From bgobbi@CHBS.CIBA.COM Wed Nov 30 02:15:58 1994 Received: from chsun.eunet.ch for bgobbi@CHBS.CIBA.COM by www.ccl.net (8.6.9/930601.1506) id CAA20420; Wed, 30 Nov 1994 02:09:53 -0500 Received: from Ciba-GW.CHBS.CIBA.COM by chsun.eunet.ch (8.6.4/1.34) id IAA03932; Wed, 30 Nov 1994 08:11:03 +0100 Received: from Central.CHBS.CIBA.COM by Ciba-GW.CHBS.CIBA.COM (4.1/Ciba2.0-R1.0) id AA29337; Wed, 30 Nov 94 08:10:10 +0100 Received: from wirz.chbs (cgchb.uss.is.chbs) by Central.CHBS.CIBA.COM id AA10457; Wed, 30 Nov 1994 08:09:41 +0100 (5.65c8/Ciba2.0-C1.1) Received: from is7w_gobbial1 ([192.37.34.17]) by wirz.chbs id AA29703; Wed, 30 Nov 94 08:09:39 +0100 (4.1/SMI-3.2-CG-1.1A) Message-Id: <9411300709.AA29703@wirz.chbs> Sender: From: "Alberto Gobbi" To: CHEMISTRY@ccl.net Date: Wed, 30 Nov 1994 08:09:12 +1 Subject: Summary: Available Chemical Databases? Reply-To: bGobbi@CHBS.CIBA.COM Priority: normal X-Mailer: Pegasus Mail/Windows (v1.22) Dear Netters, here are the answers to my quest about available chemical Databases. Thanks to all those who replied Alberto Contact Daylight support@daylight.com. We also use Cambridge Structural Database Available Chemicals Directory from MDL Maybridge catalogue Aldrich catalogue Master (octanol-water logP & pka's) from Biobyte MDL supplies a lot This is at least a start. Yvonne Martin ---------------------------------------------------------------------------------- The Cambridge Structural Database (October 1994 Release) contains data for 126,000 organic and organometallic compounds that have been studied using X-ray and neutron diffraction methods; it also contains 2500 sequences from the Brookhaven Protein Data Bank. Each entry contains bibliographic, 2D chemical and 3D crystallographic data. The data includes compound name, journal reference, molecular formula and numerical information such as unit cell parameters and R-factor. It also includes atom properties, bond properties, 3D atomic (fractional) coordinates, space-group and symmetry operators. The crystallographic connectivity is established using covalent radii and this is mapped to the 2D chemical structure. Currently, the PDB data supplied includes only sequence and bibliographic information; from April 1995 we will be distributing the coordinates as well. The CSD is the official depository for unpublished coordinate data for more than 20 major journals. The CSD Graphics System comprises software for the search, retrieval, analysis and visualisation of data in the CSD. The program QUEST can be used t o perform searches of the database for textual and numerical information, 2D structures and substructures; it can also be used to perform 3D (geometric) searches. Searches can be performed for inter- and intra-molecular non-bonded interactions. It is also possible to search for protein sequences. Various geometric parameters (bond lengths, bond angles etc.) can be defined for a search and values will be tabulated. The program VISTA allows the statistical analysis and visualisation of this data. The program PLUTO allows visualisation of the crystal structure. The System is supplied for VMS and UNIX platforms; it is available on CD-ROM and on magnetic tape. PC and Mac versions of the system are under development. Cambridge Crystallographic Data Centre 12 Union Road, Cambridge, CB2 1EZ, United Kingdom Tel: +44-223-336408 (General Office) Fax: +44-223-336033 +44-223-336022 (User Support) E-mail: software@chemcrys.cam.ac.uk World Wide Web: http://csdvx2.ccdc.cam.ac.uk/ --------------------------------------------------------------------------- I have a small database of around 25000 3D structures. These were generated >from 2-D data of compounds supplied by the Maybridge Chemical Company, Tintagel, Cornwall, England. It is available along with the 3-D structure matching program THREEDOM from QCPE. Yours sincerely Peter Bladon cbas25@vaxa.strath.ac.uk Phone/Fax +44-141-776-1718 -------------------------------------------------------------------------- nice idea, indeed. I'm aware of QCLDB and the chemical databases offered by STN. Hope this helps :-) Stefan Dapprich "to be or nut^H^H^H -- sh^Gt, how do I delete.^?^?^? Oh No Oh NO^D^D^D -- How do I get out of this thing anyway ^C^C ^C Kill it ^Z ^Z ^Z (mumble mumble) Bus error (core dumped) Dipl. Chem. Stefan Dapprich Philipps-Universitaet Marburg AK Computerchemie Hans-Meerwein-Str. D-35032 Marburg GERMANY Phone: ++49-6421-28-5549 Fax: ++49-6421-28-2189 dapprich@ps1515.chemie.uni-marburg.de --------------------------------------------------------------- I know the following database: SpecInfo Type: Commercial Spectral Database (structures and NMR, MASS and IR - Spectra) Distributor: Chemical Concepts P. O. 10 02 02 D-69442 Weinheim Fed. Rep. of Germany From toukie@zui.unizh.ch Wed Nov 30 05:16:05 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id FAA21524; Wed, 30 Nov 1994 05:14:20 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA18984; Wed, 30 Nov 94 11:14:12 +0100 X-Nupop-Charset: British Date: Wed, 30 Nov 1994 11:08:00 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <40081.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Dr. David Close, please contact me. TO: Dr. David Close, East Tennessee State University Dear Dr. Close; Kindly kind me, and send me your e-mail address. Thank you. Sincerely, (Dr.) S. Shapiro ZH, CH Internet: toukie@zui.unizh.ch From mbdtsmd@afs.mcc.ac.uk Wed Nov 30 05:29:02 1994 Received: from yama.mcc.ac.uk for mbdtsmd@afs.mcc.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA21451; Wed, 30 Nov 1994 05:01:08 -0500 Received: from afs.mcc.ac.uk (actually mchhpc.ch.man.ac.uk) by yama.mcc.ac.uk with SMTP (PP); Wed, 30 Nov 1994 10:00:42 +0100 From: mbdtsmd Message-Id: <4995.9411301000@afs.mcc.ac.uk> Subject: Kinetic isotope effects To: CHEMISTRY@ccl.net Date: Wed, 30 Nov 1994 10:00:15 +0000 (GMT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 577 Hello Everybody If anyone knows of any software for calculating secondary kinetic isotope effects from frequencies calculated using GAUSSIAN, can they let me know. Thanks Mark Davidson Computational Chemist | E-mail: mbdtsmd@afs.mcc.ac.uk Department of Chemistry | University of Manchester, | Phone: 061-275-4686 Oxford Road, Manchester, | +44-61-275-4686(international) M13 9PL, England | FAX: +44-61-275-4598 -------------------------------------------------------------------------- From mutz@ifp.mat.ethz.ch Wed Nov 30 05:39:46 1994 Received: from bernina.ethz.ch for mutz@ifp.mat.ethz.ch by www.ccl.net (8.6.9/930601.1506) id EAA21291; Wed, 30 Nov 1994 04:34:23 -0500 From: Received: from dove (actually dove.ethz.ch) by bernina.ethz.ch with SMTP inbound; Wed, 30 Nov 1994 10:33:56 +0100 Message-Id: <9411300937.AA08822@dove> Received: from ifp.mat.ethz.ch (erne) by dove.ethz.ch id AA08822; Wed, 30 Nov 94 10:37:32 +0100 Received: by erne.ethz.ch; Wed, 30 Nov 1994 10:34:10 +0100 To: XIANZ Cc: chemistry@ccl.net, mutz@ifp.mat.ethz.ch Subject: Re: CCL:looking for DFT code In-Reply-To: (Your message of Tue, 29 Nov 94 17:23:18 MST.) <941129172318.2721@ASUCHM.LA.ASU.EDU> Date: Wed, 30 Nov 94 10:34:10 +0100 Hi, I have some experience (though not very much) with the BIOSYM module Plane_Wave. It is a local DFT program that uses plane waves (who would have guessed ?) as basis functions. It is quite straightforward to use. With a cutoff energy of 21 eV in the basis set it gives you a band gap of .45 eV in Silicon. This is obviously much too small, but this is a well known feature of the local DFT. On the other hand, the band structure looks quite reasonable, and I guess the density of states is ok as well, except for the underestimation of the band gap. If you already have access to BIOSYM software, it shouldn't cost an arm and a leg to get the additional module. If not, BIOSYM might sell you the module separately (it is capable of running stand-alone) Greetings from Switzerland Marcel. ------------------------------------------------------------------------------ Marcel Utz phone: +41 1 632 5672 Institute of Polymers fax: +41 1 632 1096 ETH-Zurich CNB E 98.2 CH-8092 Zurich, Switzerland email: Marcel.Utz@ifp.mat.ethz.ch ------------------------------------------------------------------------------ From aiba@volta.vmsmail.ethz.ch Wed Nov 30 06:16:03 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id FAA21812; Wed, 30 Nov 1994 05:44:42 -0500 Message-Id: <199411301044.FAA21812@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <06506-0@bernina.ethz.ch>; Wed, 30 Nov 1994 11:44:17 +0100 X-Vms-To: ethz::"chemistry@ccl.net" To: chemistry@ccl.net From: aiba@volta.vmsmail.