From comartin@wicc.weizmann.ac.il Wed Feb 5 01:21:02 1997 Received: from wishful.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.3/950822.1) id AAA18042; Wed, 5 Feb 1997 00:47:31 -0500 (EST) Received: from winston.weizmann.ac.il (winston.weizmann.ac.il [132.76.57.114]) by wishful.weizmann.ac.il (8.6.5/8.6.5) with SMTP id GAA135277; Wed, 5 Feb 1997 06:44:11 +0200 Date: Wed, 5 Feb 1997 07:45:30 +0200 (IST) From: "Jan M.L. Martin" X-Sender: comartin@winston.weizmann.ac.il To: "Hui-Hsu (Gavin) Tsai" cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:normal modes program In-Reply-To: <199702042152.QAA04617@babar.INS.CWRU.Edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 4 Feb 1997, Hui-Hsu (Gavin) Tsai wrote: > Dear CCLers: > > Could anybody tell me what program can show the vibration normal modes > from Gaussian output files? This is one of the capabilities of gar2ped hy JML Martin and C Van Alsenoy, availableby anonymous ftp from the CCL archives. Jan Martin ---------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** temporary WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitfached k'lal ---- From toukie@zui.unizh.ch Wed Feb 5 02:21:01 1997 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id CAA18334; Wed, 5 Feb 1997 02:00:06 -0500 (EST) Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.14) id AA25044; Wed, 5 Feb 97 07:59:54 +0100 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA81478; Wed, 5 Feb 1997 07:59:53 +0100 From: "Dr. S. Shapiro" Message-Id: <9702050659.AA81478@rzurs3.unizh.ch> Subject: Proton affinities for non-nitrogens To: chemistry@www.ccl.net Date: Wed, 5 Feb 1997 07:59:53 +0100 (MET) X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text Forwarded message: From toukie@zui.unizh.ch Tue Feb 4 09:37:35 1997 Message-Id: <1.5.4.32.19970204083902.0066f4d8@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 04 Feb 1997 09:39:02 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Proton affinities for non-nitrogens Cc: toukie@zui.unizh.ch Dear Colleagues; Recently there has been some discussion in this group about the calculation of proton affinities using semi-empirical QM methods. A quick perusal (admittedly not comprehensive) of the literature has turned up numerous articles on the subject, but all of these seem to be concerned with amines of some sort: RR'R"N: + H+ <==> RR'R"N:H+, where RR'R"N: can be a primary, secondary, or tertiary amine. Whilst reading these articles, it occurred to me that a similar approach should be applicable for any Lewis base for which parametrisations exist for the elements of interest. For example, one might be able to _rank_ the Lewis acidities of various RX: derivatives (where X: = non-nitrogen heteroatom) by performing calculations on these species analogous to the abovementioned protonation reaction of amines. Even if species such as RX:H+ aren't _practically_ realistic, at least one should be able to compare the proton affinities of analogous Lewis bases and rank them accordingly. From those out there who are more knowledgeable about area than I am: is this a reasonable way of ranking the basicities within an analogous series of non-nitrogenous Lewis bases for which no experimental data are available? If not, why not? If so, then does anyone know of any publications directly addressing this matter? Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From luca@lcfs.chim.unifi.it Wed Feb 5 03:21:04 1997 Received: from cit.enscm.fr for luca@lcfs.chim.unifi.it by www.ccl.net (8.8.3/950822.1) id CAA18574; Wed, 5 Feb 1997 02:30:07 -0500 (EST) Received: from palladium.enscm.fr by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA15540; Wed, 5 Feb 1997 08:27:22 +0100 Received: from uranium (uranium [193.52.207.118]) by palladium.enscm.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id IAA13869; Wed, 5 Feb 1997 08:35:45 +0100 Sender: root@lcfs.chim.unifi.it Message-Id: <32F838D0.45A6B197@lcfs.chim.unifi.it> Date: Wed, 05 Feb 1997 08:37:52 +0100 From: Luca Pedocchi Organization: Department of Chemistry X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.0 i586) Mime-Version: 1.0 To: "Hui-Hsu (Gavin) Tsai" , chemistry@www.ccl.net Subject: Re: CCL:G:normal modes program References: <199702042152.QAA04617@babar.INS.CWRU.Edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A good one is Molden, you can find it at http://www.caos.kun.nl/b_pack/camm.html. Regards Luca -- Dr. Luca Pedocchi Laboratorio di Chimica Fisica delle Interfasi via Cavour, 82 - 50129 Firenze - ITALY http://lcfs.chim.unifi.it/solid/pedocchi e-mail luca@lcfs.chim.unifi.it phone +39-55-2757793 fax +39-55-219802 Non esistono uomini cattivi, se sono cucinati bene (Stefano Benni) From bruno@antas.agraria.uniss.it Wed Feb 5 03:28:27 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id CAA18840; Wed, 5 Feb 1997 02:54:27 -0500 (EST) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA235599221; Wed, 5 Feb 1997 08:53:41 +0100 Date: Wed, 5 Feb 1997 08:53:40 +0100 (NFT) From: "Dr. Bruno Manunza" To: "Hui-Hsu (Gavin) Tsai" Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:normal modes program In-Reply-To: <199702042152.QAA04617@babar.INS.CWRU.Edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 4 Feb 1997, Hui-Hsu (Gavin) Tsai wrote: > Dear CCLers: > > Could anybody tell me what program can show the vibration normal modes > from Gaussian output files? > Daer Hui-Hsu, there are several programs that do this, you may check MOLDEN at http://camms1.caos.kun.nl/~schaft/molden/molden.html it's free for academic users regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it From Robert.Franke@rz.ruhr-uni-bochum.de Wed Feb 5 03:36:49 1997 Received: from sun529.rz.ruhr-uni-bochum.de for Robert.Franke@rz.ruhr-uni-bochum.de by www.ccl.net (8.8.3/950822.1) id CAA18587; Wed, 5 Feb 1997 02:32:35 -0500 (EST) Received: from sun529.rz.ruhr-uni-bochum.de by mailhost.rz.ruhr-uni-bochum.de; Wed, 5 Feb 97 00:43:32 +0100 Received: from localhost.rz.ruhr-uni-bochum.de (localhost [127.0.0.1]) by sun529.rz.ruhr-uni-bochum.de (8.8.5/8.8.5) with SMTP id VAA15103 for ; Tue, 4 Feb 1997 21:12:00 +0100 (MET) Received: from rubc.rz.ruhr-uni-bochum.de by sun529.rz.ruhr-uni-bochum.de; Tue, 4 Feb 97 14:08:59 +0100 Received: from localhost (frankrbm@localhost) by rubc.rz.ruhr-uni-bochum.de (8.8.5/8.8.5) with SMTP id OAA48598 for ; Tue, 4 Feb 1997 14:08:58 +0100 Date: Tue, 4 Feb 1997 14:08:58 +0100 (MET) From: Robert Franke To: ccl Subject: VDW in Insight II (95.0) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII dear netters, does anyone know how to extract values of the van der waals radii from Insight Discover? thanks in advance robert franke /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ /\ /\ /\ Robert Franke /\ /\ Fakultaet fuer Chemie /\ /\ Lehrstuhl fuer Theoretische Chemie /\ /\ Ruhr-Universitaet Bochum /\ /\ D-44780 Bochum /\ /\ Phone: 049-234-7006751 or /\ /\ 049-234-7005294 /\ /\ Fax: 049-234-7094109 /\ /\ email: Robert.Franke@rz.ruhr-uni-bochum.de /\ /\ /\ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ From Jeffrey.Gosper@brunel.ac.uk Wed Feb 5 04:21:05 1997 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id DAA19022; Wed, 5 Feb 1997 03:29:45 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Wed, 5 Feb 1997 08:29:28 +0000 Date: Wed, 5 Feb 1997 08:29:25 GMT From: Jeffrey J Gosper Subject: Re: CCL:G:normal modes program To: CHEMISTRY@www.ccl.net cc: "Hui-Hsu (Gavin) Tsai" Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Tue, 4 Feb 1997 16:52:32 -0500 Hui-Hsu (Gavin) Tsai wrote: > From: Hui-Hsu (Gavin) Tsai > Date: Tue, 4 Feb 1997 16:52:32 -0500 > Subject: CCL:G:normal modes program > To: CHEMISTRY > > Dear CCLers: > > Could anybody tell me what program can show the vibration normal modes > from Gaussian output files? > Dear all, Re_View2 has the ability to view/animate and display displayment vectors for molcular vibrations using a 'standard file format'. I have a program that converts G94 FREQ output to this 'standard' format Further information on Re_View2 can be found at: http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view2.htm Interested persons should contact me directly. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ 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://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From grzesb@asp.biogeo.uw.edu.pl Wed Feb 5 07:21:18 1997 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.8.3/950822.1) id HAA20580; Wed, 5 Feb 1997 07:13:45 -0500 (EST) Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA05320; Wed, 5 Feb 97 13:14:54 +0100 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9702051214.AA05320@asp.biogeo.uw.edu.pl> Subject: g94 and Cray T3E (or T3D) To: chemistry@www.ccl.net Cc: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Dear CCL Readers, From Release Notes for Guassian 94 rev. D4 I've found out that g94 is NOT supported by Gaussian Inc. : *The Cray T3D & T3E and Sun UltraSparc platforms are not currently supported. My question is: Has anybody (any center) tried to port G94 on Cray T3E (or T3D) platform ? What has been results ( with success or NO) ? If YES: Has it required much efforts ? If NO: What has been main trouble ? Anyway, Anybody who can share any information on that subject is welcomed ! Thanks a lot, for your help. Grzegorz Bakalarski, Warsaw, Poland grzesb@asp.biogeo.uw.edu.pl From Jeffrey.Nauss@UC.Edu Wed Feb 5 09:21:07 1997 Received: from blues.fd1.uc.edu for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.8.3/950822.1) id JAA21180; Wed, 5 Feb 1997 09:00:57 -0500 (EST) Received: from beryllium.