From wgalazka@chem.uw.edu.pl Tue Apr 19 07:29:41 1994 Received: from sunic.sunet.se for wgalazka@chem.uw.edu.pl by www.ccl.net (8.6.4/930601.1506) id GAA28614; Tue, 19 Apr 1994 06:52:05 -0400 Received: from chem.uw.edu.pl by sunic.sunet.se (8.6.8/2.03) id MAA12149; Tue, 19 Apr 1994 12:51:08 +0200 Received: from [148.81.21.70] (caesar.chem.uw.edu.pl) by chem.uw.edu.pl (4.1/SMI-4.1) id AA10589; Tue, 19 Apr 94 12:48:34 +0200 Organization: Department of Chemistry, University of Warsaw Address: Pasteura 1, 02-093 Warsaw, Poland. Date: Tue, 19 Apr 94 13:14:30 +0100 From: "Wojciech Galazka" Message-Id: <60062.wgalazka@chem.uw.edu.pl> X-Minuet-Version: Minuet1.0_Beta_14.9 Reply-To: X-Popmail-Charset: English To: Chemistry@ccl.net Subject: CACAO program - summary Thanks to everyone who replied to my question about availability of the CACAO program. Original message ---------------------------------------------------------------------------- Dear neeters, I am looking for CACAO program - a tool to analyse molecular orbitals on PC. I though it was available on www.ccl.net, as says README file on /pub/chemistry/software. Unfortumately there's no the program anywhere. :( Does anyone know other sites where CACAO is available ? Thanking for any help ------------------------------------------------------------------------------ Here is the summary of the responses received ------------------------------------------------------------------------------ From: RAVERA@ch.unito.it (Mauro Ravera) Dear Galazka, you can find the latest version of Cacao directly from Carlo Mealli via ftp at the following address: cacao.issecc.fi.cnr.it Best wishes Mauro Ravera Dipartimento di Chimica Inorganica University of Torino (Italy) ravera@silver.ch.unito.it ------------------------------------------------------------------------------ From: Mr Andrew D Allen I see what you mean, even the mirror site www.ccl.net doesn't have it. I have tried some archie searches and they only turn up on kekule, which as I know doesn't have it now. If you get any replies I be interested also in knowing where to get the program. Andy. ------------------------------------------------------------------------------- From: davide@stinch0.csmtbo.mi.cnr.it dear Wojciech Galazka here is cacao.... have Fun, Davide Proserpio p.s. do not hesitate to contact me for any problem *********************************************************************** * * * C A C A O * * ========= * * Computer Aided Composition of Atomic Orbitals * * (A Package of Programs for Molecular Orbital Analysis) * * [PC Version 3.3, March 1993] * * * * CARLO MEALLI and DAVIDE MARIA PROSERPIO * * Symmetry routines written by KLAUS LINN (1991) * * Revisions made by Angelo Sironi and Jose A. Lopez (1992) * * * *********************************************************************** * Reference: Journal of Chemical Education 1990, (67), 399-402 * *********************************************************************** * * * Istituto per lo Studio della Stereochimica ed Energetica * * dei Composti di Coordinazione (ISSECC-C.N.R.) * * VIA J.NARDI 39 - 50132 FLORENCE (italy) * * TEL. 39-55-243990 or 2346653 - FAX: 2478366 * * e-mail= MEALLI@CACAO.ISSECC.FI.CNR.IT * * * *=====================================================================* * Present address of D.M.P. * * Istituto di Strutturistica Chimica - Universita' di Milano * * Via Venezian 21 * * 20133 Milano, ITALY * * tel. 39-2-70635120, fax 39-2-70635288, * * e-mail= davide@stinch0.csmtbo.mi.cnr.it * *=====================================================================* The PC package (usually released on a floppy diskette) is now available in a self-extracting zipped version and retrievable via the FTP type: FTP cacao.issecc.fi.cnr.it [username: anonymous] or FTP 149.139.10.2 [username: anonymous] define the option "binary" and retrieve the file with the command: get cacaozip.exe !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Although the procedure allows to identify the guest who retrieves the package, we appreciate if an e-mail message is sent to us with your generalities: name, institution, addresses (full and e-mail) telephone and Fax numbers. Use the following address: MEALLI@CACAO.ISSECC.FI.CNR.IT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! To Install and run the CACAO package in your PC (drive C:) use the following procedure. 1) Create a directory MOAN and a subdirectory FILES in DRIVE C: 2) copy the file CACAOZIP.EXE in the Directory MOAN, then enter: MOAN>CACAOZIP 3) Move all the files *.IN in the subdirectory FILES (these are the sample inputs). e.g. MOAN>copy *.IN C:\MOAN\FILES\*.* MOAN>erase *.IN 4) Read the README.DOC file to familiarize with the potentialities of the programs. 