From chemistry-request@www.ccl.net Tue Oct 13 03:25:43 1998 Received: from gamma.dou.dk (gamma.dou.dk [130.225.130.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA04423 Tue, 13 Oct 1998 03:25:42 -0400 (EDT) Received: from localhost (frj@localhost) by gamma.dou.dk (8.8.6/8.8.4) with SMTP id JAA16407; Tue, 13 Oct 1998 09:25:36 +0200 (METDST) Date: Tue, 13 Oct 1998 09:25:36 +0200 (METDST) From: Frank Jensen To: chemistry@www.ccl.net, g@CCMSD.chem.uga.edu, mmodinfo@uofto2.utoledo.edu, watoc@ic.ac.uk, amber@cgl.ucsf.edu, sybyl@extreme.chem.rpi.edu, charm-bbs@emperor.harvard.edu Subject: New Textbook in Computational Chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All I would like to announce a new textbook called Introduction to Computational Chemistry which just has been published by Wiley. The book grew out of a series of lecture notes that I have used over the years to teach a course in computational chemistry. As it stands, the book provides an introduction to many of the commonly employed theoretical models used in computational chemistry. Some of the topic covered are: Force field methods Electronic structure theory Ab initio theory DFT methods Basis set Wave function analysis Relativistic methods VB methods Molecular properties Transition state theory Optimization methods Time dependent methods Qualitative theories You may find more information on the icc-website: http://bogense.chem.ou.dk/~icc Frank Jensen PS: appology for any multiple messages you may receive. From chemistry-request@www.ccl.net Tue Oct 13 04:35:02 1998 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA04576 Tue, 13 Oct 1998 04:34:57 -0400 (EDT) Received: from [128.40.76.24] (actually host chromium.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Tue, 13 Oct 1998 09:34:53 +0100 X-Sender: uccanka@pop-server.ucl.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Oct 1998 09:36:11 +0100 To: adf-list@scm.com From: Nik Kaltsoyannis Subject: Quantum BioInorganic Chemistry (QBIC) '99 Cc: inorganic-chemistry@mailbase.ac.uk, ccwp@ulcc.ac.uk, chemistry@www.ccl.net The First Circular for the Quantum BioInorganic Chemistry (QBIC) '99 conference is now available. This meeting, which is WATOC '99 satellite symposium devoted to the application of computer modelling in bioinorganic chemistry, will be held at the University of Warwick, UK, from 29-31 July 1999. There will be no hard copy of the First Circular. Instead, interested parties are directed to the QBIC '99 website, the URL of which is http://www.warwick.ac.uk/~mssbq/qbic99.html. This site contains up-to-date information about the conference, including details of how to register on-line and how to submit abstracts and payment. Please note that deadline for abstract submission is January 15th 1999, the same date as the WATOC '99 meeting. From: Dr Nikolas Kaltsoyannis Lecturer in Chemistry Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ Email: n.kaltsoyannis@ucl.ac.uk Telephone: (0171) 504 4670 Fax: (0171) 380 7463 http://calcium.chem.ucl.ac.uk/webstuff/people/nkalt/index.html From chemistry-request@www.ccl.net Tue Oct 13 11:13:13 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA08752 Tue, 13 Oct 1998 11:13:10 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA00402; Tue, 13 Oct 98 08:11:01 -0700 Received: from unknown(146.202.7.50) by bioc1.msi.com via smap (V2.0) id xma000393; Tue, 13 Oct 98 08:10:51 -0700 Sender: osman@msi.com Message-Id: <36236D7A.4C08C7AC@msi.com> Date: Tue, 13 Oct 1998 08:10:50 -0700 From: "Osman F. Guner" Organization: Molecular Simulations Inc. X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch, isisforum-l@mdli.com Cc: chemweb@ic.ac.uk Subject: Call for papers Modeling @ Internet Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Apologies for multiple posting... MODELING AND ANALYSIS THROUGH THE INTERNET to be held at the American Chemical Society Meeting in Anaheim CA, March 21-25, 1999 Sponsored by the Division of Chemical Information As Internet is rapidly becoming an essential part of our day-to-day life more and more modeling and analysis tools are also becoming available through the Internet. This symposium will show off the current developments in this area: corporate-intranet applications, on-line modeling services, educational intiatives on the Internet, modeling and analysis tools through the Internet, and others. If you are interested in contributing to this symposium, the due date for 150 word abstracts is November 15, 1998. Electronic version of ACS abstract forms are prefered and can be obtained from http://www.acs.org/meetings/abstract/absdown.html Thx...osman -- Osman F. Guner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations, Inc. (619) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Tue Oct 13 17:19:34 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA18912 Tue, 13 Oct 1998 17:19:34 -0400 (EDT) Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id RAA11383 for ; Tue, 13 Oct 1998 17:19:25 -0400 (EDT) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.8.8/8.8.8) with SMTP id RAA27328 for <@copland.udel.edu:chemistry@ccl.net>; Tue, 13 Oct 1998 17:19:08 -0400 (EDT) Received: by wotan.duch.udel.edu (940816.SGI.8.6.9/951211.SGI) id QAA13057; Tue, 13 Oct 1998 16:33:15 -0400 Date: Tue, 13 Oct 1998 16:33:14 -0400 (EDT) From: Steve Bennett To: CCL Users Subject: G94 Polarizability units Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII What are the units of polarizabilty in G94? If you perform a frequency or polar run, you end up with values for the tensor in the form alphaxx, alphaxy, alphayy, alpha xz, alphayz, and alphazz, but I could not discern any units from the Gaussian manual. Cubic angstroms would make sense, as would atomic units but I wanted to clarify. Thanks in advance. Any assistance would be appreciated. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://udel.edu/~sbennett/steves.html In a world without walls or fences, what use do we have for windows or gates? "Scepticism is the chastity of the intellect, and it is shameful to surrender it too soon or to the first comer: there is nobility in preserving it cooly and proudly through long youth, until at last, in the ripeness of instinct and discretion, it can be safely exchanged for fidelity and happiness." George Santayana Scepticism and Animal Faith, IX From chemistry-request@www.ccl.net Tue Oct 13 18:22:25 1998 Received: from interlock.amoco.com (interlock.amoco.com [192.195.167.