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) Subject: email addresses Date: Wed, 30 Nov 1994 11:44:17 +0100 Dear netters, in July of this year, in Rev. Mod. Phys. 66 (1994) 917-983, review appeared by -- E.Deumens, A.Diz, R.Longo and Y.Oehrm -- "Time-dependent theoretical treatments of the dynamics and nuclei in molecular systems". Can I get an advice how to contact the authors - I mean email addresses ? The work was done in University of Florida, Gainesville, Florida 32611. Sincerely, Ayaz Bakasov. From grfamini@cbdcom.apgea.army.mil Wed Nov 30 07:16:03 1994 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by www.ccl.net (8.6.9/930601.1506) id GAA22551; Wed, 30 Nov 1994 06:50:19 -0500 Date: Wed, 30 Nov 94 6:40:40 EST From: George R Famini To: chemistry@ccl.net Subject: COMP Division's Preliminary Program Message-ID: <9411300640.aa09200@cbdcom.apgea.army.mil> Enclosed is the preliminary program for the Division of Computers in Chemistry at the Anaheim (April 2-6) American Chemical Society Meeting. This agenda will be posted in C&E News in the late January timeframe (the first notice for the ACS meeting). However, for those of you who may wish to come, and may need to allocate travel funds now, I am giving you a bit of a "heads up". I will post a final agenda as soon as I get the rest of the abstracts typed in. George Famini COMP Program Chair 209th ACS National Meeting, Anaheim, CA Division of Computers In Chemistry G. R. Famini, US Army, Session Title Cosponsor ing SUNDAY, APRIL 2 - AM A.Combinatorial Synthesis Division of Organic Chemistry B.Conformational Analysis Division of Carbohydrate Chemistry SUNDAY, APRIL 2 - PM A.Application of Parallel Computing to Computational Chemistry B.Conformational Analysis MONDAY, APRIL 3 - AM A.Combinatorial Synthesis Division of Organic Chemistry B.Conformational Analysis C.Density Functional Theory in Division of Chemistry Physical Chemistry MONDAY, APRIL 3 - PM A.Application of Parallel Chemistry B.Conformational Analysis C.Molecular Modeling for the Bench Division of Chemist Chemical Information MONDAY, APRIL 3 - EVE Sci-Mix 7:00 PM TUESDAY, APRIL 4 - AM A.Density Functional Theory in Division of Chemistry Physical Chemistry B.Computers in Chemistry Award Symposium Honoring Peter Kollman (Sponsored by Digital Equipment Corporation) C.Molecular Modeling for the Bench Division of Information TUESDAY, APRIL 4 - PM A.Genetic Algorithms in Chemistry B.Conformational Analysis C.Molecular Modeling for the Bench Division of Chemist Chemical Information TUESDAY, APRIL 4 - EVE General Poster Session 7:00 PM WEDNESDAY, APRIL 5 - AM A.Artifical Intelligence in Chemistry B.Molecular Modeling for the Bench Division of Chemist Chemical Information WEDNESDAY, APRIL 5 - PM A.Genetic Algorithms in Chemistry B.Density Functional Theory in Division of Chemistry Physical Chemistry C.General Oral THURSDAY, APRIL 6 - AM A.Artifical Intelligence in Chemistry B.Data-Flow Programming and Molecular Visualization THURSDAY, APRIL 6 - PM A.Artifical Intelligence in Chemistry B.Data-Flow Programming and Molecular Visualization C.General Oral From T.E.Cumper@bradford.ac.uk Wed Nov 30 07:29:08 1994 Received: from discovery.brad.ac.uk for T.E.Cumper@bradford.ac.uk by www.ccl.net (8.6.9/930601.1506) id GAA22498; Wed, 30 Nov 1994 06:37:17 -0500 From: Received: from ccw119.brad.ac.uk (user tecumper) by discovery.brad.ac.uk; Wed, 30 Nov 1994 11:36:48 GMT Date: Wed, 30 Nov 94 11:36:56 GMT Message-Id: <7697.9411301136@ccw119.brad.ac.uk> To: Chemistry@ccl.net Subject: DELETE THIS MAIL NOW!! ----- Begin Included Message ----- From J.R.Cooper@bradford.ac.uk Wed Nov 30 10:18:21 1994 From: J.R.Cooper@bradford.ac.uk Date: Wed, 30 Nov 94 10:18:26 GMT To: T.E.Cumper@bradford.ac.uk Content-Length: 4078 ----- Begin Included Message ----- >From V.Butterfield-Wallbank@maths.bath.ac.uk Wed Nov 30 09:50:28 1994 Date: Wed, 30 Nov 94 9:50:14 GMT From: V Butterfield-Wallbank To: t.e.cumper Content-Length: 3789 > > Subject: chainmail > > > > > > > > > > > > \\\|||/// \\\|||/// \\\|||/// > > > . ======= . ======= . ======= > > > / \| O O | / \| O O | / \| O O | > > > \ / \v_'/ \ / \v_'/ \ / \v_'/ > > > # _| |_ # _| |_ # _| |_ > > > (#) ( ) (#) ( ) (#) ( ) > > > #\//|* *|\\ #\//|* *|\\ #\//|* *|\\ > > > #\/( * )/ #\/( * )/ #\/( * )/ > > > # ===== # ===== # ===== > > > # (\ /) # (\ /) # (\ /) > > > # || || # || || # || || > > > .#---'| |----. .#---'| |----. .#---'| |----. > > > #----' -----' #----' -----' #----' -----' > > > > > > This message has been sent to you for good luck. The original > > > is in New England. It has been sent around the world nine times. The > > > luck has now been sent to you.You will receive good luck within four > > > days of receiving this message - Provided you, in turn send it on. > > > This is no joke. You will receive good luck in the mail. But no > > > money. > > > Send copies to people you think need good luck. Don't send money as > > > fate has no price.Do not keep this message. This message must leave > > > your hands in 96 hours. > > > A United States Air Force Officer received 470,000 Dollars. > > > Another Man received 40,000 Dollars and lost it because he broke the > > > chain. > > > Whereas in the Philippines, Gene Welch lost his wife 51 days after > > > receiving the message. He failed to circulate the message. However, > > > before his death, he received 7,555,000 dollars. > > > Please send twenty copies and see what happen in four days. > > > The chain comes from Venezuela and has written by Saul De Groda, > > > A Missionary from South America. Since the copy must tour > > > the world, you must make twenty copies and send them to friends and > > > associates - After a few days you will get a surprise > > > This is true, even if you are not superstitious. > > > Do note the following: Constantine Dias received this chain in 1958. > > > He asked his secretary to make twenty copies and send them out. A few > > > days later he won a lottery of two million dollars. Carlos Daditt, an > > > office employee, received the message and forgot that it had to leave > > his > > > hands in 96 hours.He lost his job. > > > Later, after finding that message again, He mailed twentycopies. A > > > few days later he got a better job. Dalan Fairchild received the > > message > > > and, not believing - Threw the message away. Nine days later he died. > > > In 1987, The message received by a young woman in California > > > was very faded and barely readable. She promised herself that she > > > would retype the message and send it on, But she set it aside to do it > > > later. > > > She was plagued with various problems, including expensive car > > repairs. > > > The letter did not leave her hands within 96 hours. She finally typed > > > the letter as promised and got a new car. > > > Good Luck but please remember: 20 copies of this message must leave > > > your hands in 96 hours... You must not sign on this message... > > > ----- End Included Message ----- ----- End Included Message ----- From bewilson@emn.com Wed Nov 30 09:16:04 1994 Received: from emngw1.emn.com for bewilson@emn.com by www.ccl.net (8.6.9/930601.1506) id JAA23805; Wed, 30 Nov 1994 09:06:20 -0500 Received: from stc150.kpt.emn.com by emngw1.emn.com with SMTP id AA10290 (5.67b/IDA-1.5 for ); Wed, 30 Nov 1994 09:05:43 -0500 Received: from dma095.kpt.emn.com. by stc150.kpt.emn.com (MX V4.1 VAX) with SMTP; Wed, 30 Nov 1994 09:05:47 EDT Message-Id: Date: Wed, 30 Nov 94 09:07:43 EST From: "Bruce E. Wilson" Subject: Re: the Pentium FDIV bug To: "Computational Chemistry List" X-Mailer: VersaTerm Link v1.1.1 >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). Thanks, Graham, for a reasonable evaluation