From laaksone@csc.fi Tue Feb 7 01:37:28 1995 Received: from finsun.csc.fi for laaksone@csc.fi by www.ccl.net (8.6.9/930601.1506) id BAA07429; Tue, 7 Feb 1995 01:26:12 -0500 Received: (from laaksone@localhost) by finsun.csc.fi (8.6.9/8.6.9+CSC-2.0) id IAA05038; Tue, 7 Feb 1995 08:26:07 +0200 Content-Transfer-Encoding: 8bit Date: Tue, 7 Feb 1995 08:26:07 +0200 (EET) From: Leif Laaksonen Subject: PC/Windows used in computational chemistry To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I want to thank everybody who have sent me a mail as a reply to my question about the status of the PC/Windows market for computational chemistry. As I can see it now the PC/Windows and specially (Windows NT) market is still to premature. There is excellent work going on by some software houses but not too much in other places. OS/2 Warp is also mixing up the situation in Europe. Specially in Germany shops seem to bundle OS/2 Warp with their hardware in favour of MS Windows. I don't know if this is done because they think Warp is better than Windows or if they just feel uncomfortable with Microsoft. Unix seems to be dominating the CC field more or less totally. The reply to my original question can be reached using Web. URL: http://laaksonen.csc.fi/docs/pcunix.html For those of you who can't use Web I can send you the file by mail, if you request for a copy. Regards, -leif laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 0 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- I dreamed that, as I wandered by the way, Bare winter suddenly was changed to spring. P.B. Shelley ------------------------------------------------------------------- From ross@cgl.ucsf.EDU Tue Feb 7 04:37:41 1995 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.9/930601.1506) id EAA08902; Tue, 7 Feb 1995 04:13:10 -0500 Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.9/GSC4.24) id BAA22498 for chemistry@ccl.net; Tue, 7 Feb 1995 01:13:07 -0800 Date: Tue, 7 Feb 1995 01:13:07 -0800 Message-Id: <199502070913.BAA22498@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: methods In some situations conformation A is lower then B by 7 kcal/mol using amber but B is lower that A by 5 kcal/mol using PM3. We would like to compare the calculations to gas phase experiments. So which method is better and more reliable? The one that best agrees with the experimental results :-) Bill Ross From dsg@hartree.quantchem.kuleuven.ac.be Tue Feb 7 06:37:37 1995 Received: from cc1.kuleuven.ac.be for dsg@hartree.quantchem.kuleuven.ac.be by www.ccl.net (8.6.9/930601.1506) id FAA10031; Tue, 7 Feb 1995 05:41:49 -0500 From: Received: from hartree.quantchem.kuleuven.ac.b by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP; Tue, 07 Feb 95 11:39:21 +0100 Received: by hartree.quantchem.kuleuven.ac.be id AA26160 (5.67a/IDA-1.5 for CHEMISTRY@ccl.net); Tue, 7 Feb 1995 11:31:39 +0100 Date: Tue, 7 Feb 1995 11:31:39 +0100 Message-Id: <199502071031.AA26160@hartree.quantchem.kuleuven.ac.be> To: CHEMISTRY@ccl.net Subject: L-J parameters Hi netters, Could anybody provide me the reference for the L-J parameters of NH2-C=O and CH2-C=O ? Debasis Sengupta dsg@hartree.quantchem.kuleuven.ac.be From CHEM8@vax.york.ac.uk Tue Feb 7 07:39:10 1995 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id HAA10819; Tue, 7 Feb 1995 07:04:22 -0500 Via: uk.ac.york.vax; Tue, 7 Feb 1995 12:01:39 +0000 Date: Tue, 7 Feb 95 12:01 GMT From: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Re: DIFFUSE FUNCTIONS Message-ID: <"leeman.yor.264:07.01.95.12.01.42"@york.ac.uk> In reply to Dr. Novak's question concerning diffuse functions. As was shown in J. Chem. Phys. 102,371 (1995) these can be generated as an even-tempered set using the ratio of the smallest two exponents that exist, of the requisite symmetry, in the basis to be augmented. Thus, if a diffuse p orbital is required, for a set that has the smallest p exponents, x then y, in descending order, the diffuse exponent is y*y/x. (x and y can be contracted). John Waite From cosgrove@zeneca-ph.co.uk Tue Feb 7 07:44:50 1995 Received: from eros.britain.eu.net for cosgrove@zeneca-ph.co.uk by www.ccl.net (8.6.9/930601.1506) id HAA10920; Tue, 7 Feb 1995 07:25:38 -0500 Received: from zeneca-ph.co.uk by eros.britain.eu.net with UUCP id ; Tue, 7 Feb 1995 12:24:48 +0000 From: Dave Cosgrove Date: Tue, 7 Feb 95 13:27:15 GMT Message-Id: <8828.9502071327@iciukph.zeneca-ph.co.uk> Received: from zeneca by iciukph.zeneca-ph.co.uk; Tue, 7 Feb 95 13:27:15 GMT To: chemistry@ccl.net Subject: The Hensa Archive Following my previous post