From bennett@ubaclu.unibas.ch Tue Nov 29 07:15:45 1994 Received: from swiba9.unibas.ch for bennett@ubaclu.unibas.ch by www.ccl.net (8.6.9/930601.1506) id GAA03953; Tue, 29 Nov 1994 06:21:57 -0500 Received: from yogi.urz.unibas.ch by swiba9.unibas.ch with SMTP (PP); Tue, 29 Nov 1994 12:21:45 +0100 Received: from fib.chemie.unibas.ch. (fib.chemie.unibas.ch) by ubaclu.unibas.ch (PMDF V4.3-7 #7496) id <01HK1V1H0THC8WZCOK@ubaclu.unibas.ch>; Tue, 29 Nov 1994 12:21:38 +0100 Date: Tue, 29 Nov 1994 12:21:31 +0100 From: Frederick Bennett Subject: Summary of "What is Molecular Modelling" To: chemistry@ccl.net Message-id: X-Mailer: VersaTerm Link v1.1 Content-transfer-encoding: 7BIT Hello again, a month or so ago I made the mistake of posing the question of "What is Molecular Modelling ?" to this forum. I received some interesting responses but I would say that the answers are not exactly unanimous. Since somebody asked me to summarise these replies, here they are. Regards Frederick. > > I know that most people would have no problem putting problems involving > very large systems being studied by empirically based theoretical methods > and such in the molecular modeling basket, but what about the other end ? > For example, are ab initio studies on smaller systems (say > 20 atoms) > regarded as molecular modeling. For that matter, would a diatomic be > eligable for the subject of molecular modeling after all it is a molecule? > The answer is yes and you're not splitting hairs. I can make a perfectly reasonable model of molecular motion using a linear oscillator. I can make a perfectly unreasonable one as well. By this line of logic, most of chemical physics theory falls into the catagory of molcular modeling. If it's not a model, it's not a theory. The closer your model comes to predicting the answer (as determined by experiments), the better the model. Eric R. Bittner ---------------------------------------------------------------------- Eric R. Bittner phone: (512)-471-1092 Dept. of Chemistry fax: (512)-471-8696 Univ. of Texas at Austin ----------------------------------------------------------------------- Dear Dr. Bennett: By MOLECULAR MODELING I understand "A SIMPLIFIED BUT SUFFICIENTLY ADEQUATE GENERAL DESCRIPTION OF MOLECULAR SYSTEMS BY WELL DEFINED AND EASILY EVALUATED STRUCTURAL AND ELECTRONIC FEATURES THAT REPRESENT THE MOLECULAR PROPERTIES". The idea is to describe the molecules as simple as possible compatible with the requirement of adequacy to their properties. Obviously, different properties may require different description. To my knowledge, no definition (or discussion) of this term is available in the literature. Regards, I. B. Bersuker -- ================================================================================ Note: the old address charon.chpc.utexas.edu has been changed as shown below. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Isaac B. Bersuker | E-mail: Dept. of Chemistry | cmao771@charon.cc.utexas.edu Univeristy of Texas at Austin | Vox: (512) 471-4671 Austin, TX 78712 | Fax: (512) 471-8696 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Molecular modeling originated from the Organic Chemist's method of visualizing molecular structures. They used ball-and-stick models to represent nuclear positions and covalent bonds respectively. Now the same is done on a much larger scale and using computers. Molecular Dynamics is different from Molecular Modeling but they are intimately connected through Molecular Mechanics. Electronic structure calculations using Quantum Chemistry, both theory and practice, deserve to be a separate discipline, in my humble opinion. This does not preclude interdisciplinary projects involving Q.Chem. in molecular modeling. Kottalam Phone: (USA) 612 683 3622 Cray