From jeremy@med.su.oz.au Tue Apr 18 00:30:52 1995 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.6.10/930601.1506) id AAA27257; Tue, 18 Apr 1995 00:26:24 -0400 Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.11/8.6.4) id OAA11280 for chemistry@ccl.net Tue, 18 Apr 1995 14:26:09 +1000 From: Jeremy R Greenwood Message-Id: <199504180426.OAA11280@blackburn.med.su.oz.au> Subject: Summary: 13C shift and point charge correlation To: chemistry@ccl.net Date: Tue, 18 Apr 1995 14:26:09 +1000 (EST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 7206 Summary of responses to question concerning correlation between 13C nmr shifts and point charge calculations. Thanks to all who responded. Original question: -------------------------------------------------------------------------- Firstly, it occurs to me, that since the chemical shift of a proton or carbon 13 nucleus depends on electronic shielding (in an nmr experiment), there should be some (at least loose and qualitative) correlation between point charges calculated by one or other theoretical method, and chemical shift (not withstanding solvent effects). I am attempting to identify the correct structures of some isomeric heterocycles from their 1H and 13C spectra. Would you expect changes in point charges to reflect changes in shift between equivalent centres of the isomers? If so, calculated by which method? I'm using semi-empirical (AM1, PM3), and HF calculations. My intuition is that ESP-derived charges are more likely to reflect trends in chemical shift. -------------------------------------------------------------------------- Subject: Re: CCL:nmr & point charges / free-radical visualisation To: jeremy@med.su.oz.au (Jeremy R Greenwood) Date: Wed, 12 Apr 95 12:04:31 EDT From: Lisa Emily Chirlian As a graduate student I investigated the relationship between atomic charges (ab initio electrostatic potential derived) and C-13 NMR chemical shift. While the trends were correctly predicted, individual variation was great, so I think the answer to your question is, no. If you had something you could make comparisons with (i.e. a set of isomers identified some other way), you _might_ be able to make some approximate correlations for your specific case. Lisa -- ------------------------------------------------------------------------- Lisa Chirlian lchirlia@cc.brynmawr.edu Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA 19010 ------------------------------------------------------------------------- From: snyder@euch4e.chem.emory.edu Date: Wed, 5 Apr 1995 18:31:40 -0400 (EDT) To: jeremy@med.su.oz.au Subject: POINT CHARGES AND NMR SHIFTS Dear Dr. Greenwood: Recalling a discussion with an NMR spectroscopist, I know this to be in the literature somewhere. Sorry I don't have the refs. I can suggest, however, that you look in J.Am.Chem.Soc. and Angew.Chem.Int.Edn.Engl. under the name of Paul Schleyer. He and his colleagues have lately been applying methods (in particular GIAO-MP2) for the explicit calculation of NMR chemical shifts. In some of these papers the question of charge and shift are discussed. In JACS 1994, 116, 6386 carbon charges are given for an interesting carbocation for which both experimental and calculated 13C shifts are recorded. JACS 1993, 115, 12385 focuses on 11B and 13C exp vs calculated shifts. Both of the latter paper point out the importance of including correlation effects in the calculations. This is interesting from the point of view that most charges are derived by calculations that don't include correlation; i.e. at the HF (Hartree Fock) level. The implication is that it may be very dangerous to go to far with the use of charges as a guide to relative chemical shifts. I would guess this to work only for systems that are very close in structure. Please send me a summary of the responses your receive. Good luck. Jim Snyder ********************************************************************* Dr. James P. Snyder Emerson Center Chemistry Department Tel: (404)-727-2372 or 2380 Emory University Fax: (404) 727-6586 1515 Pierce Drive E-Mail: snyder@euch4e.chem.emory.edu Atlanta, GA 30322 (USA) ********************************************************************* From: BAELL@mel.dah.csiro.au (Jonathan Baell) To: jeremy@med.su.oz.au (Jeremy R Greenwood) Subject: Re: CCL:nmr & point charges / f Date: Tue, 04 Apr 95 13:53 Dear Jeremy, I'm sure there'll be published work to