about the Statlib archive at Hensa, which I inadvertently sent to the whole list rather than just the originator of the query, several people have asked where it is. It is located at the University of Kent at Canterbury, England, and can be found at gopher://unix.hensa.ac.uk ftp: unix.hensa.ac.uk (129.12.43.16) the Statlib archive (which is only a small part of what can be found at Hensa) is also available through ftp at lib.stat.cmu.edu (128.2.241.142). Regards, Dave Cosgrove (cosgrove@zeneca-ph.co.uk) From theochem@ctc.com Tue Feb 7 08:37:49 1995 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.9/930601.1506) id IAA11729; Tue, 7 Feb 1995 08:34:44 -0500 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA17575; Tue, 7 Feb 1995 08:35:01 -0500 Received: by pauling.ctc.com (931110.SGI/930416.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA07921; Tue, 7 Feb 95 08:28:20 -0500 From: theochem@ctc.com (Douglas Smith) Message-Id: <9502071328.AA07921@pauling.ctc.com> Subject: parallel & pd DFT code? To: chemistry@ccl.net (Computational Chemistry List) Date: Tue, 7 Feb 1995 08:28:17 -0500 (EST) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 731 I would like to find out what DFT codes are out there, public domain or less than $1000 (you know, the typical academic type code), and which run in parallel. Send directly to me, I will summarize. Doug -- Douglas A. Smith Principal Technical Staff/Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. Lord, grant me the serenity to accept the things I cannot change, the courage to change the things I can and the wisdom to hide the bodies of those people I had to kill because they pissed me off. From herbert.homeier@rchs1.chemie.uni-regensburg.de Tue Feb 7 10:37:54 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id JAA13576; Tue, 7 Feb 1995 09:59:13 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA14887 (5.65c/IDA-1.4.4 for ); Tue, 7 Feb 1995 15:58:33 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA07239; Tue, 7 Feb 95 16:00:09 +0100 Date: Tue, 7 Feb 95 16:00:09 +0100 From: Herbert Homeier (t4720) Message-Id: <9502071500.AA07239@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Re: CCL:Chemistry WWW Sites and comprehensive Lists Dear CCLers, > X-Url: http://rchs1.chemie.uni-regensburg.de/~maillist/data/0056.html > CCL:Chemistry WWW Sites and comprehensive > Lists > > Steven Bachrach (smb@smb.chem.niu.edu) > Fri, 27 Jan 95 08:26:53 -0600 > Sorry for taking up this thread relatively late. > The discussions of chemistry WWW sites, while perhaps not traditionally > a part of computational chemistry, is in my opinion a legitimate topic > for discussion on this list. This list truly reaches the most computer and > network savy subsection of the chemistry community. We are the pioneers of > the web for the chemical community, and decisions we make now will likely > set the precedent and the practice for years to come. > > I strongly object to people trying to limit the discussions on this list. So do I. This discussion belongs to this list. It is good that it focuses now on WWW sites in general, and not so much on departamental home pages as such. The latter are mainly important as the primary interface to the Internet for the local users. Also, they provide the possibility to advertise a little on the net what is done locally. These places usually also provide gateways to local directory services (x.500, whois,...) and other local servers. I think a WWW site in general is an information provider. Also many departamental WWW servers do belong to this category. But there are also many non-university places of interests for chemists as evidenced in listings of external links as for instance Local list via Theoretical Chemistry Gopher via Chemistry at Uni Regensburg Gopher or the Virtual Library. There, one can find hyperlinks to such diverse resources as the Global Instructional Chemistry project, conference listings for chemists, X-ray WWW server, Protein Data Banks and the World Factbook. > One solution to a directory of WWW sites is to establish an automated > (form-based) registration procedure, following the model at the NCSA home site. > If there is interest in establishing this service, perhaps Max Kopelevich, and > Henry Rzepa, and myself and other interested parties can set this up at a > mutually agreed upon site. This is a good idea, and I would like to particate. However, such a form-based interface has to be designed carefully in order to give some sort of quality control of the WWW sites. In a sense, some sort of