From h.rzepa@ic.ac.uk Mon Jan 30 04:44:25 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id DAA27149; Mon, 30 Jan 1995 03:52:46 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 30 Jan 1995 08:51:00 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA17827; Mon, 30 Jan 95 08:50:54 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Jan 1995 08:51:03 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Re: CCL:WWW Oversight Bruce A. Luxon writes; >The idea that some self >appointed committee is going to referee the quality of my web site is >abhorent. If you don't like a particular site don't visit it anymore. >We don't need anymore control freaks than we already have. There is a distinction I think between unsolicited control, and situations where you actually submit a URL to a site known to impose it. If one turns one's mind back to 150 years ago. "Scholarly works" were often "published" privately at the author's own expense, and circulated amongst friends and peers. We are pretty much in that era now with WWW pages! However, very soon we will be awash with home pages, and quite soon career prospects might start depending on such accomplishments, or grant awards etc. At this stage, people will WANT an independent body to referee the quality of what they produce. Perhaps we have one such. They are called learned societies. Might I also point out that Chemical Abstracts are apparently investigating whether abstracting a home page is possible or worthwhile. If we solve the problem of how to ensure at least a degree of data permanency, then we have the idea of a WWW abstracts section within CA! 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 h.rzepa@ic.ac.uk Mon Jan 30 05:09:31 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id EAA27214; Mon, 30 Jan 1995 04:05:11 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 30 Jan 1995 09:04:56 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA18234; Mon, 30 Jan 95 09:04:47 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Jan 1995 09:05:00 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Propose: A Hypermail conversion of the CCL Dear all, I would like to propose that items sent to the CCL list be made available via WWW pages using Hypermail. For an example, see http://www.mailbase.ac.uk/hypermail/mac-supporters/archive.html This has several advantages a) It is far easier to retrieve an old message. b) Threads are maintained according to subject header, and hence easier to follow (provided we all use informative subject headers) c) The entire archive could be indexed, and hence easily searched using a keyword. d) Dare I say it, but those who find the sheer bulk of messages too much could unsubscribe, but still gain the advantage of browsing through what they have missed, perhaps picking up the one or two items of genuine interest to them e) Any URL submitted within the body of a text is instantly activatable f) It would increase "hypertext" awareness amongst users, and hence prepare the ground for further conference such as the ECCC last year. There are also interesting alternatives to the use of Hypermail. For example http://www.oac.uci.edu/indiv/ehood/mhonarc.doc.html is MIME RFC 1521 compliant (unlike Hypermail). I will announce to this list shortly a proposed mechanism for enclosing "chemical" message bodies in e-mail. This would automatically make available any molecule or other chemical type sent with a message as a hyperlink. Have a look at the discussion in http://www.ch.ic.ac.uk/hypermail/chemime/ as an example of what we might achieve. 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 h.rzepa@ic.ac.uk Mon Jan 30 05:41:04 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id EAA27379; Mon, 30 Jan 1995 04:50:48 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 30 Jan 1995 09:50:13 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA20313; Mon, 30 Jan 95 09:50:04 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Mon, 30 Jan 1995 09:50:13 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Chemistry symbols in HTML/WWW documents Cc: Ben Whitaker , Murray-Rust Dr P A major complaint by chemists is that HTML does not support Greek, Maths, et= c. I came across this little gem today; =AC ¬ Not sign =B0 ° Degree sign =B1 ± Plus-minus sign " ² Superscript two " ³ Superscript three =B5 µ Micro sign (Greek letter mu) =B7 · Middle dot ' ¹ Superscript one =BC ¼ lowe case pi =BD ½ upper case pi =BE ¾ less than or equal =C5 Å A ring above (Angstroms) =D7 × Multiplication sign =D8 Ø O oblique stroke (could be a null set symbol??) =F7 ÷ Division sign Note that this is how they display on a Macintosh! It is quite probable that say the pi is not a pi on a PC! Also, I send this message from a Mac. It really does show pi etc in the left hand column in my e-mail window, but I have no idea what it will look like by the time you folks get it. Try it with Netscape and the URL http://www.csci.csusb.edu/dick/iso8859-1.html The designation ½ is the so called "entity" declaration in HTML. Apparently HTML 3 will support a far larger set. 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. =46ax: (44) 171 594 5804. World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html =20 From maciekb@hypnos.chem.pg.gda.pl Mon Jan 30 05:47:59 1995 Received: from altis for maciekb@hypnos.chem.pg.gda.pl by www.ccl.net (8.6.9/930601.1506) id FAA27603; Mon, 30 Jan 1995 05:35:26 -0500 Received: from hypnos.chem.pg.gda.pl by altis (5.0/SMI-SVR4) id AA27109; Mon, 30 Jan 1995 11:39:04 --100 Received: by hypnos.chem.pg.gda.pl (931110.SGI/930416.SGI.AUTO) for @altis.chem.pg.gda.pl:CHEMISTRY@ccl.net id AA00786; Mon, 30 Jan 95 11:34:53 +0100 Date: Mon, 30 Jan 95 11:34:53 +0100 From: maciekb@hypnos.chem.pg.gda.pl (Maciej Baginski) Message-Id: <9501301034.AA00786@hypnos.chem.pg.gda.pl> To: CHEMISTRY@ccl.net Subject: MAC'95 Symposium Announcement content-length: 3291 Dear Netters, Please find enclosed the announcement of MAC'95 Symposium. The information below is part of the First Circular. Since some