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA19254 Tue, 13 Oct 1998 18:22:24 -0400 (EDT) Received: by interlock.amoco.com id RAA00115 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Tue, 13 Oct 1998 17:22:24 -0500 Message-Id: <199810132222.RAA00115@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-4); Tue, 13 Oct 1998 17:22:24 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Tue, 13 Oct 1998 17:22:24 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Tue, 13 Oct 1998 17:22:24 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Tue, 13 Oct 1998 17:22:24 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Tue, 13 Oct 1998 17:32:17 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Mass Spectrum Program Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi All! Does anyone know of a software program (or algorithm even) that can predict the species in a mass spectrum given the parent compound? I don't care about distribution or even the spectrum ... just the possibilities. This seems to be trivial at first glance BUT ... -- :Joe jtgolab@amoco.com (630) 961-7878 +-------------------------------------------------------------------------+ | The difference between reality and fiction? Fiction has to make sense. | | - Tom Clancy | +-------------------------------------------------------------------------+ From chemistry-request@www.ccl.net Tue Oct 13 03:25:43 1998 Received: from gamma.dou.dk (gamma.dou.dk [130.225.130.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA04423 Tue, 13 Oct 1998 03:25:42 -0400 (EDT) Received: from localhost (frj@localhost) by gamma.dou.dk (8.8.6/8.8.4) with SMTP id JAA16407; Tue, 13 Oct 1998 09:25:36 +0200 (METDST) Date: Tue, 13 Oct 1998 09:25:36 +0200 (METDST) From: Frank Jensen To: chemistry@www.ccl.net, g@CCMSD.chem.uga.edu, mmodinfo@uofto2.utoledo.edu, watoc@ic.ac.uk, amber@cgl.ucsf.edu, sybyl@extreme.chem.rpi.edu, charm-bbs@emperor.harvard.edu Subject: New Textbook in Computational Chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All I would like to announce a new textbook called Introduction to Computational Chemistry which just has been published by Wiley. The book grew out of a series of lecture notes that I have used over the years to teach a course in computational chemistry. As it stands, the book provides an introduction to many of the commonly employed theoretical models used in computational chemistry. Some of the topic covered are: Force field methods Electronic structure theory Ab initio theory DFT methods Basis set Wave function analysis Relativistic methods VB methods Molecular properties Transition state theory Optimization methods Time dependent methods Qualitative theories You may find more information on the icc-website: http://bogense.chem.ou.dk/~icc Frank Jensen PS: appology for any multiple messages you may receive. From chemistry-request@www.ccl.net Tue Oct 13 04:35:02 1998 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA04576 Tue, 13 Oct 1998 04:34:57 -0400 (EDT) Received: from [128.40.76.24] (actually host chromium.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Tue, 13 Oct 1998 09:34:53 +0100 X-Sender: uccanka@pop-server.ucl.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Oct 1998 09:36:11 +0100 To: adf-list@scm.com From: Nik Kaltsoyannis Subject: Quantum BioInorganic Chemistry (QBIC) '99 Cc: inorganic-chemistry@mailbase.ac.uk, ccwp@ulcc.ac.uk, chemistry@www.ccl.net The First Circular for the Quantum BioInorganic Chemistry (QBIC) '99 conference is now available. This meeting, which is WATOC '99 satellite symposium devoted to the application of computer modelling in bioinorganic chemistry, will be held at the University of Warwick, UK, from 29-31 July 1999. There will be no hard copy of the First Circular. Instead, interested parties are directed to the QBIC '99 website, the URL of which is http://www.warwick.ac.uk/~mssbq/qbic99.html. This site contains up-to-date information about the conference, including details of how to register on-line and how to submit abstracts and payment. Please note that deadline for abstract submission is January 15th 1999, the same date as the WATOC '99 meeting. From: Dr Nikolas Kaltsoyannis Lecturer in Chemistry Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ Email: n.kaltsoyannis@ucl.ac.uk Telephone: (0171) 504 4670 Fax: (0171) 380 7463 http://calcium.chem.ucl.ac.uk/webstuff/people/nkalt/index.html From chemistry-request@www.ccl.net Tue Oct 13 07:03:52 1998 Received: from anduril.Austria.EU.net (anduril.Austria.EU.net [193.154.160.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA04927 Tue, 13 Oct 1998 07:03:50 -0400 (EDT) Received: from apollon.bender.co.at (apollon.bender.co.at [193.154.107.33]) by anduril.Austria.EU.net (8.9.1/8.9.1) with SMTP id NAA02367; Tue, 13 Oct 1998 13:03:43 +0200 (MET DST) Received: from vieexch1.bender.co.at by apollon.bender.co.at via smtpd (for anduril.Austria.EU.net [193.154.160.104]) with SMTP; 13 Oct 1998 11:03:41 UT Received: by vieexch1.vie.at.bic with Internet Mail Service (5.5.1960.3) id <4X7QFM1V>; Tue, 13 Oct 1998 12:57:27 +0200 Message-ID: <4195A3C6D39BD11189C30020AFFC17588F3C2D@vieexch1.vie.at.bic> From: "LOEFFLER,DR,GERALD FEM BENAT" To: "'ccl'" Cc: "'Tu, Meihua'" Subject: SUMMARY: Graph Layout in 2D Date: Tue, 13 Oct 1998 12:57:26 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Content-Type: text/plain Dear CCL-ers! Thank you for the many reponses to my question about laying out a graph in 2D. The question was: ================= What algorithms and implementations of these algorithms (in Java?) are available to "intelligently" lay out a general graph in 2D? The resulting layout should contain a minimum number of overlaps of nodes and edges. Summary of responses: ===================== o This field is obviously quite established and is called "Graph Drawing". o Vega (http://www.ijp.si/vega/htmldoc/vinfo.htm) is a graph-theoretical package for Mathematica that handles this and many other things. Other packages for Mathematica are also available: http://www.mathsource.com o A demo-applet called GraphLayout is included in SUNs JDK and (incredibly!) slipped my attention: http://java.sun.com/applets/jdk/1.1/demo/GraphLayout/ o Petra Mutzel and her group at Max-Planck-Institut fuer Informatik do research on that subject and developed a library called AGD. o DaVinci (http://www.informatik.uni-bremen.de/~davinci/) and Graphlet (http://www.fmi.uni-passau.de/Graphlet/) are graph layout systems. o Other relevant web pages: http://www.cs.unisb.de/RW/users/sander/html/gstools.html http://www.eng.auburn.edu/department/cse/research/graph_drawing/graph_dr awing.html http://www.fmi.uni-passau.de/~himsolt/graphdrawing.html o Using an MD-like algorithm (as I suggested in my question) to optimize the layout requires calculation of forces and is thus more complicated than an MC-like algorithm. o If the graph were in fact a chemical structure this would lead to many additional problems regarding the conventions of drawing chemical structures in 2D. But in fact, my problem is unrelated to chemical structures. Many thanks to: =============== Meihua Tu Yongxing Liu Darko Babic Stephan Reiling Oliver Kohlbacher Wolf-D. Ihlenfeldt Michael E. Beck Eric Gifford Peter Bladon Many, many thanks to all of you! cheers, gerald |--------------------------------------------------------------------| Gerald Loeffler - Bioinformatics Scientist Boehringer Ingelheim R&D Vienna Email: Gerald.Loeffler@vienna.at Phone: +43 676 3289588 (and +43 1 80105 634) Fax: +43 1 80105 683 Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria From chemistry-request@www.ccl.net Tue Oct 13 10:50:33 1998 Received: from ws01.pc.chemie.tu-darmstadt.de (ws01.pc.chemie.tu-darmstadt.de [130.83.138.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA08135 Tue, 13 Oct 1998 10:49:49 -0400 (EDT) Received: (from hjb@localhost) by ws01.pc.chemie.tu-darmstadt.de (980427.SGI.8.8.8/970903.SGI.AUTOCF) id QAA18275 for chemistry@www.ccl.net; Tue, 13 Oct 1998 16:49:34 +0200 (CDT) Date: Tue, 13 Oct 1998 16:49:34 +0200 (CDT) From: hjb@ws01.pc.chemie.tu-darmstadt.de (Hans-Juergen Baer) Message-Id: <199810131449.QAA18275@ws01.pc.chemie.tu-darmstadt.de> To: chemistry@www.ccl.net Subject: Symposium on complex chemical systems International Symposium on The Treatment of Complex Chemical Systems: New Concepts in Theory and Experiment in honor of Professor Ju"rgen Brickmann on the occasion of his 60th birthday May 27 - 29, 1999 Department of Chemistry, Darmstadt University of Technology ============================================================================= Scope of the Symposium: Large and complex systems provide some of the most challenging experimental and theoretical problems in modern chemistry. By complex systems, it is meant that the systems as well as the models used should reflect chemical conditions in a realistic way. This requires the proper and simultaneous treatment of different species and phases. The purpose of this symposium is to survey recent research in the development of new model scenarios, new theoretical approaches and simulation techniques of complex systems and processes as well as subtle experimental techniques in order to study these kinds of systems. It is the aim of this meeting to discuss various ways to overcome the limitations of individual methods by combining different approaches and to demonstrate in this way the power of new concepts and technologies. The invited speakers are selected from a wide variety of fields ranging from philosophy to preparative chemistry. Therefore, the meeting is expected to be of interest to both experimentalists and theorists from all branches of science, as well as mathematicians and computer scientists. Organizing Committee: Dr. H.-J. Ba"r, Institute of Physical Chemistry, Darmstadt University of Technology Petersenstr. 20, D-64289 Darmstadt, Germany Phone: (+49) 6151/164095, Fax: (+49) 6151/164298, Email: hjb@pc.chemie.tu-darmstadt.de Prof. Dr. P. Bopp, Lab. de Physico-Chimie Moleculaire et Cristalline, Universite Bordeaux I, 351 Cours de la Liberation, F-33405 Talence CEDEX, France Phone: (+33) 556842888, Fax: (+33) 556848402, Email: pab@hulot.lsmc.u-bordeaux.fr Dr. S. M. Kast, Institute of Physical Chemistry, Darmstadt University of Technology Petersenstr. 20, D-64289 Darmstadt, Germany Phone: (+49) 6151/165397, Fax: (+49) 6151/164298, Email: kast@pc.chemie.tu-darmstadt.de Prof. Dr. R. Kniep, Institute of Inorganic Chemistry, Darmstadt University of Technology Petersenstr. 20, D-64289 Darmstadt, Germany Phone: (+49) 6151/162192, Fax: (+49) 6151/166029 Prof. Dr. M. Martin, Institute of Physical Chemistry, Darmstadt University of Technology Petersenstr. 20, D-64287 Darmstadt, Germany Phone: (+49) 6151/162498 , Fax: (+49) 6151/166024, Email: martin@e-chemie.tu-darmstadt.de Prof. Dr. E. Yurtsever, Chemistry Department, Koc University, 80860 Istanbul, Turkey Phone: (+90) 212-229 30 06, Fax: (+90) 212-229 06 80, Email: eyurtsev@ku.edu.tr Location: The symposium will be held at the Chemistry Department Kekule-Auditorium Darmstadt University of Technology Petersenstr. 20 (Lichtwiese) D-64287 Darmstadt, Germany Invited speakers (with tentative titles): D. Avnir, Jerusalem (Israel): The measurement of chirality: a two-steps model for enzymatic activity E. Aquilanti, Perugia (Italy): Exact quantum mechanics near the classical limit: Hyperquantization algorithm for structure and reactivity H. Baumga"rtel, Berlin (Germany): Homogeneous nucleation in liquids and solutions R.S. Berry, Chicago (USA): to be announced P. Bopp, Bordeaux (France): Approaches to the liquid state: Experiment, simulation, theory E. Braendas, Uppsala (Sweden): Quantum concepts and complex phenomena L. Cederbaum, Heidelberg (Germany): Intra- and intermolecular decay of molecules and clusters B. Gerber, Jerusalem (Israel): Quantum-mechanical simulations of the dynamics of large clusters and macromolecules E. Gudowska-Nowak, Krakow (Poland): Vampires story. Science, folklore and beyond R. Kniep, Darmstadt (Germany): Biomimetic materials chemistry G. Kothe, Freiburg (Germany): Quantum beats as probes of the primary events of photosynthesis H. Kubinyi, Ludwigshafen (Germany): Drug research - from serendipity to rational design R. D. Levine, Jerusalem (Israel): Theoretical considerations towards a total chemical synthesis of a computer H. Limbach, Berlin (Germany): Novel NMR views of proton transfer and hydrogen bonding in liquids and solids P. Mezey, Saskatchewan (Canada): Macromolecular quantum chemistry, new frontiers and applications J. Mittelstrass, Konstanz (Germany): Complexity: A philosophical view K. Schulten, Urbana-Champaign (USA): Interactive molecular dynamics A. Sgamellotti, Perugia (Italy): Theoretical investigations of large molecular systems: Transition metal complexes of calixarenes and fullerenes A. Skerra, Darmstadt (Germany): Molecular tools through protein design J. Weber, Geneva (Switzerland): Novel modeling tools for catalytic reaction mechanisms E. Yurtsever, Istanbul (Turkey): Quantum-classical mixed mode approaches to the chaos in vibrational motion -------------------------------------------------------------------------- Accommodation and Registration: Deadline for registration: April 1st, 1999 Registration fee: none Hotel rooms can be reserved by contacting the tourcongress bureau Darmstadt, Luisenplatz 5, D-64283 Darmstadt, phone: (+49) 6151-13 20 7, fax: (+49) 6151-13 20 75 +-----------------------------------------------------+ | | | Please register on-line at: | | | | http://www.pc.chemie.tu-darmstadt.de/symposium1999/ | | | +-----------------------------------------------------+ Please send correspondence to: Dr. Hans-Ju"rgen Ba"r Institute of Physical Chemistry Darmstadt University of Technology Petersenstr. 