Research, Inc. Dr. Bennett, You raise a valid question. I, of course, cannot say how Tim Clark will set the scope for the Journal of Molecular Modeling. However, the larger semantical question has received several pertinent discussions in "Reviews in Computational Chemistry." In particular, I would point out Volumes I, II, IV, and V. The books are published by VCH, and your library my have them. Don Boyd Hallo, In my humble opinion, any designs, works, researches dealing with molecular level which employ computational effort should be called "molecular modeling". Molecular modeling should involve the presence of model, namely, bonds, atoms, interactions and so on. best wishes, Noy ====================================================== Papernet Address : Frederick R. Bennett Institute for Physical Chemistry Klingelbergstrasse 80 CH-4056 Basel Switzerland Mouthnet Address : [41]-(61)-267-3821 Internet Address : bennett@ubaclu.unibas.ch ====================================================== From shenkin@still3.chem.columbia.edu Tue Nov 29 10:15:49 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id JAA05421; Tue, 29 Nov 1994 09:16:57 -0500 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA16806; Tue, 29 Nov 94 09:16:42 -0500 From: "Peter Shenkin" Message-Id: <9411290916.ZM16804@still3.chem.columbia.edu> Date: Tue, 29 Nov 1994 09:16:32 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: (Fwd) Pentium Papers Repository Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 The following message, which just appeared on the "numeric-interest" mailing list, ought to be of interest to those concerned about the Pentium FP bug. A Hexium on the house of Pentium! -P. --- Forwarded mail from moler@mathworks.com To: numeric-interest@validgh.com Cc: mw.biz@turing.mathworks.com Newsgroups: comp.sys.intel,comp.soft-sys.matlab,sci.math.num-analysis Subject: Pentium Papers Repository Summary: A archive of source material on the Pentium FDIV bug. Organization: The MathWorks, Inc., Natick, MA 01760 Pentium Papers Repository The MathWorks is making a collection of "primary source" material on the Pentium division bug available. If you're wired to the Web, try www.mathworks.com -- "What's New" button or, with anonymous FTP, try ftp.mathworks.com -- directory /pub/tech-support/moler/Pentium The documents available as of today, 11/28/94, are listed below. This archive is intended as a reasonably complete historical record of the events associated with the Pentium floating point division bug. All of these documents are reproduced as they originally appeared on the Net or elsewhere with full credit given to the authors and institutions involved. Some material may be copyrighted and should be treated as such. -- Cleve Moler moler@mathworks.com ------------ Nicely_original_post.txt October 30. Memo from Prof. Thomas Nicely, Lynchburg College. Calculations involving prime numbers lead to the first description of the bug. Example is 1/824633702441. Mathisen_first_post.txt October 30. A series of Internet postings by Terje Mathisen, Norsk Hydro, Norway, confirming the bug and lead to a test program, p87test.zip. EE_Times.txt November 7. Article by Alex Wolfe in the EE Times, a weekly trade publication with the headline, INTEL FIXES A PENTIUM FPU GLITCH Copyright (c) 1994 by the EE Times Coe.txt November 15. Internet posting by Tim Coe, Vitesse Semiconductor, with a model of the chip's behavior and the example 4195835/3145727. Moler_first_post.txt November 15. Internet posting by Cleve Moler, the MathWorks, summarizing results to date. Examples include Nicely's prime reciprocal and Coe's ratio. Cable_News_Network.txt November 22. Report by Steve Young on CNN's Moneyline includes interviews with Intel's Stephen Smith and