From eloranta@voimax.voima.jkl.fi Mon Mar 27 04:39:00 1995 Received: from voimax.voima.jkl.fi for eloranta@voimax.voima.jkl.fi by www.ccl.net (8.6.10/930601.1506) id EAA17282; Mon, 27 Mar 1995 04:33:10 -0500 Received: (from eloranta@localhost) by voimax.voima.jkl.fi (8.6.10/8.6.9) id MAA25721 for chemistry@ccl.net; Mon, 27 Mar 1995 12:32:57 +0300 Date: Mon, 27 Mar 1995 12:32:57 +0300 From: Jussi Eloranta Message-Id: <199503270932.MAA25721@voimax.voima.jkl.fi> To: chemistry@ccl.net Subject: Molecule orbital energies in g92? Hi, Is there a way to obtain molecule orbital energies from gaussian 92 run? I can easily get one electron energies from the eigen values but in order to get mo energies I should add the effect of coulomb and exchange terms as well. Or is there any other way to find out if a system has degenerate states (like benzene anion)? Regards, Jussi Eloranta From AZHARI@FRCU.EUN.EG Mon Mar 27 04:54:03 1995 Received: from FRCU.EUN.EG for AZHARI@FRCU.EUN.EG by www.ccl.net (8.6.10/930601.1506) id EAA17382; Mon, 27 Mar 1995 04:53:13 -0500 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01HOMOF4LDCG0002AW@FRCU.EUN.EG>; Mon, 27 Mar 1995 11:52:38 O Date: Mon, 27 Mar 1995 11:52:38 +0000 (O) Subject: cubic and quartic force fields To: chemistry@ccl.net Message-id: <01HOMOF4R9J60002AW@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netter: I am looking for a program to calculated cubic and quartic force fields but I do not like to pay for it or at least to pay the least possible. Thanks in advance. Adel El-Azhary Department of Chemistry Faculty of Science Cairo University Giza, Egypt From kupka@trilobyte.anet.cz Mon Mar 27 04:55:49 1995 Received: from pol.upce.cz for kupka@trilobyte.anet.cz by www.ccl.net (8.6.10/930601.1506) id EAA17296; Mon, 27 Mar 1995 04:38:40 -0500 Received: by pol.upce.cz (5.65/DEC-Ultrix/4.3) id AA21594; Mon, 27 Mar 1995 11:36:07 +0200 Date: Mon, 27 Mar 1995 11:36:07 +0200 Message-Id: <9503270936.AA21594@pol.upce.cz> X-Sender: kupka@pol.upce.cz X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: CHEMISTRY@ccl.net From: kupka@trilobyte.anet.cz (Karel Kupka) Subject: Chemometrics 495 Conference Announcement C H E M O M E T R I C S =B4 9 5 Announcement and call for papers 5 DAYS CONFERENCE ON CHEMOMETRICS AND COMPUTATIONAL STATISTICS IN CHEMISTRY in Pardubice, Czech Republic 4th Chemometrics Conference to be held 2-6 July 1995 Congress Center, University of Pardubice CZECH REPUBLIC The conference will cover research and latest developments in computational statistics and data analysis in analytical, inorganic and organic chemistry, environmetrics, etc. It should stimulate communication between practitioners and researchers. A competition for the best under-PhD conribution (Czech Chemometrics Society Crystal Cup) is organized for young participants. TOPICS: 1. Univariate data analysis. Statistical inference.=20 2. Multivariate data analysis. Classification and pattern recognition. 3. Quality and process control, reference material testing, GLP,= accreditation. 4. Calibration (linear and nonlinear) in quality testing. 5. Statistical models in chemical laboratory. Smoothing operations. 6. Regression model building and testing. 7. Sampling and experimental design. Time series. 8. Optimization in chemometrics. 9. Computer intensive methods in chemometrics. 10. New original software for chemometrics. 11. Education of chemometrics: tutorials, intensive courses, summer schools. 12. Miscelaneous topics related to chemometrics. =20 Abstracts of papers (one or two pages 1 inch margins, A4, single spaced 10 point Times, Courier, Pica or Elite typeface, title in bold capitals) should be submitted= to the Secretariat as soon as possible. Please send copies to the= computational chemistry convenor as well. Further information on the Chemometrics =B495 can be obtained from the CHEMOMETRICS' 95 Secretariat, TriloByte Statistical= Group Prof. Milan Meloun, DrSc. Ing. Karel Kupka Department of Analytical Chemistry, U sokolovny 21 University of Pardubice, Pardubice nam. Cs. legii 565, OR 530 02 CZ-532 10 Pardubice, Czech Republic =20 Czech Republic, tel.: +42.40.518592 Telephone: +42.40.582288, fax: +42.40.518592 Fax: +42.40.514530, kupka@trilobyte.anet.cz E-mail: meloun@hlb.upce.cz kupka@trilobyte.anet.cz -------------------------------------------------------------------------- Cheers, Milan __________________________________________________________________________ From pirard@couperin.scf.fundp.ac.be Mon Mar 27 05:09:02 1995 Received: from hermes.fundp.ac.be for pirard@couperin.scf.fundp.ac.be by www.ccl.net (8.6.10/930601.1506) id EAA17436; Mon, 27 Mar 1995 04:55:55 -0500 Received: by hermes.fundp.ac.be; id AA14452; Mon, 27 Mar 1995 12:02:48 +0200 Received: from couperin.scf.fundp.ac.be by hermes.fundp.ac.be; id AA14452; Mon, 27 Mar 1995 12:02:48 +0200 Received: by couperin.scf.fundp.ac.be (AIX 3.2/UCB 5.64/4.03) id AA23836; Mon, 27 Mar 1995 11:38:55 +0200 From: Bernard Pirard Message-Id: <9503270938.AA23836@couperin.scf.fundp.ac.be> To: chemistry@ccl.net Subject: volume computations Date: Mon, 27 Mar 95 11:38:54 +0100 dear collegues, We are interested in calculating volumes and accessible surface areas for different peptidic and non peptidic molecules. Looking in the QCPE Bulletin we found three programs that could possibly do that: 509 MOLSV QCMP053 MOLSV QMAC017 MOLSVMAC but we would like to have some advice on which to choose from these three or any other programs that calculate these kind of things. Thank you, Florence Lebon Bernard Pirard From A.T.Yagnik@exeter.ac.uk Mon Mar 27 05:39:01 1995 Received: from sun2.nsfnet-relay.ac.uk for A.T.Yagnik@exeter.ac.uk by www.ccl.net (8.6.10/930601.1506) id FAA18068; Mon, 27 Mar 1995 05:35:12 -0500 From: Via: uk.ac.exeter; Mon, 27 Mar 1995 11:34:44 +0100 Received: from cen.exeter.ac.uk by exub.exeter.ac.uk with SMTP (PP) id <06114-0@exub.exeter.ac.uk>; Mon, 27 Mar 1995 11:34:36 +0100 Message-Id: <21017.9503271034@cen> Subject: Summary: Important Modelling Books & Journals To: CHEMISTRY@ccl.net Date: Mon, 27 Mar 1995 11:34:16 +0100 (BST) Content-Type: text Content-Length: 6412 Hi all, Well here's the summary - sorry it took a bit of time to get together. I was busy and also decided to wait in case I got more replies. I have posted to CCL since the number of "me too" requests far outweighed the number of people who sent info and I cannot Email them all separately. If anyone wants to add to this list, please get in touch with me. Thanks