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IF1USM0RLQH7BHV2@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Wed, 05 Feb 1997 08:58:31 -0500 (EST) Received: by beryllium.crs.uc.edu (950413.SGI.8.6.12/940406.SGI.AUTO) for chemistry@www.ccl.net id IAA02435; Wed, 05 Feb 1997 08:59:04 -0500 Date: Wed, 05 Feb 1997 08:59:03 -0500 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Re: CCL:VDW in Insight II (95.0) In-reply-to: Robert Franke <"CCL:VDW in Insight II (95.0)"@UCBEH.SAN.UC.EDU> (Feb 4, 2:08pm) To: chemistry@www.ccl.net Reply-to: Jeffrey.Nauss@UC.EDU Message-id: <9702050859.ZM2433@beryllium.crs.uc.edu> Organization: Dept. Chemistry, University of Cincinnati MIME-version: 1.0 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT References: On Feb 4, 2:08pm, Robert Franke wrote: > does anyone know how to extract values of the van der waals > radii from Insight Discover? Good question. You might want to look at the file elements.dat or esff_elements.dat in the directory $BIOSYM/data/insight. I think that is where the information lies. Can anyone confirm this? -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From ludman@austerlitz.devinci.fr Wed Feb 5 09:28:29 1997 Received: from ns.devinci.fr for ludman@austerlitz.devinci.fr by www.ccl.net (8.8.3/950822.1) id IAA21141; Wed, 5 Feb 1997 08:51:33 -0500 (EST) Received: from austerlitz.fr. (austerlitz.devinci.fr [193.107.160.187]) by ns.devinci.fr (8.7.5/8.6.12) with SMTP id OAA28628 for ; Wed, 5 Feb 1997 14:46:26 +0100 Received: by austerlitz.fr. (SMI-8.6/SMI-SVR4) id NAA15539; Wed, 5 Feb 1997 13:03:23 GMT Date: Wed, 5 Feb 1997 13:03:23 GMT From: ludman@austerlitz.devinci.fr (Irene Ludman) Message-Id: <199702051303.NAA15539@austerlitz.fr.> To: CHEMISTRY@www.ccl.net Subject: CALL FOR PAPERS : IWCS'97 MIME-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit Content-Transfer-Encoding: 8bit CALL FOR PAPERS 1st INTERNATIONAL WORKSHOP ON COMPUTATIONAL SEMIOTICS 26th - 27th May, 1997 Pôle Universitaire Léonard de Vinci PARIS - LA DEFENSE - FRANCE TOPICS SEMIOTICS OF TEXT : Suzanne Bertrand-Gastaldy, University of Montreal Computers are increasingly used to assist text analysis for cognitive, literary, anthropological, sociological, documentary, etc. research. The workshop will focus on actual realisations, on the possibilities and limits of methodologies and existing tools to take into account the complex and multidimensional nature of texts, allowing multiple points of views for a variety of user needs. Issues such as desirable features of text analysis software, robustness and conviviality of implantations, interaction between corpora and users, constraints that actual tools put upon kinds of analyses and coding choices, the ability to elaborate models of electronic analytical tools suited to different semiotic theories, semiotical foundations of markup languages are examples of possible debates. SEMIOMETHODOLOGY : Claude Vogel, Léonard de Vinci University Several genres are currently under investigation for semiotic studies : electronic mail, news, corporate information, Web publishing. The flood of full text is overflowing semantic analysis, and this major paradigm break leads us to reconsider our approach of text processing. The size of these new corpora, the lack of consistency of information, the physical scattering of the basic units of texts, make the classical documentary solutions very uncomfortable. Instead, the semiotic based analysis seems to be a highly compelling perspective. It is focused on chronology; it provides a way to build transitive narratives throughout large amounts of data, and it does not require the understanding of the details of each local grammatical sentence in order for a global plot to be elaborated. This promising trend may give a second wind to ethnomethodology. For this reason, it is more appropriate to use the term "semiomethodology" when evoking this attempt to rationalize the computational approach of the symbolic dynamics which underlie collaborative production. ORGANIZATIONAL SEMIOTICS : Kathleen Carley, Carnegie Mellon University Organizational semiotics is the semiotics of organizations and organizational dimensions of textual semiotics. The objective of this workshop is to define the boundaries of this new specialty. Specifically, we will address the issue of : "How can semiotic analysis of interpersonal and corporate exchanges be used to reveal, evaluate, and contrast the underlying organizational logics and changes in these logics over time ?" Recent advances in textual analysis are facilitating this endeavor and creating new opportunities for understanding organizational behavior. Critical issues in the area of organizational semiotics include : 1) how to quickly and reliably analyze large quantities of texts, 2) how to reduce textual data to an empirical form that can be combined with other types of data and analyzed statistically, 3) how to identify corporate texts (those representing the "view" of the organization as an entity) and address issues of authorship, and 4) how to identify institutional constraints on the production and maintenance of corporate texts. New and innovative computational methods for empirically analyzing texts are being developed to address these and related concerns. These techniques have the potential to move textual analysis beyond counting words or locating a few themes or concepts. This section will focus on the issues involved in performing organizational semiotics with particular attention to the new computationally based techniques for facilitating organizational analysis that increase the ease, speed or reliability of coding texts and generate information that can be analyzed statistically. BIOSEMIOTICS : Jean-Claude Heudin, Léonard de Vinci University Recently, algorithms and architectures based on models derived