From b_duke@lacebark.ntu.edu.au Thu Jan 19 01:37:46 1995 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.9/930601.1506) id AAA23376; Thu, 19 Jan 1995 00:51:07 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA10479; Thu, 19 Jan 1995 14:14:00 +1000 Message-Id: <9501190414.AA10479@lacebark.ntu.edu.au> Subject: Teaching Comp Chem To: CHEMISTRY@ccl.net (chemistry) Date: Thu, 19 Jan 1995 14:13:59 +1000 (EET) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 2271 Hi folks, I hope some people are interested in this. We have recently received a grant from the Australian Government funded Committee for the Advancement of University Teaching (CAUT) for a project entittled "Learning modules for computational chemistry over AARNET". The aim is to assist the teaching of computational chemistry, particularly in Australia, by making materials available over the net. Students will access learning materials over the net and run programs on various machines in various places. The people concerned are myself, Margaret Wong (Swinburne), Ted Lloyd (VCP, Monash) and Brian Yates (Tasmania). Initially the materials will be available to students in the four institutions, later we hope to make them available through Australia and then the world. The idea is not to develop whole courses but to develop modules which can be incorporated into courses with different objectives in different places. The level is at final year undergraduate and beginning graduate, including B Sc Honours. The needs of straight chemistry students and pharmacy students will be considered. We are interested in knowing whether anyone else anywhere in the world is doing anything similar. We know of some efforts at teaching comp chem to undergraduates in the US, such at the Rev Comp Chem article and other material discussed in sci.chem and CCL, but none of this seems to have the flexibility we are seeking. We are also happy to keep people informed of our progress as we go along. The project is funded for 1995 and we will be appointing a Research Associate soon to assist in coordinating activities of the project, collecting relevant materials, writing course materials in WWW format, and installing software at the four universities involved in the project. The person we are seeking clearly needs to be multi-skilled in chemistry, computing and writing. If anyone (we would have to appoint an Australian resident) is interested in this position, please e-mail me. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University, Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From thomas@salz.phych.ba-freiberg.de Thu Jan 19 04:37:54 1995 Received: from salz.phych.ba-freiberg.de for thomas@salz.phych.ba-freiberg.de by www.ccl.net (8.6.9/930601.1506) id EAA24860; Thu, 19 Jan 1995 04:34:08 -0500 From: Received: by salz.phych.ba-freiberg.de (AIX 3.2/UCB 5.64/4.03) id AA09602; Thu, 19 Jan 1995 10:02:39 +0100 Message-Id: <9501190902.AA09602@salz.phych.ba-freiberg.de> Subject: Re: 3D-graphs To: chemistry@ccl.net Date: Thu, 19 Jan 95 10:02:38 NFT X-Mailer: ELM [version 2.3 PL2] To plot 3D-graphs you can try "pdraw" and "plotmtv", both free. The programs you can get from many servers via ftp. thomas@salz.phych.ba-freiberg.de From steve@chem.columbia.edu Thu Jan 19 09:37:54 1995 Received: from cucbs.chem.columbia.edu for steve@chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id JAA27340; Thu, 19 Jan 1995 09:18:38 -0500 Received: from amazon.chem.columbia.edu.columbia.edu (amazon.chem.columbia.edu) by cucbs.chem.columbia.edu with SMTP id AA22824 (5.65c/IDA-1.4.4 for ); Thu, 19 Jan 1995 09:18:29 -0500 Date: Thu, 19 Jan 1995 09:18:29 -0500 From: Steve Stuart Message-Id: <199501191418.AA22824@cucbs.chem.columbia.edu> Received: by amazon.chem.columbia.edu.columbia.edu (4.1/SMI-4.1) id AA13352; Thu, 19 Jan 95 09:18:24 EST To: chemistry@ccl.net Subject: expert systems for organic synthesis I would appreciate receiving any information on the current status of AI or expert system approaches to synthetic organic chemistry. I know nothing about this area, so I'm not sure what to expect - are there programs as smart as an introductory course, for example? I am most interested in references or