to all those who helped out and, to those who were interested in getting the same info, I'm glad I could help out. ******************************************************************** >From Ho Leung Ng A book I recommend is by Brooks, Karplus, and Pettitt (sp?), entitled Proteins, in the Advanced Chemical Physics series. =========================================================================== >From Alan M. Mathiowetz My favorites are: Proteins: Structure, Function, and Genetics Protein Science Journal of Computer-Aided Molecular Design Journal of Computational Chemistry. The top two have lots of articles on protein modeling and analysis. Journal of Medicinal Chemistry would also be extremely valuable if you really want to get into drug design, since it occasionally presents important new computational methods and always presents interesting experimental data. ========================================================================== >From Kenny Lipkowitz I've been editing a book series with Don Boyd on the topic of computational chemistry. The individual chapters are tutorials/reviews on topics related to your work.The series is called Reviews in Computational Chemistry, published byVCH Publishers Inc. I shall mail some info to you via snail mail. Vols. 1-5 have been published. Vol. 6 is in press and volume 8 is being prepared. ============================================================================= >From James Crabbe I can recommend the journal published by Elsevier 'Computers and Chemistry', which includes many aspects of modelling and its application to large and small molecules. The publishing editor is Dr. David Claridge, email d.claridge@elsevier.co.uk James Crabbe. Editor-in-chief ============================================================================== >From Donald Boyd Dr. Yagnik, Most chemical libraries have the book series "Reviews in Computational Chemistry." The editors are K. B. Lipkowitz and D. B. Boyd. Five volumes havebeen published: I (1990), II (1991), III (1992), IV (1993), and V (1995). Volumes VI and VII are in press. The publisher is VCH, New York and Weinheim. Descriptions of the earlier volumes are in the archives of the OSC CCL. A description of Volume VI is below. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd Volume 6 (1995) Reviews in Computational Chemistry brings together respected experts in the field of computer-aided molecular research. This new volume examines quantum chemistry of solvated molecules, molecular mechanics of inorganics and organometallics, modeling of polymers, technology of massively parallel computing, and productivity of modeling software. A guide to force field parameters and a new software compendium are added. Molecular modeling and computational chemistry are increasingly used in conjunction with organic, inorganic, medicinal, biological, physical, polymer, and analytical chemistry, as well as in biotechnology, materials science, and chemical physics. The bookseries has become a standard reference source. Unlike most review series, Reviews in Computational Chemistry considers teaching the methodologies to newcomers an important part of its mission. Most chapters have both introductory and advanced material. Chapters written as tutorials make the volumes valuable adjuncts to textbooks in more traditional disciplines. At thesame time, the advanced material in each volume will be of interest to practicing computational chemists. Table of contents- 1. Continuum Solvation Models: Classical and Quantum Mechanical Implementations Christopher J. Cramer and Donald G. Truhlar 2. Molecular Mechanics Force Fields for Modeling Inorganic and Organometallic Compounds Clark R. Landis, Daniel M. Root, and Thomas Cleveland 3. Computational Methods for Modeling Polymers: An Introduction Vassilios Galiatsatos 4. High Performance Computing in Computational Chemistry: Methods and Machines Rick A. Kendall, Robert J. Harrison, Rik J. Littlefield, and Martyn F. Guest 5. Molecular Modeling Software in Use: Publication Trends Donald B. Boyd Appendix 1: Published Force Field Parameters Eiji Osawa and Kenny B. Lipkowitz Appendix 2: Compendium of Software for Molecular Modeling Donald B. Boyd For ordering information- ISBN 1-56081-667-8. 437 pp. (The release date for the new volume is scheduledfor May). Contact VCH Publishers, 303 NW 12th Ave., Deerfield Beach, FL 33442-1788. Toll-free tel.: 800-367-8249, Toll-free fax: 800-367-8247, Tel.: 305-428-5566, fax: 305-428-8201. Editorial inquiries may be directed to boyd@chem.iupui.edu =========================================================================== >From Yvonne Martin I would suggest a subscription to Reviews in Computational Chemistry, Journal of Computer Aided Drug Design. Books: G. A. Jeffrey & W. Saenger "Hydrogen Bonding in Biological Structures" Springer-Verlag h. B. Burgi & J. D. Dunitz "Structure Correlation" Vols 1 & 2. VCH. The books deal with DATA rather than theory. ========================================================================= Well, that about complete's the info that I got. Once again, thanks to those who sent the info. Tosh. -- =============================================================================== Asutosh T Yagnik, Tel: (+44) 1392 263451 Protein Structure Group, Fax: (+44) 1392 263434 Department of Chemistry, Email: ATYagnik@exeter.ac.uk University of Exeter, * * Stocker Road, Exeter. EX4 4QD. UK. > \__/ {All opinions are my own!} "Nature can provide for the needs of people, but not the greeds" M.K.Gandhi =============================================================================== From Karl.F.Moschner@urlus.sprint.com Mon Mar 27 09:54:15 1995 Received: from sprintf.merit.edu for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.10/930601.1506) id JAA20302; Mon, 27 Mar 1995 09:45:19 -0500 X400-Received: by mta merit in /PRMD=internet/ADMD=telemail/C=us/; Relayed; Mon, 27 Mar 1995 09:42:55 -0500 X400-Received: by /ADMD=TELEMAIL/C=US/; Relayed; Mon, 27 Mar 1995 09:40:00 -0500 X400-Received: by /PRMD=SMXFL2/ADMD=TELEMAIL/C=US/; Relayed; Mon, 27 Mar 1995 09:45:48 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Mon, 27 Mar 1995 09:45:00 -0500 Date: Mon, 27 Mar 1995 09:45:00 -0500 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Mon Mar 27 09:45:41 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: RE: Molecular Mo Priority: Urgent From: Karl.F.Moschner@urlus.sprint.com Message-ID: <"Mon Mar 27 09:45:41 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: