From chemistry-request@ccl.net Mon Jun 1 04:07:38 1992 Date: 31 May 1992 22:52 -0400 (EDT) From: "DR. LAWRENCE R. SCHMITZ" Subject: Dollar Value of Y-MP time To: chemistry@ccl.net Status: RO I recently received a grant of Cray Y-MP and need to supply an approximate dollar value for publicity and other bean counting activities. I have some interest in the lowest and highest prices people pay, but am most interested in reasonable commercial rates for Y-MP time. The amount of time in the grant is measured in service units, where a service unit is meant to represent about an hour of Y-MP processor time. A service unit is defined as: SU = cpu * .75 + mem * .375 + 0.05 * connect + 0.0004 * diskspace where: cpu = system and user cpu time in hours mem = memory * cpu time in megaword hours connect = hours of interactive connect time diskspace = the sum over a month of the megaword hours of temporary files on Cray disks accumulated from snapshots of space used The people at the Pittsburgh supercomputer center said that they do not sell Cray time, but commercial rates are roughly $750/SU. Is this reasonable? What's a fair rate for Y-MP time? Larry Schmitz CHM001@MARSHALL.WVNET.EDU From chemistry-request@ccl.net Mon Jun 1 10:36:54 1992 Date: 01 Jun 92 14:33:32+0100 From: Yves chapron Subject: Re: Dollar Value of Y-MP time To: CHM001@muvms3.mu.wvnet.EDU, chemistry@ccl.net Status: R for Cray II $750/hour cpu is roughtly the price for day time but it is much cheeper at the night time and still much ceeper in the weekend time. It depend on the policy of your computing center. Yves Chapron, Grenoble France. From chemistry-request@ccl.net Mon Jun 1 12:53:02 1992 Date: Mon, 1 Jun 92 10:02:15 EDT From: rs0thp@wiz.br.rohmhaas.COM Subject: Computers and CHemistry Symposia, ACS Aug 24-28th To: chemistry@ccl.net Status: R Dear Folks, This is the Computers and Chemistry tentative schedule for the ACS meeting in Washington D.C. Thank You for your participation and I hope to see you'all there! Tom Pierce - Program Chair COMP division - 1992 American Chemical Society Washington D.C. meeting August 24-28, 1992 Computers and Chemistry Division Symposia Symposia Overview Computer Networks and Chemistry - Monday Morning Structure Searching - Monday Afternoon Poster - SCI-MIX Monday Night (Aug. 24th) Rapid Methods of Computational Chemistry - Tuesday Aug. 25th. Molecular Mechanics Force Fields - Wednesday 26th General Computational Chemistry Presentations - Thursday 26th. Symposia Titles and times Symposia - Computer Networks and Chemistry - Monday Session Chair: Dr. Dennis Gerson, IBM Comp.,1503 LBJ Freeway, Dallas, TX 75234-6032, (214)-406-7452 gerson%dfwvm04@vnet.ibm.com Monday Morning 9:00 - 1 Networking 101: Basic Tutorial in Networking and Communications, S. Gaines, IBM Communications Products Division, Research Triangle Park, Raleigh, North Carolina. 