From chatt@tniri.go.jp Tue Apr 2 01:20:15 1996 Received: from ripspost.aist.go.jp for chatt@tniri.go.jp by www.ccl.net (8.7.1/950822.1) id AAA29278; Tue, 2 Apr 1996 00:25:59 -0500 (EST) Received: from tnhost.tniri.go.jp ([150.82.48.1]) by ripspost.aist.go.jp (8.7.5/3.4W4) with SMTP id OAA00702 for ; Tue, 2 Apr 1996 14:25:34 +0900 (JST) Received: by tnhost.tniri.go.jp (4.1/6.4J.6-tniri.MASTER) id AA02834; Tue, 2 Apr 96 14:24:38 JST Date: Tue, 2 Apr 96 14:24:38 JST From: chatt@tniri.go.jp (Abhijit Chatterjee) Message-Id: <9604020524.AA02834@tnhost.tniri.go.jp> To: CHEMISTRY@www.ccl.net Subject: MEMBERSHIP Respected Sir, I was outstation for a month so my server was suspended. I am back now in the same place, please renew my membership in CCL. with regards Abhijit Chatterjee email : chatt@tniri.go.jp From tamasgunda@tigris.klte.hu Tue Apr 2 03:20:16 1996 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.7.1/950822.1) id DAA00637; Tue, 2 Apr 1996 03:00:45 -0500 (EST) Message-Id: <199604020800.DAA00637@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Tue, 02 Apr 1996 10:00:45 EST Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Tue, 2 Apr 1996 08:37:30 +1 Subject: 5th ICSA - conference CC: amber@cgl.ucsf.edu, anneal@chaco.com, c2-l@msi.com, CAChe@pacificu.edu, charmm-bbs@emperor.harvard.edu, chem-comp@mailbase.ac.uk, watoc@ic.ac.uk, chem-mod@mailbase.ac.uk, dibug@comp.bioz.unibas.ch, hyperchem@hyper.com, isisforum-l@mdli.com, pmd@cumbnd.bioc.columbia.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, anchodd@cc.utas.edu.au, mmodlist@chem.iupui.edu Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) * * * Second Announcement * * * 5th International Conference on Chemical Synthesis of Antibiotics and Related Microbial Products Debrecen (Hungary) September 1-6, 1996 The Organizing Committee has the pleasure to announce the "5th International Conference on Chemical Synthesis of Antibiotics and Related Microbial Products" which, following previous meeting in Aussois (France), Oiso (Japan), Banz (Germany) and Nashville (USA) will be held in Debrecen (Hungary) at the Lajos Kossuth University, from September 1 (Sunday) to September 6 (Friday), 1996. The conference will feature plenary lectures, invited lectures and a poster session. The purpose of the program is to bring experts together and up to date on the developments of topics including isolation, structural elucidation, total synthesis, chemical or biochemical modification and SAR of antibiotics and related natural products of bilogical importance. In order to provide you with a meaningful personal scientific atmosphere, attendance of the Symposium is limited to approximately 300 conferees. Already accepted invitation for a lecture: J.E. Baldwin (Oxford), R. Beugelmans (Gif-sur-Yvette), M. Chmielewski (Warsaw), B. Fraser-Reid (Durham), S. Hanessian (Montreal), F.W. Lichtenthaler (Darmstadt), M.J. Miller (Notre Dome) C. Monneret (Paris), W. Priebe (Houston), H. Redlich (Munster), K. Shiomi (Tokyo), K.Tatsuta (Tokyo), J. Thiem (Hamburg), A. Vasella (Zurich), J. Vilarrasa (Barcelona), A. Weis (San Antinio), D.H. Williams (Cambridge) The conference site, Lajos Kossuth University, is situated in the green belt forest area of Debrecen, the second biggest city of the country, the economic, intellectual and artistic center of Eastern Hungary. With its historical, cultural and religious relics the 631-year old Calvinist town offers plenty of sights to the visitor. Thirty kilometers away from the city the Hortobagy National Park attracts people with the ancient flora and fauna of the Great Hungarian Plain and the "puszta". The guests are also invited to the cellars of Tokaj, to taste the famous Hungarian wines. In the university campus a quiet environment is provided to the conferees for scientific discussions, and there are many opportunities for recreation on the sport grouds and in the world famous medicinal spa of the "Big Forest". Located 230 km east from Budapest, the capital of Hungary, Debrecen is easily accessible from the Budapest International Airport by train, car or in chartered buses. For more information please, write to: Prof. Ferenc Sztaricskai President of 5th ICSA Research Group of Antibiotics of the Hungarian Academy of Sciences, P.O.Box 70, H-4010 Debrecen, Hungary Telefax: (+36-52) 310 936 E-mail: antibiotics@tigris.klte.hu Second Circular is available on request. To receive further infomation and the Second Circular on the 5th International Conference on Chemical Synthesis of Antibiotics and Related Microbial Products Please, return a card to the address above with the following data: NAME:__________________________________________________ ADDRESS:_____________ FAX:___________________________________________________ I am interested in atten- I intend to I plan to bring ding the conference___ present a poster__ ___guest(s). ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From Tim_Mitchell-1@sbphrd.com Tue Apr 2 04:20:16 1996 Received: from phinet.sbphrd.com for Tim_Mitchell-1@sbphrd.com by www.ccl.net (8.7.1/950822.1) id EAA01536; Tue, 2 Apr 1996 04:09:36 -0500 (EST) Received: from pho903.um.us.sbphrd.com by phinet.sbphrd.com; (5.65v3.0/1.1.8.2/06Mar95-1250PM) id AA29910; Tue, 2 Apr 1996 04:09:03 -0500 Received: by pho903.sbphrd.com (IBM OS/2 SENDMAIL VERSION 1.3.2)/1.0) id AA4144; Tue, 02 Apr 96 04:09:14 -0800 Message-Id: <9604021209.AA4144@pho903.sbphrd.com> Received: from SB_PHARM_RD with "Lotus Notes Mail Gateway for SMTP" id 9F0D95AB481CB34D80256300003095D7; Tue, 2 Apr 96 04:09:14 To: CHEMISTRY From: Tim Mitchell-1 Date: 2 Apr 96 9:58:06 EDT Subject: DNA Transformation matrix Mime-Version: 1.0 Content-Type: Text/Plain Does anyone out there know the tranformation matrix required to generate the duplicate strand of A-form DNA. i.e. from a single strand,I want to make a copy of the backbone then rotate n degrees (180 presumably) and translate x Angstroms along a vector v to generate the backbone of the duplicate strand. It's the distance x and the vector v (relative to a backbone bond preferrably) that I'm after. Thanks for any help....... Tim Mitchell _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _____ ____ _/ SmithKline Beecham Pharmaceuticals Ltd _/ _/ / ___\\\\ _ \ _/ Brockham Park _/ _/ | |___ \\|_| | _/ Tim Mitchell, Computational Chemistry Betchworth _/ _/ \___ | | _ < _/ Phone: [0/+44] 1737 36 4535 Surrey _/ _/ ____| | | |_| | _/ Fax: [0/+44] 1737 36 4539 RH3 7AJ _/ _/ \____/ |____/ _/ E-Mail: Tim_Mitchell-1@sbphrd.com U.K. _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From vkitzing@sunny.mpimf-heidelberg.mpg.de Tue Apr 2 07:20:18 1996 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.7.1/950822.1) id GAA02265; Tue, 2 Apr 1996 06:36:52 -0500 (EST) Received: from [192.109.43.47] (mac20.mpimf-heidelberg.mpg.de) by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA11593; Tue, 2 Apr 96 13:36:30 +0200 Message-Id: <9604021136.AA11593@otto.mpimf-heidelberg.mpg.de> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 2 Apr 1996 12:44:26 +0200 To: CHEMISTRY@www.ccl.net (Computational Chemistry List) From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Mobility paradox, summary Cc: bob@aix550.phys.rpslmc.edu (Bob Eisenberg, at Rush University, Chicago), bear@ellington.pharm.arizona.edu (Soaring Bear) Dear colleges on the Computational Chemistry List, this morning I thought about an apparently simple problem where I do not know a solution jet. Consider a symmetric 1:1 electrolyte system with a single dielectric constant which is divided by a planar surface into a right hand and a left hand side. The cationic and anionic concentrations, cC and cA, on both sides are the same; to obtain global electro neutrality cC == cA is required. Exceptions from this rule are allowed only locally, e.g. within a few Debye length around the boundary. The ionic mobilities are mu1 > mu2 on the right hand side and mu2 and mu1 on the other for cations and anions, respectively. At equilibrium there is no problem. Now an external electric field E is applied and this creates the problem. On the first view one would write the individual ionic fluxes jC and jA far away from the central boundary: left hand side and right hand side cations jC(left) = + F mu1 E cC and jC(right) = + F mu2 E cC anions jA(left) = - F mu2 E cA and jA(right) = - F mu1 E cA where F is Faraday's constant. But this implies jC(left) != jC(right) and jA(left) != jA(right) which violates the particle conservation law. I would assume that such a problem has been discussed in literature. Has anybody some ideas? ========================================================================= > >I think that the current