From vaisman@gibbs.oit.unc.edu Sat Aug 7 02:55:01 1993 Date: Fri, 6 Aug 1993 21:54:01 +0501 (EDT) From: Subject: NCSMM: First Announcement and Call for Papers To: chemistry@ccl.net Message-Id: North Carolina Symposium on Molecular Modeling: Integration of Theory and Experiment Research Triangle Park, North Carolina U.S.A. October 21 - 23, 1993 Sponsored by North Carolina Section of American Chemical Society BIOSYM Technologies Molecular Design Limited Molecular Simulations, Inc. MCNC North Carolina Biotechnology Center Tripos Associates, Inc. You are invited to participate in the North Carolina Symposium on Molecular Modeling at MCNC, Research Triangle Park, NC, October 21-23, 1993. The scientific program will emphasize the integrated nature of modern chemical, biochemical, and pharmacological research that requires collaborative efforts of both theoretical and experimental scientists. The program will consist of invited lectures, posters, and software and hardware presentations. An informal picnic at Jordan Lake is planned for attendees. CALL FOR POSTERS Participants are invited to submit poster presentations on any topic related to molecular modeling. MCNC will provide 30"x40" posterboard for attendees to mount their materials. One-page abstracts of poster presentations will be included in meeting notes that will be distributed at the symposium. Abstracts must be submitted by October 4. INVITED LECTURES "Accuracy of Structure Determination and Structure Prediction: Interplay of Theory and Experiment" Axel Brunger, Yale University "Correlations vs. Simulations: Choosing the Appropriate Tool" Garland Marshall, Washington University "Monte Carlo and Molecular Dynamics Simulations with OPLS Forcefield" Julian Tirado-Rives, Yale University "Determining Protein Folds by Inverted and Evolutionary Protein Folding Algorithms" David Eisenberg, University of California at Los Angeles "Unlimited Expectations, Limited Applications" Gerald Fasman, Brandeis University "Computational Studies on Peptides and Peptoids (Poly N-Substituted Glycines)" David Spellmeyer, Chiron Corporation "A Combined Quantum Mechanical and Molecular Mechanical Approach for Modeling Chemical Reactions in Solution" Jiali Gao, SUNY at Buffalo "Complexes of HIV Protease with Inhibitors: Modeled and Experimental Structures" Alexander Wlodawer, National Cancer Institute "Site-Directed Drug Design: Methods and Applications" Richard Ogden, Agouron Pharmaceuticals Panel Discussion "Accuracy of Molecular Simulations" Vendors Displays and Demonstrations ORGANIZING COMMITTEE Alexander Tropsha, Chairman, University of North Carolina at Chapel Hill Ken Flurchick, Co-Chairman, MCNC Rebecca McCloskey, Conference Coordinator, MCNC Frank Brown, Glaxo Research Institute Michael Cory, Burroughs Wellcome Co. Jan Hermans, University of North Carolina at Chapel Hill Lee Pedersen, University of North Carolina at Chapel Hill Iosif Vaisman, University of North Carolina at Chapel Hill TRAVEL AND ACCOMMODATIONS MCNC is located in Research Triangle Park, one mile north of I-40 and five miles from Raleigh-Durham International Airport. The symposium hotel is the Holiday Inn in Research Triangle Park. The hotel rates are $72 plus tax per night. Please make your reservation directly with the hotel by calling 919-941-6000. Indicate that the registration is for the ACS Symposium. The hotel registration deadline is October 1. After this deadline, reservations will be accepted depending on availability. Rental cars are available at the airport. For additional administrative information, contact Rebecca McCloskey at 919-248-1841. REGISTRATION Complete the attached registration form and return with payment by October 10 to MCNC, P.O. Box 12889, Research Triangle Park, NC 27709 Attn: R. G. McCloskey. Only checks and money orders will be accepted (no credit cards). Make checks payable to the ACS Symposium. Payment must be included with registrations. For further technical information, call Alex Tropsha at 919-966-2955 (e-mail tropsha@gibbs.oit.unc.edu) or Ken Flurchick at 919-248-1121 (e-mail kenf@ncsc.org). For administrative information, call Rebecca McCloskey at 919-248-1841 or send e-mail to gebuhr@mcnc.org. REGISTRATION FEES Industrial participants $170 Academia $ 65 Post-doctorates $ 35 Graduate students $ 25 Registration fees include the reception, the picnic dinner at Jordan Lake, two lunches, refreshment breaks, and meeting materials. REGISTRATION FORM Symposium on Molecular Modeling: Integration of Theory and Experiment Registration is limited and will be accepted on a