From qocruces@usc.es Mon May 15 03:06:38 1995 Received: from uscmail.usc.es for qocruces@usc.es by www.ccl.net (8.6.10/930601.1506) id CAA07184; Mon, 15 May 1995 02:52:46 -0400 Received: by uscmail.usc.es (5.67b/1.34) id AA11209; Mon, 15 May 1995 08:56:42 +0200 Date: Mon, 15 May 1995 08:56:42 +0200 From: qocruces@usc.es (Jacobo Cruces Colado) Message-Id: <199505150656.AA11209@uscmail.usc.es> To: chemistry@ccl.net Subject: CCL: NMR Analyzer package I want to announce the availability of a new spin system simulator, called NMR Analyzer. The program allows the calculation up to seven nuclei, but non-calculated signals can also be incorporated into the spectrum. Other program feature allows the analysis of AB, ABX, AB2 and AA'XX' spin systems through the spectral frequencies. Examples of these types of spin systems, and parame- ters for calculating the theoretical 1H-NMR spectrum of some molecules (methyl acrylate, beta-D-glucopyranose pentaacetate...) are included in the package. The program has been uploaded to the CICA FTP site and to Infomeister The program runs on 386-486 based computers under Microsoft Windows 3.x, and requires the library VBRUN100.DLL, which can be easily found in many FTP sites. Questions, comments and suggestions will be very appreciated. Jacobo Cruces Colado Department of Organic Chemistry University of Santiago de Compostela Avda. de las Ciencias s/n 15706 SPAIN e-mail: qocruces@uscmail.usc.es jcruces@sfdzuma.usc.es From ahirasim@agr.kyushu-u.ac.jp Mon May 15 06:51:41 1995 Received: from nogakubu.agr.kyushu-u.ac.jp for ahirasim@agr.kyushu-u.ac.jp by www.ccl.net (8.6.10/930601.1506) id GAA08904; Mon, 15 May 1995 06:49:18 -0400 Received: from [133.5.200.49] (pestic3.ach.agr.kyushu-u.ac.jp [133.5.200.49]) by nogakubu.agr.kyushu-u.ac.jp (8.6.9+2.4W/3.4Wbeta3) with SMTP id TAA20643 for ; Mon, 15 May 1995 19:49:52 +0900 Message-Id: <199505151049.TAA20643@nogakubu.agr.kyushu-u.ac.jp> Date: Mon, 15 May 1995 19:52:29 +0900 To: chemistry@ccl.net From: ahirasim@agr.kyushu-u.ac.jp (Akinori Hirashima) X-Sender: ahirasim@nogakubu.agr.kyushu-u.ac.jp Subject: summary of web for chemistry Return-Receipt-To: ahirasim@agr.kyushu-u.ac.jp MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear CCL'ers: This is the summary of the responses I received to my question on web for chemistry. I feel quite strongly that the following should be "de facto" collections: http://hackberry.chem.niu.edu:70/0/cheminf.html http://www.chem.ucla.edu/chempointers.html http://www.ccl.net/ccl/chemurls.html Thanks for your input. ahirasim@agr.kyushu-u.ac.jp (Akinori Hirashima) From toukie@zui.unizh.ch Mon May 15 07:06:42 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/930601.1506) id GAA08896; Mon, 15 May 1995 06:46:09 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA29700; Mon, 15 May 95 12:46:03 +0200 X-Nupop-Charset: Swiss Date: Mon, 15 May 1995 12:45:56 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <45957.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Conformer generator for MOPAC Dear Colleagues; Is anyone aware of a conformer generating programme that can be inter- faced with MOPAC 6.0 or MOPAC7 (or possibly MOPAC 93)? The programme I seek should be able to rotate designated bonds in a molecule, systematically (fixed rotational angle) and/or (preferably) using a Monte Carlo stochastic procedure, to generate an ensemble of molecules plus their Z-matrices (or some other coordinate file format that can be readily converted to a Z- matrix); I would then wish to feed the resultant Z-matrices one at a time into MOPAC in order to obtain heats of formation and other information. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Institut fuer orale Mikrbiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund- und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich 7 Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From Daniel.Vercauteren@fundp.ac.be Mon May 15 07:06:45 1995 Received: from hermes.fundp.ac.be for Daniel.Vercauteren@fundp.ac.be by www.ccl.net (8.6.10/930601.1506) id HAA09010; Mon, 15 May 1995 07:00:11 -0400 Received: by hermes.fundp.ac.be; id AA13855; Mon, 15 May 1995 13:07:42 +0200 Received: from telemann.scf.fundp.ac.be by hermes.fundp.ac.be; id AA13855; Mon, 15 May 1995 13:07:42 +0200 Received: from pci-dpv.scf.fundp.ac.be by telemann.scf.fundp.ac.be (AIX 3.2/UCB 5.64/4.03) id AA32777; Mon, 15 May 1995 12:46:45 +0200 Date: Mon, 15 May 1995 12:46:45 +0200 Message-Id: <9505151046.AA32777@telemann.scf.fundp.ac.be> X-Sender: vercau@telemann.scf.fundp.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: chemistry@ccl.net From: Daniel.Vercauteren@fundp.ac.be (Daniel Vercauteren) Subject: NN courses in Namur (Belgium) The "Societe Royale de Chimie de Belgique" (Namur Section) and the "Laboratoire de Physico-Chimie Informatique des Facultes Universitaires Notre Dame de la Paix", Namur (Belgium) propose in the framework of the "Advanced Lectures in Computational Chemistry and Physics" of the Namur SCF Center a series of specialized lectures on: NEURAL NETWORKS FOR CHEMISTS By Jure Zupan Kemijski Institut, Ljubljana, Slovenija National Institute of Chemistry, Slovenia Monday, June 12th, 1995, 16h00-18h30 (including coffee break) Theoretical Background: error-back propagation, Kohonen, and counter-propagation. Application Possibilities: supervised and unsupervised learning, classifications and experimental design, models and inverse models, models and optimisations. Tuesday, June 13th, 1995, 16h00-18h30 (including coffee