density at the cathode is > > j(K)=(mu+ + mu- )F E |Z+|(n+ - (mu-/mu+)dn- - dn-(diff)) > >and at the anode: > > j(A)=(mu+ + mu- )F E |Z-|(n- - dn- + dn-(diff)) > >and for kinetic equilibrium j(K)= j(A) obtains, because the diffusion > >current dn-(diff) will balance the unequal changes in particle density > >in the left and right parts of the cell which stem from the inequality > >of mobility values. > > This may be the situation close to the boundary. But one cannot have > a non-zero concentration gradient over macroscopic distances. I did not realize that by 'planar surface' you meant a material division which separates the cell into two compartments (that is, a membrane).In this case there will of course be no diffusion gradient over macroscopic distances, but instead a diffusion poential which influences the field strength in the left and right compartment.The faster ions will be slowed down and vice versa until the current densities are equal again. I do not think that under these conditions concentration differences between left an right part can be stationary. But if the concentrations are equal again,the diffusion potential should vanish, which gives rise to concentration differences,this again to diffusion potential, ... . I suppose therefore an oscillatory behaviour. Best Wishes, M. Mauksch, CCC uni-erlangen ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From owner-chemistry@ccl.net Tue Apr 2 09:20:18 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id JAA04954; Tue, 2 Apr 1996 09:06:31 -0500 (EST) Received: from cook.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id JAA25275; Tue, 2 Apr 1996 09:06:20 -0500 (EST) Received: from molnir.brunel.ac.uk by cook.brunel.ac.uk with SMTP (PP); Tue, 2 Apr 1996 14:57:31 +0100 From: Jeffrey J Gosper Message-Id: <14684.9604021357@molnir.brunel.ac.uk> Subject: Window's MOPAC GRID viewer To: chemistry@ccl.net Date: Tue, 2 Apr 1996 14:57:19 +0100 (BST) Cc: ca92ccm2@brunel.ac.uk X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Jeff Gosper and Conor McMenamin are pleased to announce the beta-test release of a Window's program, named 'GRID'. The program enables the results from GRID MOPAC calculations to be analysed and viewed. These GRID calculations involve the systematic variation of two geometrical parameters to produce an array of chemical structures. GRID has been developed by Jeff Gosper and Conor McMenamin as part of one of Conor's final year undergraduate research project. The program allows various types of 2D-'contour' maps (including 'Feature' maps) to be viewed. These maps are 'live' in that the user can then select one, or more, points on the map and view the corresponding structure(s) in 3D (NB: this option requires Re_View, Raswin, or similar viewing software to be installed on your computer). The program enables geometrical and energy trends to be explored, such that saddle point, minima, etc can the be readily located and MOPAC input files constructed for further optimization/exploration. The beta test version of GRID is being freely distributed from Re_View's WWW home page: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm We welcome any comments, suggestions, bug reports, etc (as Conor would like to quote some comments in his thesis). Thanks Jeff Gosper From owner-chemistry@ccl.net Tue Apr 2 10:20:28 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id JAA05858; Tue, 2 Apr 1996 09:49:05 -0500 (EST) Received: from gatekeeper.tripos.com for goddette@xhost1.tripos.com by bedrock.ccl.net (8.7.1/950822.1) id JAA28133; Tue, 2 Apr 1996 09:49:04 -0500 (EST) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id IAA05415 for ; Tue, 2 Apr 1996 08:49:03 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma005412; Tue Apr 2 08:48:45 1996 Received: from xhost1.tripos (xhost1.tripos.com [192.160.145.212]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id IAA13903 for ; Tue, 2 Apr 1996 08:46:44 -0600 Received: by xhost1.tripos (940816.SGI.8.6.9/5.6) id OAA01755; Tue, 2 Apr 1996 14:46:31 GMT Date: Tue, 2 Apr 1996 08:46:31 -0600 (CST) From: Dean Goddette Subject: Web Chemistry To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A few weeks ago there was some discussion about Web tools and chemistry. We (Tripos, Inc.) have recently put on-line one example of how the Web can be used for chemistry. We