From JeanLuc.Verschelde@rug.ac.be Wed Sep 7 03:44:27 1994 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id CAA04106; Wed, 7 Sep 1994 02:46:28 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA00189 (5.67b/IDA-1.5 for ); Wed, 7 Sep 1994 08:45:44 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA24559; Wed, 7 Sep 94 08:42:21 +0200 Date: Wed, 7 Sep 1994 08:42:20 +0200 (MET DST) From: Jean-Luc Verschelde Subject: pdb on cdrom To: OHIO SUPER Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 682 Hi all, Can someone tell me where I can buy the pdb-files on cdrom. I already tried pdb@bnl.bitnet but without result. Thanks. jean-luc =================================================================================== Verschelde Jean-Luc University of Ghent Lab. for Mathematical Physics | Lab. for Biochemistry | Krijgslaan 286 S9 | K.L. Ledeganckstraat 35 9000 Ghent | 9000 Ghent Belgium. | Belgium. Tel.:09/264 47 94 Fax:09/264 49 89 Email:Jeanluc.Verschelde@rug.ac.be =================================================================================== From CHMORA@LSUVAX.SNCC.LSU.EDU Wed Sep 7 05:44:26 1994 Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by www.ccl.net (8.6.9/930601.1506) id FAA04890; Wed, 7 Sep 1994 05:03:01 -0400 Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426) id <01HGTFHZXY688X03IA@LSUVAX.SNCC.LSU.EDU>; Wed, 7 Sep 1994 04:05:13 CST Date: Wed, 07 Sep 1994 04:05:13 -0600 (CST) From: CHMORA@LSUVAX.SNCC.LSU.EDU Subject: Summary about MOPAC. To: chemistry@ccl.net Message-id: <01HGTFHZY7TE8X03IA@LSUVAX.SNCC.LSU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters: Last week I asked if there was anything in the literature about how to use MOPAC's keywords, how to find Transition States, etc. According to the replies I received there 4 major sources of information about how to use MOPAC: 1) Mopac's manual. 2) "Handbook of Computational Chemistry" by Tim Clark, Wiley and Sons, N.Y., 1985, pp. 152-188 3) "MOPAC: A Semiempirical Molecular Orbital Program" by James J. P. Stewart, Journal of Computer-Aided Molecular Design, Vol. 4, pp. 1-105 (1990) 4) "Semiempirical Molecular Orbital Methods" by James J. P. Stewar, Reviews in Computational Chemistry Vol. 1 (Boyd and Lipkowitz) In addition to these references, I did some literature search myself and I found 6 publications contain general information on semiempirical calculations. 1) Deward, M.J.S.; Healy, E.F.; Stewart, J.J.P. "Location of Transition States in Reaction Mechanisms" J. Chem. Soc., Faraday Trans. 2, 1984, 80, pp. 227-233 2) Gundertofte, K.; Palm, J.; Petterson, I.; Stamvik, A. "A Comparison of Conformational Energies Calculated by Molecular Mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and Semiempirical (AM1 and PM3) Methods" J. Computational Chemistry 1991, 12, pp. 200-208 3) Rios, M.A.; Rodriguez, J. "Semiempirical Study of Compounds with O-H--O Intramole- cular Hydrogen Bond" J. Computational Chemistry 1992, 7, pp.860-866 4) Orti, J.; Branchadell, V.; Ortun~o, R.M.; Oliva, A.; Font, J.; Bertran, J. "Theoretical study of the regioselectivity in the Diels-Alder reactions of protoanemnin with substituted dienes" J. Molecular Structure (Theochem) 1993, 284, pp. 37-41 5) Jurema, M.W.; Shields, G.C. "Ability of the PM3 Quantum-Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules" J. Computational Chemistry 1993, 14, pp. 89-104 6) Rzepa, H.S.; Yi, M.Y. "An AM1 and PM3 Molecular Orbital and Self-consisted Reaction-field Study of the Aqueous Solvation of Glycine, Alanine and Proline in their Neutral and Zwitterionic Forms" J. CHem. Soc. Perkin Trans. 