From qftramos@usc.es Mon Sep 30 04:58:44 1996 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.7.5/950822.1) id EAA01574; Mon, 30 Sep 1996 04:10:45 -0400 (EDT) Received: by uscmail.usc.es (5.67b/1.34) id AA06583; Mon, 30 Sep 1996 10:09:19 +0100 Date: Mon, 30 Sep 1996 10:09:18 +0100 (MET) From: Antonio Fernandez Ramos To: Lista computacional Subject: Latex Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: How can I get a version of Latex for a Indy by SGI. Thanks, Antonio Fernandez Ramos Departamento de quimica Fisica Facultade de Quimica Avda des Ciencias s/n Santiago de Compostela (SPAIN) From peon@medchem.dfh.dk Mon Sep 30 05:15:00 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.7.5/950822.1) id EAA01714; Mon, 30 Sep 1996 04:25:41 -0400 (EDT) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id JAA03178; Mon, 30 Sep 1996 09:25:32 +0100 (MET) Received: from [130.225.177.59] by medchem.dfh.dk via SMTP (940816.SGI.8.6.9/940406.SGI) id JAA16612; Mon, 30 Sep 1996 09:38:44 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Date: Mon, 30 Sep 1996 10:25:33 +0200 To: U54632%UICVM.BITNET@phem3.acs.ohio-state.edu From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:MM2 parameters Cc: chemistry@www.ccl.net Chaya Duraiswami wrote: >Hi! I would like to have MM2 torsion parameters (i.e. v1,v2, & v3 >values) for the following bonds: > >Csp2 - Csp3 - Csp - Csp >Osp3 - Csp3 - Csp - Csp >Csp3 - Csp - Csp - Csp2 >Csp2 - Csp2 - Csp - Csp >Osp3 - Csp2 - Csp - Csp >Csp2 - Osp3 - Csp2 - Csp All except the last one are linear so even though the program requires parameters, they should be set to 0.0. You can't very well rotate around a bond when one of the central atoms is sp, can you ?-) Note that if you are using a "real", modern MM2, with pi-calculations, you may encounter a nasty bug here. Some interfaces set up the calculation so that the sp-carbons are considered conjugated. Since the torsion is used in determining overlap, you will get a division-by-zero error for linear atoms, which will cause the program to crach. The workaround is to exclude the sp-carbons from the list of conjugated atoms. MM2 was, as far as I know, parameterized for non-conjugated acetylenes anyway. For the last parameter, shouldn't you rat´her use the special furan-O atom type? I believe it's 41 or something close. Best Regards, Per-Ola Norrby PS. If you are NOT using Allingers MM2, you should specify the source, as there are many MM2 implementations out there, not all as good as the original. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * 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 steve@bellatrix.pcl.ox.ac.uk Mon Sep 30 08:13:07 1996 Received: from oxmail4.ox.ac.uk for steve@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.7.5/950822.1) id IAA00702; Mon, 30 Sep 1996 08:03:24 -0400 (EDT) Received: from joule.pcl.ox.ac.uk by oxmail4 with SMTP (PP) with ESMTP; Mon, 30 Sep 1996 13:03:53 +0100 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.6.10/8.6.5) with ESMTP id NAA22416 for <@joule.pcl:chemistry@www.ccl.net>; Mon, 30 Sep 1996 13:03:08 +0100 Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) id MAA21353; Mon, 30 Sep 1996 12:05:16 GMT Date: Mon, 30 Sep 1996 13:05:14 +0100 (BST) From: Steve Doughty To: chemistry@www.ccl.net Subject: MGMS EC-1: Summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII FIRST ELECTRONIC MOLECULAR GRAPHICS AND MODELLING SOCIETY CONFERENCE ******************************************************************** The First Electronic Molecular Graphics and Modelling Society Conference (MGMS EC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Oct 7-18, 1996 and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. The conference is sponsored by Elsevier, the Molecular Graphics and Modelling Society, Molecular Simulations Inc, Oxford Molecular, NASA, Springer-Verlag, Wyeth-Ayerst, and GlaxoWellcome and is designed and operated by Greenlea Communications. The conference is being served from the following UK and US sites at Oxford University and Wesleyan University: UK - http://bellatrix.pcl.ox.ac.uk/mgms/ USA - http://linus.chem.wesleyan.edu/~mirror/mgms/ Conference registration