break) Chemical Applications Part I: spectroscopies (IR, UV, EDX spectra), property predictions (origin of olive oils, ageing of TiO2-based paints, mechanical properties of paint coatings), control of chemical processes (fault predictions, direct and inverse models for continuously stirred tank reactor - CSTR). Wednesday, June 14th, 1995, 16h00-18h30 (including coffee break) Chemical Applications Part II: reactivity of bonds, electrostatic potentials, secondary structure of proteins (moving window), etc=8A Ref.: J. Zupan & J. Gasteiger, Neural Networks for Chemists, VCH, Weinheim, Germany, 1993. Informations: Prof. D.P.Vercauteren, Dr. L. Leherte Laboratoire de Physico-Chimie Informatique Facult=E9s Universitaires Notre-Dame de la Paix Rue de Bruxelles, 61 B-5000 NAMUR T=E9l.: +32-81-724534 -- FAX: +32-81-724530 e-mail: vercau,leherte@scf.fundp.ac.be Address of the Courses: =46acult=E9s Universitaires Notre-Dame de la Paix Auditorium CH1, rue J.Graf=E9, 2 B-5000 Namur, Belgium =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D | Prof. Daniel P. Vercauteren | tel +32 (81) 72 45 34 | | Departement de Chimie | fax +32 (81) 72 45 30 | | F.U.N.D.P. | e-mail Daniel.Vercauteren@fundp.ac.be | | Rue de Bruxelles, 61 | | | B-5000 Namur Belgium | | =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From SERGEI@ps1515.chemie.uni-marburg.de Mon May 15 08:06:56 1995 Received: from Mailer.Uni-Marburg.DE for SERGEI@ps1515.chemie.uni-marburg.de by www.ccl.net (8.6.10/930601.1506) id HAA09770; Mon, 15 May 1995 07:58:45 -0400 Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA109479; Mon, 15 May 1995 13:58:30 +0200 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 15 May 95 13:59:05 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 15 May 95 13:58:46 GMT+2 To: chemistry@ccl.net From: "Sergei Vyboishchikov" Date: 15 May 95 13:58:41 MDT Subject: Gear method: summary Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Message-Id: <28D0D5B7ADC@ps1515.chemie.uni-marburg.de> Dear Netters: Recently I have posted a question concerning Fortran implementations of the Gear method. I would like to express my sincere gratitude to the netters whose responses I received. Some of the replies were very helpful. One of the programs is available, for example, from ftp://ftp.uni-bayreuth.de/mounts/pubdsk2/math/netlib/sodepack The book by Vetterling et al. "Numerical Receipts..." does not contain any Fortran code for Gear method. Here is the summary of the responses (in part shortened): -------------------------------------------------------------------- From: uscgckc3@ibmmail.com Hello Sergei, The QCPE has a very nice pc program set called "GEAR ITERATOR" which is available in Microsoft Fortran. I believe they will even supply the executable. The QCPE number is QCMP022. Regards, Anthony DeBellis Ciba Corp. uscgckc3@ibmmail.com -------------------------------------------------------------------- From: "FREDERICK IGNATZ-HOOVER" Try "gear" from the QCPE at the University of Indiana in Bloomington, In. USA -------------------------------------------------------------------- From: doherty@msc.edu (David C. Doherty) ..... -- On the other hand, you may have some luck poking around at netlib, for instance: http://www.netlib.org/ode/index.html ftp://ftp.netlib.org/ode/index http://www.netlib.org/odepack/index.html ftp://ftp.netlib.org/odepack/index -------------------------------------------------------------------- From: Dave Edelson A reasonable implementation of Gear is found in the IMSL Library, routine IVPAG, which can be switched between Adams-Moulton or Gear. However, it requires the entire library to be implemented, since the routine calls other subroutines from the library. Fortran code for older versions of Gear are found in several places in the literature. D. Edelson College of Engineering Florida A&M/State Universities -------------------------------------------------------------------- From: ars@ari.net (ARSoftware Corporation) Though not fortran, Kinetics for Windows is an easy to use Microsoft Windows based software package for modeling complex chemical reactions and reaction mechanisms. This unique program computes the concentrations of the chemical species in a system as a function of time for multistep reversible reactions, given the reaction mechanism, the forward and reverse rate constants, and the initial concentrations of reactants and products. KINETICS easy to use Windows interface allows you to input complex chemical systems by simply typing in the reaction equations and the associated rate constants. The program automatically formulates the differential equations necessary to describe the kinetics of the chemical system. The rate equations are then numerically integrated using a modified GEAR algorithm. ..... For more information, contact ars@ari.net Sincerely, Sat Want S. Khalsa ARSoftware ===================================================== ARSoftware Corporation 8201 Corporate Drive Landover, MD 20785 Phone: (301) 459-3773 FAX: (301) 459-3776 e-mail: ars@ari.net -------------------------------------------------------------------- From: jcw@biosym.com (Jack Wathey ) Dear Sergei, The program you want is "lsoda" (acronym for Livermore Solver of Ordinary Differential equations: Automatic). It's a robust and highly optimized FORTRAN implementation with automatic integration step size control. Unfortunately I don't remember where it is on the net, but you should be able to find it with Archie or some similar net-searching tool. Best wishes, Jack Wathey Biosym