From chemistry-request@server.ccl.net Mon Sep 4 03:25:56 2000 Received: from herald.cc.purdue.edu (herald.cc.purdue.edu [128.210.11.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA27048 for ; Mon, 4 Sep 2000 03:25:56 -0400 Received: from [209.178.158.86] by herald.cc.purdue.edu with ESMTP; Mon, 4 Sep 2000 02:25:42 -0500 Mime-Version: 1.0 Message-Id: Date: Mon, 4 Sep 2000 00:32:13 -0800 To: philchem@vm.sc.edu From: Eric Scerri Subject: Now Free On-line/ issue 3 of FOCH Cc: chemed-l@atlantis.uwf.edu, chemistry@ccl.net, CHEM-HIST@LISTSERV.NGATE.UNI-REGENSBURG.DE, Chem-education@mailbase.ac.uk, HOPOS-L@listerv.nd.edu, Ian Cresshull , raf_dahlquist Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear Colleagues, I thought you might like to know that the whole of issue 3 of Foundations of Chemistry is now available and can be dowloaded free of charge from this journal web page. You need Acrobat 3 or any later version. This too can be dowloaded in you don't have it. Just search for Acrobat http://www.wkap.nl/sample.pdf?240323 click on any of the articles and they will be dowloaded onto your machine. ---------------------------------------------------------------------- ---------------- Foundations of Chemistry Philosophical, Historical, Educational and Interdisciplinary Studies of Chemistry Table of Contents Volume 1, Issue 3, October 1999 Editorial 3 Eric R. Scerri pp. 221-223 Circulation of Concepts Pierre Laszlo pp. 225-238 Opus Magnum: An Outline for the Philosophy of Chemistry Hrvoj Vancik pp. 239-254 On the Relationship Between Instrument and Specimen in Chemical Research Daniel Rothbart pp. 255-268 Towards a Useful Philosophy of Biochemistry: Sketches and Examples Roger Strand pp. 269-292 The Atomic Shell-Structure Formula 2n2 Richard D. Harcourt pp. 293-294 A Critique of Atkins' Periodic Kindom and Some Writings on Electronic Structure Eric R. Scerri pp. 295-303 25 Centuries of Atoms and Void William R. Everdell pp. 305-309 Authors index pp. 311-311 Volume contents pp. 312-314 ------------------------------------------------- Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095 USA E-mail: scerri@chem.ucla.edu Editor of "Foundations of Chemistry" http://www.wkap.nl/journalhome.htm/1386-4238 Also see, International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Mon Sep 4 09:22:26 2000 Received: from holyrood.ed.ac.uk (holyrood.ed.ac.uk [129.215.16.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA29336 for ; Mon, 4 Sep 2000 09:22:26 -0400 Received: from localhost (mhp02@localhost) by holyrood.ed.ac.uk (8.8.7/8.8.7) with ESMTP id OAA12565 for ; Mon, 4 Sep 2000 14:22:14 +0100 (BST) Date: Mon, 4 Sep 2000 14:22:14 +0100 (BST) From: Alistair Nelson To: chemistry@ccl.net Subject: Looking for Sang Yon-Lee Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I am trying to get in touch with a man called Sang Yon-Lee from Korea, he was with me in Japan in 1999 working with Professor Iwata at the IMS. If anyone here knows his email address could he please let me know? Cheers Alistair Nelson -- /------------------------------------------------------\ | Email: Alistair.nelson@ed.ac.uk ICQ# 16297649 | | http://truegallery.50g.com/ (The true Gallery) | | http://www.nelsona.co.uk/ (trueSpace Stuff) | | http://www.ed.ac.uk/~zeke/ (PhD Stuff) | \------------------------------------------------------/ From chemistry-request@server.ccl.net Sun Sep 3 05:30:48 2000 Received: from lrz.uni-muenchen.de (root@f-238.munchen.ipdial.viaginterkom.de [62.180.172.238]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21845 for ; Sun, 3 Sep 2000 05:30:42 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id BAA01011; Sun, 3 Sep 2000 01:19:50 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14770.2470.555484.292964@lrz.uni-muenchen.de> Date: Sun, 3 Sep 2000 01:19:50 -0700 (PDT) To: , Cc: Subject: Chemists Toy With the Preprint Future X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid http://www.sciencemag.org/cgi/content/full/289/5484/1445a SCIENTIFIC PUBLISHING: Chemists Toy With the Preprint Future Robert F. Service After watching their physics colleagues explore the digital landscape of electronic preprints over the past decade, chemists are sending out a survey party of their own. Last week, the giant publishing house Elsevier Science launched the first electronic archive for chemistry preprints through its ChemWeb subsidiary. The new site (preprint.chemweb.com) will be a common repository for reports on a wide range of chemistry topics and a forum for authors and readers to discuss the results. But ChemWeb could face an uphill battle in convincing authors to post their papers on the site, as many of the field's premier journals decline to accept papers that have already been posted on the Web. Physics envy. Elsevier is hoping its chemistry preprint archive will prove as popular as the Los Alamos physics archive, use of which by U.S.