of the implications of the Pentium bug in a practical application. The question I'd worry about more than MD or semi-empirical methods would be ab initio calcs. In MD or semi-empirical, the numbers come back in rational units, where a difference out several significant figures is well past the practical utility of the method. ab initio methods generate energies in atomic units, so one is often faced with the issue that the energy differences of interest start in the fifth or sixth significant digit. Even then, an error out in the 12th or 13th digit is of comparatively small importance, but if it moves much in from there, I'd start to be concerned. Has anyone done the sort of analysis on ab initio calcs with a buggy Pentium that Graham mentions for MD? Tx. Bruce E. Wilson (bewilson@emn.com) Eastman Chemical Company From vijaya@chem.psu.edu Wed Nov 30 10:16:06 1994 Received: from PSUVM.PSU.EDU for vijaya@chem.psu.edu by www.ccl.net (8.6.9/930601.1506) id JAA24320; Wed, 30 Nov 1994 09:29:00 -0500 From: Received: from portal.chem.psu.edu by PSUVM.PSU.EDU (IBM VM SMTP V2R2) with TCP; Wed, 30 Nov 94 09:28:28 EST Received: from xeno.chem.psu.edu by portal.chem.psu.edu (AIX 3.2/UCB 5.64/RS6000-Server-1.0) id AA18619; Wed, 30 Nov 1994 09:28:54 -0500 Received: by xeno.chem.psu.edu (AIX 3.2/UCB 5.64/Client-1.0) id AA14113; Wed, 30 Nov 1994 09:30:38 -0500 Date: Wed, 30 Nov 1994 09:30:38 -0500 Message-Id: <9411301430.AA14113@xeno.chem.psu.edu> To: chemistry@ccl.net Subject: text book on femtochemistry Hi I am interested in buying a book entitled "FEMTOCHEMISTRY" by Ahmed H. Zewail. I am particularly interested in bying part I. Can someone post the list of contents of this volume? Thank you in advance. vijaya kumar vijaya@chem.psu.edu From becky@msi.com Wed Nov 30 10:20:57 1994 Received: from msi.com for becky@msi.com by www.ccl.net (8.6.9/930601.1506) id JAA24939; Wed, 30 Nov 1994 09:46:00 -0500 Received: from franz.MSI.COM by msi.com (4.1/SMI-4.1) id AA10959; Wed, 30 Nov 94 09:47:17 EST Received: by franz.MSI.COM (AIX 3.2/UCB 5.64/4.03) id AA16660; Wed, 30 Nov 1994 09:47:15 -0500 Date: Wed, 30 Nov 1994 09:47:15 -0500 From: becky@msi.com (Becky Rone X 276) Message-Id: <9411301447.AA16660@franz.MSI.COM> To: LONCHARICH_RICHARD_J@Lilly.com, chemistry@ccl.net Subject: Re: CCL:Cambridge fractional to cartesian coordinates I think QUANTA can perform the translation you are interested in. Then you can view the molecule on-screen, build the crystal copies and export the cartesion coordinates of the molecule, with or without crystal copies. Also, you can perform CHARMm calculations with mirror image crystal copies or independent copies, depending on the space group. From chakravo@cs.purdue.edu Wed Nov 30 10:27:10 1994 Received: from arthur.cs.purdue.edu for chakravo@cs.purdue.edu by www.ccl.net (8.6.9/930601.1506) id KAA25412; Wed, 30 Nov 1994 10:00:28 -0500 Received: from akhil.cs.purdue.edu (chakravo@akhil.cs.purdue.edu [128.10.16.37]) by arthur.cs.purdue.edu (8.6.4/PURDUE_CS-1.3) with ESMTP id for ; Wed, 30 Nov 1994 10:00:26 -0500 Received: from localhost (chakravo@localhost) by akhil.cs.purdue.edu (8.6.4/PURDUE_CS-1.3) id for CHEMISTRY@ccl.net; Wed, 30 Nov 1994 10:00:25 -0500 Date: Wed, 30 Nov 1994 10:00:25 -0500 From: chakravo@cs.purdue.edu (Subhas Chakravorty) Message-Id: <199411301500.KAA01870@akhil.cs.purdue.edu> To: CHEMISTRY@ccl.net Subject: The Pentium Bug It is curious to find that a number of researchers from respectable organisations are coming to the defense of a lost cause. The Pentium processor performs incorrect arithmatic "sometimes". Considering that several floating point operations are performed per second what is the guarantee that it at least one bug doesnt occur during a calculation which ranges between O(1) to O(N^4) sec,mins,hrs. Running a specific input for a specific program and producing a specific output that matches with that produced by another computer is a hilarious example of an ostrich with its head buried in the sand. Of course there have been a number of computer manufacturers with buggy software and hardware in the past and in the present. If the user only knows that he purchased or uses an "incorrect calculator" he/she would get rid of it in a hurry, which I want to do with my P-90 which I use very sparingly. Being unaware of a bug in a a product is okay but to defend a bug seems a bit ridiculous, at least to me. Sorry for the outburst. Subhas Chakravorty From Harold_Helson@camsci.com Wed Nov 30 10:34:15 1994 Received: from camsci.com for Harold_Helson@camsci.com by www.ccl.net (8.6.9/930601.1506) id KAA25838; Wed, 30 Nov 1994 10:14:06 -0500 Received: from by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AB04106; Wed, 30 Nov 94 10:13:58 EST Received: from QuickMail by mercury.camsci.com id qm-00003; Wed, 30 Nov 1994 10:11:55 +0000 Message-Id: <199411301011556511@mercury.camsci.com> X-Mailer: InterCon Dispatcher/SMTP for QuickMail X-Priority: 4 Date: Wed, 30 Nov 1994 10:11:55 +0000 From: Harold Helson Subject: RE>CCL:Synthesis design To: RobertK Szilagyi , Dimitris Agrafiotis Cc: chemistry Date 11/30/94 Subject RE>CCL-Synthesis design >From Harold Helson To Robert K Szilagyi, Dimitris Agrafiotis CC chemistry Reply to: RE>CCL:Synthesis design Another program is CAMEO, on which I worked as a graduate student. It operates in the forward (as opposed to retrosynthetic) direction, predicting the products of organic reactions given starting materials and conditions. For further information contact Professor William Jorgensen at bill@adrik.chem. yale.edu. Harold Helson -------------------------------------- Date: 11/29/94 3:02 PM To: Harold Helson >From: Dimitris Agrafiotis >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) To: "Robert K. Szilagyi" Subject: CCL:Synthesis design Cc: chemistry@ccl.net Sender: Computational Chemistry List 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 ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV From jkl@ccl.net Wed Nov 30 10:40:15 1994 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA24970; Wed, 30 Nov 1994 09:47:09 -0500 Date: Wed, 30 Nov 1994 09:47:09 -0500 From: Jan Labanowski Message-Id: <199411301447.JAA24970@www.ccl.net> To: chemistry@ccl.net Subject: Recent list abuses Cc: jkl@ccl.net Dear Netters, Since there are many inappropriate messages on the list lately (address inquires, chain letters, etc.) I am introducing the following rule: "The addresses of people who post inappropriate material to the list will be placed in the "reject" file. Messages from these people will be first reviewed before being posted to the list. Since I am extremely busy lately, the review process may take even a week or more, or may never be done." To avoid being placed in the "reject" file please read the "help" file for the list. It can be obtained by sending an e-mail message: HELP CHEMISTRY to MAILSERV@ccl.net Please help me in keeping the list useful by sending explanation to offenders who abouse the list. Jan Labanowski jkl@ccl.net From DWARKNTH@ACFcluster.NYU.EDU Wed Nov 30 11:16:21 1994 Received: from axp1.acf.nyu.edu for DWARKNTH@ACFcluster.NYU.EDU by www.ccl.net (8.6.9/930601.1506) id KAA26249; Wed, 30 Nov 1994 10:27:02 -0500 From: Received: from ACFcluster.NYU.EDU by ACFcluster.NYU.EDU (PMDF V4.3-13 #8043) id <01HK355DYQ9CX6WGNR@ACFcluster.NYU.EDU>; Wed, 30 Nov 1994 10:27:40 -0400 (EDT) Date: Wed, 30 Nov 1994 10:27:40 -0400 (EDT) Subject: Absurd mail on this BBoard To: Chemistry@ccl.net Message-id: <01HK355DYQ9EX6WGNR@ACFcluster.NYU.EDU> X-VMS-To: IN%"Chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi Netters, I received a message on this BBoard today about some good Luck stuff. Some of you may have received too. Once I posted a requested on X windows for PC and the everybody was stry. At least my request was concerning my work with CHEMISTRY. What IS Going ON ?????? S.Dwarakanath New York University Dept. of Biology NY From LONCHARICH_RICHARD_J@Lilly.com Wed Nov 30 11:22:29 1994 Received: from Lilly.com for LONCHARICH_RICHARD_J@Lilly.com by www.ccl.net (8.6.9/930601.1506) id KAA26019; Wed, 30 Nov 1994 10:18:53 -0500 Received: from DECNET-MAIL (RX82788@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-10 #6224) id <01HK34YO6EDS004F2L@INET.D48.LILLY.COM>; Wed, 30 Nov 1994 10:18:05 -0500 (EST) Date: Wed, 30 Nov 1994 10:18:05 -0500 (EST) From: Rick Loncharich Subject: Re: CCL:Cambridge fractional to cartesian coordinates To: chemistry@ccl.net Message-id: <01HK34YO6XOI004F2L@INET.D48.LILLY.COM> X-VMS-To: MCDEV1::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT SUBJ: RE: CCL:Cambridge fractional to cartesian coordinates Many thanks to all those who replies to my search for a simple fortran program to convert CSD fractional coordinates to cartesian coordinates. I have been overwhelmed by the number of replies. I received many programs some well known programs FRACT2XYZ (Rene Kanters) and CRYSTAL (Cynthia A. Jolly), and some private stock including FRAC2XYZ (phung), XYZ (Metz), CRYSTAL (Facelli) CRYSTOCART (Su), CRYSTAL (Bywater), and TRANSC (Braendle) from: James T. Metz, Eli Lilly Dongchul Lim, Yale Julio Facelli, Univ of Utah David Heisterberg, Ohio State Univ Dave Doherty, Minnesota Supercomputer Center phung@spin.chem.utah.edu Zhengwei Su, SUNY at Buffalo Robert Bywater, Novo Nordisk A/S I also received suggestions such as how to do it in the CSD system software from Ian Bruno (CSD), and by using other well know programs such as CHEM-X, Babel, Macromodel v.4.x, QUANTA from: W. Pat Walters, Univ of Arizona Jerry Perlstein, Univ of Rochester Jesus M. Castagnetto Mizuaray, New York Univ Leslie Glasser, Univ of Witwatersrand, South Africa Robert R. Zinn, Louisiana State Univ becky@msi.com Martin Braendle, Univ of Berne, Switzerland Jose Ignacio Garcia, Instituto de Cienciade Materiales de Aragon,Spain Once again thanks to all those who replied to my email. Sincerely, Rick Loncharich Eli Lilly & Co. From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net") From gulden@chemie.uni-wuerzburg.de Wed Nov 30 11:25:43 1994 Received: from wrzx01.rz.uni-wuerzburg.de for gulden@chemie.uni-wuerzburg.de by www.ccl.net (8.6.9/930601.1506) id KAA26050; Wed, 30 Nov 1994 10:19:48 -0500 Received: from wocx03.chemie.uni-wuerzburg.de by wrzx01.rz.uni-wuerzburg.de (4.1/uniwue-M-3.2) id AA02167; Wed, 30 Nov 94 16:19:39 +0100 Received: by wocx03.chemie.uni-wuerzburg.de (931110.SGI/uniwue-S-3.0) id AA19490; Wed, 30 Nov 94 16:19:28 +0100 Date: Wed, 30 Nov 1994 16:19:27 +0100 (MET) From: Klaus-Peter Gulden Subject: Re: CCL:MOPAC on PC's To: David Close Cc: chemistry@ccl.net In-Reply-To: <01HK20K75GWI94E0ZI@phem3.acs.ohio-state.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 29 Nov 1994, David Close wrote: > 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 I've ported MOPAC6.0 on Linux! I don't know whether this seems to be an appropriate solution for you. All test files have been successfully calulated. It's compiled with the f2c converter and subsequent gcc compilation. Only minor changes were neccessary to make the program run on a LinuX-platform. You don't mention your operating system, but if you are interested I would like to give either the sources or the executables. > 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? Are the sources to MOPAC7.1 free to the public? In this case you can give the FORTRAN-files and I try to port it on LinuX. So after that we can see whether the numerical problems are due to the PENTIUM-division bug or due to the Microsoft SUPER POWER HYPER ..... (and so on) Compiler (or what do the comercials say?). ok, see you and bye Klaus-Peter ------------------------------------------------------------------------ | Klaus-Peter Gulden | Institut fuer Org. Chemie, Universitaet Wuerzburg | | Am Hubland | mail : gulden@chemie.uni-stuttgart.de | | D-97074 Wuerzburg | voice : (0049)-(0)-931-888-4750 | | Germany | fax : (0049)-(0)-931-888-4750 | ------------------------------------------------------------------------ From shenkin@still3.chem.columbia.edu Wed Nov 30 11:28:39 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id KAA26555; Wed, 30 Nov 1994 10:37:04 -0500 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA13613; Wed, 30 Nov 94 10:33:13 -0500 From: "Peter Shenkin" Message-Id: <9411301033.ZM13611@still3.chem.columbia.edu> Date: Wed, 30 Nov 1994 10:33:01 -0500 In-Reply-To: hurst@hyper.hyper.com (Graham Hurst) "CCL:Comp. Chem. and the Pentium FDIV bug" (Nov 29, 4:41pm) References: <9411292141.AA27643@hyper.hyper.com.hyper.com> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: hurst@hyper.hyper.com (Graham Hurst), hyperchem@granite.sentex.net, chemistry@ccl.net Subject: Re: CCL:Comp. Chem. and the Pentium FDIV bug Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 29, 4:41pm, Graham Hurst wrote: > 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 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... ... > 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... Graham, I believe that your analysis is based on a misinterpretation of the nature of the bug. The nature of the bug is that for a very few specific floating point values, division is very, very wrong. The probability of this happening is of the order of parts per 10^12. The odds of your having even encountered the bug while running your test suite is only about 1/1000, even if each of your tests performed ~10^6 floating-point calculations. If you did encounter it, it might or might not have affected your results significantly, depending on where it was encountered. If it was encountered during an update of coordinates in an otherwise converged MD run, for example, presumably it would be averaged out of visibility. But if the bug had been encountered during, say, a scale-factor division just prior to output, the effect would have been disasterous. Thus the Pentium FDIV bug is one of those cases of "low probability, but high potential for disaster if encountered." In a certain sense, you're correct when you say: > The magnitude of the error as manifested in molecular modelling > calculations seems almost immeasurable... But this is in part because you're unlikely to encounter it. The FP differences you see between 486 and 586 are unlikely to have anything whatsoever to do with this bug; you probably never encountered it. The Pentium FP bug differs in a fundamental way from the look-up-table bugs to which you compare it. The look-up table bugs are, at worst, close to the threshold of floating-point precision. The Pentium bug, when encountered, gives a result which, in contrast, is nearly as wrong as it could possibly be. -P. -- *********** 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 doherty@msc.edu Wed Nov 30 12:16:42 1994 Received: from noc.msc.edu for doherty@msc.edu by www.ccl.net (8.6.9/930601.1506) id MAA28627; Wed, 30 Nov 1994 12:01:53 -0500 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA11144; Wed, 30 Nov 94 11:01:50 -0600 Received: from mac3.msc.edu by uh.msc.edu (5.65/MSC/v3.1r(920220)) id AA26852; Wed, 30 Nov 94 11:01:48 -0600 Message-Id: <9411301701.AA26852@uh.msc.edu> X-Sender: doherty@uh.msc.