From MAILER-DAEMON@www.ccl.net Tue Sep 19 16:11:53 1995 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.6.10/950822.1) id QAA17423; Tue, 19 Sep 1995 16:11:49 -0400 Received: by schiele (950215.SGI.8.6.10/940406.SGI.AUTO) for chemistry@www.ccl.net id WAA21612; Tue, 19 Sep 1995 22:11:31 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9509192211.ZM21610@schiele> Date: Tue, 19 Sep 1995 22:11:28 -0600 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@www.ccl.net Subject: ANNOUNCE: Free Chemistry Software Tools Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit Status: R Version 1.2.1 of the CACTVS tools collection has been released. This is a collection of Tcl/Tk-based scripts running on a generic chemistry-aware data manager program. Among the tools are a full-featured 2D structure editor, a 2D structure browser, an IR spectra display tool and a number of additional goodies. Information about the context of these tools as well as downloading instructions can be obtained from http://schiele.organik.uni-erlangen.de/cactvs/index.html This is a binary-only release. Precompiled executables are provided for SunOS4.1, Solaris2.4 and Irix5.3. Versions for Linux and HPUX can be expected sometime later. A number of external test users have successfully installed and run the software. However, please tell me about any problem you might encounter. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From jkl@ccl.net Wed Sep 20 03:17:58 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA24437; Wed, 20 Sep 1995 03:14:46 -0400 Received: from shiva.jussieu.fr for bouyer@ext.jussieu.fr by bedrock.ccl.net (8.6.10/950822.1) id DAA04704; Wed, 20 Sep 1995 03:14:42 -0400 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id JAA18537 ; Wed, 20 Sep 1995 09:14:36 +0200 Received: from [134.157.11.12] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Wed, 20 Sep 1995 09:14:30 +0200 X-Sender: bouyer@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Sep 1995 09:21:13 +0100 To: "Victor M. Rosas Garcia" , chemistry@ccl.net From: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: Re: CCL:M:Calculation of entropy Hi Victor, I would say that in general I had the same problems with negative frequencies to calculate vibrational contributions to thermochemical functions. I used DMol and DGauss, and I tried always to get all frequencies, even those of small energy. Why? First, did you try to change (or pertubate) your geometry in order to fully re-optimize your structure? Did you optimize with strong Keywords (PRECISE, small gradients ...) Generally speaking, I would say you got the wrong geometry and you had a local maximum (a so called transition state with one negative frequency or a local maximum of the order n if you have n negative frequencies). Second, I would say that frequencies of small energy are **very** important in vibrational contributions because of the analytical expression ! Small frequencies of the order of 50 cm-1 (with my clusters) completely change thermochemical functions (S, H, and G(T), and DeltaG(T) of reaction ) if you either not take them into account or replace them by 35 cm-1 or 65 cm-1 ! But for frequencies that are normally in the order of 200 cm-1, they not strongly influence thermochemical functions. See how frequencies change thermodynamical quantities with your molecules. If you are interested in more comments, send me an email. You would probably be interested by (and references therein) : F. Bouyer, G. Picard and J. J. Legendre, "Computational chemistry : a way to reach spectroscopic and thermodynamic data for exotic compounds", to be published in Journal of Chemical Information and Computer Science [special issue of the ICCCRE XI (XIth International Conference on Computers in Chemical Research and Education, Paris, France, July 17-21), 1995.] Hope this helps. Frederic Bouyer ____________________________________________________________________ Frederic BOUYER Laboratoire d'Electrochimie et de Chimie Analytique Equipe "Reactivite en Milieux Ioniques Liquides" (G. PICARD) ENSCP 11, rue Pierre et Marie Curie 75231 PARIS Cedex 05 FRANCE Tel : (33)-1-43-54-53-84 ou (33)-1-44-27-67-51 ou (33)-1-44-27-66-94 Fax : (33)-1-44-27-67-50 E-mail : bouyer@ext.jussieu.fr http://alcyone.enscp.jussieu.fr/ created, in progress ... http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/ From steller@structchem.uni-essen.de Wed Sep 20 09:48:02 1995 Received: from gaby.structchem.uni-essen.de for steller@structchem.uni-essen.de by www.ccl.net (8.6.10/950822.1) id JAA28613; Wed, 20 Sep 1995 09:38:09 -0400 Received: by gaby.structchem.uni-essen.de (911016.SGI/910805.SGI) for CHEMISTRY@www.ccl.net id AA27498; Wed, 20 Sep 95 15:37:54 +0200 From: steller@structchem.uni-essen.de (Ingo Steller) Message-Id: <9509201337.AA27498@gaby.structchem.uni-essen.de> Subject: Spartan and LoadLeveler? To: CHEMISTRY@www.ccl.net Date: Wed, 20 Sep 1995 15:37:53 +0100 (MDT) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 688 Der CCL's: I am looking for a possibility to submit Spartan-jobs from the interface to a queuing system like IBM's LoadLeveler. Does anyone did the job to write appropiate scripts? If not, I will start working on it in the near future. I'll summarize all responces in the usual way. Sincerely, Ingo Steller -- Ingo Steller e-mail: steller@structchem.uni-essen.de Universitaet-Gesamthochschule Essen URL: http://www.structchem.uni-essen.de/ Fachbereich 08 - Chemie Tel.: ++49 (0)201 183 3599 Institut fuer Anorganische Chemie Fax : ++49 (0)201 183 2535 Abteilung Roentgenstrukturanalyse Universitaetsstrasse 3-5 45117 Essen From acp37@rs1.rrz.Uni-Koeln.DE Wed Sep 20 11:03:04 1995 Received: from rs1.rrz.Uni-Koeln.DE for acp37@rs1.rrz.Uni-Koeln.DE by www.ccl.net (8.6.10/950822.1) id KAA00452; Wed, 20 Sep 1995 10:50:17 -0400 Received: by rs1.rrz.Uni-Koeln.DE id AA127543 (5.67b/IDA-1.5 for CCL ); Wed, 20 Sep 1995 16:49:49 +0200 Date: Wed, 20 Sep 1995 16:49:49 +0200 (MST) From: "T. Koch" To: CCL Subject: Exact symmetries needed Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I am looking for a cute little program which would be so kind and generate exact symmetric coordinates from my approximate ones. I already tried newzmat from the Gaussian package, but it seems to be too far from the desired symmetry for it. Any help would be great. Thorsten Koch /-----------------------------------------------------------------\ | 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 Wed Sep 20 11:33:18 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA01244; Wed, 20 Sep 1995 11:18:06 -0400 Received: from biocad.ba.msi.com for scott@paganini.ba.msi.com by bedrock.ccl.net (8.6.10/950822.1) id LAA07486; Wed, 20 Sep 1995 11:18:03 -0400 Received: from paganini.ba.msi.com by biocad.ba.msi.com via SMTP (920330.SGI/911001.SGI) for chemistry@ccl.net id AA11369; Wed, 20 Sep 95 08:15:28 -0700 Received: by paganini.ba.msi.com (950413.SGI.8.6.12/930416.SGI) id IAA05403; Wed, 20 Sep 1995 08:15:16 -0700 Date: Wed, 20 Sep 1995 08:15:16 -0700 From: scott@paganini.ba.msi.com (Scott Kahn) Message-Id: <199509201515.IAA05403@paganini.ba.msi.com> To: ISISFORUM-L@mdli.com, DIBUG@comp.bioz.unibas.ch, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemistry@ccl.net, chemind-l@derwent.co.uk, chem_comp@mailbase.ac.uk, CHMINF-L@IUBVM.UCS.INDIANA.EDU Subject: Call for Papers - 3D databasing The following call for papers has been posted to several list servers. Sorry for any redundant messages (in advance). >> CALL FOR PAPERS << --------------- I am organizing a symposium for the Division of Chemical Information (CINF) of the ACS entitled "Managing Information in Databases of Three-Dimensional Structures" at the Spring ACS meeting in New Orleans, 24-29 March 1996. I would like to broadly focus of the symposium on the several aspects of _3D_ information management (e.g. integration with modeling/relational data, generation/storage of 3D structures, flexibiliy in searching, efficient indexing methods, etc.), and especially those that are potentially problematic as the compound generation process becomes more automated (i.e., via combinatorial methods). All _scientific_ presentations are welcomed; sales/ marketing presentations are actively discouraged (commercial and academic alike!). If you would like to contribute to this symposium, please send me four (4) copies of a 150 word abstract, including the original ACS abstract form, before 30 October 1995 at: Scott D. Kahn Biosym/Molecular Simulations 555 Oakmead Parkway Sunnyvale, California 94086-4023 Phone: (408) 522-0100 (secretary) FAX: (408) 522-0199 Email: skahn@msi.com or sdk@biosym.com ACS abstract forms can be obtained from me or from ACS Headquarters (Tel. 202-872-4396; email: natlmtg@acs.org). ------ Scott D. Kahn, Biosym/MSI (408) 522-0100 Email : scott@ba.msi.com or skahn@msi.com FAX (408) 522-0199 From tamaki@vt.edu Wed Sep 20 15:18:07 1995 Received: from holodeck.cc.vt.edu for tamaki@vt.edu by www.ccl.net (8.6.10/950822.1) id PAA06921; Wed, 20 Sep 1995 15:08:50 -0400 Message-Id: <199509201908.PAA06921@www.ccl.net> Received: from as2511-2.sl005.cns.vt.edu by holodeck.cc.vt.edu with SMTP (8.6.12/16.2) id PAA19948; Wed, 20 Sep 1995 15:08:47 -0400 X-Sender: tkurusu@mail.vt.edu X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Sep 1995 15:05:44 +0600 To: chemistry@www.ccl.net From: tamaki@vt.edu (Tamaki Kurusu) Subject: Torsion constraint in MOPAC 6.0 Hi, all! I have a question about the ways to constrain a torsion angle in MOPAC 6.0 run. (We use SGI Iris Workstation.) I set the optimization flag for the particular torsion angle to 0 so that it would not be optimized during the run, but that torsion was actually optimized/changed. What is the right method to constrain a torsion/angle/bond length in MOPAC? Thank you for your help in advance! tamaki From hou@agouron.com Wed Sep 20 17:03:08 1995 Received: from agouron.com for hou@agouron.com by www.ccl.net (8.6.10/950822.1) id RAA10040; Wed, 20 Sep 1995 17:00:45 -0400 Received: from duck by agouron.com via ESMTP (950215.SGI.8.6.10/930901.SGI) for <@tbone.agouron.com:CHEMISTRY@www.ccl.net> id OAA01797; Wed, 20 Sep 1995 14:00:33 -0700 Received: by duck (950215.SGI.8.6.10/930416.SGI) for CHEMISTRY@www.ccl.net id OAA08710; Wed, 20 Sep 1995 14:01:10 -0700 Date: Wed, 20 Sep 1995 14:01:10 -0700 From: hou@agouron.com (Xinjun Hou) Message-Id: <199509202101.OAA08710@duck> To: CHEMISTRY@www.ccl.net Subject: ether vs thioether in H bond Dear CCL'er, Is there any recent study, theoretical and/or experimental, to compare the relative hydrogen bond strengths of ether and thioether? Any points on this would be appreciate. I would post a summary Thank you Xinjun Hou C Xinjun J. Hou hou@agouron.com C Agouron Pharmaceuticals, Inc. San Diego, CA 92121 C10110000110100101101110011010100111010101101110010010000110111101110101 From david@helium.ch.ntu.edu.tw Wed Sep 20 21:48:12 1995 Received: from helium.ch.ntu.edu.tw for david@helium.ch.ntu.edu.tw by www.ccl.net (8.6.10/950822.1) id VAA13087; Wed, 20 Sep 1995 21:46:03 -0400 Received: by helium.ch.ntu.edu.tw; id AA30159; Thu, 21 Sep 1995 09:45:55 +0800 Date: Thu, 21 Sep 1995 09:45:55 +0800 From: Tsu-chien Weng Message-Id: <9509210145.AA30159@helium.ch.ntu.edu.tw> To: CHEMISTRY@www.ccl.net, steller@structchem.uni-essen.de Subject: Re: CCL:Spartan and LoadLeveler? Dear Ingo: I have no idea about IBM's LoadLevel, but I have tried to submit my jobs in SGI one by one. My method is to write down a script. The content of the file is as following spartan -x jobname1 spartan -x jobname2 ...... Now, go back shell and change its mode by typing "chmod u+x scriptname". Execute the script and it will submit those files one by one. Maybe I misunderstand your words. Hope it helpful. sincerely, David Weng