selection according to quality is ensured by the model which is used now, namely that some webmaster maintains a list of WWW sites which he thinks are valuable (in fact, most users on machines running a WWW server can do that, too: Use a directory public_html in your home directory. Data there can be accessed via WWW using the "URL" http://machinename.domain.somewhere/~username/data.xyz). In the long run, the refereeing process known from journals could be applied, mutatis mutandis, to lists of WWW sites as well. The sites could be refereed, and each list itselve, too. The criteria, however, are rather difficult to find: Number of accesses, nice interface with lots of graphics (not my main interest), useful local data, useful links, searchable indices, reasonable access times via the net (this would be a sort of geographical sorting according to continent/country like 'oh, no, that WWW course can not be recommended, because it is so sloow due to graphical data transfer across the atlantic'), or ...? But one should keep in mind that not only the links are important. They have to point to real data, useful ones. In chemistry, more of the following data might be helpful: - preprint servers and electronic journals - data on materials (Is there any server providing free-access, searchable data bases of experimental and/or theoretical results on transition metals, for instance) ? - software indices (where to find programs on a given topic) - educational material (school, university, industry(!, for instance handbooks)) - easy-to-use tools for information providers (perl-script programming is not exactly, what is needed, for instance). - data bases for graphical images of molecules (to be viewed and/or embedded in manuscripts) - Form-based builletin boards where information can be entered freely for databases as conference listings, software products, ... (corresponding news groups would not be that useful due to their transient nature) - ... This list is obviously incomplete. But it means that developing of such data bases, tools and interfaces should become part of the research activities. besides the "usual" ones. Diploma and PhD theses on data bases and web tools are too rare, and I fear that many people would not regard such work as proper research. But it is highly important work in my opinion. Best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From WADE@EMBL-Heidelberg.DE Tue Feb 7 11:38:40 1995 Received: from Eros.EMBL-Heidelberg.DE for WADE@EMBL-Heidelberg.DE by www.ccl.net (8.6.9/930601.1506) id LAA16002; Tue, 7 Feb 1995 11:32:40 -0500 Received: from EMBL-Heidelberg.DE by EMBL-Heidelberg.DE (PMDF V4.3-7 #2491) id <01HMRYAD03KWGIBYV2@EMBL-Heidelberg.DE>; Tue, 7 Feb 1995 17:32:18 +0100 Date: Tue, 07 Feb 1995 17:32:18 +0100 From: Rebecca Wade Subject: workshop on protein-ligand interactions: correction To: CHEMISTRY@ccl.net Message-id: <01HMRYAD0WIQGIBYV2@EMBL-Heidelberg.DE> X-FAX-defaults: /STN=+49 6221 387 0/SFN=+49 6221 387 306 X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT N.B. Original posting had incorrect e-mail and www addresses. They are correct in the following. Apologies for error. ************************************************************** Workshop on PROTEIN-LIGAND INTERACTIONS: Theoretical Approaches on April 6-7, 1995 at the European Molecular Biology Laboratory, Heidelberg, Germany ************************************************************** The workshop will address biophysical aspects of molecular recognition focusing on the interactions of proteins with other molecules such as drugs, nucleic acids and proteins. Topics will include: Intermolecular force fields; Ligand docking; Drug design; Protein hydration; Molecular Simulation; Neural Networks. Speakers will include: A Buckingham, Cambridge P. Goodford, Oxford K. Gubernator, Basel G. Klebe, Ludwigshafen A. Martin, London P. Wolynes, Illinois Contributions for oral and poster presentations are invited. Registration forms are available from: A. Retzmann, Molecular Biophysics (0810) German Cancer Research Centre Im Neuenheimer Feld 280 69120 Heidelberg, Germany Tel. (+49) 6221 - 422372 Fax (+49) 6221 - 422333 email: A.Retzmann@dkfz-heidelberg.de or on the World Wide Web: http://genome.dkfz-heidelberg.de/nnga/pl-registration.html Deadline for receipt of abstracts is March 10, 1995 Deadline for receipt of registration forms is April 1, 1995 Organizing Committee: R. Wade, H. Bohr and M. Reczko Sponsored by the European Union, EMBL and the German Cancer Research Centre *********************************************************** From