2 1991, pp.531-537 These references cover different topics that many of you are interested in. I've read a lot of messages requesting infor- mation about hydrogen bonding, if this calculation is better compare to this other, etc. I truly hope that all this information that I am providing here will be useful for you. Thanks to all of you that e-mailed me answering my questions. Sincerely, Guillermo A. Morales Department of Chemistry Louisiana State University Baton Rouge, LA. 70803-1804 Phone: (voice) 504/388-2706 (fax) 504/388-3458 E-mail: chmora@sn01.sncc.lsu.edu From czarek@sun1.chem.univ.gda.pl Wed Sep 7 06:44:28 1994 Received: from chemik.chem.univ.gda.pl for czarek@sun1.chem.univ.gda.pl by www.ccl.net (8.6.9/930601.1506) id GAA05542; Wed, 7 Sep 1994 06:14:31 -0400 Received: from sun1.chem.univ.gda.pl by chemik.chem.univ.gda.pl with SMTP (1.37.109.4/16.2) id AA12378; Wed, 7 Sep 94 12:12:58 +0100 Date: Wed, 7 Sep 94 12:10:05 +0200 From: czarek@sun1.chem.univ.gda.pl (Cezary Czaplewski) Received: from sun2.univ.gda.pl (sun2.ARPA) by sun1.chem.univ.gda.pl (4.1/1.2-Univ. of Gdansk Chemistry) id AA05434; Wed, 7 Sep 94 12:10:05 +0200 Message-Id: <9409071010.AA05434@sun1.chem.univ.gda.pl > To: chemistry@ccl.net Subject: benchmarks CCL:REQUEST FOR INFO ABOUT MAC POWER PC I send a information about benchmarks - anybody can calculate how many Mflops does his PC or workstation himself. ------- ########################################################################## LATEST RESULTS AS OF 26 Jun 1994: ########################################################################## This directory contains a collection of the source code and the results of a number of public benchmarks (in 'c'). It is maintained by Al Aburto of the Naval Command, Control and Ocean Surveillance Center (NCCOSC) RDT&E Division (NRaD) in San Diego, CA. If you have contributions (program results or programs) or any comments please send them to aburto@marlin.nosc.mil. All 'c' programs and tables of results ('.tbl') are available via anonymous ftp to 'ftp.nosc.mil' in directory 'pub/aburto'. The IP address for ftp.nosc.mil is: 128.49.192.51 PLEASE NOTE: The file 'bench.tar.gz' is a gzip compressed tar file of all programs and results. This is the only BINARY file. All other files are ASCII. To get bench.tar.gz be sure to set ftp to BINARY mode. A brief description of the test programs available follows: (1) sim An integer program that compares DNA segments for similarity. Source: sim.shar Result: sim.tbl (2) fhourstones An integer program to find solutions to the 'connect-4' game. Source: c4.shar Result: c4.tbl (3) dhrystone A synthetic integer program which provides a MIPS rating based upon a 'typical' instruction mix. Very sensitive to optimization and results will appear erratic unless degree of optimization is carefully tracked. Source: dhry.shar Result: dhry.tbl (4) nsieve An integer program which generates prime numbers based on the Sieve of Eratosthenes using array sizes from 8 KBytes to 2 MBytes. A nsieve MIPS rating is provided but the nsieve instruction mix is NOT 'typical'. Nsieve can reveal the 'knees' in performance relative to memory and cache size as illustrated below (item 14). Source: nsieve.c Result: nsieve.tbl (5) heapsort An integer program which uses the 'heap sort' method of sorting a random array of long integers up to 2 MBytes in size. A heapsort MIPS rating is provided but it is NOT representative of a 'typical' instruction mix. Source: heapsort.c Result: heapsort.tbl (6) hanoi An integer program which solves the Towers of Hanoi puzzle using recursive function calls. Source: hanoi.c Result: hanoi.tbl (7) flops Estimates MFLOPS rating for specific FADD, FSUB, FMUL, and FDIV instruction mixes. Four distinct MFLOPS ratings are provided based on the