which you get plenty of references, but just in case you don't, here's my 1000 lire worth. I think charge would correlate in certain instances to chemical shift, but I don't think some effects would be accommodated, particularly conformationally-related ones. I would be interested to know, for example, whether the changes in point charges of the protons of a methyl group in going from a strong aromatic deshielding zone to a shielding one could explain the great difference in anticipated chemical shift. And chemical shift changes between protons and attached carbons, of course are not necessarily in proportion, connectivity versus field effects having a great bearing on the ultimate resonance. Re charge calculation methods: some of this has been worked over the list in the last year or so. I think MNDO ESP is the way to go. Recent improvements in available AMPAC/MOPAC versions have made the calculations much faster. Faster and even better methods have been published and I think are in the pipeline for the software. Two recent papers by Ford and Wang represent breakthroughs (see Bingze Wang and George P. Ford "Atomic Charges Derived from a Fast and Accurate Method for Electrostatic Potentials Based on Modified AM1 Calculations, J. Comp. Chem. 15, 200-207 (1994); George P. Ford and Bingze Wang "New Approach to the Rapid Semiempirical Calculation of Molecular Electrostatic Potentials Based on the AM1 Wave Function: Comparison with Ab Initio HF/6-31G* Results" J. Comp. Chem. 14, 1101-1111 (1993)). Say hello to Hugh Jonathan Ball ---------------------------------------------------------------------- From: Neil McKelvie Subject: C-13 and other chemical shifts To: "Jeremy.R.Greenwood" Status: OR In general, chemical shifts are NOT just dependent on electron densities around the atom in question. They depend on the magnetic field strength at this atom's nucleus. The first paper I know about dealing with this was by H.S.Gutowsky over 30 years ago, on F-19 NMR. This must be in the old Pople, Bernstein, and Schneider book, which of course is showing its age in many ways but is still valuable. A simplified explanation is that a magnetic field causes mixing in of the p-orbitals with m(l) + or -1 (which are complex) into the real p-orbitals px and py. Now, if there is "p-orbital imbalance" either >from different electronegativities of attached atoms, or because one p-orbital is involved in pi-bonding and the others in sigma-bonding, you get more of the p(+1) mixed in, and so a considerable paramagnetic effect. This is why the C-13 shifts of carbonyl groups are so far downfield, not just because of any partial (+) charge on the carbon. Attached protons are affected also - look at the downfield shift of alkene hydrogens. (Prof.) Neil McKelvie; Chemistry Dept., The City College; NY,NY 10031 USA (Voice) 212-650-6062 (Fax) 212-650-6107 NEMCC@CUNYVM.CUNY.EDU ---------------------------------------------------------------------------- Jeremy Greenwood Adrien Albert Laboratory of Medicinal Chemistry Department of Pharmacology University of Sydney NSW 2006 Australia From jeremy@med.su.oz.au Tue Apr 18 00:45:52 1995 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.6.10/930601.1506) id AAA27261; Tue, 18 Apr 1995 00:27:47 -0400 Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.11/8.6.4) id OAA11344 for chemistry@ccl.net Tue, 18 Apr 1995 14:27:44 +1000 From: Jeremy R Greenwood Message-Id: <199504180427.OAA11344@blackburn.med.su.oz.au> Subject: Summary: visualisation of free radicals To: chemistry@ccl.net Date: Tue, 18 Apr 1995 14:27:44 +1000 (EST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 9891 Summary of responses to question concerning visualisation of localisation of free-radicals. Thanks to all who responded. Original question: -------------------------------------------------------------------------- Secondly, I am interested in visualising localisation of free radicals calculated by MOPAC or G92. Some kind of map of spin density would seem to be an appropriate method. Can anyone suggest software (preferably cheap or free!) which can extract and produce this kind of output? I believe that Spartan has this capability, but is outside our price-range. -------------------------------------------------------------------------- From: Peter Fluekiger To: jeremy@blackburn.med.su.oz.au Subject: Molekel Dear Jeremy, thank you for your interest in Molekel. It is