20 D-64289 Darmstadt Germany Fax: (+49) 6151/164298 Email: hjb@pc.chemie.tu-darmstadt.de ========================================================= Dr.-Ing. Hans-Juergen Baer Physical Chemistry I, TU Darmstadt Petersenstr. 20, D-64287 Darmstadt phone: (x49) 6151 16 4095 ; fax: (x49) 6151 16 4298 email: hjb@pc.chemie.tu-darmstadt.de ========================================================= From chemistry-request@www.ccl.net Tue Oct 13 11:04:36 1998 Received: from cz2.chem.niu.edu (cz2.chem.niu.edu [131.156.9.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA08625 Tue, 13 Oct 1998 11:04:35 -0400 (EDT) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA09501; Tue, 13 Oct 98 09:06:02 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA04160; Tue, 13 Oct 98 10:14:15 -0500 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id KAA24693; Tue, 13 Oct 1998 10:03:33 -0500 Sender: smb@smb.chem.niu.edu Message-Id: <36236BC4.7DE1@smb.chem.niu.edu> Date: Tue, 13 Oct 1998 10:03:32 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: ECCC5 Abstracts and Registration Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The abstracts of the 71 articles that will be presented at the Fifth Electronic Computational Chemistry Conference (ECCC-5) are now available from the conference web page: http://hackberry.chem.niu.edu/ECCC5/ The full articles will be available at the start of the conference on November 2, 1998. Registration is free for the conference and can also be found at the ECCC5 home page. Steve -- Steven Bachrach Department of Chemistry and Biochemistry Northern Illinois University DeKalb, IL 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From chemistry-request@www.ccl.net Tue Oct 13 11:07:04 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA08647 Tue, 13 Oct 1998 11:06:59 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA00252; Tue, 13 Oct 98 08:04:28 -0700 Received: from unknown(146.202.7.50) by bioc1.msi.com via smap (V2.0) id xma000245; Tue, 13 Oct 98 08:04:23 -0700 Sender: osman@msi.com Message-Id: <36236BF6.1FE07CA0@msi.com> Date: Tue, 13 Oct 1998 08:04:22 -0700 From: "Osman F. Guner" Organization: Molecular Simulations Inc. X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch, isisforum-l@mdli.com, mol-diversity@listserv.arizona.edu, chemweb@ic.ac.uk Subject: Call for papers TECHNIQUES IN PHARMACOPHORE DEVELOPMENT Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Apologies for posting at multiple listservers. TECHNIQUES IN PHARMACOPHORE DEVELOPMENT to be held at the American Chemical Society Meeting in Anaheim CA, March 21-25, 1999 Sponsored by the Division of Chemical Information Co-sponsored by Division of Computers in Chemistry While "3D Searching" has established itself as one of the essential tools in Computer-Aided Drug Design and combinatorial library focusing, the ability to ask better questions to retrieve better hit lists from 3D databases is still a challenging task. The questions in 3D Searching involve a search queries that represent "pharmacophore models." Pharmacophore development may involve a range of activities from a simple visual pattern recognition, to fully automated model generation, to receptor-based methods. In this symposium, we will try to cover new developments in the area of pharmacophore development as well as validation studies on the existing methods, experimental prototypes, and in short, full spectrum of techniques in pharmacophore development. If you are interested in contributing to this symposium, the due date for 150 word abstract is November 15, 1998. Electronic version of ACS abstract forms are prefered and can be obtained from http://www.acs.org/meetings/abstract/absdown.html Thx...Osman -- Osman F. Guner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations, Inc. (619) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Tue Oct 13 11:13:13 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA08752 Tue, 13 Oct 1998 11:13:10 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA00402; Tue, 13 Oct 98 08:11:01 -0700 Received: from unknown(146.202.7.50) by bioc1.msi.com via smap (V2.0) id xma000393; Tue, 13 Oct 98 08:10:51 -0700 Sender: osman@msi.com Message-Id: <36236D7A.4C08C7AC@msi.com> Date: Tue, 13 Oct 1998 08:10:50 -0700 From: "Osman F. Guner" Organization: Molecular Simulations Inc. X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch, isisforum-l@mdli.com Cc: chemweb@ic.ac.uk Subject: Call for papers Modeling @ Internet Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Apologies for multiple posting... MODELING AND ANALYSIS THROUGH THE INTERNET to be held at the American Chemical Society Meeting in Anaheim CA, March 21-25, 1999 Sponsored by the Division of Chemical Information As Internet is rapidly becoming an essential part of our day-to-day life more and more modeling and analysis tools are also becoming available through the Internet. This symposium will show off the current developments in this area: corporate-intranet applications, on-line modeling services, educational intiatives on the Internet, modeling and analysis tools through the Internet, and others. If you are interested in contributing to this symposium, the due date for 150 word abstracts is November 15, 1998. Electronic version of ACS abstract forms are prefered and can be obtained from http://www.acs.org/meetings/abstract/absdown.html Thx...osman -- Osman F. Guner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations, Inc. (619) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Tue Oct 13 12:08:25 1998 Received: from gateway.chiroscience.com (firewall-user@gateway.chiroscience.com [194.203.52.61]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA09342 