From chemistry-request@www.ccl.net Mon Feb 1 18:46:57 1999 Received: from teapot28.domain6.bigpond.com (teapot28.domain6.bigpond.com [139.134.5.197]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA04899 Mon, 1 Feb 1999 18:46:53 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by teapot28.domain6.bigpond.com (NTMail 3.02.13) with ESMTP id oa884144 for ; Tue, 2 Feb 1999 09:40:30 +1000 Received: from BDIP-T-009-p-236-35.tmns.net.au ([139.134.236.35]) by mail6.bigpond.com (Claudes-Ultra-Violet-MailRouter V2.2a); 02 Feb 1999 09:40:24 Message-ID: <000f01be4e3c$cd535f30$09007a81@hnlsyd8> Reply-To: "Dr Huang" To: From: "Dr Huang" Subject: Polarography Software available in CCL archives Date: Tue, 2 Feb 1999 10:44:22 +1100 Polar 3.2 for Windows: Electrochemical simulation and data analysis W.S. Ping Company 124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia Phone: 61 2 96620516, 0413 008 019 mailto:polarography@bigfoot.com, showing@bigfoot.com http://www.bigfoot.com/~polarography/ http://www.bigfoot.com/~showing/ ftp://www.ccl.net/pub/chemistry/software/MS-WIN95-NT/Polarograms It analytically and digitally simulates voltammograms (polarograms) on about 20 mechanisms at 8 electrode geometries (planar, spherical, semi- spherical, cylindrical, semi-cylindrical, microdisc, thin film, and rotating electrodes) in over 5 techniques (linear sweep and CV, DC, normal pulse, differential pulse, and square wave voltammetries), and outputs current, resitance, conductivity and surface concentration. It also simulates effects of charge current, resistance, noise, electrolyte, stripping time, stripping potential, etc. It analyses any x-y data for detecting peak location, peak value, semi-derivative, derivative, intergral, semi-intergral, curve fitting, and separating overlapped peaks. It shows a tip when the user put mouse cursor over a lable. It can separate overlapped voltammograms into individuals, and extract real peaks from voltammogram with noise and baseline. Users can compare by the theoretical peak values, analytically and digitally simulation, and choose to extract which kinetic pararmeters. Its data can be imported into other program (e.g. MS Excel). It has been successfully applied to fit experimental polarograms (voltammograms) of In(III), Cd(II), Pb(II), Tl(I), Cr(III). Zn(II), and binuclear copper complex in aqueous and non-aqueous media at mercury, solid metal and non-metal electrodes (specifically the dropping mercury, hanging mercury drop, gold, platinum and glassy carbon electrodes) by various electrochemical techniques (differential pulse, sqware wave, and pseudo-derivative normal pulse polargraphies) [1]. Its 32-bit version Polar32 runs on IBM PC under Windows 3.11/95/98/NT while its 16-bit version Polar32b runs under Windows 3/3.1/3.11/95/98/NT. They are available from the author or download from my Web site. REFERENCES [1] W. Huang, T. Henderson, A.M. Bond and K.B. Oldham, Curve fitting to resolve overlapping voltammetric peaks: model and examples, Anal. Chim. Acta, 1995, 304, 1-15. From chemistry-request@www.ccl.net Tue Feb 2 03:31:32 1999 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA06890 Tue, 2 Feb 1999 03:31:31 -0500 (EST) From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id JAA07282 for ; Tue, 2 Feb 1999 09:37:50 +0100 (MET) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id DAA05695 for CHEMISTRY@www.ccl.net;Tue, 2 Feb 1999 03:29:40 -0500 ("EST) X-OpenMail-Hops: 5 Date: Tue, 2 Feb 1999 09:31:24 +0100 X-OpenMail-Transport-Id: <0312336B6B7DC044/NL/400net/DSM/36B6B6C2.10DD.1586.000> Message-Id: <"36B6B6C2.10DD.1586.