reviews describing progress and/or techniques, but pointers to specific programs would also be fine. I will summarize any responses for the list, of course. -Steve Stuart steve@chem.columbia.edu echo "a'rfg cnf Crpv | har" | tr '[a-m][n-z] ' '[n-z][a-m]\012' | sort | tr "\012" " " ; echo " " From h.rzepa@ic.ac.uk Thu Jan 19 10:55:33 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA28331; Thu, 19 Jan 1995 10:07:39 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Thu, 19 Jan 1995 14:55:22 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA16544; Thu, 19 Jan 95 14:55:09 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jan 1995 14:55:16 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: chemically cognisant E-mailers As a result of the recent ECCC conference, and with others planned, I find one vital tool that is missing are E-mail programs that might support chemical MIME enclosures. In brief, I would like to enclose, lets say a molfile or a pdb file, and have it received at the other end in an instantly openable form, either within the e-mail window (wishful thinking; lets wait for OpenDoc) or with an external helper such as RasMol. This can be done now within say Mac-to-Mac e-mails, but would not work with Mac-to-Windows, or Windows-to-Unix etc etc. I have tried some experiments with Mac Eudora. However, the only way I could get it to work was to manually insert entries such as the one below. Even then, a bit of Resedit hacking is needed! Clearly, we need a custom job done! Does anyone know of a mailer which might be user configured to do this? Indeed, is there a "most common" mailer in use. Would Eudora be such a beast? Or is the chemistry mailer market fragmented into an entire variety, ranging from elm on Unix, ccmail in commerce, etc etc? --========================_13836636==_ Content-Type: chemical/x-chemdraw; name="scheme.cd"; charset="us-ascii" Content-Disposition: attachment; filename="scheme.cd" scheme.cd 54 57 0 0 0 0 0 0 0 0 24 -4.2967 5.0233 0.0000 C 0 0 0 0 0 etc etc Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.1.1, Tel (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804. World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html From REISSNER@pembvax1.pembroke.edu Thu Jan 19 11:37:54 1995 Received: from papa.pembroke.edu for REISSNER@pembvax1.pembroke.edu by www.ccl.net (8.6.9/930601.1506) id LAA29228; Thu, 19 Jan 1995 11:07:27 -0500 From: Received: by pembvax1.pembroke.edu (MX V4.1 VAX) id 44; Thu, 19 Jan 1995 11:05:53 EST Date: Thu, 19 Jan 1995 11:05:52 EST To: U54632%UICVM.BITNET@phem3.acs.ohio-state.edu CC: chemistry@ccl.net Message-ID: <0098AB15.16995854.44@pembvax1.pembroke.edu> Subject: RE: CCL:Software for plotting 3D-graphs > I'm a graduate student at the University of Illinois at Chicago > and I'm looking for a freeware, or a public domain software to plot 3D-graphs. > Any suggestions or help in this regard, would be greatly appreciated. > If there is enough interest, I shall summarize the responses > that I get on the net. Let me hitch-hike on Chaya's query: most anything, like wonderful GNUPLOT, will do OK contouring data given on a rectangular grid, i.e. xi=x0+ia,yi=y0+jb, and moreover the points lie on a rectangular domain. The newest GNUPLOT even works on a non-rectangular grid... but stalls on oallowing triangular, or more wildly non-rectangular domains. Suggestions as to that functionality would be appreciated. John John Reissner Pembroke State University Pembroke NC 28372 USA reissner@pembvax1.pembroke.edu vox: (910)521-6425 fax: (910)521-6649 From craig@hobbes.gh.wits.ac.za Thu Jan 19 12:38:00 1995 Received: from hobbes.gh.wits.ac.za for craig@hobbes.gh.wits.ac.za by www.ccl.net (8.6.9/930601.1506) id LAA29876; Thu, 19 Jan 1995 11:53:38 -0500 Received: (from craig@localhost) by hobbes.gh.wits.ac.za (8.6.9/8.6.9) id SAA20388; Thu, 19 Jan 1995 18:51:25 +0200 Date: Thu, 19 Jan 1995 18:51:24 +0200 From: Craig Taverner Subject: Hartree-Fock-Slater SCF atomic orbitals To: computational chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know of recent programs for the calculation of atomic orbitals by the self consistent field approach. I am particularly interested