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 30 Nov 1994 11:03:10 -0500 To: chakravo@cs.purdue.edu (Subhas Chakravorty), CHEMISTRY@ccl.net From: doherty@msc.edu (David C. Doherty) Subject: Re: CCL:The Pentium Bug At 10:00 AM 11/30/94 -0500, Subhas Chakravorty wrote: >[...] >Being unaware of a bug in a a product is okay but >to defend a bug seems a bit ridiculous, at least to me. The above statement is true. Let me point out, however, that what these people have actually done is to put the bug into perspective. I'd be hard pressed to imagine that they have attempted to "defend" it. approximations, parameterization, coding errors, precision errors, compiler bugs... You seem to evince absolute faith that we have conquered all of these ;-). Back to work on my bug-free Motorola processor... --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From jan@EROS.CCC.Uni-Erlangen.DE Wed Nov 30 12:21:18 1994 Received: from enar.organik.uni-erlangen.de for jan@EROS.CCC.Uni-Erlangen.DE by www.ccl.net (8.6.9/930601.1506) id MAA29213; Wed, 30 Nov 1994 12:12:38 -0500 Received: from kochab.eros.edu (kochab.organik.uni-erlangen.de) by enar.organik.uni-erlangen.de with SMTP id AA24785 for CHEMISTRY@ccl.net (5.65c/IDA-1.4.4/bs-02); Wed, 30 Nov 1994 18:09:27 +0100 From: Jan Schuur Received: from izar.erosnet by kochab.eros.edu (5.0/SMI-4.1/client) id AA19547; Wed, 30 Nov 1994 18:09:27 --100 Date: Wed, 30 Nov 1994 18:09:27 --100 Message-Id: <9411301709.AA19547@kochab.eros.edu> To: CHEMISTRY@ccl.net Subject: Slow macro execution with Microsoft Excel 5.0 Cc: jan.schuur@EROS.CCC.uni-erlangen.de Content-Length: 697 Dear Netters, I using a MS Excel 5.0 macro written in Visual Basic which sorts a lot of numbers in an Excel spreadshead just by coping it to an other one. First I used it on an 386 PC with the original MS VGA driver and it runs nearly two ours but then I wanted to use an fast 486 PC with a myroChrital 16si graphik card and themyro driver for speed up. All I got was the expierence that with the myro driver the execution takes 3 hours and using the MS VGA driver with the 486 only 40 minutes. My questions are, is there anybody out there with the same expierence? Is there a way to tell Excel to jump over an screen update after the execution of each instruction? Please let me know! Jan From jkl@ccl.net Wed Nov 30 12:24:20 1994 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA28135; Wed, 30 Nov 1994 11:45:34 -0500 Date: Wed, 30 Nov 1994 11:45:34 -0500 From: Jan Labanowski Message-Id: <199411301645.LAA28135@www.ccl.net> To: chemistry@ccl.net Subject: Re: CCL:Recent list abuses In-Reply-To: Mail from 'bittner@hpcf.cc.utexas.edu (bittner)' dated: Wed, 30 Nov 1994 10:42:55 -0600 (CST) Cc: jkl@ccl.net Dear Netters, It is me again. Please do not post to the list what should be done to prevent list abuse. Send it to me. We have enough noise on the list already... Your coordinator, Jan Labanowski jkl@ccl.net From hinsenk@ERE.UMontreal.CA Wed Nov 30 14:16:13 1994 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id NAA00967; Wed, 30 Nov 1994 13:35:43 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA27470 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Wed, 30 Nov 1994 13:33:47 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA10768; Wed, 30 Nov 94 13:33:46 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA02176; Wed, 30 Nov 94 13:33:46 -0500 Date: Wed, 30 Nov 94 13:33:46 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9411301833.AA02176@cyclone.ERE.UMontreal.CA> To: CHEMISTRY@ccl.net In-Reply-To: <9411301701.AA26852@uh.msc.edu> (doherty@msc.edu) Subject: Re: CCL:The Pentium Bug David C. Doherty wrote: At 10:00 AM 11/30/94 -0500, Subhas Chakravorty wrote: >[...] >Being unaware of a bug in a a product is okay but >to defend a bug seems a bit ridiculous, at least to me. The above statement is true. Let me point out, however, that what these people have actually done is to put the bug into perspective. I'd be hard pressed to imagine that they have attempted to "defend" it. approximations, parameterization, coding errors, precision errors, compiler bugs... You seem to evince absolute faith that we have conquered all of these ;-). Not at all, but the Pentium bug is of a different quality. All the problems you have mentioned are common; any serious scientist doing numerical work is aware of them. On the other hand, floating point arithmetic is something that on the vast majority of systems works correctly. I doubt that anyone exploring the cause of a dubious result would start to check the FPU - I certainly wouldn't. And the problems you have listed above keep us sufficiently busy that we don't need to add another one, especially not one that is so easy to avoid (simply don't use a defective Pentium for numerical work). And I would like to see a similar attitude towards software development. The quality of many scientific programs, including widely used systems, is alarmingly low. A course in software engineering should be obligatory for all computational scientists. And if we throw in a course in user interface design, we might finally get rid of those programs that waste everyone's time with silly idiosyncrasies. It's about time that scientists realize that human time is more valuable than CPU time. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From hyper@sentex.net Wed Nov 30 14:21:13 1994 Received: from granite.sentex.net for hyper@sentex.net by www.ccl.net (8.6.9/930601.1506) id NAA00942; Wed, 30 Nov 1994 13:32:03 -0500 Received: (from hyper@localhost) by granite.sentex.net (8.6.9/8.6.9) id KAA08511; Wed, 30 Nov 1994 10:43:24 -0800 Received: by hyper.hyper.com.hyper.com (920330.SGI/890607.SGI) (for emn.com!bewilson) id AA03478; Wed, 30 Nov 94 13:47:15 -0500 Date: Wed, 30 Nov 94 13:47:15 -0500 From: hurst@hyper.hyper.com (Graham Hurst) Message-Id: <9411301847.AA03478@hyper.hyper.com.hyper.com> To: "Bruce E. Wilson" Subject: Re: CCL:the Pentium FDIV bug Cc: chemistry@ccl.net Bruce E. Wilson writes (in response to my post): > Thanks, Graham, for a reasonable evaluation of the implications of > the Pentium bug in a practical application. The question I'd worry > about more than MD or semi-empirical methods would be ab initio > calcs. In MD or semi-empirical, the numbers come back in rational > units, where a difference out several significant figures is well > past the practical utility of the method. ab initio methods generate > energies in atomic units, so one is often faced with the issue that > the energy differences of interest start in the fifth or sixth > significant digit. Even then, an error out in the 12th or 13th > digit is of comparatively small importance, but if it moves much > in from there, I'd start to be concerned. Has anyone done the sort > of analysis on ab initio calcs with a buggy Pentium that Graham > mentions for MD? Tx. > > Bruce E. Wilson (bewilson@emn.com) > Eastman Chemical Company You're welcome! Actually units per se are irrelevent (since they are simply scaling factors) and one is typically interested in energy differences in the fifth or sixth digit with semi-empirical calculations as well. I do agree that, because of explicit core electrons and two-electron integrals, an ab initio calculation will do orders of magnitude more divisions than an equivalent semi-empirical calculation. In ab initio calculations, most of the floating point divisions occur in the calculation of integrals (mostly two electron), and though I don't have specific results for buggy Pentiums doing ab initio calculations, I do have some experience in errors resulting from imprecision in ab initio integrals. In my earlier life as an ab initio chemist, I wrote some pipelined FPS assembler code to pack two-electron integrals to a fixed point accuracy. All integrals were truncated with rounding to the integral cutoff, thus if the integral cutoff was 1E-9, then the bits of the mantissa less than 1E-9 were thrown away. The remaining variable-length mantissa bits were were packed into words (lots of shifts and or's!), resulting in packing factors of 0.2 to 0.4 (depending on the cutoff). Details are in Hurst & Dupuis, J. Comp. Chem. 9:148-157 (1988). What does this shameless self promotion have to do with the pentium bug? Well this effectively introduced a known (and definable) imprecision into *every* two-electron integral (including those discarded), and I measured this effect on some sample calculations. The details are in the paper, but in general total energies differed less than two orders of magnitude (in atomic units) more than the integral imprecision (compared to the same cutoff without the integral compression). For imprecision less than 1E-8 for all integrals, geometry optmization results were identical for seven printed decimal places (Angstroms and degrees). Thus if imprecision in *every* integral at the eighth decimal place (in atomic units) gives total energies differing in the 7th or 8th decimal place, I think that the one in eight billion chance of getting and imprecise divide on a Pentium while calculating integrals is not cause for concern. Though the correspondence isn't strict, I think this gives an idea for an upper bound on the effect of the pentium bug in ab initio calculations. Of course quantum chemistry is like weighing a ship's captain by weighing the ship with and without the captain (I wish I could remember who said that), but I think that the pentium bug is like having a fly around the captain! Most of the time it won't make any difference (when the fly is flying) and when it does (when the fly lands briefly) the difference is almost imperceptible! By the way, Intel will replace your chip if you are doing floating-point intensive calculations. I had no trouble convincing them that HyperChem was such an app (though they informed me that the pentium also had improved accuracy for transcendentals which could cause differences from 486 results) and they added it to their list of apps that warranted high priority (but of course not immediate!) replacement. Sorry for the bandwidth... 