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: CCL:CoMFA software MIME-Version: 1.0 TO: CHEMISTRY@www.ccl.net Hi All, can anybody point me to some CoMFA software packages (both commercial and academic). Thank you Steven Creve From chemistry-request@www.ccl.net Tue Feb 2 05:39:36 1999 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA07326 Tue, 2 Feb 1999 05:39:35 -0500 (EST) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA19489 for ; Tue, 2 Feb 1999 11:35:10 +0100 Received: from localhost by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA13684; Tue, 2 Feb 1999 11:39:34 +0100 Date: Tue, 2 Feb 1999 11:39:34 +0100 (MET) From: John Marelius Reply-To: John Marelius To: chemistry@www.ccl.net Subject: Re: Alpha based computers in computational chemistry In-Reply-To: <85256708.004BD21D.00@bdc-notes003.na.pg.com> Message-Id: On Fri, 29 Jan 1999 shelley.jc@pg.com wrote: > > Hello, > In the context of individual research laboratories looking for > workstations or low to mid-range compute servers, are alpha based computers > used much in computational chemistry laboratories and if so how? In the group I work in we use Alpha workstations with WindowsNT for computational chemistry, mostly running our own molecular dynamics software. The Alpha + WindowsNT combination has proven to be a powerful combination of a high-performance number-cruncher and a desktop computer for word processing (MS Office etc) in one box. We find systems based on the Alpha processor not only to be the fastest but also to give the highest performance/price ratio. Systems based on the new generation of Alpha chips ("21264") are starting to become available, promising another large jump in performance. WindowsNT still has some drawbacks as a compute server operating system. * A third-party batch queue package is needed. * It's not a (simultaneous) multi-user system although remote login by telnet is possible (although sometimes problematic) by means of additional software. John Marelius +-----------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: john@alpha2.bmc.uu.se | | address: Box 590, S-751 24 Uppsala, Sweden | +-----------------------------------------------------------------+ From chemistry-request@www.ccl.net Tue Feb 2 08:35:11 1999 Received: from chris2.u-strasbg.fr (maerker@chris2.u-strasbg.fr [130.79.34.140]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA08205 Tue, 2 Feb 1999 08:35:10 -0500 (EST) Received: (from maerker@localhost) by chris2.u-strasbg.fr (8.8.8/8.8.8) id OAA11165; Tue, 2 Feb 1999 14:35:46 +0100 From: Christoph Maerker Message-Id: <199902021335.OAA11165@chris2.u-strasbg.fr> Subject: problem with G94 volume runs To: chemistry@www.ccl.net (ccl) Date: Tue, 2 Feb 1999 14:35:46 +0100 (MET) Cc: maerker@chris2.u-strasbg.fr (Christoph Maerker) Organization: Laboratoire de Chimie biophysique, Institut Le Bel, Universite Louis Pasteur Postal-Address: 4, rue Blaise Pascal, F- 67000 Strasbourg FRANCE Phone: +33/3-88-41-53-19 Fax: +33/3-88-60-63-83 X-Mailer: ELM [version 2.4ME+ PL37 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 650 Dear CClers, I wanted to do some G94 runs with the Volume keyword. In some cases I got zero volumes computed: Box volume =13970.821 fraction occupied=0.000 Molar volume = 0.000 bohr**3/mol ( 0.000 cm**3/mol) Recommended a0 for SCRF calculation = 0.50 angstrom ( 0.94 bohr) In other instances, however, I got non-zero volumes of the correct size; but from the few cases I have I cannot see any regular pattern. It seems to me that the molecule of interest is not positioned in the box at all (zero occupation fraction ?!). Has anybody ever hit this problem ? What is the cause, and how to solve the problem ? Sincerely yours, C. Maerker From chemistry-request@www.ccl.net Tue Feb 2 13:29:35 1999 Received: from sumter.awod.com (sumter.awod.com [198.81.225.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA14431 Tue, 2 Feb 1999 13:29:30 -0500 (EST) Received: from [208.140.97.215] (wa0215.tnt2.awod.com [208.140.97.215]) by sumter.awod.com (8.8.7/8.8.8) with SMTP id NAA08082; Tue, 2 Feb 1999 13:29:23 -0500 (EST) (envelope-from netsci@awod.com) X-Sender: arichon@awod.com Message-Id: Date: Tue, 2 Feb 1999 13:30:39 +0100 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: The 1999 Charleston Conference A few spaces are available for The 1999 Charleston Conference. If you plan to attend, please check http://www.netsci.org for registration details. From chemistry-request@www.ccl.net Wed Feb 3 03:42:59 1999 Received: from frederik.pml.tno.nl (frederik.pml.tno.nl [134.221.122.