Tue, 13 Oct 1998 12:08:23 -0400 (EDT) Received: by gateway.chiroscience.com; id RAA16966; Tue, 13 Oct 1998 17:04:09 +0100 Received: from mailhost(192.168.3.253) by gateway.chiroscience.com via smap (4.0a) id xma016954; Tue, 13 Oct 98 17:03:38 +0100 Received: from chiroscience.com (unverified [192.168.5.205]) by cb002.chiroscience.com (Integralis SMTPRS 2.04) with ESMTP id ; Tue, 13 Oct 1998 17:04:42 +0100 Sender: will@chiroscience.com Message-Id: <36237925.336BE020@chiroscience.com> Date: Tue, 13 Oct 1998 17:00:37 +0100 From: Will Pitt Organization: Chiroscience R&D Ltd X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Announcement: MGMS Young Molecular Modellers' Forum Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ANNOUNCEMENT: MGMS Young Molecular Modellers' Forum November 18th 1998, Glaxo Stevenage, UK. This meeting features 13 young researchers presenting results from their Ph.D. studies. We would like to invite you attend this meeting to support these talented researchers. Registration is via the web at: http://www.mgmg.org/young.htm Cost is 5 pounds. For more information contact: David Manallack Chiroscience R&D Ltd. Cambridge Science Park Milton Road Cambridge CB4 4WE UK +44 1223 420430 davidmanallack@chiroscience.com From chemistry-request@www.ccl.net Tue Oct 13 12:22:35 1998 Received: from mx02.uni-tuebingen.de (root@mx02.uni-tuebingen.de [134.2.3.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA09515 Tue, 13 Oct 1998 12:22:24 -0400 (EDT) Received: from apollo.pharm.chemie.uni-tuebingen.de (apollo.pharm.chemie.uni-tuebingen.de [134.2.68.23]) by mx02.uni-tuebingen.de (8.8.8/8.8.8) with SMTP id SAA23172 for ; Tue, 13 Oct 1998 18:22:15 +0200 Date: Tue, 13 Oct 1998 18:22:15 +0200 Message-Id: <199810131622.SAA23172@mx02.uni-tuebingen.de> X-Sender: cpcmu01@cpcmu01.mail.uni-tuebingen.de X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Inge Muszynski Subject: bioisosterism Dear CCl'lers, does anybody has an idea how the bioisosteric groups Ester and 1,2,4-Oxadiazole could be aligned in biological targets. I am looking forward to any references or crystallographic data. Inge Muszynski University of Tuebingen Auf der Morgenstelle 8 72076 Tuebingen From chemistry-request@www.ccl.net Tue Oct 13 12:22:35 1998 Received: from mx02.uni-tuebingen.de (root@mx02.uni-tuebingen.de [134.2.3.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA09515 Tue, 13 Oct 1998 12:22:24 -0400 (EDT) Received: from apollo.pharm.chemie.uni-tuebingen.de (apollo.pharm.chemie.uni-tuebingen.de [134.2.68.23]) by mx02.uni-tuebingen.de (8.8.8/8.8.8) with SMTP id SAA23172 for ; Tue, 13 Oct 1998 18:22:15 +0200 Date: Tue, 13 Oct 1998 18:22:15 +0200 Message-Id: <199810131622.SAA23172@mx02.uni-tuebingen.de> X-Sender: cpcmu01@cpcmu01.mail.uni-tuebingen.de X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Inge Muszynski Subject: bioisosterism Dear CCl'lers, does anybody has an idea how the bioisosteric groups Ester and 1,2,4-Oxadiazole could be aligned in biological targets. I am looking forward to any references or crystallographic data. Inge Muszynski University of Tuebingen Auf der Morgenstelle 8 72076 Tuebingen From chemistry-request@www.ccl.net Tue Oct 13 15:04:15 1998 Received: from mail.wesleyan.edu (mail.wesleyan.edu [129.133.1.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA10638 Tue, 13 Oct 1998 15:04:15 -0400 (EDT) Received: from dkombo.wesleyan.edu (jellyfish.chem.wesleyan.edu [129.133.20.75]) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id PAA26635 for ; Tue, 13 Oct 1998 15:04:17 -0400 (EDT) Date: Tue, 13 Oct 1998 15:04:17 -0400 (EDT) Message-Id: <199810131904.PAA26635@mail.wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Yongxing Liu Subject: Basic Water Dimer Question Dear CCLers, Would any one please help with the following question? Is it possible to calculate water dimer interaction energy without calculating the monomer? This is a prototype question for a real problem. Say we have two boxes of classical particles. we may calulate their interactions bewtween these two boxes without calulating the energy of each box. Let's look water dimer as two boxes of clouds(divided by population analysis). There should be a way to do this using QM. Its just a degree of accuracy. I do not have much experience with QM, please help! Thanks a lot in advance. Sincerely -------------------------------------------------------------------------- Yongxing Liu, Graduate Student | E-Mail: yliu@wesleyan.edu Department of Chemistry | Tel.:860-685-2777 Wesleyan University | Fax: 860-685-2211 Middletown CT 06459 | URL: http://ludwig.chem.wesleyan.edu/yliu --------------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Oct 13 17:19:34 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA18912 Tue, 13 Oct 1998 17:19:34 -0400 (EDT) Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id RAA11383 for ; Tue, 13 Oct 1998 17:19:25 -0400 (EDT) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.8.8/8.8.8) with SMTP id RAA27328 for <@copland.udel.edu:chemistry@ccl.net>; Tue, 13 Oct 1998 17:19:08 -0400 (EDT) Received: by wotan.duch.udel.edu (940816.SGI.8.6.9/951211.SGI) id QAA13057; Tue, 13 Oct 1998 16:33:15 -0400 Date: Tue, 13 Oct 1998 16:33:14 -0400 (EDT) From: Steve Bennett To: CCL Users Subject: G94 Polarizability units Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII What are the units of polarizabilty in G94? If you perform a frequency or polar run, you end up with values for the tensor in the form alphaxx, alphaxy, alphayy, alpha xz, alphayz, and alphazz, but I could not discern any units from the Gaussian manual. Cubic angstroms would make sense, as would atomic units but I wanted to clarify. Thanks in advance. Any assistance would be appreciated. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://udel.edu/~sbennett/steves.html In a world without walls or fences, what use do we have for windows or gates? "Scepticism is the chastity of the intellect, and it is shameful to surrender it too soon or to the first comer: there is nobility in preserving it cooly and proudly through long youth, until at last, in the ripeness of instinct and discretion, it can be safely exchanged for fidelity and happiness." George Santayana Scepticism and Animal Faith, IX From chemistry-request@www.ccl.net Tue Oct 13 18:22:25 1998 Received: from interlock.amoco.com (interlock.amoco.com [192.195.167.