FDIV weightings from 25% to 0% and using register-register operations. Works with both scalar and vector machines. Since the program trys to maximize register usage the results are NOT sensitive to main memory speed. In this sense flops yields a peak rating. Source: flops20.c Result: flops_1.tbl, flops_2.tbl, flops_3.tbl, flops_4.tbl (8) clinpack This is the Linpack program (floating-point) converted to c. Results here are sensitive to cache effects and memory speed. Source: clinpack.c Result: clinpack.dpr, clinpack.dpu, clinpack.spr, clinpack.spu (9) tfftdp This program performs FFT's using the Duhamel-Hollman method for FFT's from 32 to 262,144 points in size. Source: tfftdp.c Result: tfftdp.tbl (10) matrix multiply (mm) This program (mm.c) contains 9 different algorithms for doing matrix multiplication (500 X 500 standard size). Results illustrate the enormous effects of cache thrashing versus algorithm, machine, compiler, and compiler options. Source: mm.c Result: mm_1.tbl, mm_2.tbl (11) SPEC results SPEC results from vendor Performance Briefs and results collected off the network are also available. Result: specin89.tbl, specfp89.tbl, specin92.tbl, specfp92.tbl speccorr.tbl (12) Timer programs Timer routines in 'c' are also available. Source: timers_a.c, timers_b.c (13) FAQ's Some helpful FAQ files are also available: FAQ: spec.faq, nistlib.faq, briefs.faq (14) Nsieve example results: ----------------------------------------------------------------------- Sieve of Eratosthenes (Scaled to 10 Iterations) Version 1.2b, 26 Sep 1992 R4400 100 MHz, 16 KByte I/D internal caches, 1 MByte external cache cc -DUNIX -mips2 -sopt-so=4 -O3 -non_shared nsieve.c -o nsieve Array Size Number Last Prime Linear RunTime MIPS caches (Bytes) of Primes Time(sec) (Sec) 8191 1899 16381 0.022 0.022 76.2 10000 2261 19997 0.027 0.026 76.8___ 16KB 20000 4202 39989 0.053 0.060 69.0 40000 7836 79999 0.106 0.152 55.0 80000 14683 160001 0.213 0.326 51.7 160000 27607 319993 0.425 0.680 50.2 320000 52073 639997 0.850 1.432 48.1 640000 98609 1279997 1.700 3.451 40.3___ 1 MB 1280000 187133 2559989 3.401 11.772 23.9 2560000 356243 5119997 6.801 44.810 12.6 ----------------------------------------------------------------------- R4000PC 100 MHz CPU, 8 KByte I/D internal caches, NO external cache cc -DUNIX -mips2 -sopt-so=4 -O3 -non_shared nsieve.c -o nsieve Array Size Number Last Prime Linear RunTime MIPS (Bytes) of Primes Time(sec) (Sec) 8191 1899 16381 0.023 0.023 72.1___ 8 KB 10000 2261 19997 0.028 0.047 43.6 20000 4202 39989 0.056 0.184 22.4 40000 7836 79999 0.112 0.435 19.1 80000 14683 160001 0.225 0.944 17.9 160000 27607 319993 0.449 1.984 17.2 320000 52073 639997 0.899 4.133 16.7 640000 98609 1279997 1.797 8.733 15.9 1280000 187133 2559989 3.594 18.228 15.4 2560000 356243 5119997 7.188 38.085 14.9 Al Aburto aburto@marlin.nosc.mil ------- From rull@RUUCI19.chem.ruu.nl Wed Sep 7 09:44:30 1994 Received: from ruucv1.chem.ruu.nl for rull@RUUCI19.chem.ruu.nl by www.ccl.net (8.6.9/930601.1506) id JAA07339; Wed, 7 Sep 1994 09:24:28 -0400 Received: from ruuci19.chem.ruu.nl by ruucv1.chem.ruu.nl (5.65b/4.13) with SMTP id AA07812; Wed, 7 Sep 94 15:24:26 +0200 Received: by RUUCI19 (931110.SGI/930416.SGI.AUTO) for @RUUCV1.chem.ruu.nl:CHEMISTRY@ccl.net id AA17163; Wed, 7 Sep 94 15:22:52 +0100 From: rull@RUUCI19.chem.ruu.nl (Ton Rullmann) Message-Id: <9409071422.AA17163@RUUCI19> Subject: CCL:pdb on cdrom To: CHEMISTRY@ccl.net Date: Wed, 7 Sep 1994 15:22:49 +0100 (WDT) Reply-To: rull@ruuci9.chem.ruu.nl X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 608 Jean-Luc Verschelde writes: > > Can someone tell me where I can buy the pdb-files > on cdrom. > I already tried pdb@bnl.bitnet