from biological systems have been receiving an increasing amount of interest. This section will explore how such new approaches and techniques could be used for managing large amount of information exchanges on Internet or Intranet. Topics of particular interest include, but are not limited to, applications of agent-based systems, autonomous and evolving agents, genetic algorithms and programming, neural networks, cellular automata etc. to text stream analysis and in the more general framework of semiotics analysis. SUBMISSION OF PAPERS Send four copies of an abstract (approximately 500 words) in english or email it to : Irène Ludman - IWCS'97 Pôle Universitaire Léonard de Vinci 92916 PARIS-LA DEFENSE-CEDEX, FRANCE Phone: (33) 01 41 16 73 05 Fax : (33) 01 41 16 73 35 Email : irene.ludmann@devinci.fr DEADLINES Submission of abstracts by 1st April 1997 Acceptance notification to authors by 15th April 1997 Submission of full papers by 12th May 1997 ORGANIZING COMMITTEE Claude Vogel (chairman) Suzanne Bertrand-Gastaldy Kathleen Carley Jean-Claude Heudin PROGRAM COMMITTE Pierre Boudon (canada) Guillaume Deffuant (France) Evelyne Lutton (France) Joe Porac (USA) Carl Roberts (USA) J. Sebeok (Canada) Peter Stockinger (France) Bill Turner (France) For more information please visit the following Web page : http://www.devinci.fr/home/actua.htm From ludman@austerlitz.devinci.fr Wed Feb 5 09:31:24 1997 Received: from ns.devinci.fr for ludman@austerlitz.devinci.fr by www.ccl.net (8.8.3/950822.1) id IAA21142; Wed, 5 Feb 1997 08:51:33 -0500 (EST) Received: from austerlitz.fr. (austerlitz.devinci.fr [193.107.160.187]) by ns.devinci.fr (8.7.5/8.6.12) with SMTP id OAA07138 for ; Wed, 5 Feb 1997 14:46:32 +0100 Received: by austerlitz.fr. (SMI-8.6/SMI-SVR4) id NAA15542; Wed, 5 Feb 1997 13:03:25 GMT Date: Wed, 5 Feb 1997 13:03:25 GMT From: ludman@austerlitz.devinci.fr (Irene Ludman) Message-Id: <199702051303.NAA15542@austerlitz.fr.> To: CHEMISTRY@www.ccl.net Subject: CALL FOR PAPERS : IWCS'97 MIME-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit Content-Transfer-Encoding: 8bit CALL FOR PAPERS 1st INTERNATIONAL WORKSHOP ON COMPUTATIONAL SEMIOTICS 26th - 27th May, 1997 Pôle Universitaire Léonard de Vinci PARIS - LA DEFENSE - FRANCE TOPICS SEMIOTICS OF TEXT : Suzanne Bertrand-Gastaldy, University of Montreal Computers are increasingly used to assist text analysis for cognitive, literary, anthropological, sociological, documentary, etc. research. The workshop will focus on actual realisations, on the possibilities and limits of methodologies and existing tools to take into account the complex and multidimensional nature of texts, allowing multiple points of views for a variety of user needs. Issues such as desirable features of text analysis software, robustness and conviviality of implantations, interaction between corpora and users, constraints that actual tools put upon kinds of analyses and coding choices, the ability to elaborate models of electronic analytical tools suited to different semiotic theories, semiotical foundations of markup languages are examples of possible debates. SEMIOMETHODOLOGY : Claude Vogel, Léonard de Vinci University Several genres are currently under investigation for semiotic studies : electronic mail, news, corporate information, Web publishing. The flood of full text is overflowing semantic analysis, and this major paradigm break leads us to reconsider our approach of text processing. The size of these new corpora, the lack of consistency of information, the physical scattering of the basic units of texts, make the classical documentary solutions very uncomfortable. Instead, the semiotic based analysis seems to be a highly compelling perspective. It is focused on chronology; it provides a way to build transitive narratives throughout large amounts of data, and it does not require the understanding of the details of each local grammatical sentence in order for a global plot to be elaborated. This promising trend may give a second wind to ethnomethodology. For this reason, it is more appropriate to use the term "semiomethodology" when evoking this attempt to rationalize the computational approach of the symbolic dynamics which underlie collaborative production. ORGANIZATIONAL SEMIOTICS : Kathleen Carley, Carnegie Mellon University Organizational semiotics is the semiotics of organizations and organizational dimensions of textual semiotics. The objective of this workshop is to define the boundaries of this new specialty. Specifically, we will address the issue of : "How can semiotic analysis of interpersonal and corporate exchanges be used to reveal, evaluate, and contrast the underlying organizational logics and changes in these logics over time ?" Recent advances in textual analysis are facilitating this endeavor and creating new opportunities for understanding organizational behavior. Critical issues in the area of organizational semiotics include : 1) how to quickly and reliably analyze large quantities of texts, 2) how to reduce textual data to an empirical form that can be combined with other types of data and analyzed statistically, 3) how to identify