in C code that is publically available. A particularly useful feature would be the dropping of the assumption of spherical symmetry, if such a think is possible or has been attepted, or possibly the use of HF SCF methods for the calculation of molecular orbitals. I'm quite new in this field and would appreciate any help I can get. Thanks Craig Taverner Structural Chemistry University of the Witwatersrand, South Africa craig@hobbes.gh.wits.ac.za From jle@toyota.wavefun.com Thu Jan 19 13:37:56 1995 Received: from wavefun.com for jle@toyota.wavefun.com by www.ccl.net (8.6.9/930601.1506) id NAA01423; Thu, 19 Jan 1995 13:00:41 -0500 Received: from toyota.wavefun.com by wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA02795; Thu, 19 Jan 95 10:00:37 -0800 Received: by toyota.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA11701; Thu, 19 Jan 95 10:01:02 -0800 From: "Joe Leonard" Message-Id: <9501191001.ZM11699@toyota.wavefun.com> Date: Thu, 19 Jan 1995 10:01:02 -0800 Reply-To: jle@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Ghose-Crippen LogP estimation questions Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Folks, I have been working with the Ghose-Crippen LogP estimation method (J. Comp. Chem. 9,80(1990)), and have several questions regarding the atom-typing rules described in the paper(s): 1. They refer to a program called CLASIF as being able to take structural information and generate the atom type. Obviously, having this program would "answer" all questions - is it available anywhere? 2. They make a distinction between "groups linked through carbon" (R-) and aliphatic groups (Al-). In this model, do aliphatic groups only contain carbon and hydrogen atoms, or can they contain any atom as long as they are singly-bound. Also, can H- match Al-? 3. They discuss aromatic groups - as with (2) are these carbon/hydrogen aromatics only, or can they contain heteroatoms? 4. Their Type 51 is called "H bound to alpha-C" - is this the alpha carbon of peptides or is it something else? 5. How are "formal oxidation numbers" handled for aromatic systems. The model refers to carbons with integer oxidation numbers. Since aromatic systems could have non-integer oxidation numbers (1.5, etc), should they be rounded up or down? In general, how are such systems handled? 6. Does Type 57 (phenol, enol, carboxyl OH) include Csp-OH oxygens? 7. Is Type 72 amide nitrogens RC(=O)-N or is RCO-N something like R-C-O-N compounds? 8. Is Type 76 R(=O)-NO2 or R-O-NO2? Looking at the other groups in Type 76, it seems like the former is correct... 9. The model does not include cationic nitrogens - has this been dealt with in a later paper? Are there later papers? 10. Type 78 is Ar-N=X and X-N=X - what about Al-N=X? 11. The Types associated with Sulfur seem incorrect. All specify R- groups, which I assumed to be -C-???, but there is at least one example (sulfapyridine) which has S(O2)-N- bonding... Should the sulfur groups be "any atom" connections, or am I misunderstanding the terminology throughout? I realize this is a large number of questions, but they're basically the same kinds of problems. I think folks have implemented this model in their work (and if Arup and/or Gordon are lurking, I'd appreciate their input!), so there should be some expertise out there - how folks have resolved these ambiguities. Thanks in advance - I welcome all comments! Please flame me directly, unless they're particularly interesting (I've always hated reading boring flames). Joe -- ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com From felice@bioorganic.ucsb.edu Thu Jan 19 15:48:45 1995 Received: from hub.ucsb.edu for felice@bioorganic.