Moler. MathWorks_press_release.txt November 23. MathWorks issues a press release with the title THE MATHWORKS DEVELOPS FIX FOR THE INTEL PENTIUM(tm) FLOATING POINT ERROR New_York_Times.txt November 24. New York Times article by John Markoff with headline CIRCUIT FLAW CAUSES PENTIUM CHIP TO MISCALCULATE, INTEL ADMITS Copyright (c) 1994 by the New York Times Associated_Press.txt November 24. News story circulated by the Associated Press. Copyright (c) 1994 by the Associated Press Moler_second_post.txt November 24. Internet posting by Moler describing a software/ hardware workaround for the FDIV bug. Moler_third_post.txt November 24. Internet posting by Moler announcing a Pentium-Aware Release of MATLAB. Intel_support.txt November 24. America OnLine and Internet posting by Ken Hendren, Intel Applications Support Manager. Intel_FAX.txt Intel FAXBACK Document #7999 Obtained from FAXBACK system at 800 628-2283 Nicely_second_post.txt November 25. Memo from Prof. Nicely entitled "Pentium Bug and the Intel NDA". Andy_Grove.txt November 27. Internet posting by Intel CEO Andy Grove entitled "My Perspective on Pentium". --- End of forwarded mail from moler@mathworks.com -- *********** World music: What bluegrass is to a Bulgarian. ********** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************************ Make love, THEN war. ************************ From fercu@cwgk.chem.cwru.edu Tue Nov 29 10:32:31 1994 Received: from CWGK.cwru.edu for fercu@cwgk.chem.cwru.edu by www.ccl.net (8.6.9/930601.1506) id JAA05390; Tue, 29 Nov 1994 09:16:23 -0500 From: Received: by cwgk.chem.cwru.edu (MX V4.1 VAX) id 1; Tue, 29 Nov 1994 09:17:32 EST Date: Tue, 29 Nov 1994 09:17:56 EST To: CHEMISTRY@ccl.net CC: fercu@cwgk.chem.cwru.edu Message-ID: <009882F2.8FAB6BAF.1@cwgk.chem.cwru.edu> Subject: Re: Look for Refs. of Rational Drug Design Arthur Wang writes: To: CHEMISTRY@ccl.net Subject: CCL: T.A.Halgren email Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does somebody know the email of Dr. Thomas A. Halgren (Merck Research Labs.) ? Thanks in advance, Edgardo Garcia From szilagyi@indy.mars.vein.hu Tue Nov 29 12:21:06 1994 Received: from sztaki.hu for szilagyi@indy.mars.vein.hu by www.ccl.net (8.6.9/930601.1506) id LAA08819; Tue, 29 Nov 1994 11:37:34 -0500 Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id lD29914; Tue, 29 Nov 1994 17:31:32 +0100 Received: by miat0.vein.hu with SMTP (5.61++/Vein-1.0) id AA03533; Tue, 29 Nov 94 17:40:43 +0100 Received: by indy.mars.vein.hu (931110.SGI/930416.SGI.AUTO) for @miat0.vein.hu:chemistry@ccl.net id AA18401; Tue, 29 Nov 94 17:39:58 +0100 From: "Robert K. Szilagyi" Message-Id: <9411291739.ZM18399@indy.mars.vein.hu> Date: Tue, 29 Nov 1994 17:39:51 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Synthesis design Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Charset: US X-Char-Esc: 0 Dear Netters, we are looking for expert systems in synthesis design, more precisely, retro- and non-retro-synthetic databases, management softwares. They should be applicable in education and in research, too. If possible, please attach the name of the software, price and the mailing address of producer company to your query. Any experienced user's comments are welcome! Yours, Rob ps.: Of course as every time, I will summarize for the net! -- ----------------------------------------------------------------------------- Robert K. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 szilagyi@indy.mars.vein.hu Egyetem u. 10 >W=C< Phone: +36-(88)-422022/156 P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 http://indy.mars.vein.hu:8000/molmod.html ----------------------------------------------------------------------------- From LONCHARICH_RICHARD_J@Lilly.com Tue Nov 29 13:17:21 1994 Received: from Lilly.com for LONCHARICH_RICHARD_J@Lilly.com by www.ccl.net (8.6.9/930601.1506) id MAA09931; Tue, 29 Nov 1994 12:47:54 -0500 Received: from DECNET-MAIL (RX82788@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-10 #6224) id <01HK1VRURPY8004LZC@INET.D48.LILLY.COM>; Tue, 29 Nov 1994 12:47:14 -0500 (EST) Date: Tue, 29 Nov 1994 12:47:14 -0500 (EST) From: Rick Loncharich Subject: CCL: Cambridge fractional to cartesian coordinates To: chemistry@ccl.net Message-id: <01HK1VRUWT76004LZC@INET.D48.LILLY.COM> X-VMS-To: MCDEV1::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Is there any public domain software that will read a,b,c,alpha,beta,gamma and fractional coordinates >from the cambridge database and write out cartesian coordinates? I am looking for a simple fortran program that will read data of the type: 8.9500 18.7240 7.2890 90.0 101.980 90.0 Na1 .70040 .82610 .03040 Na2 .04290 .72310 .19540 N1 .93600 .42570 .58010 . . . and do the conversion. Rick rjl@lilly.com From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net") From Tim_Mitchell-1%notes@sb.com Tue Nov 29 13:24:06 1994 Received: from phinet.smithkline.com for Tim_Mitchell-1%notes@sb.com by www.ccl.net (8.6.9/930601.1506) id NAA10239; Tue, 29 Nov 1994 13:08:49 -0500 Received: by phinet.smithkline.com (5.57/ULTRIX-az-040392); id AA11593; Tue, 29 Nov 94 12:59:11 -0500 Received: by pho018.sb.com (IBM OS/2 SENDMAIL VERSION 1.2.15T (03/09/94)/1.0) id AA1316; Tue, 29 Nov 94 13:08:02 -0800 Message-Id: <9411292108.AA1316@pho018.sb.com> Received: from SB_PHARM_RD with "Lotus Notes Mail Gateway for SMTP" id 72B37E093D21E0E2802561160063873C; Tue, 29 Nov 94 13:08:01 To: CHEMISTRY From: Tim Mitchell-1 Date: 29 Nov 94 18:10:07 ES Subject: CCL: Distance Geometry programs that read line notation Mime-Version: 1.0 Content-Type: Text/Plain Does anyone out there know of any distance geometry programs that can take line notation (smiles etc.) as input? I believe Rubicon from Daylight is one -- I'd appreciate it if anyone knows about any others. Thanks in advance ...... Tim. _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _____ ____ _/ SmithKline Beecham Pharmaceuticals Ltd _/ _/ / ___\\\\ _ \ _/ Brockham Park _/ _/ | |___ \\|_| | _/ Tim Mitchell, Comp. Chem. Betchworth _/ _/ \___ | | _ < _/ Phone: (0)737 36 4535 Surrey _/ _/ ____| | | |_| | _/ Fax: (0)737 36 4539 RH3 7AJ _/ _/ \____/ |____/ _/ E-Mail: Tim_Mitchell-1%notes@sb.com U.K. _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From dimitris@3dp.com Tue Nov 29 14:15:55 1994 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id OAA11864; Tue, 29 Nov 1994 14:12:52 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA02849; Tue, 29 Nov 94 14:19:51 -0500 Received: by europa.3dp.com (931110.SGI) id AA01642; Tue, 29 Nov 94 14:51:45 -0500 From: "Dimitris Agrafiotis" Message-Id: <9411291451.ZM1640@europa.3dp.com> Date: Tue, 29 Nov 1994 14:51:45 -0500 In-Reply-To: "Robert K. Szilagyi" "CCL:Synthesis design" (Nov 29, 5:39pm) References: <9411291739.ZM18399@indy.mars.vein.hu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Robert K. Szilagyi" Subject: Re: CCL:Synthesis design Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 29, 5:39pm, Robert K. Szilagyi wrote: > Subject: CCL:Synthesis design > Dear Netters, > > we are looking for expert systems in synthesis design, more precisely, > retro- and non-retro-synthetic databases, management softwares. They should be > applicable in education and in research, too. If possible, please attach the > name of the software, price and the mailing address of producer company to > your query. > Any experienced user's comments are welcome! There are a few around, but the most advanced is LHASA (Logic and Heuristics Applied to Synthetic Analysis) out of EJ Corey's group at Harvard. For more information, contact: Dr. Alan Long Director Department of Chemistry Harvard University 12 Oxford Street Cambridge, MA 02138 tel: (617) 495-4283 e-mail: long@chemistry.harvard.edu. or EJ himself at the same address. Please let me know if you need more information or can't get through to Alan. Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From dimitris@3dp.com Tue Nov 29 14:21:03 1994 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id NAA11080; Tue, 29 Nov 1994 13:41:58 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA02783; Tue, 29 Nov 94 13:49:45 -0500 Received: by europa.3dp.com (931110.SGI) id AA01642; Tue, 29 Nov 94 14:51:45 -0500 From: "Dimitris Agrafiotis" Message-Id: <9411291451.ZM1640@europa.3dp.com> Date: Tue, 29 Nov 1994 14:51:45 -0500 In-Reply-To: "Robert K. Szilagyi" "CCL:Synthesis design" (Nov 29, 5:39pm) References: <9411291739.ZM18399@indy.mars.vein.hu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Robert K. Szilagyi" Subject: Re: CCL:Synthesis design Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 29, 5:39pm, Robert K. Szilagyi wrote: > Subject: CCL:Synthesis design > Dear Netters, > > we are looking for expert systems in synthesis design, more precisely, > retro- and non-retro-synthetic databases, management softwares. They should be > applicable in education and in research, too. If possible, please attach the > name of the software, price and the mailing address of producer company to > your query. > Any experienced user's comments are welcome! There are a few around, but the most advanced is LHASA (Logic and Heuristics Applied to Synthetic Analysis) out of EJ Corey's group at Harvard. For more information, contact: Dr. Alan Long Director Department of Chemistry Harvard University 12 Oxford Street Cambridge, MA 02138 tel: (617) 495-4283 e-mail: long@chemistry.harvard.edu. or EJ himself at the same address. Please let me know if you need more information or can't get through to Alan. Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From dimitris@3dp.com Tue Nov 29 14:24:28 1994 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id OAA11756; Tue, 29 Nov 1994 14:07:25 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for szilagyi@indy.mars.vein.hu id AA02814; Tue, 29 Nov 94 14:04:49 -0500 Received: by europa.3dp.com (931110.SGI) id AA01642; Tue, 29 Nov 94 14:51:45 -0500 From: "Dimitris Agrafiotis" Message-Id: <9411291451.ZM1640@europa.3dp.com> Date: Tue, 29 Nov 1994 14:51:45 -0500 In-Reply-To: "Robert K. Szilagyi" "CCL:Synthesis design" (Nov 29, 5:39pm) References: <9411291739.ZM18399@indy.mars.vein.hu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Robert K. Szilagyi" Subject: Re: CCL:Synthesis design Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 29, 5:39pm, Robert K. Szilagyi wrote: > Subject: CCL:Synthesis design > Dear Netters, > > we are looking for expert systems in synthesis design, more precisely, > retro- and non-retro-synthetic databases, management softwares. They should be > applicable in education and in research, too. If possible, please attach the > name of the software, price and the mailing address of producer company to > your query. > Any experienced user's comments are welcome! There are a few around, but the most advanced is LHASA (Logic and Heuristics Applied to Synthetic Analysis) out of EJ Corey's group at Harvard. For more information, contact: Dr. Alan Long Director Department of Chemistry Harvard University 12 Oxford Street Cambridge, MA 02138 tel: (617) 495-4283 e-mail: long@chemistry.harvard.edu. or EJ himself at the same address. Please let me know if you need more information or can't get through to Alan. Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From dimitris@3dp.com Tue Nov 29 14:25:21 1994 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id NAA10903; Tue, 29 Nov 1994 13:37:24 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for szilagyi@indy.mars.vein.hu id AA02754; Tue, 29 Nov 94 13:32:05 -0500 Received: by europa.3dp.com (931110.SGI) id AA01642; Tue, 29 Nov 94 14:51:45 -0500 From: "Dimitris Agrafiotis" Message-Id: <9411291451.ZM1640@europa.3dp.com> Date: Tue, 29 Nov 1994 14:51:45 -0500 In-Reply-To: "Robert K. Szilagyi" "CCL:Synthesis design" (Nov 29, 5:39pm) References: <9411291739.ZM18399@indy.mars.vein.hu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Robert K. Szilagyi" Subject: Re: CCL:Synthesis design Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 29, 5:39pm, Robert K. Szilagyi wrote: > Subject: CCL:Synthesis design > Dear Netters, > > we are looking for expert systems in synthesis design, more precisely, > retro- and non-retro-synthetic databases, management softwares. They should be > applicable in education and in research, too. If possible, please attach the > name of the software, price and the mailing address of producer company to > your query. > Any experienced user's comments are welcome! There are a few around, but the most advanced is LHASA (Logic and Heuristics Applied to Synthetic Analysis) out of EJ Corey's group at Harvard. For more information, contact: Dr. Alan Long Director Department of Chemistry Harvard University 12 Oxford Street Cambridge, MA 02138 tel: (617) 495-4283 e-mail: long@chemistry.harvard.edu. or EJ himself at the same address. Please let me know if you need more information or can't get through to Alan. Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From R29CLOSE@ETSU.EAST-TENN-ST.EDU Tue Nov 29 15:15:58 1994 Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by www.ccl.net (8.6.9/930601.1506) id OAA13001; Tue, 29 Nov 1994 14:59:33 -0500 Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HK20K74XLS94E0ZI@phem3.acs.ohio-state.edu>; Tue, 29 Nov 1994 14:59:29 EDT Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 4068; Tue, 29 Nov 1994 14:48:13 -0500 Date: Tue, 29 Nov 1994 14:38:11 -0500 (EST) From: David Close Subject: MOPAC on PC's To: chemistry@ccl.net Message-id: <01HK20K75GWI94E0ZI@phem3.acs.ohio-state.edu> Organization: East Tennessee State University Content-transfer-encoding: 7BIT Dear Netters: I would like to know if others have had success with MOPAC or AMPAC on a PC. I am trying to use Ivar Koppel's MOPAC 7.1 on my Gateway Pentium (P5-66). Ivar sent me the FORTRAN code which I compiled using Microsoft's Powerstation 32-bit compiler. The program executes, but gives results that differ from some of the popular tests examples. I need to know if others have had similar problems. Some users have mentioned the use of compilers from Microway or Leahey. I am wondering if this is important. Also it would help to know if Ivar's program has given reliable results in other situations. Then there is this Pentium division error that everyone is discussing. Can this influence MO calculations? Regards, Dave Close. From hyper@sentex.net Tue Nov 29 17:15:53 1994 Received: from granite.sentex.net for hyper@sentex.net by www.ccl.net (8.6.9/930601.1506) id RAA15439; Tue, 29 Nov 1994 17:12:38 -0500 Received: (from hyper@localhost) by granite.sentex.net (8.6.9/8.6.9) id OAA27553; Tue, 29 Nov 1994 14:17:14 -0800 Received: by hyper.hyper.com.hyper.com (920330.SGI/890607.SGI) (for ccl.net!chemistry) id AA27643; Tue, 29 Nov 94 16:41:32 -0500 Date: Tue, 29 Nov 94 16:41:32 -0500 From: hurst@hyper.hyper.com (Graham Hurst) Message-Id: <9411292141.AA27643@hyper.hyper.com.hyper.com> To: hyperchem@granite.sentex.net, chemistry@ccl.net Subject: Comp. Chem. and the Pentium FDIV bug Here are some observations on the pentium FDIV bug and computational chemistry