corporate texts (those representing the "view" of the organization as an entity) and address issues of authorship, and 4) how to identify institutional constraints on the production and maintenance of corporate texts. New and innovative computational methods for empirically analyzing texts are being developed to address these and related concerns. These techniques have the potential to move textual analysis beyond counting words or locating a few themes or concepts. This section will focus on the issues involved in performing organizational semiotics with particular attention to the new computationally based techniques for facilitating organizational analysis that increase the ease, speed or reliability of coding texts and generate information that can be analyzed statistically. BIOSEMIOTICS : Jean-Claude Heudin, Léonard de Vinci University Recently, algorithms and architectures based on models derived from biological systems have been receiving an increasing amount of interest. This section will explore how such new approaches and techniques could be used for managing large amount of information exchanges on Internet or Intranet. Topics of particular interest include, but are not limited to, applications of agent-based systems, autonomous and evolving agents, genetic algorithms and programming, neural networks, cellular automata etc. to text stream analysis and in the more general framework of semiotics analysis. SUBMISSION OF PAPERS Send four copies of an abstract (approximately 500 words) in english or email it to : Irène Ludman - IWCS'97 Pôle Universitaire Léonard de Vinci 92916 PARIS-LA DEFENSE-CEDEX, FRANCE Phone: (33) 01 41 16 73 05 Fax : (33) 01 41 16 73 35 Email : irene.ludmann@devinci.fr DEADLINES Submission of abstracts by 1st April 1997 Acceptance notification to authors by 15th April 1997 Submission of full papers by 12th May 1997 ORGANIZING COMMITTEE Claude Vogel (chairman) Suzanne Bertrand-Gastaldy Kathleen Carley Jean-Claude Heudin PROGRAM COMMITTE Pierre Boudon (canada) Guillaume Deffuant (France) Evelyne Lutton (France) Joe Porac (USA) Carl Roberts (USA) J. Sebeok (Canada) Peter Stockinger (France) Bill Turner (France) For more information please visit the following Web page : http://www.devinci.fr/home/actua.htm From mbigi@farm.unipi.it Wed Feb 5 10:21:08 1997 Received: from mixer.unipi.it for mbigi@farm.unipi.it by www.ccl.net (8.8.3/950822.1) id JAA21301; Wed, 5 Feb 1997 09:21:23 -0500 (EST) Organization: Centro SERRA University of Pisa - Italy Received: from pippo.cnuce.cnr.it (pippo.cnuce.cnr.it [131.114.1.249]) by mixer.unipi.it (8.8.0/8.8.0) with SMTP id QAA01620 for ; Wed, 5 Feb 1997 16:21:47 -0100 (GMT) Date: Wed, 5 Feb 1997 16:21:47 -0100 (GMT) Message-Id: <199702051721.QAA01620@mixer.unipi.it> X-Sender: mbigi@dial-up.unipi.it 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: "Michele U. Bigi" Subject: Partial Charge in Big Molecule Dear CCLers, I search some fast algoritms for the calculus of the partial charge of the atoms in a proteic system. Now I use a Iteractive Partial Equalization Of Orbital Electronegativity (Gasteiger, J., Marsili, M., Tetrahedron, 36(1980), 3219). Thanks Michele Bigi From giovanni@sg2.csrsrc.mi.cnr.it Wed Feb 5 10:25:11 1997 Received: from sg2.csrsrc.mi.cnr.it for giovanni@sg2.csrsrc.mi.cnr.it by www.ccl.net (8.8.3/950822.1) id JAA21586; Wed, 5 Feb 1997 09:41:17 -0500 (EST) Received: from localhost by sg2.csrsrc.mi.cnr.it via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) id GAA19704; Wed, 5 Feb 1997 06:40:43 -0800 Date: Wed, 5 Feb 1997 06:40:35 -0800 (PST) From: Giovanni Scalmani To: Grzegorz Bakalarski cc: chemistry@www.ccl.net Subject: Re: CCL:G:g94 and Cray T3E (or T3D) In-Reply-To: <9702051214.AA05320@asp.biogeo.uw.edu.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Feb 1997, Grzegorz Bakalarski wrote: > Dear CCL Readers, > > >From Release Notes for Guassian 94 rev. D4 I've found out that g94 is NOT supported > by Gaussian Inc. : > > *The Cray T3D & T3E and Sun UltraSparc platforms are not > currently supported. > > My question is: Has anybody (any center) tried to port G94 on Cray T3E (or T3D) > platform ? What has been results ( with success or NO) ? If YES: Has it > required much efforts ? If NO: What has been main trouble ? > Anyway, Anybody who can share any information on that subject is welcomed ! > Thanks a lot, for your help. > Dear Grzegorz, right now I am running the test suite of g94 on a Cray-T3E. I also ported it on Cray-T3D, but I haven't tested it deeply, essentially because of the little (on Gaussian scale) memory which T3D has on each processor (T3D has 8Mw/PE while T3E has 16Mw/PE). Some general remarks follow: 1) on Cray T3E you run applications on a pool of PEs (processing elements) in which there is 1 (and 1 only) process on each PE. Gaussian 94 uses UNIX function like execl() or the fortran system() call to execute the sequence of the links: on T3E the only way to run g94 appear to use an option of the Makefile which build a one-executable version of the whole Gaussian system ... but Gaussian, Inc. does not support that option anymore. I actually build such a one-executable version (>20 Mbytes) by looking at Gaussian92's makefile and by carefully checking for duplicate subroutines, functions and commons within the whole source code. 2) Gaussian94 can run in parallel using the fork/wait UNIX calls or by using Linda(tm) from Scientific Computing Associate, Inc.. On T3E I used MPI. 3) as a general warning I must say that Gaussian94 contains still a lot of serial code (it is quite puzzling to get into a huge and complex code like Gaussian and try to parallelize it). When you use a little number of PEs, from 2 to 8, all goes fine, but on T3E you can go far beyond and, using 16, 32 or more PEs, you find out new bottlenecks (for example in the SCF procedure the bottleneck moves from integral evaluation and Fock matrix formation to matrix diagonalization, which is performed by a single PE while the others do nothing!). I am implementing the use of SCALAPACK routines within my g94 on T3E and things are getting better. 4) the true limitation is again the memory available to each T3E processing element: into the available 16Mw you must find room for the operating system (quite little UNICOS/mk), the g94 executable (about 20Mbytes, i.e. more than 2 Mw), the BLACS-SCALAPACK buffer (for the moment I use 4Mw, but I will try to tailor its size better) ... .. so there are about 8-10 Mw left for the g94 job, which is enough for many kinds of calculations, but not for all. Sincerely, Giovanni P.S.: We must remember the Gaussian94 is not a public domain code. ---------------------------------------------------------------------- ^^^ | SCALMANI Giovanni giovanni@sg2.csrsrc.mi.cnr.it o o | Universita' degli Studi di Milano | | Dipartimento di Chimica Fisica ed Elettrochimica \_/ | via C.Golgi, 19 Phone: ++39-2-26603254 | 20133 Milano (Italy) Fax : ++39-2-70638129 ---------------------------------------------------------------------- From ludman@austerlitz.devinci.fr Wed Feb 5 11:21:10 1997 Received: from ns.devinci.fr for ludman@austerlitz.devinci.fr by www.ccl.net (8.8.3/950822.1) id LAA22676; Wed, 5 Feb 1997 11:09:10 -0500 (EST) Received: from austerlitz.fr. (austerlitz.devinci.fr [193.107.160.187]) by ns.devinci.fr (8.7.5/8.6.12) with SMTP id RAA22248 for ; Wed, 5 Feb 1997 17:05:32 +0100 Received: by austerlitz.fr. (SMI-8.6/SMI-SVR4) id PAA03197; Wed, 5 Feb 1997 15:22:25 GMT Date: Wed, 5 Feb 1997 15:22:25 GMT From: ludman@austerlitz.devinci.fr (Irene Ludman) Message-Id: <199702051522.PAA03197@austerlitz.fr.> To: chemistry@www.ccl.net Subject: CALL FOR PAPERS : IWCS'97 MIME-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit Content-Transfer-Encoding: 8bit CALL FOR PAPERS 1st INTERNATIONAL WORKSHOP ON COMPUTATIONAL SEMIOTICS 26th - 27th May, 1997 Pôle Universitaire Léonard de Vinci PARIS - LA DEFENSE - FRANCE TOPICS SEMIOTICS OF TEXT : Suzanne Bertrand-Gastaldy, University of Montreal Computers are increasingly used to assist text analysis for cognitive, literary, anthropological, sociological, documentary, etc. research. The workshop will focus on actual realisations, on the possibilities and limits of methodologies and existing tools to take into account the complex and multidimensional nature of texts, allowing multiple points of views for a variety of user needs. Issues such as desirable features of text analysis software, robustness and conviviality of implantations, interaction between corpora and users, constraints that actual tools put upon kinds of analyses and coding choices, the ability to elaborate models of electronic analytical tools suited to different semiotic theories, semiotical foundations of markup languages are examples of possible debates. SEMIOMETHODOLOGY : Claude Vogel, Léonard de Vinci University Several genres are currently under investigation for semiotic studies : electronic mail, news, corporate information, Web publishing. The flood of full text is overflowing semantic analysis, and this major paradigm break leads us to reconsider our approach of text processing. The size of these new corpora, the lack of consistency of information, the physical scattering of the basic units of texts, make the classical documentary solutions very uncomfortable. Instead, the semiotic based analysis seems to be a highly compelling perspective. It is focused on chronology; it provides a way to build transitive narratives throughout large amounts of data, and it does not require the understanding of the details of each local grammatical sentence in order for a global plot to be elaborated. This promising trend may give a second wind to ethnomethodology. For this reason, it is more appropriate to use the term "semiomethodology" when evoking this attempt to rationalize the computational approach of the symbolic dynamics which underlie collaborative production. ORGANIZATIONAL SEMIOTICS : Kathleen Carley, Carnegie Mellon University Organizational semiotics is the semiotics of organizations and organizational dimensions of textual semiotics. The objective of this workshop is to define the boundaries of this new specialty. Specifically, we will address the issue of : "How can semiotic analysis of interpersonal and corporate exchanges be used to reveal, evaluate, and