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id PAA05723; Thu, 19 Jan 1995 15:15:08 -0500 Received: from bioorganic (bioorganic.ucsb.edu) by hub.ucsb.edu; id AA05186 sendmail 4.1/UCSB-2.1-sun Thu, 19 Jan 95 12:14:56 PST for CHEMISTRY@ccl.net Received: by bioorganic (931110.SGI/930416.SGI) for @hub.ucsb.edu:CHEMISTRY@ccl.net id AA00212; Thu, 19 Jan 95 12:20:04 -0800 Date: Thu, 19 Jan 95 12:20:04 -0800 From: felice@bioorganic.mechanisms.ucsb.edu (Felice Chu) Message-Id: <9501192020.AA00212@bioorganic> To: CHEMISTRY@ccl.net Subject: gaussian2gamess HELP CHEMISTRY I was wondering if anyone might have a program that converts a Gaussian92 force constant matrix to a Gamess HESS group or anything like it. Thanks Felice felice@bioorganic.ucsb.edu From E.A.Wilinska@open.ac.uk Thu Jan 19 15:52:59 1995 Received: from venus.open.ac.uk for E.A.Wilinska@open.ac.uk by www.ccl.net (8.6.9/930601.1506) id OAA03624; Thu, 19 Jan 1995 14:40:05 -0500 Message-Id: <199501191940.OAA03624@www.ccl.net> Received: from acsvax.open.ac.uk by venus.open.ac.uk with Mail-11 (PP) id <14617-0@venus.open.ac.uk>; Thu, 19 Jan 1995 19:39:41 +0000 Date: Thu, 19 Jan 1995 19:39:41 +0000 From: Elzbieta Wilinska To: chemistry@ccl.net X-VMS-To: MAIL1::"chemistry@ccl.net" Cc: E.A.Wilinska@open.ac.uk X-VMS-Cc: EA_WILINSKA Subject: Stability constant for Bistris-K complex. Hi, I am calculating concentrations of ion complexes in solution and I have been using table values of experimentally measured stability constants. However I can't find the stability constant for Bistris-K+ complex, where Bistris is: bis[2-hydroxyethyl]iminotris[hydroxymethyl]methane or C8H19NO5. I wonder if it is possible to compute stability constants and perhaps someone on CCL has calculated it already for this particular complex. Ela Wilinska e.a.wilinska@open.ac.uk From U54632@UICVM.CC.UIC.EDU Thu Jan 19 21:38:01 1995 Received: from phem3 for U54632@UICVM.CC.UIC.EDU by www.ccl.net (8.6.9/930601.1506) id UAA10999; Thu, 19 Jan 1995 20:40:03 -0500 Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HM1LB14YJ48Y6DTE@phem3.acs.ohio-state.edu>; Thu, 19 Jan 1995 20:40:01 EDT Received: from UICVM (NJE origin U54632@UICVM) by UICVM.CC.UIC.EDU (LMail V1.2a/1.8a) with BSMTP id 8245; Thu, 19 Jan 1995 19:40:00 -0600 Date: Thu, 19 Jan 1995 19:32:13 -0600 (CST) From: Chaya Duraiswami Subject: Software for plotting 3D-graphs To: CCL Message-id: <01HM1LB14YJ68Y6DTE@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I'd like to thank each one of you, that took the time to respond to my query posted on the net. The GNUPLOT seems to be the best suited alternative for my needs. I'm summarizing the responses received for the net, as there did seem to be sufficient interest generated on this subject. -Chaya ------------------------------------------------------------------- My inital posting on the net was: >Hi Netters! > > I'm a graduate student at the University of Illinois at Chicago >and I'm looking for a freeware, or a public domain software to plot 3D-graphs. >Any suggestions or help in this regard, would be greatly appreciated. > If there is enough interest, I shall summarize the responses >that I get on the net. > >Thanks in advance, >-Chaya ========================================================================= Try gnuplot. Versions exist for Mac, Windows, DOS, Unix and Vax. For more info, check out the gnuplot FAQ via FTP from rtfm.mit.edu/pub/usenet/news.answers/graphics/gnuplot-faq You can find the FAQ and a lot of other stuff at the gnuplot archive at Dartmouth College on WWW http://www.cs.dartmouth.edu/gnuplot_info.html -Brad ---------------------------------------------------------------------------- Brad Isbister Duke University longshot@chem.duke.edu Department of Chemistry Computational/Biophysical chemistry E.J. Toone group DukeChem Home Page http://eyring.chem.duke.edu/ ========================================================================== To plot 3D-graphs you can try "pdraw" and "plotmtv", both free. The programs you can get from many servers via ftp. thomas@salz.phych.ba-freiberg.de ========================================================================== I know a program called 'xmgr' (on RS6000 platforms) that can solve " probably your problem. You can download it by anonymous ftp from aixpdbslib.seas.ucla.edu (128.97.2.211) The programme was originaly written for Silycon and was named 'xvgr'. --------------------------------------------------------------------------- "M. De Wil" Name : Marc De Wil Address : Facultes Universitaires Notre-Dame de la Paix Departement de Chimie Theorique Appliquee rue de Bruxelles 61 B - 5000 NAMUR ===========================================================================