subjects of the Symposium is devoted to computer-aided drug design I am sending the announcement also to CCL list. Please note that the full information about MAC'95 is available through mosaic: http://www.pg.gda.pl/chem/mac95.html You can also use e-mail: mac@altis.chem.pg.gda.pl to order the Second Circular or to registrate. Sincerely, Maciej Baginski Department of Pharmaceutical Technology and Biochemistry Technical University of Gdansk Gdansk, Poland fax: (++48) 58-471993 e-mail: maciekb@altis.chem.pg.gda.pl begining of the Announcement ------------------------------------ 5th International Symposium on MOLECULAR ASPECTS OF CHEMOTHERAPY ******************************************************************* under the auspices INTERNATIONAL SOCIETY OF CHEMOTHERAPY organized by Committee on Drug Research Polish Academy of Sciences and Technical University of Gdansk Gdansk, Poland, August 21-24, 1995 GENERAL PROGRAM The Symposium is intended to bring together scientists representing different disciplines related to molecular aspects of chemotherapy: biorganic and physical organic chemists, biochemists, enzymologists, biophysicists, crystallographers, quantum chemists, clinicians. Molecular approaches to immune defense modulating agents, control of gene expression, etc. will also be included. While aimed primarily at problems of control in eukaryotic systems, prokaryotes will be included. The meeting should contribute to further development of a rational basis for drug design. SCIENTIFIC PROGRAM Five half-day sessions are scheduled for plenary and half-hour lectures by invited authorities. Several poster and oral presentation sessions are also planned. The following topics will be covered: - structural basis of biological properties of active agents - molecular mechanisms of drug-target interactions (nucleic acids, proteins and enzymes, membranes, etc.) - molecular mechanisms of selectivity of drug action - molecular mechanisms of drug resistance - new targets and drug prototypes - availability of drugs at target sites (transport, metabolic activation and inactivation, drug targeting) - rational drug design - bioorganic chemistry of immunomodulating agents The Proceedings, comprising the text of invited speakers, and extended abstracts of selected free communications, will be published in a special volume. ORGANIZING COMMITTEE E. Borowski (chairman) D. Sugar J. Konopa B. Lesyng M. Gniazdowski T. Kulikowski W. Rode M. Bontemps-Gracz (organizing secretary) INTERNATIONALY ADVISORY COMMITTEE F. Arcamone, Italy P. Borst, Holland J.A. McCammon, USA P. Janssen, Belgium A. Krayevsky, Russia L. Montagnier, France S. Omura, Japan W.H. Prusoff, USA A. Sartorelli, USA J.D. Williams, UK H. Zur Hausen, Germany ADDRESS FOR CORESPONDENCE 5th International Symposium on Molecular Aspects of Chemotherapy, c/o Department of Pharmaceutical Technology and Biochemistry Technical University of Gdansk 11/12 Narutowicza St, 80-952 Gdansk, POLAND Tel.: (++48) (58) 472523; Telex: 0512302; Fax: (++48) (58) 472694 e-mail: mac@altis.chem.pg.gda.pl http://www.pg.gda.pl/chem/mac95.html --------- end From oscar@bilbo.edu.uy Mon Jan 30 06:42:09 1995 Received: from seciu.uy for oscar@bilbo.edu.uy by www.ccl.net (8.6.9/930601.1506) id GAA28067; Mon, 30 Jan 1995 06:19:41 -0500 Received: from bilbo.edu.uy by seciu.uy with smtp (Smail3.1.28.1 #27) id m0rYt82-000lygC; Mon, 30 Jan 95 08:14 GMT-3:00 Received: by bilbo.edu.uy (AIX 3.2/UCB 5.64/4.03) id AA23510; Mon, 30 Jan 1995 08:18:30 -0300 Date: Mon, 30 Jan 1995 08:18:29 -0300 (TZ ) From: "Oscar N. Ventura" To: chemistry@ccl.net Subject: Re: CCL:WWW Oversight Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Netters, In principle, I don't consider abhorent that an independent comittee nay referee anyone's home page. In that I agree with Henry's message today. But (there's always a but, isn't it?) what are the criteria this comitee (eventually the "learned societies"?) will use for the evaluation? I'm sure everybody agrees that the essential content is new and valuable information. Na gut! But what about presentation? We all know that a very well designed home page viewed with Netscape may have a completely disgusting appearence viewed with Mosaic! Or that a beatifully designed, plenty of images home page in Europe, may be really never appreciated for instance here because I will need some 5 minutes to load it and then I will prefer simply to delay image loading! And what about content (i.e. new and valuable info)? What is that? The apparent state of mind here in this net is that a home page is a bit like a paper (or a set of papers). I would say it is much more like a whole journal, or (what it is really) the front end of a laboratory or institution. In my opinion a page must be alive for been useful. A certain degree of freezing is necessary (some valuable material should always stay there!) but mostly it should be changing so that the page is attractive, not only for new users but also for old ones. By the way, how many times in one's life one rereads classical, beautifully written, extremely valuable for their moment, papers? 10? But, how loyal are we to reading JACS or JChemSoc? Then, I agree that some discussion about independent refereeing is healthy. But, I think, we are not yet at the point of agreeing on what are the external parameters to be used in assessing quality. After all, very few people in our profession is building up home pages at this moment without thinking that they will be inmediately noticed by the colleagues. So, I don't think somebody is simply saying "ok, I have a low quality thing, but let's show it anyway, nobody will notice!". O. ------------------------------------------------------------------------------- Dr. Oscar N. Ventura Tel. +(5982)941860 MTC-Lab Fax +(5982)941906 Gral.Flores 2124, C. C. 1157 E-mail oscar@bilbo.edu.uy Montevideo, URUGUAY MTC-Lab http://bilbo.edu.uy/MTC-Lab.html ------------------------------------------------------------------------------- From ccl@probe.ac1.uni-duesseldorf.de Mon Jan 30 