5) Run some of the tests provided. P.S. We are not authorized to distribute the PRINTGL.EXE file (Ravitz Software) that allows to process and dump on a printer the drawings made by CACAO (HPGL files). The user can purchase his own copy or obtain it by FTP connection to: wsmr-simtel20.army.mil directory pd1: file PRTGL118.ZIP However, we supply three files (PL.BAT, VIEW.BAT, POSTSCR.BAT) which organize and process the HPGL files made by CACAO (provided that PRINTGL.EXE has been imported in the directory MOAN) ------------------------------------------------------------------- Davide M. Proserpio - Istituto di Chimica Strutturistica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch0.csmtbo.mi.cnr.it ------------------------------------------------------------------- ------------------------------------------------------------------------------ From: YELKADI@CCIT.ARIZONA.EDU Wojciech, CACAO is a program to do EHMO calculations; graphicize numerical resultson screen of PC; draw Walsh diagrams; along with a 3D reps of any MO and its components. A reference for CACAO is, "MO Theory Made Visible"-J Chem Ed. 67 (1990) 399. You can get it using anonymous FTP "FTP CACAO.issecc.fi.cnr.it" or "FTP 149.139.10.2" . Username: Anonymous; Password: Your E-mail address. Get the files cacao.txt and cacaozip.exe. Read cacao.txt. Define option binary. ------------------------------------------------------------------------------ From: molsol@wucmd.wustl.edu (Molecular Solutions) You should be able to get information about the program from Davide M. Proserpie (stinch@imisiam.mi.cnr.it) at the Universita di Milano in Milan. His telephone is 38-2-70635120. Merry Ambos ----------------------------------------------------------------------------- From: ascanio@salve3.salve.edu Please use cacao.issecc.fi.cnr.it (149.139.10.2) Ciao /////////// |/////| | 3 | Ascanio Giuseppe DiPippo, C.H.S. ////// / liter \ Salve Regina University |//| / \ Newport, Roe Dylin 02840 / \ | et cum | ascanio@salve3.salve.edu | H2O | | spiriti | 401-847-6650 | | | vini | 41 30'N 71 20'W -------- --------------- **************************************************************** * " Neva trusst n nee won whoo kan ownly spel a wird won whey" * ******************** Mock Twane ******************************** ----------------------------------------------------------------------------- From: "John M. Simmie, University College, Galway, Ireland" ftp stinch0.csmtbo.mi.cnr.it ------------------------------------------------------------------------------ From: "stefano chimichi" Hi, you can get the last version of the program writing to Dr. Carlo Mealli at mealli@cacao.issecc.fi.cnr.it Cheers Stefano ------------------------------------------------------------------------------- Wojciech Galazka ///////////////////////////////////////////////////****************** // Wojciech Galazka // * // Computer Center // Chemistry - yes,* // Chemistry Department, University of Warsaw // Distortions- no * // Pasteura 1, 02-093 Warsaw, Poland // * ///////////////////////////////////////////////////****************** From szeinfel@fox.cce.usp.br Tue Apr 19 08:29:42 1994 Received: from bee08.uspnet.usp.br for szeinfel@fox.cce.usp.br by www.ccl.net (8.6.4/930601.1506) id IAA29067; Tue, 19 Apr 1994 08:18:50 -0400 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.8.1/RISC-CCE2.0) id JAA72304 Received: from localhost (szeinfel@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id JAA15122 Date: Tue, 19 Apr 1994 09:14:41 -0300 (BDT) From: Rafael N Szeinfeld Subject: Re: CCL:helix dipole To: Margaret Wong cc: CHEMISTRY@ccl.net In-Reply-To: <9404182218.AA27929@chem1.chem.swin.oz.au> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Apr 1994, Margaret Wong wrote: > > Dear Networkers > > Is there any way to calculate the dipole on a helix > in a protein. Several papers I have read recently talk > about the importance of the helix-dipole but none quantify > this value. > > > THANKS > > > Margaret Wong > > _ Dr Margaret Wong V marg@chem1.chem.swin.oz.au _--_|\ > (_)o Chemistry Dept | | mgw@stan.xx.swin.oz.au / \ > /\ \ Swinburne Uni /___\ Ph. 03 819 8542 \_.--.x/ > Hawthorn,OZ,3122 /_____\ Fax 03 819 0834 v > For each pair of opposite charges in the helix you have a dipole momentum vector that points from the positive to the negative charge so I suppose the total dipole momenta vector of that helix will be the vectorial sum of all these vectors. How to calculate it in practice (that is, if there are approximation methods or computer algorhitms) I don't know. Hope this help. Rafael Najmanovich From loki@amethyst.Chemie.Uni-Dortmund.DE Tue Apr 19 09:29:46 1994 Received: from nx1.HRZ.Uni-Dortmund.DE for loki@amethyst.Chemie.Uni-Dortmund.DE by www.ccl.net (8.6.4/930601.1506) id IAA29839; Tue, 19 Apr 1994 08:53:01 -0400 Received: from amethyst.Chemie.Uni-Dortmund.DE by nx1.hrz.uni-dortmund.de with SMTP (PP); Tue, 19 Apr 1994 