calculations. The results are for HyperChem, though I would expect similar results for calculations with other modelling programs. A regression test that we use for the testing of HyperChem uses HyperChem's scripting to perform around 3,000 calculations, including geometry optimizations, CI, molecular dynamics, vibration calculations, and uv-vis spectra, logging all results to files that we can then compare to reference files. When we run this test on a Pentium 90 with the bug (verified by finding 4195835 - (4195835/3145727*3145727) = 256 with the Windows calculator) and on a 486 without the bug, we do find differences for 4 (out of roughly 3000) calculations. The four cases are all geometry optimizations, (two with MNDO and one each with AM1 and CNDO) where the final optimized electronic and core-core repulsion energies differ. For one the difference is one in the 12th significant digit and for the other three the differences are in the 13th siginificant digit. For comparison, we find larger differences (but still relatively insignificant) comparing results from 486, SGI, DEC Alpha or IBM PowerPC computers, which we have found is due to very small differences in math library routines (like sqrt and arccos). Based on the above, I'd suggest not panicking about the Pentium FDIV bug. The magnitude of the error as manifested in molecular modelling calculations seems almost immeasurable, and is certainly far smaller than the "errors" introduced by the numerous approximations that are used routinely (like integral cutoff thresholds or non-bonded distance cutoffs). This kind of thing is hardly new - the Paranoia program was written long ago to characterize floating-point weaknesses of chip/library combinations. (Has anyone run this on a buggy Pentium 90? I've misplaced my copy, but would guess that it passes with flying colours.) I remember Clemens Roothaan showing me that the ROM for the table lookup square root in FPS-164 and FPS-264 array processors had several errors in it, leading to small but measurable imprecision, but I wouldn't advocate tossing out the wealth of published results from the mid-80s that used those once-popular computers! For what it's worth, my advice (if you've got a buggy Pentium) is to call Intel and tell them that the bug is detectable in some computational chemistry calculations (including off-the-shelf, shrink-wrapped HyperChem) and see if they'll replace it, but in the meantime carry on with calculations! Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com From rachelle@picard.niehs.nih.gov Tue Nov 29 18:16:29 1994 Received: from kamakazi.niehs.nih.gov for rachelle@picard.niehs.nih.gov by www.ccl.net (8.6.9/930601.1506) id RAA15713; Tue, 29 Nov 1994 17:25:40 -0500 Received: from picard.niehs.nih.gov by kamakazi.niehs.nih.gov via SMTP (920330.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA08992; Tue, 29 Nov 94 17:18:50 -0500 Received: by picard.niehs.nih.gov (931110.SGI/930416.SGI.AUTO) for @kamakazi.niehs.nih.gov:chemistry@ccl.net id AA01714; Tue, 29 Nov 94 17:25:32 -0500 Date: Tue, 29 Nov 94 17:25:32 -0500 From: rachelle@picard.niehs.nih.gov (Rachelle J. Bienstock) Message-Id: <9411292225.AA01714@picard.niehs.nih.gov> To: chemistry@ccl.net Subject: Calculating A and B -the nonbonded Lennard-Jones Parameters in Biosym's CVFF In Biosym's CVFF, the nonbonded Lennard-Jones potential is written as E=Aij/r^12-Bij/r^6 and values of A and B are listed. Can anyone suggest a good reference which would explain or have information as to what is needed to calulate A and B? and as to units? Thanks, Rachelle ##### (o o) +------------------------oooO---(__)---Oooo----------------------------+ | | | Dr. Rachelle Bienstock INTERNET :rachelle@picard.niehs.nih.gov | | National Institute of | | Environmental