09:40:58 1995 Received: from probe.ac1.uni-duesseldorf.de for ccl@probe.ac1.uni-duesseldorf.de by www.ccl.net (8.6.9/930601.1506) id IAA29846; Mon, 30 Jan 1995 08:52:12 -0500 Received: by probe.ac1.uni-duesseldorf.de (5.61/1.34) id AA29389; Mon, 30 Jan 95 05:51:52 -0800 From: ccl@probe.ac1.uni-duesseldorf.de (CCL-LIST) Message-Id: <9501301351.AA29389@probe.ac1.uni-duesseldorf.de> Subject: Compute uv/spectra for p/containing substances To: chemistry@ccl.net Date: Mon, 30 Jan 1995 14:51:51 +0100 (MEZ) X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 228 Dear Reader! I wood like to know if there is any parameter set for Phosphorus containing Substances. Zindo/s does not have it. I want to compute UV-spectra. Thank you for response! C.Arendt, University of Duesseldorf, Germany From gregory@wucmd.wustl.edu Mon Jan 30 09:53:46 1995 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by www.ccl.net (8.6.9/930601.1506) id JAA00851; Mon, 30 Jan 1995 09:53:46 -0500 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA08733; Mon, 30 Jan 1995 08:53:38 -0600 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA11310; Mon, 30 Jan 95 06:36:26 -0600 Date: Mon, 30 Jan 1995 06:30:43 -0600 (CST) From: Gregory Nikiforovich Subject: Re: CCL:WWW Oversight To: h.rzepa@ic.ac.uk Cc: CHEMISTRY@ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 30 Jan 1995 h.rzepa@ic.ac.uk wrote: > There is a distinction I think between unsolicited control, and > situations where you actually submit a URL to a site known > to impose it. If one turns one's mind back to > 150 years ago. "Scholarly works" were often "published" > privately at the author's own expense, and circulated amongst > friends and peers. We are pretty much in that era now with > WWW pages! 150 years ago people like Pasteur and Faraday had ideas. Now it seems that people like those proposing censoring of WWW pages have no ideas, but a lot of imagination how to sell their sixpence of knowledge for a pound. Nice to hear from you, fellows progressists! ############################################################################## Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130 ############################################################################## From jtgolab@amoco.com Mon Jan 30 10:41:25 1995 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.6.9/930601.1506) id KAA01411; Mon, 30 Jan 1995 10:28:37 -0500 Received: by interlock.amoco.com id AA09332 (InterLock SMTP Gateway 3.0 for CHEMISTRY@ccl.net); Mon, 30 Jan 1995 09:28:33 -0600 Message-Id: <199501301528.AA09332@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Mon, 30 Jan 1995 09:28:33 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Mon, 30 Jan 1995 09:28:33 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Mon, 30 Jan 1995 09:28:33 -0600 From: jtgolab@amoco.com (Joe Golab) Date: Mon, 30 Jan 1995 09:26:51 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: WWW page Cc: jtgolab@amoco.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 In regards the WWW Chemistry homepage conversations: A recent Forbes article talks about the "Internet". One quote is especially pertinent: "Some observers point out that humans rarely react to technology the way that technologists think they should, and success usually isn't realized for a decade or two after a technology is developed." (Forbes 1/30/95 p.100) Seen in this light, it looks like WWW still has a long way to go. For my $0.02, I would like to see a National Lab or one of the Supercomputer centers pick this up, i.e. "a science WWW" of which chemistry is one branch. If it is done in the right way, - eventually - we will all have something that will be a useful tool in getting research done/ideas explained/a public memory started. Or, we could petition NetScape or SpyGlass that this kind of functionality be implemented in Mosaic. -- :Joe jtgolab@amoco.com (708) 961-7878 +----------------------------------------------------------------+ | In theory, there is no difference between theory and practice; | | but in practice, there is a great deal of difference. | +----------------------------------------------------------------+ From cbas25@vms.strath.ac.uk Mon Jan 30 10:46:43 1995 Received: from harris.cc.strath.ac.uk for cbas25@vms.strath.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA01571; Mon, 30 Jan 1995 10:36:51 -0500 Received: from vaxa.cc.strath.ac.uk (actually host vaxa.strath.ac.uk) by harris with SMTP (PP); Mon, 30 Jan 1995 15:32:49 +0000 Received: by vms.strath.ac.uk (MX V4.1 VAX) id 28; Mon, 30 Jan 1995 15:28:24 EST Date: Mon, 30 Jan 1995 15:28:20 EST From: "CBAS25 ::P_BLADON ::CBAS25" To: chemistry@ccl.net Message-ID: <0098B3DE.93E1102C.28@vms.strath.ac.uk> Subject: pKa Calculation summary Dear Colleagues, Here as promised is the summary of the responses I got from the enquiry on calculation of pKa values. Very many thanks to all who replied to this. I had looked at the archives but it is obvious that I missed the recent enquiry on a similar topic. I shall be looking into the the avenues afforded by the replies. Yours sincerely Peter Bladon First the enquiry I made: ______________________________________________________________________________ >Dear Colleagues, >I am writing to ask if anyone knows of software for calculation of pKa >values of organic compounds. Ideally I would like to calculate the full >range of organic structures, but if necessary it could be applicable >to structures with conventional ionizable groups. Methods using >addition of functional group parameters would be ideal. > >If there is any interest in this topic I will summarise for the group. >Yours sincerely >Peter Bladon >Department of Pure and Applied Chemistry >University of Strathclyde >Glasgow G1 1XL Scotland UK >cbas25@vms.strath.ac.uk >Phone/Fax (+44)(0)141-776-1718 ______________________________________________________________________________ From: MX%"rudolphc@sbh.Cyanamid.COM" Dear colleague, please try the demo version on gopher://www.ccl.net:73/11/software/MS-WINDOWS/pKa_logP_logD-demo This can