14:51:15 +0200 Received: by amethyst.Chemie.Uni-Dortmund.DE (AIX 3.2/UCB 5.64/HRZ-V1.0-AIX-12/20/93-15:39:02) id AA19000; Tue, 19 Apr 1994 14:53:11 +0100 From: loki@amethyst.Chemie.Uni-Dortmund.DE (Lothar Koniczek) Message-Id: <9404191353.AA19000@amethyst.Chemie.Uni-Dortmund.DE> Subject: CCL: CACAO the Software To: CHEMISTRY@ccl.net Date: Tue, 19 Apr 1994 14:53:10 +0100 (NFT) X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 733 As i haven't read answering Wojciech Galazka's question, i will do it: CACAO is available at cacao.issecc.fi.cnr.it but the version ist dated Apr 13 1993, so it may not be any longer PD? that's it Lothar Koniczek KEYBOARD FAILURE PRESS ANY KEY TO RESUME ---IBM ---------------------------------------------------------------------------- | Name: Dipl.-Chem. Lothar Koniczek | | Working at: University of Dortmund (Germany) / Department of Chemistry | | E-mail: loki@amethyst.chemie.uni-dortmund.de | | Voice: +49 0231 755-3891 | ---------------------------------------------------------------------------- From ppaneth1@itr1.p.lodz.pl Tue Apr 19 10:29:58 1994 Received: from itr1.p.lodz.pl for ppaneth1@itr1.p.lodz.pl by www.ccl.net (8.6.4/930601.1506) id JAA00554; Tue, 19 Apr 1994 09:44:46 -0400 From: Piotr Paneth To: chemistry@ccl.net Subject: parametrizations X-Mailer: ScoMail 1.0 Date: Tue, 19 Apr 1994 15:44:13 +0200 (MESZ) Message-ID: <9404191544.aa19877@itr1.itr1.p.lodz.pl> I'd like to argue with Andy's last comment on parametrizations which are crafted for a particular property. I'm with Cris in this respect although my reasoning is a bit diffrent. I represent 'users' end rather than 'developers' point of view and therefore any hamiltonian is just a tool for me (and not a precious baby). A tool is good only when it does what it was invented for and of course, yes, I'd like to have an universal tool. But if this is unavailable I'd much prefer to have five different good tools for what I need them for rather that one so so for everything. Having said so much here comes my "request" to developers; is there someone with a good parametrizations for vibrational analysis? I'm calculating isotope effects and a method yielding reliable frequencies (not even necessary in absolute sense but isotopic shifts) would be a blessing. By the by, I'd appreciate any references to QM calculations of heavy-atoms isotope effects - I was recently browsing through the literature and found surprizingly few of these. Piotr ************************************************************************* Piotr Paneth Ph.D., D.Sc. Professor and Vice-chairman Department of Chemistry Technical University of Lodz Zwirki 36, 90-924 Lodz, Poland phone: (+48 42) 31-31-95 fax: (+48 42) 55-29-02 e-mail: ppaneth1@plearn.bitnet or ppaneth1@itr1.p.lodz.pl ************************************************************************* From CHAKRAVO@ucs.indiana.edu Tue Apr 19 11:31:54 1994 Received: from PO3.indiana.edu for CHAKRAVO@ucs.indiana.edu by www.ccl.net (8.6.4/930601.1506) id KAA01594; Tue, 19 Apr 1994 10:56:31 -0400 Message-Id: <199404191456.KAA01594@www.ccl.net> Received: from LOCAL:.prism.DECnet by PO3.Indiana.EDU; id AA00272 (5.65c+jsm/2.5.1jsm); Tue, 19 Apr 1994 09:51:34 -0500 Date: Tue, 19 Apr 94 09:56:31 EST From: Subhas Chakravorty X-To: PO%"chemistry@ccl.net" Subject: Different recipes for diffrent molecules To: chemistry@ccl.net How about a model hamiltonian for every different molecule. I think that is adequate. We only need countably infinite number of methods for each different molecule or atom namely the one which gives the right answer That will keep us in business too! Considering that there is an excess of me types ? Happy computing ? Subhas From mealli@cacao.issecc.fi.cnr.it Tue Apr 19 12:32:15 1994 Received: from cacao.issecc.fi.cnr.it for mealli@cacao.issecc.fi.cnr.it by www.ccl.net (8.6.4/930601.1506) id LAA02215; Tue, 19 Apr 1994 11:45:32 -0400 From: Received: by cacao.issecc.fi.cnr.it (5.57/Ultrix3.0-C) id AA05168; Tue, 19 Apr 94 17:43:03 GMT Message-Id: <9404191743.AA05168@cacao.issecc.fi.cnr.it> To: chemistry@ccl.net Subject: A notice from the authors about CACAO4.0 Date: Tue Apr 19 17:42:00 1994 To the old and new CACAO users, A beta version of CACAO 4.0 has been available at www.ccl.net for a limited time but it was withdrawn because of some known bugs. Now, most of the problems are about to be solved and the new version will be made available soon from our FTP site (149.139.10.2). A notice will be sent through this computer list. In the meanwhile, new users can get the older version from the same source. Among the features of the announced PC version, a new 32 bits compiler helps to bypass the DOS 640K limit and large molecules can be handled at increased speed. Also thanks to an improved algorhythm, the MO drawings are obtained in a fraction of the