demonstrate the use of java applets for searches in chemical databases. The application can be accessed from: Tripos home page: http://www.webcom.com/~tripos2 Silicon Graphics: http://www.sgi.com/ChemBio (under What's New) Please check it out and sent us your comments. All feedback is welcome. We wish to thank Chapman & Hall, Derwent, and Current Drugs for their permission to use subsets of their databases for this demo; and Silicon Graphics for their assistance and for their cooperation in providing access to their web servers, making this application available worldwide. ------------------------------------------------------------------------------ Dean Goddette, Ph.D. Senior Product Manager TRIPOS, Inc., 1699 S. Hanley Road, St. Louis, MO 63144 ph. (314) 647-1099 X3386 fax: (314) 647-9241 Tripos Delivers Chemical Expertise to the Web Tripos has created a chemical searching application based on Web technology. We believe that Web technologies offer an effective means to provide access to design tools on a range of hardware platforms such as Mac's and PC's. This application is the first step in delivering the molecular design and analysis expertise of Sybyl and UNITY at the desktop. To separate reality from hype, we built an application called "Sketch and Fetch" which is now available on the web with access from multiple sites including the Tripos homepage (www.webcom.com/~tripos2) and under What's New on the Silicon Graphics ChemBio page (www.sgi.com/ChemBio). "Sketch & Fetch" is a Web-based application built with Java applets. Sketch & Fetch provides a simple WebSketcher(tm) to (1) enter a 2D query, (2) choose a UNITY database and (3) initiate a search. Structures matching the query are returned and displayed in a 3D viewer in the page (also a Java applet). The structures can be rotated and manipulated. Subsets from three commercial databases are on-line for searching -- Chapman & Hall, Current Drugs and Derwent's WDI. Hyperlinks provide information about each of the databases. The complete databases (and others) are available in UNITY format from Tripos. "Sketch and Fetch" requires Java and was developed using Netscape Navigator(tm) 2.0. Navigator 2.0 is available for most platforms and can be downloaded from their web page (www.netscape.com). Other Java-capable browsers may also work. A user without a Java-capable Browser is given a description of the applet's function but cannot use the sketcher. I encourage you to give this application a try and let us know what you think. Participants who register are eligible for a prize drawing. Comments and inquiries can be made directly from the web page or can be sent directly to the Database Product Manager, Sheila Ash (sash@tripos.com). This application is the first step in delivering the drug design expertise of Sybyl and UNITY at the desktop using web technology. Tripos would like to thank Silicon Graphics for their assistance and for their cooperation in providing access to their web servers, making this application available worldwide; Derwent, Chapman and Hall and Current Drugs for allowing us to make a subset of their data available on-line. ------------------------------------------------------------------------------ Dean Goddette, Ph.D. Senior Product Manager TRIPOS, Inc., 1699 S. Hanley Road, St. Louis, MO 63144 ph. (314) 647-1099 X3386 fax: (314) 647-9241 goddette@tripos.com Sketch & Fetch: http://www.sgi.com/ChemBio (under What's New) Tripos Home Page: http://www.webcom.com/~tripos2 Sheila Ash e-mail: sash@tripos.com From rsjuds@california.sandia.gov Tue Apr 2 12:20:24 1996 Received: from california.sandia.gov for rsjuds@california.sandia.gov by www.ccl.net (8.7.1/950822.1) id MAA08621; Tue, 2 Apr 1996 12:15:57 -0500 (EST) Received: (from rsjuds@localhost) by california.sandia.gov (8.7.3/1.15) id JAA26458 for CHEMISTRY@www.ccl.net; Tue, 2 Apr 1996 09:15:56 -0800 From: rsjuds@california.sandia.gov (judson richard s) Message-Id: <199604021715.JAA26458@california.sandia.gov> Subject: Internal coordinat MD codes To: CHEMISTRY@www.ccl.net Date: Tue, 2 Apr 1996 09:15:56 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text I am looking for information on MD/MM codes that work in internal (dihedral coordinates) and that calculate analytic gradients (dE/dphi, where phi is a dihedral), and that also return the total energy. I'd appreciate any information on code names and availabilities that you could provide. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering, MS 9214 | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | (510)294-2234 (FAX) | | email: rsjuds@ca.sandia.gov | | | ----------------------------------------------- From herrmann@hermes.informatik.uni-stuttgart.de Tue Apr 2 14:20:20 1996 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.7.1/950822.1) id NAA09561; Tue, 2 Apr 1996 13:30:25 -0500 (EST) Date: Tue, 2 Apr 1996 20:30:22 +0200 Message-Id: <199604021830.UAA26779@odysseus.informatik.uni-stuttgart.de> Received: by odysseus.informatik.uni-stuttgart.de; Tue, 2 Apr 1996 20:30:22 +0200 From: Frank Herrmann To: rsjuds@california.sandia.gov CC: CHEMISTRY@www.ccl.net In-reply-to: <199604021715.JAA26458@california.sandia.gov> (rsjuds@california.sandia.gov) Subject: Re: CCL:Internal coordinat MD codes Hello, here are two references regarding minimizations in dihedral space: @article{fantom, title={The program FANTOM for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in Torsion Angle Space}, author={Thomas Schaumann and Werner Braun and Kurt W"uthrich}, journal= BIOPOL , volume={29}, number={}, pages={679-694}, year=1990} @article{fantom2, title={Efficient Search for All Low Energy Conformations of Polypeptides by Monte Carlo Methods}, author={Berthold von Freyberg and Werner Braun}, journal= JCC , volume={12}, number={9}, pages={1065-1076}, year=1991} they refer to @article{dihderiv, title={Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations}, author={H. Abe and W. Braun and T. Noguti and N. Go}, journal={Computers \& Chemistry}, volume={8}, number={}, pages={239}, year=1984} for the calculation of the derivatives. Regards, ----------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Dept. of Molecular Biophysics 0810 German Cancer Research Center Im Neuenheimer Feld 280, D-69120 Heidelberg Tel: (49) 6221-422336, FAX: (49) 6221-422333 email: Herrmann@odysseus.informatik.uni-stuttgart.de From goddette@xhost1.tripos.com Tue Apr 2 14:34:16 1996 Received: from gatekeeper.tripos.com for goddette@xhost1.tripos.com by www.ccl.net (8.7.1/950822.1) id OAA09734; Tue, 2 Apr 1996 14:01:59 -0500 (EST) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id NAA06622 for ; Tue, 2 Apr 1996 13:01:59 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma006620; Tue Apr 2 13:01:41 1996 Received: from xhost1.tripos (xhost1.tripos.com [192.160.145.212]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id MAA17582 for ; Tue, 2 Apr 1996 12:59:40 -0600 Received: by xhost1.tripos (940816.SGI.8.6.9/5.6) id SAA05302; Tue, 2 Apr 1996 18:59:27 GMT Date: Tue, 2 Apr 1996 12:59:26 -0600 (CST) From: Dean Goddette Subject: Web Chemistry To: CHEMISTRY@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A few weeks ago there was some discussion about Web tools and chemistry. We (Tripos, Inc.) have recently put on-line one example of how the Web can be used for chemistry. We demonstrate the use of java applets for searches in chemical databases. The application can be accessed from: Tripos home page: http://www.webcom.com/~tripos2 Silicon Graphics: http://www.sgi.com/ChemBio (under What's New) Please check it out and sent us your comments. All feedback is welcome. We wish to thank Chapman & Hall, Derwent, and Current Drugs for their permission to use subsets of their databases for this demo; and Silicon Graphics for their assistance and for their cooperation in providing access to their web servers, making this application available worldwide. ------------------------------------------------------------------------------ Dean Goddette, Ph.D. Senior Product Manager TRIPOS, Inc., 1699 S. Hanley Road, St. Louis, MO 63144 ph. (314) 647-1099 X3386 fax: (314) 647-9241 Tripos Delivers Chemical Expertise to the Web Tripos has created a chemical searching application based on Web technology. We believe that Web technologies offer an effective means to provide access to design tools on a range of hardware platforms such as Mac's and PC's. This application is the first step in delivering the molecular design and analysis expertise of Sybyl and UNITY at the desktop. To separate reality from hype, we built an application called "Sketch and Fetch" which is now available on the web with access from multiple sites including