CHEMISTRY@ccl.net Subject: RE: Molecular Modeling Packages for ALPHA systems Surprisingly DEC doesn't seem to be pursuing the computational chemistry market as vigorously as it had in the VAX and DECsystem days. Still, there are a slew of QCPE programs which have been ported to the DEC Alphas. Also: DEC Alpha Software Supplier Contact --------------------------------------------------------------------------- QCPE qcpe@ucs.indiana.edu For info and catalagoue login: anonymous@qcpe6.chem.indiana.edu Gaussian 92/DFT Gaussian Inc. info@gaussian.com Spartan Wavefunction Inc. sales@wavefun.com (?)HyperChem(?) Hypercube Inc. (800) 960-1871 --------------------------------------------------------------------------- Note that Gaussian 92/DFT and most of the QCPE software is non-graphical. Some programs may not support both Open VMS and OSF/1; e.g., Spartan only supports OSF/1 but Gaussian 92/DFT supports both but is non-graphical. I'm not sure about HyperChem, now from Hypercube Inc. but their software was fairly portable and the graphics were X-based. Good luck! _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ From qftramos@usc.es Mon Mar 27 10:54:07 1995 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.6.10/930601.1506) id KAA21632; Mon, 27 Mar 1995 10:44:56 -0500 Received: by uscmail.usc.es (5.67b/1.34) id AA12323; Mon, 27 Mar 1995 17:47:56 +0200 Date: Mon, 27 Mar 1995 17:47:56 +0200 From: qftramos@usc.es (Antonio Fernandez Ramos) Message-Id: <199503271547.AA12323@uscmail.usc.es> To: chemistry@ccl.net Subject: least squares again Dear netters, Through the fault of my terminal, I lost the answers to the following mail: I am trying to do a non linear least squares fit, using a Marquardt type algoritm, but I need to restrict some parameters to make my function behaves correctly. Is available any program to constrain parameters to be positive? Thanks. I am gratefully if you answer the question again. Thanks in advice. From lma@univ-orleans.fr Mon Mar 27 11:24:11 1995 Received: from centre.univ-orleans.fr for lma@univ-orleans.fr by www.ccl.net (8.6.10/930601.1506) id LAA22187; Mon, 27 Mar 1995 11:14:52 -0500 Received: from mailhost.univ-orleans.fr ([193.49.81.10]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id SAA12978 for ; Mon, 27 Mar 1995 18:20:03 +0200 LD?Resent-Date: Mon, 27 Mar 1995 18:20:03 +0200 Date: Mon, 27 Mar 1995 18:20:03 +0200 Message-Id: <199503271620.SAA12978@centre.univ-orleans.fr> X-Sender: lma@mailhost.univ-orleans.fr X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: lma@univ-orleans.fr (Luc Morin-Allory) Subject: Chemistry for computers dear netters, This list is mainly based on the use of computers in chemistry but I have a question about the use of chemistry in computers. Some of my students are looking for information about the different ways of recycling old computers. They need to know: The chemical process used for the recycling of metals from I.C. ( mainly gold) The economical aspect of the operation The interest ( and the chemical process) of the recovery of the rare earths of the color screens Which are the organisationsor companies involved in this area and all other information or references in this field. Thanks in advance for any help. **************************************************************************** ********* Luc Morin-Allory Modelisation- Chemometrics Group Laboratoire de Chimie Bioorganique et Analytique ( LCBA) ICOA, URA CNRS 499 University of Orleans B.P. 6759 45067 Orleans Cedex 2 France Tel (33) 38 41 70 42 Fax: (33) 38 41 72 81 e.Mail: lma@univ-orleans.fr **************************************************************************** ********* From polowin@hyper.hyper.com Mon Mar 27 11:54:13 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id LAA23611; Mon, 27 Mar 1995 11:50:21 -0500 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id LAA01226 for <@www.hyper.com:CHEMISTRY@ccl.net>; Mon, 27 Mar 1995 11:45:11 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA18666; Mon, 27 Mar 95 11:49:51 -0500 Date: Mon, 27 Mar 95 11:49:51 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9503271649.AA18666@hyper.hyper.com> To: everyone@hyper.hyper.com, --@hyper.hyper.com, CHEMISTRY@ccl.net Subject: Re: Molecular Modeling Packages for ALPHA systems > DEC Alpha Software Supplier Contact > --------------------------------------------------------------------------- > QCPE qcpe@ucs.indiana.edu > For info and catalagoue login: anonymous@qcpe6.chem.indiana.edu > > Gaussian 92/DFT Gaussian Inc. info@gaussian.com > > Spartan Wavefunction Inc. sales@wavefun.com > > (?)HyperChem(?) Hypercube Inc. (800) 960-1871 > --------------------------------------------------------------------------- > > Note that Gaussian 92/DFT and most of the QCPE software is non-graphical. > Some programs may not support both Open VMS and OSF/1; e.g., Spartan only > supports OSF/1 but Gaussian 92/DFT supports both but is non-graphical. I'm > not sure about HyperChem, now from Hypercube Inc. but their software was > fairly portable and the graphics were X-based. At the moment, the software that we have for the DEC Alpha is the back-end modules, which let the heavy number-crunching be off-loaded from the PC front end to a network-linked UNIX box. We can work under OSF/AXP 1.2; under NT or USF but not on a DEC VAX. (The back-end modules are also available for SGI Irix 4.0 to 4.0.5F and 5.2, and IBM AIX 3.2.5 and 4.0 .) Regards, Joel Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 weifan@gibbs.oit.unc.edu Mon Mar 27 12:09:07 1995 Received: from gibbs.oit.unc.edu for weifan@gibbs.oit.unc.edu by www.ccl.net (8.6.10/930601.1506) id LAA23982; Mon, 27 Mar 1995 11:58:23 -0500 Received: from localhost by gibbs.oit.unc.edu (8.6.4.3/10.1) id LAA12713; Mon, 27 Mar 1995 11:58:21 -0500 Date: Mon, 27 Mar 1995 11:58:20 -0500 (EST) From: Weifan Zheng Subject: Residue Based Solvent Accessible Area To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Can anyone out there tell me where I can get a program for calculating the solvent accessible area for each individual residue in a given protein? Thank you! Weifan Lab for Molecular Modeling School of Pharmacy UNC-Chapel Hill From tripos!metis!matt@uunet.uu.net Mon Mar 27 12:24:11 1995 Received: from relay3.UU.NET for tripos!metis!matt@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id MAA24570; Mon, 27 Mar 1995 12:18:18 -0500 Received: from uucp5.UU.NET by relay3.UU.NET with SMTP id QQyiwz12706; Mon, 27 Mar 1995 12:17:45 -0500 Received: from tripos.UUCP by uucp5.UU.NET with UUCP/RMAIL ; Mon, 27 Mar 1995 12:17:45 -0500 Received: from metis.UUCP by tripos (4.1/SMI-4.0) id AA13663; Mon, 27 Mar 95 10:39:16 CST Received: by metis.UUCP (4.0/4.7) id AA07089; Mon, 27 Mar 95 10:39:05 CST Message-Id: <9503271639.AA07089@metis.UUCP> To: uunet!ccl.net!CHEMISTRY@uunet.uu.net Subject: Seminar tour on new compound discovery Date: Mon, 27 Mar 95 10:39:04 CST From: Matthew Clark -------------- World Seminar Tour on "Optimizing Chemical Information -------- ------------------------- for New Compound Discovery" ------------------------ Tripos, Inc is holding a world tour of seminars on important topics for new compound discovery in April, May and June. There are two seminar topics to choose from: o New ways to get more from your drug discovery research This seminar will discuss how to use information technology to handle data overload from research, to manage access and communicate the information among the scientific disciplines in the research process. Learn how the new UNISON chemical information management system can accelerate your research efforts. Topics discussed: 2D structure searches Corporate data access and data mining Customizing data access for the research team Integration with molecular analysis tools. o A new era of lead discovery: Optimally Diverse Screening Libraries This seminar will discuss ways to manage the process of high-througput screening. Tripos and Panlabs have collaborated to develop screening libraries with optimally diverse properties. These libraries increase the chances of finding better leads. Learn how to analyze and evaluate screening libraries. Topics discussed: creating combinatorial libraries managing the diversity of your libraries selecting libraries for screening apply data mining techniques Dates for "New Ways to get more from your drug discovery research" April 3, Workshop at ACS Anaheim April 24 Houston, TX May 3 Rutgers, NJ May 4 Chicago, IL May 8 Frankfurt, Germany May 10 Paris, France May 11 Stockholm, Sweden May 15 Milan, Italy May 17 London, England Dates for "A new era of lead discovery, optimally diverse screening libraries" April 18 San Diego, CA April 18 London, England April 19 Seattle, WA April 20 Paris, France May 2 Boston, MA May 9 Frankfurt, Germany May 12 Stockholm, Sweden May 16 Milan, Italy June 5 Tokyo, Japan June 6 Osaka, Japan June 8 Teijin, Korea Email or Fax Marthellen Cain (mcain@tripos.com, fax 314 647 9241) for a Fax back sheet with the agenda and details for the location nearest you. From biosym.com!tony@biosym.com Mon Mar 27 13:39:12 1995 Received: from bioc1.biosym.com for biosym.com!tony@biosym.com by www.ccl.net (8.6.10/930601.1506) id NAA27524; Mon, 27 Mar 1995 13:37:38 -0500 Received: from biosym.com by bioc1.biosym.com (5.64/0.0) id AA08473; Mon, 27 Mar 95 10:24:57 -0800 Received: by east1.biosym.com (920330.SGI/920502.SGI) for bioc1!ccl.net!chemistry-request id AA08521; Mon, 27 Mar 95 13:10:53 -0500 Date: Mon, 27 Mar 95 13:10:53 -0500 From: biosym.com!tony@biosym.com (Tony Schmidt) Message-Id: <9503271810.AA08521@east1.biosym.com> To: ccl.net!chemistry-request@bioc1.biosym.com Subject: Re: CCL:Residue Based Solvent Accessible Area Cc: chemistry@ccl.net, tony@biosym.com >Can anyone out there tell me where I can get a program for calculating >the solvent accessible area for each individual residue in a given protein? You may use Biosym's Solvation module provided with the Delphi program. Tony Schmidt tony@biosym.com From polowin@hyper.hyper.com Mon Mar 27 13:55:26 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id NAA27481; Mon, 27 Mar 1995 13:35:24 -0500 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id NAA01644 for <@www.hyper.com:CHEMISTRY@ccl.net>; Mon, 27 Mar 1995 13:30:03 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA20639; Mon, 27 Mar 95 13:34:48 -0500 Date: Mon, 27 Mar 95 13:34:48 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9503271834.AA20639@hyper.hyper.com> To: CHEMISTRY@ccl.net Subject: Re: Residue Based Solvent Accessible Area > Can anyone out there tell me where I can get a program for calculating > the solvent accessible area for each individual residue in a given protein? This can be done with HyperChem and the QSAR Properties module of ChemPlus. One would select each residue, one at a time, and import the complete structure into the module. The solvent-accessible area is calculated only for the selected part. The process would be automated by an Excel macro or a Visual Basic program. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 young@slater.cem.msu.edu Mon Mar 27 14:39:13 1995 Received: from slater.cem.msu.edu for young@slater.cem.msu.edu by www.ccl.net (8.6.10/930601.1506) id OAA29232; Mon, 27 Mar 1995 14:35:49 -0500 Received: by slater.cem.msu.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA01829; Mon, 27 Mar 95 14:36:33 -0500 Date: Mon, 27 Mar 95 14:36:33 -0500 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9503271936.AA01829@slater.cem.msu.edu> To: chemistry@ccl.net Subject: Summary of Random Number Generators Hello, The following is a summary of the replies to my question about random number generators. **************************************************************** The original question. Hello, I am starting to do Quantum Monte Carlo calculations and I am interested in the performance of random number generators. There have been a number of tests developed, the most trusted seem to be those in "Seminumerical Algorithms" by Knuth. And there are a number of supplemental random number generators, such as the ran3 generator in "Numerical Recipies". It has also been demonstrated that in the past the random number generators built into various programming languages were not to be trusted. My question is - Do the random number generators built into the current generation of compilers pass statistical tests? I have tested the built in random number generators in Borland C++ and GNU C++ and so far they have passed all tests (working out of Knuth). I would like to know if it is only C++ that has a reliable random number generator implemented or if all compilers are now reliable, or if it is only certain vendors even within the C++ language? The reason that I would like to use built in random number generators is that Knuth indicates that code written directly in assembly language can accomplish the task faster than code written in standard source code. The GNU C++ built in random number generator