-based users is shown above. CREDIT: ARXIV.ORG ChemWeb's new preprint service is modeled closely on the physics preprint archive started in 1991 by Paul Ginsparg at Los Alamos National Laboratory in New Mexico, which today serves as a storehouse for some 146,000 articles. Although readers of the new chemistry preprints will be able to rank the papers, there will be no formal peer review, says ChemWeb's preprint manager James Weeks. The service is free to both authors and readers. (They need only register with ChemWeb, which is also free.) ChemWeb, says Weeks, hopes that its new service will generate enough Internet traffic to lure advertisers to fund the site. For now, about all the site is attracting is heated debate. "A preprint server is highly controversial among chemists," said Daryle Busch, president of the American Chemical Society (ACS), speaking at the society's national meeting in Washington, D.C., last week. Busch, a chemist at the University of Kansas, Lawrence, says he and his colleagues are lured by the Web's speed, wide dissemination, and low cost of publishing new scientific results. But many researchers fear that the absence of peer review will reduce the quality of submissions and force readers to wade through electronic mounds of poor-quality results in search of tidbits of worthwhile science. Says Peter Stang, a chemist at the University of Utah, Salt Lake City, "It's a dilemma." Apparently, it's one that a broad cross section of chemists are struggling with. According to Robert Bovenschulte, head of ACS publications, the association conducted a survey of some 8000 of its members last summer on the question of non-peer- reviewed electronic preprints. The results "are a very mixed bag," Bovenschulte says. "A lot of people were in favor of it. A lot of people were against it." Nevertheless, the new preprint archive likely faces a tough future, because ACS journal editors themselves are lined up against it. ACS, the world's largest scientific membership organization, with 161,000 members, also publishes many of the premiere journals in the field including the flagship Journal of the American Chemical Society. But nearly all ACS journal editors consider posting results on the Web to constitute "prior publication," says Bovenschulte. (Science maintains the same policy.) As a result, Bovenschulte says, those ACS journals will not publish papers that appear first on ChemWeb's preprint server. And that, says Ralph Nuzzo, a chemist at the University of Illinois, Urbana-Champaign, would convince him and most of his colleagues not to post their articles on ChemWeb. "If I couldn't publish my paper [in a conventional journal], I probably wouldn't do it," Nuzzo says. In an effort to find a compromise, Weeks says ChemWeb will remove the full text of papers from the site when they are published in a print journal, keeping an abstract and a link to the journal article. But Bovenschulte says ACS journals would still not consider such papers, because the results would already be public knowledge. Not all journals are playing hardball. Ginsparg points out that American Physical Society journals, including the prominent Physical Review Letters, not only publish articles already posted on the Los Alamos preprint server, but even provide the electronic connections for authors to submit to the journals at the click of a button. Elsevier's own journals will publish articles that appear first on ChemWeb. Indeed, Elsevier--which is ACS's chief competitor in the chemistry journal publishing business--may be counting on ChemWeb to give its journals an edge among some chemists. Elsevier officials may be hoping that researchers interested in distributing results quickly will then send their articles to Elsevier journals, says Bovenschulte. For Elsevier, he says, "this could be considered a cost of attracting the best authors." Whatever the motivation, chemistry preprints are long overdue, says R. Stephen Berry, a chemist at the University of Chicago. The culture among chemists--with their history of close ties to industry--is more conservative than that among physicists, says Berry. Still, Berry believes that chemistry preprints have a shot. "We just have to wait and see if it works," he says. "But this is the kind of experiment we should