contrast the underlying organizational logics and changes in these logics over time ?" Recent advances in textual analysis are facilitating this endeavor and creating new opportunities for understanding organizational behavior. Critical issues in the area of organizational semiotics include : 1) how to quickly and reliably analyze large quantities of texts, 2) how to reduce textual data to an empirical form that can be combined with other types of data and analyzed statistically, 3) how to identify corporate texts (those representing the "view" of the organization as an entity) and address issues of authorship, and 4) how to identify institutional constraints on the production and maintenance of corporate texts. New and innovative computational methods for empirically analyzing texts are being developed to address these and related concerns. These techniques have the potential to move textual analysis beyond counting words or locating a few themes or concepts. This section will focus on the issues involved in performing organizational semiotics with particular attention to the new computationally based techniques for facilitating organizational analysis that increase the ease, speed or reliability of coding texts and generate information that can be analyzed statistically. BIOSEMIOTICS : Jean-Claude Heudin, Léonard de Vinci University Recently, algorithms and architectures based on models derived from biological systems have been receiving an increasing amount of interest. This section will explore how such new approaches and techniques could be used for managing large amount of information exchanges on Internet or Intranet. Topics of particular interest include, but are not limited to, applications of agent-based systems, autonomous and evolving agents, genetic algorithms and programming, neural networks, cellular automata etc. to text stream analysis and in the more general framework of semiotics analysis. SUBMISSION OF PAPERS Send four copies of an abstract (approximately 500 words) in english or email it to : Irène Ludman - IWCS'97 Pôle Universitaire Léonard de Vinci 92916 PARIS-LA DEFENSE-CEDEX, FRANCE Phone: (33) 01 41 16 73 05 Fax : (33) 01 41 16 73 35 Email : irene.ludmann@devinci.fr DEADLINES Submission of abstracts by 1st April 1997 Acceptance notification to authors by 15th April 1997 Submission of full papers by 12th May 1997 ORGANIZING COMMITTEE Claude Vogel (chairman) Suzanne Bertrand-Gastaldy Kathleen Carley Jean-Claude Heudin PROGRAM COMMITTE Pierre Boudon (canada) Guillaume Deffuant (France) Evelyne Lutton (France) Joe Porac (USA) Carl Roberts (USA) J. Sebeok (Canada) Peter Stockinger (France) Bill Turner (France) For more information please visit the following Web page : http://www.devinci.fr/home/actua.htm From hebant@ext.jussieu.fr Wed Feb 5 12:21:10 1997 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.8.3/950822.1) id LAA23056; Wed, 5 Feb 1997 11:28:29 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.5/jtpda-5.2) with ESMTP id RAA17962 for ; Wed, 5 Feb 1997 17:28:18 +0100 (MET) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with ESMTP; Wed, 5 Feb 1997 17:28:14 +0100 Date: Wed, 5 Feb 1997 17:28:14 +0100 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: Pascal HEBANT Subject: Eigenvectors normalization with Gamess Content-Transfer-Encoding: 8bit Hi netters, It seems that Eigenvectors given in Gamess output files are not normalized. Is there a keyword in order to do it. Regards Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel:+33 - 01 44 27 66 94 fax: +33 - 01 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/Pascal.html ***************************************************************************** Yü From huang@nissan.wavefun.com Wed Feb 5 13:21:10 1997 Received: from volvo.wavefun.com for huang@nissan.wavefun.com by www.ccl.net (8.8.3/950822.1) id MAA23710; Wed, 5 Feb 1997 12:41:42 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA04390; Wed, 5 Feb 97 09:42:41 -0800 Received: from nissan.wavefun.com(198.147.95.2) by volvo.wavefun.com via smap (V1.3) id sma004388; Wed Feb 5 09:42:24 1997 Received: by nissan.wavefun.com (931110.SGI/940406.SGI.AUTO) for @volvo.wavefun.com:chemistry@www.ccl.net id AA03741; Wed, 5 Feb 97 09:41:17 -0800 From: "Wayne Huang" Message-Id: <9702050941.ZM3739@nissan.wavefun.com> Date: Wed, 5 Feb 1997 09:41:08 -0800 In-Reply-To: "Hui-Hsu (Gavin) Tsai" "CCL:G:normal modes program" (Feb 4, 4:52pm) References: <199702042152.QAA04617@babar.INS.CWRU.Edu> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: "Hui-Hsu (Gavin) Tsai" Subject: Re: CCL:G:normal modes program Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Feb 4, 4:52pm, Hui-Hsu (Gavin) Tsai wrote: > Subject: CCL:G:normal modes program > Dear CCLers: > > Could anybody tell me what program can show the vibration normal modes > from Gaussian output files? > > Thanks a lot! > > Hui-Hsu (Gavin) Tsai > Ph.D. student in the Chemistry Department > Case Western Reserve University > E-mail : hxt10@po.cwru.edu > Tel : (O)(216)368-3730 > (H)(216)229-5913 > Spartan has external interface with Gaussian which enables to the vibration animation of the normal