first-come, first-served basis. Make checks payable to the ACS Symposium. Registrations will not be accepted without payment. Send your registration to the following address: MCNC P.O. Box 12889 3021 Cornwallis Road Research Triangle Park, NC 27709 Attn: R. G. McCloskey Name Position/Title Affiliation Address City State, Zip Phone Fax Email __I will be presenting a poster and will require 30"x40" posterboard to mount my presentation. Indicate dietary restrictions ___________________________________________ From feng@lisboa.ks.uiuc.edu Sat Aug 7 05:32:56 1993 From: Zhou Feng Message-Id: <9308071533.AA09733@lisboa.ks.uiuc.edu> Date: Sat, 7 Aug 93 10:32:56 -0500 To: chemistry@ccl.net Subject: MD program Hello there: I posted a message on MD program a few days ago in the net. Some people asked for a numerical address of lisboa.ks.uiuc.edu (the public ftp site for the program), the address is 128.174.214.14. There was also a minor error in the unix commands to get the file. After ftp, do the following: > mkdir md; > cd md; > zat ../md2.0.tar.Z | tar xvf - ^^^^^ zat should be zcat. Thanx --- Feng Zhou +-------------------------------------------------------------------- |Theoretical Biophysics feng@lisboa.ks.uiuc.edu |University of Illinois Tel: (217)-244-1612 |3121 Beckman Institute Fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok +-------------------------------------------------------------------- From mbdtsdd@hpb.ch.man.ac.uk Sat Aug 7 19:20:55 1993 From: David Dos Santos Message-Id: <19460.9308071832@hpb.ch.man.ac.uk> Subject: IR and Raman spectra To: chemistry@ccl.net Date: Sat, 7 Aug 93 19:32:50 BST Hi All, I wish to calculate the IR and Raman spectra of liquid water from its autocorrelation functions. Does anyone know of some code which will do this given raw dipole and polarizability data. -- Many Thanks...... David dos Santos. ********************************* * * * "The more innocuous * * a design change appears, * * the further its influence * * will extend." * * * ********************************* From wipke@SECS.UCSC.EDU Sat Aug 7 09:37:19 1993 Date: Sat, 07 Aug 1993 16:37:19 PDT From: "W. Todd Wipke" To: chemistry@ccl.net Message-Id: <00970AC9.95B30221.14927@SECS.UCSC.EDU> Subject: Re: SECS Simulation and evaluation of Chemical Synthesis) I would like to correct some of David Winkler's (CSIRO) comments regarding the SECS synthesis planning program. First, SECS was developed beginning in 1969 at Princeton and then later at the University of California, Santa Cruz. Molecular Design Limited had nothing to do with the program. Second, the installation at CSIRO Melborne used a computer 3000 miles away going through a pretty strange national network not designed for handling interactive graphics. It wasn't an optimal setup and his comments are at odds with many other users. A number of companies including E. Merck, Roche, Sandoz, BASF, Hoechst, Ciba-Geigy, Bayer, Kureha, Mitsubishi have used SECS since as early as 1973 with the usage continuing to today. Publicity about their usage has been minimized to prevent possible challenges to their process patents that were developed using the SECS program. (see Blick, A.R. "Computer-Assisted Chemical Synthesis packages: Is this a new problem in Patentability?". J. Infor. Sci., 1979, 1, 227-229) Using the ALCHEM language for chemical transform description, they extended the transform library to include their own specialized areas of chemistry. The REACCS program that I designed at MDL was designed for a different purpose, namely retrieval of reactions in the form of complete experiments that had been performed whereas SECS stored chemical transforms as conceptual generalizations of reactions without any explicit molecules involved. REACCS provided the ability to start capturing reaction information in computer readible form searchable efficiently by computer graphics. Many synthetic chemists are mainly interested in just retrieving reactions >from the literature, preferring to do their own synthesis planning. In my humble opinion (IMHO) synthesis planning was the first and most successful application of artificial intelligence to chemistry. And the first synthesis planning program ran on a PDP-1 with 24K 18-bit words, three graphic CRTs (DEC340 displays) with a drum for storage, OCSS was its name, the program. This machine also had the first head-mounted display and the first image displayed on the head mounted display was a molecule, so you can impress your friends with the role of chemistry in virtual reality back in 1968. -Todd Wipke wipke@chemistry.ucsc.edu