also be reached via WWW as http://www.ccl.net/chemistry.html (software archive MS-Windows). Kind regards, Christine Rudolph Dr. Christine Rudolph phone: ++49 - 6130 - 911 - 403 Molecular Modelling fax: ++49 - 6130 - 911 - 113 Cyanamid Forschung GmbH e-mail:rudolphc@sbh.cyanamid.com Zur Propstei 55270 Schwabenheim Germany ______________________________________________________________________________ From: MX%"E.A.Wilinska@open.ac.uk" I asked the same question a few months ago and I am forwarding you a reply (the only one) that I got. Hope this helps. Ela Wilinska """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" >From: MAIL1::"butch@sunlac.chem.uga.edu" >If you can send the structures, we have a reasonable >pKa calculator (pka's in water). The SMILES string >if you're familiar with it would be best. >Butch Carreira butch@sunlac.chem.uga.edu Department of Chemistry (706) 542-2050 or 2051 >The University of Georgia (706) 542-9454 FAX >Athens, GA 30602 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" ______________________________________________________________________________ From: MX%"nxb96@acs.org" Dear Peter, There is a peer-reviewed pKa calculater appropriately called pKalc by CompuDrug. I will be sending you a demonstration diskette as well as marketing and spec information to your adress posted. This package is available to ACs members for 695 through the ACS order department. I will send you a complete catalog and ordering information as well. Hope this helps! NB ______________________________________________________________________________ From: MX%"adit@extreme.chem.rpi.edu" Peter, Check the archives of this list. I think that this was discussed not too long ago. I think that the best one for your purposes is CAMEO written by the Jorgensen group at Yale University. Adi T. ______________________________________________________________________________ From: MX%"gilson@indigo12.carb.nist.gov" Dear Peter, I don't know of software, but here are two references of possible interest. I would guess that the authors could make their programs available. @Article{dixon_pka, author = "Steven J. Dixon and Peter C. Jurs", title = "Estimation of p{K}a for Organic Oxyacids using calculated atomic charges", OPTcrossref = "", OPTkey = "", journal = "J. Comput. Chem.", year = "1993", volume = "14", OPTnumber = "", pages = "1460-1467", OPTmonth = "", OPTnote = "", OPTannote = "" } @Article{pka_qsar1, author = "Gilles Klopman and Dan Fercu", title = "Application of the {M}ultiple {C}omputer {A}utomated {S}tructure {E}valuation methodology to a quantitative structure-activity relationship study of acidity", OPTcrossref = "", OPTkey = "", journal = "J. Comput. Chem.", year = "1994", volume = "15", OPTnumber = "", pages = "1041-1050", OPTmonth = "", OPTnote = "", OPTannote = "" } Good luck, Mike Gilson Center for Advanced Research in Biotechnology gilson@indigo12.carb.nist.gov ______________________________________________________________________________ From: MX%"jaeger@3dp.com" Peter, I would appreciate hearing any replies that you get to your message about pKa calculations. Thanks. Ed Jaeger ..... em: jaeger@3dp.com -- ______________________________________________________________________________ From: MX%"MARTIN@cmda.abbott.com" Let me know what you find. The one thing I know about is CAMEO from Bill Jorgensen's group. I haven't tried it out, but am about to do so. Yvonne Martin Abbott Laboratories ______________________________________________________________________________ From: MX%"kcousins@wiley.csusb.edu" This topic was discussed and I believe summarized recently on this list (in the last 6 mos?). Check the archives. Kimberley Cousins Department of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@wiley.csusb.edu ______________________________________________________________________________ From: MX%"jborn@triton.unm.edu" Peter I would like to have a copy of your responses to the pKa question. Thanks __________________________________________________________ Jerry L. Born Ph. D. Professor of Pharmacy Voice (505) 277-3657 The College of Pharmacy Fax (505) 277-6749 The University of New Mexico Email jborn@triton.unm.edu Albuquerque, NM 87131 __________________________________________________________ From: MX%"elewars@alchemy.chem.utoronto.ca" There was a request for info on the calc of pKa on the Comp Chem Net about 6- 12 months ago; the results may be in the archives, which you can search. I have some refs to the calc of pKa, and will be happy to send them to you if you're interested: M. J. S. Dewaret al used AM1 to calc scidities, i.e. pKa, in a paper in JACS ca. 1986. Also, the calc of pKa is described in *Experiments in Computational Organic Chemistry*, byHehre, Burke, Shusterman and Pietro, published by Wavefunction, Inc, the company that makes the Spartan computational chemistry program. If you have Spartan, calculating pKa from electrostatic potentials should be quite easy. Try to get hold of Spartan and this book. If you can't get the book, I could send you Xerox copies of the relevant parts. Good Luck (Prof) Errol Lewars elewars@trentu.ca ______________________________________________________________________________ From: MX%"WallyR@netcom.com" Please do summarize...I would be interested in seeing it. Thank you. Wally Walter E. Reiher III, Ph.D. WallyR@netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 ______________________________________________________________________________ From: MX%"HMARQUES@AURUM.CHEM.WITS.AC.ZA" You may want to try CompuDrug Chemistry Ltd in Budapest. Their e-mail address is MKTG@cdk-cgx.hu and the programme they sell is called pKalc. I've looked at a demo version and it seems very useful. Prof. Helder M. Marques, Department of Chemistry University of the Witwatersrand, P.O. Wits 2050 Johannesburg, South Africa Fax: Int + 27 + 11 + 339-7967 ______________________________________________________________________________ From: MX%"butch@sunlc2.chem.uga.edu" Peter, Our group has been working on a program to calculate ionization pKa's. Currently the only module we have is a PC-Windows winsock client that accesses a server in our dept. We have tested the system on ~4000 IUPAC approved pKa's with an RMS of ~0.36. The program can also calculate all possible microconstants and generate speciation as a fn of pH curves. I can 1) Send you the testing results and references to the calculator. 