is a factor of 2 faster than the ran3 generator using all available compiler optimization. **************************************************************** From: TOPPER ROBERT My best advice is to beware of using random number generators as black-boxes, especially in the context of Monte Carlo integrations and simulations. When using random number generators in Monte Carlo, you have to not only worry about whether the samples are uniform on the plane and uncorrelated in hyperdimensions but also about the period of the random number sequence (all random number generators, as you know, have a period for a given seed - and if your program requires a # of random numbers which is on the order of the period of the algorithm, better watch out). What's more, RNGs which perform perfectly well against a battery of statistical tests have been known to fail when used, for example, in 3D Ising lattice calculations...there is a good bit of literature on this subject. I personally wouldn't use any random number generator in my Monte Carlo work unless I knew exactly what the algorithm was, had a reference for it, and had subjected it to my personal battery of tests, which includes statistical tests ala Knuth and application tests (path-integral and classical Monte Carlo computations). At least then, if there is a bug in the algorithm I know who to blame for all those wasted cycles... Finally, in every Monte Carlo calculation I have ever carried out, the limiting factor has not been the speed of the random number generator, but the evaluation of the potential energy. But then I've never done QMC calculations, so I don't know what the "rate-determining step" is for such calcs. Because of this, I tend to err on the side of slow, but solid random number generation. hope this helps, best to all- rqt ************************************************************************ From: "Trevor Creamer" Dave, What you want to do is use the most reliable (statistically) random number generator available. I haven't done any Quantum Monte Carlo, but I've a lot of experience using MC to study peptides and polyelectrolytes. The fraction of time in a simulation spent generating the random numbers is miniscule compared to the time spent calculating the energies. It is essential that you use a reliable generator, much more important than using the fastest generator. You probably want to spend your time optimising your energy calculation code - this is where the bulk of simulation time is spent. Cheers, Trevor **************************************************************** From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) My question is - Do the random number generators built into the current generation of compilers pass statistical tests? In general, I doubt that. Random number generators are usually provided for games and other less demanding applications. The exception is the set of generators in the GNU C++ library. Others might also be good, but I would always check them first. (working out of Knuth). I would like to know if it is only C++ that has a reliable random number generator implemented or if all compilers are now reliable, or if it is only certain vendors even within the C++ language? I would assume the latter... The reason that I would like to use built in random number generators is that Knuth indicates that code written directly in assembly language can accomplish the task faster than code written in standard source code. The GNU C++ built in random number generator is a factor of 2 faster than the ran3 generator using all available compiler optimization. Nevertheless the GNU C++ random generators are written entirely in C++ (remember that GNU C++ is meant to be a portable compiler). **************************************************************** From: rs0thp@rohmhaas.com (Dr. Tom Pierce) Previously, Dave Young wrote: > I am starting to do Quantum Monte Carlo calculations and > I am interested in the performance of random number generators. > > There have been a number of tests developed, the most trusted > seem to be those in "Seminumerical Algorithms" by Knuth. And there > are a number of supplemental random number generators, such as the > ran3 generator in "Numerical Recipies". It has also been demonstrated > > My question is - Do the random number generators built into > the current generation of compilers pass statistical tests? > A simple answer is "No". I think this topic is a permanent flame-war in sci.math.stat. The current publications of interest are "Monte Carlo Simulations: Hidden errors from "Good" Random number generators" Phys. Rev. Letters 69(23), pp 3382 1992 Specifically this article says ".. a specific algorithm must be tested together with the random number generator being used REGARDLESS of the tests which the generator has passed." "Latest Development in Random Numbers", CERN Computer Newsletter 213, July-Sept. pp 5-7, 1993. and "Ultra, The greatest random number generator that ever was or ever will be", by Arif Zaman (arif@stat.fsu.edu) and George Marsaglia (geo@stat.fsu.edu), 1992. My painful experience with compiler random number generators is that one is far better off using a known and tested generator. **************************************************************** From: Gislason Jason I have used the random number generators found in "Numerical Recipes" and I have found them to work very well. Personally, I would not trust the generators built into compilers. You just don't know how good it works unless you or someone else has tested it. Jason Gislason **************************************************************** From: brianh@scg.scg.fujitsu.com (Brian Hammond) For QMC calculations the "quality" of pseudo-random numbers depends on the algorithm used. Most modern Fortran- or C-library pseudo-random number generators are good enough, particularly if you are doing branching in which you are using a random number of pseudo-random numbers. Also you must consider how to create Gaussian distributed random numbers if your algorithm calls for them. I have seen presentations where the overall cycle length of the underlying pseudo-random number generator is quite noticeable due to creating Gaussian numbers by adding 12 uniformly distributed numbers. So, in general use a pseudo-random number generator with a long cycle length and use Box-Muller if you want Gaussian pseudo-random numbers. -Brian **************************************************************** From: Markus.Wagener@EROS.CCC.Uni-Erlangen.DE Hello Dave, I always use the following random number generator. I might not be the fastest one, but it is portable and therefore gives the same results on all platforms. It is a linear congruential one. Additive random number generators, like those given in Knuth's book should be a lot faster! I hope tis helps! Markus <<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> #include #include /****************************************************************/ /* Rand computes a psuedo-random */ /* double value between 0 and 1, excluding 1. Randint */ /* gives an integer value between low and high inclusive. */ /****************************************************************/ #define Randomize() (Seed = time((time_t)0)) #define Randint(low,high) ( (int) ((low) + ((high)-(low)+1) * Rand())) #define Flip(P) ((P == 1.0) ? 