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 hyper@sentex.net Wed Nov 30 15:17:44 1994 Received: from granite.sentex.net for hyper@sentex.net by www.ccl.net (8.6.9/930601.1506) id OAA02246; Wed, 30 Nov 1994 14:30:42 -0500 Received: (from hyper@localhost) by granite.sentex.net (8.6.9/8.6.9) id LAA09543; Wed, 30 Nov 1994 11:42:04 -0800 Received: by hyper.hyper.com.hyper.com (920330.SGI/890607.SGI) (for granite.sentex.net!hyperchem) id AA04021; Wed, 30 Nov 94 14:44:24 -0500 Date: Wed, 30 Nov 94 14:44:24 -0500 From: hurst@hyper.hyper.com (Graham Hurst) Message-Id: <9411301944.AA04021@hyper.hyper.com.hyper.com> To: "Peter Shenkin" , chemistry@ccl.net, hyperchem@granite.sentex.net Subject: Re: CCL:Comp. Chem. and the Pentium FDIV bug References: <9411292141.AA27643@hyper.hyper.com.hyper.com> Peter Shenkin wrote: > Graham, > > I believe that your analysis is based on a misinterpretation > of the nature of the bug. The nature of the bug is that for a > very few specific floating point values, division is very, very > wrong. The probability of this happening is of the order of parts > per 10^12. I'll agree about the rarity, though one in eight billion pairs of floating point numbers is the probability I've seen, but I haven't seen anything about the divisions per se being "very, very wrong". Of course small errors can be magnified with later operations, but with a "wrong" (extremely low probability) pair of numbers where the bug is manifested, the result of the division is only slightly wrong. I haven't seen a definitive "worst case" yet, but the worst I've seen so far is for 4195835 / 3145727, where the relative error is 8.1E-5. The statistical analyses I've seen posted have typical relative errors around 4E-9. What *division* example have you seen that is "very, very wrong"? I like to know if I've missed it! ;-) > The odds of your having even encountered the bug while running your > test suite is only about 1/1000, even if each of your tests performed > ~10^6 floating-point calculations. If you did encounter it, it > might or might not have affected your results significantly, depending > on where it was encountered. If it was encountered during an update > of coordinates in an otherwise converged MD run, for example, > presumably it would be averaged out of visibility. Our test suite ran many *billion* floating point operations and off the top of my head I'd guess 1 % were divisions. I agree that we might not have tickled the bug, but the odds were much better than 1/1000. (I didn't know about the immproved transcendentals and assumed that we had indeed tickled the bug when we saw any differences.) > But if the bug had been encountered during, say, a scale-factor > division just prior to output, the effect would have been > disasterous. Not if the maximum relative error is ~1e-4, and the usual error is orders of magnitude smaller. > Thus the Pentium FDIV bug is one of those cases of "low probability, > but high potential for disaster if encountered." I disagree - it's extremely low probability and low potential for disaster if encountered. I've deleted the rest of your points since it all follows from the your premise that the bug causes "very, very wrong" divisions. I'm not trying to defend the bug or Intel. Indeed it is fun to see them squirm after the "Intel Inside" marketing blitz (which among other things implied imprecision in competitors floating point chips), but I think a little less hysteria and more perspective is called for. I'd be happy to take further discussions offline to save bandwidth... 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 smap@agouron.com Wed Nov 30 17:17:22 1994 Received: from agouron.com for smap@agouron.com by www.ccl.net (8.6.9/930601.1506) id QAA04390; Wed, 30 Nov 1994 16:18:15 -0500 Received: by agouron.com (940715.SGI.52/930901.SGI) for chemistry@ccl.net id AA24319; Wed, 30 Nov 94 13:19:15 -0800 Received: from humbert.agouron.com(192.135.144.98) by tbone.agouron.com via smap (V1.3mjr) id sma024313; Wed Nov 30 13:19:09 1994 Message-Id: Date: 30 Nov 1994 13:16:00 -0800 From: "Nobuyuki Okajima" Subject: Summary-3D database search To: "chemistry osc" X-Mailer: Mail*Link SMTP/QM 3.0.0 Dear Netters, Here are the answers to my question about 3D-Database Searching . I summarized all reply here in stead of Chris Chen who submitted this question for me. Thanks to all who replied. Nobu Okajima =================================================== Nobuyuki Okajima, Ph.D. (okajima@agouron.com) Agouron Pharmaceuticals, Inc. 3565 General Atomics Court San Diego, CA 92121 Voice: (619) 622-7940, FAX: (619) 622-7999 =================================================== ##################################################### Original question was as follows. ---- [ I post it for a friend ] Hi, netters! We are looking for good literatures of 3D database searching for drug design purpose. The databases are ones such as Cambridge crystal database, and other 3D structure databases. -- Chris Chen ##### Summary #################################### 1) From: Garcia Edgardo Hi Chris, You can search the J. Chem. Information and Computer Science, the volumes of 1993 and 1994 have lots of good references about 3D database search. There is one from Akzo Company in the 93 volume about the SPERM 3D search program (that I remember). You will find many references cited there. Best regards, Edgardo Garcia Cristol Chem. & Biochem. University of Colorado Boulder CO 80303 USA ##################################################### 2) From: "Dr. Dave Winkler" Try the NCI database (~120,000 compounds) available via FTP or from software vendors such a Tripos (support@tripos.com). See also Milne et al, J. Chem. Inf. Comput. Sci., 1994, 34, 1219-24 and references within. Cheers, Dave _____________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. ##################################################### 3) From: David Clark A few papers on 3-D database searching for drug design: @article{Mart92 , author = "Martin, Y.C. ", title = " 3D Database Searching in Drug Design", journal = "Journal of Medicinal Chemistry ", year = "1992 ", volume = "35 ", pages = "2145--2154 ", } @article{Bure94 , author = "Bures, M.G., Martin, Y.C. and Willett, P. ", title = "Searching Techniques for Databases of Three--Dimensional Chemical Structures ", journal = "Topics in Stereochemistry ", year = "1994 ", volume = "21 ", pages = "467--511 ", } @article{Humb93 , author = "Humblet, C. and Dunbar, J.B. ", title = "3D Database Searching and Docking Strategies ", journal = "Annual Reports in Medicinal Chemistry ", year = "1993 ", volume = "28 ", pages = "275--284 ", } @article{Mooc94 , author = "Moock, T.E., Henry, D.R., Ozkabak, A.G. and Alamgir, M. ", title = "Conformational Searching in ISIS/3D Databases ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1994 ", volume = "34 ", pages = "184--189 ", } @article{Hurs94 , author = "Hurst, T. ", title = "Flexible 3D Searching: The Directed Tweak Technique ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1994 ", volume = "34 ", pages = "190--196 ", } @article{Ho93 , author = "Ho, C.W.M. and Marshall, G.R. ", title = "FOUNDATION: A Program to Retrieve All Possible Structures Containing a User-defined Minimum Number of Matching Query Elements from Three--Dimensional Databases ", journal = "Journal of Computer--Aided Molecular Design ", year = "1993 ", volume = "7 ", pages = "3--22 ", } @article{Miln94 , author = "Milne, G.W.A., Nicklaus, M.C., Driscoll. J.S. and Wang, S. ", title = "National Cancer Institute Drug Information System 3D Database ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1994 ", volume = "34 ", pages = "1219--1224 ", } @article{Mart94 , author = "Martin, Y.C. ", title = "Utility and Challenges of 3D Database Searching in New Drug Discovery ", journal = "European Journal of Pharmaceutical Sciences ", year = "1994 ", volume = "2 ", pages = "34--35 ", } @article{vanG90 , author = "van Geerestein, V.J., Perry, N.C., Grootenhuis, P.D.J. and Haasnoot, C.A.G. ", title = "3D Database Searching on the Basis of Ligand Shape Using the SPERM Prototype Method ", journal = "Tetrahedron Computer Methodology ", year = "1990 ", volume = "3 ", pages = "595--613 ", } @article{Perr92 , author = "Perry, N.C. and van Geerestein, V.J. ", title = "Database Searching on the Basis of Three--Dimensional Molecular Similarity Using the SPERM Program ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1992 ", volume = "32 ", pages = "607--616 ", } @article{Hara90 , author = "Karaki, K.S., Sheridan, R.P. and Venkataraghavan, R. ", title = "Looking for Pharmacophores in 3--D Databases: Does Conformational Searching Improve the Yield of Actives ", journal = "Tetrahedron Computer Methodology ", year = "1990 ", volume = "3 ", pages = "565--573 ", } @article{Hadl92 , author = "Hadlington, S. ", title = "3--D Structure Searching: A New Dimension to Drug Discovery ", journal = "Chemistry and Industry ", year = "1992 ", volume = "6 January ", pages = "10--11 ", } @article{Alle93 , author = "Allen, F.H. and Kennard, O. ", title = "3D Search and Research Using the Cambridge Structural Database ", journal = "Chemical Design Automation News ", year = "1993 ", volume = "8 (January) ", pages = "1--37 ", } @article{Rusi93 , author = "Rusinko III, A. ", title = "Commercially Available Databases of Three--Dimensional Structures ", journal = "Chemical Design Automation News ", year = "1993 ", volume = "8 (September/October) ", pages = "44--47 ", } @article{Fisa93 , author = "Fisanick, W., Cross, K.P., Forman, J.C. and Rusinko III, A. ", title = "Experimental System for Similarity and 3D Searching of CAS Registry Substances. 1. 3D Substructure Searching ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1993 ", volume = "33 ", pages = "548--559 ", } @article{Bure91 , author = "Bures, M.G., Black--Schaefer, C. and Gardner, G. ", title = "The Discovery of Novel Auxin Transport Inhibitors by Molecular Modeling and Three-Dimensional Pattern Analysis ", journal = "Journal of Computer--Aided Molecular Design ", year = "1991 ", volume = "5 ", pages = "323--334 ", } Some of these may be more technical than applied, but hopefully there may be some useful stuff. David David E. Clark | Email: D.E.Clark@proteus.co.uk Proteus Molecular Design Ltd. | Tel: 0625-500555 Lyme Green Business Park | Fax: 0625-500666 Macclesfield | Cheshire | SK11 0JL, United Kingdom | ##################################################### 4) From: "Mi-Youn Kim" Yvonne Martin has good 3D searching review paper: Mark G. Bures and Yvonne C. Martin "Searching Techniques for Database of 3D chemical structures" Topics in Stereochemistry Volume 21 p467. Mi-Youn Kim Brusniak Collage of Pharmacy University of Texas at Austin ##################################################### 5) From: "Mi-Youn Kim" Yvonne Martin has good 3D searching review paper: Mark G. Bures and Yvonne C. Martin "Searching Techniques for Database of 3D chemical structures" Topics in Stereochemistry Volume 21 p467. I would be very happy if you could share your findings with me. Good luck. Mi-Youn Kim Brusniak Collage of Pharmacy University of Texas at Austin ##################################################### 6) From: "McDaniel, Joe" We are looking at various alternative for stereochemistry searching for 2D databases. I suspect that some of the problems are very similar. I have looked at the parity approach so far. I look forward to your synopsys of responses -- please do include the 2D responses (if any). Our interest is for adding stereo searching to our RS^3 (RS cubed) relational substructure search system (hence the name), not true 3D searching. Joe McDaniel PSI INTERNATIONAL 810 Gleneagles Ct. #300 Baltimore, MD 21286 joe@psiint.com ##################################################### 7) From: PEARLMAN@VAX.PHR.UTEXAS.EDU I wrote the CONCORD program which has been used to generate almost all of the 3D databases now available for searching. I've also been involved in developing the searching software itself and I present an Overview of 3D Searching at the biannual ACS short course on molecular modeling. I could send you a copy of a review chapter I wrote. Alternatively, I could visit and provide a more up-to-date indication of the current state of the art. Let me know how I can help. Regards, -- Bob Pearlman ##################################################### 8) From: shaomeng@helix.nih.gov (Shaomeng Wang) We have published a paper this year in J. Chem. Inf. Comput. Sci. about the NCI 3D-Database. Another paper about using the NCI 3D-database for the discovery of PKC Agonists will be soon appeared in J. Med. Chem. (probably in Jan. 95 or Dec. 94 issue). Besides these, there is another paper by Sheridan, Rusinko et al, published in 1989 in PNAS, worthwhile cited. The details about these references are: Milne et al, The NCI drug information system 3D database, J. Chem. Inf. Comput. Sci., 1994, 34, 1219-1224. Wang et al, The discovery of Novel Structurally Diverse PK-C Agonists through Computer 3D-database pharmacophore search. Molecular modeling studies. J. Med. Chem. in press ( Dec. 1994 or Jan. 1995). Sheridan, et al. Searching for pharmacophore in large coordinate data base and its use in drug design, PNAS, 1989, 86, 8165-8169. -Shaomeng Wang Computational Chemist National Cancer Institute National Institutes of Health, Bethesda, MD 20892 (301)402-3111 shaomeng@helix.nih.gov ##################################################### 9) From: MARTIN%cmda@randb.abbott.com (1) Bures, M. G.; Martin, Y. C.; Willett, P. "Searching Techniques for Databases of Three-Dimensional Chemical Structures," In Topics In Stereochemistry; (Vol.21 of ; E. L. E. a. S. H. Wilen, Ed.; Wiley: New York, 1994; pp 467-511. (2) Martin, Y. C.; Bures, M. G.; Willett, P. ""Searching Databases of Three-Dimensional Structures," In Reviews in Computational Chemistry; (Vol.1 of ; K. B. Lipkowitz and D. B. Boyd, Ed.; VCH Publishers: New York, 1990; pp 213-263. (3) Martin, Y. C., "3D Database Searching in Drug Design," J. Med. Chem. 1992, 35, 2145-2154. Also (1) Kuntz, I. D., "Structure-based Strategies for Drug Design and Discovery," Science 1992, 257, 1078-1082. Yvonne Martin Abbott Laboratories ##################################################### 10) From: cgp@ussu.Ciba.Com (Greg Paris) Bures, M. G., Hutchins, C. W., Maus, M., Kohlbrenner, W., Kadam, S., and Erickson, J. W. (1990, published 1992). Using Three-Dimensional Substructure Searching to Identify Novel, Non-Peptidic Inhibitors of HIV-1 Protease. Tetrahedron Comput. Methodol. 3 (6C), 673-680. Christie, B. D., Henry, D. R., Guner, O. F., and Moock, T. E. (1990a). MACCS-3D: a tool for three-dimensional drug design. In "Proceedings of the 14th International Online Information Meeting" (D. Raitt, ed.), pp. 137-161, Learned Information, Oxford. DesJarlais, R. L., Sheridan, R. P., Seibel, G. L., Dixon, J. S., Kuntz, I. D., and Venkataraghavan, R. (1988). Using Shape Complementarity as an Initial Screen in Designing Ligands for a Receptor Binding Site of Known Three-Dimensional Structure. J. Med. Chem. 31, 722-729. DesJarlais, R. L., Seibel, G. L., Kuntz, I. D., Furth, P. S., Alvarez, J. C., Ortiz de Montellano, P. R., DeCamp, D. L., Babe, L. M., and Craik, C. S. (1990). Structure-based design of non-peptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc. Natl. Acad. Sci. USA 87, 6644-6648. Gonnella, N. C., Bohacek, B., Zhang, X., Kolossvary, I., Paris, C. G., Melton, R., Winter, C., Hu, S.