9:45 - 2 High Performance National Networks, J. Becker, Advanced Network and Services Inc, 100 Clearbrook Road, Elmsford, NY 1052 10:15 - 3 CLUSTER COMPUTING AND NETWORK COMPUTING: THE SUCCESSES AND THE PITFALLS D.Gerson, J.Tesch, IBM National Engineering/Scientific Support Center, Dallas TX 75234 USA 10:45 - 4 DISTRIBUTED COMPUTING OF CHEMICAL STRUCTURE INFORMATION, K. P. Cross, T. R. Couvreur, L. H. Wibberley, Chemical Abstracts Service, P. O. Box 3012, Columbus, OH 4321O. 11:15 - 5 WORKGROUP COMPUTING IN IBM: CONFERENCING AND TOOLS DEVELOPMENT, S. K. Boyer, D.Silverman, T. Haine and A. Miller, IBM European Center for Chemical Computing and IBM Almaden Research Center. Structure Searching - Monday Afternoon Session Chair Dr. G.W. Milne, Building 37, Room 5C28,NIH, Bethesda, MD 20892 301- 402-3115 1:30-- 6 Substructural Searching Methods: Old and New, J. M. Barnard, Barnard Chemical Information Ltd. ,46 Uppergate Road, Stannington, Sheffield S6 6BX, UK 2:00-7 SUBSTRUCTURE SEARCHING A DATABASE OF "RIGID" 3D STRUCTURES. W. Fisanick, K. P. Cross, A. Rusinko III, Chemical Abstracts Service, P. O. Bo.: 3012, Columbus, OH 43210. 2:30 - 8 A MEMORY-BASED STRUCTURE SEARCH SYSTEM PROTOTYPE. D. H. Lillie and A. Rusinko III, Chemical Abstracts Service, Research Department, Columbus OH 43210. 3:00 - 9 HOW CAN PARALLEL ALGORITHMS HELP TO FIND NEW SEQUENTIAL ALGORITHMS, Z. M. Nagy, BUDAPEST, TOROKVESZ 143/A. 3:30 - 10 SUBSTRUCTURE SEARCH ON VERY LARGE FILES BY USING MULTIPLE STORAGE TECHNIQUES, Dr. A. Bartmann, Dr. H. Maier, Dr. B. Roth, D. Walkowiak, Softron GmbH, Rudolf-Diesel-Str. 1,D-8032 Grafelfng 4:00 - 11 Substructure Search Of Diverse Chemical Structures and Data., J.G.Norse, B.D. Christie, B.A. Leland, T.Wilson, W.D. Hounshell, A.J. Gushurst, T.E. Moock, D.R. Henry, A.Ozkabak, D.H. Smith., Molecular Design Ltd., San Leandro, CA. Poster - SCI-MIX Monday Night (Aug. 24th) Session Chairman : Dr. Thomas Pierce, Rohm and Haas, PO Box 219, Bristol, PA 19007 (215)-785-8989 12 APPLICATION OF THE HAUSDORFF DISTANCE FOR A MEASURE OF MOLECULAR CHIRALITY AND MOLECULAR SIMILARITY. Andrzej B. Buda and Kurt Mislow, Department of Chemistry, Princeton University, Princeton, NJ 08544 13 Use of Computational Chemistry for Teaching Secondary Chemistry, Bob Gotwals , Blair Magnet Program , 313 Wayne Avenue, Silver Spring, MD 20910 (301) 650-6688/6690 14 tubular Graphitic Carbon Structures. Y.-D. Gao and W. C. Herndon, Department of Chemistry, University of Texas at El Paso, TX 79968, USA 15 Selective Cyclodimerization of Acetylene and Related Molecules : A Computational Approach K. Jayasuriya, R. Damavarapu and N. Slagg,U. S. ARDEC, Bldg. 3O28, Picatinny Arsenal, NJ 078O6-5000 16 CALCULATION OF ASSOCIATION FREE ENERGIES OF SULFONA-MIDE/13-CYCLODEXTRIN COMPLEXES. G. King and R. A. Barford, USDA, ARS, Eastern Regional Center. 6OO East Mermaid Lane, Philadelphia, PA 19118. 17 COMPUTER REPRESENTATION OF TAUTOMERS: A GRAPH-THEORETICAL NORMALIZATION ALGORITHM. A. H. Lipkus, Chemical Abstracts Service, P. O. Box 3012, Columbus, OH 43210. 