From salb@sbu.ac.uk Thu Mar 21 01:17:45 1996 Received: from psb.sbu.ac.uk for salb@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id AAA01701; Thu, 21 Mar 1996 00:53:31 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Thu, 21 Mar 1996 05:53:53 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Thu, 21 Mar 1996 05:53:09 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Thu, 21 Mar 1996 05:52:21 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:13:40 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 01:40:56 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id UAA00728; Fri, 15 Mar 1996 20:19:01 -0500 (EST) Received: from ix3.ix.netcom.com for jsalb@ix.netcom.com by www.ccl.net (8.7.1/950822.1) id TAA00612; Fri, 15 Mar 1996 19:44:05 -0500 (EST) Received: from lax-ca25-28.ix.netcom.com by ix3.ix.netcom.com (8.6.13/SMI-4.1/Netcom) id QAA29338; Fri, 15 Mar 1996 16:43:37 -0800 Originally-From: jsalb@ix.netcom.com To: chemistry@www.ccl.net Subject: CCL:Pronunciation of "Conformer" Date: Sat, 16 Mar 1996 00:43:36 GMT Message-ID: <314a0e15.34336363@smtp.ix.netcom.com> I apologize for wasting valuable bandwidth, but is the preferred pronunciation of "conformer" either "con' form er" or "con form' er"? Thanks. -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: jsalb@ix.netcom.com -- Original Sender From: Address: jsalb@ix.netcom.com 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 aussian.com@sbu.ac.uk Thu Mar 21 01:25:59 1996 Received: from psb.sbu.ac.uk for aussian.com@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id BAA01758; Thu, 21 Mar 1996 01:09:03 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Thu, 21 Mar 1996 06:09:24 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Thu, 21 Mar 1996 06:08:35 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Thu, 21 Mar 1996 06:07:48 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:49:11 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Fri, 15 Mar 1996 16:58:36 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id LAA24145; Fri, 15 Mar 1996 11:21:50 -0500 (EST) Received: from relay5.UU.NET for gaussian.com!moses@lorentzian.com by www.ccl.net (8.7.1/950822.1) id LAA24046; Fri, 15 Mar 1996 11:11:42 -0500 (EST) Received: from uucp6.UU.NET by relay5.UU.NET with SMTP id QQahdw24763; Fri, 15 Mar 1996 11:11:38 -0500 (EST) Message-ID: Received: from m10.UUCP by uucp6.UU.NET with UUCP/RMAIL ; Fri, 15 Mar 1996 11:11:40 -0500 Received: by m10.lorentzian.com; Fri, 15 Mar 1996 11:09:12 -0500 Received: by mousse.gaussian.com; Fri, 15 Mar 1996 10:10:15 -0500 Originally-From: gaussian.com Subject: CCL:G:Come see us at ACS To: CHEMISTRY@www.ccl.net Date: Fri, 15 Mar 1996 10:10:15 -0500 (EST) Representatives from Gaussian, Inc. will be demonstrating Gaussian 94 in the IBM booth (#417) at the ACS Exposition in New Orleans, March 25-27. We will also sponsor a drawing, in which you could win a FREE copy of G94W. Be sure to stop by and say hello, and register for the drawing. *------------------------*------------------------*-----------------------* | David J. Moses, Ph.D. | Carnegie Office Park | info@gaussian.com | | Vice President, C.O.O. | Building Six | 412-279-6700 (Voice) | | Gaussian, Inc. | Pittsburgh, PA 15106 | 412-279-2118 (FAX) | *------------------------*------------------------*-----------------------* -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: gaussian.com!moses@lorentzian.com -- Original Sender From: Address: gaussian.com!moses@lorentzian.com 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 ariane@WAPinorg.chemie.uni-halle.de Thu Mar 21 03:17:45 1996 Received: from WAPinorg.chemie.uni-halle.de for ariane@WAPinorg.chemie.uni-halle.de by www.ccl.net (8.7.1/950822.1) id CAA02434; Thu, 21 Mar 1996 02:43:39 -0500 (EST) Received: by WAPinorg.chemie.uni-halle.de (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id IAA16680; Thu, 21 Mar 1996 08:10:10 +0100 Date: Thu, 21 Mar 1996 08:10:10 +0100 From: ariane@WAPinorg.chemie.uni-halle.de (Ariane) Message-Id: <199603210710.IAA16680@WAPinorg.chemie.uni-halle.de> To: CHEMISTRY@www.ccl.net Subject: CCL: How to get information Dear colleagues, maybe this is a FAQ, but I would like to know if there are any opportunities to get information about the table of contents (authors, title, brief summary) of the latest issues of journals like - J. Am. Chem. Soc. J. Chem. Phys. J. Phys. Chem. Int. J. Quant. Chem. Theor. Chim. Acta Organometallics J. Organometallic Chemistry Inorg. Chemistry J. Comp. Chem. Chem. Phys. Letters ... by surfing within the web-space or via STN-access ( a free of charge access would be preferable). Any references or pointers are highly appreciated. Regards, Ariane From wieland@btm2d1.mat.uni-bayreuth.de Thu Mar 21 06:17:55 1996 Received: from btm2d1.mat.uni-bayreuth.de for wieland@btm2d1.mat.uni-bayreuth.de by www.ccl.net (8.7.1/950822.1) id GAA03531; Thu, 21 Mar 1996 06:05:02 -0500 (EST) From: Received: by btm2d1.mat.uni-bayreuth.de (IBM OS/2 SENDMAIL VERSION 1.3.14/2.12um) id AA0241; Thu, 21 Mar 96 12:05:03 +0100 Message-Id: <9603211105.AA0241@btm2d1.mat.uni-bayreuth.de> Mime-Version: 1.0 Date: Thu, 21 Mar 96 11:56:00 +0100 To: Bernd.Hartke@RUS.Uni-Stuttgart.DE, chemistry@www.ccl.net Subject: Re: pronunciation of conformer X-Mailer: Ultimedia Mail/2 Lite, IBM T. J. Watson Research Center Content-Id: <64_109_1_827427360> Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Today, Bernd.Hartke@RUS.Uni-Stuttgart.DE wrote: > > Incidentally, in German we would say "konFORmer" for someone who conforms -- > if we had such a word. But all German chemists say "/con/-for-MER" (secondary > stress on first syllable, primary stress on the last; or "MOnoMER" with about > equal stress on the first and last syllables). I guess this clever way out > is not open for English chemists... > > Bernd > The stress on the last syllable is not incidental. Quite a number of chemical expression in German (and I think in some other languages, too) are not derived from Latin/Greek directly but came via French. For example, "Molek"ul" has the umlaut from French - the Latin origin is "moles". So the stress on the last syllable in word ending with "-mer" is probably also due to the French background. But perhaps the French emphasizing was too unusual to the English such that the stress was shifted. So my suggestion is to make use of the analogy to "isomer" and say "CONformer" - or just "conforMAtional ISOmer". Best regards, Thomas Wieland Lehrstuhl II f. Mathematik Universitaet Bayreuth **** Do you know MOLGEN? **** http://btm2xd.mat.uni-bayreuth.de/molgen **** From owner-chemistry@ccl.net Thu Mar 21 06:24:30 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id FAA03379; Thu, 21 Mar 1996 05:26:21 -0500 (EST) Received: from fstgds01.tu-graz.ac.at for hassler@fscm1.dnet.tu-graz.ac.at by bedrock.ccl.net (8.7.1/950822.1) id FAA04896; Thu, 21 Mar 1996 05:26:17 -0500 (EST) From: Received: from FSCM1.DECnet MAIL11D_V3 by fstgds01.tu-graz.ac.at (5.57/Ultrix3.0-C) id AA18462; Thu, 21 Mar 96 11:26:05 +0100 Date: Thu, 21 Mar 96 11:26:04 +0100 Message-Id: <9603211026.AA18462@fstgds01.tu-graz.ac.at> To: FULTRX"chemistry@ccl.net"@ccl.net Subject: MM3-summary Dear members of CCL! Best greetings to all those who answered my request: I need MM3 parameters (stretching constants, torsional constants, bending parameters, etc.) for bonds containing Si,C,H,X (X=F,Cl,Br,I) (atoms arranged in all possible variations). Can you tell me, where I can find these parameters (literature, or another existing force field program already providing such parameters)? All replies are highly acknowledged! Best wishes to everyone Doz.Dr.K. Hassler Institut fuer Anorganische Chemie, Technische Universitaet Graz, Stremayrgasse 16 present e-mail: hassler@fscm1.tu-graz.ac.at Here are the answers! 