From chemistry-request@server.ccl.net Wed Oct 6 18:40:49 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA02073 for ; Wed, 6 Oct 1999 18:40:49 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id SAA10144; Wed, 6 Oct 1999 18:32:45 -0400 (EDT) Date: Wed, 6 Oct 1999 18:32:35 -0400 (EDT) From: Iraj Daizadeh To: John Mackin cc: chemistry@ccl.net Subject: Re: CCL:computational chem for high school students In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Run--Run Fast to Huck"el/Extended Huck"el Calculators! Then rush the molecular orbital viewer Spartan. This is the Trick! Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh On Wed, 6 Oct 1999, John Mackin wrote: > > I am interested in any very basic applications which will help high school > chemistry students appreciate the use of technology and math in the current > development of chemistry. These students have algebra capability > (no calculus) so the math component must be more simple than I suspect is > used in computational chemistry. The graphics results, though, will spark > interest in the students. Again, the key word is appreciation. Are there > applications which would excite and motivate some students to pursue > a chemistry career in college? > > From chemistry-request@server.ccl.net Wed Oct 6 17:12:34 1999 Received: from toronto.acdlabs.com (toronto.acdlabs.com [207.176.233.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA01528 for ; Wed, 6 Oct 1999 17:12:34 -0400 Received: from gavin (gavin.acdlabs.com [207.176.233.80]) by toronto.acdlabs.com (8.9.0/8.9.0) with SMTP id RAA24036 for ; Wed, 6 Oct 1999 17:08:51 -0400 (EDT) Date: Wed, 6 Oct 1999 17:08:51 -0400 (EDT) Message-Id: <199910062108.RAA24036@toronto.acdlabs.com> X-Sender: chemist@acdlabs.com (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: chemist@acdlabs.com (ACD Chemist) Subject: Re: CCL:computational chem for high school students We at Advanced Chemistry Development have an ongoing commitment to contribute to education. Our products are an excellent way to demonstrate chemical phenomena in a versatile, enjoyable fashion. Students learn faster due to the interactive nature of the software as well as the intuitive interface. Please visit www.acdlabs.com for more information, including examples of ACD in the Curriculum. Chemistry Department, Advanced Chemistry Development, Inc. 133 Richmond St. W., Suite 605 Toronto, ON M5H 2L3 CANADA Phone: (416) 368-3435 US & Canada: (800) 304-3988 Facsimile: (416) 368-5596 e-mail: chemist@acdlabs.com URL: http://www.acdlabs.com ------------------------------------------------------------------------ Advanced Chemistry Development announces even MORE Free Stuff for download at www.acdlabs.com/download. FREE structure drawing software, NMR viewer, SpecViewer (NMR, MS, UV, IR), Cambridgesoft Integration and Spectral Databases! ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Oct 6 17:17:27 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA01588 for ; Wed, 6 Oct 1999 17:17:27 -0400 Received: from tandoori.schrodinger.com (tandoori.schrodinger.com [166.84.149.99]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id OAA06855; Wed, 6 Oct 1999 14:13:32 -0700 Received: from avarice (hazel.schrodinger.com [166.84.149.150]) by tandoori.schrodinger.com (8.8.5/8.8.5) with SMTP id RAA14003; Wed, 6 Oct 1999 17:13:01 -0400 From: "Hege S. Beard" To: "Bruno Bienfait" , "Computer Chemistry List" Subject: RE: Summary: Automatic docking with Macromodel Date: Wed, 6 Oct 1999 17:12:05 -0400 Message-ID: <001401bf103f$71216020$969554a6@avarice.schrodinger.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 In-Reply-To: <37FA9329.3BCAC017@helix.nih.gov> X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Importance: Normal Hello Bruno, I was planning on answering your CCL posting, but never got around to it until I just now noticed your summary... > Subject: CCL:Summary: Automatic docking with Macromodel > > > Dear CCL, > > One week ago I posted : > " > I am interested in automatic docking of small molecules to a protein > using a program equipped with a non explicit solvent model. > I plan to use the MMFF with the GB/SA water solvation model as > implemented in Macromodel 6.5 for this task. I also would like selected > > residues of the binding site to be flexible whereas the rest of the > receptor would be fixed. > There is (or will soon be appearing) a JCC article from Istvan Kolossvary and Wayne C. Guida, titled "Low-Mode Conformational Search Elucidated. Application to C39H80 and Flexible Docking of 9-Deazaguanine Inhibitors into PNP" This article covers just what you are mentioning above; flexible docking, allowing flexibility of inhibitor, as well as a number of binding site residues. I would be happy to send you a pre-print if you send me your mailing address. Best regards, Hege -------------------------------------------------------------------- Hege S. Beard Schrödinger, Inc. One Exchange Place, Suite 604 hege@schrodinger.com Jersey City, NJ 07302 Phone:201-433-2014 x101 USA Fax: 201-433-2065 www.schrodinger.com -------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Oct 7 11:26:57 1999 Received: from europe.std.com (europe-e.std.com [192.74.137.