be doing." From chemistry-request@server.ccl.net Sun Sep 3 20:00:29 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA25566 for ; Sun, 3 Sep 2000 20:00:28 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id QAA04558 for ; Sun, 3 Sep 2000 16:55:58 -0700 (PDT) Received: from unknown(146.202.11.79) by mailhost.msi.com via smap (V2.0) id xma004556; Sun, 3 Sep 00 16:55:57 -0700 Message-Id: <4.3.1.2.20000903162527.00b32d20@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 4.3.1 Date: Sun, 03 Sep 2000 16:47:59 -0700 To: CHEMISTRY@ccl.net From: Don Gregory Subject: Re: CCL:I/O in Charmm In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi all, Really, there are two separate issues here; (a) using InsightII to create CHARMm input files, and (b) what to do when a chosen force-field is missing parameters. The easy one first: Indeed, InsightII can write CHARMm PSF and RTF files. Whenever your research leads you to modify the (more or less) 'standard' molecule/residue types that are provided in the RTF files that come with InsightII, we heartily recommend you use the PSF creation capabilities of InsightII to make the 'whole-system' unique molecular topology description that CHARMm needs, i.e. the PSF file. That is what this capability is intended for. However, even given this, missing parameters are still a possibility since creating a topology is trivial comapred to developing a well optimized force-field that will cover all the esoteric molecular types you might encounter in your on-going research. MSI provides numerous force-fields, and are committed to extending our force-field coverage as we go forward. However if the force-field you are using (not specified in the original email) is missing parameters, we'd suggest CFF if that is not being used already. If CFF also is missing the parameters, then we're in the same boat as we've seen in dozens of emails here on the CCL, i.e. you can research the literature to see if someone has developed parameters *for that specific force-field* (if for another force-field, then you have to make the decision as to whether to accept the *approximation* that those parameters will be reasonably transferrable into the force-field you would like to use), or you can ask your collegues on CCL (remembering to specify the force-field you are using, and a complete description of the atoms (atom-types) involved [*not* as I've seen numerous time "has anyone developed parameters for X?"; not saying for which force-field and simply *assuming* transferrability is acceptable), or contact MSI to see if we have developed these parameters, ir ..... well, resort to a force-field optimization project yourself! In fact, it is 'fair' (?) to provide numbers from any of the sources mentioned above, but what is *really* crucial, is to note the original force-field used, and any added/modified parameters to that force-field, when publishing your results. This is a step that I think is missing all too often in molecular mechanics studies I've seen in the literature. There are additional comments to be found at MSI's scientific support FAQ site, under the heading of "ForceFields", http://www.msi.com/support/FAQ.html Hope this helps; sorry for such a long email. DG At 06:37 PM 9/3/00 -0400, Xiang(Simon) Wang wrote: >Dear CCLers: > >Can someone help me on how to read small molecule structure in Charmm? >For example, phosphoribosyldiphosphate (PRPP), which can not be found in >top_all22_model.inp file. I could get the PSF file from InsightII. But >when running, Charmm gave the warning of lacking of parameters. Can >someone help me out of it? > >Thanks a lot, > >X. Wang > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > Dr. Don Gregory (dgregory@msi.com) CHARMm Product Marketing Manager Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (858) 799-5331 http://www.msi.com Mobile Ph.: (619) 200-3613 From chemistry-request@server.ccl.net Sun Sep 3 23:25:59 2000 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA26224 for ; Sun, 3 Sep 2000 23:25:59 -0400 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id UAA15885 for ; Sun, 3 Sep 2000 20:25:54 -0700 (PDT) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma015883; Sun, 3 Sep 00 20:25:53 -0700 Received: from shepherd.