indeed esily possible to visualize 3D (and 2D) representations of the spin density distribution with Molekel, just based on the results of a Gaussian 92 computation (you need to launch it with the keywords GFPRINT and POP=REG or POP=FULL). Unfortunately, Mopac is not included yet - it wouldn't be that much work, but time is lacking... Here, I append a short description of Molekel: Molekel is a tool for visualizing results of computational chemistry. Two points have been stressed: first, it can be used as a routine tool for rapidly generating views of electron or spin densities, orbitals, meps or vibrational modes from the standard output files of the compoutational packages (or simply molecular structures), and second, very nice and sophisticated views can be generated for conferences or posters using recent techniques such as 1D-textures for representing surface properties and others. What is still missing, even though it is planned for the future, is a molecule editor. And well, it's a university development which means that we cannot guarantee the reliability and support such as a commercial enterprise, and the user's guide is still quite sparse. Several research groups in Switzerland have been using Molekel for quite some time to their entire satisfaction, and last year, we started commercializing the package for 500.- swiss francs for non-profit organizations, and 5000.- for commercial ones (i.e. ~US $ 380.- and 3800.-) for the licence for one group. Molekel is running on practically all SGI workstations with hard- or software zbuffer. Unfortunately, we cannot provide test-licenses. I hope these indications are helpful for you! sincerely yours peter Here is a cut-and-paste from a small leaflet describing Molekel: ------------------------------------------------------------------------------- MOLEKEL is a powerful 3-dimensional molecular graphics package for the interactive visual representation of molecular structures and properties. It is mainly designed for generating detailed, easily interpretable and esthetically appealing graphical output based on structural data and the results of physico-chemical calculations. Due to the flexibility of the data- and program-structure, various chemical systems ranging from small organic compounds to large macro-molecules may be investigated, and due to its modularity, additional interfaces and tools can easily be implemented. MOLEKEL offers an intuitive and userfriendly graphical user-interface with mouse-driven menus, file-browser, dialog-boxes and mouse-driven tools for manipulating the represented 3D-objects. Various models for data visualization can be chosen in MOLEKEL: wire-frame, ball-and-stick, stick-only or spacefilling representation for the molecules; dotted, chicken-wire, solid or semi-transparent representation for the surfaces which may be cut by clipping planes. Object- and background colors can be modified individually, and on machines which support texture-mapping, different textures can be applied to all objects. For maximum realism, shadows can be added to the scenes. MOLEKEL contains various data-interfaces to external electronic structure calculation program-packages: Gaussian, a library of ab initio quantum-chemistry methods Gamess, Hondo, Amoss, direct ab initio quantum-chemistry code deMon, density functional calculation code ADF, density functional calculation code Icon8, semi-empirical calculations based on the Extended Hueckel method EHProp, semi-empirical calculations of interaction energies based on the Extended Hueckel method (Soon: Mopac, Mndo, Prddo). For all of these packages, the standard output files can be read, the structures can be extracted and the molecular orbitals, the spin density and the electron density can be calculated and visualized. For ICON8 and EHProp (and soon for Gaussian and Amoss) the input can be generated and the calculations can be launched from within MOLEKEL. Supplementary packages can easily be added to this list. Connolly's MS-program is equally interfaced for generating molecular dot-surfaces. Internal modules of MOLEKEL allow the generation of solid models of different properties: a fast (!) surface triangulation tool transforms dot-surfaces into solid surfaces, and an iso-surface tool generates solid representations of densities and wavefunctions. A contour tool allows the generation of 2D-contour-plots within the 3D-scene. Surface