Technologies, Inc. -------------------------------------------------------------------- From: jpool@ccsf.caltech.edu (J.C.T. Pool) Have you looked at Netlib for ODE codes? See http://www.netlib.org/index.html or send a message to netlib.org with the text send index -------------------------------------------------------------------- From: "Dr. Chris L. Waller" Numerical Recipes in Fortran book and program diskette. ==================================================================== Yours, Sergei. From h.rzepa@ic.ac.uk Mon May 15 10:36:48 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.10/930601.1506) id KAA12540; Mon, 15 May 1995 10:28:32 -0400 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 15 May 1995 15:21:07 +0100 Received: from [155.198.224.89] by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA06338; Mon, 15 May 95 15:21:03 +0100 X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 15 May 1995 14:21:08 +0000 To: chemistry@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Re: CCL:summary of web for chemistry >Dear CCL'ers: > >This is the summary of the responses I received to my question >on web for chemistry. I feel quite strongly >that the following should be "de facto" collections: > >http://hackberry.chem.niu.edu:70/0/cheminf.html >http://www.chem.ucla.edu/chempointers.html >http://www.ccl.net/ccl/chemurls.html We went through this some time ago. The selection by any individual of three "de facto" sites is bound to create dissent from those whose other three favourite sites are omitted. In no way should the above individual opinion be taken as an acceptance that we have all "voted" and that the above is the result. I do not wish to necessarily dissent from the three selected, except to point out they are all in the USA. As we are all aware, the three sites contain a great many pointers, and that access from non-USA sites can be VERY problematic (and indeed vice versa). A good non-USA site is http://www.shef.ac.uk/uni/academic/A-C/chem/chemistry-www-sites.html I am sure that colleagues in other part of Europe, Austalia etc can provide other alternatives. An important issue becomes the need to establish automatic mirrors of the best sites. Unless we do this urgently, the grid-lock that some expect to occur very soon in the global Internet may make all this discussion irrelevant anyway. Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.1.1; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. World-Wide Web URL: http://www.ch.ic.ac.uk/rzepa.html From marty@ionchannel.med.harvard.edu Mon May 15 13:51:51 1995 Received: from ns2.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.10/930601.1506) id NAA18002; Mon, 15 May 1995 13:41:41 -0400 Received: by ns2.harvard.edu (5.65/DEC-Ultrix/4.3) id AA19527; Mon, 15 May 1995 13:41:32 -0400 Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA28994; Mon, 15 May 95 13:35:23 EDT Received: from [134.174.159.173] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:chemistry@ccl.net id AA00278; Mon, 15 May 95 13:28:20 -0700 Date: Mon, 15 May 95 13:28:20 -0700 Message-Id: <9505152028.AA00278@ionchannel.med.harvard.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Subject: differential H-bonds Could someone please direct me to references that discuss pharmacophores that preferentially H-bond with alcohols rather than corboxylates, and vice versa. I will summarize if there is interest. Thank you in advance, Marty Gallagher ========================================================================= Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave http://ionchannel.med.harvard.edu/~marty Boston, MA 02115 =========================================================================== Finger, or WWW for PGP Public Key =========================================================================== -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From jkg1000@cus.cam.ac.uk Mon May 15 14:05:13 1995 Received: from bootes.cus.cam.ac.uk for jkg1000@cus.cam.ac.uk by www.ccl.net (8.6.10/930601.1506) id NAA17954; Mon, 15 May 1995 13:39:17 -0400 Received: from apus.cus.cam.ac.uk [131.111.8.2] (ident = root) by bootes.cus.cam.ac.uk with smtp (Smail-3.1.29.0 #36) id m0sB3N2-000C0QC; Mon, 15 May 95 17:51 BST Received: by apus.cus.cam.ac.uk (Smail-3.1.29.0 #36) id m0sB3N2-00034IC; Mon, 15 May 95 17:51 BST Date: Mon, 15 May 1995 17:51:50 +0100 (BST) From: "J.K. Gregory" To: chemistry@ccl.net cc: Jiri Czernek Subject: ab initio request Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A summary of the replies to the following message: > I would like to know if there is an ab initio program that will allow me > to apply a static electric field to a molecule and still be able to > calculate derivatives. I want to calculate a reaction path in the presence > of a field and so I still need the derivatives. Cadpac can apply a field > but cannot do derivatives in this field. Many thanks in advance. Hi, GAMESS can now do first derivatives (and thus geometry optimizations) with a static electric field. If you are interested send an email to that effect to mike@si.fi.ameslab.gov Thanks, Brett -- ____________________________________ Brett Bode 201 Spedding Hall Iowa State University Ames Iowa 50011 (515) 294-4604 FAX (515) 294-0105 E-Mail: brett@si.fi.ameslab.gov ____________________________________ I'm not sure if what we've got will meet your needs -- but Release 4.5 of HyperChem will do ab initio calculations, including gradients, and allows the user to include the effects of point charges from other atoms in the system as a classical static field. If you need a homogeneous field, then I'm afraid that we can't help. Release 4.5 for Windows will be shipping in a few weeks; the SGI version will be along by the end of July. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ I guess that Gamess ( mike@si.fi.ameslab.gov (Mike Schmidt) ) and Gaussian allow such calculations. DMol (DFT) too. Thank you for sharing, if it is possible, replies you could receive. I am interested in answers you could receive. Regards, Frederic Bouyer ____________________________________________________________________ Frederic BOUYER Laboratoire d'Electrochimie et de Chimie Analytique Equipe "Reactivite en Milieux Ioniques Liquides" (G. PICARD) ENSCP 11, rue Pierre et Marie Curie 75231 PARIS Cedex 05 FRANCE Tel : (33)-1-43-54-53-84 ou (33)-1-44-27-67-51 ou (33)-1-44-27-66-94 Fax : (33)-1-44-27-67-50 E-mail : bouyer@ext.jussieu.fr http://alcyone.enscp.jussieu.fr/ created, in progress ... http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/frederic.html Jon, Turbomole (ab initio package from Biosym) has the capabilty to calculate energy 1st derivatives in the presence of an external electric field. - Andy -- ================================================================ Andrew C. Scheiner Phone: (619) 546-5346 Biosym Technologies, Inc. scheiner@biosym.com ================================================================ Gaussian can do derivatives (first and second) including the static electric field at differents leves levels of theory. I have been doing these calculations since 1989. Someone else in our group has aldo done IRC calculations including the electric field. (Jordi Mestres) Best regards, Jose L. Andres Institute of Computational Chemistry Dept. of Chemistry University of Girona c/ albereda 3-5 17071 Girona SPAIN From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon May 15 14:22:46 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.10/930601.1506) id OAA19069; Mon, 15 May 1995 14:18:35 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA15280 (5.65c/IDA-1.4.4 for ); Mon, 15 May 1995 20:16:12 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16045; Mon, 15 May 95 20:16:43 +0200 Date: Mon, 15 May 95 20:16:43 +0200 From: Herbert Homeier (t4720) Message-Id: <9505151816.AA16045@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net, chem-comp@mailbase.ac.uk, na.digest@na-net.ornl.gov, scicomp@informatik.tu-muenchen.de, maple-list@daisy.uwaterloo.ca, molecular-dynamics-news@mailbase.ac.uk Subject: Server Announcement Cc: sweidman@nas.edu >>>>>>>>>>>>>>>>>>>>>>>>>>> Announcement <<<<<<<<<<<<<<<<<<<<<<<<<<< The combined WWW/gopher/ftp server at rchs1.uni-regensburg.de (IP 132.199.48.1) now provides Preprints, Technical Reports, and Theses in the fields Computational Chemistry, Scientific Computing, and Numerical Analysis. ------------------------------------------------------------------ WWW: http://rchs1.uni-regensburg.de:80/preprint.html ftp://rchs1.chemie.uni-regensburg.de/pub/preprint gopher://rchs1.chemie.uni-regensburg.de:70/11./pub/preprint ------------------------------------------------------------------ gopher: gopher rchs1.uni-regensburg.de --> 8. Data files (= /pub ) --> 45. preprint ------------------------------------------------------------------ ftp: ftp rchs1.uni-regensburg.de Name(...) : anonymous Password: cd /pub/preprint --------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From mvaul@altern.com Fri May 12 06:48:07 1995 Received: from fog for mvaul@altern.com by www.ccl.net (8.6.10/930601.1506) id GAA27845; Fri, 12 May 1995 06:48:03 -0400 Received: by fog (Linux Smail3.1.29.1 #1) id m0s9uIz-0003I7C; Fri, 12 May 95 12:58 GMT Message-Id: Date: Fri, 12 May 95 12:58 GMT To: chemistry@ccl.net Subject: heat of formation From: mvaul@altern.com (mvaul) Do you know calculation codes available to compute heat of formation for nitro compounds.? I ve attemped to use MOPAC 6 but there s a big difference with the EOF found in the scentific litterature. thanks for replying. mvaul@altern.com (mvaul) From toukie@zui.unizh.ch Mon May 15 06:46:13 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/930601.1506) id GAA08896; Mon, 15 May 1995 06:46:09 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA29700; Mon, 15 May 95 12:46:03 +0200 X-Nupop-Charset: Swiss Date: Mon, 15 May 1995 12:45:56 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <45957.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Conformer generator for MOPAC Dear Colleagues; Is anyone aware of a conformer generating programme that can be inter- faced with MOPAC 6.0 or MOPAC7 (or possibly MOPAC 93)? The programme I seek should be able to rotate designated bonds in a molecule, systematically (fixed rotational angle) and/or (preferably) using a Monte Carlo stochastic procedure, to generate an ensemble of molecules plus their Z-matrices (or some other coordinate file format that can be readily converted to a Z- matrix); I would then wish to feed the resultant Z-matrices one at a time into MOPAC in order to obtain heats of formation and other information. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Institut fuer orale Mikrbiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund- und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich 7 Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From TSHEHLA@che.und.ac.za Mon May 15 15:51:50 1995 Received: from owl.und.ac.za for TSHEHLA@che.und.ac.za by www.ccl.net (8.6.10/930601.1506) id PAA22099; Mon, 15 May 1995 15:45:23 -0400 Received: from Charon1.CC.und.ac.za by owl.und.ac.za with SMTP (PP) id <04706-6@owl.und.ac.za>; Mon, 15 May 1995 17:05:15 +0200 Received: From STUD-AFF/WORKQUEUE by charon1.cc.und.ac.za via Charon-4.0A-VROOM with IPX id 100.950515161040.2880; 15 May 95 17:05:14 -0200 Message-ID: From: TSHEHLA Organization: University of Natal - Durban To: chemistry@ccl.net Date: Mon, 15 May 1995 16:10:16 +0200 (SAST) Subject: Converting g92 standard orientation to a z-matrix orientation... Priority: normal X-mailer: PMail v3.0 (R1a) Hi out there! Does anyone out there have a fortran routine that converts g92 standard orientation into a z-matrix. Any pointers will be appreciated. Thanking you all in advance T M Tshehla From overney@pegasus.unm.edu Mon May 15 16:06:50 1995 Received: from pegasus.unm.edu for overney@pegasus.unm.edu by www.ccl.net (8.6.10/930601.1506) id QAA22402; Mon, 15 May 1995 16:00:51 -0400 Received: by pegasus.unm.edu (Smail3.1.28.1 #7) id m0sB6Ju-0000PlC; Mon, 15 May 95 14:00 MDT Date: Mon, 15 May 1995 14:00:50 -0600 (MDT) From: "gregor t. overney" To: chemistry@ccl.net cc: Gregor Overney Subject: Are methods based on DFT ab initio? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Are methods based on density functional theory (DFT) ab initio? --------------------------------------------------------------- Recently, I had a conversation about theories based on DFT with some of my colleagues. Some support Dr. Jerzy Cioslowski's idea to put those methods into the same category as semiempirical methods and some, including myself, do not. I would like to ask quantum chemists to answer the above question. Are methods based on density functional theory (DFT) of an ab initio nature? If yes, why? And if not, why not? Thanks for your comments. Gregor -------------------------------------------------------------------------- Gregor T. Overney, Ph.D. Department of Chemistry Senior Research Associate The University of New Mexico Albuquerque, NM 87131-1096 Voice: (505) 277-1665 FAX: (505) 277-2609 WWW: http://enke.unm.edu/gregor/gregor.htm -------------------------------------------------------------------------- From THOMPSON@bobcat.csc.wsu.edu Mon May 15 16:21:52 1995 Received: from bobcat.csc.wsu.edu for THOMPSON@bobcat.csc.wsu.edu by www.ccl.net (8.6.10/930601.1506) id QAA22851; Mon, 15 May 1995 16:20:12 -0400 Date: Mon, 15 May 1995 13:07:54 -0700 (PDT) From: "Steve Thompson: VADMS genetics" To: Sogin@evol1.MBL.EDU, gary@phylo.life.uiuc.edu, Davison@UH.EDU, Joe@Genetics.Washington.EDU, gilbertd@bio.indiana.edu, danj@dev.gdb.ORG, KRobison@nucleus.harvard.edu, ernest@lenti.med.umn.edu, tree@ag.Arizona.EDU X-Vmsmail-To: @MAILDIS:EDUCATION.DIS Message-Id: <950515130754.20400abe@JAGUAR.CSC.WSU.EDU> Subject: PSB Biocomputing Educ' Call: final version Dear Colleague, Please find enclosed a "Call for Papers, Demonstrations and Participation" for the upcoming workshop on Biocomputing Education: Challenges and Opportunities to be held as part of the First Pacific Symposium on Biocomputing (PSB-I), the agenda of which can be found following the Call. We are excited about this meeting and the workshop. To the best of our knowledge (and please correct us if you have knowledge that we are wrong), this will be the first time that a forum on educational issues will be included in a meeting on computational approaches to molecular biology. Please take a few minutes to fill out and return the enclosed questionnaire. We would especially like your comments regarding what you think are the most important issues in biocomputing education. Plan to submit a paper if you can, but at least mark the meeting on your calendar and consider joining us in Hawaii next year. Regards, Susan J. Johns Steven M. Thompson A. Keith Dunker ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ CALL FOR PAPERS, DEMONSTRATIONS AND PARTICIPATION Biocomputing Education: Challenges and Opportunities First Pacific Symposium on Biocomputing Ritz Carlton Hotel, Big Island, Hawaii --- January 3-6, 1996 Susan J. Johns, Steven M. Thompson, and A. Keith Dunker Center for Visualization, Analysis and Design in the Molecular Sciences (VADMS) and the Department of Biochemistry and Biophysics Washington State University Pullman, WA 99164-1224 & 4660 Phone: (509) 335-0424 & 335-5322 FAX: (509) 335-0540 & 335-9688 E-mail: prcadms@jaguar.csc.wsu.edu thompson@jaguar.csc.wsu.edu dunker@jaguar.csc.wsu.edu The need for a forum on educational issues: Philosophically, we have come to the view that computer science is to molecular biology as calculus is to physics, yet at present there is really no well defined curriculum for computational molecular biology. Although specific individuals have developed courses or workshops, educational materials such as textbooks or laboratory exercises based on existing courses or workshops are not widely available. In addition to the absence of formal materials, there is also a lack of communication among those of us who are now teaching courses in this domain. Correcting the deficiencies regarding the lack of educational materials and the lack of communication on educational issues represents both a challenge and an opportunity for the community of scientists who are currently doing research in biocomputing. A workshop: Recognizing the need for the development of an educational forum, the Pacific Symposium on Biocomputing (PSB) has included our workshop on biocomputing education as part of its overall program. Our hope is that this workshop on biocomputing education