From owner-chemistry@ccl.net Mon Jun 26 01:18:38 1995 Received: from aqua.chem.nagoya-u.ac.jp for mito@aqua.chem.nagoya-u.ac.jp by www.ccl.net (8.6.10/930601.1506) id BAA21288; Mon, 26 Jun 1995 01:09:11 -0400 Received: from localhost (mito@localhost) by aqua.chem.nagoya-u.ac.jp (8.6.9+2.4W/3.3Wb-94112516) with SMTP id OAA23614; Mon, 26 Jun 1995 14:06:25 +0900 Message-Id: <199506260506.OAA23614@aqua.chem.nagoya-u.ac.jp> X-Authentication-Warning: aqua.chem.nagoya-u.ac.jp: Host localhost didn't use HELO protocol To: hommes@derioc1.organik.uni-erlangen.de Cc: CHEMISTRY@ccl.net Subject: Re:g94 on HP9000/735: makefile patch included In-reply-to: Your message of "Sat, 24 Jun 1995 15:13:49 JST." Date: Mon, 26 Jun 1995 14:06:24 JST From: Masakatsu Ito Thank you for your quick response and usefull comments, Dr. Hommes. I've successfully installed g94 on HP after replacing the makefile and changing l609.F as gaussian.com instructed me. I cannot know whether your patch is essentially same as the one which gaussian.com send me. But I will post the patchfile, if they allow me to do so. Masakatsu Ito Department of Structual Molecular Science The Graduate University for Advanced Studies Tel 81(Japan)-52-789-3656 Fax 81(Japan)-52-789-3551 E-mail mito@aqua.chem.nagoya-u.ac.jp From owner-chemistry@ccl.net Mon Jun 26 02:48:39 1995 Received: from hobbes.gh.wits.ac.za for craig@hobbes.gh.wits.ac.za by www.ccl.net (8.6.10/930601.1506) id CAA26218; Mon, 26 Jun 1995 02:39:59 -0400 Received: (from craig@localhost) by hobbes.gh.wits.ac.za (8.6.11/8.6.9) id IAA00805; Mon, 26 Jun 1995 08:35:14 +0200 Date: Mon, 26 Jun 1995 08:35:13 +0200 (GMT+0200) From: Craig Taverner To: FS300627@Sol.YorkU.CA cc: chemistry@ccl.net Subject: Re: CCL:Chemical structures as GIF files In-Reply-To: <01HS4KRE3CSY8WWS3M@Sol.YorkU.CA> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 25 Jun 1995 FS300627@Sol.YorkU.CA wrote: > Greetings, > > Does anybody know what chemical drawing programs will allow > the user to export a structure as a GIF file. I have tried > several options by exporting a file as a WMF file and then > use a program to convert WMF to GIF but it doesn't do a good > job. > > Any ideas? Egbert Keller (kell@ruf.uni-freiburg.de) provides the program SCHAKAL (commercial) for both DOS and unix/X. Although it only produces screen, hpgl, PCL5 and SIF formats, not only is there some support for PCX and TIFF in the pipeline, I have had very good results simply doing a screen grab on high res X window screens with xv and then exporting as GIF (and several other formats). Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From owner-chemistry@ccl.net Mon Jun 26 04:03:40 1995 Received: from swifr9 for Olivier.Schafer@unifr.ch by www.ccl.net (8.6.10/930601.1506) id DAA29785; Mon, 26 Jun 1995 03:49:09 -0400 Message-Id: <199506260749.DAA29785@www.ccl.net> Received: from UFPER6.UNIFR.CH by swifr9 with SMTP (PP); Mon, 26 Jun 1995 09:48:51 +0200 Received: from UFPER6.UNIFR.CH via Pony Express VMS Mail FPI (v8.1.1-fpi001); Mon, 26 Jun 95 09:48:00 MET Date: Mon, 26 Jun 95 09:48:00 MET From: Olivier Schafer To: chemistry@ccl.net Cc: Olivier.Schafer@unifr.ch Subject: CCL:Compiling ADF on SGI Power Challenge X-Vms-To: PONY%"CHEMISTRY@ccl.net" X-Vms-Cc: SCHAFER Hi, I am trying to compile the Amsterdam Density Functional program (ADF V1.1.4) on our brand new Sgi Power Challenge. I get core dumps at run time when compiling with the 64bit compiler (32bit is OK). Even with no optimization the program dumps core at a WRITE(FORMAT,'(I2)')N statement (FORMAT is a string). There must be a problem with memory pointers somewhere. Any help ? Olivier Schafer Institut de Chimie Inorganique 1700 Fribourg Switzerland From owner-chemistry@ccl.net Mon Jun 26 04:18:43 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.10/930601.1506) id EAA00533; Mon, 26 Jun 1995 04:01:00 -0400 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 26 Jun 1995 09:00:31 +0100 Received: from [155.198.224.89] by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA15999; Mon, 26 Jun 95 09:00:26 +0100 X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 26 Jun 1995 08:01:33 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Re: CCL:Chemical structures as GIF files >On Sun, 25 Jun 1995 FS300627@Sol.YorkU.CA wrote: > >> Greetings, >> >> Does anybody know what chemical drawing programs will allow >> the user to export a structure as a GIF file. I have tried >> several options by exporting a file as a WMF file and then >> use a program to convert WMF to GIF but it doesn't do a good >> job. >> >> Any ideas? I believe