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA19254 Tue, 13 Oct 1998 18:22:24 -0400 (EDT) Received: by interlock.amoco.com id RAA00115 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Tue, 13 Oct 1998 17:22:24 -0500 Message-Id: <199810132222.RAA00115@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-4); Tue, 13 Oct 1998 17:22:24 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Tue, 13 Oct 1998 17:22:24 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Tue, 13 Oct 1998 17:22:24 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Tue, 13 Oct 1998 17:22:24 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Tue, 13 Oct 1998 17:32:17 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Mass Spectrum Program Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi All! Does anyone know of a software program (or algorithm even) that can predict the species in a mass spectrum given the parent compound? I don't care about distribution or even the spectrum ... just the possibilities. This seems to be trivial at first glance BUT ... -- :Joe jtgolab@amoco.com (630) 961-7878 +-------------------------------------------------------------------------+ | The difference between reality and fiction? Fiction has to make sense. | | - Tom Clancy | +-------------------------------------------------------------------------+ From chemistry-request@www.ccl.net Tue Oct 13 18:58:14 1998 Received: from anugpo.anu.edu.au (anugpo.anu.edu.au [150.203.2.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA19374 Tue, 13 Oct 1998 18:58:11 -0400 (EDT) Received: from hannes.anu.edu.au (hannes.anu.edu.au [150.203.193.229]) by anugpo.anu.edu.au (8.8.8/8.8.8) with SMTP id IAA26262 for ; Wed, 14 Oct 1998 08:58:07 +1000 (EST) Message-Id: <199810132258.IAA26262@anugpo.anu.edu.au> From: "Johannes Zuegg" Organization: JCSMR To: CHEMISTRY@www.ccl.net Date: Wed, 14 Oct 1998 08:57:01 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: One letter code for Sugars Reply-to: johannes.zuegg@anu.edu.au Priority: normal Dear Net, I'm modelling oligosaccharide and built a residue library (for AMBER) where I am restricted to a three letter code for the sugar residue, ending up with the following code: - The first letter is a code for the type of sugar (M=Man, G=Glc S=silaic acid, H=GlcNAc ... I used just letters which do not interfer with the amino acids), - thes econd for the glycosidic conformation (A=alpha, B=beta, N=N-alpha as the partial charges are different,....) and - the third is for the linkage (1= only at 1, 2=at 1 and 2,... A=at 1,2 and 6, ... Z= at 1,2,3,4 and 6 ). a-Glc 1----4 b-Man 1 ---- 3 a- Man 1 ---- GA1 MB4 MA3 My questions is, are there any one letter code for the saccharide type, as I used just one which doesn't interfer with the amino acids, and/or is there already a standard three letter code for oligsaccharides? Thanks Johannes --------------------------------------------------------------------- John Curtin School of Medical Research Australian National University Dept. Biochemistry and Molecular Biology PO Box 334 Canberra, ACT 2612, Australia Tel: +61 2 6279 8301 Fax: +61 2 6249 0415 EMail: johannes.zuegg@anu.edu.au --------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Oct 13 22:36:47 1998 Received: from multi11.netcomi.com (cwohlers@multi11.netcomi.com [204.58.155.211]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA20516 Tue, 13 Oct 1998 22:36:47 -0400 (EDT) Received: (from cwohlers@localhost) by multi11.netcomi.com (8.8.5/8.7.4) id VAA20303; Tue, 13 Oct 1998 21:35:57 -0500 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by multi11.netcomi.com (8.8.5/8.7.4) with ESMTP id VAA20296 for ; Tue, 13 Oct 1998 21:35:56 -0500 Received: (from ccl@localhost) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) id KAA08552 Tue, 13 Oct 1998 10:59:28 -0400 (EDT) X-Authentication-Warning: www.ccl.net: ccl set sender to chemistry-request@www.ccl.net using -f Received: from eagle.molsoft.com (eagle.molsoft.com [209.122.85.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA01870 Mon, 12 Oct 1998 12:26:51 -0400 (EDT) Received: by eagle.molsoft.com (5.65v4.0/1.1.19.2/13Jun98-0140AM) id AA16656; Mon, 12 Oct 1998 12:25:33 -0400 Date: Mon, 12 Oct 1998 12:25:33 -0400 From: Molsoft Info Message-Id: <199810121625.AA16656@eagle.molsoft.com> Subject: CCL:A One Day Course on Computational Structural Biology Apparently-To: chemistry@www.ccl.net Sender: chemistry-request@www.ccl.net Errors-To: ccl@ccl.net Precedence: bulk X-Loop: kmtakita@knowledgefoundation.com To: kmtakita@ix.netcom.com Dear Colleague, Molsoft announces a one day course in computational structural biology. Lecturer and instructor: Dr. Ruben Abagyan Date: Thursday, October 29, 1998 Location: Molsoft LLC office, 200 Middlesex-Essex Tpke, Iselin, New Jersey NJ Turnpike, exit 11 Garden State Parkway, exit 131-A/B Time: 10 a.m. - 4 p.m. The course is directed at scientists with an interest in protein structure and structure prediction who wish to learn what can be accomplished with the cutting edge methods of computational structural biology. The following topics will be covered: Sensitive sequence searches Multiple sequence alignments and trees Secondary structure prediction, pattern recognition, functional annotation Modeling by homology Structure-based analysis of sequence conservation Protein surfaces and structure analysis Introducing mutation Ab initio peptide folding Advanced molecular vizualization For additional information and registration please visit our web-site at www.molsoft.com. --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- From chemistry-request@www.ccl.net Tue Oct 13 12:09:42 1998 Received: from earth.ox.ac.uk (darwin.earth.ox.ac.uk [163.1.22.