will become an important node with regard to the dissemination of educational materials, information, and approaches in this field. To the end of improving communication, we encourage your formal or informal participation at our workshop on educational issues. Bring your course outlines, syllabi, laboratory exercises, videotapes, CD-ROMS or whatever educational materials you have developed or that you use for teaching computational approaches to biology, especially molecular biology. We hope to have a very open discussion about what works and what does not and what needs to be done in the future. Submission of papers: We also encourage you to submit full technical papers or abstracts for posters on biocomputing education to be included in the general refereeing process. We envision that such papers could range from philosophical discussions on biocomputing education to the nuts-and-bolts of particular courses or workshops that are enjoying significant success. Given a sufficient number of refereed papers submitted on biocomputing education, additional time will be allocated by the PSB organizers for their presentation. Submitted papers and abstracts will be carefully peer reviewed by at least 3 independent referees for publication in an archival proceedings. Publication of a full paper is required for oral presentation. Submissions from researchers who desire to present their work at the conference without the publication of a full paper are eligible for exhibition space in the poster and demonstration sessions. Publication: In addition to traditional print options, PSB is exploring the possibility of publishing its proceedings as the first in a series of peer-reviewed electronic conference publications from a major scientific publisher. Authors would have the ability to include extensive color graphics, animations, datasets and source code in papers published electronically and to obtain printed versions of individual papers by facsimile. The publisher would offer attractive licensing arrangements for the series, intending to insure the greatest possible availability in libraries and other institutions. Whether we opt for electronic publication or not, we hope to have the contents of the proceedings indexed in Medline and elsewhere. PSB is also exploring the possibility of CD-ROM distribution, as well as a follow-up book with extended versions of the best papers. We hope that these forward-looking publication efforts will encourage you to submit your best upcoming work to this conference. Key dates: Immediate -- Return of questionnaire June 15 -- Abstract of papers, presentation or demonstration July 1 -- Feedback from us on abstracts July 27 -- Full papers due September 11 -- Notification of acceptance, with comments October 2 -- Final, revised manuscripts due Conference registration for authors is required along with the submission of the final paper on October 2. There will be an early registration discount for people who register on or before that date. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ First Pacific Symposium on Biocomputing (PSB-I) Ritz Carlton Hotel, Big Island, Hawaii --- January 3-6, 1996 The conference will consist of several tracks: § The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution Chairs: Richard A. Goldstein & Russ B. Altman Contact: altman@comis.stanford.edu § Interactive Molecular Visualization Chairs: Michael Teschener and Chris Henn Contact: micha@basel.sig.com § Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics Chairs: Tom Head, Takashi Yokomori, Katsumi Nitta & Kiyoshi Asai Contact: tom@binghamton.edu § Discovering, Learning, Analyzing and Predicting Protein Structure Chairs: Richard H. Lathrop & A. Keith Dunker Contact: dunker@jaguar.csc.wsu.edu minitracks: § Population Modeling Chair: John Conery Contact: conery@cs.uoregon.edu § Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution Chairs: Martin Field & Jiali Gao contact: mjfield@ubs.fr § Models of Control Systems in Biology Chair: Seth Michelson contact: seth.michelson@syntex.com § Computational Studies on the Design of Protease Inhibitors Chair: C. N. Hodge Contact: hodgecn@lldmpc.dnet.dupont.com and workshops: § Internet Tools for Computational Biology Chair: Reinhard Doelz Contact: doelz@ubaclu.unias.ch § Biocomputing Education: Challenges and Opportunities Chairs: Susan J. Johns, Steven M. Thompson & A. Keith Dunker Contact: thompson@jaguar.csc.wsu.edu Key dates: July 27 -- Full papers due September 11 -- Notification of acceptance, with comments October 2 -- Final, revised manuscripts due ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Pacific Symposium on Biocomputing --- Educational Issues Questionnaire Please provide us with the following information: Name: E-Mail: Address: Telephone: FAX: General comments on Biocomputing Education: Courses or workshops you are teaching in the broadly defined field of "Biocomputing" and the year such courses or workshops began: A brief statement of your willingness to participate in the 1996 meeting as one: § Who would submit a paper by early June describing course, workshop or curriculum issues and who would subsequently attend the meeting to present the paper if accepted; (yes or no): if yes, tentative title: § Who would plan to attend the meeting, participate in panel discussions, software demonstrations, and workshops on educational issues, but who would not submit a paper; (yes or no): § Who might or might not attend the meeting, but who would be willing to review papers. (yes