time. A user-friendly interface allows the user to analyze and compare the results of many different calculations during a single interactive section. Hard copies of each drawing can be produced in real time. Further information will be found in the release notes. The authors: Carlo Mealli and Davide M. Proserpio Dr. Carlo Mealli ISSECC, CNR Via J.NARDI 39, 50132 Firenze, ITALY e-mail: mealli@cacao.issecc.fi.cnr.it Tel. 0039-55-2346653 (243990) - Fax 2478366 - Home 4492709 From cletner@remcure.bmb.wright.edu Tue Apr 19 12:39:36 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.4/930601.1506) id MAA02656; Tue, 19 Apr 1994 12:06:43 -0400 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA22165; Tue, 19 Apr 94 11:55:16 -0700 Date: Tue, 19 Apr 1994 10:48:46 -0700 (PDT) From: Charles Letner Subject: Re: CCL:Semiempirical parameterization yet again... To: Computational Chemistry List In-Reply-To: <01HBBXIOSRFQ9S3U9X@VAX1.UMKC.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 18 Apr 1994 AHOLDER@VAX1.UMKC.EDU wrote: > ("The snake oil salesman mounted the soapbox to confront the angry > crowd. He began to speak:") > ... > I can safely say that MM has nothing to do with chemistry, > but is more or less a fit to a convenient set of functions. It > does have chemical validity in that it gives us good answers to some > questions. > QM is an entirely different situation, in that the actual arbiters of > chemistry, the electrons, are treated directly by mathematical functions. > The chemistry come OUT of a model that describes the electrons. > ... > ("The snake oil salesman descends from the soapbox to thunderous applause.") ("Then the one lone dissenter humbly approaches the soapbox.") I'd like to address the issue that MM "has nothing to do with chemistry". How can this be? Is this to imply that molecular structure is not in the realm of chemistry? MM invokes the Born-Oppenhimer approximation (a QM idea if I'm not mistaken) to allow us to ignore electrons. Of course by doing this we have to leave bond making and bond breaking (electronic processes) behind. However, nuclear motions are still allowed. Because MM takes a more simplified approach to modeling structure than does QM does not mean it has nothing to do with chemistry. However MM force fields do have terms that model chemical phenomenon. Examples include bond angles, bond lengths, etc. Granted, these are parmeterized based on chemical data. However, they do attempt to model chemically meaningfull aspects of molecular structure. Further, is not any mathmatical fomalism a model? This is to include QM, a more detailed and complicated model of atomic events. Yes, QM may have a higher level of theory involed than does MM but that does not relegate MM to the pesudo-chemistry domain. Each has their place in solving chemical problems. There are questions that MM can answer that QM and semi-emperical methods can not yet answer because of practical conciderations (Size of molecules). This is not to imply that MM can answer any question that QM can. Remember, processes that involve electrons have been left behind with this model of molecular structure. It is fair to say that one aspect of computational chemistry is knowing which methods can answer the question possed in the most efficent way. ("And with this the lone dissenter prays to the god that be that his life will be spared by the restless crowd") Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 From matt@mercury.aichem.arizona.edu Tue Apr 19 14:29:47 1994 Received: from mercury.aichem.arizona.edu for matt@mercury.aichem.arizona.edu by www.ccl.net (8.6.4/930601.1506) id OAA04600; Tue, 19 Apr 1994 14:20:57 -0400 Received: by mercury.aichem.arizona.edu (5.57/Ultrix3.0-C) id AA03010; Tue, 19 Apr 94 11:10:19 -0700 Date: Tue, 19 Apr 1994 11:02:06 -0700 (MST) From: Matthew Stahl Subject: MM calc's of stereoisomers To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Netters, Is it appropriate to apply molecular mechanics to the determination of the relative stability of two stereoisomers? In other words, if a single stereocenter is inverted, should I be able to calculate which one is more stable? Mechanics is normally applied to conformational isomers, but not configurational isomers. Where do stereoisomers fit into the picture? Thanks in advance, matt <-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-> _/_/_/ _/_/_/_/_/ Mr. Matthew Stahl _/ _/ _/ Artificial Intelligence in Chemistry _/_/_/_/_/ _/ University of Arizona _/ _/ _/ Tucson, AZ 85721 _/ _/ _/_/_/_/_/ matt@mercury.aichem.arizona.edu <-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-><-> From gerard@scripps.edu Tue Apr 19 14:39:35 1994 Received: from scripps.edu for gerard@scripps.edu by www.ccl.net (8.6.4/930601.1506) id OAA04224; Tue, 19 Apr 1994 14:08:07 -0400 Received: from