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA19557 Wed, 3 Feb 1999 03:42:57 -0500 (EST) Received: by frederik.pml.tno.nl; id JAA29336; Wed, 3 Feb 1999 09:42:44 +0100 Received: from postoffice.pml.tno.nl(134.203.134.74) by frederik.pml.tno.nl via smap (4.1) id xma029226; Wed, 3 Feb 99 09:42:14 +0100 Received: by postoffice.pml.tno.nl with Internet Mail Service (5.5.2232.9) id <1F751DVT>; Wed, 3 Feb 1999 09:41:31 +0100 Message-ID: <97C27A97BB05D211B37100805FE2A63814A3D8@postoffice.pml.tno.nl> From: "Gurp, Ron van" To: chemistry@www.ccl.net Cc: "Zelst, Michel van" Subject: Drawing Lewis structures Date: Wed, 3 Feb 1999 09:41:29 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Dear netters, We are looking for software (Linux/Windows95/98 or NT) that can draw Lewis structures of organic molecules, depicting all electron lone pairs as well as bonding pairs. Is there any computer program available that generates such structures semi-automatically? I appreciate all your answers and I will summarize. Kind Regards, Ron A. Rumley- Van Gurp, M.Sc. TNO Prins Maurits Laboratory Chemical Toxicology E-mail: gurp@pml.tno.nl From chemistry-request@www.ccl.net Wed Feb 3 05:16:12 1999 Received: from uldns2.unil.ch (uldns2.unil.ch [130.223.4.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA20135 Wed, 3 Feb 1999 05:16:09 -0500 (EST) Received: from pcbch3207h.unil.ch ([130.223.143.63] ident=aborel) by uldns2.unil.ch with esmtp (Exim 2.10 #1) for chemistry@www.ccl.net id 107zLj-0000l0-00; Wed, 3 Feb 1999 11:15:59 +0100 Message-ID: X-Mailer: XFMail 1.3 [p0] on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 Date: Wed, 03 Feb 1999 12:15:58 +0100 (MET) Organization: Universiy of Lausanne Sender: aborel@pcbch3207h.unil.ch From: Alain Borel To: chemistry@www.ccl.net Subject: CCL:G: gaussian98 for Linux using g77 Dear sirs, did anybody try and build gaussian98 using g77 on Linux? I do not have the option of using the officially supported Portland compiler. I managed to compile the util library but linking fails with 2 undefined symbols (wait_ and fork_). In case this plays a role I am using g77 shipping with egcs release 1.1.1. Thank you in advance Alain Borel Institute of Inorganic and Analytical Chemistry University of Lausanne (Switzerland) ---------------------------------- E-Mail: Alain Borel Date: 03-Feb-99 Time: 12:10:14 From chemistry-request@www.ccl.net Wed Feb 3 10:29:01 1999 Received: from natick-emh2.army.mil (NATICK-EMH2.ARMY.MIL [153.103.2.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA22505 Wed, 3 Feb 1999 10:29:00 -0500 (EST) Received: by natick-emh2.army.mil with VINES-ISMTP; Wed, 3 Feb 1999 10:28:44 EST Date: Wed, 3 Feb 1999 10:38:59 EST Message-ID: X-Priority: 3 (Normal) To: From: "Michael Sennett" Reply-To: Errors-to: Subject: CALL FOR PAPERS X-Incognito-SN: 461 X-Incognito-Version: 4.25.293 MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii American Chemical Society Division of Polymeric Materials: Science and Engineering Call for Papers Adhesion: Chemistry, Process and Mechanics New Orleans, Louisiana August 1999 The American Chemical Society Division of Polymeric Materials: Science and Engineering is sponsoring a symposium on chemistry, mechanics, and process engineering aspects of adhesion, adhesive bonding, paint adhesion, and related subjects. The symposium will be held in conjunction with the National meeting of the American Chemical Society in New Orleans, Louisiana, August 22-26, 1999. Original research papers are solicited in the following areas: Fundamentals of Surface and Interface Chemistry Modeling and Simulation of Interfaces and Adhesion Surface Chemistry, Cure Chemistry and Adhesion Process Effects on Chemistry and Adhesion Surface Chemistry and Mechanics of Durability Mechanics and Fracture Mechanics of Adhesion