1) Dipl.Ing. Zuegg (Institute of Organic Chemistry, University of Technology Graz, Stremayrgasse 16) wrote, that one can find some useful literature about SiC SiO SiCl SiS MM2 parameters in Review of Computational chemistry Vol. 6. 2) From: FULTRX::"peon@medchem.dfh.dk" 12-MAR-1996 10:25:09.56 Dear Dr. Hassler, The basis for the "parameter estimator" in MM3(94) was published a while ago, "Allinger et al., J.Mol.Struct. (THEOCHEM) 312 (1994) 69-83". In there, you can find methods for generating parameters for the entire periodic table. You should be aware that such parameters are prone to errors, but they will let you start calculations while you are hunting for more accurate values. I've had fairly good experience with them so far. Best Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ 3) From: SMTP%"shim@anion.herl.epa.gov" 12-MAR-1996 15:58:19.15 Hellow, Dr. Hassler As you may know, C, H, and Si are fundamental elements for constructing force field. Therefore, they belong to primary ones to be parameterized. For MM3 parameters, you can find from literatures or MM3 program manual. You may ask directly Professor Allinger's group. Here is their WWW address; http://europa.chem.uga.edu. For MM3 halogen parameters, Cl and I are parameterized, and F is almost ready, and Br is not ready, I think. I guess it will take a while to complete the MM3 halogen parameters. I am the guy who parametrized MM3 monochloroalakanes. This work has just been done, and submitted for publication. Let me know if you need further information. Good Bye! Sincerely, JY Shim ***************************************************************** *Joong-Youn Shim, Ph.D. Tel:919-541-0814 * *UNC/EPA Post-Doc Fax:919-541-0694 * * * *Curriculum in Toxicology Environ. Carcinogen. Div. * *School of Medicine NHEERL * *U. of North Carolina U.S. EPA * *Chapel Hill, NC 27599 Research Triangle Park, NC 27711* * shim@anion.herl.epa.gov * ***************************************************************** 4) From: FULTRX::"lipkowitz@chem.iupui.edu" 12-MAR-1996 16:20:27.99 Appendix 1 in Reviews in Computational Chemistry, Volume 7, VCH Publishers, 1995 is called "Published Force Field Parameters" and it may contain what you need. _______________________________________________________________________________ 5) From: FULTRX::"profeta~s@glaxo.com" 12-MAR-1996 21:13:34.05 Dear Dr. Hassler, I do not have my bibliography on these items with me curretnly, but I can tell you if you look at the papers published in JOC, JCompChem, JMolStruct and Tetrahedron by my co-workers S.G. Cho, R. J. Unwalla, F. K. Cartledge and I, you will find a good starting place for the MM2 values which can accurately supplement or replace those in the public domain versions of MM2. We published all parameters to be used with MM2. I was s student of Allinger who worked on MM1 and MM2 with him, thus I understand the process better than most. You will also see that we used good ab initio data to help develop parameters where exp data was missing. Also recognize that this data was generated 10 years ago, when widespread use of full geometry optimization was rare! I cannot vouch for the accuracy of any MM3 parameters for silicon systems, as I have not worked in that area, nor have I funded Prof. Allinger to do so. I would be very careful with use of MM3 in that context. Let me know if I can be of further assistance. ++++++De mortuis nil nisi bonum.++++++++++* Dr. Salvatore Profeta, Jr. Computational Polymorphism, Ltd. 104 Cottage Lane Durham, NC 27713-9387 (919) 544-2299/5304 (Fax) email: sal@rti.org (neutral zone) email: profeta~s@glaxo.com (courtesy acct) ++++++Sic transit gloria mundi++++++++++++ 6) From: FULTRX::"polowin@hyper.hyper.com" 13-MAR-1996 22:42:11.28 Hi, Dr. Hassler. I don't know of any force field that can definitely provide you with explicit parameters for all possible combinations of those atoms. But you might look at the Dreiding force field proposed by Mayo, Olafson and Goddard (_J. Phys. Chem._ *94*, 8897 (1990)) -- it provides a scheme to extrapolate parameters from atomic hybridizations, bonding, and covalent radii. We use a related scheme to determine missing parameters in the MM+ force field in our HyperChem software. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com From joubert@ext.jussieu.fr Thu Mar 21 07:17:48 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.7.1/950822.1) id HAA04766; Thu, 21 Mar 1996 07:16:00 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.3/jtpda-5.2) with ESMTP id NAA22803 for ; Thu, 21 Mar 1996 13:15:53 +0100 (MET) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Thu, 21 Mar 1996 13:15:51 +0100 Date: Thu, 21 Mar 1996 13:15:51 +0100 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (laurent JOUBERT) Subject: f orbitals in Hartree-Fock programs Dear Netters, It's well known that Gaussian 92 (or 94) can't compute derivatives of integrals using higher than d functions with ECP's. It seems there is the same problem with Gamess, but I'm not sure indeed ... 1) Does anybody know another Hartree-Fock calculations program which can compute these derivatives of integrals ? 