or no): Names and addresses of others who might be interested in participating in the educational session, especially the names and addresses of possible referees: Finally, as there might be some funds available to support speakers, please indicate whether you would require financial support to attend the meeting as a speaker. Funds would be absolutely required, yes or no: Please FAX the filled-out questionnaire to (509) 335-9688 or e-mail to: thompson@jaguar.csc.wsu.edu or mail to: Steve Thompson Washington State University VADMS Center Pullman WA 99164-1224 From nobes@theor.ch.cam.ac.uk Mon May 15 17:21:51 1995 Received: from ppsw3.cam.ac.uk for nobes@theor.ch.cam.ac.uk by www.ccl.net (8.6.10/930601.1506) id RAA24097; Mon, 15 May 1995 17:14:30 -0400 Received: from theor.ch.cam.ac.uk (actually host gmos.ch.cam.ac.uk) by mauve.csi.cam.ac.uk with SMTP-CAM (XTPP8.1) as ppsw.cam.ac.uk; Mon, 15 May 1995 22:13:54 +0100 Received: by theor.ch.cam.ac.uk (931110.SGI/930416.SGI) for @ppsw.cam.ac.uk:chemistry@ccl.net id AA19817; Mon, 15 May 95 22:15:01 +0100 From: nobes@theor.ch.cam.ac.uk (Ross Nobes) Message-Id: <9505152115.AA19817@theor.ch.cam.ac.uk> Subject: Use of localized orbitals To: chemistry@ccl.net Date: Mon, 15 May 1995 22:15:01 +0100 (BST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 617 Could anyone please point me to a recent review on the use of localized orbitals in chemistry? Thanks, Ross -- +---------------------------------------------------------------------+ | Ross Nobes | | Department of Chemistry Phone: + 44 1223 336384 | | University of Cambridge Fax: + 44 1223 336362 | | Lensfield Road | | Cambridge CB2 1EW, UK E-mail: nobes@theor.ch.cam.ac.uk | +---------------------------------------------------------------------+ From elewars@alchemy.chem.utoronto.ca Mon May 15 18:36:50 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/930601.1506) id SAA25392; Mon, 15 May 1995 18:27:47 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id SAA20006 for chemistry@ccl.net; Mon, 15 May 1995 18:27:43 -0400 Date: Mon, 15 May 1995 18:27:43 -0400 From: "E. Lewars" Message-Id: <199505152227.SAA20006@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: RE IS DFT AB INITIO? Those interested in this question may want to think about the remarks in *Quantum Chemistry* by Ira N. Levine (4th ed., 1991), p 525: "Because density functional calculations do not use the exact E(XC) and V(XC) [in the Kohn-Sham eqs on p 521 & 522] they are not, strictly speaking, ab initio calculations. However, they do not use parameters fitted to experimental data, as do ...semiempirical methods..., and so are closer in spirit to ab initio calculations than to semiempirical ones." Errol Lewars === From dickson@zinc.chem.ucalgary.ca Mon May 15 19:21:54 1995 Received: from zinc.chem.ucalgary.ca for dickson@zinc.chem.ucalgary.ca by www.ccl.net (8.6.10/930601.1506) id TAA25858; Mon, 15 May 1995 19:13:30 -0400 Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA33725; Mon, 15 May 1995 17:15:47 -0600 Date: Mon, 15 May 1995 17:15:47 -0600 From: dickson@zinc.chem.ucalgary.ca (Ross M. Dickson) Message-Id: <9505152315.AA33725@zinc.chem.ucalgary.ca> To: chemistry@ccl.net, overney@unm.edu Subject: Re: CCL:Are methods based on DFT ab initio? Cc: I don't normally get into nomenclature arguments, but I'll bite this time. I'm not familiar with Prof. Cioslowski's arguments in favour of calling DFT "semi-empirical", so I can't answer them directly, but I take the position that DFT is better characterized as a branch of the ab initio family. I most often hear this question raised in connection with one functional or another which contains some parameter (usually one, sometimes as many as three) determined by fitting to experiment. A classic example is the local exchange functional variously known as X-alpha, Hartree-Fock-Slater (HFS), or Slater exchange. There were non-empirical physical arguments for a value of either 2/3 or 1 (one) for alpha. Eventually many workers settled on a compromise value of 0.7 for empirical reasons. Does this make HFS a semi-empirical theory? I think not: There is one and only one adjustable parameter, and the functional should be equally applicable in any part of any molecule. If you insisted on calling such a scheme semi-empirical, then you'd have to call Hartree- Fock frequencies adjusted by the famous 10% factor semi-empirical as well. (If you already do, that's fine with me. You're a purer man than I am, Gunga Din.) In a semi-empirical method, parameters are chosen for *each atom*, and if you don't have parameters for cesium, you simply cannot do semi-empirical calculations on cesium chloride. But once you have this one DFT parameter -- or even two or three -- you can do calculations anywhere on the periodic table (modulo relativity). Now there have been calculations carried out in which this HFS alpha parameter *was* different for each atomic environment (the so-called muffin-tin method), and those I *would* call semi-empirical. But that does not represent the main body of present-day density functional theory. There are certainly more recent examples of density functionals containing one or more fitted parameters; my former boss Axel Becke frequently ends up with one unknown left over when he's inventing a new functional. Nevertheless, in every case I know of the result after the fitting has been a density functional intended to be universally applicable. What we are pursuing, after all, is Hohenberg's and Kohn's universal functional of the density -- you