properties can either be visualized using a color-code, or, on machines which support texture-mapping, by quantized colors and contour-lines on the surfaces. MOLEKEL allows the rapid investigation of results from external packages, as well as the construction of complex graphical representations for publications or conferences, and on demand, additional features for special applications may be implemented additionally. -- ----------------------------------------------------------------------------- Peter F. Fluekiger, Ph. D. Scientific Visualization Centro Svizzero di Calcolo Scientifico Tel : (41) 91 50 83 27 Via Cantonale Fax : (41) 91 50 67 11 CH-6928 Manno (Switzerland) E-mail : Peter.Flukiger@cscs.ch ----------------------------------------------------------------------------- From: mayer@cric.chemres.hu Date: Wed, 5 Apr 1995 17:44:08 +0200 Message-Id: <9504051544.AA07658@cric.chemres.hu> To: jeremy@blackburn.med.su.oz.au Subject: Free radicals Dear Dr. Greenwood, I think, you need the "free valence indices" for visualizing free radicals. These were introduced in my paper I. Mayer, Chem. Phys. Lett. 27, 290 (1983) with some correction in Addendum to that paper: CPL 117, 396 (1985); also see IJQC 26, 151 (1984) [addendum 28, 419 (1985)]; and papers TCA 67, 315 (1985); IJQC 29, 73, 477 (1986) , etc. You will get for each atom a number which is the measure of the free spin on it - something as a "dot" on a chemical formula of a radical. If you are interested, I can send you routines which then you can adapt to your programs. Best regards, Prof. Istvan Mayer Central Research Institute for Chemistry of the Hungarian Academy of Sciences E-mails: mayer@cric.chemres.hu and IB13LVIB@HUEARN.sztaki.hu (or IB13LVIB@HUEARN.bitnet); H1376May@ella.hu (or H1376May@HUELLA.bitnet) >From landin@membrana.mednet.gu.se Mon Apr 10 20:24:49 1995 ------------------------------------------------------------------------- From: "Johan Landin" Date: Mon, 10 Apr 1995 12:23:20 -0600 To: jeremy@med.su.oz.au Subject: RE: free-radical visualisation Cc: landin@clavicula.mednet.gu.se > Secondly, I am interested in visualising localisation of free radicals > calculated by MOPAC or G92. Some kind of map of spin density would > seem to be an appropriate method. Can anyone suggest software (preferably > cheap or free!) which can extract and produce this kind of output? > I believe that Spartan has this capability, but is outside our price-range. Dear Dr. Greenwood, The MOLEKEL program is able to produce 3D plots of the spin density superimposed on the molecular strucuture. The price for acacademics are ~500 sFr. (Swiss Francs) Contact Dr. Peter Fluekiger at the Swiss Scientific Computing Center (flukiger@cscs.ch) for more information. Yours Sincerely /Johan Landin ___________________________________________________________________ Johan Landin Tel: +46 31 773 3767, 773 3762 Dept. of Medical Biochemistry Fax: +46 31 41 6108 Medicinaregatan 9 Home: +46 31 14 7554 S-413 90 Goteborg, Sweden Email: landin@mednet.gu.se -------------------------------------------------------------------------- Date: Thu, 6 Apr 1995 07:17:24 -0800 To: Jeremy R Greenwood From: jim@volvo.wavefun.com (jim Parisi) Subject: Re: CCL:nmr & point charges / free-radical visualisation Hello, I am the sales and marketing coordinator for Wavefunction. I know Jill Gready has several licenses, but she is in a different department. As such, Spartan is $1,900 for new academic customers. Is this the price you had referenced as out of price range? Let me know if I can be of any assistance. Thanks! Jim Parisi Marketing/Sales Coordinator _________________________________________________________________ WAVEFUNCTION, INC. Phone: 714-955-2120 18401 Von Karman, Suite 370 FAX: 714-955-2118 Irvine, CA e-mail: jim@wavefun.com 92715 USA WEB: http://wavefun.com ----------------------------------------------------------------- C A R P E D I E M _________________________________________________________________ Jeremy Greenwood Adrien Albert Laboratory of Medicinal Chemistry Department of Pharmacology University of Sydney NSW 2006 Australia From rull@rhino.chem.ruu.nl Tue Apr 18 04:45:56 1995 Received: from ruucv1.chem.ruu.nl for rull@rhino.chem.ruu.nl by www.ccl.net (8.6.10/930601.1506) id EAA29623; Tue, 18 Apr 1995 04:31:04 -0400 Received: from rhino by ruucv1.chem.ruu.nl (5.65/4.13) with SMTP id AA21711; Tue, 18 Apr 1995 10:30:48 +0200 