Health Sciences | | P.O. Box 12233 Mail Drop 10-03 Telephone : 919-541-3397 | | Research Triangle Park, NC 27709 Fax : 919-541-1578 | +----------------------------------------------------------------------+ || || (__) (__) From haney@netcom.com Tue Nov 29 18:18:04 1994 Received: from netcom4.netcom.com for haney@netcom.com by www.ccl.net (8.6.9/930601.1506) id SAA16751; Tue, 29 Nov 1994 18:13:57 -0500 Received: by netcom4.netcom.com (8.6.9/Netcom) id PAA02372; Tue, 29 Nov 1994 15:12:33 -0800 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199411292312.PAA02372@netcom4.netcom.com> Subject: Re: CCL:Distance Geometry programs that read line notation To: Tim_Mitchell-1%notes@sb.com (Tim Mitchell-1) Date: Tue, 29 Nov 1994 15:12:32 -0800 (PST) Cc: CHEMISTRY@ccl.net In-Reply-To: <9411292108.AA1316@pho018.sb.com> from "Tim Mitchell-1" at Nov 29, 94 06:10:07 pm X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 969 Tim Mitchell writes: > > Does anyone out there know of any distance geometry programs that can take line > notation (smiles etc.) as input? I believe Rubicon from Daylight is one -- I'd > appreciate it if anyone knows about any others. > HINT provides (in addition to hydrophobicity calculation) an option for InsightII to convert SMILES to 2D structures. The remaining tools to convert 2D to 3D using DGII exist in InsightII/Sketch, and a more general interface to DGII exists through the NMR interface from Biosym. Similarly, Sybyl is interfaced to both Concord (for SMILES conversion) and Diana (for distance geometry). -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From mwd@lenti.med.umn.edu Tue Nov 29 19:15:54 1994 Received: from mail.unet.umn.edu for mwd@lenti.med.umn.edu by www.ccl.net (8.6.9/930601.1506) id SAA16912; Tue, 29 Nov 1994 18:19:20 -0500 Received: from lenti.med.umn.edu by mail.unet.umn.edu (5.65c) id AA07887; Tue, 29 Nov 1994 17:19:19 -0600 From: "Mark Dalton (Cray)" Message-Id: <9411292319.AA24397@lenti.med.umn.edu> Received: by lenti.med.umn.edu; Tue, 29 Nov 94 17:19:17 CST Subject: Phospholipid 3d structure and forces To: chemistry@ccl.net Date: Tue, 29 Nov 1994 17:19:16 -0600 (CST) X-Mailer: ELM [version 2.4 PL23beta] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 951 Hi! I was wondering if anyone has suggestions or know of places where I could get 3D structures (PDB format) of (cell membrane) phospholipids, also if there are any formulas/information on strengths and rate of decrease of the hydrophilic/phobic interactions, pH and ionic strength of various phospholipids, proteins. Basically, I am looking for good, accurate and complete information of characteristics/properties of the various parts of cell membranes. Does anyone have good references? Thanks! Mark -- Mark Dalton CH3-S-CH2 H H O H | | | \ | CH2-C-COOH //\ ---C--CH2-C-COO C-CH2-C-COO mwd@lenti.med.umn.edu | | || || | // | NH2 \\/ \ / CH NH3 O NH3 NH URL = http://lenti.med.umn.edu/~mwd/mwd.html From XIANZ@ASUCHM.LA.ASU.EDU Tue Nov 29 20:15:55 1994 Received: from ASUCHM.LA.ASU.EDU for XIANZ@ASUCHM.LA.ASU.EDU by www.ccl.net (8.6.9/930601.1506) id TAA17552; Tue, 29 Nov 1994 19:23:02 -0500 From: Date: Tue, 29 Nov 1994 17:23:18 -0700 (MST) To: chemistry@ccl.net Message-Id: <941129172318.2721@ASUCHM.LA.ASU.EDU> Subject: looking for DFT code Dear netters: I am looking for some software on the basis of Density Functional Theory ( free or commercial but not too expensive), with which the energy band structure and densities of states for crystals can be performed. Orbital- free-DFT or orbital-based hybrid-HF-DFT methods are OK but the later is prefered. Please send your reply to me at xianz@asuchm.la.asu.edu I'll summerize to the list. Thank you in advance! Xianzhang Gu Department of Chemistry Arizona State University