the new version of ChemWindow/Chemintosh will export structures as GIF, although whether GIF87 or 89a I am uncertain. Also Raster3D as used at the Molecules R Us site produces superb rendered GIF images. Take a look also at our hyperglossary which uses this concept; http://www.ch.ic.ac.uk/ectoc/glossary/ Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.1.2; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. World-Wide Web URL: http://www.ch.ic.ac.uk/rzepa.html From owner-chemistry@ccl.net Mon Jun 26 04:48:43 1995 Received: from gauss.uib.es for guillem@gauss.uib.es by www.ccl.net (8.6.10/930601.1506) id EAA02660; Mon, 26 Jun 1995 04:43:24 -0400 From: Received: by gauss.uib.es; id AA15207; Mon, 26 Jun 1995 10:43:13 +0100 Message-Id: <9506260943.AA15207@gauss.uib.es> To: chemistry@ccl.net Subject: summary: Carnegie-Mellon Quantum Archive Date: Mon, 26 Jun 95 10:43:13 +0100 X-Mts: smtp Dear Netters, Here is the summary of the responses answering my question about the Carnegie-Mellon Quantum Archive. I regret to say that my email sent to Gaussian Inc. asking for info has not been yet replied. My original question was: >Dear Netters, > >I would like to know if the Carnegie-Mellon Quantum Archive (from Prof. >Pople's group) is still operational and how it can be accessed via INTERNET, >if possible. > > Many thanks for your help. And the answers: *********************************************************************** Hello! Prof. Pople retired from Carnegie Mellon (CMU) three years ago. He is now at Northwestrn University at Chicago. There is a conputational chemistry archive at CMU's chemistry department. I am not sure if that is the Archive you mentioned. You might want to take a look. You can access it through WWW. Get into CMU's front door, (http://www.cmu.edu/), then go to "colleges", etc. The other computer in my lab is down, I one I am using is slow to get into WWW, otherwise I could have found the exact address for you. Good luck! Jingfeng Zhang postdoc at Chemistry Department, CMU zhang@chem.cmu.edu *********************************************************************** Dear Dr Suner, Its available for Netscape or Mosaic the access to Gaussian Basis Set in: http://www.emsl.pnl.gov:2080/forms/basisform.html Optimizations of atoms its possible! But, the program (originated in the group of Pople at Carnegie-Melon) is now developed by Gaussian Inc. and the information can be obtained via e-mail at: info@gaussian.com I would be interested in seeing a summary of any responses your receive to your questions. Thanks and best wishes Angelica -- _________________________________________________ Claudia Angelica Garcia Zacarias Quimica Inorganica. Fisica y Quimica Teorica DEPg., Facultad de Quimica, UNAM Mexico, D.F. 04510 Tel/Fax: (525) 622 3724; (525) 622 3776 e-mail: zacarias@papalotl.pquim.unam.mx zac@servidor.unam.mx *********************************************************************** Hola Guillermo: Recientemente he tratatdo de localizar por email al Prof. Pople pero no parece ser un asiduo lector del mismo. Si le quieres contactar, lo mejor es llamarle por telefono o mandar un fax. Sus datos son: Prof. John A. Pople Northwestern University Tel: (708) 491 3403 (708) 491 5372 Fax: (708) 491 7713 Tengo entendido que el viernes pasado salio de viaje. Espero que esta informacion te sirva. Saludos Alberto ========================================================================== Dr. Alberto Vela Tel: (525) 724 4675 Departamento de Quimica Fax: (525) 724 4666 Area de Fisicoquimica Teorica Universidad Autonoma Metropolitana email: ava@xanum.uam.mx Unidad Iztapalapa A.P. 55-534 Mexico D.F. 09340 MEXICO *********************************************************************** The last spanish e-mail says that Prof. Pople is not a regular email user, and it includes his phone and fax number. Many thanks to you all who replied to my question. Guillem ------------------------------------------------------------------------ Dr Guillermo A. Suner; Dep. de Quimica, UNIVERSITAT DE LES ILLES BALEARS E-07071-Palma de Mallorca, SPAIN. E-mail: guillem@gauss.uib.es Tel: + 34 71 173498 Fax: + 34 71 173426 WWW URL: http://www.uib.es/depart/dqu/dquo/suner.html From owner-chemistry@ccl.net Mon Jun 26 08:03:44 1995 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2x2.mat.uni-bayreuth.de by www.ccl.net (8.6.10/930601.1506) id IAA12391; Mon, 26 Jun 1995 08:00:20 -0400 Received: from btm2x2.