Received: by rhino (931110.SGI/930416.SGI.AUTO) for @RUUCV1.chem.ruu.nl:chemistry@ccl.net id AA29446; Tue, 18 Apr 95 10:30:33 +0100 From: rull@rhino.chem.ruu.nl (Ton Rullmann) Message-Id: <9504180930.AA29446@rhino> Subject: Re: CCL:PROCHECK located WWW_page... To: chemistry@ccl.net (ccl) Date: Tue, 18 Apr 1995 10:30:30 +0100 (WDT) In-Reply-To: <199504121900.PAA21269@destrier.acsu.buffalo.edu> from "Emil Marcus" at Apr 12, 95 03:00:34 pm X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 796 A correction to an earlier mail: > > WWW Page: Procheck 3.2 > Roman Laskovski et al. > http://bsmchal.biochem.ucl.ac.uk/~roman/procheck/procheck.html ^ should be 1 (digit, not letter). The current version is 3.3. Source code to be found in ftp://bsmcha1.biochem.ucl.ac.uk/pub/procheck/source3_3 (vms users) or ftp://bsmcha1.biochem.ucl.ac.uk/pub/procheck/tar3_3 (unix users) See first ftp://bsmcha1.biochem.ucl.ac.uk/pub/procheck/README -- | Ton Rullmann NMR Spectroscopy | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533641 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | 3584 CH Utrecht, The Netherlands | Email: rull@nmr.chem.ruu.nl | From gadre@unipune.ernet.in Tue Apr 18 05:30:57 1995 Received: from sangam.ncst.ernet.in for gadre@unipune.ernet.in by www.ccl.net (8.6.10/930601.1506) id FAA29880; Tue, 18 Apr 1995 05:20:16 -0400 Received: from unipune.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id OAA09009 for CHEMISTRY@ccl.net; Tue, 18 Apr 1995 14:50:13 +0530 Received: from unipune.UUCP by iucaa (4.1/SMI-4.1) id AA01281; Tue, 18 Apr 95 14:47:42+050 Received: by unipune.unipune.ernet.in (5.0/SMI-SVR4) id AA04688; Tue, 18 Apr 1995 14:32:08 +0500 Date: Tue, 18 Apr 1995 14:32:08 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9504181932.AA04688@unipune.unipune.ernet.in> To: CHEMISTRY@ccl.net Subject: Micellar molecules Cc: gadre@unipune.ernet.in Content-Length: 407 Hi. I posted a query recently but either did not get replies OR they were lost. The question is : Is there a fundmental difference in the electronic environment of the "hydrophobic" tail of say dodecane and dodecylsulfate? Please send the reply again if already replied. Thanks. Shridhar Gadre April 18, 1995. From h0159cap@rz.hu-berlin.de Tue Apr 18 07:01:05 1995 Received: from hpcom.rz.hu-berlin.de for h0159cap@rz.hu-berlin.de by www.ccl.net (8.6.10/930601.1506) id GAA00924; Tue, 18 Apr 1995 06:53:22 -0400 Received: from ejoker.rz.hu-berlin.de by hpcom.rz.hu-berlin.de with SMTP (1.38.193.5/15.6-10.92) id AA06004; Tue, 18 Apr 1995 12:53:10 +0200 Received: from localhost by joker.rz.hu-berlin.de (8.6.4/X1.00.syb) id MAA19114; Tue, 18 Apr 1995 12:54:58 +0200 From: h0159cap@rz.hu-berlin.de (Frank Eisenmenger) Message-Id: <199504181054.MAA19114@joker.rz.hu-berlin.de> Subject: CCL: autocorrelation for dihedrals To: chemistry@ccl.net Date: Tue, 18 Apr 1995 12:54:56 +0200 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1124 Hi All, during conformational analysis of peptides the following question occurred: given a (time-)series of conformations for a linear,four-atom molecule described by one dihedral angle (=tau, range 180 ... +180) How calculate the autocorrelation function for tau, taking into account the "cyclic" behaviour of dihedrals ? Thanks for your ideas, Frank Eisenmenger +------------------------------------------------------------------------+ | Institute of Biochemistry | | Medical Faculty of the Humboldt University (Charite) | | | | Hessische Str. 3-4 | | 10115 Berlin, Germany | | | | Phone: +49-30-28468-612 or -239 FAX: +49-30-28468-600 | | E-mail: h0159cap@joker.rz.hu-berlin.de | +------------------------------------------------------------------------+ From lutz@ricx.royal-institution.ac.uk Tue Apr 18 08:46:01 1995 Received: from sun2.nsfnet-relay.ac.uk for lutz@ricx.royal-institution.ac.uk by www.ccl.net (8.6.10/930601.1506) id IAA02129; Tue, 18 Apr 1995 08:43:49 -0400 Via: uk.ac.royal-institution.ricx; Tue, 18 Apr 1995 13:43:17 +0100 From: Lutz Ackermann Date: Tue, 18 Apr 95 13:38:41 +0100 Message-Id: <20096.9504181238@ricx.ri.ac.uk> To: CHEMISTRY@ccl.net Subject: re:relativistic corrections on TM systems in response to CCL request by zacarias@papalotl.pquim.unam.mx (e-mail ok???) Hola Se~nor Zacarias, you were asking for results on the relevance of relativistic tratment of transition metal systems. You may want to check out a recent article by Roesch and