From chemistry-request@ccl.net Sun Jan 11 22:26:13 2004 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0C3QBld016321 for ; Sun, 11 Jan 2004 22:26:11 -0500 Expiry-Date: Wed, 31 Mar 2004 -1:-1:-1 +0000 Reply-To: training)at(accelrys.com To: CHEMISTRY)at(ccl.net Cc: judith.madeley)at(accelrys.com Subject: CCL: Accelrys Customer Training for March MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Jeff Nauss Date: Sun, 11 Jan 2004 19:26:42 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 01/11/2004 19:26:44, Serialize complete at 01/11/2004 19:26:44 Content-Type: text/plain; charset="US-ASCII" X-Spam-Status: No, hits=0.0 required=7.0 tests=LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Accelrys Inc. are holding the following training workshops at locations in the US and Europe during March. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic. MACROMOLECULAR MODELING Structure Based Drug Design 1-2 March in San Diego, CA CHARMm 3-4 March in San Diego, CA Modeling of GPCR Proteins with InsightII 11 March in San Diego, CA Introduction to InsightII for Life Sciences 16-17 March in Cambridge, UK Homology-Based Protein Design 18-19 March in Cambridge, UK Structure Based Drug Design with InsightII 22-23 March in Cambridge, UK CHARMm 24-25 March in Cambridge, UK Modeling of GPCR Proteins with InsightII 26 March in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/macro/schedule.html CHEMINFORMATICS Accord Visual Controls 1 March in Burlington, MA Accord SDK 2-3 March in Burlington, MA Accord Chemistry Cartridge 4 March in Burlington , MA Accord CombiChem Add-on 5 March in Burlington, MA DS AccordEnterprise Client 8 March in Burlington, MA DS Accord for Excel Enterprise 9 March in Burlington, MA Accord Inventory 10 March in Burlington, MA Accord HTS 11 March in Burlington, MA DIVA 12 March in Burlington, MA Accord Enterprise Informatics Database Admin. 15-16 March in Burlington, MA For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html Rational Drug Design Introduction to Cerius2 for Life Sciences 16-17 March in San Diego, CA Small Molecule and Drug Design with Cerius2 18-19 March in San Diego, CA Library Design and Analysis 22-23 March in San Diego, CA Pharmacophore Generation with Catalyst 24-25 March in San Diego, CA Introduction to Cerius2 for Life Sciences 30-31 March in Cambridge, UK Small Molecule and Drug Design with Cerius2 1-2 April in Cambridge, UK Library Design and Analysis 5-6 April in Cambridge, UK Pharmacophore Generation with Catalyst 7-8 April in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html Materials Science Modeling of Nanomaterials 11 March in San Diego, CA Introduction to Materials Studio 22 March in Burlington, MA Introduction to Polymer Modeling 23-24 March in Burlington, MA Introduction to Quantum Mechanics 25-26 March in Burlington, MA Workshop on Crystal Structure Determination 29 March in Burlington, MA Pharmacophore Generation with Catalyst 24-25 March in San Diego, CA For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss)at(accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Mon Jan 12 01:37:31 2004 Received: from kdmail2.netcologne.de (kdmail2.netcologne.de [194.8.194.86]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0C6bSld022721 for >ccl.net>; Mon, 12 Jan 2004 01:37:29 -0500 Received: from cosmologic.de (xdsl-213-168-111-183.netcologne.de [213.168.111.183]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id ACP74369 (AUTH klamt<>cosmologic.de); Mon, 12 Jan 2004 07:37:56 +0100 (CET) Message-ID: <400240BE.5010109<>cosmologic.de> Date: Mon, 12 Jan 2004 07:37:50 +0100 From: Andreas Klamt >cosmologic.de> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Don Steiger >bioeng.ucsd.edu>, "chemistry<>ccl.net" >ccl.net> Subject: Re: CCL:Alternative to dielectric for polarization in Poisson equation. References: >be-research.ucsd.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit 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 Don, my COSMO-RS is exactly made for the corrections of the dielectric model beyond the limits of dielectric continuum solvation. A list of relevant papers can be found on our home page. I suggest that you first have a look to the papers and we then discuss the specific applicability of COSMO-RS to your problem. Regards Andreas Don Steiger wrote: >Hello, > >I would like to use the Poisson Boltzmann equation to model >polymerization. This approach requires the use of a dielectric value for >the monomers. When the monomers are far apart, this may produce >reasonable results. However, as the monomers approach each other, a >constant scalar dielectric model will break down. Does anybody know of >any papers that correct for polarization using some other approach? > > >Thanks, > >Don > > >-= 