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA01551; Mon, 26 Jun 95 13:36:31 +0200 Received: by btm2x2.mat.uni-bayreuth.de (4.1/SMI-4.1) id AA08991; Mon, 26 Jun 95 13:35:21 +0200 Date: Mon, 26 Jun 95 13:35:21 +0200 From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland) Message-Id: <9506261135.AA08991@btm2x2.mat.uni-bayreuth.de> To: FS300627@Sol.YorkU.CA Subject: Chemical structures as GIF files Cc: chemistry@ccl.net >On Sun, 25 Jun 1995 FS300627@Sol.YorkU.CA wrote: > >> Greetings, >> >> Does anybody know what chemical drawing programs will allow >> the user to export a structure as a GIF file. I have tried >> several options by exporting a file as a WMF file and then >> use a program to convert WMF to GIF but it doesn't do a good >> job. >> >> Any ideas? You could try RASMOL by R. Sayle which is available from various ftp servers (try ARCHIE) for MS-Windows and UNIX X-Windows. It doesn't allow to draw interactively, but has very nice pictures with several export formats (including gif). It accepts as input e.g. PDB-format. Hope this helps Thomas Thomas Wieland +---------------+ Dipl. Math. |+---- +----+| Lehrstuhl II f. Mathematik |\ \ | || Universitaet Bayreuth | \ \ | || | \ \ | || 95440 Bayreuth | \ \\ || Germany | \ \\ || Tel. +49 (921) 553386 | \ \\ || Fax +49 (921) 553385 | \-------|| +---------------+ From owner-chemistry@ccl.net Mon Jun 26 08:18:46 1995 Received: from tigger.jvnc.net for frccgate.sandoz.com!snell.chris@sandoz.com by www.ccl.net (8.6.10/930601.1506) id HAA11847; Mon, 26 Jun 1995 07:50:05 -0400 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA00248 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Mon, 26 Jun 1995 07:50:06 -0400 From: snell.chris@frccgate.sandoz.com Received: from umc by sndzeh via MR/HANNET with conversational-MRIF; Mon, 26 Jun 95 03:48:04 -0400 Posted: Mon, 26 Jun 95 08:27:01 -0400 Date: Mon, 26 Jun 95 08:27:01 -0400 Sender: snell.chris@frccgate.sandoz.com Author: snell~chris@HANNET.umc Message-Id: <25738062605991/221499@SCDC01> To: chemistry@ccl.net Cc: m.dooley@mailbox.uq.oz.au Subject: Re: CCL:Quantitative assessment of novel ligands In response to your question - 'what molecular parameters can be generated to convince an organic chemist to synthesise a molecule you have designed?' Before embarking on this process you should also view the question from the organic chemists point of view. He will be considering your compound and prioritising it with other compounds he is already synthesising and will probably make this assessment based on i) synthesisability (a major problem with de novo designed ligands) ii) the state of the project (is it early days and leads are scarce, or is it towards the end of the project when fine tuning is the focus?) iii) how far is the structure away from the known SAR iv) in the light of ii and iii what are the chances of success and are the risks worth taking. There are probably other questions, but I doubt whether any other parameters will make a great difference to your ability to persuade a busy organic chemist to synthesise your compounds. Presumably you are convinced that the molecules you have designed are worth making, therefore your best approach is to present your argument based on how you have designed the molecules, but most important of all, you should have your chemist collaborators on board at an early stage in the modelling and involve them as much as possible in the process. Along with the basic tenet of modelling: 'No modelling without experimentation' (A. Vintner) we should possibly add: 'No synthesis without dialog' ?! If you are not convinced yourself that these molecules are worth making and that their synthesis will answer this question, then you need to get into activity prediction, i.e. QSAR using MOPAC generated parameters, principal component analysis etc, or using Comfa (Tripos). These are not trivial exercises but do give a prediction that may help to decide whether the molecules are worth synthesising. Good luck anyway! Chris Snell Molecular Modelling and Computational Chemistry Sandoz Institute for Medical Research 5 Gower Place London WC1E 6BN E-Mail snell@sandoz.com Tel 0171-333-2165 Fax 0171-387-4116 ______________________________ Reply Separator _________________________________ Subject: CCL:Quantitative assessment of novel ligands Author: M.DOOLEY@MAILBOX.UQ.OZ.AU@UMC@HANNET at DECPostmaster Date: 25/06/95 21:21 I'm searching for a protocol or recipe of 'vital statistics' to assess novel ligands that i've designed, so that i'll have firm arguments to convince organic chemists to synthesise a molecule. I'm using biosym software + intuition to de novo design ligands for a target with good x-ray data and also have access to Oxford Molecular software. If