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA09380 Tue, 13 Oct 1998 12:09:41 -0400 (EDT) Received: from metropolis.earth.ox.ac.uk (metropolis [163.1.22.59]) by earth.ox.ac.uk (8.9.1a/8.9.1) with SMTP id RAA05742 for ; Tue, 13 Oct 1998 17:09:35 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <13859.31550.844016.543322@metropolis> Date: Tue, 13 Oct 1998 17:09:34 +0100 (BST) To: chemistry@www.ccl.net Subject: Recommendations for textbooks and teaching software X-Mailer: VM 6.62 under Emacs 20.3.1 Content-Transfer-Encoding: 7bit This is slightly off-topic for CCL, but I'm guessing there might be some people on the list who will be able to help. I'm in the position of having to teach an elementary undergraduate course on chemical bonding and structure of solids. It will be a short course (12 teaching hours) and the students will not have had any quantum mechanics or atomic structure beyond (high-)school level. I am having trouble finding a decent textbook at the right level (ie very introductory) and I'd appreciate any recommendations you may have. I also wish to make heavy use of computer-assisted learning so I'm also looking for recommendations of teaching software -- perhaps for visualization of atomic orbitals and bonding. The students will be Earth scientists, not chemists or physicists and I don't want to take too a rigorous approach. So though I may display the 3D solutions of the Schroedinger equation for the H atom I won't do the solution. I hope to rely on computer graphics to illustrate wavefunctions orbitals and hopefully bonding. I'd like to cover at least some of the following topics from a solid-state point of view using mineralogical examples. * the schroedinger equation and QM in 1 dimension - quantization. * The H atom. Atomic structure, orbitals, the aufbau principle and the periodic table. * Ionic bonding. Ionization energies, electronegativities. Ionic radii and mineral crystal structures. * covalent bonding, H2, sp2, sp3 bonding in molecules and solids using the LCAO approach. * Structural trends and polymorphism in the solid state. Silicate structures. * Substitutional defects. So if anyone knows of a textbook which covers this material at an introductory level and/or any educational software (Windows 95 or Linux) which could be used in support of such a course I'd like to hear from you. (I'd also welcome any comments from anyone who has taught a similar course on the amount of material given the 12 hours teaching time!) I'll summarize if requested. Thanks in advance. Keith Refson -- ------------------------------------------------------------------------------ Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | Spam: root@cyberpromo.com | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------------------ From chemistry-request@www.ccl.net Wed Oct 14 04:21:37 1998 Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA22172 Wed, 14 Oct 1998 04:21:36 -0400 (EDT) Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA15511; Wed, 14 Oct 1998 09:20:36 +0100 (BST) Message-ID: <36245CBB.353F5E2C@nibsc.ac.uk> Date: Wed, 14 Oct 1998 09:11:39 +0100 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: David Chalmers , chemistry@www.ccl.net Subject: Re: CCL:Utility to superimpose pdb files References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear David, One thing is not clear from your question: Do the two PDB files represent the same protein and hence have the same number of (say C-alpha) atoms. If this is the case then the CCL archives have a program called Quatfit which could surely do this job, although I have not yet used it for this purpose. If they are different proteins rather than different conformations Quatfit could still be used but you would need an alignment to establish the atom correspondance. If you have want to align a given protein structure against those in PDB then try the DALI server at http://www2.ebi.ac.uk/dali/ Hope this helps. David Chalmers wrote: > Hi all, > > I am after a utility to perform a best fit superimposition of two pdb > files that I can incorporate in to a shell or perl script. Does anybody > have such a useful thing? > > Thanks > > David > > _____________________________________________________________________________ > > David Chalmers Lab: 9903 9623 > Victorian College of Pharmacy Fax: 9903 9582 > 381 Royal Pde, Parkville, Vic 3053 http://synapse.vcp.monash.edu.au > Australia David.Chalmers@vcp.monash.edu.au > _____________________________________________________________________________ > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@www.ccl.net Wed Oct 14 06:03:24 1998 Received: from sc2a.unige.ch (sc2a.unige.ch [129.194.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA22352 Wed, 14 Oct 1998 06:03:23 -0400 (EDT) Received: from PC-Pascal.unige.ch ([129.194.52.113]) by sc2a.unige.ch (PMDF V5.1-10 #U3242) with SMTP id <01J2YKRK5N0Q001MJ3@sc2a.unige.ch> for chemistry@www.ccl.net; Wed, 14 Oct 1998 12:03:22 MET Date: Wed, 14 Oct 1998 12:02:17 +0200 From: pascal boulet Subject: Look for potential parameters for ZrO2 To: ccl Message-id: <01bdf759$b9e3b560$7134c281@PC-Pascal.unige.ch> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.71.1712.3 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 X-Priority: 3 Dear CCL'ers, I am looking for references where I could find the parameters for ZrO2 for the following potentials: 1- Buckingham 2- Lennard-Jones 3- Morse 4- Harmonic Thank you very much for your help, Pascal ****************************************************************** Pascal BOULET Pascal.Boulet@chiphy.unige.ch Department of Physical Chemistry University of Geneva 30, Quai e-Ansermet 1211 Geneva 4 Switzerland tel: (00 41) (22) 702 65 77 or (00 41) (22) 702 65 32 fax: (00 41) (22) 702 65 18 and Institut de Recherche sur la Catalyse, UPR 5401 CNRS Groupe de Chimie Theorique 43, Bd du 11 Novembre 1918 69622 Villeurbanne Cedex France **************************************************************** From chemistry-request@www.ccl.net Wed Oct 14 09:54:41 1998 Received: from hera.math.uni.wroc.pl (hera.math.uni.wroc.pl [156.17.86.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA23659 Wed, 14 Oct 1998 09:54:35 -0400 (EDT) Received: from wchuwr.chem.uni.wroc.pl [156.17.103.193] by hera.math.uni.wroc.pl with esmtp (Exim 1.70 #1) id 0zTRM7-0000EB-00; Wed, 14 Oct 1998 15:52:47 +0200 Received: from ICHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.43); 14 Oct 98 15:54:04 +0200 Received: from SpoolDir by ICHUWR (Mercury 1.43); 14 Oct 98 15:53:48 +0200 From: "Ludmila Szterenberg" Organization: University of Wroclaw (Chemistry) To: chemistry@www.ccl.net Date: Wed, 14 Oct 1998 15:53:45 GMT+2 Subject: aromaticity Priority: normal X-mailer: Pegasus Mail v3.40 Message-ID: <79D9E039B@wchuwr.chem.uni.wroc.pl> Dear Colleagues; I would be very gratefully for references to papers about theoretical studies of molecule aromaticity. Ludmila From chemistry-request@www.ccl.net Wed Oct 14 10:22:26 1998 Received: from sg2-rsa.univ-reims.fr (sg2-rsa.univ-reims.fr [194.199.64.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA23942 Wed, 14 Oct 1998 10:21:45 -0400 (EDT) Received: from localhost (chanteau@localhost) by sg2-rsa.univ-reims.