the Tripos homepage (www.webcom.com/~tripos2) and under What's New on the Silicon Graphics ChemBio page (www.sgi.com/ChemBio). "Sketch & Fetch" is a Web-based application built with Java applets. Sketch & Fetch provides a simple WebSketcher(tm) to (1) enter a 2D query, (2) choose a UNITY database and (3) initiate a search. Structures matching the query are returned and displayed in a 3D viewer in the page (also a Java applet). The structures can be rotated and manipulated. Subsets from three commercial databases are on-line for searching -- Chapman & Hall, Current Drugs and Derwent's WDI. Hyperlinks provide information about each of the databases. The complete databases (and others) are available in UNITY format from Tripos. "Sketch and Fetch" requires Java and was developed using Netscape Navigator(tm) 2.0. Navigator 2.0 is available for most platforms and can be downloaded from their web page (www.netscape.com). Other Java-capable browsers may also work. A user without a Java-capable Browser is given a description of the applet's function but cannot use the sketcher. I encourage you to give this application a try and let us know what you think. Participants who register are eligible for a prize drawing. Comments and inquiries can be made directly from the web page or can be sent directly to the Database Product Manager, Sheila Ash (sash@tripos.com). This application is the first step in delivering the drug design expertise of Sybyl and UNITY at the desktop using web technology. Tripos would like to thank Silicon Graphics for their assistance and for their cooperation in providing access to their web servers, making this application available worldwide; Derwent, Chapman and Hall and Current Drugs for allowing us to make a subset of their data available on-line. ------------------------------------------------------------------------------ Dean Goddette, Ph.D. Senior Product Manager TRIPOS, Inc., 1699 S. Hanley Road, St. Louis, MO 63144 ph. (314) 647-1099 X3386 fax: (314) 647-9241 goddette@tripos.com Sketch & Fetch: http://www.sgi.com/ChemBio (under What's New) Tripos Home Page: http://www.webcom.com/~tripos2 Sheila Ash e-mail: sash@tripos.com From crawford.ra@pg.com Tue Apr 2 16:20:23 1996 Received: from oldspice.pg.com for crawford.ra@pg.com by www.ccl.net (8.7.1/950822.1) id QAA13483; Tue, 2 Apr 1996 16:18:42 -0500 (EST) From: Received: by oldspice.pg.com (8.6.11/8.6.9) id QAA07802 for ; Tue, 2 Apr 1996 16:12:16 -0500 Received: by smtp400.pg.com via Worldtalk with X400 (3.0.4/1.64) id WT04333.1741; Tue, 02 Apr 1996 13:25:40 EST Date: 2 Apr 96 10:55:00 -0500 To: CHEMISTRY@www.ccl.net Subject: Calcium Basis Sets Message-Id: Hello -- Recently, I began some structural calculations on calcium complexes. So far, I have only found 3 RHF basis sets which allow me to have Ca as an atom -- PM3 (parameterized by Spartan), STO-3G, and 3-21G(*). The calculations which I am doing require a bit more precision than these basis sets allow, but I cannot find any other basis sets which are parameterized for Calcium. If anyone can help, it will be greatly appreciated. Thanks, Ray Crawford Research Associate The Procter & Gamble Company crawford.ra@pg.com PS--> Beings that I AM NOT A MEMBER OF THIS LIST, please send all responses directly to the above mentioned address. Thanks!!!! From owner-chemistry@ccl.net Tue Apr 2 17:20:23 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA14199; Tue, 2 Apr 1996 16:48:33 -0500 (EST) Received: from B.PSC.EDU for HECKATHO@B.PSC.EDU by bedrock.ccl.net (8.7.1/950822.1) id QAA07445; Tue, 2 Apr 1996 16:48:31 -0500 (EST) From: Date: Tue, 2 Apr 1996 16:48:31 -0500 (EST) To: chemistry@ccl.net Message-Id: <960402164831.2040a12c@B.PSC.EDU> Subject: CCL: Supercomputing Techniques Workshop The Pittsburgh Supercomputing Center (PSC) is offering a new kind of supercomputing techniques workshop for biomedical researchers this May. We invite you to review the description below and consider returning an application for it. If you have any questions, please contact Nancy Blankenstein Biomedical Assistant biomed@psc.edu ******************************************************************************* SUPERCOMPUTING TECHNIQUES FOR BIOMEDICAL RESEARCHERS Pittsburgh Supercomputing Center May 5-9, 1996 This newly developed Supercomputing Techniques workshop is aimed at researchers