it might not be possible to roughly predict binding constants for novel compounds that differ greatly from known ligands, are there methods to predict the effects of modifications to known ligands. I'm aware of scoring functions such as Bohm Comput-aided mol des (1994) 243, but I'm not sure if this would be appropriate. Eagerly awaiting any suggestions. Michael Dooley Ph.D. Centre for Drug Design and Development University of Queensland -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: owner-chemistry@ccl.net -- Original Sender From: Address: M.Dooley@mailbox.uq.oz.au CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV From owner-chemistry@ccl.net Mon Jun 26 09:18:47 1995 Received: from srv.cip.physik.tu-muenchen.de for thuber@Physik.TU-Muenchen.DE by www.ccl.net (8.6.10/930601.1506) id JAA16542; Mon, 26 Jun 1995 09:17:41 -0400 Received: from speedy.cip.physik.tu-muenchen.de by srv.cip.physik.tu-muenchen.de with SMTP id AA19889 for (5.67a/IDA-1.5/bs04); Mon, 26 Jun 1995 12:47:59 +0200 Received: by speedy.cip.physik.tu-muenchen.de (4.1/SMI-4.1) id AA27104; Mon, 26 Jun 95 12:47:58 +0200 Date: Mon, 26 Jun 95 12:47:58 +0200 From: Thomas.Huber@Physik.TU-Muenchen.DE Message-Id: <9506261047.AA27104@speedy.cip.physik.tu-muenchen.de> To: chemistry@ccl.net Subject: Re: Mol mod Linux progs Dr. Shapiro wrote: We are in the process of installing Linux version 1.2.1 on our Pentium/ 90 MHz PC. If anyone can recommend good molecular modelling/QSAR programmes for Linux, I would appreciate your contacting me directly. If these pro- grammes are available by FTP, kindly send me the exact FTP address, subdirec- tory, and programme name. Please note: I do _not_ yet have access to the WWW. 1. Molecular Mechanics/Dynamics, MolMod Tools: We have adapted AMBER 4.1beta for Linux w/ f2c & gcc, you'll find a Linux compatible version in the official 4.1 release. [ Contact Prof.Kollman's group, try amber@cgl.ucsf.edu ] 2. Distance Geometry We also have a running C language version of DGEOM 95. (The original FORTRAN file could not be compiled with f2c/gcc (neither 2.5.8 nor 2.6.3)!) [ Contact QCPE for the DGEOM license ] 3. Quantum Mechanics The GAMESS package is also ready to compile on linux. [ Contact mike@si.fi.ameslab.gov for details ] 4. Mol. Graphics The RasMol program is included in some Linux distributions and can compiled on linux/X11R6. [ Contact "rasmol@dcs.ed.ac.uk" or "rasmol@ggr.co.uk" or get the source from any larger ftp server near your site (I think there is a nic.switch.ch?!) ] 5. Tools&Development If you are interested in running parallel jobs with Linux, try TCGMSG. This is the only Message Passing Library which could be used to test parallel jobs on one CPU _and_ distributing jobs on several CPUs. The more popular PVM could not be tested in parallel on one node/CPU. I didn't succeed in porting ANL/MPI or MPICH. As a replacement for the f77 script from f2c I would highly recommend to use the fort1.6 PERL script instead. It is also available on most ftp sites. If you have any questions, feel free to contact me! Thomas Huber Institut fuer Physikalische Biochemie der Universitaet Muenchen Schillerstrasse 44 80336 Muenchen Germany (email: thuber@physik.tu-muenchen.de) ----------- End Forwarded Message ----------- From owner-chemistry@ccl.net Mon Jun 26 09:23:18 1995 Received: from unb.ca for AJIT@UNB.CA by www.ccl.net (8.6.10/930601.1506) id JAA16193; Mon, 26 Jun 1995 09:07:06 -0400 Received: from UNBVM1.CSD.UNB.CA by unb.ca (8.6.12/950414-15:35) id KAA03286; Mon, 26 Jun 1995 10:07:06 -0300 Received: from UNBVM1.CSD.UNB.CA by UNBVM1.CSD.UNB.CA (IBM VM SMTP V2R2) with BSMTP id 3677; Mon, 26 Jun 95 10:05:37 ADT Received: from UNB.CA (NJE origin MUSIC@UNBVM1) by UNBVM1.CSD.UNB.CA (LMail V1.2a/1.8a) with BSMTP id 3676; Mon, 26 Jun 1995 10:05:36 -0300 Message-Id: <26JUN95.10899772.0197.MUSIC@UNB.CA> Date: Mon, 26 Jun 95 10:05:32 -0300 From: "Ajit J. Thakkar" To: Cc: Baukje Miedema Subject: CSTC-12 symposium program X-Mailer: MUSIC/SP V3.1.1 ******************************** * * * R E M I N D E R * * * * HAVE YOU REGISTERED? * * * ******************************** 12th Canadian Symposium on Theoretical Chemistry 12ieme Symposium Canadien sur la Chimie Theorique Fredericton, 6-11 August/Aout 1995 Co-chairmen: William J. Meath and Ajit J. Thakkar The 12th Canadian Symposium on Theoretical Chemistry will be held August 6-11, 1995 at the Wu Conference Centre, University of New Brunswick, Fredericton, NB, under the co-chairmanship of William J. Meath (University of Western Ontario) and Ajit J. Thakkar (University of New Brunswick). The