2) Stuttgart's ECP's include f orbitals in core for lantanides elements. Does anybody know other ECP's also including f orbitals in core ? (Stevens' ECP's don't include them in core) Thanks in advance for your answers. Laurent JOUBERT ------------------------------------------------------------------ Laurent JOUBERT Ecole Nationale Superieure de Chimie de Paris Laboratoire d'Electrochimie et de Chimie Analytique 11, rue Pierre et Marie Curie 75231 PARIS CEDEX 05- FRANCE Tel : 44-27-66-94 Fax : 44-27-67-50 E-Mail : joubert@ext.jussieu.fr WWW site : http://www.enscp.jussieu.fr ------------------------------------------------------------------ From gfruzze@junix.ju.edu Thu Mar 21 08:17:54 1996 Received: from junix.ju.edu for gfruzze@junix.ju.edu by www.ccl.net (8.7.1/950822.1) id HAA04787; Thu, 21 Mar 1996 07:17:51 -0500 (EST) Received: by junix.ju.edu (5.61/1.39) id AA03906; Thu, 21 Mar 96 07:17:50 -0500 From: gfruzze@junix.ju.edu (Giancarlo Fruzzetti) Message-Id: <9603211217.AA03906@junix.ju.edu> Subject: Computational chemistry/drug industry (fwd) To: chemistry@www.ccl.net Date: Thu, 21 Mar 1996 07:17:49 -0500 (EST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Forwarded message: > > To all list members: > > I have a question for anyone on the list with knowledge about research in > the pharmaceutical industry. I am going to begin graduate school > in a Ph.D. medicinal chemistry program this fall. I am curious as to > whether individuals with specialized knowledge in quantitative aspects of > chemistry, such as quantum chemistry, molecular modeling, and chemical > kinetics are in demand in the pharmaceutical industry. I have a great > deal of personal interest in these areas, and I would like to know if > concentrating my graduate studies in applying these areas to drug design > would be a profitable use of time. > > Thank you for your responses, which may be sent to my e-mail address. > > Giancarlo Fruzzetti > gfruzze@junix.ju.edu > > From erich@cma.univie.ac.at Thu Mar 21 08:26:47 1996 Received: from homer.cma.univie.ac.at for erich@cma.univie.ac.at by www.ccl.net (8.7.1/950822.1) id IAA06284; Thu, 21 Mar 1996 08:04:47 -0500 (EST) Received: from solon.cma.univie.ac.at by homer.cma.univie.ac.at; (5.65v3.2/1.1.8.2/12Jan95-0202PM) id AA22962; Thu, 21 Mar 1996 13:08:05 +0100 Received: by solon.cma.univie.ac.at; (5.65v3.2/1.1.8.2/21Jun95-0858AM) id AA01587; Thu, 21 Mar 1996 13:00:05 +0100 Date: Thu, 21 Mar 1996 13:00:05 +0100 (MET) From: Erich Bornberg-Bauer Subject: PSB97-Call for Papers:Biopolymer Evolution To: chemistry@www.ccl.net Cc: mike@santafe.edu, steen@santafe.edu, andrews@biology.ucla.edu, pbinder@cdcnet.uniandes.edu.co, tbi@tbi.univie.ac.at, hs@mdy.univie.ac.at, gl@mdy.univie.ac.at, walter@santafe.edu, mah@santafe.edu, asl@santafe.edu, duck@imb-jena.de, robo@imb-jena.de, chris@imb-jena.de, casari@embl-heidelberg.de, sander@embl-heidelberg.de, abseher@embl-heidelberg.de, harmen@Glue.umd.edu, lboehmer@math.ucla.edu, rupp1@llnl.gov, Joachim.Selbig@gmd.de, sippl@Olga.came.sbg.ac.at, shosh@ucmbsun1.ulb.ac.be, MDZorn@lbl.gov, Gert.Vriend@EMBL-Heidelberg.DE, tbi@dkfz-heidelberg.de, olson@scripps.edu, Pat.Argos@embl-heidelberg.de, head@math.binghamton.edu, kol@cgi.nsk.su, sklenar@iris3.biosim.mdc-berlin.de, lcyagil@weizmann.weizmann.ac.il, langowsk@cvx12.inet.dkfz-heidelberg.de, artemis@dkfz-heidelberg.de, akutsu@cs.gunma-u.ac.jp, rudi@csdec1.tuwien.ac.at, andr@scripps.edu, pkarp@ai.sri.com, seth.michelson@syntex.com Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, please find enclosed the announcement for a seminar track and consider if this might be of interest for you. Forward the message to people you know who might be interested and suggest appropriate places to post this announcement to us (f.i. news-groups, email-exploders, inhouse-lists etc.). The full call can be found at http://www.dkfz-heidelberg.de/tbi/people/bornberg/psb2/eop.html with corresponding links. ``Mahalo'' for your cooperation Erich , Richard ----------------------------------------------------------------------- Conference Announcement And Call for Papers BIOPOLYMER STRUCTURES: WHERE DO THEY COME FROM? WHERE ARE THEY GOING? EVOLUTIONARY PERSPECTIVES ON BIOPOLYMER STRUCTURE AND FUNCTION A Seminar Track in the Second Pacific Symposium on Biocomputing January 6-9, 1997 Ritz-Carlton Kapalua, Maui, Hawaii info at: http://www.dkfz-heidelberg.de/tbi/people/bornberg/psb2/eop.html Biological macromolecules are the result of eons of evolution. In order to understand these macromolecules, it is necessary to understand the evolutionary pressures that determined their current form. Conversely, the properties of these macromolecules encode this heritage, and can provide insight into the process of evolution. The effort to understand, reconstruct and simulate the evolution of biopolymers, including their structure and function, has become a key task involving such diverse fields as evolutionary biology, molecular biology, structural biology, biophysical chemistry, and bio-informatics. This track, part of the Second Pacific Symposium on Biocomputing, invites scientists from related disciplines to present original papers that discuss new techniques, theories, insights and approaches for understanding the evolution of biopolymers. We welcome papers describing results from a wide range of possible methodologies, including analyses of the databases of biomolecular sequences and structures, simple conceptual and computational evolutionary models, and computational perspectives on experimental results. DEADLINES Submission of Full Papers: July 1 Notification of Acceptances: August 22 Camera ready copy due: September 15 Conference: January 6-9, 1997 Further Information concerning possible topics, literature and organisation of the conference can be obtained from the web: http://www.dkfz-heidelberg.de/tbi/people/bornberg/psb2/eop.html For questions about the symposium track and about possible manuscript submissions, please contact the track organizers: Erich Bornberg-Bauer, German Cancer Research Center Tel.: (+49 - 62 21) 42 - 27 25 Fax.: (+49 - 62 21) 42 - 28 49 email: bornberg@dkfz-heidelberg.de , erich@santafe.edu Richard A. Goldstein, University of Michigan tel: (+1 - 313) 763 - 80 13 fax: (+1 - 313) 747 - 48 65 email: richardg@chem.lsa.umich.edu For general questions about the conference, contact the conference coordinator: Sharon Surles, IS, Inc., phone: +1 (619) 658-9782 fax: +1 (619) 658-9463 email: psb@intsim.com url: http://cgl.ucsf.edu/psb/psb.html ----------------------------------------------------------------------- From acp37@rs1.rrz.Uni-Koeln.DE Thu Mar 21 09:17:49 1996 Received: from rs1.rrz.Uni-Koeln.DE for acp37@rs1.rrz.Uni-Koeln.DE by www.ccl.net (8.7.1/950822.1) id IAA06956; Thu, 21 Mar 1996 08:52:01 -0500 (EST) Received: by rs1.rrz.Uni-Koeln.DE id AA41395 (5.67b/IDA-1.5 for CCL ); Thu, 21 Mar 1996 14:51:49 +0100 Date: Thu, 21 Mar 1996 14:51:49 +0100 (MET) From: "T. Koch" To: CCL Subject: Pronounciation of conformer Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters! It would be very kind if we could stop the very interesting discussion about the pronounciation and origins of conformers, isomers and so on and could come back to computational chemistry. Thank you, Thorsten /-----------------------------------------------------------------\ | Thorsten Koch | | Institut fuer Physikalische Chemie II der Universitaet zu Koeln | | Luxemburger Str. 116, 50939 Koeln, Germany | | acp37@rrz.uni-koeln.de | | Tel. +49 [0]221 470 4816 | \-----------------------------------------------------------------/ From jkl@ccl.net Thu Mar 21 10:17:50 1996 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.7.1/950822.1) id JAA08333; Thu, 21 Mar 1996 09:35:13 -0500 (EST) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id JAA07275; Thu, 21 Mar 1996 09:35:13 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id JAA11363; Thu, 21 Mar 1996 09:35:10 -0500 Date: Thu, 21 Mar 1996 09:35:10 -0500 Message-Id: <199603211435.JAA11363@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Re: CCL:How to get information In-Reply-To: Mail from 'ariane@WAPinorg.chemie.uni-halle.de (Ariane)' dated: Thu, 21 Mar 1996 08:10:10 +0100 Cc: jkl@ccl.net > I would like to know if there are any opportunities > to get information about the table of contents (authors, title, brief summary) > of the latest issues of journals like Int. J. Quant. Chem., and J. Comp. Chem. table of contents is available in CCL archives under periodicals Jan Labanowski jkl@ccl.net From Jeffrey.Gosper@brunel.ac.uk Thu Mar 21 10:24:14 1996 Received: from cook.