: 19081 - Zip: 81531-990 - Phone: +55(41)361-3300 From chemistry-request@ccl.net Thu Jan 22 09:45:50 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MEjijs015697; Thu, 22 Jan 2004 09:45:49 -0500 To: "chemistry*at*ccl.net" , "Computational Chemistry List" Subject: ForTran and C compilers under IRIX? MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy*at*givaudan.com Date: Thu, 22 Jan 2004 15:47:05 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.07a |May 14, 2001) at 22/01/2004 15:47:32, Serialize complete at 22/01/2004 15:47:32 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i0MEjojs015708 Dear Colleagues, Has anyone compared g77 and gcc with other ForTran and C compilers under IRIX? I will spread the answers. Many thank, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy*at*givaudan.com From chemistry-request@ccl.net Thu Jan 22 17:09:53 2004 Received: from med-gwia-02a.med.umich.edu (med-gwia-02a.med.umich.edu [141.214.93.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MM9qjs003911 for ; Thu, 22 Jan 2004 17:09:52 -0500 Received: from gwia-02-MTA by med-gwia-02a.med.umich.edu with Novell_GroupWise; Thu, 22 Jan 2004 17:11:20 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Beta Date: Thu, 22 Jan 2004 17:10:49 -0500 From: "Renxiao Wang" To: Subject: Marketed drugs by structure-based design? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, all! Would anybody please provide some references for marketed drugs whose development were largely aided by structure-based design methods? Some review papers/books must have mentioned this, but I cannot recall any at this moment. Any clue is appreicated. I will put back the summary. Thanks in advance! Regards, -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao=at=med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- From chemistry-request@ccl.net Thu Jan 22 17:59:19 2004 Received: from front3.chartermi.net (front3.chartermi.net [24.213.60.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MMxGjs005869 for ; Thu, 22 Jan 2004 17:59:17 -0500 Received: from [24.236.135.230] (HELO mmserver) by front3.chartermi.net (CommuniGate Pro SMTP 4.0.6) with SMTP id 530646756; Thu, 22 Jan 2004 18:00:47 -0500 Message-ID: <002a01c3e13b$9220a980$0901a8c0@mmserver> From: "Jim Kress" To: "Tackley Daniel R" , "Comp Chem Mailing List \(E-mail\)" References: <67DFB9481700D111900E00805F59F86104C0472D@UKHX14> Subject: Re: CCL:Gaussian 98 Cube File Error Date: Thu, 22 Jan 2004 18:00:45 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=2.6 required=7.0 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Did you explicitly specify the cube parameters in your input file or did you let the program select them for you? What does your input file look like? Jim ----- Original Message ----- From: "Tackley Daniel R" To: "Comp Chem Mailing List (E-mail)" Sent: Thursday, January 22, 2004 9:01 AM Subject: CCL:Gaussian 98 Cube File Error > Has anyone else seen / solved this problem: > > I want to visualise some electron density differences between ground and > excited state molecules calculated using G98W. To do this I need to create > two cube files which I can then subtract. The problem I am getting is that > in many cases, the structure in the cube file is offset from the points > describing the density. Also, the density doesn't seem to be centred within > the box defined by the cube dimensions and on visualising, spills out of the > box, thereby wrapping round to the other side of the box. > > Result - a complete mess. There seems to be spurious density points all over > the place and the cubes cannot be subtracted due to the offset structures. > > This seems to be the case when either the molecule is greater than a certain > size (which is not very big) or when the number of points to evaluate in > each dimension are greater than a certain number (again not very big). It > also makes no difference whether the CUBE keyword is used or the > post-processing cubegen program is. > > I have tried contacting Gaussian multiple times with no respose. > > Any ideas anyone? > > Thanks, > > Daniel Tackley > > -- > Dr Daniel Tackley > Computational Chemistry Group > Avecia Ltd > Manchester > UK > Tel: +44 (0)161 721 2541 > Email: daniel.tackley*at*avecia.com > > > > -= This is automatically added to each message by the 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, jlabanow*at*nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Jan 22 18:48:49 2004 Received: from ms1.usu.edu (ms1.usu.edu [129.123.104.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0MNmljs007856 for ; Thu, 22 Jan 2004 18:48:47 -0500 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by ms1.usu.edu (8.12.8/8.12.8) with SMTP id i0MNnOuR026646; Thu, 22 Jan 2004 16:49:25 -0700 Reply-To: From: "Tapas Kar" To: "Tackley Daniel R" , "Comp Chem Mailing List \(E-mail\)" Subject: RE: Gaussian 98 Cube File Error Date: Thu, 22 Jan 2004 16:40:00 -0700 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) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 In-reply-to: <67DFB9481700D111900E00805F59F86104C0472D@UKHX14> Importance: Normal X-USU-MailScanner-Information: Please contact the USU HelpDesk for more information (http://helpdesk.usu.edu) X-USU-MailScanner: Found to be clean X-USU-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0, required 5) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I guess you don't have correct dimensions of the cub files. If you send me your input files, I can check the result. Thanks Tapas -------------------------------------------- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar=at=cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request=at=ccl.net]On Behalf Of Tackley Daniel R Sent: Thursday, January 22, 2004 7:01 AM To: Comp Chem Mailing List (E-mail) Subject: CCL:Gaussian 98 Cube File Error Has anyone else seen / solved this problem: I want to visualise some electron density differences between ground and excited state molecules calculated using G98W. To do this I need to create two cube files which I can then subtract. The problem I am getting is that in many cases, the structure in the cube file is offset from the points describing the density. Also, the density doesn't seem to be centred within the box defined by the cube dimensions and on visualising, spills out of the box, thereby wrapping round to the other side of the box. Result - a complete mess. There seems to be spurious density points all over the place and the cubes cannot be subtracted due to the offset structures. This seems to be the case when either the molecule is greater than a certain size (which is not very big) or when the number of points to evaluate in each dimension are greater than a certain number (again not very big). It also makes no difference whether the CUBE keyword is used or the post-processing cubegen program is. I have tried contacting Gaussian multiple times with no respose. Any ideas anyone? Thanks, Daniel Tackley -- Dr Daniel Tackley Computational Chemistry Group Avecia Ltd Manchester UK Tel: +44 (0)161 721 2541 Email: daniel.tackley=at=avecia.com -= This is automatically added to each message by the 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, jlabanow=at=nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+