planti.scripps.edu by scripps.edu (5.61/1.34) id AA29077; Tue, 19 Apr 94 11:04:53 -0700 Received: by planti (920330.SGI/911001.SGI) for @riscsm.scripps.edu:chemistry@ccl.net id AA13356; Tue, 19 Apr 94 10:57:31 -0700 Date: Tue, 19 Apr 94 10:57:31 -0700 From: gerard@scripps.edu (Gerard Jensen) Message-Id: <9404191757.AA13356@planti> To: chemistry@ccl.net Subject: Helix Dipole Dear Net-people, In response to: ******************************************************************** Dear Networkers Is there any way to calculate the dipole on a helix in a protein. Several papers I have read recently talk about the importance of the helix-dipole but none quantify this value. THANKS Margaret Wong ******************************************************************** In response to the above, fewer and fewer people I think believe in the so-called macrodipole anymore. A nice alternative was presented by Aqvist and Warshel cited below. AQVIST J; LUECKE H; QUIOCHO FA; WARSHEL A. DIPOLES LOCALIZED AT HELIX TERMINI OF PROTEINS STABILIZE CHARGES. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1991 MAR, V88 N5:2026-2030. --------------------------------------------------------------------------------- stereo pair stereo pair Gerard M. Jensen, Ph.D. The Scripps Research Institute-MB8 H H H H Department of Molecular Biology \ | | \ 10666 N. Torrey Pines Road H--C---C--H H---C---C---H La Jolla, California, 92037 / | | / gerard@scripps.edu H H H H Ph: 619-554-4325 Fax: 619-554-6188 --------------------------------------------------------------------------------- From cmartin@rainbow.uchicago.edu Tue Apr 19 14:48:18 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id OAA04618; Tue, 19 Apr 1994 14:23:21 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Tue, 19 Apr 94 13:23:19 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA24546; Tue, 19 Apr 94 13:55:56 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9404191855.AA24546@rainbow.uchicago.edu> Subject: Ab Initio Theory of Semiempirical Methods To: mail@rainbow.uchicago.edu, chemistry@ccl.net Date: Tue, 19 Apr 1994 13:55:56 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2641 Netters, More on the discussion about semiempirical methods: I have been working with Karl Freed at the University of Chicago also trying to develop a "new model" for semiempirical methods. We have had quite a bit of success producing semiempirical parameters for pi-electron systems soley from correlated ab initio calculations using the effective valence shell Hamiltonian (Hv) method. Note that our ``parameters'' involve no tweaking and no number-twiddling (Some of this will come out in JCP soon, but right now the papers are tied up in press. They will also be available online via JCP express. Of course, we will be happy to send anyone reprints or preprints if they are interested) The Hv method provides a rigorous derivation of the semiempirical Hamiltonians directly >from the Schr\"odinger Equation. Granted, we are not not upto the all-valence-electron case, but there are two reasons for that. First, the computations are very complicated and slow, and second, the standard semiempirical Hamiltonians seem to average three-electron correlation contributions which appear in the exact theory. We do not yet understand the all of the details of this averaging, and as a result, we can not yet produce all-valence electron parameters. We are very close to solving this problem, but it is not trivial. From our point of view, there is alot more going on in these methods than just number-twiddling, and there is a lot of room for advancement in both the ab initio theory of semiempirical methods and the computational implementation of the effective Hamiltonian method. Also, from our studies of semiempirical theory, we have learned how to perform better ab initio calculations. The Hv method is a decent multi-reference ab initio method, albiet it is a bit slow in it's current implementation. We would be happy to discuss some of these problems with researchers trying to build new semiempirical methods, and we also have a post doc position (see the CCL job listings) open in this area. I would also like to know if this work is being duplicated. I know that some people use effective Hamiltonians for Ligand Field Theory, Effective-Spin Hamiltonians, etc. ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From rickr@scripps.edu Tue Apr 19 15:29:51 1994 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.4/930601.1506) id OAA04745; Tue, 19 Apr 1994 14:32:12 -0400 Received: from ppg.scripps.edu by scripps.edu (5.61/1.34) id AA00946; Tue, 19 Apr 94 11:31:00 -0700 Received: by ppg.