supplying userid, password and payment details, is available through: UK - http://bellatrix.pcl.ox.ac.uk/mgms/register.html USA - http://linus.chem.wesleyan.edu/~mirror/mgms/register.html Conference subject areas are: Protein Structure (Rod Hubbard); Membranes and Membrane Proteins (Terry Stouch and Alan Robinson); Computational Nanotechnology (Al Globus); Protein Folding (Jeffrey Skolnick); Modelling of In Vivo Activity (Ed Hodgkin); Knowledge-based Library Design (Mike Hann); Surface Science (Donald Brenner); Host-guest interactions (Jon Essex); Carbohydrates and Protein-Carbohydrate Interactions (Anne Imberty); Enzyme Mechanisms (Guy Grant); Conformational Sampling (Robert Topper); Nucleic Acids (David Beveridge and Dennis Sprous); Quantum Chemistry (Tim Clark); Structure-based Design (David Winkler); Visualization (Art Olson); and Perspectives (Graham Richards). Presentations are in Hypertext Markup Language (HTML), graphics (GIF,JPEG) and other web-compatible formats (VRML,Java,PDF) so that participants can view material via the World Wide Web (WWW). During the conference meetings and discussions will take place via the Internet in real-time using a virtual conference centre based on a MOO (multiple-user domain, object oriented) and via Internet- accessible electronic mailing lists and discussion areas. The conference contains a Virtual Job Center and a Virtual Trade Center where commercial vendors, software and hardware developers, consultants, and contractors are able to display their goods and services and provide software demonstrations in return for exhibition fees to support conference activities. Any potential exhibitors should contact Barry Hardy at barry@bellatrix.pcl.ox.ac.uk Registration If you intend to participate in MGMS EC-1 please use the registration form accessible via http://bellatrix.pcl.ox.ac.uk/mgms/register.html which is available for electronic registration. The registration is used to construct a registrant database for the conference, generates the conference mailing list and handles assignment of userids and passwords. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 35 pounds sterling (50 US dollars) with a special rate for students of 20 pounds sterling (30 US dollars). A copy of a suitable student identification or a letter from the supervisor will be required to be charged at the lower rate. Registration payments can be accepted by credit card, direct bank transfer, cheque or bank draft. Credit card payments can be accepted by fax at 4 4 (0) 1865 875581 where the (0) is not used outside the UK. Regardless of method of payment we ask you to supply accompanying correspondence with your complete name, address, fax and phone number, and email address which should be mailed or faxed directly to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Fax: 44 (0) 1865 875581 Payment Instructions: a) Credit Card We can currently accept Visa, Mastercard, Switch or JCB. Please send your credit card type, number and expiration date via fax to 44 (0) 1865 875581 or via regular mail to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Fax is recommended for registration carried out close to the conference commencement. b) Bank Transfer Your payment can be made in sterling by direct bank transfer into the folowing account: Account Number: 20-6518 50772712 Account Name: Greenlea Communications Bank: Barclays Bank, Oxford City Centre Branch, P.O. Box 333, Oxford, OX1 3HS, UK --Please ensure your full name is listed with the transfer details. --You are responsible for any bank charges associated with the transfer from your bank. --Please notify us directly of your transfer payment. 3) Cheque/Bank Draft Cheques or bank orders (in pounds or dollars) should be made out to Greenlea Communications and mailed to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Acknowledgement of Registration and Payment: When you first register at the conference site you should receive an acknowledgement email with a password and userid. After receipt of your registration fee you will receive a further acknowledgement and your userid and password will be validated to allow access to the conference site. Hot line Any general emails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, MOO queries, etc.) should be sent to: mgmsorg@bellatrix.pcl.ox.ac.uk Barry Hardy barry@bellatrix.pcl.ox.ac.uk ---------------------------------------------------------------------- ------------------------------------------------------------------ // || \\ // Stephen Doughty || "The best and most \\ // Physical & Theoretical Chemistry Lab.