bartberg@server.chem.ufl.edu Tue Feb 7 11:42:22 1995 Received: from server.chem.ufl.edu for bartberg@server.chem.ufl.edu by www.ccl.net (8.6.9/930601.1506) id LAA15347; Tue, 7 Feb 1995 11:03:14 -0500 Received: (from bartberg@localhost) by server.chem.ufl.edu (8.6.9/8.6.9) id LAA00194; Tue, 7 Feb 1995 11:06:57 -0500 Date: Tue, 7 Feb 1995 11:06:57 -0500 (EST) From: "Michael D. Bartberger" To: Computational Chemistry List Subject: Prediction of reactive sites Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I would very much appreciate references concerning any methods used to correlate a given molecule's regioselectivity in a given reaction with a property calculable with ab initio methods. For example, using a simple FMO approach, we are taught that "attack" by a nucleophile on a given substrate are predicted / rationalized by looking at the AO coefficients at the LUMO of the substrate and envisioning maximum overlap in the transition state, etc etc. The same goes for electrophilic reactions using the HOMO of the substrate; that (in this case) the electron density and overlap in a TS is greatest at the site with the greatest coefficient. Now, AO coefficients are easily generated in semiempirical programs, where they are generated from a minimal basis, and seem to mimic what one would generate from a valence-only, Huckel-type approximation (for example, look at the AM1 coefficients for ethylene, allyl radical, etc.) With ab initio methods and extended basis sets, "reading" the coefficients in such a manner doesn't seem as plausible, as one obtains coefficients for each of the sets of functions used in the basis. I had asked a question similar to this some time ago; asking whether it is possible to obtain a "total" coefficient of a given AO at a certain MO, or whether one of the coefficients generated in this way should be "plucked out" and used as "the" coefficient. The question was met with mixed sentiments without really ever getting any concrete answer. (By the way, I'm still very much open for suggestions here.) :-) This brings me to the main question. What is the "best" (if any) method for correlating the types of reactivities I've discussed above, whether in polar (like discussed above) or in radical reactions, with either calculated coefficients, or some other property caclulable by ab initio methods. Of course, total TSs can be calculated and the energetics compared, but it would be nice to have some sort of qualitative or semi-quantitative rationale for what governs these reactivities. I will certainly summarize if there is sufficient interest. I hope what I have written makes some sense. :-) Thanks very much! Regards, Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (904) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (904) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________ From jkl@ccl.net Tue Feb 7 11:45:38 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA15217; Tue, 7 Feb 1995 10:59:14 -0500 Date: Tue, 7 Feb 1995 10:59:14 -0500 From: Jan Labanowski Message-Id: <199502071559.KAA15217@www.ccl.net> To: chemistry@ccl.net Subject: Re: support the CCL, once again Cc: jkl@ccl.net Sorry, I made a mistake in my last posting on how to retrieve the original plea for help... It should be: --------- I forgot about get command in GET message.txt ----- If some of you missed my original appeal, it can be retrieved by sending a message: select chemistry cd ccl-proposal ls get message.txt quit to MAILSERV@ccl.net Jan Labanowski CCL Coordinator jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From gregory@wucmd.wustl.edu Tue Feb 7 12:08:40 1995 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by www.ccl.net (8.6.9/930601.1506) id MAA16994; Tue, 7 Feb 1995 12:08:40 -0500 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA14145; Tue, 7 Feb 1995 11:08:34 -0600 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA28347; Tue, 7 Feb 95 08:28:24 -0600 Date: Tue, 7 Feb 1995 08:14:00 -0600 (CST) From: Gregory Nikiforovich Subject: Re: CCL:Semiempirical vs. empirical force fields? To: Gert von Helden Cc: CHEMISTRY@ccl.net In-Reply-To: <9502070239.AA39685@gaucho.ucsb.