program will include invited papers and contributed posters in all areas of theoretical chemistry. Contributed papers are welcome in all areas of theoretical chemistry. All contributed papers will be given in poster format. For registration forms, contact the Conference Secretary, 12th CSTC, Department of Chemistry, University of New Brunswick, Fredericton, NB E3B 6E2, Canada. Fax: 506-453-4981. Internet: coyy@unb.ca The schedule for the plenary lectures is given below: MONDAY, August 7 Session 1; Chair: M.C. Zerner, University of Florida H.A. Scheraga, Cornell University Theoretical Studies of Protein Folding A. Rauk, University of Calgary Oxidative Damage to Peptides: Breaking the Ground Session 2; Chair: R.A. Poirier, Memorial University W.L. Jorgensen, Yale University Molecular Recognition in Organic and Biochemical Systems P.G. Mezey, University of Saskatchewan Molecular Shape Analysis from Diatomics to Proteins: Ab Initio Quality Local and Global Electron Density Representations by the Medla Method J.T. Hynes, University of Colorado How Do Acids Ionize in Water? Session 3; Chair: S.G. Whittington, University of Toronto J.M. Andre, Universitaires Notre-Dame de la Paix Theoretical Aspects of the Calculation of Polarizabilities of Organic Polymers D.W. Sumners, Florida State University Topological Entanglement in Polymers Session 4; Chair: R.S. Dumont, McMaster University W.H. Miller, University of California, Berkeley Quantum Theory of Chemical Reaction Rates D.M. Wardlaw, Queen's University The Influence of Hindered Rotations in the Recombination Kinetics of Radicals TUESDAY, August 8 Session 5; Chair: S.M. Rothstein, Brock University D. Ceperley, University of Illinois at Urbana-Champaign Quantum Monte Carlo Methods for Electronic Structure R.E. Kapral, University of Toronto Reaction Dynamics in Mesoscopic Molecular Clusters Session 6; Chair: T.T. Nguyen-Dang, Laval University H.A. Rabitz, Princeton University Intervention and Interrogation of Molecular Dynamics A.D. Bandrauk, Universite de Sherbrooke Molecules in Intense Laser Fields: Dissociation, Ionization, Coulomb Explosions and Stabilization K.C. Showalter, West Virginia University Stabilizing and Tracking Stationary States and Periodic Orbits in Chaotic Systems Session 7; Chair: J. Paldus, University of Waterloo D.J. Moore, Universite de Geneve Berry Phases: Theory and Applications W. Yang, Duke University Linear Scaling Methods for Electronic Structure Calculations: The Divide-and-Conquer Strategy Session 8; Chair: W.G. Laidlaw, University of Calgary D.R. Salahub, Universite de Montreal Structure, Properties, and Reactivity of Clusters and Surfaces from Density Functional Theory K.B. Whaley, University of California, Berkeley Clusters - interpolations and surprises in the science between molecules and bulk phases WEDNESDAY, August 9 Session 9; Chair: J.S. Wright, Carleton University E.R. Davidson, Indiana University Unconventional Applications of Conventional Ab Initio Methods J. Simons, University of Utah Chemically Incorrect Molecular Structures Session 10; Chair: R.J. Boyd, Dalhousie University R.J. Bartlett, University of Florida Excited States Using the Equation-of-Motion Coupled Cluster Method S.D. Peyerimhoff, Universitat Bonn Multi-Reference CI Calculations of Molecular Spectra: From small to large molecules P. Botschwina, Universitat Gottingen Interaction Between Theory and Experiments in the Molecular Spectroscopy of Reactive Species THURSDAY, August 10 Session 11; Chair: B.C. Sanctuary, McGill University M.A. Ratner, Northwestern University Electron Transfer in Molecules and Molecular Wires (tentative) H.J. Kreuzer, Dalhousie University Oscillating Hydrogen-Water Reactions on a Platinum Field Emitter Session 12; Chair: T. Ziegler, University of Calgary D.M. Bishop, University of Ottawa Linear and Nonlinear Optical Properties: the Magnetic Story J. Oddershede, Odense University Response Calculations of Dipole Oscillator Strength Sum Rules and Related Quantities P. Pyykko, University of Helsinki Relativistic Effects on Molecular Properties Session 13; Chair: T. Carrington, Jr., Universite de Montreal C.E. Dykstra, Indiana University-Purdue University,Indianapolis Ab Initio and Model Studies of Weakly Bound Trimers and Other Clusters B. Jeziorski, University of Warsaw Symmetry adapted Perturbation Approach to Intermolecular Potential Energy Surfaces Session 14; Chair: I.P. Hamilton, Wilfred Laurier University D.G. Truhlar, University of Minnesota Kinetics and Reaction Dynamics and their Interface with Potential Energy Surfaces R.J. LeRoy, University of