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06919 for ; Thu, 7 Oct 1999 11:26:57 -0400 Received: from world.std.com (root@world-f.std.com [199.172.62.5]) by europe.std.com (8.9.3/8.9.3) with ESMTP id LAA04813 for ; Thu, 7 Oct 1999 11:23:01 -0400 (EDT) Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id LAA10237 for chemistry@ccl.net; Thu, 7 Oct 1999 11:20:56 -0400 (EDT) Date: Thu, 7 Oct 1999 11:20:56 -0400 (EDT) From: Joe M Leonard Message-Id: <199910071520.LAA10237@world.std.com> To: chemistry@ccl.net Subject: PLP - piecewise linear potential? Folks, I am trying to parse my notes from ACS, New Orleans, and I wonder whether anybody has references to the PLP docking/scoring function which was mentioned by several speakers. I think this is the "piecewise linear potential" method, but I'm not sure of this... Any pointers appreciated! Joe Leonard jle@world.std.com From chemistry-request@server.ccl.net Thu Oct 7 12:20:54 1999 Received: from nmr.utmb.edu (dggin1.utmb.edu [129.109.73.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA00403 for ; Thu, 7 Oct 1999 12:20:52 -0400 Received: from nmr.utmb.edu (morass.utmb.edu [129.109.73.39]) by nmr.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id LAA02218 for ; Thu, 7 Oct 1999 11:12:39 -0500 Sender: bruce@nmr.utmb.edu Message-ID: <37FCC6BB.230CA320@nmr.utmb.edu> Date: Thu, 07 Oct 1999 11:13:47 -0500 From: "Bruce A. Luxon" Reply-To: bruce@nmr.utmb.edu Organization: Sealy Center for Structural Biology X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: SGI sleds Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Re: Sleds for SGI Indigo2 Does anyone know of a vendor who sells sleds for mounting hard drives, etc into SGI Indigo2 workstations? Especially for a reasonable price. Saw a 3.5" one for almost $300 a month or so ago. I'm particularly interested in several 5.25" sleds so I can use the few remaining open bays I have left in our machines. Thanks, Bruce -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Bruce A. Luxon, Ph.D. Associate Professor Sealy Center for Structural Biology Dept. of Human Biological Chemistry & Genetics University of Texas Medical Branch Galveston, TX 77555-1157 (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ http://www.nmr.utmb.edu/ mailto:bruce@nmr.utmb.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Oct 7 12:43:58 1999 Received: from phare.univ-lille2.fr (root@phare.univ-lille2.fr [193.51.138.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA00648 for ; Thu, 7 Oct 1999 12:43:57 -0400 Received: from icpl6 (icpl6.univ-lille2.fr [193.51.138.127]) by phare.univ-lille2.fr (8.8.7/8.8.7) with SMTP id SAA02605 for ; Thu, 7 Oct 1999 18:38:23 +0200 Message-ID: <001901bf10e2$3bf309a0$7f8a33c1@icpl6.univ-lille2.fr> From: "Philippe CHAVATTE" To: "CCL" Subject: Amber 4.1 parameters for benzothiazolinone Date: Thu, 7 Oct 1999 18:37:23 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Dear CCLers, I would appreciate any help in getting Amber 4.1 parameters for benzothiazolinone Best regards Philippe ----------------- Philippe CHAVATTE Institut de Chimie Pharmaceutique Albert Lespagnol BP 83 59006 LILLE CEDEX FRANCE E-Mail : pchavatt@phare.univ-lille2.fr From chemistry-request@server.ccl.net Thu Oct 7 15:00:01 1999 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA01192 for ; Thu, 7 Oct 1999 15:00:01 -0400 Message-ID: Date: 7 Oct 1999 14:01:56 -0500 From: "Boyd" Subject: COMP's journal To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear CCLers, Last year the Journal of Molecular Graphics and Modelling became of the official publication of the ACS Division of Computers in Chemistry (COMP). The scope of the journal has expanded. Interest has been steadily increasing. We invite you to read about the journal at our new website: http://chem.iupui.edu/~boyd/jmgm.html Thanks, Don Donald B. Boyd, Ph.D. Co-Editor, Journal of Molecular Graphics and Modelling Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Thu Oct 7 16:32:31 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01941 for ; Thu, 7 Oct 1999 16:32:30 -0400 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA15951 for ; Thu, 7 Oct 1999 16:28:41 -0400 (EDT) Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id NAA24561; Thu, 7 Oct 1999 13:27:23 -0700 (PDT) Message-Id: <199910072027.NAA24561@bioc1.msi.com> Received: from osman-pc.msi.com(146.202.7.202) by bioc1.msi.com via smap (V2.0) id xma024551; Thu, 7 Oct 99 13:26:56 -0700 X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Thu, 07 Oct 1999 13:28:19 -0700 To: CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch, chemweb@ic.ac.uk