From peon@medchem.dfh.dk Fri Mar 13 06:09:44 1998 Return-Path: Received: from danpost.uni-c.dk (danpost.uni-c.dk [129.142.6.64]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id GAA13868 for ; Fri, 13 Mar 1998 06:09:38 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.8.7/8.6) with SMTP id MAA05733 for <@danpost.uni-c.dk:jkl@ccl.net>; Fri, 13 Mar 1998 12:09:37 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA24380 for ; Fri, 13 Mar 1998 12:28:30 +0100 Message-Id: From: Per-Ola Norrby Content-Type: text/plain; charset="us-ascii" Subject: QSAR-98 12th European Symposium on QSAR Date: Fri, 13 Mar 1998 12:09:37 +0100 To: chemistry@www.ccl.net QSAR '98 The "12th European Symposium on Quantitative Structure-Activity Relationships", with subtitle "Molecular Modelling and Prediction of Bioactivity" will be held in Copenhagen, Denmark, August 23-28, 1998. Conference information can be found at: http://compchem.dfh.dk/qsar98/ NOTE! The original deadline for abstracts has been extended to April 1 (only announced here!), so there is still some time if you wish to submit a contribution. There is no online registration: please allow sufficient time for your abstract to reach us by regular mail. The second announcement, with information about abstract submission, is now available: http://compchem.dfh.dk/qsar98/2nd_circular.html Information about registering can be found at: http://compchem.dfh.dk/qsar98/registration.html Sincerely, The Organising Committee /Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From WILLECKE@oc1.chemie.uni-oldenburg.de Tue Mar 17 05:18:22 1998 Received: from hp9000.hrz.uni-oldenburg.de for WILLECKE@oc1.chemie.uni-oldenburg.de by www.ccl.net (8.8.3/950822.1) id EAA23821; Tue, 17 Mar 1998 04:28:11 -0500 (EST) Received: from oc1.chemie.uni-oldenburg.de (fb9oc1.chemie.uni-oldenburg.de [134.106.64.20]) by hp9000.hrz.uni-oldenburg.de (8.8.8/8.8.8/09.12.97) with ESMTP id KAA16370 for ; Tue, 17 Mar 1998 10:27:51 +0100 (MET) Received: from FB9OC1/MAILQUEUE by oc1.chemie.uni-oldenburg.de (Mercury 1.21); 17 Mar 98 10:27:52 MEZ-1MESZ Received: from MAILQUEUE by FB9OC1 (Mercury 1.21); 17 Mar 98 10:27:32 MEZ-1MESZ From: "Andreas Willecke" Organization: Inst. Of Org. Chem. Univ. Oldenburg To: chemistry@www.ccl.net Date: Tue, 17 Mar 1998 10:27:26 MEZ-1MESZ Subject: AMBER Pyrophosphate parameters X-Confirm-Reading-To: "Andreas Willecke" X-pmrqc: 1 Return-receipt-to: "Andreas Willecke" Priority: normal X-mailer: Pegasus Mail for Windows (v2.01) Message-ID: <20FE84E280B@oc1.chemie.uni-oldenburg.de> Dear CCLer, I want to calculate molecules with a pyrophosphate linkage, like ATP, with the AMBER 4.1 force field, but unfortunately no such parameters exist. Can anybody kindly tell me about such a parameter set for the AMBER FF ? Thanks in advance, Andreas **************************************** Andreas Willecke Universitaet Oldenburg Institut fuer Organische Chemie Carl-von-Ossietzky-Str. 9-11 26111 Oldenburg e-mail: willecke@fb9oc1.uni-oldenburg.de **************************************** From martin@mousy.chemie.unibas.ch Tue Mar 17 08:18:23 1998 Received: from mousy.chemie.unibas.ch for martin@mousy.chemie.unibas.ch by www.ccl.net (8.8.3/950822.1) id HAA24557; Tue, 17 Mar 1998 07:34:56 -0500 (EST) Received: from anne.chemie.unibas.ch by mousy.chemie.unibas.ch (AIX 3.2/UCB 5.64/4.03) id AA14535; Tue, 17 Mar 1998 13:37:06 +0100 Sender: martin@mousy.chemie.unibas.ch Message-Id: <350E6D6E.41C6@mousy.chemie.unibas.ch> Date: Tue, 17 Mar 1998 13:32:46 +0100 From: Martin Spichty Organization: Institut fuer Organische Chemie der Universitaet Basel X-Mailer: Mozilla 3.0Gold (X11; I; AIX 2) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: selenium parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am looking for Lennard-Jones parameters (sigma, epsilon) for selenium. I would like to