18 THEORETICAL DESCRIPTORS FOR THE POTENCY OF SUBSTITUTED COCAINES, A. H. Lowre Laboratory for the Structure of Matter Naval Research Laboratory Washington DC 2O37S George R. Famini Chemometrics Branch US Army CRDEC Aberdeen Proving Ground MD 21OlO 19 SEMI-EMPIRICAL MOLECULAR ORBITAL CALCULATION OF THE BILIRUBIN DIANION. W. L. Shelver, H. Rosenberg, W. H. Shelver, Department Pharmaceutical Sciences, North Dakota State University, Fargo, ND S81OS 20 HYDROGEN BONDING IN GELLMAN'S AMIDES. CAN MM3 AND AM1 FREE ENERGY CALCULATIONS RESOLVE THE DICHOTOMY BETWEEN MODELING AND EXPERIMENT? D. A. Smith and S. Vijayakumar, Department of Chemistry, The University of Toledo, Toledo, OH 43606-3390 21 MICROSCOPIC MODELING OF LIGAND DIFFUSION THROUGH A PROTEIN: CARBON MONOXIDE IN LEGHEMOGLOBIN. G. Verkhivker and R. Elber Department of Chemistry M/C 111, University of Illinois at Chicago, Chicago, Il-linois 60680. 22 EXPERIMENTAL DESIGN IN THE PROCESS DEVELOPMENT OF MUSCARINIC AGONIST CI-979, R. A. Wade, P. Giri, T. M. Zennie. Parke-Davis Chemical Development, Warner-Lambert Co., 188 Howard Ave., Holland, MI 49424 Rapid Methods of Computational Chemistry Tuesday Aug. 25th. Session Chairman: Dr. Allen Richon , P.O. Box 32101, St. Louis. MO 63132 Tel: (314) 567-3927 8:3O - 23 A MOLECULAR INFORMATION SERVER. K. M. Smith, J.-L. Escobar, and R. S. Pearlman, College of Pharmacy, University of Texas, Austin, TX 78712. 9:15 - 24 CONSTRAINED SEARCH OF CONFORMATIONAL HYPERSPACE: SEGMENTATION AND PARALLELISM, R. A. Dammkoehler, Center for Molecular Design and Department of Computer Science, Washington University, St. Louis, Missouri 6313O. 9:45- lO:OO Break l0:00- 25 APPLICATION OF INNOVATIVE MULTIBODY METHODS To MOLECULAR DYNAMICS. J. Turner, H. C., Moldyn, Inc., 1O33 Mass Ave. Cambridge, MA O2138, S. Gallion, P. Weiner, Amber Systems, Inc., 28 Tower St. Somerville, MA O2143, J. Nicholas, Battelle Pacific Northwest Labs., Richmond, WA 99352, Chandra Singh, Scripps Research Clinic, LaJolla, CA 92121 10:30 26 A FAST NEW APPROACH TO PHARMACOPHORE MAPPING, M. Bures, J. DeLazzer, Y. Martin, Abbott Laboratories, Pharmaceutical Prod. Div.,One Abbott Park Road, Abbott Park, IL 60064-3500. 11:OO - 27 LATTICE CONFORMATIONAL ENUMERATION APPROACHES TO PROTEIN FOLDING. H. S. Chan and K. A. Dill, Department of Pharmaceutical Chemistry, University of California at San Francisco, CA 94143-1204. Rapid Methods of Computational Chemistry Tuesday Aug. 25th. Session Chairman: Dr. Allen Richon , P.O. Box 32101, St. Louis. MO 63132 Tel: (314) 567-3927 2:0O - 28 APPLICATION OF MOST RESTRICTED PATH THEORY TO 4D DATABASE STRATEGY AND OTHER MODELLING PROBLEMS, J. Bradshaw and E. Maliski, Computational Chemistry Group, Glaxo Group Research, Ware, Hertfordshire, UK and Research Computing, Glaxo Research Institute, Research Triangle Park, NC 277O9 2:3O- 29 INTERPRETING PEPTIDE ACTIVITY DATA AND OPTIMIZING EXPERIMENTAL DESIGN USING QSAR., W. E. Reiher, Tripos Associates, 1699 S. Hanley Road, Suite 3O3, St. Louis, MO 63144. 3:0O- 30 APPLICATIONS OF ROTATIONAL ISOMERIC STATE THEORY TO THE EVALUATION OF CONFORMATIONAL PROPERTIES OF LARGE MOLECULES, W. L. Mattice, Institute of Polymer Science, The University of Akron, Akron, Ohio 44325 3:30 - 31 RECENT PROGRESS TOWARDS THE DEVELOPMENT OF A CONFORMATION DEPENDENT HYDROPHOBICITY INDEX N. G J Richards, Department of Chemistry, University of Florida, Gainesville, FL 32611, USA 4:00 - 32 RAPID GEOMETRY OPTIMIZATION USING SEMIEMPIRICAL MOLECULAR ORBITAL THEORY. J. D. Mohr, James W. McIver, Jr., State University of NY at Buffalo, Buffalo, NY 14214. Molecular Mechanics Force Fields - Session Chairman Dr. Thomas Pierce, Rohm and Haas, P.O. Box 219, Bristol PA 19007, 215-785-8989 Wednesday 830 - 33 A SYSTEMATIC METHOD FOR ESTIMATING MM2 FORCE FIELD PARAMETERS, S.