2) If the number of molecules is less than 20-30, I would be willing to do the calculations and/or speciation plots for you. 3) Make the winsock client available to you for testing. Let me know if you are interested. Butch Carreira Department of Chemistry (706) 542-2050 or 2051 The University of Georgia (706) 542-9454 FAX Athens, GA 30602 ______________________________________________________________________________ From: MX%"bowlus@palres.dnet.sandoz.com" This is a real problem for us, and I would appreciate a summary of any replies you get. My own experience: _Delta_ pKa can be estimated in the DelPhi module marketed by Biosym, if their advertising can be believed. I haven't experience with this program, but the blurbs sent out are reasonably impressive. We have in the past tried to use a correlation approach, using a number of model compounds of known pKa, and calculating and correlating these with heats of formation of the acid and anion. I usually use AM1 for this, but the results are at best mixed, and for the most part, I don't consider them reliable (these are all gas phase). We are extending some studies to the AMSOL SM2 model, and I am optimistic that this will be more successful. In neither case, however, do I expect an absolute pKa to be obtained, but only grist for a correlation. sb Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 ______________________________________________________________________________ From: MX%"west@qtp.ufl.edu" Dear Dr. Bladon, I am responding to let you know that I am interested in the summary that you suggested. Thank You, John West west@qtp.ufl.edu ______________________________________________________________________________ From: MX%"walterse@mis.fuhscms.edu" Please summarize! Thanks. * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.fuhscms.edu ______________________________________________________________________________ From mmadrid@gardel.psc.edu Mon Jan 30 11:41:11 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.9/930601.1506) id KAA02044; Mon, 30 Jan 1995 10:55:53 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA01310; Mon, 30 Jan 95 10:55:51 -0500 From: "Marcela Madrid" Message-Id: <9501301055.ZM1308@gardel.psc.edu> Date: Mon, 30 Jan 1995 10:55:42 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: MM/MD workshop offered at PSC Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages will are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From mmadrid@gardel.psc.edu Mon Jan 30 12:03:27 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.9/930601.1506) id KAA01907; Mon, 30 Jan 1995 10:52:17 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA00890; Mon, 30 Jan 95 10:52:11 -0500 From: "Marcela Madrid" Message-Id: <9501301052.ZM888@gardel.psc.edu> Date: Mon, 30 Jan 1995 10:52:01 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: Molecular Mechanics and Dynamics Workshop Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP MOLECULAR MECHANICS AND DYNAMICS WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages will are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From WORSNOP@chem1.chem.dal.ca Mon Jan 30 12:41:06 1995 Received: from Snoopy.UCIS.Dal.Ca for WORSNOP@chem1.chem.dal.ca by www.ccl.net (8.6.9/930601.1506) id LAA03128; Mon, 30 Jan 1995 11:54:40 -0500 Received: from chem1.chem.dal.ca (CHEM1.Chem.Dal.Ca [129.173.17.47]) by Snoopy.UCIS.Dal.Ca (8.6.9/8.6.6) with SMTP id MAA21673 for ; Mon, 30 Jan 1995 12:53:44 -0400 Received: from CHEM1/MERCURYQUEUE by chem1.chem.dal.ca (Mercury 1.13); Mon, 30 Jan 95 12:53:45 -0400 Received: from MERCURYQUEUE by CHEM1 (Mercury 1.13); Mon, 30 Jan 95 12:53:33 -0400 From: "S. Kent Worsnop" To: chemistry@ccl.net Date: Mon, 30 Jan 1995 12:53:29 AST Subject: CCL:Installation of RPAC Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <6AD0CCD5BA1@chem1.chem.dal.ca> Hello Netters, My group is trying to install the newest version of RPAC on a RS6000 machine running AIX. However we are having problems with getting it up and running. We would appreciate any help other with this installation by those who are knowledgable of this program. All answers can be sent to worsnop@chem1.chem.dal.ca Thank You, Kent Worsnop Dept. of Chemistry Dalhousie University From adrian@silver.chem.nwu.edu Mon Jan 30 12:48:09 1995 Received: from silver.chem.nwu.edu for adrian@silver.chem.nwu.edu by www.ccl.net (8.6.9/930601.1506) id MAA03872; Mon, 30 Jan 1995 12:16:03 -0500 Received: by silver.chem.nwu.edu (921113.SGI.UNSUPPORTED_PROTOTYPE/921111.SGI.jml) for chemistry@ccl.net id AA04113; Mon, 30 Jan 95 11:16:02 -0600 From: adrian@silver.chem.nwu.edu (Adrian Roitberg) Message-Id: <9501301716.AA04113@silver.chem.nwu.edu> Subject: Midwest Theoretical Chemistry Coference, First Announcement To: chemistry@ccl.net Date: Mon, 30 Jan 95 11:16:02 CST X-Mailer: ELM [version 2.3 PL9] First Announcement 28th Midwest Theoretical Chemistry Conference Northwestern University Evanston, IL May 11-13, 1995 This year the Midwest Theoretical Chemistry Conference will be held in conjunction with a special symposium in honor of the appointment of John Pople to Trustees Professor at Northwestern University, Evanston Il on May 11-13, 1995. The Pople Symposium will be held on May 11, and will include the following invited speakers: R. Bartlett, N. Handy, M. Newton, M. Gordon, M. Head- Gordon, R. Parr as well as Pople himself. The Midwest Theoretical Chemistry conference will then follow its usual format of poster and oral sessions on May 12 and 13. A second announcement will be sent out in March, with instructions for abstracts, registration and housing. Contact Adrian Roitberg (mwtcc@chem.nwu.edu) if you like