use them to run a MC solution simulation with the program BOSS. Is there any publication referring to these values or do you know a method to estimate them? Sincerely yours, Martin Spichty ======================================================================== Martin Spichty Institute of Organic Chemistry Email: martin@anne.chemie.unibas.ch St. Johanns-Ring 19 Phone: 0041 61 267 11 57 CH-4056 Basel Fax: 0041 61 267 11 05 ======================================================================== From raji@ymail.yu.edu Tue Mar 17 10:18:23 1998 Received: from acis.mc.yu.edu for raji@ymail.yu.edu by www.ccl.net (8.8.3/950822.1) id JAA24974; Tue, 17 Mar 1998 09:19:58 -0500 (EST) Received: (from raji@localhost) by acis.mc.yu.edu (8.8.5/8.8.5) id JAA96378; Tue, 17 Mar 1998 09:18:06 -0500 Date: Tue, 17 Mar 1998 09:18:05 -0500 (EST) From: Raji Viswanathan X-Sender: raji@acis.mc.yu.edu To: chemistry@www.ccl.net Subject: Sun vs silicon graphics Message-ID: Organization: Yeshiva University MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We are interested in buying a workstation that will satisfy the needs of our chemistry and physics departments. We would appreciate any input regarding the pros and cons of a sun vs silicon graphics workstation. The Chemistry department would be using it for some molecular modeling (using spartan, CAche, and GAMESS) as well as some Monte Carlo and molecular dynamics calculations. The physics department is also interested in some Monte Carlo simulations using this workstation. Thanks in advance for your input. ******************* R. Viswanathan Dept. of Chemistry Yeshiva University 500 West 185th street NY, NY 10033 (212) 960 - 5443 raji@ymail.yu.edu ******************** From perla@sun.che.sc.edu Tue Mar 17 10:22:08 1998 Received: from charlie.ece.sc.edu for perla@sun.che.sc.edu by www.ccl.net (8.8.3/950822.1) id JAA25119; Tue, 17 Mar 1998 09:42:27 -0500 (EST) From: Received: by charlie.ece.sc.edu (5.57/Ultrix3.0-C) id AA08224; Tue, 17 Mar 98 09:40:50 -0500 Received: by che.sc.edu (4.1/SMI-4.1) id AA13807; Tue, 17 Mar 98 10:05:21 EST Date: Tue, 17 Mar 1998 10:05:20 -0500 (EST) To: chemistry@www.ccl.net Subject: Call for Papers- AIChE meeting, November, Miami Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 1998 AIChE Annual Meeting Call for Papers Area 1a: Thermodynamics and Transport Properties Group 9: Environmental Division Molecular Modeling for Solving Environmental Problems Tuesday Afternoon, November 17, 1998 Chair: Prof. J. Thomas McKinnon Dept of Chemical Engineering Colorado School of Mines Golden, CO 80401 Phone: (303) 273-3098 Fax: (303) 273-3730 Email: jmckinno@mines.edu Co-Chair: Prof. Perla B. Balbuena Department of Chemical Engineering University of South Carolina Columbia SC 29208 Phone: (803) 777-8022 telephone Fax: (803) 777-8265 Email: perla@sun.che.sc.edu Topics include but are not limited to applications of quantum mechanics and classical molecular simulations to: Evaluation of thermodynamic properties for engineering design. Computational phase equilibrium. Estimation of reaction pathways and rates of elementary gas-phase reactions. Elementary reaction analysis of heterogeneous catalytic reaction mechanisms related to environmental problems. New computational methods or validation of model chemistries. Proposals to present should be submitted electronically and can be prepared on the World-wide Web at: http://www.aiche.org/docs/meetapp/programming/cfp.htm From perla@sun.che.sc.edu Tue Mar 17 10:24:36 1998 Received: from charlie.ece.sc.edu for perla@sun.che.sc.edu by www.ccl.net (8.8.3/950822.1) id JAA25086; Tue, 17 Mar 1998 09:36:54 -0500 (EST) From: Received: by charlie.ece.sc.edu (5.57/Ultrix3.0-C) id AA08216; Tue, 17 Mar 98 09:35:57 -0500 Received: by che.sc.edu (4.1/SMI-4.1) id AA13763; Tue, 17 Mar 98 10:00:28 EST Date: Tue, 17 Mar 1998 