From: "Osman F. Guner" Subject: Cal for Papers - ADME/Tox in early drug discovery EXPERIMENTAL, COMPUTATIONAL, AND INFORMATICS CHALLENGES OF ADME/TOX IN EARLY STAGE DRUG DISCOVERY To be held at the 219th National American Chemical Society Meeting in San Francisco California, March 26-31, 2000 Sponsored by Division of Chemical Information (CINF) Co-sponsored by Divisions of Medicinal Chemistry (MEDI), Toxicology (TOXI), and Computers in Chemistry (COMP) Open symposia will be followed by a plenary session that will feature the following speakers: Christopher A. Lipinski, Ph.D. Senior Research Fellow, Pfizer Central Research Dale E. Johnson, Pharm.D., Ph.D. Vice President Preclinical Development, Chiron John J. Baldwin, Ph.D. Chief Science and Technology Officer, Pharmacopeia Stephen K. Durham, Ph.D. Distinguished Research Fellow, Bristol Myers Squibb Mark A. Murcko, Ph.D. Vice President and Senior Research Fellow, Vertex The titles of the plenary lectures will be announced shortly. This is an invitation for you to present your views and research results in the above topics. Papers will be organized with respect to experimental, computational, informatics aspects as well as others. If you have an opinion on this topic, or research results, or if you know of success stories or failures in this area, you may want to consider presenting your views in this symposium. Please use the On-line Abstract System (OASys) to submit your abstracts. At http://acs.confex.com/acs/219nm/cinf/papers/index.cgi, select the symposium with the above title. The deadline for submitting abstracts is November 1, 1999. Although use of the OASys is strongly encouraged for your abstract submission, should you have difficulties with the OASys, feel free to E-mail me an electronic copy of your abstract by filling out the word template that can be downloaded at http://www.acs.org/meetings/abstract/absdown.html. Cheers...Osman --- Osman F. G=FCner, Ph.D. Sr.Product Manager, Rational & Combinatorial Drug Design Molecular Simulations Inc. (858)799-5341 osman@msi.com http://www.msi.com From chemistry-request@server.ccl.net Thu Oct 7 16:43:10 1999 Received: from saratoga.orconet.com (saratoga.orconet.com [206.66.136.11] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01994 for ; Thu, 7 Oct 1999 16:43:09 -0400 Received: from molecules.com ([216.98.228.87]) by saratoga.orconet.com (Netscape Messaging Server 3.6) with ESMTP id AAA53E5 for ; Thu, 7 Oct 1999 13:42:26 -0700 Message-ID: <37FD03EF.BC831D75@molecules.com> Date: Thu, 07 Oct 1999 13:34:55 -0700 From: James Givens X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re: CCL:computational chem for high school students References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit John Mackin wrote: > > I am interested in any very basic applications which will help high school > chemistry students appreciate the use of technology and math in the current > development of chemistry. These students have algebra capability > (no calculus) so the math component must be more simple than I suspect is > used in computational chemistry. The graphics results, though, will spark > interest in the students. Again, the key word is appreciation. Are there > applications which would excite and motivate some students to pursue > a chemistry career in college? For a simple-to-use chemistry program that is graphics-oriented yet contains some reasonably sophisticated computational aspects, try: Molecules-3D, ver 2.5 3D Molecular Model Builder for Windows and Macintosh Go to: http://www.molecules.com/m3d25int.shtml for additional information. -- James Givens ---------------------------------------------------------------- Molecular Arts Corporation | Hanover Corporate Centre, Suite 1000 | http://www.molecules.com 1532 East Katella Avenue | Main: (714) 634-8100 Anaheim, California 92805-6627 USA | FAX: (714) 634-1999 ---------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Oct 7 17:20:04 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02392 for ; Thu, 7 Oct 1999 17:20:03 -0400 Received: from zosia (zosia.dorf.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with SMTP id <01JGVCN6T2FA0000CA@mail.rwth-aachen.de> for chemistry@ccl.net; Thu, 7 Oct 1999 23:17:39 +0200 Date: Thu, 07 Oct 1999 23:16:03 +0200 From: Krzysztof Radacki Subject: gaussian link l1002 X-Sender: kradacki@mail.rwth-aachen.de To: chemistry@ccl.net Message-id: <3.0.6.32.19991007231603.007d3100@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Content-type: text/plain; charset="us-ascii" Hi, can somebody write me if link L1002 in gaussian98 is or not parallel? I'm a little supprised but this one I've never seen working with more than one processor on our HP9000. regards Krzys Radacki ___________________---------------------------------------------------- ------------------ e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------------