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA01658; Tue, 19 Apr 94 11:17:53 PDT Date: Tue, 19 Apr 94 11:17:53 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9404191817.AA01658@ppg.Scripps.EDU> To: chemistry@ccl.net Subject: chemical information databases Folks, Greetings. I was wondering if anyone might have any suggestions for database software to optimally hold the following info for molecules: Molecule, molecular structure, related reactions, related literature data and information I would be glad to post a summary. Thanks Rick Ross PPG Industries P.O. Box 9 Allison Park, PA 15101 rickr@ppg.scripps.edu (412)492-5359 From burkhart@goodyear.com Tue Apr 19 15:38:45 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id OAA04893; Tue, 19 Apr 1994 14:40:32 -0400 Received: from rdsrv2 by goodyear.com (4.1/SMI-4.1) id AA04981; Tue, 19 Apr 94 14:40:32 EDT Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA01910; Tue, 19 Apr 94 14:40:31 EDT Received: by rds325 (920330.SGI/920502.SGI.AUTO) for @rdsrv2:chemistry@ccl.net id AA21683; Tue, 19 Apr 94 14:40:30 -0400 Date: Tue, 19 Apr 94 14:40:30 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9404191840.AA21683@rds325> To: chemistry@ccl.net Subject: Snake Oil... Cc: burkhart@goodyear.com Don't worry Chuck, you're not alone in this escapade. I have read the "snake oil" position. Needless to say, I'm NOT a happy camper. I second the reaction by Chuck Letner. I'm also sure that molecular forcefield developers will be happy to know that what they do is not REALLY chemistry. REALLY NOW. I'm sure that anyone that does molecular statistical mechanics will be resting better knowing that their need for accuracy is nothing more than "number-twiddling of the highest order". Indeed, all those people trying to compute macroscopic thermodynamic properties will be relieved that they no longer have to worry about the CHEMISTRY of the problem. This is nothing more than a question of scale. If you accept that following electrons is a finer-scale problem than following atoms (a reasonable one to me), it is not true that because it is a more finely grained problem that we should abandon the thought that chemistry is NOT in the coarser one. Since the majority of my work is in molecular mechanics, I would be the first to call it empirical. But because we fit things to a different functional form (one that London derived from quantum principles in the 30's) that lumps some of the "chemistry" into a more generic equation, then it is not as worthy of being called CHEMISTRY. I guess that because I do statistical mechanics problems, then MY work is REAL CHEMISTRY compared to people who do phase separation modeling or other forms of morphology modeling. WRONG. This form of argument, as it is not substantial, makes me more than a little irritated. The point about ab initio methods being a parameterization also misses the mark. The great advantage of standard Hartree-Fock ab initio methods over semi-empirical methods is that they normally CONVERGE to an answer that you can have some faith in. The faith comes in the numbers...the better the numbers, the better the faith. No more, no less. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From cmartin@rainbow.uchicago.edu Tue Apr 19 15:47:29 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id OAA04886; Tue, 19 Apr 1994 14:40:02 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for CHEMISTRY@ccl.net Tue, 19 Apr 94 13:40:02 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:CHEMISTRY@ccl.net id AA25040; Tue, 19 Apr 94 14:12:43 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9404191912.AA25040@rainbow.uchicago.edu> Subject: Other Models for Semiempirical Hamiltonians To: CHEMISTRY@ccl.net Date: Tue, 19 Apr 1994 14:12:42 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2700 Netters, More on the discussion about semiempirical methods: I have been working with Karl Freed at the University of Chicago also trying to develop a "new model" for semiempirical methods. We have had quite a bit of success producing semiempirical parameters for pi-electron systems soley from correlated ab initio calculations using the effective valence shell Hamiltonian (Hv) method. Note that our ``parameters'' involve no tweaking and no number-twiddling (Some of this will come out in JCP soon, but right now the papers are tied up in press. They will also be available online via JCP express. Of course, we will be happy to send anyone reprints or preprints if they are interested) The Hv method provides a rigorous derivation of the semiempirical Hamiltonians directly >from the Schr\"odinger Equation. Granted, we are not not upto the all-valence-electron case, but there are two reasons for that. First, the computations are very complicated and slow, and second, the standard semiempirical Hamiltonians seem to average three-electron correlation contributions which appear in the exact theory. We do not yet understand the all of the details of this averaging, and as a result, we can not