Krueger (Munich), in which relativistic and montelativistic benchmark calculations for MO and MCO are compared (both LDF and gradient corrected DFT results), M being Ni, Pd and (I think) also Pt. It appeared in JCP a few weeks ago. With best regards L. Ackermann <^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^> < Dr. Lutz Ackermann > < Davy-Faraday Research Laboratory > < The Royal Institution of Great Britain > < 21 Albemarle Street > < London W1X 4BS > < UK > < > < phone: +44-171-409 2992 ext 424 > < FAX: +44-171-629 3569 > < e-mail: lutz@ricx.ri.ac.uk > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv ps: Por que no alegran Uds. con nuestras flores tambien? -------- From stevens@rainbow.uchicago.edu Tue Apr 18 11:03:50 1995 Received: from midway.uchicago.edu for stevens@rainbow.uchicago.edu by www.ccl.net (8.6.10/930601.1506) id KAA04912; Tue, 18 Apr 1995 10:56:22 -0400 Received: from rainbow.uchicago.edu (rainbow.uchicago.edu [128.135.136.33]) by midway.uchicago.edu (8.6.10/8.6.4) with SMTP id JAA10656 for <@midway.uchicago.edu:chemistry@ccl.net>; Tue, 18 Apr 1995 09:56:21 -0500 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA17402; Tue, 18 Apr 95 09:56:03 -0500 From: stevens@rainbow.uchicago.edu (Jonathan Stevens) Message-Id: <9504181456.AA17402@rainbow.uchicago.edu> Subject: hondo8 To: chemistry@ccl.net Date: Tue, 18 Apr 1995 09:56:02 -0500 (CDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 227 I would like to thank everyone who responded to my query concerning a manual for hondo8. Jonathan Stevens University of Chicago James Franck Institute Chicago, Illinois 60637 312-702-9003 stevens@rainbow.uchicago.edu From mmadrid@gardel.psc.edu Tue Apr 18 11:10:54 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id LAA05146; Tue, 18 Apr 1995 11:00:45 -0400 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA01081; Tue, 18 Apr 95 11:00:43 -0400 From: "Marcela Madrid" Message-Id: <9504181100.ZM1079@gardel.psc.edu> Date: Tue, 18 Apr 1995 11:00:37 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: 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. DEADLINE FOR SUBMITTING APPLICATIONS IS FRIDAY, APRIL 21, 1995. Enrollment is lmited 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 21, 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 Apr 18 11:17:48 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id LAA05169; Tue, 18 Apr 1995 11:01:15 -0400 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA01220; Tue, 18 Apr 95 11:01:13 -0400 From: "Marcela Madrid" Message-Id: <9504181101.ZM1218@gardel.psc.edu> Date: Tue, 18 Apr 1995 11:01:06 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: NMR workshop 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 AFFILIATED 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. From mmadrid@gardel.psc.edu Tue Apr 18 11:17:52 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id LAA05198; Tue, 18 Apr 1995 11:01:49 -0400 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA01359; Tue, 18 Apr 95 11:01:47 -0400 From: "Marcela Madrid" Message-Id: <9504181101.ZM1357@gardel.psc.edu> Date: Tue, 18 Apr 1995 11:01:41 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: MOLECULAR DYNAMICS 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 AFFILIATED 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 jkl@ccl.net Tue Apr 18 13:01:06 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id MAA07867; Tue, 18 Apr 1995 12:47:16 -0400 Date: Tue, 18 Apr 1995 12:47:16 -0400 From: Jan Labanowski Message-Id: <199504181647.MAA07867@www.ccl.net> To: chemistry@ccl.net Subject: ACES II workshop at UnFlorida@Gainesville Cc: jkl@ccl.net ACES II WORKSHOP May 17-20, 1995 University of Florida Dear Colleague, For you, your students, or associates who would like to learn more about ab initio, correlated quantum chemistry, and particularly the benefits that the ACES II program system can provide in your research, this is a special opportunity. We have designed a four-day workshop, conducted by some of the authors, to provide an outstanding opportunity to learn about the flexibility of ACES II and the wealth of different calculations possible, many of which are unique to ACES II. Our hands-on ACES II Workshop, conducted on SGI Indigos (courtesy of Silicon Graphics, Inc.), will take place from May 17-20, 1995, in the Reitz Union at the University of Florida, Gainesville, Florida. The workshop