but without result. > The newsletter of the PDB gives information. See: http://www.pdb.bnl.gov/newsletter.txt. Several e-mail and postal addresses are given at the end. -- | Ton Rullmann NMR Spectroscopy | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533641 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | 3584 CH Utrecht, The Netherlands | Email: rull@nmr.chem.ruu.nl | From setlik@acsu.buffalo.edu Wed Sep 7 12:44:31 1994 Received: from lictor.acsu.buffalo.edu for setlik@acsu.buffalo.edu by www.ccl.net (8.6.9/930601.1506) id LAA10560; Wed, 7 Sep 1994 11:45:50 -0400 Received: (setlik@localhost) by lictor.acsu.buffalo.edu (8.6.8/8.6.4) id LAA22526 for CHEMISTRY@ccl.net; Wed, 7 Sep 1994 11:45:23 -0400 Date: Wed, 7 Sep 1994 11:45:23 -0400 From: "Robert F. Setlik" Message-Id: <199409071545.LAA22526@lictor.acsu.buffalo.edu> To: CHEMISTRY@ccl.net Subject: DISCOVER with AMBER params. Content-Length: 690 Hi netters, Recently, there have been a few papers which describe work using DISCOVER with AMBER parameters for energy minimization and MD: MD: Fritsch and Wolf, J. Biomol. Str. Dyn., 11(6), 1161-1174 (1994) EM/structural refinement: Chou et al., J. Mol. Biol., 241, 467-479 (1994). Both of these papers deal with nucleic acid structural biology. I am curious as to whether any tests have been done to show that if you use AMBER parameters on DISCOVER, you indeed get answers that are the same as if you had used the actual AMBER programs. Any references would be helpful. Cheers, Rob Setlik Biophysics Dept. Roswell Park Cancer Inst. Elm and Carlton Streets Buffalo, N.Y. 14263 From jsb2@camsci.com Wed Sep 7 22:44:45 1994 Received: from camsci.com for jsb2@camsci.com by www.ccl.net (8.6.9/930601.1506) id WAA18576; Wed, 7 Sep 1994 22:06:24 -0400 From: Date: Wed, 7 Sep 94 22:05:58 EDT Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA06040; Wed, 7 Sep 94 22:05:58 EDT Message-Id: <9409080205.AA06040@camsci.com> To: CHEMCORD@UMDD.UMD.EDU, CHEMIC-L@VM.TAU.AC.IL, anchodd@cc.utas.edu.au, aschin-list@nuscc.nus.sg, chemed-l@UWF.CC.UWF.EDU, chemind-l@derwent.co.uk, chemistry@ccl.net, chemistrytm@dhvx20.csudh.edu Subject: Desktop Chemists' WWW Server Cc: ICS-L@UMDD.UMD.EDU, INFOCHIM@ICINECA.CINECA.IT, MICROSCALE-L@merrimack.edu, ORGANOMET@MAILSERV.ZDV.UNI-TUEBINGEN.DE, chminf-l@IUBVM.UCS.INDIANA.EDU, cmts-l@cornell.edu, org-geochem@uk.ac.mailbase, polyed-l@bgu.edu Cambridge Scientific Computing, Inc., is pleased to announce our new WWW server, located at http://www.camsci.com. From this site we will be able to better support the current and potential users of CS ChemOffice, including CS ChemDraw, CS Chem3D and CS ChemFinder. We also have press releases and information about the other services we provide. Shortly we will provide tech notes, selections from our CS Catalyst newsletter, and lots of other good stuff. You want something you don't see? We'll take requests, too. Because we are dedicated to providing the best information available the desktop chemist worldwide, we have tried to include links to other resources as we've found them across the Web. The one thing that really struck us was how little information there is on WWW about desktop chemistry software. This is unfortunate. Accordingly, we would like to offer space on our WWW server to anyone who wants to provide information about software that would be useful to chemists. If finding a server is stopping people from providing information, we want to help. Please contact us (info@camsci.com) for details, because there are a few limits to our generosity (no multi-megabyte mpegs allowed, sorry!). Let's hear what you think! Jonathan Brecher Cambridge Scientific Computing, Inc. jsb@camsci.com