Waterloo Determining Potential Energy Surfaces from the Spectra of Van der Waals Complexes FRIDAY, August 11 Session 15; Chair: G.N. Patey, University of British Columbia S.A. Rice, University of Chicago Properties of Langmuir Monolayers and other Pseudo-Two Dimensional Systems W. Meyer, Universitat Kaiserslautern Theoretical Investigation of the Autoionization Process in Molecular Collision Complexes Session 16; Chair: V.H. Smith, Jr., Queen's University J.N. Murrell, University of Sussex Potentials for Elemental Solids, Surfaces and Clusters; A Unified Scheme From owner-chemistry@ccl.net Mon Jun 26 10:17:54 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/930601.1506) id KAA01485; Mon, 26 Jun 1995 10:11:56 -0400 From: Received: from rzurs10.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA08539; Mon, 26 Jun 95 16:11:36 +0200 Received: by rzurs10.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA119490; Mon, 26 Jun 1995 16:11:35 +0200 Message-Id: <9506261411.AA119490@rzurs10.unizh.ch> Subject: Reflecting stereoscope To: chemistry@ccl.net Date: Mon, 26 Jun 1995 16:11:35 +0200 (MEST) X-Mailer: ELM [version 2.4 PL24 PGP2] Content-Type: text Content-Length: 425 Dear Colleagues; In order to assist me in visualising the pictures generated in "split image" format using Hyperhem release 3.0 for Windows as stereoscopic images, I have been advised to obtain a "reflecting stereoscope". Can anyone explain to me just what one of those things is, from where they may be obtained, and the $$$? Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From owner-chemistry@ccl.net Mon Jun 26 10:30:58 1995 Received: from Lilly.com for JOHNSON_DOUGLAS_W@Lilly.com by www.ccl.net (8.6.10/930601.1506) id KAA01492; Mon, 26 Jun 1995 10:12:03 -0400 Received: from DECNET-MAIL (RX23376@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-10 #6224) id <01HS5N80RXN4001VKI@INET.D48.LILLY.COM>; Mon, 26 Jun 1995 09:11:32 -0500 (EST) Date: Mon, 26 Jun 1995 09:11:32 -0500 (EST) From: "Doug Johnson/MC625/dwj@lilly.com" Subject: Ampicillin structure To: chemistry@ccl.net Message-id: <01HS5N80T082001VKI@INET.D48.LILLY.COM> X-VMS-To: CHEMISTRY X-VMS-Cc: ME MIME-version: 1.0 Content-transfer-encoding: 7BIT There was a recent post regarding ampicillin not being in Cambridge Structural Database; I had retrieved this structure several years ago from CSD; it is in fact present with the refcode being AMCILL: AMCILL Ampicillin 6-(D-(-)-alpha-Aminophenyl-acetamido)-penicillanic acid antibiotic activity C16 H19 N3 O4 S1 M.O.Boles,R.J.Girven Acta Crystallogr.,Sect.B, 32, 2279,1976 Hope this helps. Doug Johnson Lilly Research Labs dwj@lilly.com Indianapolis, IN 46285 From: JOHNSON DOUGLAS W (MCVAX0::RX23376) To: VMS MAIL ADDRESSEE (IN::"chemistry@ccl.net") cc: JOHNSON DOUGLAS W (MCVAX0::RX23376) From owner-chemistry@ccl.net Mon Jun 26 12:16:24 1995 Received: from gsusgi1.Gsu.EDU for chessyx@gsusgi1.Gsu.EDU by www.ccl.net (8.6.10/930601.1506) id MAA05100; Mon, 26 Jun 1995 12:13:53 -0400 Received: (from chessyx@localhost) by gsusgi1.Gsu.EDU (8.6.10/8.6.10) id MAA24793 for chemistry@ccl.net; Mon, 26 Jun 1995 12:13:53 -0400 Date: Mon, 26 Jun 1995 12:13:53 -0400 From: Shijie Yao Message-Id: <199506261613.MAA24793@gsusgi1.Gsu.EDU> To: chemistry@ccl.net Subject: How to get QM contribution to Free Energy Dear Netters We are using free energy perturbation calculation to get the solvation free energy difference for this reaction. H R | | /\/\/\ /\/\/\ |O|O|O| -----> |O|O|O| \/\/\/ \/\/\/ anthracene 9-R anthracene R could be anything (e.g. CH3, CH2CH3 etc.) Could some one please tell us how to treat the quantum mechanical energy contribution in the reaction of anthracene ---> 9-R anthracene (R could be anything e.g. CH3, CH2CH3 etc.)? According to Prof. Kollman's papers, we need to add the quantum mechanical energy contribution of changing anthracene to substituted anthracene and the zero point vibrational energy difference between the two systems to the solvation free energy to get the total free energy change for the reaction (We also would like to know an explanation why we need to add the quantum mechanical energy contribution and zero point vibrational energy difference). Please write directly to me at chessyx@gsusgi1.gsu.edu I'll summarize the responses if there is enough interest. Thanks for your help. chessyx From owner-chemistry@ccl.net Mon Jun 26 12:46:25 1995 Received: from canastra for dantas@canastra.fisica.ufjf.br by www.ccl.net (8.6.10/930601.1506) id MAA05565; Mon, 26 Jun 1995 12:29:44 -0400 Received: by canastra (Linux Smail3.1.28.1 #1) id m0sQRbs-000Mz4C; Tue, 