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<>ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>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<>nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt<>cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Jan 12 10:42:19 2004 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0CFgIld011188 for >ccl.net>; Mon, 12 Jan 2004 10:42:19 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1Ag4DL-000NHLC; Mon, 12 Jan 2004 16:42 +0100 Message-ID: <4002C121.10206<>chem.vu.nl> Date: Mon, 12 Jan 2004 16:45:37 +0100 From: Anton Feenstra >chem.vu.nl> Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL posting >ccl.net> Subject: CCL: Multiple Simulations 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 Hi CCL-ers! I've been looking through literature, but was unable to locate papers that rigorously treat how to combine trajectories from multiple simulations of the same system. In principle, one has to assign a (statistical) weight to each of the simulations before taking, e.g., averages over the combination. Can anyone give me a hint or a few pointers? -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra<>chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Mon Jan 12 10:47:17 2004 Received: from solar.pharma.hr ([161.53.121.4]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0CFl4ld011348 for ; Mon, 12 Jan 2004 10:47:07 -0500 Received: from solar (localhost [127.0.0.1]) by scanned (Postfix) with ESMTP id 5D0FEDB9C9; Mon, 12 Jan 2004 16:46:58 +0100 (CET) Received: from localhost ([127.0.0.1]) by solar.pharma.hr (MailMonitor for SMTP v1.2.2 ) ; Mon, 12 Jan 2004 16:46:58 +0100 (CET) Received: from bf7 (unknown [161.53.121.94]) by solar.pharma.hr (Postfix) with SMTP id 7D200DB9C9; Mon, 12 Jan 2004 16:46:57 +0100 (CET) Message-ID: <001801c3d923$c218e500$5e7935a1)at(pharma.hr> From: "vgomzi" To: Cc: "Close, David M." References: Subject: electron affinities in P3 method Date: Mon, 12 Jan 2004 16:50:09 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-Spam-Status: No, hits=1.2 required=7.0 tests=DEAR_SOMETHING 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 Dear Sir/Ms, partial third-order propagator method (P3) as implemented in Gaussian 98 program code and described in several papers of V. Ortiz has recently successfully been used for calculation of ionization potentials of molecules by choosing IOp(9/11=10010) modification of ROVGF keyword. Now, I'm interested what should that IOp mean, since in G98 IOp list there is no such value described and therefore I'm not sure what is the numerical meaning of the above procedure. Furthermore, has anybody tried to calculate electron affinity of a compound using the same method? (Or do any of the readers know of such a work?) If yes, what would be the relevant IOp modification for such a method/calculation? (I apologize if the question is trivial.) Please, respond to my e-mail. I thank You very much in advance, Vjeran Gomzi, Ph.D. Student, Department of Biophysics Faculty of Pharmacy and Biochemistry, Ante Kovacica 1, 10000 Zagreb CROATIA tel. +385 1 4812128 fax. +385 1 4856 201 From chemistry-request@ccl.net Mon Jan 12 11:53:10 2004 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0CGr9ld013914 for ; Mon, 12 Jan 2004 11:53:09 -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 i0CGrh411949 for ; Mon, 12 Jan 2004 11:53:43 -0500 Message-ID: <4002D117.3080001/at/chem.utoronto.ca> Date: Mon, 12 Jan 2004 11:53:43 -0500 From: Jeremy Schofield Reply-To: jmschofi/at/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/at/ccl.net Subject: Chemical Biophysics Symposium, Toronto, March 19 - 21, 2004 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 First Announcement Chemical Biophysics Symposium 2004 Toronto, Canada March 19-21, 2004 http://www.chembiophys.ca We are pleased to announce that the third annual Chemical Biophysics Symposium will be held in Toronto, Canada on March 19-21, 2004. Chemical Biophysics is an emerging interdisciplinary field bridging the physical sciences and biology. The past two meetings were overwhelmingly successful in bringing together a diverse set of researchers and stimulating the exchange of ideas in an informal environment, and this year will build upon that success. The meeting will be held on the campus of the University of Toronto, with inexpensive rooms available 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 minimal (Students/Post-docs: $75-$85 (credit card) and all others $135-$145 in Canadian dollars), and will cover registration as well as several meals (see the web page for more details). A number of outstanding researchers have agreed to speak at the Chemical Biophysics Symposium, including: Robert Blankenship, ASU Chris McKay, NASA-Ames David Weitz, Harvard Benoit Roux, Cornell Medical Steve Ferguson, UWO Terry Beveridge, Guelph Michelle Wang, Cornell The bulk of the meeting will consist of oral presentations and posters selected from submitted abstracts. In order to keep