-Y. Liu and G. D. Purvis III, CAChe Scientific, PO Box 500, 13-400, Beaverton, Oregon 97077 9:05 - 34 REACTIVITY MODELING BY FORCE FIELD METHODS. F. Jensen, Department of Chemistry, Odense University, DK-5230 Odense M, Denmark. 9:40 - 35 A COMPARATIVE STUDY OF FORCE FIELD PARAMETERS FOR USE IN POLYMER SIMULATIONS. D. C. Doherty, Minnesota Supercomputer Center, Inc.,1200 Washington Avenue South,Minneapolis, MN 55415, 612.625.7311 doherty@msc.edu 10:15 - 36 "CONTEXT-SPECIFIC FORCE FIELD PARAMETERS IN MACROMODEL" W. C. STILL, DEPt.OF CHEMISTRY, COLUMBIA UNIVERSITY, NEW YORK, NY 10027 10:50 - 37 DERIVATION OF A CLASS II FORCE FIELD: METHODOLOGY AND APPLICATIONS. M.-J. Hwang, J. R. Maple, T. P. Stockfisch, and A.T. Hagler, Biosym Technologies, Inc., San Diego, California 92191. 11:25 - 38 THE MERCK MOLECULAR FORCE FIELD: FORM, SCOPE, PARAMETERIZATION AND PERFORMANCE. T. A. Halgren, Merck Research Laboratories, Rahway, NJ, O7O65 Wednesday Afternoon Molecular Mechanics Force Fields - Session Chairman: Dr. Angelo Rossi, T. J. Watson Research Center, IBM Corporation, 914-945-3834 1:30 - 39 RECENT DEVELOPMENTS AND APPLICATIONS OF THE MM3 FORCE FIELD, J. P. Bowen*, P. C. Fox, G. Liang, G. McGaughey, J.-Y. Shim, E. L. Stewart, Computational Center for Molecular Structure and Design, Department of Chemistry, University of Georgia, Athens, Georgia 3O6O2. 2:05 - 40 A SECOND GENERATION FORCE FIELD FOR THE SIMULATION OF PROTEINS NUCLEIC ACIDS, AND SMALL MOLECULES. W.D. Cornell, P. Cieplak, I.R. Gould, K.M. Merz Jr., J.W. Caldwell, D.C. Spellmeyer, and P.A. Kollman, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94122. 2:40 - 41 Recent Developments of the Chem-X force-field, K. Davies , M. Baird, Chemical Design Ltd., Unit 12, 7 West Way, Oxford, England OX2 0JB 3:15 - 42 QUANTA3.3/CHARMm22 PARAMETERS, F. A. Momany, R. Rone, H. Kunz, Molecular Simulations Inc., Waltham, MA 02254, and L. Schafer, Department of Chemistry, University of Arkansas, Fayetteville, AR 72701 3:50 - 43 THE OPLS FORCE FIELD FOR ORGANIC AND BIOMOLECULAR SYSTEMS. J. Tiado-Rives and W. L. Jorgensen, Department of Chemistry, Yale University,New Haven, Connecticut 06511. 4:25 - 44 A COMPARISON OF FORCE FIELDS AND SOLVATION METHODS FOR STUDYING INTRAMOLECULAR HYDROGEN BONDING IN THE ALANINE DIPEPTIDE. D. A. Smith, K. J. Seger, and S. Vijayakumar, Department of Chemistry, The University of Toledo, Toledo, OH 43606-3390. General Computational Chemistry Session Chair : Dr. Peter C. Jurs, Chemistry Department, Pennsylvania State University. 830 - 45 The Advanced Combustion Modeling Environment, M. L. Koszykowski, R. Armstrong, R. E. Cline Jr.,Sandia National Laboratories, Livermore, CA 94566 and J. Macfarlane, J.