who want to determine if they need supercomputing resources to solve their biomedical research problem(s). It differs from both the Biomedical Applications workshops, which focus on science, and other PSC Techniques workshops, which focus on programming details. The emphasis here will be on practical concepts and assumes no prior supercomputing experience. Applicants should have a working knowledge of either Fortran or C. Participants will learn what resources are potentially available to them through PSC's Biomedical Initiative, including hardware, software and PSC staff expertise. By participating in this course, you should be able to answer the following questions as they pertain to your research computing needs: How can my application benefit from supercomputing? What must I examine to determine this? Is my application massively parallel in nature? Is it more vector oriented? Should I consider a heterogeneous solution involving both vector and massively parallel machines? Are there ways to restructure my application to get more computing power out of the machines already at my disposal? How much effort would be involved to accomplish the necessary modifications, and what are the potential payoffs? Is it worth pursuing at this time? Where do I go from here? The workshop will include informal discussion times to encourage participants to collaborate with one another as well as PSC researchers and scientific support staff. A panel discussion will be held on the final day to further promote discussions between participants and members of the Biomedical Supercomputing Initiative. This workshop is NOT intended to provide detailed information on the use of any one computer system. Other techniques workshops are available that address the details of programming either the C90 or the T3D. Expenses/Registration Fees: Researchers affiliated with a U.S. academic institutions will have their hotel accommodations paid and receive complimentary breakfasts and lunches the days of the workshop. No registration fee will be charged but participants are responsible for all other expenditures connected with attending the workshop, i.e., travel, meals outside the workshop, ground transportation, parking, etc. A few openings may be available for government and industrial researchers: U.S. Government researchers will be charged a registration fee to cover their documentation and workshop meals. They will be responsible for all expenses incurred in travel, accommodations, other meals, etc. Industrial researchers will be charged a registration fee to cover their service units, documentation and the workshop meals. They are responsible for all expenses incurred in travel, accommodations, other meals, etc. This program is sponsored by a National Institutes of Health grant. Enrollment is limited to 20 participants. Deadline for applications: April 5, 1996 A tentative agenda and an on-line application are below. ******************************************************************************* SUPERCOMPUTING TECHNIQUES FOR BIOMEDICAL RESEARCHERS May 5-9, 1996 TENTATIVE AGENDA Sunday: May 5, 1996 Introduction to PSC and the Biomedical Supercomputing Initiative Introduction to PSC Environment (Interactive) Optional computer lab time (each evening of the workshop) Monday: May 6, 1996 Introduction to Supercomputing Parallel Computing Concepts and Hardware C90 and T3D Architecture Overview Parallel Computing Paradigms Tuesday: May 6, 1996 PVM Basics MPI Basics Heterogeneous Computing Westinghouse Tour Wednesday: May 7, 1996 Performance Monitoring Optimization Techniques Practical Considerations Thursday: May 8, 1996 Heterogeneous Scientific Applications Panel Discussion Collaborations/Optional Lab Time ******************************************************************************* PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE SUPERCOMPUTING TECHNIQUES FOR BIOMEDICAL RESEARCHERS May 5-9, 1996 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 and with FORTRAN or C programming language. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by April 5, 1996 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Room 230C Pittsburgh, PA 15213 For additional information: http://www.psc.edu/biomed/workshops.html Direct inquiries to Nancy Blankenstein, biomed@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.