to be added to the conference mailing list. (Those who attended either of the last two meetings will automatically be included on the list.) Further questions concerning this conference may be directed to George Schatz(708-491-5657) or Mark Ratner(708-491-5652). We are looking forward to seeing you in Evanston this May. Mark Ratner George Schatz Adrian E. Roitberg ============================================================================= Dept. of Chemistry | Phone: (708) 491-3423 Northwestern University | Fax : (708) 491-7713 2145 Sheridan Road. Evanston, IL |E-mail:adrian@chem.nwu.edu 60208-3113 | ============================================================================= From mmadrid@gardel.psc.edu Mon Jan 30 12:59:35 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.9/930601.1506) id MAA03323; Mon, 30 Jan 1995 12:04:42 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA02065; Mon, 30 Jan 95 12:04:40 -0500 From: "Marcela Madrid" Message-Id: <9501301204.ZM2063@gardel.psc.edu> Date: Mon, 30 Jan 1995 12:04:31 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: NMR workshop offered at PSC Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: April 28, 1995. * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION USING NMR June 25-28, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by APRIL 28, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From h.rzepa@ic.ac.uk Mon Jan 30 13:41:15 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id NAA04984; Mon, 30 Jan 1995 13:22:13 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 30 Jan 1995 18:21:50 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA07646; Mon, 30 Jan 95 18:21:39 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Jan 1995 18:21:50 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Refereeing Presentational Quality in WWW pages Oscar N. Ventura writes, > Then, I agree that some discussion about independent refereeing is >healthy. But, I think, we are not yet at the point of agreeing on what >are the external parameters to be used in assessing quality. Everyone is learning the answer to this one. I should point out that the collected proceedings of the Electronic Computational Chemistry Conference, after due refereeing of purely the scientific content, will be recognised by Chemical Abstracts. I might also point out that the referee's comments on our own paper to this conference also related in part to the "presentation", offering helpful suggestions for improvements which we were happy to act upon. I think therefore that the first signs are there. 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 toni@athe.wustl.edu Mon Jan 30 13:45:13 1995 Received: from wugate.wustl.edu for toni@athe.wustl.edu by www.ccl.net (8.6.9/930601.1506) id NAA05498; Mon, 30 Jan 1995 13:45:13 -0500 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA17346; Mon, 30 Jan 1995 11:50:11 -0600 Received: by athe.WUStL.EDU (8.6.9/SMI-SVR4) id LAA16177; Mon, 30 Jan 1995 11:50:09 -0600 Date: Mon, 30 Jan 1995 11:50:09 -0600 From: toni@athe.wustl.edu (Toni Kazic) Message-Id: <199501301750.LAA16177@athe.WUStL.EDU> To: CHEMISTRY@ccl.net In-Reply-To: (h.rzepa@ic.ac.uk) Subject: Re: CCL:WWW Oversight Netters, I'd like to reiterate that open, do-it-yourself expression on the Web and refeered databases are ***not*** binary choices. Both are appropriate for different types of information, and the Web is already a mix of such data (you just don't see the quality control mechanisms for databases like GenBank or PIR, but they're there). Henry Rzepa properly points out that the global infrastructure for URNs is expensive and therefore probably distant. But I think it would benefit all of us to tinker with some of the issues ---- including what we want refeered and the mechanics of distributed databases ---- in advance. I was heartened by Steve Bachrach's and others' offers to get some form of this ball rolling. The hard issues are less technical, and more sociological --- what do we want reviewed, how do we do it. Quality control and sifting through the Web are different issues technically, though to a user they often collude. Toni Kazic Institute for Biomedical Computing Washington University From thep@risc1.lrm.fi.cnr.it Mon Jan 30 15:41:17 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id PAA08003; Mon, 30 Jan 1995 15:36:21 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA23807; Mon, 30 Jan 1995 21:31:00 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9501302031.AA23807@risc1.lrm.fi.cnr.it> Subject: ps2hp or gif2hp To: CHEMISTRY@ccl.net Date: Mon, 30 Jan 1995 21:31:00 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 169 Hello Does anybody know of any program that can convert the postscript/gif format into the hp format. Any reponse will be appreciate. Thanks in advance Pornthep From ANTHONY@admis.med.usf.edu Mon Jan 30 15:58:45 1995 Received: from pharm1.pharm.med.usf.edu for ANTHONY@admis.med.usf.edu by www.ccl.net (8.6.9/930601.1506) id PAA07989; Mon, 30 Jan 1995 15:35:05 -0500 Received: from admis.med.usf.edu ([131.247.70.101]) by pharm1.pharm.med.usf.edu (8.6.5/8.6.5) with SMTP id PAA21911 for ; Mon, 30 Jan 1995 15:35:03 -0500 Received: from COM_ADM/MERCURY-MAIL by admis.med.usf.edu (Mercury 1.1); Mon, 30 Jan 95 15:39:12 +1100 To: Chemistry@ccl.net From: "Anthony Lemus" Organization: USF College of Medicine Date: 30 Jan 95 15:38:43 EST Subject: Graduate Programs X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v2.3 (R5). Message-ID: <65F5E027DB6@admis.med.usf.edu> I would appreciate Email pointing me to schools in the US with Ph.D. programs in compuataional chemistry. thanks, ______________________________________________________________________ Anthony Lemus (813) 974-3427 -Systems Analyst University of South Florida Anthony@admis.med.usf.edu College of Medicine ______________________________________________________________________ From ryszard@msi.com Mon Jan 30 16:02:30 1995 Received: from msi.com for ryszard@msi.com by www.ccl.net (8.6.9/930601.1506) id PAA07275; Mon, 