-Y. Chen, and N. Brown, Lawrence Berkeley Laboratory, Berkeley CA, 94590 8:55 - 46 GLOBAL MINIMA OF MOLECULAR MECHANICS FORMULATIONS, N. V. Sahinidis, Dept. Mech. & Ind. Eng., University of Illinois at U- C, Urbana, IL 61801 9:20 - 47 ATOMIC CHARGES IN MOLECULAR MECHANICS FORCE FIELDS: THE DEPENDENCE OF ELECTROSTATIC POTENTIAL DERIVED CHARGES FOR DOPAMINE oN CoNFoRMATIoN. J. J. Urban, G. R. Famini, U..S. Army Chemical Research, Devel-opment and Engineering Center, Aberdeen Proving Ground, Maryland 21010-5423 9:45 - 48 13C NMR SPECTRAL SIMULATION USING NEURAL NETWORKS TO SELECT REGRESSION MODELS. J. W. Ball and P. C. Jurs, Department of Chemistry, The Pennsylvania State University, University Park, PA 168O2. 10:10 - 49 MACROSEARCH: a new program for generating structures from NMR constraints using systematic conformational search. D. D. Beusen, J. D. Clark, R. D. Head, R. A. Dammkoehler, S. F. Karasek, and E.F. Berkley Shands. Center for Molecular Design, Washington University, Box 1099, One Brookings Drive, St. Louis, MO 63130. 10:35 - 50 Transferable Atom Equivalents. The Construction of Molecular Properties from Atomic Electron Density Fragments. C. M. Breneman, T. R. Schroeder and M. Dung, Department of Chemistry , Rensselaer Polytechnic Institute,Troy, NY 12180, breneman@quant.chem.rpi.edu 11:00 - 51 ENVIRONMENTAL APPLICATIONS OF PATTERN RECOGNITION TECHNIQUES. B.K.Lavine, Department of Chemistry, Clarkson University, Potsdam, NY 13699-581O 11:25- 52 SIMULATION OF THE VIBRATIONAL SPECTRA OF LARGE MOLECULES E. L. McMaster, Department of Applied Physics, Cornell University, Ithaca, New York 14853 General Computational Chemistry - Thursday Afternoon Session Chair: Dr. Kate Holloway,Merck Research Laboratories,West Point, PA 1:30- 53 THEORETICAL EXAMINATIONS OF POLYPEPTIDE FOLDING, B.T. Luke, IBM, MS 284, Kingston, NY 12401. 1:55- 54 CONFORMATIONAL ENERGY ANALYSIS OF THE PENTAPEPTIDE AC-GLY-ARG-GLY-ASP-SER-NMA AND SEVERAL ANALOGS. S. S. Zimmerman, S. E. Christensen, and S. D. Brown, Graduate Section of Biochemistry and Department of Chemistry, Brigham Young University, Provo, Utah 48602. 2:20- 55 CONSTANT PRESSURE MOLECULAR DYNAMICS AND COHESION PARAMETERS. G. E. Whitwell, Akzo Research Laboratories, Dobbs Ferry, NY 10522-3401 2:45- 56 RELATIVE STABILITIES OF CH3Co-L1-L2-NHCH3 DIPEPTIDES IN FOUR MAJOR b-TURN CONFORMATION FROM FREE ENERGY SIMULATIONS. Alexander Tropsha#, Yibing Yan, Jan Hermans and Bruce W. Erickson, #Laboratory for Mo-lecular Modeling, School of Pharmacy, and Departments of *Chemistry and Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599. 3:10- 57 MOLECULAR DYNAMICS SIMULATIONS IN WATER OF A DESIGNED 44-RESIDUE COILED-COIL PROTEIN. J. E. Rozzelle Jr.*, B. W. Erickson*, and A. Tropsha#, *Department of Chemistry and #Laboratory for Mo-lecular Modeling, School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 3:35-4:00 3:35- 58 CALCULATION OF RELATIVE SOLVATION AND BINDING FREE ENERGY DIFFERENCES OF HIV-1 PROTEASE INHIBITORS PRIOR TO SYNTHESIS: A THERMODYNAMIC CYCLE PERTURBATION (TCP) APPROACH. M. R. Reddy, Gensia Pharmaceuticals, 4575 Eastgate Mall, San Diego, CA 92121, V. Kalish, C. Palmer, J. Tat-lock, M. D. Varney, B.W. Wu, K. Appelt, Agouron Pharmaceuticals, 3565 General Atomic Court, San Diego, CA 92121. 