||beautiful things in \\ // Oxford University, ||this world cannot be \\ // South Parks Road, OXFORD, OX1 3QZ, UK||seen or even touched.\\ // ||They must be felt \\ // Tel: +44 1865 275475 ||with the heart." \\ //--------------------------------------------------------------\\ // Email : steve@bellatrix.pcl.ox.ac.uk \\ // WWW : http://bellatrix.pcl.ox.ac.uk/people/steve/ \\ ------------------------------------------------------------------ From SATYAM@vms.cis.pitt.edu Mon Sep 30 10:13:07 1996 Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.7.5/950822.1) id JAA01053; Mon, 30 Sep 1996 09:38:14 -0400 (EDT) From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #10002) id <01IA32E4AKG090TR78@vms.cis.pitt.edu>; Mon, 30 Sep 1996 09:37:42 -0400 (EDT) Date: Mon, 30 Sep 1996 09:37:42 -0400 (EDT) Subject: Program(S) to Model SAM's -- ?? To: chemistry@www.ccl.net Message-id: <01IA32E4CRK290TR78@vms.cis.pitt.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, An experimental group is interested in obtaining information about an simple to use program for generating Self-Assembled Monolayers (SAM's) of alkane chain. They want to generate coordinates and visualize them. Send reply to me. Thanks Satyam ---------------------------------------------------- Dr. Satyam Priyadarshy satyam+@pitt.edu Research Assistant Prof. satyam@vms.cis.pitt.edu Department of Chemistry Phone: 412-624 8589 University of Pittsburgh FAX : 412-624 8552 Pittsburgh, PA 15260 Emerg: 412-624 8200 ---------------------------------------------------- From Steven.Creve@chem.kuleuven.ac.be Mon Sep 30 12:13:09 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.5/950822.1) id LAA01674; Mon, 30 Sep 1996 11:18:21 -0400 (EDT) Received: from localhost by hartree.quantchem.kuleuven.ac.be with SMTP id AA30118 (5.67b/IDA-1.5 for ); Mon, 30 Sep 1996 17:18:13 +0100 Date: Mon, 30 Sep 1996 17:18:12 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:G: CUBE/VISUALIZATION Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone know which program can visualize the CUBE output files from a Gaussian94 job? Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From berriz@chasma.harvard.edu Mon Sep 30 12:18:11 1996 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.7.5/950822.1) id MAA02041; Mon, 30 Sep 1996 12:12:46 -0400 (EDT) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA14123; Mon, 30 Sep 1996 12:12:15 -0400 Date: Mon, 30 Sep 1996 12:12:15 -0400 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9609301612.AA14123@chasma.harvard.edu> To: chemistry@www.ccl.net Subject: Q: Pure Rotational Diffusion (Langevin) I am studying the behavior of a three-dimensional arrangement of rigid particles that are translationally fixed, but may rotate around any axis. (No symmetries are assumed for the particles, so no axis is privileged.) To each pair of particles corresponds a potential energy, which depends on the orientations of the particles relative to each other, and the distance between them. (The internal energy of the ensemble is the sum of all the pairwise energies). I am currently using a Langevin-type formalism to study the effect of applying a thermal rotational fluctuation (to each particle) on the ensemble's steady-state configuration. These studies have yielded some rather strange results (briefly, the stability of the system decreases dramatically when going from 6 to 7 particles, plus some other strange details). Therefore, I am now conducting a detailed and thorough troubleshooting of my system. To this end, I am interested in learning as much as possible about existing work on Langevin models of (purely) rotational diffusion of (asymmetrical) particles. I would greatly appreciate the readership's pointers to the literature.