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.1/950822.1) id JAA08477; Thu, 21 Mar 1996 09:49:16 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by cook.brunel.ac.uk with SMTP (PP); Thu, 21 Mar 1996 13:58:51 +0000 Date: Thu, 21 Mar 1996 13:58:22 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Problems running IRC + COSMO in MOPAC93 To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear colleagues, I have just implemented MOPAC93 at our site and was interested in performing a number of IRC calculations which included the COSMO solvation model. However, I have been unable to get the calculation to produce an output in which the coordinates of the steps are included. The input and output files are provided below. I know that Dr Klamt does not recommend the use of COSMO in FORCE calculations, but what about IRC calculations? As they are linked, is it not recommended that COSMO be used in IRC calculations? Taken a step further does this mean that COSMO is not recommended even for TS optimization? Has anyone succeed in running a similar calculation or is will to provide some help on this matter. Yours thankfully Jeff Gosper (Brunel) ****************input file************************ AM1 NSPA=60 EPS=10 CHARGE=-1 T=600M ISOTOPE RESTART IRC=1 X-PRIO LARGE Optimized under COSMO TS Br -2.2567 1 0.0000 1 -0.0017 1 C 0.0000 1 0.0000 1 -0.0017 1 H -0.0001 1 1.0994 1 -0.0017 1 H 0.0013 1 -0.5483 1 -0.9545 1 H -0.0012 1 -0.5500 1 0.9502 1 Br 2.2567 1 0.0000 1 0.0020 1 the output is as follows ******************************************************************************* ** MOPAC 93 (c) Fujitsu ** ******************************************************************************* AM1 CALCULATION RESULTS ******************************************************************************* * MOPAC 93.00 CALC'D. Wed Mar 20 16:55:50 1996 * LARGE - EXPANDED OUTPUT TO BE PRINTED * X-PRIOR - GEOMETRY CHANGES TAKE PRIORITY IN DRC * RESTART - CALCULATION RESTARTED * IRC=N - INTRINSIC REACTION COORDINATE 1 DEFINED * * * * CHARGE ON SYSTEM = -1 * * * * T= - A TIME OF 600.000 MINUTES REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 3600.000 SECONDS * AM1 - THE AM1 HAMILTONIAN TO BE USED * ISOTOPE - FORCE MATRIX WRITTEN TO DISK (CHAN. 9 ) * EPS= 10.000 * NSPA= 60 ***********************************************************************024BY024 AM1 NSPA=60 EPS=10 CHARGE=-1 T=600M ISOTOPE RESTART IRC=1 X-PRIO LARGE TS Optimized and characterized under COSMO ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES) (I) NA:I NB:NA:I NC:NB:NA:I NA NB NC 1 Br 2 C 2.25670 1 3 H 1.09940 89.99479 2 1 4 H 1.09930 90.06776 -119.91878 2 1 3 5 H 1.09937 89.93746 120.01897 2 1 3 6 Br 2.25670 179.90606 90.00000 2 1 3 CARTESIAN COORDINATES NO. ATOM X Y Z 1 Br 0.0000 0.0000 0.0000 2 C 2.2567 0.0000 0.0000 3 H 2.2566 1.0994 0.0000 4 H 2.2580 -0.5483 -0.9528 5 H 2.2555 -0.5500 0.9519 6 Br 4.5134 0.0000 0.0037 H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) C: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) Br: (AM1): M.J.S. DEWAR AND E. G. ZOEBISCH, THEOCHEM, 180, 1 (1988). MOLECULAR POINT GROUP : D3h RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 11 INTERATOMIC DISTANCES Br 1 C 2 H 3 H 4 H 5 Br 6 ------------------------------------------------------------------------------ Br 1 0.000000 C 2 2.256700 0.000000 H 3 2.510164 1.099400 0.000000 H 4 2.511379 1.099301 1.903351 0.000000 H 5 2.509162 1.099370 1.904373 1.904702 0.000000 Br 6 4.513402 2.256703 2.510347 2.510449 2.509919 0.000000 MAXIMUM NUMBER OF SEGMENTS ALLOWED: 800 TIME USED UP TO RESTART = 56.04 FOR POINT-GROUP D3h THERE ARE 12 UNIQUE SYMMETRY FUNCTIONS. MOLECULAR WEIGHT = 174.84 INITIAL VELOCITY IN DRC -0.03367 0.00000 0.00000 0.47243 0.00000 0.00039 -0.09735 0.00000 -0.00008 -0.09737 0.00000 -0.00008 -0.09734 0.00000 -0.00008 -0.03367 0.00000 -0.00005 GEOMETRY PRIORITY, STEP = 0.05 ANGSTROMS IRC CALCULATION COMPLETE TOTAL CPU TIME: 178.97 SECONDS == MOPAC DONE == JOB FINISHED /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From owner-chemistry@ccl.net Thu Mar 21 11:18:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA09523; Thu, 21 Mar 1996 10:33:05 -0500 (EST) Received: from hrz-sun1 for gdanitz@hrz.uni-kassel.de by bedrock.ccl.net (8.7.1/950822.1) id KAA08416; Thu, 21 Mar 1996 10:33:04 -0500 (EST) Received: from hrz-serv1.hrz.uni-kassel.de by hrz-sun1 (4.1/SMI-4.1) id AA21917; Thu, 21 Mar 96 16:34:02 +0100 Received: by hrz-serv1.hrz.uni-kassel.de (AIX 3.2/UCB 5.64/HRZ-GhK/HRZ-SERV1/pm) id AA51498; Thu, 21 Mar 1996 16:32:26 +0100 From: gdanitz@hrz.uni-kassel.de (Robert Gdanitz) Message-Id: <9603211532.AA51498@hrz-serv1.hrz.uni-kassel.de> Subject: Program for Crystal Energies To: chemistry@ccl.net (Computational Chemistry List) Date: Thu, 21 Mar 1996 16:32:26 +0100 (MEZ) +-----+ Robert J. Gdanitz email: gdanitz@hrz.uni-kassel.de | GhK | Gesamthochschule Kassel Tel.: +(49) 561-804-4556 | | Fachbereich 18 (Physik) Fax: +(49) 561-804-4006 +-----+ 34109 Kassel X-Mailer: ELM [version 2.4 PL24 PGP3 *ALPHA*] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 996 Dear Netters, I'm looking for software to compute the energy and its gradient of molecular crystals. Since I intend to predict crystal structures using the algorithm des- cribed in Chem. Phys. Lett. 190 (1992) 391 and J. Comp. Chem. 13 (1992) 1171, *fast performance* (i.e. e.g. no heavy usage of trigonometric functions) is mandatory. The list of desirable features includes * Application to all crystallographic space groups * Build-up of the crystal fragment from images of the asymmetric unit rather than of the unit cell * Use of the minimum image convention * Ewald summation of the electrostatic contribution (only for the energy). However, since the molecules will be treated as rigid bodies, only non-bonded interactions need to be taken into account. It should be possible to get the *source code* written in C or preferably in Fortran for usage in commercial research. It should be free or at least mode- rately