1 : (Rand() <= P) ) extern double Rand(void); <<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> int Seed = 707559297; /**********************************************************************/ /* Rand */ /*--------------------------------------------------------------------*/ /* Minimal standard random number generator as defined in: */ /* "Random Number Generators: Good ones are hard to find", */ /* Communications of the ACM, 31(1988)1192. */ /**********************************************************************/ #define A 16807 #define M 2147483647 #define Q 127773 #define R 2836 double Rand(void) { int hi, lo, test; hi = Seed / Q; lo = Seed % Q; test = A * lo - R * hi; if (test > 0) Seed = test; else Seed = test + M; return((double)Seed / (double)M); } **************************************************************** From: dario@rs5.csrsrc.mi.cnr.it (Dario Bressanini) Dear Dave, If I may add something to what Brian Hammond wrote, if you are going to do Quantum Monte Carlo for Electronic structure, the time you spend computing the value of the trial wavefunction is much more than the time you spend to generate random deviates I am working on QMC since 1991 and the only thing i can say is: don't use a system provided generator: they usually have a too short cycle. Happy Quantum Monte Carlo computing. dario bressanini dario@rs5.csrsrc.mi.cnr.it **************************************************************** From: Kari Kankaala Dear Dave, Your posting was forwarded to me by a colleague. Our group has been recently playing much with pseudorandomnumber generation, testing a variety of generators etc (e.g. Phys. Rev. Lett, 73, 2513 (1994), Phys. Rev. E, 48, R4211 (1993), see also Nature, 372, Dec 1, 1994, p. 403). I'll try to comment your questions briefly below. > > I am starting to do Quantum Monte Carlo calculations and >I am interested in the performance of random number generators. Our interest in the work on PRNGs was due to the fact that we mainly weork on classical MC simulations of Stat Mech Systems (surfaces, polymers, complex systems in general). > > There have been a number of tests developed, the most trusted >seem to be those in "Seminumerical Algorithms" by Knuth. And there >are a number of supplemental random number generators, such as the >ran3 generator in "Numerical Recipies". It has also been demonstrated >that in the past the random number generators built into various >programming languages were not to be trusted. > Do not touch RAN3. It is one of the worst we tested. > My question is - Do the random number generators built into >the current generation of compilers pass statistical tests? > Generally, do not use any built in generators unless you have demonstrated data that these generators are "good". Cray has a decent generator in Fortran library but e.g. Convex has a extremely poor one available. > I have tested the built in random number generators in >Borland C++ and GNU C++ and so far they have passed all tests >(working out of Knuth). I would like to know if it is only C++ that >has a reliable random number generator implemented or if all >compilers are now reliable, or if it is only certain vendors even within >the C++ language? The language does not matter. It is a question of converting the algorithm into a code correctly. It can be only correct or incorrect, nothing in between. This can be done in any language. If you have disrecpancies with two implementations of the same algortihm, it would suggest that one of them is wrong. Whether it is the C++,C, Fortran or wahtever version, has to be checked. What comes to vendor supplied PRNGs, I would reiterate the earlier comment, that never use those unless someone has demonstarted to you, how reliable both the algorithm and the vendor implementation of them are. > > The reason that I would like to use built in random number >generators is that Knuth indicates that code written directly in >assembly language can accomplish the task faster than code written in >standard source code. The GNU C++ built in random number generator >is a factor of 2 faster than the ran3 generator using all available >compiler optimization. > You can find good algorithms and references to them e.g. in our papers. I can provide you with some codes if you need them. But basically relying on vendor supplied stuff, is like relying on a variety of black boxes and then claiming that your results are significant even if you do not know all the steps in between. Hope this scared you from using vendor supplied stuff :-) But putting pressure on vendors, would be a very good thing. Still, most vendors consider random number generation as a some kind of sidetrack, and do not understand its meaning in modern modelling and simulation. Questions? Comments? I'd be happy to reply. Regards, -kari kankaala **************************************************************** Thank you to everyone who replied. I hope this helps some others as much as it has helped me. Dave Young young@slater.cem.msu.edu youngdc@msucem -------------------------------------------------------------------------- It can be easily shown that certain methods are not applicable to solving the many particle Schrodinger equation. However, it has not been shown that it is impossible to find an analytic solution. The only question remaining is "Who will have the honor?" -------------------------------------------------------------------------- From mmadrid@gardel.psc.edu Mon Mar 27 15:24:12 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id PAA00219; Mon, 27 Mar 1995 15:11:00 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA15634; Mon, 27 Mar 95 15:10:58 -0500 From: "Marcela Madrid" Message-Id: <9503271510.ZM15632@gardel.psc.edu> Date: Mon, 27 Mar 1995 15:10:38 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: NMR workshop offered at PSC Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 - STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: April 28, 1995. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION FROM NMR June 25-28, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by APRIL 28, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. --- End of forwarded mail from MAILER-DAEMON (Mail Delivery Subsystem) From mmadrid@gardel.psc.edu Mon Mar 27 15:24:16 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id PAA00234; Mon, 27 Mar 1995 15:11:16 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA15773; Mon, 27 Mar 95 15:11:14 -0500 From: "Marcela Madrid" Message-Id: <9503271511.ZM15771@gardel.psc.edu> Date: Mon, 27 Mar 1995 15:11:05 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: MM/MD workshop offered at PSC Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From mmadrid@gardel.psc.edu Mon Mar 27 15:24:18 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id PAA00336; Mon, 27 Mar 1995 15:11:49 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA15912; Mon, 27 Mar 95 15:11:45 -0500 From: "Marcela Madrid" Message-Id: <9503271511.ZM15910@gardel.psc.edu> Date: Mon, 27 Mar 1995 15:11:36 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: Nucleic Acid and Protein Sequencing Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. The deadline for submitting applications is April 17, 1995. Enrollment is limited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 1995 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 17, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From WANG@IRBM.IT Mon Mar 27 15:39:09 1995 Received: from V1.IRBM.IT for WANG@IRBM.IT by www.ccl.net (8.6.10/930601.1506) id PAA00941; Mon, 27 Mar 1995 15:34:25 -0500 From: Date: Mon, 27 Mar 1995 22:33:11 +0200 (WET-DST) To: CHEMISTRY@ccl.net CC: WANG@IRBM.IT Message-Id: <950327223311.49d@IRBM.IT> Subject: re:Residue Based Solvent Accessible Area >From: Weifan Zheng >Can anyone out there tell me where I can get a program for calculating >the solvent accessible area for each individual residue in a given protein? Hi Weifan, If you are unable to access to a $_package, you can make it based on a QCPE program, such as those kindly donated by Prof. Pearlman, Dr. Connolly and ... As I know, all calculate surface area by atoms. You can insert a subroutine and get the area by residues without too much effort. Ciao, Bingze Wang >From IRBM, Italy From gilson@indigo14.carb.nist.gov Mon Mar 27 15:54:10 1995 Received: from ENH.NIST.GOV for gilson@indigo14.carb.nist.gov by www.ccl.net (8.6.10/930601.1506) id PAA01202; Mon, 27 Mar 1995 15:47:03 -0500 Received: from indigo14.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HOMWIS8PBK00A17F@ENH.NIST.GOV>; Mon, 27 Mar 1995 15:44:31 EST Received: by indigo14.carb.nist.gov (931110.SGI/930416.SGI) for @enh.nist.gov:chemistry@ccl.net id AA16041; Mon, 27 Mar 95 15:39:53 -0500 Date: Mon, 27 Mar 1995 15:39:53 -0500 From: gilson@indigo14.carb.nist.gov (Michael K. Gilson) Subject: Predicting protein-ligand structures. To: chemistry@ccl.net Message-id: <9503272039.AA16041@indigo14.carb.nist.gov> Content-transfer-encoding: 7BIT Given a flexible ligand and a relatively rigid protein whose 3-D structure in the absence of the ligand is known, is there a way of reliably generating a several-thousand member (or smaller) set of protein-ligand complex structures, which is highly likely to include something close (say 1.5 Angstrom RMSD) to the true structure of the complex? Thanks, Mike Gilson gilson@indigo14.carb.nist.gov From srheller@origin.nalusda.gov Mon Mar 27 16:24:09 1995 Received: from cliff.nalusda.gov for srheller@origin.nalusda.gov by www.ccl.net (8.6.10/930601.1506) id QAA01818; Mon, 27 Mar 1995 16:17:34 -0500 Received: from origin.nalusda.gov by cliff.nalusda.gov (4.1/SMI-4.1) id AA28033; Mon, 27 Mar 95 16:20:06 EST Received: by origin.nalusda.gov (5.x/SMI-SVR4) id AA16158; Mon, 27 Mar 1995 16:14:49 -0500 Date: Mon, 27 Mar 1995 16:14:48 -0500 (EST) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software for Review Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 27 March, 1995 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have 4 new software and database products. I am looking for people who are willing to review these software/databases products. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE AVAILABLE. Messages with such replies are trashed! I have tried this approach for about the past four years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 29 March 1995 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@NALUSDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. NIST Mass Spectrometry database for Windows, Version 1.0. The database contains 62,235 high quality mass spectra. The database comes on a CD-ROM or 28 floppy disks. 2. HSC Chemistry for Windows, Version 2.0 from ARS Software. This program allows one to calculate seven different kinds chemical reactions and chemical equilibria: reaction equations, heat and materials balance, equilibrium compositions, electrochemical cell equilibria, formula weights, phase stability diagrams, and Eh-pH diagrams. 3. Chemkey (IBM), from Heterodata in Atlanta, GA, is a database of some 40,000 reactions is available IBM PC/Windows. 4. Chemkey (Mac), from Heterodata in Atlanta, GA, is a database of some 40,000 reactions is available for the Mac. Steve Heller, USDA, ARS, Plant Genome Program Bldg. 005, Room 337 Beltsville, MD 20705-2350 E-Mail: srheller@nalusda.gov Phone: 301-504-6055 FAX: 301-504-6231 From aiba@ir.phys.chem.ethz.ch Mon Mar 27 16:54:59 1995 Received: from bernina.ethz.ch for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.6.10/930601.1506) id QAA03552; Mon, 27 Mar 1995 16:52:42 -0500 Received: from volta (actually volta.ethz.ch) by bernina.ethz.ch with SMTP inbound; Mon, 27 Mar 1995 23:52:32 +0200 Date: Mon, 27 Mar 1995 23:51:56 +0200 Message-Id: <95032723515588@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net, AMFERREIRA@msuvx2.memphis.edu Subject: Re: Complex Valued Hartree-Calculations X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA smtp%"AMFERREIRA@msuvx2.memphis.edu" Dear Netters, I think the question posted by Antonio M. Ferreira is a very interesting one. Should I dare to pass this discission