27 Jun 95 00:46 EST Message-Id: Date: Tue, 27 Jun 95 00:46 EST From: dantas@canastra.fisica.ufjf.br (Socrates de Oliveira Dantas) To: chemistry@ccl.net Subject: Internet address... Cc: -v@canastra.fisica.ufjf.br Dear Colleagues; We are interested in the e-mail of Prof. Ari Aviram. Can you help me? Thank you in advance. Yours sincerely, (Dr.) Socrates de Oliveira Dantas Departamento de Fisica Instituto de Ciencias Exatas Universidade Federal de Juiz de Fora Minas Gerais - Brasil e-mail: dantas@fisica.ufjf.br Phone: (055032) 229-3307/229-3313 Fax: (055032) 229-3312 From owner-chemistry@ccl.net Mon Jun 26 12:48:27 1995 Received: from actcom.co.il for boris@dcl.co.il by www.ccl.net (8.6.10/930601.1506) id MAA05684; Mon, 26 Jun 1995 12:35:08 -0400 Received: from dclpc by actcom.co.il with SMTP (8.6.12/actcom-0.1) id TAA11596 for ; Mon, 26 Jun 1995 19:35:35 +0300 (rfc931-sender: dcl.co.il [192.114.194.1]) Received: from elan1.dcl.co.il by dclpc (5.65/SMI-4.1) id AA19638; Mon, 26 Jun 95 18:54:07 +0100 Received: by elan1.dcl.co.il (940816.SGI.8.6.9/SMI-4.1) id SAA14040; Mon, 26 Jun 1995 18:59:46 +0300 Date: Mon, 26 Jun 1995 18:59:46 +0300 From: boris@dcl.co.il (Boris Vesterman) Message-Id: <199506261559.SAA14040@elan1.dcl.co.il> To: chemistry@ccl.net Subject: Re:Quantitative assessment of novel ligands Michael Dooley recently asked about software for quantitative assessment of novel ligands. > I'm searching for a protocol or recipe of 'vital statistics' > to assess novel ligands that i've designed, so that > i'll have firm arguments to convince organic chemists > to synthesise a molecule. I'm using biosym software + > intuition to de novo design ligands for a target with good > x-ray data and also have access to Oxford Molecular software. > If it might not be possible to roughly predict binding > constants for novel compounds that differ greatly from known > ligands, are there methods to predict the effects of > modifications to known ligands. I'm aware of scoring functions Dear Michael, According to your question in CCL about tools for the ligands design, I want to turn your attention to the program Apex-3D integrated with insightII (BIOSYM). It allows among other things to build 3D QSAR models and predict binding constants for novel compounds. A short description of the methods incorporated into Apex-3D can be found in the http://www.dcl.co.il/apex3d.html. More detailed description is in the Apex-3D Manual available from BIOSYM. Please feel free to contact me for additional information. Sincerely yours Boris Vesterman *---------------------------------------------------* | Boris Vesterman, Ph.D. | | | | DCL Systems International Ltd. | | 20 Galgalei Haplada St. Herzlia Industrial Area | | P.O.B. 544 Herzlia 46105 Israel | | Phone: 972-9-584684 | | Fax: 972-9-543917 | | E-mail: boris@dcl.co.il | *---------------------------------------------------* From owner-chemistry@ccl.net Mon Jun 26 13:16:24 1995 Received: from beavis.chemse.gatech.edu for sahmed@beavis.chemse.gatech.edu by www.ccl.net (8.6.10/930601.1506) id NAA06401; Mon, 26 Jun 1995 13:06:54 -0400 Received: by beavis.chemse.gatech.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id NAA04610; Mon, 26 Jun 1995 13:06:48 -0400 From: "Savant Ahmed" Message-Id: <9506261306.ZM4608@beavis.chemse.gatech.edu> Date: Mon, 26 Jun 1995 13:06:48 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: SCRF in Gaussian92 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, While trying to run a SCRF geometry optimization and frequency job on a molecule with 261 basis functions[HF/6-311+G(2d,p)] with Mem=4000000 I get the following error: NBasis is 261 maximum for raffinetti integral format is 255. Dimensioning error detected by BadBas. Error termination in Lnk1e. Is there a way to fix this? Thanks in advance. Savant -- Savant Ahmed From owner-chemistry@ccl.net Mon Jun 26 15:31:26 1995 Received: from relay3.UU.NET for frisch@lorentzian.com by www.ccl.net (8.6.10/930601.1506) id PAA11124; Mon, 26 Jun 1995 15:29:39 -0400 Received: from uucp1.UU.NET by relay3.UU.NET with SMTP id QQyvvh13019; Mon, 26 Jun 1995 15:29:36 -0400 Received: from m10.UUCP by uucp1.UU.NET with UUCP/RMAIL ; Mon, 26 Jun 1995 15:29:36 -0400 Received: from mjf by m10.lorentzian.com; Mon, 26 Jun 1995 16:57:59 -0400 Received: by mjf (AIX 4.1/UCB 5.64/4.03) id AA20610; Mon, 26 Jun 1995 15:29:01 -0400 From: frisch@lorentzian.com (Mike Frisch) Message-Id: <9506261929.AA20610@mjf> Subject: Re: CCL:SCRF in Gaussian92 To: chemistry@ccl.net Date: Mon, 26 Jun 1995 15:29:01 -0400 (EDT) In-Reply-To: <9506261306.ZM4608@beavis.chemse.gatech.edu> from "" at Jun 26, 95 01:06:48 pm X-Mailer: ELM [version 2.4 PL24] Content-Type: text Content-Length: 742 Savant Ahmed writes: > > Hi, > > While trying to run a SCRF geometry optimization and frequency job on a > molecule with 261 basis functions[HF/6-311+G(2d,p)] with Mem=4000000 I get the > following error: > > NBasis is 261 maximum for raffinetti integral format is 255. > Dimensioning error detected by BadBas. > Error termination in Lnk1e. > > Is there a way to fix this? > > Thanks in advance. > > Savant > If you're doing anything above 100 basis functions, you should be using SCF=Direct. It's much faster than conventional SCF (the default) for larger systems, does not require disk to store integrals, and doesn't have the basis set size limits of the sort you've encountered. Mike Frisch frisch@lorentzian.com From owner-chemistry@ccl.net Mon Jun 26 15:37:05 1995 Received: from relay3.UU.NET for frisch@lorentzian.com by www.ccl.net (8.6.10/930601.1506) id PAA11124; Mon, 26 Jun 1995 15:29:39 -0400 Received: from uucp1.UU.NET by relay3.UU.NET with SMTP id QQyvvh13019; Mon, 26 Jun 1995 15:29:36 -0400 Received: from m10.UUCP by uucp1.UU.NET with UUCP/RMAIL ; Mon, 26 Jun 1995 15:29:36 -0400 Received: from mjf by m10.lorentzian.com; Mon, 26 Jun 1995 16:57:59 -0400 Received: by mjf (AIX 4.1/UCB 5.64/4.03) id AA20610; Mon, 26 Jun 1995 15:29:01 -0400 From: frisch@lorentzian.com (Mike Frisch) Message-Id: <9506261929.AA20610@mjf> Subject: Re: CCL:SCRF in Gaussian92 To: chemistry@ccl.net Date: Mon, 26 Jun 1995 15:29:01 -0400 (EDT) In-Reply-To: <9506261306.ZM4608@beavis.chemse.gatech.edu> from "" at Jun 26, 95 01:06:48 pm X-Mailer: ELM [version 2.4 PL24] Content-Type: text Content-Length: 742 Savant Ahmed writes: > > Hi, > > While trying to run a SCRF geometry optimization and frequency job on a > molecule with 261 basis functions[HF/6-311+G(2d,p)] with Mem=4000000 I get the > following error: > > NBasis is 261 maximum for raffinetti integral format is 255. > Dimensioning error detected by BadBas. > Error termination in Lnk1e. > > Is there a way to fix this? > > Thanks in advance. > > Savant > If you're doing anything above 100 basis functions, you should be using SCF=Direct. It's much faster than conventional SCF (the default) for larger systems, does not require disk to store integrals, and doesn't have the basis set size limits of the sort you've encountered. Mike Frisch frisch@lorentzian.com From owner-chemistry@ccl.net Mon Jun 26 19:22:03 1995 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by www.ccl.net (8.6.10/930601.1506) id TAA04255; Mon, 26 Jun 1995 19:14:35 -0400 Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id IAA13585; Tue, 27 Jun 1995 08:15:33 +0900 Message-Id: <199506262315.IAA13585@inetnif.niftyserve.or.jp> Date: Tue, 27 Jun 1995 08:13:00 +0900 From: "JDA03546@niftyse" Subject: conference/symposium on catalyst To: chemistry@ccl.net Sorry to take the band width. I live in Japan. I was suddenly offered the oppotunity to attend the international conference or symposium or whatever on the catalyst research being held overseas. The condition is 1. within this year (1995) 2. must make a presentation 3. preferably in North America It seems too late if I have to make a presentation. Any information will be appreciated. ** JDA03546@niftyserve.or.jp/Kazuo Teraishi <95/06/24 10:09:02> ** From owner-chemistry@ccl.net Mon Jun 26 21:22:05 1995 Received: from camsci.com for jsb2@camsci.com by www.ccl.net (8.6.10/930601.1506) id VAA05295; Mon, 26 Jun 1995 21:07:05 -0400 From: Date: Mon, 26 Jun 95 21:07:04 EDT Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA16725; Mon, 26 Jun 95 21:07:04 EDT Message-Id: <9506270107.AA16725@camsci.com> To: CHEMISTRY@ccl.net Subject: Re: CCL:Chemical structures as GIF files >On Sun, 25 Jun 1995 FS300627@Sol.YorkU.CA wrote: > >> Greetings, >> >> Does anybody know what chemical drawing programs will allow >> the user to export a structure as a GIF file. I have tried >> several options by exporting a file as a WMF file and then >> use a program to convert WMF to GIF but it doesn't do a good >> job. >> >> Any ideas? Using ChemDraw on the Mac in conjunction with clip2gif (free) and AppleScript (included with System 7.5), you can get a nice automatic process. If you're using ChemDraw 3.5, you can even add a Save as GIF menu item. Unfortunately, while ChemDraw is available on Windows and UNIX platforms as well as Macintosh, AppleScript isn't, so this trick only works on Macs. If using a Mac is an option, email me for details. Jonathan Brecher CambridgeSoft Corporation jsb@camsci.com