-I., and Ganu V. (in press) Bioactive conformation of stromelysin inhibitors determined by transferred nuclear overhauser effects. Proc. Natl. Acad. Sci. USA Greene, J., Kahn, S., Savoj, H., Sprague, P., and Teig, S. (1994). Chemical function queries for 3D database search. J. Chem. Inf. Comput. Sci. 34, 1297-1308. Lam, P. Y. S., Jadhav, P. K., Eyermann, C. J., Hodge, C. N., Ru, Y., Bacheler, L. T., Meek, J. L., Otto, M. J., Rayner, M. M., Wong, Y. N., Chang, C.-H., Weber, P. C., Jackson, D. A., Sharpe, T. R., and Erickson-Viitanen, S. (1994). Science 263, 380-384. Martin, Y. C. (1992). 3D Database Searching in Drug Design. J. Med. Chem. 35, 2145-2154. Martin, Y. C., Bures, M. G., and Willett, P. (1990). Searching Databases of Three-Dimensional Structures. In "Reviews in Computational Chemistry" (K. B. Lipkowitz, and D. B. Boyd, eds.), pp. 213-263, VCH, New York, Weinheim and Cambridge. Sheridan, R. P., Rusinko III, A., Nilakantan, R., and Venkataraghavan, R. (1989). Searching for pharmacophores in large coordinate data bases and its use in drug design. Proc. Natl. Acad. Sci. USA 86, 8165-8169. Van Drie, J. H., Weininger, D., and Martin, Y. C. (1989). ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. J. Comput.-Aided Mol. Des. 3, 225-251. Willett, P. (1991). "Three-Dimensional Chemical Structure Handling" (chapter 6). Research Studies Press Ltd., Taunton, Somerset, England and John Wiley & Sons, Inc., New York. Greg Paris Ciba-Geigy Pharmaceuticals, Research Dept. Internet: cgp@ussu.ciba.com Biophysical Chemistry, CAMM, Bldg. SIC-235 Voice: 908 277 5421 556 Morris Ave, Summit, NJ 07901 USA Fax: 908 277 4876 ##################################################### ###### End of Summary ################################### From steve@carbo.cc.binghamton.edu Wed Nov 30 18:16:12 1994 Received: from carbo.cc.binghamton.edu for steve@carbo.cc.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id RAA05985; Wed, 30 Nov 1994 17:18:46 -0500 Received: by carbo.cc.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA17657; Wed, 30 Nov 94 16:59:40 -0500 Date: Wed, 30 Nov 1994 16:49:59 -0500 (EST) From: Steven Schafer Subject: Q:GAMESS MOs To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have been doing some geometry optimizations on transistion metal carbonyl complexes. When the MOs are printed out, the energies do not always increase with each MO. This is the case however for my other work on di-Methyl-ether. One of these systems is Mn(CO)5 using ROHF and C4v symmetry. Are these valid MOs that are just not outputted in order, or is there another problem? Thanks in advance, Steven Schafer S.U.N.Y. Binghamton Chemistry Department From b_duke@lacebark.ntu.edu.au Wed Nov 30 19:16:24 1994 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.9/930601.1506) id SAA07312; Wed, 30 Nov 1994 18:37:25 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA10121; Thu, 1 Dec 1994 08:01:51 +1000 Message-Id: <9411302201.AA10121@lacebark.ntu.edu.au> Subject: Weighing the captain. To: CHEMISTRY@ccl.net (chemistry) Date: Thu, 1 Dec 1994 08:01:46 +1000 (EET) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 736 The reference to weighing the Captain of a ship is by Charles Coulson in "Valence" 1st Ed, 1952, footnote on page 88:- "It has laughingly been said that calculating the dissociation energy of a heavy molecule is like weighing the the captain of a ship by determining the difference in displacement of his ship when he is, or is not, on board!". This raises the question "laughingly said by whom?". Does anybody know? BTW, by a heavy molecule he meant H2! Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University, Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From yinona@niva.tau.ac.il Wed Nov 30 19:50:59 1994 Received: from niva.tau.ac.il for yinona@niva.tau.ac.il by www.ccl.net (8.6.9/930601.1506) id TAA08619; Wed, 30 Nov 1994 19:50:59 -0500 Date: Thu, 1 Dec 1994 00:04:24 +0200 (IST) From: yinon ashkenasy Subject: XYZ CO. of dna bases To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters I need coordinates for very few bases of DNA bonded together. It doesn't matter to me what is the medium there in or how accurate the coordinates are. I searched through databases like pdb but they have only large structures, while I need VERY simple one. I want only few bases bonded together (even one is good enough!!!) preferably single stranded. even the coordinates of adenine, thymine etc. alone will be helpful. I would deeply appreciate any help cheers yinon :-) p.s. I would gladly accept any kind of co. (amber, pdb, xyz..) yinon ashkenazy dept. of phys. TEL-AVIV U. From d3e102@ames.pnl.gov Wed Nov 30 20:16:12 1994 Received: from pnlg.pnl.gov for d3e102@ames.pnl.gov by www.ccl.net (8.6.9/930601.1506) id TAA08734; Wed, 30 Nov 1994 19:57:27 -0500 Received: from ames.pnl.gov by pnlg.pnl.gov (PMDF V4.2-15 #6012) id <01HK3IYHRXGG8WY1WB@pnlg.pnl.gov>; Wed, 30 Nov 1994 16:57:13 PST Received: by ames.pnl.gov (931110.SGI/890607.SGI) id AA15504; Wed, 30 Nov 94 16:57:06 -0800 Date: Wed, 30 Nov 1994 16:57:06 -0800 From: d3e102@ames.pnl.gov (Dave Feller) Subject: Ab Initio Benchmarks To: CHEMISTRY@ccl.net Message-id: <9412010057.AA15504@ames.pnl.gov> Content-transfer-encoding: 7BIT Occassionally people post inquiries on the Comp. Chem. List about benchmarks of various ab initio packages. Since version 2.0 of the EMSL Ab Initio Benchmarks Report is currently being cleared for publication, this seemed like a good time to announce its impending availability. In July of 1993 we released version 1.0 in both hardcopy and anonymous ftp forms suitable for downloading. The new version will probably be available near the end of December (in electronic form) or sometime in January (for printed copies). Since we rapidly ran out of the 300 copies of version 1.0 that we had printed and this year's edition is considerable larger, we intend to make this new release available through Mosaic (under the EMSL home page at URL http://www.emsl.pnl.gov:2080/) as well as have a limited number of hardcopies. This year's edition will include an initial sample of parallel benchmarks run by Dr. Rick Kendall and Matt Brightman of PNL and Dr. Martin Feyereisen of Cray Research. The report contains information on the following methods, packages and machines. Method Method ---------------------------------------------- 1. Conventional RHF 12. MP4(SDTQ) 2. Direct RHF 13. SDCI 3. Analytical RHF Gradient 14. CCSD 4. Analytical RHF Hessian 15. CCSD(T) 5. Conventional UHF 16. QCISD 6. Conventional MP2 17. QCISD(T) 7. Direct MP2 18. CASSCF 8. Analytical MP2 Gradient 19. CAS-CI 9. Analytical MP2 Hessian 10. DFT/SVWN (LSD) 11. DFT/BLYP (NLSD) Codes ---------------------------------- 1. Gaussian 90 2. Gaussian 92 and G92/DFT 3. MOLPRO 92.3 and 94.3 4. DISCO 1.82 5. GAMESS(US) 6/17/92 and 7/17/93 6. HONDO 8.3 and 8.4 7. GAMESS(UK) 8. ACES II 9. SPARTAN 3.0 10.SUPERMOLECULE 1.08 Machine Machine ------------------------------------------------------------------------ 1. Intel 486 DX2 (50 MHz) 16. DEC AXP model 300 (150 MHz) 2. Intel 486 DX2 (66 MHz) 17. DEC AXP model 600 (175 MHz) 3. Sun SPARCstation 2 (40 MHz) 18. DEC AXP model 800 (200 MHz) 4. Sun SPARCstation 10/41 (40 MHz) 19. DEC AXP model 900 (300 MHz) 5. IBM PowerPC 250 (66 MHz) 20. SGI Indigo (50/100 MHz R4000) 6. IBM RS/6000 340 (33 MHz) 21. SGI Onyx (50/100 MHz R4400) 7. IBM RS/6000 370 (63 MHz) 22. SGI Indigo (75/150 MHz R4400) 8. IBM RS/6000 550 (42 MHz) 23. SGI PowerChallenge (75 MHz R8000) 9. IBM RS/6000 580 (63 MHz) 24. Fujitsu VPX240/10 (300 MHz) 10.IBM RS/6000 590 (66 MHz) 25. HP 9000 model 730 (66 MHz) 11.KSR2 (80 processors) 26. HP 9000 model 735 (99 MHz) 12.Cray YMP 27. HP 9000 model 735/125 (125 MHz) 13.Cray YMP EL 28. Intel Paragon (512 processors) 14.Cray C90 15.Cray T3D (1000 processors) We are always looking for external contributions if people wish to see other machines or platforms than the ones listed. Input files for a variety of applications are available to hopefully make the benchmarking easier. Constructive criticism is always welcomed. David Feller David Feller Molecular Science Research Center Battelle Pacific Northwest Labs Mail Stop K1-96 Battelle Blvd Richland, WA 99352