4:00- 59 THEORETICAL STUDIES ON HYDRATION OF PYRROLE, IMIDAZOLE AND PROTONATED IMIDAZOLE IN THE GAS PHASE AND AQUEOUS SOLUTION. P. I. Nagy1*, G. J. Durant1 and D. A. Smith2* 1Department of Medicinal and Biological Chemistry and 2Department of Chemistry, The University of Toledo, Toledo, OH Dr. Thomas Pierce COMP Program Chair thpierce@rohmhaas.com or rs0thp@rohvm1 Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From chemistry-request@ccl.net Mon Jun 1 21:23:23 1992 Date: Mon, 1 Jun 92 19:00:44 -0500 From: molsol@wucmd.wustl.EDU (Molecular Solutions) Subject: The Computational Chemistry Yellow Pages To: chemistry@ccl.net Status: R Molecular Solutions, Inc. (Allen Richon and Merry Ambos) and Custom Consulting and Research (Bruce Gelin) are collaborating to produce and sell The Computational Chemistry Yellow Pages. This is to be a general resource guide for computational chemistry software and services. It is designed to: act as an introduction to new users; provide a resource for experienced users; summarize sources of information available in the field. If you have software, services, data or publications which you would like to have included in the publication at no charge, please send us a brief description and pricing, a contact name, address, telephone number, FAX number and e-mail address if available. The deadline for inclusion is July 1, 1992. You can e-mail your response to molsol@wucmd.wustl.edu, mail it to Molecular Solutions, P.O. Box 32101, St. Louis, MO 63132 or FAX it to us at 314-997-6760. From chemistry-request@ccl.net Mon Jun 1 23:07:36 1992 Date: Tue, 2 Jun 1992 10:52:21 +1000 From: Weiguang Huang Subject: <> and <> comment on SymbMath To: cayley@maths.su.oz.AU, chemistry@ccl.net, esljiang@vax.ox.ac.UK, Status: R This is news. ------------ In the magazine <>, June 1992, page 119, Mr. Geoff Long wrote, "SymbMath 1.4 belongs in a more esoteric field, that of symbolic mathematics. If you've ever had need for programs such as Maple or Mathematica, you'll know about symbolic mathematics, also called algebraic computation or symbolic manipulation. SymbMath is a symbolic calculator that can manipulate complicated formulas and return answers in terms of symbols. It solves the same sort of problems as programs like Mathematica, but still runs in 640 K of RAM as opposed to Mathematica's 4 Mb plus. Although SymbMath is still being added to, it has generated interest in the scientific sections of some overseas electronic bulletin board, being one of the most frequently download programms at some monitored sites". The Journal <> on February 1992, page 76, said, "SymbMath, an expert system that solves mathematic problems in symbolic formula or through numeric computation ... requires significantly less RAM than most comparable software - 640 Kbytes, as opposed to as much as 4 Mbytes". ********************************************************************** * Dr. Weiguang HUANG * * 5/6 Cara Road, Geelong, Vic. 3216, Australia * * Email: huang@deakin.oz.au, Phone: (052)443282 * * ------------------------------------------------------------------ * * SymbMath - a symbolic calculator with learning * * PlotData - a plotter with analysing data * **********************************************************************