modes calculated from Gaussian. Check our Web page for more info (http://www.wavefun.com). --Wayne -- +---------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92612 | | Wavefunction, Inc. | 714-955-2120 <> 955-2118(fax)| | huang@wavefun.com | Web: http://www.wavefun.com | +---------------------------------------------------------------+ From DAVID@UCONNVM.UCONN.EDU Wed Feb 5 13:25:35 1997 Received: from UConnVM.UConn.Edu for DAVID@UCONNVM.UCONN.EDU by www.ccl.net (8.8.3/950822.1) id MAA23762; Wed, 5 Feb 1997 12:49:09 -0500 (EST) Received: from UCONNVM.UCONN.EDU by UConnVM.UConn.Edu (IBM VM SMTP V2R2) with BSMTP id 0700; Wed, 05 Feb 97 12:49:17 EST Received: from UConnVM.UConn.Edu (NJE origin DAVID@UCONNVM) by UCONNVM.UCONN.EDU (LMail V1.2c/1.8c) with BSMTP id 5325; Wed, 5 Feb 1997 12:49:18 -0500 Date: Wed, 05 Feb 97 12:48:45 EST From: Carl David Subject: Can you look at some Java for Mathematics Inputting? To: chemistry@www.ccl.net X-Mailer: MailBook 96.01.000 Message-Id: <970205.124917.EST.DAVID@UConnVM.UConn.Edu> MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT In Computer Assisted Testing using the World Wide Web, when applying the method to mathematics based subjects, one needs the ability to allow students to input equations as well as numbers as answers to individual questions. In a separate posting, several months ago, I asked for criticism of a java module which allowed students to input chemical formulae into the Web for grading: http://www.chem.uconn.edu/~chem12x/cgi-bin/c127fin2.pl Now, I am asking for guidance in evaluating the equation entry scheme which is under development. If you are inter- ested, could you try the location: http://www.chem.uconn.edu/~cdavid/cgi-bin/HowToUseWebEQ.pl where R. Miner's WebEQ(2) is implemented in a framed envi- ronment. This implementation requires the student to write his/her equation in (what I call) pseudo-LaTeX. Actually, the current implementation uses only a subset of LaTeX, and needs excessive curly brackets to demark ambiguous opera- tors. ======================= I have tried using EqnWriter, the point and click applet, but it spasmodically works differ- ently on different platforms, making it (so far) unsuitable for students. ====================== There is no question that the implemented method (above) is cumbersome, but the question is, is it so cumbersome that its use should not be attempted with undergraduates? Thanks for any advice, suggestions, etc., which you can provide with respect to this problem. Carl W. David bitnet : david@uconnvm internet : david@uconnvm.uconn.edu http://www.sp.uconn.edu/~.cdavid/chem263.html http://www.sp.uconn.edu/~/chem12x From dimitris@3dp.com Wed Feb 5 14:21:10 1997 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.8.3/950822.1) id NAA24311; Wed, 5 Feb 1997 13:47:27 -0500 (EST) From: Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA03843; Wed, 5 Feb 97 13:53:01 -0500 Received: by europa.3dp.com (950413.SGI.8.6.12) id NAA29697; Wed, 5 Feb 1997 13:46:06 -0500 Date: Wed, 5 Feb 1997 13:46:06 -0500 Message-Id: <199702051846.NAA29697@europa.3dp.com> To: chemistry@www.ccl.net Subject: ACD fingerprints Has anyone out there computed Daylight-like fingerprints for the ACD, NCI Open, or any other public collection of compounds, that they would be willing to share with us for some diversity studies? Please let me know if you can help. Thanks, Dimitris K. Agrafiotis, PhD | E-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | Tel: (610) 458-6045 665 Stockton Drive, Suite 104 | Fax: (610) 458-8249 Exton, PA 19341 From bruno@antas.agraria.uniss.it Wed Feb 5 15:21:16 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id PAA24960; Wed, 5 Feb 1997 15:12:59 -0500 (EST) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA018923626; Wed, 5 Feb 1997 21:13:47 +0100 Date: Wed, 5 Feb 1997 21:13:43 +0100 (NFT) From: "Dr. Bruno Manunza" To: "Michele U. Bigi" Cc: chemistry@www.ccl.net Subject: Re: CCL:Partial Charge in Big Molecule In-Reply-To: <199702051721.QAA01620@mixer.unipi.it> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Feb 1997, Michele U. Bigi wrote: > Dear CCLers, > I search some fast algoritms for the calculus of the partial charge > of the atoms in a proteic system. Now I use a Iteractive Partial > Equalization Of Orbital Electronegativity (Gasteiger, J., Marsili, M., > Tetrahedron, 36(1980), 3219). > > > Thanks > Michele Bigi > Dear Michele, the best way to compute partial atomic charges is to fit them in order to reproduce the electrostatic potential (EP) computed at a convenient distance from the molecule. The EP may be computed by ab initio or with the AM1 hamiltonian. Of course it's an unaffordable task to use such methods for a protein as a whole. So you may use charges computed for the single residues. You may found tables reporting these charges for most of the aminoacids and the nucleic acid residues in the DLPOLY suite (http://gserv1.dl.ac.uk/TCSC/Software/DL_POLY/main.html) or among the public AMBER (http://www.amber.ucsf.edu/amber/amber.html) files at this page: http://www.amber.ucsf.edu/amber/ff94.html. Hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it