10:00:28 -0500 (EST) To: chemistry@www.ccl.net Subject: Call for Papers Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CALL FOR PAPERS 1998 AIChE Annual MeetingPMiami Beach, FLP November 15-20, 1998 Supercritical Fluid Science and Technology Session sponsored by Area 1f- High Pressure SIMULATIONS OF SUPERCRITICAL FLUIDS PROPERTIES Session 01f05 Contributions are solicited for a session on applications of computational chemistry (ab initio and semiempirical methods) and molecular simulations to characterize thermodynamic and transport properties of relevance for processes involving supercritical fluids. Topics of interest include but are not limited to supercritical fluids effects on thermochemistry, kinetics, transport properties, solution structure and interfacial phenomena. Session Chair: Session Co-Chair: Perla B. Balbuena Karl Johnson Dept. of Chemical Engineering Dept. of Chem. and Petroleum Eng. University of South Carolina University of Pittsburgh Columbia, SC 29208 Pittsburgh, PA 15260 (803)-777-8022 (412)-624-5644 perla@sun.che.sc.edu karlj@puccini.che.pitt.edu Deadlines: 1 April 1998: Electronic submission of Proposal-to-Present http://www.aiche.org/docs/meetapp/programming/cfp.htm 1 October 1998: Mail hard copy of extended abstracts* to AIChE Manuscript Center 345 East 47th Street New York, NY 10017 *Extended abstracts must include an introduction, results, discussion, and references. The is no minimum length requirement. From smb@smb.chem.niu.edu Tue Mar 17 10:26:45 1998 Received: from cz2.chem.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id JAA25059; Tue, 17 Mar 1998 09:33:26 -0500 (EST) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA20034; Tue, 17 Mar 98 07:57:44 -0600 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA21636; Tue, 17 Mar 98 08:30:43 -0600 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) id IAA05017; Tue, 17 Mar 1998 08:29:52 -0600 Sender: smb@smb.chem.niu.edu Message-Id: <350E88DE.41C6@smb.chem.niu.edu> Date: Tue, 17 Mar 1998 08:29:50 -0600 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: tj@eecs.uic.edu Cc: Brian Beck , CHEMISTRY@www.ccl.net Subject: Re: CCL:Digital Unix PDB viewer plugin References: <9803161558.AA29376@Ba.Chem.UH.EDU> <350DB77A.2B21@eecs.uic.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit No, I don't think this is the problem. Since Brian has created pages with the EMBED tag before and obviously gotten them to work, the MIME tage is set properly. The real probelm here is, as Brain mentioned, a lack of a plugin for the DEC machine. The last I spoke with the MDL folks, and this was about 6 months ago, and there was no plan to expand the CHIME product to other platforms (being an SGI user, I wanted them to enhance the plugin to 24-bit from 8-bit, something we are still waitng for). The problem remains - plugins are platform specific and until the developer ports to your platform, you are out of luck. To avoid the problem you need to avoid using the EMBED tag - you could create two pages, one with one without the EMBED tag - then on the page without the embed, you can offer the file as a straight download which the browser canthen direct to helper application to view the structure. An alternative is to use a java utility to display your molecules. I recommend ChemSymphony (http://www.cherwell.com/)for this. Steve TJ O'Donnell wrote: > > Brian Beck wrote: > > > > Does anyone know of a PDB (or other molecular format) viewer > > PLUGIN for netscape that will work with Digital Unix on a > > DEC Alpha? > > > > I can use a helper application for straight links to PDB > > files, but the tags trip me up, and most chem > > related web pages (including my own) with links to pdb files > > use tags. > > > > -Brian > > I bet is tripping you up because you need to configure > your web server to recognize .pdb (or whatever) files and serve > them up with the appropriate mime type. > If you can't reconfigure your server, you can use a cgi program > to produce the "Content-type: chemical/x-pdb" mime type (or > whichever mime type you want to associate with your molecular > structure files). > -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From mforster@nibsc.ac.uk Tue Mar 17 11:18:26 1998 Received: from nibsc.ac.uk for mforster@nibsc.