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 6 Feb 1995, Gert von Helden wrote: > In some situations conformation A is lower then B by 7 kcal/mol > using amber but B is lower that A by 5 kcal/mol using PM3. > We would like to compare the calculations to gas phase experiments. > So which method is better and more reliable? The real point is that most uncertainties in your calculations would probably come from your protocol (annealing) than from the type of force field you use. To compare calculations with any experiment you have to be sure you have found all (at least, the most of) low energy conformers. If any of them (or any of combinations of them) could explain the experimental data, you win. Now, in my experience, with AMBER you can safely assume that any conformer of your peptide within relative energy ca 0.5-0.7 kcal/mol*residue belongs to the low-energy family. It probably would give you up to 30 different possible conformers for the nonapeptide backbone alone. With this level of uncertainty, why be bothered with the question, which force field is "better"? None of them would correspond to the true Boltzmann distribution of conformers. Good luck. ############################################################################## Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130 ############################################################################## From herbert.homeier@rchs1.chemie.uni-regensburg.de Tue Feb 7 12:37:44 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id MAA17072; Tue, 7 Feb 1995 12:12:33 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA20860 (5.65c/IDA-1.4.4 for ); Tue, 7 Feb 1995 18:12:10 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA07687; Tue, 7 Feb 95 18:13:46 +0100 Date: Tue, 7 Feb 95 18:13:46 +0100 From: Herbert Homeier (t4720) Message-Id: <9502071713.AA07687@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Re: CCL:Propose: A Hypermail conversion of the CCL Dear CCLers, > From: h.rzepa@ic.ac.uk (Rzepa,Henry) > I would like to propose that items sent to the CCL list be made available > via WWW pages using Hypermail. For an example, see > http://www.mailbase.ac.uk/hypermail/mac-supporters/archive.html There is now a hypermail entry point to the Automated Archive of Mailing Lists (that presently mirrors new CCL messages). It works, maybe it could be improved. See: http://rchs1.chemie.uni-regensburg.de/gopher/.maillist/ Best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From mmadrid@gardel.psc.edu Tue Feb 7 16:37:52 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.9/930601.1506) id QAA23015; Tue, 7 Feb 1995 16:16:57 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA08166; Tue, 7 Feb 95 16:16:54 -0500 From: "Marcela Madrid" Message-Id: <9502071616.ZM8164@gardel.psc.edu> Date: Tue, 7 Feb 1995 16:16:46 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: NMR workshop offered by 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 USING 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. From mmadrid@gardel.psc.edu Tue Feb 7 16:44:42 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.9/930601.1506) id QAA23058; Tue, 7 Feb 1995 16:18:31 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA08307; Tue, 7 Feb 95 16:18:30 -0500 From: "Marcela Madrid" Message-Id: <9502071618.ZM8305@gardel.psc.edu> Date: Tue, 7 Feb 1995 16:18:23 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: MM and MD of Biopolymers workshop 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 Tue Feb 7 16:45:40 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.9/930601.1506) id QAA23085; Tue, 7 Feb 1995 16:19:57 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA08447; Tue, 7 Feb 95 16:19:56 -0500 From: "Marcela Madrid" Message-Id: <9502071619.ZM8445@gardel.psc.edu> Date: Tue, 7 Feb 1995 16:19:50 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: Nucleic Acid and Protein Sequence Analysis workshop 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 itsigeln@chem.UCSD.EDU Tue Feb 7 18:37:53 1995 Received: from ucsd.edu for itsigeln@chem.UCSD.EDU by www.ccl.net (8.6.9/930601.1506) id SAA25091; Tue, 7 Feb 1995 18:11:21 -0500 Received: from chem.chem.ucsd.edu by ucsd.edu; id PAA17928 sendmail 8.6.9/UCSD-2.2-sun via SMTP Tue, 7 Feb 1995 15:11:16 -0800 for Received: by chem.chem.ucsd.edu (5.51) id AA05674; Tue, 7 Feb 95 15:09:43 PST Received: by chemod0.ucsd.edu (931110.SGI) id AA12871; Tue, 7 Feb 95 15:11:25 -0800 Date: Tue, 7 Feb 95 15:11:25 -0800 From: itsigeln@chem.UCSD.EDU (Igor Tsigelny) Message-Id: <9502072311.AA12871@chemod0.ucsd.edu> To: CHEMISTRY@ccl.net Subject: charges Recently we discussed partial charges in phosphorylated a.acids and I could not find some reasonable references for this problem. Can you help me with the references and data of partial charges for phospho- serine, threonine and tirosine? ------------------------------------------------ IGOR TSIGELNY itsigeln@ucsd.edu