30 Jan 1995 15:01:32 -0500 Received: from aga.msi.com by msi.com (4.1/SMI-4.1) id AA27383; Mon, 30 Jan 95 15:03:00 EST Received: by aga.msi.com (5.65/DEC-OSF/1-29Feb92); id AA01018; Mon, 30 Jan 1995 15:02:50 -0500 Date: Mon, 30 Jan 1995 15:02:50 -0500 From: ryszard@msi.com (Ryszard Czerminski X 217) Message-Id: <9501302002.AA01018@aga.msi.com> To: CHEMISTRY@ccl.net, toni@athe.wustl.edu Subject: Re: CCL:WWW Oversight As a side commentary to ongoing discussion about chemistry, WWW, homepages ratings, censorship, etc... let me point those of you who will find time to an article by John Perry Barlow ---------------------------------------------------------- John Perry Barlow (barlow@eff.org) is a retired cattle rancher, a lyricist for the Grateful Dead, and co-founder and executive chair of the Electronic Frontier Foundation. ---------------------------------------------------------- in magazine "WIRED", March 1994. The title is "The Economy of Ideas", subtitle "A framework for rethinking patents and copyrights in the Digital Age (Everything you know about intellectual property is WRONG)" To give you a feel what it is all about I list here few chapter titles. I. Information is an activity II. Information is a life form Information wants to be free Information replicates into the cracs of possibility Information wants to change III. Information is a relationship Exclusivity has value Point of view and authority have value etc... It is worth reading. Ryszard Czerminski +------------------------------------------------------------------+ | Molecular Simulations Incorporated | phone : (617)229-8875 x 217 | | 16 New England Executive Park, | fax : (617)229-9899 | | Burlington, MA 01803-5297 | e-mail: ryszard@msi.com | +------------------------------------------------------------------+ From pbays@saintmarys.edu Mon Jan 30 16:41:09 1995 Received: from jade.saintmarys.edu for pbays@saintmarys.edu by www.ccl.net (8.6.9/930601.1506) id PAA08143; Mon, 30 Jan 1995 15:41:57 -0500 Received: by jade.saintmarys.edu (1.37.109.11/16.2) id AA101358865; Mon, 30 Jan 1995 15:47:45 -0500 Date: Mon, 30 Jan 1995 15:47:45 -0500 (EST) From: Phil Bays To: chemistry@ccl.net Subject: gcc on SGI R8000 In-Reply-To: <6AD0CCD5BA1@chem1.chem.dal.ca> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looing for someone who has built gcc on a SGI R8000 machine (Power indigo^2) using Irix 6.0.1. If you have done so, please send me a note. I am interested in getting the object file. Phil Bays Saint Marys College Notre Dame IN 46556 pbays@chem.saintmarys.edu From tps@iris27.biosym.com Mon Jan 30 16:44:49 1995 Received: from bioc1.biosym.com for tps@iris27.biosym.com by www.ccl.net (8.6.9/930601.1506) id QAA08979; Mon, 30 Jan 1995 16:37:35 -0500 Received: from iris27.biosym.com by bioc1.biosym.com (5.64/0.0) id AA03925; Mon, 30 Jan 95 13:37:47 -0800 Received: by iris27.biosym.com (931110.SGI/930416.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA13126; Mon, 30 Jan 95 13:36:02 -0800 Date: Mon, 30 Jan 95 13:36:02 -0800 From: tps@iris27.biosym.com (Tom Stockfisch) Message-Id: <9501302136.AA13126@iris27.biosym.com> To: chemistry@ccl.net Subject: Re: Terminology > METMOD A > All of the geometrical parameters (bond lenghts, angles, distances and > torsions) are calculated.... > METMOD B. > The diferences are presented in RMS and/or AVERAGE fitting error. > I tried to create simple names for these methods. Here comes my > version. Please send me a note, if you know better, than mine. > METMOD A is the Parametric Method > METMOD B is the Molecular Method If you named these "internals metric" and "cartesian metric" I think most people would guess correctly what you are doing even if they never read your definition. -- Tom Stockfisch, BIOSYM Technologies tps@biosym.com From michael@bch48.bch.ncsu.edu Mon Jan 30 18:41:09 1995 Received: from bch48.bch.ncsu.edu for michael@bch48.bch.ncsu.edu by www.ccl.net (8.6.9/930601.1506) id RAA10537; Mon, 30 Jan 1995 17:54:24 -0500 Received: by bch48.bch.ncsu.edu (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA07081; Mon, 30 Jan 95 17:54:40 -0500 From: "Michael R Rothwell" Message-Id: <9501301754.ZM7079@bch48.bch.ncsu.edu> Date: Mon, 30 Jan 1995 17:54:33 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: How about a "Democratic" Chemistry WWW site... Cc: michael@bch48.bch.ncsu.edu Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 It would not be too difficult to set up a WWW site here (at NCSU). My idea for i is: It will keep track of the number of accesses each link gets. It would then, for the Web Page, rank the links according to popularity, most popular first. New links would come in at the highest rank, and then slip downward (or perhaps not) as people evaluate them. Anyone could add a link. Links which stay at the bottom of the list for more than a certain length of time would get deleted (taking out the garbage, so to speak). The links would be divided into several sections, such as "Software" "computational Chemistry" "Biochemistry" or whatever. What do you think? From MARTIN@cmda.abbott.com Mon Jan 30 18:45:56 1995 Received: from abtlabs.abbott.com for MARTIN@cmda.abbott.com by www.ccl.net (8.6.9/930601.1506) id RAA10502; Mon, 30 Jan 1995 17:52:55 -0500 Received: from randb.pprd.abbott.com (randb.abbott.com) by abtlabs.abbott.com with SMTP id AA05162 (5.65c/IDA-1.4.4 for ); Mon, 30 Jan 1995 16:49:58 -0600 Received: from DECNET-MAIL (MARTIN@CMDA) by RANDB.PPRD.Abbott.Com (PMDF V4.3-13 #5551) id <01HMGQJ65I2O8YV9EK@RANDB.PPRD.Abbott.Com>; Mon, 30 Jan 1995 16:52:50 -0600 (CST) Date: Mon, 30 Jan 1995 16:52:50 -0600 (CST) From: MARTIN%CMDA Subject: Symposium: Computer Evaluation of Synthetic Feasibility To: chemistry@ccl.net Message-Id: <01HMGQJ66UAQ8YV9EK@RANDB.PPRD.Abbott.Com> X-Vms-To: RANDB::IN%"chemistry@ccl.net" X-Vms-Cc: MARTIN Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Call for contributions: Symposium: Computer Evaluation of Synthetic Feasibility ACS Division of Computers in Chemistry Aug. 20-24, 1995 Chicago, IL There has been