on to our list ? Here is his original question and my (perhaps a bit hastily made) reply. Sincerely, Ayaz Bakasov. > Date: 27-MAR-1995 22:22:28.46 > From: ETHZ::""Antonio M. Ferreira" > " > Subj: Complex Valued Hartree-Calculations > To: chem-comp@mailbase.ac.uk > > I am looking for any information concerning > complex-valued HF calculatoins. I understand > that this has been done in the past, however > I have been unable to find the references. > I would appreciate any information out there, > particularly on such calculations using > complex basis functions leading to complex > density matricies. > >To anyone who can help me, I offer my appreciation > and sincere thanks. > >Tony > Dear Antonio M. Ferreira, I believe that the rejection of complex valued SCF in quantum chemistry is a historical mistake -- it will be eventually improved. The physical ground is that as long as the main features of molecular behavour are concerned, the Coulomb interaction is the leading one - it strongly dominates other interactions like spin-orbit or hyperfine. The Coulomb interaction (taken solely) produces a wave function which has a GLOBAL complex phase which can be put equal to zero everywhere in configuration space (at zero external fields). ONLY magnetic interactions lead to the physical necessity to compexify the wave function and to introduce LOCAL complex phase which depends on coordinates. For instance, in NMR it is a routine to use complex wave functions in ab initio calculations though the magnetic fields are EXTERNAL. Take as example the IGLO package. There are internal magnetic fields but the bulk of quantum chemists believe that they are not significant for most of applications. It is a prejudice and chemists have no motivation to give it up yet. And they make the weather in the field -- the orthodox physicists left long time ago for high energy physics, nuclear physics and so forth (to look for "fundamental problems"), so the molecular physics was left to people who were really interested in it - to chemists. :-) So, "no need to use complex SCF" for zero external magnetic fields. No reason to laugh - one has to have more education in physics, and it will require some time to overcome the inertia to use MOSTLY real wave functions. G92 provides with quite strange means (from physical point of view) which allow to complexify wave function -- look up the manual on page 40, option 'Complex'. It has no great meaning, >from a point of view of a physicist. One idea, is however, accepted (under the pressure of Pople's authority): it is that one has to complexify wave function in the crossing region. The reference is this: J.A.Pople, "Electronic States and Wave Functions Associated with Orbital Energy Crossing" Int. J. Quantum Chem, Symposium, No.5, 175-182 (1971). Beware: it is just TECHNICAL way to avoid (or "solve", as you wish) a purely technical problem INHERENT TO MO APPROACH. It, again, has NO physical significance. I contacted MANY distinguished people in computational molecular physics or in "quantum chemistry" (asking them this "silly" question). It is a very firm consensus NOT to use complex wave functions - and no clear reason to that. I wish you to go ahead in this field and to succeed to create a good HF-code, you will find numerous users to it (I will be the first in queue :-) ). I myself regret to say that present constraints don't allow me to spend more time on this though I will be very glad to cooperate on the topic and to put on the table what I already have about it. I didn't abandon the hope yet that one day I will be working on the problem. If there will be enough material for a summary, it would be nice to have it posted, on CCL for instance. Once more, the best wishes. Sincerely, Ayaz Bakasov. From gavin@vangogh.chem.uab.edu Mon Mar 27 17:09:11 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id QAA03899; Mon, 27 Mar 1995 16:55:44 -0500 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA10847; Mon, 27 Mar 1995 15:49:51 -0600 Date: Mon, 27 Mar 1995 15:49:51 -0600 Message-Id: <9503272149.AA10847@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: TEST! DONOT READ! Cc: Gavin@vangogh.chem.uab.edu TEST!!!! From nauss@ucmod2.che.uc.EDU Mon Mar 27 17:24:11 1995 Received: from ROCK.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/930601.1506) id RAA05526; Mon, 27 Mar 1995 17:22:10 -0500 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-10 #7238) id <01HOMZUKNK6O8WWY62@UCBEH.SAN.UC.EDU>; Mon, 27 Mar 1995 17:20:26 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA03365; Mon, 27 Mar 95 17:23:33 -0500 Date: Mon, 27 Mar 1995 17:23:33 -0500 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: UC Department of Chemistry WWW Site To: CHEMISTRY@ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9503272223.AA03365@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT The Department of Chemistry at the University of Cincinnati is pleased to announce the public unveiling of our WWW page. The URL for our welcome page is: http://www.che.uc.edu This file is to be used by prospective students and other interested parties to learn about our department and university. From there, users may access our internal home page which provides links to other chemistry related sites of interest to our department. Please feel free to stop in for a look and if you have any questions or comments, I will be happy to address them. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From raman@bioc01.uthscsa.edu Mon Mar 27 19:54:12 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id TAA14025; Mon, 27 Mar 1995 19:47:45 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 27 Mar 1995 18:50:27 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA15924; Mon, 27 Mar 95 18:47:46 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9503280047.AA15924@bioc01.uthscsa.edu> Subject: Re: CCL:Residue Based Solvent Accessible Area To: weifan@gibbs.oit.unc.edu (Weifan Zheng) Date: Mon, 27 Mar 1995 18:47:42 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: from "Weifan Zheng" at Mar 27, 95 11:58:20 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1807 Weifan: > Can anyone out there tell me where I can get a program for calculating > the solvent accessible area for each individual residue in a given protein? > Contact Art Perlo in Fred Richards' group at Yale regarding the program ACCESS which will do what you want (perlo@hhvms8.csb.yale.edu). Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/