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA25603; Tue, 17 Mar 1998 10:30:12 -0500 (EST) Received: from chalsig.nibsc.ac.uk by nibsc.ac.uk via ESMTP (951211.SGI.8.6.12.PATCH1502/940406.SGI.1(NIBSC)) for id PAA09315; Tue, 17 Mar 1998 15:30:00 GMT Received: by chalsig.nibsc.ac.uk (951211.SGI.8.6.12.PATCH1502/client-1.3.1(NIBSC)) id PAA05126; Tue, 17 Mar 1998 15:29:59 GMT Date: Tue, 17 Mar 1998 15:29:59 GMT From: mforster@nibsc.ac.uk (mforster) Message-Id: <199803171529.PAA05126@chalsig.nibsc.ac.uk> To: chemistry@www.ccl.net Subject: summary Dear Net Chemists Here is a summary of responses to my recent question concerning calculation of intermolecular interactions by electronic structure methods. There were no responses to the part of the query asking how the use of numerical basis sets, as opposed to contracted gaussians, would alter the effect of basis set superposition error. Here is the question itself. > Could some Quantum chemistry experts please offer some advice or > comments on the computation of intermolecular interactions by > quantum methods. > > I noticed a recent paper in which the the difference in the (SCF) > energy of an ion pair at some separation (r) relative to the the sum > of the energies of the individual ions was used to estimate the stabilisation > of the ion pair. Does this approach neglect basis set superposition effects > where the 'effective' basis set size grows as the two separate molecules > are brought together. In addition how would such calculations be affected > by numerical basis sets (eg as used by DMOL). Here are the responses: From: scheiner@chem.siu.edu (Steve Scheiner) intermolecular interactions in reply to your question on the net about interactions, your question is a good one, and one that has generated quite a bit of work over the years. the approach you mention may or many not have included a BSSE correction; you would have to read the details to know for sure. about the second part of your question, the basis set has a great deal to do with the result computed. so i can't answer your question except to refer you to the original paper. for more details, you might consult a book which i recently edited for wiley. the title of the book is Molecular Interactions. you would probably be most interested in chapters 3, 5 and 9. ----- Steve Scheiner, Professor scheiner@chem.siu.edu Dept. of Chemistry & Biochemistry Mail Stop 4409 Southern Illinois University Carbondale Illinois 62901 ph: 618/453-6476 fax: 618/453-6408 From: noertema@theochem.tu-muenchen.de (Folke Noertemann) Dear Dr Forster, since I am not really an expert, I may be telling you things that you are already aware of. Of course the effective basis, as you call it, grows if the distance between two molecular fragments is decreased. However, it is possible to correct the energies for the BSSE and so I think your first question cannot be answered without having seen the paper. Moreover the BSSE does not depend on the distance alone but also one the quality of the basis. It is for example possible to get a very low BSSE with a minimal basis-set calculation because for reasonble distances only the diffuse functions centered on fragment a can be used for the representation of orbitals on fragment b. Unfortunately I do not have any experience at all with numerical basis sets and thus I am unable to comment on your second question. I hope this is of some help to you, F. Noertemann