priced (i.e. below 1000 US$). With Regards Robert Gdanitz From shawn@wavefun.com Thu Mar 21 13:17:51 1996 Received: from volvo.wavefun.com for shawn@wavefun.com by www.ccl.net (8.7.1/950822.1) id MAA12541; Thu, 21 Mar 1996 12:45:38 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA27149; Thu, 21 Mar 96 09:45:55 -0800 Received: from fiat.wavefun.com(198.147.95.116) by volvo.wavefun.com via smap (V1.3) id sma027146; Thu Mar 21 09:45:49 1996 X-Sender: shawn@acura Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Mar 1996 09:51:38 -0800 To: chemistry@www.ccl.net From: shawn@wavefun.com (Shawn Butler) Subject: Wavefunction @ ACS New Orleans Dear CCLers: This seems to be the trend, so . . . Wavefunction will be live and kicking at ACS New Orleans in booth 1017. Please drop by just to say "uh . . . hello . . . where's the souvenir booth?" or to see: * Spartan 4.1 with a new interface to Schrodinger's PS-GVB software * MacSpartan, our new modeling product (Power Macintosh Computer System) * FREE CD-ROM demos of MacSpartan, with tutorial introduction * FREE "mini" Lab Manual Dr. Warren Hehre will be present in the booth, and we look forward to addressing any and all questions/concerns you might have about Wavefunction, our software and/or computational chemistry. See you there! Shawn Butler, Wavefunction, Inc. shawn@wavefun.com ****************************************************************************** Wavefunction, Inc. 18401 Von Karman Ave., Ste. 370 Irvine, CA 92715 WWW: http://www.wavefun.com Spartan Sales: (714) 955-2120 - sales@wavefun.com MacSpartan Sales: (714) 660-6101 - macsales@wavefun.com Fax: (714) 955-2118 ****************************************************************************** This Space for Rent (Cheap!) **************************************************************************** ** From vuckovic@hyper.com Thu Mar 21 14:17:53 1996 Received: from www.hyper.com for vuckovic@hyper.com by www.ccl.net (8.7.1/950822.1) id OAA14055; Thu, 21 Mar 1996 14:13:19 -0500 (EST) Received: from dragan2.hyper.com (dragan2.hyper.com [204.50.97.30]) by www.hyper.com (8.6.12/8.6.12) with SMTP id OAA05920 for ; Thu, 21 Mar 1996 14:30:27 -0500 Date: Thu, 21 Mar 1996 14:30:27 -0500 Message-Id: <199603211930.OAA05920@www.hyper.com> X-Sender: vuckovic@hyper.com 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: Dragan Vuckovic Subject: Last Call for HyperChem Workshop - Santa Clara There are some more spaces available for HyperChem Workshop on Computational Chemistry, Santa Clara, CA, April 10-12. If you respond quickly, we can extend the deadline for early registration prices. Contact me as soon as possible. ____________________________________________________________________________ _________ Dr. Dragan Lj. Vuckovic E-mail: vuckovic@hyper.com HyperCube Inc. Tel.: (519) 725-4040 419 Phillip St. Fax: (519) 725-5193 Waterloo, On N2L 3X2 URL: http://www.hyper.com Canada From owner-chemistry@ccl.net Thu Mar 21 14:26:59 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id OAA14072; Thu, 21 Mar 1996 14:14:36 -0500 (EST) Received: from anny.psgvb.com for info@anny.psgvb.com by bedrock.ccl.net (8.7.1/950822.1) id OAA14744; Thu, 21 Mar 1996 14:14:34 -0500 (EST) Received: by anny.psgvb.com (931110.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA04044; Thu, 21 Mar 96 11:14:28 -0800 Date: Thu, 21 Mar 96 11:14:28 -0800 From: info@anny.psgvb.com (Info at Schrodinger Inc.) Message-Id: <9603211914.AA04044@anny.psgvb.com> To: chemistry@ccl.net Subject: Schrodinger, Inc.'s move (and ACS booth) Dear CCLers, If you'll be in New Orleans for the ACS meeting, please visit Schrodinger, Inc. in Booth 606 in the Exhibit Hall, where we'll be demonstrating our quantum chemical software, PS-GVB. We're also pleased to announce that we are moving our headquarters to Portland, Oregon at the end of this month. Our new address is 121 SW Morrison, Suite 1212 Portland, OR 97204 Phone: (503) 299-1150 Fax: (505) 299-4532 Our sales phone number, (800) 20-PS-GVB (800-207-7482), our email address, info@psgvb.com, and our URL, http://www.psgvb.com/, will be the same after the move. Thanks for your attention. -- Schrodinger, Inc. / info@psgvb.com / (800) 20-PS-GVB / http://www.psgvb.com/ Address after March 31: 121 SW Morrison, Suite 1212, Portland, OR 97204 From owner-chemistry@ccl.net Thu Mar 21 15:13:53 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id NAA12827; Thu, 21 Mar 1996 13:31:52 -0500 (EST) Received: from si.fi.ameslab.gov for brett@si.fi.ameslab.gov by bedrock.ccl.net (8.7.1/950822.1) id NAA13646; Thu, 21 Mar 1996 13:31:51 -0500 (EST) Received: by si.fi.ameslab.gov (AIX 3.2/UCB 5.64/4.03) id AA42789; Thu, 21 Mar 1996 12:35:24 -0600 From: brett@si.fi.ameslab.gov (Brett Bode) Message-Id: <9603211835.AA42789@si.fi.ameslab.gov> Subject: GAMESS at the New Orleans ACS meeting To: chemistry@ccl.net Date: Thu, 21 Mar 1996 12:35:24 -0600 (CST) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Since I have seen several "Come see us at the ACS meeting" postings in the past few days I thought I might as well add one more. Stop by the IBM booth (#417) to see a demonstration of GAMESS on an IBM SP2. We will also demonstrate a prototype graphical interface for GAMESS which runs on Macintosh computers. The interface is capable of building input files for GAMESS and then graphically displaying the output of most GAMESS runs (IRCs, DRCs, and hessians included) including 3D display of MO's. For more information about either program check out our WWW site: http://www.msg.ameslab.gov/GAMESS/GAMESS.html See you at the ACS meeting... 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 ____________________________________ From te_meehan@ccmail.pnl.gov Thu Mar 21 16:18:03 1996 Received: from pnl.gov for te_meehan@ccmail.pnl.gov by www.ccl.net (8.7.1/950822.1) id PAA16996; Thu, 21 Mar 1996 15:59:31 -0500 (EST) From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01I2LNMOTZGGCMHJ5T@pnl.gov>; Thu, 21 Mar 1996 12:58:50 -0800 (PST) Date: Thu, 21 Mar 1996 12:56 -0800 (PST) Subject: triflic acid To: chemistry@www.ccl.net Message-id: <01I2LNMQC0D6CMHJ5T@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Does anyone know the dielectric constant of triflic acid,CF3SO3H, and the reference thereof? tim meehan te_meehan@pnl.gov From elewars@alchemy.chem.utoronto.ca Thu Mar 21 16:34:24 1996 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.7.1/950822.1) id QAA17117; Thu, 21 Mar 1996 16:07:15 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id QAA22420 for chemistry@www.ccl.net; Thu, 21 Mar 1996 16:07:13 -0500 (EST) Date: Thu, 21 Mar 1996 16:07:13 -0500 (EST) From: "E. Lewars" Message-Id: <199603212107.QAA22420@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: PROBLEMS WITH DFT ETC 1996 March 21 A few comments on some recent queries on the Net: (1) _re_ DFT and transition states: B.G. Johnson recently reported that "regular Kohn-Shawm DFT is a complete failure for radical H abstractions" (Chem Phys Lett 221, 100 (1994)). Another failure of DFT with transition states is reparted in S. Gronert, G. L. Merrill and S.R. Kass, J. Org. Chem., _60_, 488-489 (1995): DFT failed to handle the transition state for eliminatiion of fluoride ion from C2F5F. The ability of DFT "to elucidate complex reaction pathways" was questioned. Clearly, any one thinking of using DFT to calculate transition state properties or reaction barriers should take a look at these papers. (2) _re_ Titles of (presumably computationally oriented) papers in chemical journals: this isn't free or (I think) online, but it's cheap and very useful: QCPE publishes the QCPE current awareness profile on quantum chemistry, 26 issues a year; you get more than titles, as "each issue... represents an exhaustive computerized search of two consecutive issues of Chemical Abstracts." Quantum Chemistry Program Exchange, Creative Arts Building 181, Indiana University, Bloomington, Indiana 47405, USA. (3) Final words on the very important matter of correct pronunciation: Berndt Hartke and Thomas Wieland haben mich fast ueberzeugt dass...oops, have almost convinced me that the analogy with ISOmer, MONOmer, POLYmer, etc. provides a compelling case for CONformer. Errol Lewars =================== From owner-chemistry@ccl.net Thu Mar 21 17:17:55 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id RAA17951; Thu, 21 Mar 1996 17:06:32 -0500 (EST) Received: from crash.cts.com for wanger@cts.com by bedrock.ccl.net (8.7.1/950822.1) id RAA18361; Thu, 21 Mar 1996 17:06:26 -0500 (EST) Received: by crash.cts.com (Smail3.1.29.1 #5) id m0tzsUZ-0000QcC; Thu, 21 Mar 96 14:05 PST Date: Thu, 21 Mar 1996 14:05:59 -0800 (PST) From: Len Wanger X-Sender: wanger@crash.cts.com To: chemistry@ccl.net Subject: Announcing Sculpt for PowerMac Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Interactive Simulations, Inc. will be introducing Sculpt for the Macintosh PowerPC in Booth #538 at the ACS Exposition in New Orleans, March 25-27. Also look for Sculpt for the Macintosh PowerPC in the CambridgeSoft (#301) and Apple Computer (#305) Booths. Len Wanger -- wanger@intsim.com Interactive Simulations, Inc. (619) 658-9462 (619) 658-9463 (fax) http://www.intsim.com From owner-chemistry@ccl.net Thu Mar 21 17:22:54 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id RAA17946; Thu, 21 Mar 1996 17:06:00 -0500 (EST) Received: from crash.cts.com for wanger@cts.com by bedrock.ccl.net (8.7.1/950822.1) id RAA18351; Thu, 21 Mar 1996 17:05:51 -0500 (EST) Received: by crash.cts.com (Smail3.1.29.1 #5) id m0tzsTk-0000CGC; Thu, 21 Mar 96 14:05 PST Date: Thu, 21 Mar 1996 14:05:08 -0800 (PST) From: Len Wanger X-Sender: wanger@crash.cts.com To: chemistry@ccl.net Subject: ACS workshop: Sculpt Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Interactive Simulations, Inc. will be presenting a workshop on their new product Sculpt for the Macintosh at: Title: Computerized Drieding Models Date: Tuesday, March 26, 9 AM - Noon Location: Room 82, 3rd Floor, Convention Center New Orleans, LA If you are interested in attending, please call Interactive Simulations to reserve a space: 619-658-9462 Computerized Drieding Models ---------------------------- Learn how the physical models such as CPK, Kendrew, and Drieding have been re-created in a SGI, PC, and Mac application called Sculpt. Bend and twist 3D computer models while the conformation adjusts in real-time. By interactively modeling atomic forces, this new paradigm applies to medicinal, peptide, and organic chemistry, receptor modeling and protein engineering. This is an introductory workshop. Also look for Sculpt in the Interactive Simulations, Inc. (#538), CambridgeSoft (#301) and Apple Computer (#305) Booths at the ACS Exposition in New Orleans, March 25-27. Len Wanger -- wanger@intsim.com Interactive Simulations, Inc. (619) 658-9462 (619) 658-9463 (fax) From KGRAFTON@aardvark.ucs.uoknor.edu Thu Mar 21 17:27:25 1996 Received: from aardvark.ucs.uoknor.edu for KGRAFTON@aardvark.ucs.uoknor.edu by www.ccl.net (8.7.1/950822.1) id QAA17338; Thu, 21 Mar 1996 16:35:16 -0500 (EST) From: Received: from aardvark.ucs.uoknor.edu by aardvark.ucs.uoknor.edu (PMDF V4.3-13 #7521) id <01I2LT484N5C0029EK@aardvark.ucs.uoknor.edu>; Thu, 21 Mar 1996 15:36:17 -0600 (CST) Date: Thu, 21 Mar 1996 15:36:17 -0600 (CST) Subject: G94 'Cube' Option: The Responses To: CHEMISTRY@www.ccl.net Message-id: <01I2LT4884J60029EK@aardvark.ucs.uoknor.edu> X-Envelope-to: CHEMISTRY@www.ccl.net X-VMS-To: IN%"CHEMISTRY@www.ccl.net" X-VMS-Cc: KGRAFTON MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT A few days ago I posted a question about the proper use of the 'Cube' option in Gaussian94. Below are the responses I received. Thanks to all who replied! *************************************************************** From: Gerd Raether I had also problems with this option - but there were also some bugs in the A & B version. You should ask Douglas J. Fox Director of Technical Support help@gaussian.com for more information. Gerd In the C version the following example should work: #p hfs/sto-3g density=current Cube=(50,density) H2 0 1 h1 h2 1 r Variables: r=1. h2dens.xyz *************************************************************** From: Nathaniel (noj) Malcolm there should be little problems with the G94-cube option IF you are looking at densities, as far as i remember , BUT when being used for plotting orbitals, then you MUSt input the cube info (origin, step-size, no. of steps) as was the case for g92. You may also encounter problems if your wavefunction is of the ROHF type and you are plotting orbitals as g94 tries to find the (non-existant) beta-orbital co-efficients. Dr. Noj Malcolm Noj.Malcolm@man.ac.uk *************************************************************** From: mccarthy@convx1.ccit.arizona.edu (William Mccarthy) Here is a sample of generation of a cube of points of total density: $ RunGauss # rhf 3-21g scf=direct Cube=density water 0 1 H O, 1, r1 H, 2, r1, 1, a1 r1=.90 a1=107. h2o.out -1, 2.5, 2.5, 2.5 10, -.50, 0.0, 0.0 10, 0.0, -.50, 0.0 10, 0.0, 0.0, -.50 Here is a sample of a cube of points from a MO: $ RunGauss # rhf 3-21g scf=direct Cube=orbital water 0 1 H O, 1, r1 H, 2, r1, 1, a1 r1=.90 a1=107. h2o.out -1, 2.5, 2.5, 2.5 10, -.50, 0.0, 0.0 10, 0.0, -.50, 0.0 10, 0.0, 0.0, -.50 LUMO,HOMO *************************************************************** From: victor@xhost1.tripos.com (Vic Lewchenko) Kurt, The Gaussian input file below generates a cube output file for ethanol and seems to work (at least using GAUSSIAN92). Vic Lewchenko Tripos, Inc. victor@tripos.com %chk=ethenol.chk # HF/STO-3G NOSYMM CUBE=ORBITALS " " 0 1 6 -0.63052 -0.36707 -0.00228 6 0.64729 0.36372 -0.00749 8 0.78656 1.45548 0.75102 1 1.64855 1.85125 0.67460 1 -0.76070 -1.25882 -0.61472 1 -1.45710 -0.01953 0.61629 1 1.45217 -0.01705 -0.64159 ethenol.cube -22 -3.057100 -2.858820 -2.241590 16 0.400000 0.000000 0.000000 16 0.000000 0.400000 0.000000 12 0.000000 0.000000 0.400000 HOMO *************************************************************** From: IN%"djh@ccl.net" "David Heisterberg" Good luck! Gaussian has had a problem with this forever. The documentation has been wrong forever as well. CUBE doesn't work. You need to use CUBEDENSITY, but the defaults may not work either. You may have to specify all the cube data. An easy way is to use CUBEDENSITY and just specify a file name. This may die, but the output will have the default cube dimenions and numbers of points. Use this (or modify it) in the input and rerun and it should be successful. Step 1) --------#P TEST RHF/6-31G* CUBEDENSITY Water CUBE test 0 1 O H 1 R H 1 R 2 A R 0.96 A 109.471221 water.cube -------- This may die but in the output you'll find IGUnit= -31 Origin= -2.630400 -2.630400 -2.519549 N1= 80 XYZInc= 0.066592 0.000000 0.000000 N2= 80 XYZInc= 0.000000 0.066592 0.000000 N3= 80 XYZInc= 0.000000 0.000000 0.066592 So change the above to -------- water.cube -31 -2.630400 -2.630400 -2.519549 80 0.066592 0.000000 0.000000 80 0.000000 0.066592 0.000000 80 0.000000 0.000000 0.066592 -------- And all should be well. The other options for HOMO, LUMO, etc. should work just fine. Of course for anything non-trivial you'll want to pick up the wavefunction from the checkpoint file. Dave Heisterberg *************************************************************** From: IN%"aldert@chemde4.leidenuniv.nl" Hi Kurt, I guess you want to use your own defined grid, weel here is my "standard" .com: ___________________________________________________________________ #p rhf/6-31g** scf=tight density=scf cube=(cards,density,full) test CH4 rhf/6-31g**//opt - 1/4 space +core 0 1 c h 1 r h 1 r 2 a h 1 r 2 a 3 a 1 h 1 r 2 a 3 a -1 r=1.08354 a=109.4712206 /scratch/aldert/CH4-scf.cub -99 0.0 0.0 -5.46 -57 0.0975 0.0 0.0 57 0.0 0.0975 0.0 113 0.0 0.0 0.0975 ___________________________________________________________________ So, with cube=cards you force the G92 default input. The minus sign in front of 99 results in a formatted cube-file, the one in front of 57 sets the unit of distance to bohr (if I am correct, else Angs, any way the sign switches between these units !-). Hope this helps. Ciao, Aldert ------------------------------------------- A.J.A. Westra Hoekzema Conformational Analysis (Organic Chemistry) Leiden Institute of Chemistry, Gorlaeus Laboraties, Leiden University P.O. Box 9502, 2300 RA Leiden The Netherlands Phone : +31 715274505 Fax : +31 715274488 E-mail: aldert@chemde4.LeidenUniv.nl ------------------------------------------- *************************************************************** From: IN%"mxw@cedar.nesc.epa.gov" "Dr Manton Frierson" Dear Colleague, I also believe the manuals were not too clear on how to make the option work. Taking the defaults on most options (i.e., cube size, etc.), here is an example of input I am pretty confident will work. I do not know what property or functions you are trying to visualize, but I am here looking at an M.O. of benzoquinone, the HOMO explicitly. I think the extensions to other properties should now be obvious. Also, there are obviously site specific paths here which you will have to substitute for the ones appropriate to your location, etc. The structure (benzoquinone) has already been optimized and most data is being read from the checkpoint file. Good Luck! ____________________Begin Input__________________ %Chk=/work/aster/bzq/output/bzq001_d # HF/6-31+G* SCF=Direct Guess=(Read,Only) Cube=orbital Gaussian generated by Cerius2 -1 2 C C 1 r2 C 2 r3 1 a3 C 3 r4 2 a4 1 t4 C 4 r5 3 a5 2 t5 C 5 r6 4 a6 3 t6 O 4 r7 3 a7 2 t7 O 1 r8 2 a8 3 t8 H 2 r9 1 a9 3 t9 H 3 r10 2 a10 1 t10 H 5 r11 4 a11 3 t11 H 6 r12 5 a12 4 t12 r2 1.449170 r3 1.360240 r4 1.449900 r5 1.448980 r6 1.361990 r7 1.264330 r8 1.263920 r9 1.099260 r10 1.098700 r11 1.098880 r12 1.099410 a3 122.347940 a4 121.772260 a5 115.990120 a6 122.107010 a7 121.971920 a8 122.166400 a9 116.661370 a10 121.266250 a11 116.835290 a12 121.078700 t4 -0.389690 t5 0.622370 t6 -0.544670 t7 -179.502690 t8 -179.945440 t9 179.812830 t10 179.814420 t11 179.531150 t12 -179.911850 /work/aster/bzq/output/bzq001_d_homo.cube HOMO ________________________End of Input_________________ -- ==================================================================== Manton R. Frierson, Ph.D. /\ /\ R Senior Scientific Applications Consultant / \/ \/ Lockheed Martin Services Group, Inc. |/\ |/\| National Environmental Supercomputing Center |\/ |\/| 135 Washington Ave. \ /\ / Bay City, MI 48708 \/ \/ (517)894-7612(Office) (517)894-7676(FAX) FRIERSON.MANTON@CEDAR.NESC.EPA.GOV ==================================================================== *************************************************************** From: IN%"rbw@msc.edu" Kurt, Here is an example that I think still works. Richard Walsh Minnesota Supercomputer Center %chk=h2o.chk %mem=8000000 #p rhf sto-3g opt scf=incore cube=(density,cards) cube of water 0 1 8 1 1 R2 1 1 R3 2 A3 R2 = 0.95000 R3 = 0.95000 A3 = 104.5000 h2o_den1.cub -1 0.000000 0.000000 0.000000 10 1.000000 0.000000 0.000000 10 0.000000 1.000000 0.000000 10 0.000000 0.000000 1.000000 h2o_den2.cub -1 0.000000 0.000000 0.000000 10 1.000000 0.000000 0.000000 10 0.000000 1.000000 0.000000 10 0.000000 0.000000 1.000000 *************************************************************** From: IN%"aefrisch@lorentzian.com" Here is the simplest possible file: #T HF/6-31G* Cube=Orbital water 0,1 o h 1 1. h 1 1. 2 120. water.dat LUMO If you look for this in the output, you will see the values used for the cube: IGUnit= -31 Origin= -2.630400 -2.630400 -2.530400 N1= 80 XYZInc= 0.066592 0.000000 0.000000 N2= 80 XYZInc= 0.000000 0.066592 0.000000 N3= 80 XYZInc= 0.000000 0.000000 0.066592 You can also specify this stuff in the input if you want. See the manual for details. AEleen Frisch aefrisch@lorentzian.com *************************************************************** From: IN%"c.s.page@ic.ac.uk" "Mr C. S. Page" Kurt, It is not entirely clear from your message what the problem is. However, I have attached a sample file. This makes use of the 'cards' option, which is probably the most difficult part as regards setting up the input goes, although g94 does calculate a suitable grid spec by default. The 'nosymm' keyword is included as it prevents reorientation of the molecule. Both of these things are extremely useful if you wish to compare/manipulate the output of two or more cube calculations together. I hope that this helps somewhat. If you have any further difficulties, could you please send the log file... :-) Chris Page __________ Department of Chemistry Tel: +44 (0)171 594 5795 Imperial College GB-LONDON SW7 2AY ---1681465336-505359091-827321245=:15485 Content-ID: Content-Description: Content-type: TEXT/PLAIN; charset="US-ASCII"; name="benzeneesp.com" Content-transfer-encoding: BASE64 I3AgaGYvc3RvLTNnIGN1YmUocG90ZW50aWFsLCBjYXJkcykgbm9zeW1tDQoN CmJlbnplbmUgZWxlY3Ryb3N0YXRpYyBwb3RlbnRpYWwNCg0KMCAgMQ0KQw0K QyAgIDEgICByMg0KQyAgIDIgICByMyAgIDEgICBhMw0KQyAgIDMgICByNCAg IDIgICBhNCAgIDEgICBkNCAgIA0KQyAgIDQgICByNSAgIDMgICBhNSAgIDIg ICBkNSAgIA0KQyAgIDEgICByNiAgIDIgICBhNiAgIDMgICBkNiAgIA0KSCAg IDEgICByNyAgIDIgICBhNyAgIDMgICBkNyAgIA0KSCAgIDIgICByOCAgIDEg ICBhOCAgIDMgICBkOCAgIA0KSCAgIDMgICByOSAgIDIgICBhOSAgIDEgICBk OSAgIA0KSCAgIDQgIHIxMCAgIDMgIGExMCAgIDIgIGQxMCAgIA0KSCAgIDUg IHIxMSAgIDQgIGExMSAgIDMgIGQxMSAgIA0KSCAgIDYgIHIxMiAgIDEgIGEx MiAgIDIgIGQxMiAgIA0KDQpyMiAgPSAgICAxLjQwMDEwODIyDQpyMyAgPSAg ICAxLjQwMzU4Nzc5DQphMyAgPSAgMTE4LjgyOTUzNDQwDQpyNCAgPSAgICAx LjQwMjg3NjY5DQphNCAgPSAgMTIwLjQ3NjcxNTY1DQpkNCAgPSAgIC0wLjAx MjYwNTU4DQpyNSAgPSAgICAxLjQwMzEyODQ3DQphNSAgPSAgMTE5Ljc2Nzkx NDcyDQpkNSAgPSAgIC0wLjAwODM5MjAyDQpyNiAgPSAgICAxLjQwMDU0OTky DQphNiAgPSAgMTIxLjYxODU0MjAwDQpkNiAgPSAgIC0wLjAwMjUyNjI0DQpy NyAgPSAgICAxLjA5MDUyMjY0DQphNyAgPSAgMTE5LjIwNDY2NjgzDQpkNyAg PSAtMTc5Ljk5MTU3NTkzDQpyOCAgPSAgICAxLjA4ODcxODQ5DQphOCAgPSAg MTIwLjIwMTI2Mzc0DQpkOCAgPSAgMTc5Ljk4NDQxMzQ0DQpyOSAgPSAgICAx LjA5MDUwNTc5DQphOSAgPSAgMTE5LjI2MTY2MDI4DQpkOSAgPSAtMTc5Ljk5 NjMzNTQ1DQpyMTAgPSAgICAxLjA5MDE0ODMwDQphMTAgPSAgMTIwLjEyMjY2 NDY4DQpkMTAgPSAtMTc5Ljk4Njc2MDEzDQpyMTEgPSAgICAxLjA5MDUyMjY0 DQphMTEgPSAgMTIwLjIzNTg3MzQwDQpkMTEgPSAtMTc5Ljk5NjMxNDg1DQpy MTIgPSAgICAxLjA4ODcwODk4DQphMTIgPSAgMTIwLjE2MjEwNjg0DQpkMTIg PSAgMTc5Ljk5OTkzODQ5DQoNCmJlbnplbmVlc3AuY3ViDQogICAtMSAgIC01 Ljg2NDg4MiAgIC00LjMwNzc3MSAgIC01LjE3ODI3OA0KICAgOTEgICAgMC4x Mjk5OTggICAgMC4wMDAwMDAgICAgMC4wMDAwMDANCiAgIDY3ICAgIDAuMDAw MDAwICAgIDAuMTI5OTk4ICAgIDAuMDAwMDAwDQogICA4MyAgICAwLjAwMDAw MCAgICAwLjAwMDAwMCAgICAwLjEyOTk5OA0KCQkNCg== ---1681465336-505359091-827321245=:15485-- From hinsenk@ERE.UMontreal.CA Thu Mar 21 14:38 EST 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id OAA14427; Thu, 21 Mar 1996 14:38:06 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id JAA14767 (8.6.11/IDA-1.6 for ); Thu, 21 Mar 1996 09:28:43 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id JAA11403; Thu, 21 Mar 1996 09:28:06 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id JAA20424; Thu, 21 Mar 1996 09:26:14 -0500 Date: Thu, 21 Mar 1996 09:26:14 -0500 Message-Id: <199603211426.JAA20424@cyclone.ERE.UMontreal.CA> To: CHEMISTRY@www.ccl.net Subject: Connectivity in XMol From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) Content-Type: text Content-Length: 1278 Status: RO A few days ago I asked about ways to feed a bond list into XMol for display. Judging from the many responses I received, this seems to be a popular problem. The solution that worked best for me is to load the structure in whatever format into XMol, save in Alchemy format, edit the bond list in the Alchemy file, and load it back into XMol. While no one seems to have a precise description of the Alchemy format, its structure is rather obvious and I had no problems in modifying it. The second most frequently proposed method was to add more atom types and adjust their radii to make the bonds come out correctly. But for my application, and probably for most others, this procedure is a lot more tedious than the previous one. Thanks to everyone who responded to my question. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Mar 21 07:54 EST 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id HAA06256; Thu, 21 Mar 1996 07:54:35 -0500 (EST) Received: from focus.ftn.net for amt@ftn.net by bedrock.ccl.net (8.7.1/950822.1) id HAA05841; Thu, 21 Mar 1996 07:54:33 -0500 (EST) Received: from 172.27.99.1 by focus.ftn.net with smtp (Smail3.1.28.1 #7) id m0tzjtY-000NxSC; Thu, 21 Mar 96 07:55 EST Message-Id: Date: Thu, 21 Mar 96 07:55 EST X-Sender: amt@172.27.99.1 (Unverified) X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 To: chemistry@ccl.net From: amt@ftn.net (Adi Treasurywala) Subject: FINAL call for Validation Symposuim Content-Type: text/plain; charset="us-ascii" Content-Length: 2323 Status: RO =============================================================== Abstract deadline: April 19 on official ACS abstract form. ACS abstract forms may be requested from (1) http://www.acs.org/memgen/meetings/abrqst.htm (2) Ann Nelson (a_nelson@acs.org) (3) one of the organizers. =============================================================== -- Final call for papers -- VALIDATION METHODS IN COMPUTATIONAL CHEMISTRY American Chemical Society COMP Division 212th National Meeting Orlando, Florida August 25-29, 1996 What we are hoping to highlight through this Symposium is how experts evaluate the relevance and the completeness of a validation experiment in Comp Chem. All aspects of this topic are welcome from software release validation to validation of the results of a particular experiment etc. We hope to have some good examples to offer of the choices of positive and negative controls in such experiments. If you are planning to make a presentation in this symposium please ensure that your abstract reaches one of us on the official abstract form **BEFORE** the deadline. It will be very difficult or impossible to add you in if this is not done. If you are one of those who has already written in earlier asking if you could be a part of this symposium please go ahead and send in an abstract. We will do our best to fit you in. The response to this one has been large-to-overwhelming and we both thank you for that. Dr. A.M.Treasurywala Dr.E.P.Jaeger Allelix Biopharm Inc., 3D Pharm. 6850 Goreway Drive, Eagleview Corporate Center Mississauga Ont 665 Stockton Drive Suite 104 L4V 1V7 CANADA Exton PA 19341 amt@ftn.net jaeger@3dp.com (905)6770831 (610)4586052 FAX (905)6779595 FAX (610)4588249 ******************************** All views expressed here are only my own. Adi M Treasurywala Allelix Biopharma., 6850 Goreway Drive, Mississauga, Ontario. CANADA L4V 1V7. (905)677-0831 FAX (905)677-5344 ******************************** From chpajt@bath.ac.uk Thu Mar 21 04:31 EST 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.1/950822.1) id EAA03098; Thu, 21 Mar 1996 04:31:05 -0500 (EST) Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Thu, 21 Mar 1996 09:30:57 +0000 Date: Thu, 21 Mar 1996 09:30:43 +0000 (GMT) From: A J Turner To: TOPPER ROBERT cc: CHEMISTRY@www.ccl.net, topper@cooper.edu, freeman@mozart.chm.uri.edu, truhlar@t1.chem.umn.edu Subject: Re: CCL:WWW Molecular Monte Carlo Page In-Reply-To: <199603202105.AA29564@zeus.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 484 Status: RO Hi! I am interested in the Monticarlo driving routine. IE I give it energy and gradients - and it comes back with a step vector. Does anyone know of a public domane version of such a thing. Also - has anyone done Monticarlo with Charmm? Thanks in advance Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+