only need, in principle, one functional and you can then calculate all nondegenerate ground states. If we try to derive this functional from physics, we are working "from first principles" -- or "ab initio". The other sense in which I can imagine DFT being characterized as "semi-empirical" is the manner in which the recent proliferation of functionals has been greeted by the user community. I've seen more papers and talks and posters than I can count that had the nature of "try six different density functionals and see which one gives the best results for my systems." If some thought then goes into the relationship between the underlying physics of the functionals and their performance, this is quite reasonable. But if the lowest average deviation from experiment -- sometimes by a vanishingly small margin -- is then taken as the only reason for choosing functional X over functional Y for further studies on analogs of these systems, then we are at some risk of passing straight through semi-empirical methods into pure empiricism, and neither DFT nor semi-empirical specialists might care to claim such work as characteristic of their field. (Although I should confess I'm prone to this disease myself. Mea culpa.) In conclusion, I don't really care what DFT is called except inasmuch as naming affects understanding. I myself try not to use language which classes DFT as either ab initio or semi-empirical, because those terms have accreted fairly specialized meanings over the last twenty years and DFT really doesn't fit comfortably into either. Cheers, Ross M. Dickson, Ph.D. (dickson@zinc.chem.ucalgary.ca) Chemistry Dept., The University of Calgary, Alberta, Canada. From tony@schroeder.newcastle.edu.au Mon May 15 21:21:51 1995 Received: from schroeder.newcastle.edu.au for tony@schroeder.newcastle.edu.au by www.ccl.net (8.6.10/930601.1506) id VAA26714; Mon, 15 May 1995 21:11:36 -0400 Received: by schroeder.newcastle.edu.au (AIX 3.2/UCB 5.64/4.03) id AA20533; Tue, 16 May 1995 11:11:12 GMT Date: Tue, 16 May 1995 11:11:11 +0000 (CUT) From: Tony Dyson To: Computational Chemistry List Subject: CCL: Is DFT ab initio? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It seems to me that the choice of pseudopotentials goes a long way towards determining whether a DFT calculation can really be called ab initio. Comments? Tony ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +49 21 5425 University of Newcastle fax: +49 21 6907 Callaghan, Australia, 2308 ================================================================ From overney@pegasus.unm.edu Mon May 15 21:35:05 1995 Received: from pegasus.unm.edu for overney@pegasus.unm.edu by www.ccl.net (8.6.10/930601.1506) id VAA26663; Mon, 15 May 1995 21:07:53 -0400 Received: by pegasus.unm.edu (Smail3.1.28.1 #7) id m0sBB6z-0000NuC; Mon, 15 May 95 19:07 MDT Date: Mon, 15 May 1995 19:07:49 -0600 (MDT) From: "gregor t. overney" To: chemistry@ccl.net cc: Gregor Overney Subject: Are methods based on DFT ab initio? (More information) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Are methods based on density functional theory (DFT) ab initio? A quick summary ----------------------------------------------------------------------- I am very grateful for the feedback I am currently receiving on this issue. So far, I can subdivide the different opinions into three groups (one more than I thought). The first one wants to have DFT-based methods to be considered as ab initio (which is my personal opinion). The second one likes to put it into a category placed between semiempirical and ab initio, where some researchers still like to use the expression "from first principles" but not "ab initio". (And I always thought that ab initio means nothing more than from first principles). Last but not least, the third group sees DFT-based methods to be more of a semiempirical rather than an ab initio nature. Since quite a few readers asked me to be more specific with my statement regarding Dr. Jerzy Cioslowski's point of view, I cite from the conclusions of a book contribution written by Dr. Jerzy Cioslowski ("Reviews In Computational Chemistry", edited by K.B. Lipkowitz and D.B. Boyd, VCH Publishers, Inc. 1993, Volume 4, Chapter 1, "Ab Initio Calculations on Large Molecules: Methodology and Applications"): "A subject that has not been covered here is that of the methods based on density functional theory (DFT). It is the author's view that these methods, although without doubt having a legitimate place in quantum chemistry, are more of a semiempirical rather than an ab initio (as often claimed) nature. The functionals used in the DFT programs (such as DMOL [1]) are quite simple, and it is not currently known how they can be methodically improved. This is in contrast to the molecular orbital methods, in which the accuracy is limited only by the available computer resources." [1] B. Delley, J. Chem. Phys., 92, 508 (1990). Some people have pointed out that it is not so important how we are going to classify DFT-based methods. But I think that expressions in quantum theory shall be exactly defined to make sure that the risk of mis- communication is strongly reduced. Gregor Overney -------------------------------------------------------------------------- Gregor T. Overney, Ph.D. Department of Chemistry Senior Research Associate The University of New Mexico Albuquerque, NM 87131-1096 Voice: (505) 277-1665 FAX: (505) 277-2609 WWW: http://enke.unm.edu/gregor/gregor.htm --------------------------------------------------------------------------