Folke Noertemann Lehrstuhl f. Theoretische Chemie TU Muenchen Lichtenbergstr.4 85748 Garching noertema@theochem.tu-muenchen.de From: Richard Wheatley This is an extremely widely studied area of chemistry. Despite the many hundreds of postdoc-years and hundreds of postgrad-years spent on it, there is still no way of doing accurate, cheap calculations for any system with more than about 20 electrons or more than about 3 degrees of freedom. By accurate I mean guaranteed within about 10%, and by cheap I mean less than a few months of supercomputer time for the surface. Don't let anyone convince you otherwise! Having said that, SCF calculations will be (1) in error due to the incorrect polarizability of the negative ion. This is easy to look up (both SCF and correlated results are known). Also the (fairly small) dispersion interaction energy is neglected. If the ions are not spherical, SCF will also get the multipoles wrong and this will give major errors. (2) free of BSSE (reasonably!) provided that at least 10 - preferably more - Gaussian functions are used per spin-orbital, so 100 Gaussians would just be tolerable for F- and Na+, for example. The Counterpoise method can always be used to estimate BSSE if in doubt. I don't know about numerical basis sets. Note that BSSE gets MUCH WORSE, not better, for correlated calculations with the same basis set. For light reading, try B Jeziorski, S S Xantheas, A J Stone or possible some of the P W Fowler work. Or me. Best wishes Richard Wheatley, Department of Chemistry, University of Nottingham. Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk From laaksone@csc.fi Tue Mar 17 12:18:33 1998 Received: from pobox.csc.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id MAA26128; Tue, 17 Mar 1998 12:13:20 -0500 (EST) Received: from voxopm.minedu.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with SMTP id TAA28991; Tue, 17 Mar 1998 19:11:47 +0200 (EET) Date: Tue, 17 Mar 1998 19:11:46 +0200 (EET) From: Leif Laaksonen X-Sender: laaksone@voxopm.minedu.fi To: Steven Bachrach cc: tj@eecs.uic.edu, Brian Beck , CHEMISTRY@www.ccl.net Subject: Re: CCL:Digital Unix PDB viewer plugin In-Reply-To: <350E88DE.41C6@smb.chem.niu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would also recommend the WebMol Java PDB Viewer from EMBL Heidelberg and its various development tracks. It's a very good piece of software. http://www.embl-heidelberg.de/cgi/viewer.pl Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From fgonzale@lauca.usach.cl Tue Mar 17 15:18:26 1998 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id OAA27387; Tue, 17 Mar 1998 14:54:03 -0500 (EST) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.8.5/8.8.8) with ESMTP id PAA08043 for ; Tue, 17 Mar 1998 15:54:15 -0400 (CST) Received: from danilo (kekule.usach.cl [158.170.16.6]) by lauca.usach.cl (8.6.12/8.6.12) with ESMTP id PAA16058 for ; Tue, 17 Mar 1998 15:59:56 -0400 Message-ID: <34C11A5B.18653338@lauca.usach.cl> Date: Sat, 17 Jan 1998 16:53:48 -0400 From: Danilo Gonzalez Organization: Universidad de Santiago de Chile X-Mailer: Mozilla 4.01 [en] (WinNT; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: G94W and GopenMol X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all! We tried to visualize the molecular orbital and density from G94W (PC) calculation with the GopenMol 1.10. We used the option cubegen and cubeman at G94W, for make the file *.cube and *.data. But we have problem for do it. Anybody knows how can I get display (MO, density, etc.) on GopenMol? Thanks a lot! Sincerely Marcela and Danilo -- Fdo. Danilo González Nilo University of Santiago de Chile, Faculty of Chemistry and Biology, Computational Chemistry Lab. Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108 URL : http://quimbio.usach.cl/~danilo/ E-mail: fgonzale@lauca.usach.cl @@@@@@@@@@@@@@@@@@@@@@@@@@@@@