yet produce all-valence electron parameters. We are very close to solving this problem, but it is not trivial. From our point of view, there is alot more going on in these methods than just number-twiddling, and there is a lot of room for advancement in both the ab initio theory of semiempirical methods and the computational implementation of the effective Hamiltonian method. Also, from our studies of semiempirical theory, we have learned how to perform better ab initio calculations. The Hv method is a decent multi-reference configuration ab initio method which can reproduce multiple potential energy surfaces for reasonable size molecules very accurately. We would be happy to discuss some of these problems with researchers trying to build new semiempirical methods, and we also have a post doc position (see the CCL job listings) open in this area. I would also like to know if this work is being duplicated. I know that some people use effective Hamiltonians for Ligand Field Theory, Effective-Spin Hamiltonians, etc. ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From jle@world.std.com Tue Apr 19 16:29:48 1994 Received: from news.std.com for jle@world.std.com by www.ccl.net (8.6.4/930601.1506) id PAA06092; Tue, 19 Apr 1994 15:53:03 -0400 Received: from world.std.com by news.std.com (5.65c/Spike-2.1) id AA03075; Tue, 19 Apr 1994 15:52:55 -0400 Received: by world.std.com (5.65c/Spike-2.0) id AA21225; Tue, 19 Apr 1994 15:52:54 -0400 Date: Tue, 19 Apr 1994 15:52:54 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199404191952.AA21225@world.std.com> To: chemistry@ccl.net Subject: Seeking information re: polarization maps... Folks, In the latest J. Mol. Graphics (3/94), the lead article describes polarization maps, obtained from the difference between an interaction and electrostatic potential (expressed as grids?). My question - when generating the interaction grid, a +1 probe is used - is that an H+ with the associated basis set, or a "bare" point charge? Does it matter either way? Joe From jtgolab@amoco.com Tue Apr 19 17:29:50 1994 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.6.4/930601.1506) id RAA08162; Tue, 19 Apr 1994 17:03:52 -0400 Received: by interlock.amoco.com id AA19119 (InterLock SMTP Gateway 1.1 for CHEMISTRY@ccl.net); Tue, 19 Apr 1994 16:03:49 -0500 Received: by interlock.amoco.com (Internal Mail Agent-3); Tue, 19 Apr 1994 16:03:49 -0500 Received: by interlock.amoco.com (Internal Mail Agent-2); Tue, 19 Apr 1994 16:03:49 -0500 Received: by interlock.amoco.com (Internal Mail Agent-1); Tue, 19 Apr 1994 16:03:49 -0500 From: jtgolab@amoco.com (Joe Golab) Message-Id: <9404191602.ZM17960@vacc47.nap.amoco.com> Date: Tue, 19 Apr 1994 16:02:33 -0500 X-Mailer: Z-Mail (2.1.5 20sep93) To: CHEMISTRY@ccl.net Subject: Comments from the Peanut Gallery Cc: jtgolab@amoco.com OKay, I can't resist anymore. First a small correction: The BO does NOT "allow us to ignore electrons" actually just the opposite. The BO states that to a good approximation, one can consider the electrons in a molecule to be moving in the field of fixed nuclei. This allows QM to neglect the KE of the nuclei and makes the repulsion between nuclei effectively constant. The electrons are still there and handled explicitly, self-consistently. Basically, I agree with the assertion that if MM models are used to do "structure" things - like determine the relative energies of conformers - then everything is OK. Finally, Please Stop The Debate About "REAL CHEMISTRY". Unless you are also an experimentalist, we all MODEL chemistry - some of it as unreal as you can imagine! "Can't we all just get along?" -- :Joe jtgolab@amoco.com (708) 961-7878 From mercie@mail.med.cornell.edu Tue Apr 19 18:29:58 1994 Received: from mail.med.cornell.edu for mercie@mail.med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id RAA08552; Tue, 19 Apr 1994 17:32:06 -0400 Received: (from mercie@localhost) by mail.med.cornell.edu (8.6.8/ech1.65) id RAA14693; Tue, 19 Apr 1994 17:31:27 -0400 Date: Tue, 19 Apr 1994 17:31:27 -0400 (EDT) From: Gustavo Mercier Subject: Re: CCL:helix dipole To: Margaret Wong cc: CHEMISTRY@ccl.net In-Reply-To: <9404182218.AA27929@chem1.chem.swin.oz.au> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Apr 1994, Margaret Wong wrote: > > Is there any way to calculate the dipole on a helix > in a protein. Several papers I have read recently talk > about the importance of the helix-dipole but none quantify > this value. > Hi! The initial suggestion of a helix dipole moment was by Hol et. al. Nature v. 273, p. 443-446, 1978. If I remember correctly in this paper the dipole was approximated by 0.5xL where L is the length of the alpha helix. This is crude but occassionally useful. How to compute the helix - dipole, or for that matter the moment associated with a given element of a protein