the meeting informal, the number of attendees will be limited to 150 researchers, also selected on the basis of submitted abstracts. We strongly encourage you and any interested colleagues to visit the conference web page, submit an abstract, and attend the third of what we hope will be many meetings devoted to growing field at the interface between the physical and biological sciences. Abstract submission deadline: February 7, 2004 Early registration deadline: January 15, 2004 (rates increase by C$60 after this date) For additional information about the meeting, travel, and accommodations, please consult the conference web page: http://www.chembiophys.ca We hope to see you there! Please forward this message to any interested colleagues. The Organizing Committee: Cynthia Goh Ray Kapral Dwayne Miller Jeremy Schofield Greg Scholes Michael Menzinger Darren Anderson Gabriel Hanna Jan Rainey Bernie Sattin Alexander Doust Mayrose Salvador Mark Sinyor Gabriel Hanna Andrea Nagy Tieneke Dykstra Alessandro Sergi Zuzana Ecerova Paul Trudeau Jordan Dinglasan Nicolas Taulier Dave McMillen Robin Stoodley Cecile Fradin Anja Nohe From chemistry-request@ccl.net Mon Jan 12 16:46:59 2004 Received: from jilau1.Colorado.EDU (jilau1.Colorado.EDU [128.138.140.5]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0CLkwld022914 for ; Mon, 12 Jan 2004 16:46:58 -0500 Received: from [127.0.0.1] (jilau1.Colorado.EDU [128.138.140.5]) by jilau1.Colorado.EDU (8.12.10/8.12.10/UnixOps+Hesiod) with ESMTP id i0CLlUwp122808 for ; Mon, 12 Jan 2004 14:47:30 -0700 (MST) Subject: Re: CCL:Auguste Comte on Mathematical Methods in Chemistry From: The Matt To: CCL List In-Reply-To: <200401091124.41428.hinsen*at*cnrs-orleans.fr> References: <3FFD5D9B.19309.B96194@localhost> <200401091124.41428.hinsen*at*cnrs-orleans.fr> Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Organization: JILA Message-Id: <1073944050.28048.34.camel*at*ixion.colorado.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.5 (1.4.5-7) Date: Mon, 12 Jan 2004 14:47:30 -0700 On Fri, 2004-01-09 at 03:24, Konrad Hinsen wrote: > On Thursday 08 January 2004 13:39, Jens Spanget-Larsen wrote: >=20 > > I got it several years ago from an Internet page, without any > > details. Does anybody know this text? A. Comte must be the > > philosopher Auguste Comte, and the year 1830 may indicate his > > work "Cours de philosophie positive" which was published in > > this and the following years. But what can he have meant? Any > > comments? >=20 > I have seen that quote with the explicit attribution to the "Cours de=20 > philosophie positive" by Auguste Comte, but I never verified it. A large = part=20 > of that book deals with the philosophy of science, so it would fit in the= re.=20 > I suppose he refers to the potential contradiction between the empirical=20 > approach of science (including chemistry) and the deductive approach of=20 > mathematics, but that's just a guess. Well, I decided to walk to the library to clear my head and picked up "The Positive Philosophy" of Auguste Comte. And, a little reading, there it was: Every attempt to refer chemical questions to mathematical doctrines must be considered, now and always, profoundly irrational, as being contrary to the nature of the phenomena.=20 In the case of physics, the mischief would be, as we have seen, merely from the misuse of an instrument which, properly directed, may be of admirable efficacy; but if the employment of mathematical analysis should ever become so preponderant in chemistry (an aberration which is happily almost impossible) it would occasion vast and rapid retrogradation, by substituting vague conceptions for positive ideas, and an easy algebraic verbiage for a laborious investigation of facts. These two sentences (yes, two!) are interesting, and more philosophy follows. Namely, Comte believed the order of the sciences was: Mathematics, Astronomy, Physics, Chemistry, Physiology, Social Physics This led to the comment: =20 ...(I)t is only by having always before their eyes such an exemplification of the true spirit of natural philosophy, that chemists can rightly estimate the inanity of the metaphysical explanations which vitiate their doctrine, and can acquire an adequate sense of the true character, conditions, and destiny of chemical science. Under this point of view, astronomy is more useful to chemists than even physics, in proportion to the superiority of its method. I guess I need to go tell my college that astronomy should have been a prerequisite for chemistry. Of course, it was always full, so maybe that should have told me something. Now I'm going to have to read this a bit more. Just to see what he says about astronomy v. physics v. chemistry...when I have time. Matt=20 --=20 I am a theoretical chemist. Fear me! Matt Thompson -- http://ucsub.colorado.edu/~thompsma/ 440 UCB, Boulder, CO 80309-0440 JILA A510, 303-492-4662