will be tailored to address your individual needs; from molecular structures, to searching for transition states, to excited states, hyperpolarizabilities, etc., all using state-of-the-art correlated methods and density functional theory. Please retrieve postscript files from CCL archives for further information and registration form: ftp www.ccl.net Name: anonymous Password: Your_True_e-mail_address cd pub/chemistry/info get ACESII-form.ps get ACESII-info.ps quit Tuition, which includes lodging, reception, two special dinners, daily continental breakfasts, and detailed lecture notes, is at an inclusive $750 per person. Enrollment will be limited to 20 participants, housed conveniently in single rooms at the Reitz Union on the University of Florida campus. Although the course is intense, companions are invited to accompany a participant by payment of an additional $100 to cover the social affairs. Don't miss out on this unique opportunity to get all your questions about ab initio theory answered by experts, and to expand the depth and breadth of your applications with ACES II. Please reserve space now by returning the attached registration form (in postscript file) today to: Rodney J. Bartlett Quantum Theory Project University of Florida P.O. Box 118435 Gainesville, FL 32611-8435 OR FAX TO: (904) 392-8722 OR, FOR MORE INFORMATION, CALL: (904) 392-1597 From talafous@curly.chem.cwru.edu Tue Apr 18 14:01:09 1995 Received: from thor.INS.CWRU.Edu for talafous@curly.chem.cwru.edu by www.ccl.net (8.6.10/930601.1506) id NAA09383; Tue, 18 Apr 1995 13:57:35 -0400 Received: from curly.chem.cwru.edu (curly.CHEM.CWRU.Edu [129.22.200.87]) by thor.INS.CWRU.Edu with SMTP (8.6.10+cwru/CWRU-2.3) id NAA24240; Tue, 18 Apr 1995 13:55:52 -0400 (from talafous@curly.chem.cwru.edu) Received: by curly.chem.cwru.edu (931110.SGI/920502.SGI.AUTO) for mxz12@po.cwru.edu id AA12867; Tue, 18 Apr 95 14:03:54 -0400 From: talafous@curly.chem.cwru.edu (Joe Talafous) Message-Id: <9504181803.AA12867@curly.chem.cwru.edu> Subject: protein modelers To: chemistry@ccl.net Date: Tue, 18 Apr 1995 14:03:45 -0500 (EDT) Cc: mxz12@po.cwru.edu X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 908 Dear Fellows, I'd like to get a feel for the feasibility of a project for the Ohio Supercomputer for which I might write a possible grant. Could you drop me your phone number and/or e-mail address if you've worked with a Cray Y/MP before with CHARMm? I'd like to get an idea of the number of picoseconds that I can get out of molecular dynamics per CRAY hour in CHARMm, within an order of magnitude. Please tell me of any reasonable CPUtime approximations that you used. I'm working on a 45 residue peptide that is extremely important, yet very difficult to study experimentally. Its bioactivity is conformationally dependent and folding is driven by both charges and hydrophobicity, so solvent will have to be included. An accurate modeling may provide some idea as to what is going on... Thank you for any insights you may have, Joseph Talafous, Ph. D. Case Western Reserve University From ar1z+@andrew.cmu.edu Tue Apr 18 15:16:06 1995 Received: from andrew.cmu.edu for ar1z+@andrew.cmu.edu by www.ccl.net (8.6.10/930601.1506) id PAA10867; Tue, 18 Apr 1995 15:15:03 -0400 Received: (from postman@localhost) by andrew.cmu.edu (8.6.12/8.6.9) id PAA12909; Tue, 18 Apr 1995 15:14:49 -0400 Received: via switchmail; Tue, 18 Apr 1995 15:14:48 -0400 (EDT) Received: from unix6.andrew.cmu.edu via qmail ID ; Tue, 18 Apr 1995 15:13:49 -0400 (EDT) Received: from unix6.andrew.cmu.edu via qmail ID ; Tue, 18 Apr 1995 15:13:35 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.44.27.pmax.ul4.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix6.andrew.cmu.edu.pmax.ul4 via MS.5.6.unix6.andrew.cmu.edu.pmax_ul4; Tue, 18 Apr 1995 15:13:34 -0400 (EDT) Message-ID: <0jZ0xSS00WB7FWtlVg@andrew.cmu.edu> Date: Tue, 18 Apr 1995 15:13:34 -0400 (EDT) From: "Alexander J. Ropelewski" To: Outbound News Subject: CCL:Sequence Analysis Workshop Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , chemistry@ccl.net, rna@net.bio.net, Outbound News 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 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. DEADLINE FOR SUBMITTING APPLICATIONS IS FRIDAY, APRIL 21, 1995. Enrollment is lmited 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 21, 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.