an explosive rise in the number of 3D structures of biomacromolecules and in the number of computer programs that design molecules that bind to a macromolecule of known 3D structure. These accomplishments highlight a new challenge: how to distinguish, in the multitude of designed compounds, those that are relatively easy to synthesize. This symposium will feature the different strategies taken to attack this problem. It is hoped that it will not only inform others of the state-of-the-art but also stimulate other work on the problem. Invited speakers: o Johann Gasteiger, Universitat Erlangen-Nurnberg o Stephen Hanessian, University of Montreal o Peter Johnson, University of Leeds Do you have a contributed paper to offer? Can you suggest someone who might? The deadline for abstracts is April 15, however I would like to hear from potential speakers before then. Yvonne C. Martin Computer Assisted Molecular Design D-47E, AP10 2fl Abbott Laboratories 100 Abbott Park Rd. Abbott Park, IL 60064 martiny@abbott.com FAX: 708 937 2625 From bkarlak@ren.onyx-pharm.com Mon Jan 30 20:41:05 1995 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.9/930601.1506) id TAA11615; Mon, 30 Jan 1995 19:47:05 -0500 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (5.67/1.37) id AA08615; Mon, 30 Jan 95 16:47:02 -0800 Received: by ren.onyx-pharm.com (931110.SGI/921111.SGI.AUTO) for @iserver.onyx-pharm.com:CHEMISTRY@ccl.net id AA07054; Mon, 30 Jan 95 16:47:00 -0800 From: "Brian Karlak" Message-Id: <9501301646.ZM7052@ren.onyx-pharm.com> Date: Mon, 30 Jan 1995 16:46:58 -0800 In-Reply-To: "Michael R Rothwell" "CCL:How about a "Democratic" Chemistry WWW site..." (Jan 30, 5:54pm) References: <9501301754.ZM7079@bch48.bch.ncsu.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Michael R Rothwell" , CHEMISTRY@ccl.net Subject: Re: CCL:How about a "Democratic" Chemistry WWW site... Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jan 30, 5:54pm, Michael R Rothwell wrote: > Subject: CCL:How about a "Democratic" Chemistry WWW site... > It would not be too difficult to set up a WWW site here (at NCSU). My idea for i > is: > > It will keep track of the number of accesses each link gets. It would then, > the Web Page, rank the links according to popularity, most popular first. > > New links would come in at the highest rank, and then slip downward (or > not) as people evaluate them. > > Anyone could add a link. > > Links which stay at the bottom of the list for more than a certain length of > time would get deleted (taking out the garbage, so to speak). > What do you think? An excellent idea. zenkat -- "Update all information. Pod into cosmos." Jeffffff said it. i believe it. That settles it. From bkarlak@ren.onyx-pharm.com Mon Jan 30 20:46:13 1995 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.9/930601.1506) id UAA11854; Mon, 30 Jan 1995 20:26:54 -0500 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (5.67/1.37) id AA08932; Mon, 30 Jan 95 17:23:25 -0800 Received: by ren.onyx-pharm.com (931110.SGI/921111.SGI.AUTO) for @iserver.onyx-pharm.com:pmr1716@ggr.co.uk id AA07332; Mon, 30 Jan 95 17:23:07 -0800 From: "Brian Karlak" Message-Id: <9501301723.ZM7330@ren.onyx-pharm.com> Date: Mon, 30 Jan 1995 17:23:05 -0800 In-Reply-To: h.rzepa@ic.ac.uk (Rzepa,Henry) "CCL:Chemistry symbols in HTML/WWW documents" (Jan 30, 9:50am) References: X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: h.rzepa@ic.ac.uk (Rzepa,Henry), CHEMISTRY@ccl.net Subject: Re: CCL:Chemistry symbols in HTML/WWW documents Cc: Ben Whitaker , Murray-Rust Dr P Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jan 30, 9:50am, Rzepa,Henry wrote: > Subject: CCL:Chemistry symbols in HTML/WWW documents > A major complaint by chemists is that HTML does not support Greek, Maths, et= > c. > > I came across this little gem today; > =AC ¬ Not sign > =B0 ° Degree sign > =B1 ± Plus-minus sign {snip} > Note that this is how they display on a Macintosh! It is quite probable > that say the > pi is not a pi on a PC! Also, I send this message from a Mac. It really > does show > pi etc in the left hand column in my e-mail window, but I have no idea what > it will > look like by the time you folks get it. Try it with Netscape and the > URL http://www.csci.csusb.edu/dick/iso8859-1.html Well, out here in Unix-land (SGI IRIX 5.2 with Z-mail/MediaMail for reading mail) it comes out like you see it above. Brian Karlak Onyx Pharmaceuticals "MIME? What's that? In my day, son, we used ASCII and were happy about it. None of this modern newfangled stuff you kids flash around like HTML and WWW and URL. Sounds dangerous to me. What's a matter with FTP and Telnet, eh? Spoiled brats, I tell you!" ;) -- "Update all information. Pod into cosmos." Jeffffff said it. i believe it. That settles it. From mspackma@metz.une.edu.au Mon Jan 30 23:41:10 1995 Received: from metz.une.edu.au for mspackma@metz.une.edu.au by www.ccl.net (8.6.9/930601.1506) id XAA12888; Mon, 30 Jan 1995 23:07:16 -0500 Received: from [129.180.52.150] ([129.180.52.150]) by metz.une.edu.au (8.6.9/8.6.9) with SMTP id PAA29735 for ; Tue, 31 Jan 1995 15:07:00 +1100 Message-Id: <199501310407.PAA29735@metz.une.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 31 Jan 1995 15:08:34 +0800 To: CHEMISTRY@ccl.net From: mspackma@metz.une.edu.au (Mark Spackman) Subject: Fax/e-mail address for J Comp Chem Does anyone out there have a Fax number or e-mail address for the Journal of Computational Chemistry? I know it sounds bizarre, especially for a journal with that title, but I can't find either anywhere in the journal, and wish to contact one of the editors (Dr N Allinger) without waiting several weeks for the snail-mail turnaround from downunder. cheers Mark ======================================================================== Dr Mark Spackman _/ _/ _/ _/ _/_/_/_/ Department of Chemistry _/ _/ _/_/ _/ _/ University of New England _/ _/ _/ _/ _/ _/_/_/_/ Armidale, NSW 2351 _/ _/ _/ _/_/ _/ AUSTRALIA _/__/ _/ _/ _/_/_/_/ TEL: +61 67 732722 FAX: +61 67 711563 E-mail: mspackma@metz.une.edu.au