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id QAA25861 for ; Wed, 14 Oct 1998 16:18:26 +0200 Date: Wed, 14 Oct 1998 16:18:26 +0200 (CEST) From: Frederic Chanteau To: chemistry@www.ccl.net Subject: CCL:gaussian 94 problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I am using Gaussian94 installed on a silicon graphic machine and doing geometry optimization on molecule with mp2/6-31g(d) level, but I am always getting a write error in the first geometry optimization step. In files .out the error is: Cycle 5 Pass 1: Errorneous write -1 instead 405768. fd = 5 writwa. and when i want to submit, the error is space left on device disk. It seems to be a read/write problem. Did anyone experience this problem before or have an idea to resolve it. thank you in advance. e-mail: chanteau@sg2-rsa.univ-reims.fr From chemistry-request@www.ccl.net Wed Oct 14 10:54:47 1998 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA24313 Wed, 14 Oct 1998 10:54:45 -0400 (EDT) Received: from elptrs1.rug.ac.be (elptrs1.rug.ac.be [157.193.112.1]) by mserv.rug.ac.be (8.9.0/8.9.0) with SMTP id QAA26654 for ; Wed, 14 Oct 1998 16:54:18 +0200 (MET DST) Received: from pc3bu4.rug.ac.be by elptrs1.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA14100; Wed, 14 Oct 1998 16:49:09 +0200 Received: by pc3bu4.rug.ac.be with Microsoft Mail id <01BDF793.D67CD3C0@pc3bu4.rug.ac.be>; Wed, 14 Oct 1998 16:58:16 +-200 Message-Id: <01BDF793.D67CD3C0@pc3bu4.rug.ac.be> From: Steven Brillant To: "'chemistry@www.ccl.net'" Subject: CCL: Gamess calculation of chloro-fluoro-compounds Date: Wed, 14 Oct 1998 16:58:14 +-200 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi CCL'ers, In order to calculate transition states of several reactions involving C2 chloro-fluoro-compounds and the standard heats of formation of chloro-fluoro-compounds, I am using GAMESS US. For the calculating of both TS and standard heats of formation, I have used a STO NGAUSS=3 basis and a SBK NPFUNC=1 NDFUNC=1 basis Both basis's give poor results for the standard heat of formation for fluorine containing molecules Does anyone have experience with the calculation of chloro-fluoro- compounds and is it possible to advise me for the selection of a better basis for my calculations. Thank you in advance Steven Brillant sb@elptrs1.rug.ac.be PhD student Laboratorium voor Petrochemische Techniek University of Ghent From chemistry-request@www.ccl.net Wed Oct 14 14:40:50 1998 Received: from leona.harvard.edu (daizadeh@leona.harvard.edu [128.103.96.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA25778; Wed, 14 Oct 1998 14:40:50 -0400 (EDT) Received: from localhost (daizadeh@localhost) by leona.harvard.edu (8.8.7/8.8.7) with SMTP id OAA08416; Wed, 14 Oct 1998 14:42:02 -0400 Date: Wed, 14 Oct 1998 14:42:02 -0400 (EDT) From: Iraj Daizadeh To: chemistry@www.ccl.net, chemistry-request@www.ccl.net Subject: BioInformatics. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. I am interested in obtaining codes (written in any language) that are free or relatively free (< $500.00) for members in academia that can visualize and manipulate Genetic Database Information (nucleic acid sequences, etc...) for problems in BioInformatics. I will summarize all respones as is traditional on the CCL. Sincerely, Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Chemistry and Chemical Biology 12 Oxford Street, Box #35 Cambridge, MA 02138-2902 Phone: 617-495-2654 Fax: 617-495-1823 email: daizadeh@lhasa.harvard.edu From chemistry-request@www.ccl.net Wed Oct 14 19:27:31 1998 Received: from anugpo.anu.edu.au (anugpo.anu.edu.au [150.203.2.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA00705 Wed, 14 Oct 1998 19:27:28 -0400 (EDT) Received: from hannes.anu.edu.au (hannes.anu.edu.au [150.203.193.229]) by anugpo.anu.edu.au (8.8.8/8.8.8) with SMTP id JAA04400 for ; Thu, 15 Oct 1998 09:27:15 +1000 (EST) Message-Id: <199810142327.JAA04400@anugpo.anu.edu.au> From: "Johannes Zuegg" Organization: JCSMR To: CHEMISTRY@www.ccl.net Date: Thu, 15 Oct 1998 09:26:09 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Q: One letter code for Sugars Reply-to: johannes.zuegg@anu.edu.au Priority: normal Dear CCL-List, I am modelling oligosaccharide on proteins and had to build up a residue library (within AMBER), where I could use only 3 letters for the residues. Is there any standard way of naming sugar-units in oligosaccharides ? I used a code were: - the first letter is a code for the sugar type (M=Man, G=Glc, N=GlcNAc, K=Gal, S=sialic acid...) - the second is the glycosidic linkage type (A=alpha, B=beta, N=alpha with N as different partial charges ...) - the third is the type of linkage to other sugars (1=only at 1, 2= 1 and 2, 6=1 and 6, A=1,2 and 6, Z= 1,2,3,4 and 6) eg: 1- a-D-Man 4 - a-D-GlcNAc 1(N) --- ASN | MA1 | NN4 2 1 a-D-Gal 1 ----- 6 b-D-Man 2 --- 1 a-D-Man KA2 MBA MA1 For the sugar code I just used a letter which does not interfere with the amino acids. But, do you know if there is a default one letter code for saccharides ? Thanks for any comments and suggestions Johannes --------------------------------------------------------------------- John Curtin School of Medical Research Australian National University Dept. Biochemistry and Molecular Biology PO Box 334 Canberra, ACT 2612, Australia Tel: +61 2 6279 8301 Fax: +61 2 6249 0415 EMail: johannes.zuegg@anu.edu.au --------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Oct 14 23:36:29 1998 Received: from leona.harvard.edu (daizadeh@leona.harvard.edu [128.103.96.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA01459; Wed, 14 Oct 1998 23:36:28 -0400 (EDT) Received: from localhost (daizadeh@localhost) by leona.harvard.edu (8.8.7/8.8.7) with SMTP id XAA13051; Wed, 14 Oct 1998 23:38:12 -0400 Date: Wed, 14 Oct 1998 23:38:12 -0400 (EDT) From: Iraj Daizadeh To: chemistry@www.ccl.net, chemistry-request@www.ccl.net Subject: Protein Vis/Mani. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. I am in search of a program that is able to display multiple protein structures at the same time (viz. on the screen) and is able to manipulate them independently. The resolution of the structures displayed may be primitive. I know that RasMol is able to do this for up to five molecules. Any information concerning other programs prefereable free would be appreciated. A summary will be posted on the CCL as is customary. Thank you. Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Chemistry and Chemical Biology 12 Oxford Street, Box #35 Cambridge, MA 02138-2902 Phone: 617-495-2654 Fax: 617-495-1823 email: daizadeh@lhasa.harvard.edu