Two copies of 150-word abstract (original on ACS abstract form) and three copies of PMSE preprint (original on PMSE preprint paper) are due to the symposium chairs by APRIL 1, 1999. Detailed instructions for authors can be obtained from the Symposium Chairs or from the PMSE website at: http://www.umd.umich.edu/~rpotts/acs/; the website can also accessed from the ACS website, http://www.acs.org. Symposium Chairs Dr. Ray A. Dickie Ford Research Laboratory P. O. Box 2053, MD3083SRL Dearborn, MI 48121-2053, USA (313)337-4059 (313)621-0646 (fax) rdickie1@ford.com Prof. A. J. Kinloch Department of Mechanical Engineering Imperial College Exhibition Road London SW7 2BX, UK 0171 594 7082 0171 823 8845 (fax) a.kinloch@ic.ac.uk From chemistry-request@www.ccl.net Wed Feb 3 10:41:23 1999 Received: from hera.wku.edu (hera.wku.edu [161.6.20.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA22639 Wed, 3 Feb 1999 10:41:22 -0500 (EST) Received: (from adler@localhost) by hera.wku.edu (8.9.1b+Sun/8.9.1) id JAA05098; Wed, 3 Feb 1999 09:41:18 -0600 (CST) Date: Wed, 3 Feb 1999 09:41:18 -0600 (CST) Message-Id: <199902031541.JAA05098@hera.wku.edu> X-Authentication-Warning: hera.wku.edu: adler set sender to adler@hera.wku.edu using -f From: Allen Adler To: chemistry@www.ccl.net, adler@hera.wku.edu Subject: Re: Drawing Lewis structures Disclaimer: I am a mathematician, not a chemist. Ron A. Rumley- Van Gurp writes: >We are looking for software (Linux/Windows95/98 or NT) that can draw Lewis >structures of organic molecules, depicting all electron lone pairs as well >as bonding pairs. Is there any computer program available that generates >such structures semi-automatically? I asked about this several years ago. At the time, people referred me to ChemTeX, which draws chemical formulas, but it doesn't seem to handle Lewis structures. In Latex, one could probably use the resident graphics capabilities to write macros or enhance the ones that come with ChemTeX. If I were to do it, I would probably write some programs directly in PostScript, but that is a matter of taste and endurance. Does "semi-automatically" imply that the program will figure out the Lewis structure as well as draw it? The problem with that, in my perception, is that, at least as it is described in textbooks, the procedures for determining Lewis structures are not consistent. There is an exception in the case of books which dumb down the rules to apply only to a small class of examples (the "This is a course on how to pass this course" approach), but let's not even mention that. People have been complaining about this all the way back to Lewis, who never intended that his innovation should be used to prop up the same kind of arbitrary rule-based pedagogy about bonding that he himself had to go through and which he had hoped to dispel by inventing Lewis structures. I have a list somewhere, guaranteed not to be complete, which I compiled when I was thinking of writing an article about how screwed up pedagogy seems to be on this point. I abandoned the project when I realized that people have long complained about this in print and it has had no effect whatsoever on pedagogical practice. Apart from such inconsistencies, different authors try to do different things with Lewis structures. For example, Wheland's book on resonance has much fancier versions of Lewis structures with different kinds of electrons, and if I remember correctly he refers to other literature that I was unable to obtain that takes it even further. At any rate, there seem to be a lot of versions of "Lewis structures" in the literature. Allan Adler adler@hera.wku.edu From chemistry-request@www.ccl.net Wed Feb 3 15:00:04 1999 Received: from adams.moldyn.com (gateway.photon.com [206.71.176.98]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA03481 Wed, 3 Feb 1999 15:00:03 -0500 (EST) Received: by adams.moldyn.com with Internet Mail Service (5.0.1460.8) id ; Wed, 3 Feb 1999 14:50:50 -0500 Message-ID: <22E7F3D5131DD2119E3700A0C9D18F6D0706B9@adams.moldyn.com> From: Hon M Chun To: CHEMISTRY@www.ccl.net Subject: Request for comment: interest in various comp chem capabilities Date: Wed, 3 Feb 1999 14:50:48 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Content-Type: text/plain Dear netters, I'd like to get some feedback on the level of interest in the following topics. The purpose of this request is to gather information that will allow Moldyn to determine what features to incorporate into potential future products. * Free energy from MD calculations How practical are these calculations perceived to be, compared to the alternatives? Is the accuracy mostly limited by the forcefield parameter set, or by the length of the simulation trajectory? * High throughput molecular dynamics High throughput screening and docking of molecules are commonplace. How about high throughput molecular dynamics of the docked compounds (ligand and protein)? How important is it to analyze dynamic motions of the docked ligand/receptor complexes? * Coarse-grained dynamics modeling of large macromolecules, such as viral capsids How much interest is there for a coarse-grained modeling approach for the dynamics of large macromolecules that can be completed in a reasonably short amount of time? By coarse-grained, I mean grouping together atoms at the sub-residue level, residue level, or beyond. We therefore sacrifice many atomic details for greater speed and access to larger scale properties. Interaction forces are calculated at corresponding levels, and not at the atomistic level, resulting in significantly higher computational speed (approximately 2 orders of magnitude faster) than atomistic models. Such a dynamics model will not include explicit solvent, but will implicitly include solvent in the parameter set or via some form of continuum model. I recognize that there are many groups that are developing this class of simulation methods. I'd like to hear from potential users of such methods, to gauge the level of commercial and academic interest. * Dynamics of Self-assembly How much interest is there in studying the assembly or aggregation process? Would you use it for nanotechnology or molecular biology? Thank you in advance for your comments. Hon Chun hon@moldyn.com Hon M. Chun, Ph.D. Vice President & Chief Technical Officer Moldyn, Inc., 955 Massachusetts Avenue, Cambridge, MA 02139-3180 Phone:(617)354-3124 Voicemail: X16, Fax:(617)491-4522 From chemistry-request@www.ccl.net Wed Feb 3 20:08:12 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA07651 Wed, 3 Feb 1999 20:08:11 -0500 (EST) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id UAA26511 for ; Wed, 3 Feb 1999 20:08:13 -0500 Sender: richard@tc.cornell.edu Message-ID: <36B8F2FB.41C6@tc.cornell.edu> Date: Wed, 03 Feb 1999 20:08:11 -0500 From: Richard Gillilan X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: uniform random orientations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone have a pointer to methods of obtaining uniformly randomly distributed orientations of a rigid body? Richard Gillilan Cornell Theory Center From chemistry-request@www.ccl.net Wed Feb 3 20:18:01 1999 Received: from chu.Chem.nthu.edu.tw (Chu.Chem.nthu.edu.tw [140.114.45.233]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA07806 Wed, 3 Feb 1999 20:17:55 -0500 (EST) Received: by chu.Chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA12635; Thu, 4 Feb 1999 08:54:11 +0800 From: lin@chu.Chem.nthu.edu.tw (Chiu-Ling Lin) Message-Id: <9902040054.AA12635@chu.Chem.nthu.edu.tw> Subject: 6-31G* basis set of Sn in Gaussian Type? To: CHEMISTRY@www.ccl.net Date: Thu, 4 Feb 1999 08:54:10 +0800 (TAIST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear Netters, Does anyone have the 6-31G* basis set of the element Sn in Gaussian type? Any hits will be appreciated ! Regards, Chiu-Ling Lin **************************************** e-mail: lin@chu.chem.nthu.edu.tw NTHU, Hsin-Chu, Taiwan, R. O. C. ****************************************