structure is not a trivial matter. For example, 1) Excluding solvent effects, you can simply use SUM(i) qixRi for the segment you are interested. You may or may not include the sidechains. Other variations in this theme are also possible, like vectorial sums of the the C=O bond moment that contributes to the helix macrodipole 2) If you want to include solvent effects using state of the art techniques, things are a bit more complex. You may consider a finite element solution to the Poisson equation as done by M K. Gilson and coworkers. You may also like to look at R. Zauhar's work who uses boundary elements methods for the same purpose. Programs that implement the finite element method include UHBD and Delphi. I have not seen Zauhar's boundary element method in a program available for distribution. Good Luck, gus mercier mercie@cumc.cornell.edu From dave%@mel.dit.csiro.au Tue Apr 19 20:29:55 1994 Received: from shark.mel.dit.csiro.au for dave%@mel.dit.csiro.au by www.ccl.net (8.6.4/930601.1506) id UAA10629; Tue, 19 Apr 1994 20:13:46 -0400 Received: from ([138.194.40.143]) by shark.mel.dit.csiro.au with SMTP id AA09795 (5.65c/IDA-1.4.4/DIT-1.3 for ); Wed, 20 Apr 1994 10:12:48 +1000 Date: Wed, 20 Apr 94 10:13:14 EST From: "Dr. Dave Winkler" Subject: Re: CCL:chemical information databases To: rickr@scripps.edu (Rick Ross), chemistry@ccl.net X-Mailer: LeeMail 2.0.4 Message-Id: >Folks, > Greetings. I was wondering if anyone might have any suggestions for >database software to optimally hold the following info for molecules: > > Molecule, molecular structure, related reactions, related literature > data and information > > I would be glad to post a summary. Thanks > > We use the REACCS chemical database on our VAX and ISIS on a Mac to do this (Molecular Design Ltd, support@molecular.com). I have also looked at the new database capabilities in Chem-X (chemical Design Ltd, Oxford, Chemdesign@applelink.apple.com), which also allow this. I used a beta version and had some problems but the new version may be OK. Runs on Mac, PC, VAX and Unix boxes. I believe Tripos are adding reaction database capabilities to their Unity database (support@tripos.com). Of these, Mac/Isis and Unity (if available) would be my first choice. There are, of course, vast chemical reaction databases for sale (up to 1.8 million reactions) as well. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From ECCLES@cmda.abbott.com Tue Apr 19 20:36:17 1994 Received: from abtlabs.abbott.com for ECCLES@cmda.abbott.com by www.ccl.net (8.6.4/930601.1506) id UAA10650; Tue, 19 Apr 1994 20:15:57 -0400 Received: from randb.pprd.abbott.com (randb.abbott.com) by abtlabs.abbott.com with SMTP id AA24738 (5.65c/IDA-1.4.4 for ); Tue, 19 Apr 1994 19:12:59 -0500 Received: from DECNET-MAIL (ECCLES@CMDA) by RANDB.ABBOTT.COM (PMDF #2795 ) id <01HBDC60NJM8CDRZ5S@RANDB.ABBOTT.COM>; Tue, 19 Apr 1994 19:15:50 CST Date: 19 Apr 1994 19:15:50 -0600 (CST) From: "Bev Eccles,x70346,D42T/AP6B" Subject: Position available: Chemical Information Scientist/Abbott Labs To: CHEMISTRY@ccl.net Message-Id: <01HBDC60NJMACDRZ5S@RANDB.ABBOTT.COM> X-Envelope-To: CHEMISTRY@ccl.net X-Vms-To: RANDB::IN%"CHEMISTRY@ccl.net" X-Vms-Cc: ECCLES Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Abbott Laboratories has an immediate opening for a CHEMICAL INFORMATION SCIENTIST You will develop and support chemical information systems for application in pharmaceutical products R&D. These systems support drug sample inventory, chemical modeling, substructure queries, reaction databases and integration with other databases and applications. Databases include proprietary and commercial information. You will have broad responsibilities including project leadership, full software lifecycle planning, development, maintenance and support, conformance to federal regulations, chemical database administration and technology evaluation. We require a PhD in Chemistry or equivalent, at least two years of project leadership experience, and four years of scientific software development background, preferably in chemical information systems. Since 1888, Abbott Laboratories has been a pioneer in the development of advanced health care products and services. Today you could join us and contribute to research that is improving the quality of human life in 130 countries worldwide. Abbott provides an excellent salary and benefits package including profit sharing and a stock retirement plan. We are located in an attractive suburban area, approximately 30 miles north of Chicago. For confidental consideration, please send your resume via email (not the list) to: ECCLESB@ABBOTT.COM or snail mail to: Linda DeLavallade Job #69074 D393/AP6B Abbott Laboratories One Abbott Park Road Abbott Park, IL 60064. Abbott is an Affirmative Action Employer/Smoke-Free Environment - Bev Eccles, Ph.D.