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id UAA42084; Sun, 3 Sep 2000 20:25:52 -0700 (PDT) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2650.21) id ; Sun, 3 Sep 2000 20:25:52 -0700 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE50451FD72@shepherd.mdli.com> From: Bob Snyder To: "'List Server, CCL'" Cc: Bob Snyder Subject: CALL FOR PAPERS: Structure-Based Data Mining Date: Sun, 3 Sep 2000 20:25:51 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" To: CHMINF-L, ACSMEDI, CCL, ISISFORUM-L, MOL-DIVERSITY, TOXLIST The Division of Chemical Information (CINF) is planning a session on "Structure-Based Data Mining" at the Spring ACS meeting in San Diego (April 1-5, 2001). The session will focus on new technologies for mining structure databases, including: data warehousing, descriptor calculations, physicochemical parameter estimation, visualization, in silico screening, and model building. For additional information regarding the ACS meeting in San Diego please see http://www.acs.org/meetings/sandiego2001/. If you would like submit a talk for this sessions please refer to the URL above and follow the links through the "Submitting a Paper" button and links to the Division of Chemical Information. The OASys system used for submitting abstracts for the meeting will be open for speakers beginning on September 11th. If you have any questions regarding the session please send an email message to the session organizer, Bob Snyder at bobs@mdli.com. Bob Snyder ------------------------------------- Robert W. Snyder, Ph.D. Director, Chemistry Marketing MDL Information Systems email: bobs@mdli.com telephone: 510-357-2222 Never stop searching. From chemistry-request@server.ccl.net Sun Sep 3 23:42:53 2000 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA26288 for ; Sun, 3 Sep 2000 23:42:52 -0400 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id UAA16281 for ; Sun, 3 Sep 2000 20:42:48 -0700 (PDT) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma016279; Sun, 3 Sep 00 20:42:44 -0700 Received: from shepherd.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id UAA71450; Sun, 3 Sep 2000 20:42:43 -0700 (PDT) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2650.21) id ; Sun, 3 Sep 2000 20:42:43 -0700 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE50451FD79@shepherd.mdli.com> From: Bob Snyder To: "'List Server, CCL'" Cc: Bob Snyder , Jean Holt Subject: CALL FOR PAPERS: Web-Based Information Sources Date: Sun, 3 Sep 2000 20:42:42 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" To: CHMINF-L, ACSMEDI, CCL, ISISFORUM-L, MOL-DIVERSITY, TOXLIST The Division of Chemical Information (CINF) is planning a session on "Web-Based Information Sources" at the Spring ACS meeting in San Diego (April 1-5, 2001). The session will focus on two areas: technologies associated with searching & browsing chemical information via the web and applications that deliver chemical information via the web. For additional information regarding the ACS meeting in San Diego please see http://www.acs.org/meetings/sandiego2001/. If you would like submit a talk for this session please refer to the URL above and follow the links through the "Submitting a Paper" button and links to the Division of Chemical Information. The OASys system used for submitting abstracts for the meeting will be open for speakers beginning on September 11th. If you have any questions regarding the session please send an email message to the session organizers, Jean Holt for the web technology section at jeanh@mdli.com or Bob Snyder for the application section at bobs@mdli.com. Jean Holt and Bob Snyder ------------------------------------- Robert W. Snyder, Ph.D. Director, Chemistry Marketing MDL Information Systems email: bobs@mdli.com telephone: 510-357-2222 Never stop searching. From chemistry-request@server.ccl.net Mon Sep 4 07:43:52 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA28994 for ; Mon, 4 Sep 2000 07:43:51 -0400 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id NAA08692; Mon, 4 Sep 2000 13:44:02 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14771.35582.116251.340062@yogi.pc1.uni-duesseldorf.de> Date: Mon, 4 Sep 2000 13:43:58 +0200 (CEST) From: Jochen Kuepper To: Eric Scerri Cc: philchem@vm.sc.edu, chemed-l@atlantis.uwf.edu, chemistry@ccl.net, CHEM-HIST@LISTSERV.NGATE.UNI-REGENSBURG.de, Chem-education@mailbase.ac.uk, HOPOS-L@listerv.nd.edu.pc1.uni-duesseldorf.de Subject: CCL:Now Free On-line/ issue 3 of FOCH In-Reply-To: References: X-Mailer: VM 6.72 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA28995 Eric Scerri writes: > I thought you might like to know that the whole of issue 3 of > Foundations of Chemistry is now available and can be dowloaded free Well, the correct address is http://www.wkap.nl/sampletoc.htm?1386-4238+1+3+1999 > http://www.wkap.nl/sample.pdf?240323 While this points to his own paper only;-(!? Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195