From thys@schs.uia.ac.be Fri Sep 9 05:48:06 1994 Received: from sch2.uia.ac.be for thys@schs.uia.ac.be by www.ccl.net (8.6.9/930601.1506) id EAA05224; Fri, 9 Sep 1994 04:51:03 -0400 Received: from localhost by sch2.uia.ac.be (8.6.4/Ultrix3.0-C) id KAA15111; Fri, 9 Sep 1994 10:49:31 +0200 Date: Fri, 9 Sep 1994 10:49:27 +0200 (MET DST) From: Gerd Thys To: CCL Subject: QCPE-651 (Semiempirical MO Package for Spectroscopy) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I'm looking for references on the 'MOS'-program (QCPE 651) by Azuma Matsuura. References on calculations, done with this program, or people who want to share their experience are also welcome. Thanks in advance... Gerd ------------------------------------------------------------------------ Gerd Thys Dienst voor structuurchemie Universiteitsplein 1 B-2610 wilrijk BELGIUM E-mail: thys@uia.ac.be ------------------------------------------------------------------------ From JEREMYW@num-alg-grp.co.uk Fri Sep 9 05:52:38 1994 Received: from ben.britain.eu.net for JEREMYW@num-alg-grp.co.uk by www.ccl.net (8.6.9/930601.1506) id EAA05228; Fri, 9 Sep 1994 04:51:19 -0400 Received: from iec.co.uk by ben.britain.eu.net via JANET with NIFTP (PP) id ; Fri, 9 Sep 1994 09:50:27 +0100 Message-Id: <16013.9409090850@nags2.nag.co.uk> Received: from vax.nag.co.uk (nagvax) by nags2.nag.co.uk (4.1/UK-2.1) id AA16013; Fri, 9 Sep 94 09:50:06 BST Date: 9 Sep 94 09:48:00 WET From: JEREMY WALTON Subject: Re: Q:Explorer Modules To: CHEMISTRY Cc: bob Hi Steven, >> Does anyone know of any Explorer modules, for use with the SGI >> version, that allow you to visualize data from the ab initio package >> GAMESS or dynamics files generated by the SYBYL package? Any information >> on such topics would be of great help. >> >> Thanks in advance, >> >> Steven Schafer >> S.U.N.Y. Binghamton Chemistry Department >> Binghamton, NY Version 2.2 of IRIS Explorer (currently bundled with IRIX 5.2) contains some chemistry modules in the 'unsupported' category which were contributed by Omer Casher (o.casher@ic.ac.uk). One of these - EyeSybyl - reads molecular data from a Sybyl mol file and builds a Chemistry Pyramid for passing around within explorer. Is this the sort of thing you were looking for? Hope this is helpful. Please let me know if you need any more here. Cheers, Jeremy -------------------------------------------------------------------------------- | Jeremy Walton nagjpw@vax.oxford.ac.uk | | The Numerical Algorithms Group Ltd, Oxford, UK jeremyw@nag.co.uk | | Tel: +44 865 511245 | | Fax: +44 865 310139 | -------------------------------------------------------------------------------- From TILBROOK@chem.surrey.ac.uk Fri Sep 9 06:48:06 1994 Received: from mail-server.surrey.ac.uk for TILBROOK@chem.surrey.ac.uk by www.ccl.net (8.6.9/930601.1506) id GAA06070; Fri, 9 Sep 1994 06:37:54 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <14782-0@mail-server.surrey.ac.uk>; Fri, 9 Sep 1994 11:37:30 +0100 Received: from chemcharon.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (1.37.109.8/16.2) id AA26255; Fri, 9 Sep 1994 11:37:23 +0100 Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.940909113741.704; 09 Sep 94 11:40:43 +500 Message-Id: To: CHEMISTRY@ccl.net From: Dave Organization: Chemistry Department, Uni of Surrey Date: Fri, 9 Sep 1994 11:26:43 GMT Subject: Cerius-2 and Vibrational Calculations? Reply-To: tilbrook@chem.surrey.ac.uk Priority: normal X-Mailer: WinPMail v1.0 (R1) I was just wondering if anyone out there could help with a question regarding the capabilities of the MSI Cerius-2 package. I have been using the MSI package POLYGRAF PROFESSIONAL with the VIBRATE module to carry out normal mode calculations on organic systems. Our apparently POLYGRAF will be discontinued as an individual product lin the near future and thus we have elected to transfer our work to the Cerius-2 package which has had the POLYGRAF capabilities incorporated in the form of the CERIUS POLYMER WORKBENCH. This suite of tools seems to cover all of the basic POLYGRAF operations and provides an interface to MOPAC. However, I do not seem to be able to find a module to handle the normal modes calculations and spectral visualisation that we carried out with the old POLYGRAF VIBRATE tool. Does anyone out there know of a CERIUS module that can be used for IR spectral simulation via normal modes calculations? Does the CERIUS MOPAC interface incorporate means of visualising the MOPAC vibrational force constant data or is it more of a means of simplifying the task of running conformational plots etc.? I would welcome any comments and advice that you can provide me with. I can be contacted my mail at tilbrook@chem.surrey.ac.uk Thanks in advance David Tilbrook ********************************************************** David Tilbrook * Tel: 44 483 300 800 x 2632 Polymer Group, * x 2617 Chemistry Department, * University of Surrey, * Fax: 44 483 300 803 Guildford, Surrey, GU2 5XH * U.K. * ********************************************************** From markm@portal.vpharm.com Fri Sep 9 10:49:21 1994 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.9/930601.1506) id KAA09525; Fri, 9 Sep 1994 10:42:24 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA14492; Fri, 9 Sep 1994 10:41:08 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9409091441.AA14492@portal.vpharm.com> Subject: Bond strengths -- table? book? To: chemistry@ccl.net Date: Fri, 9 Sep 1994 10:41:08 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 278 Can anyone suggest a book or table that has just about every reasonable bond strength? Organics, Inorganics, etc. I am looking for something that goes way beyond the kind of truncated lists you find in the back of most inorganic textbooks. Thanks! / Mark (markm@vpharm.com) From rsefeck@watson.ibm.com Fri Sep 9 11:48:11 1994 Received: from watson.ibm.com for rsefeck@watson.ibm.com by www.ccl.net (8.6.9/930601.1506) id LAA10517; Fri, 9 Sep 1994 11:22:17 -0400 Message-Id: <199409091522.LAA10517@www.ccl.net> Received: from YKTVMV by watson.ibm.com (IBM VM SMTP V2R3) with BSMTP id 8131; Fri, 09 Sep 94 11:22:21 EDT Date: Fri, 9 Sep 94 11:22:21 EDT From: RSEFECK@watson.ibm.com To: chemistry@ccl.net Subject: New chemistry tools for IBM Visualization Data Explorer Along with the release of IBM's Visualization Data Explorer 2.1 are a new chemistry tools. These tools are available through the Data Explorer public repository at Cornell University. The tools consist of a number of user contributed modules and Data Filters. The newest of these tools are: Any2DX: A filter for converting various molecular structure file formats from widely used computational chemistry programs into Data Explorer format. As currently implemented, it can be used to prepare PDB, CHARMn CRD, Sybyl MOL2 and generic free format files for molecular model representation using Visualization Data Explorer. The output of Any2DX is a file containing a single DX field which specifies the molecular structure in terms of the atomic numbers of the atoms, their positions, and the connections specifying the covalent bonds, and optionally, a colors and radii components. Gauss2DX: This filter converts Gaussian92 grid files to the Data Explorer format. It creates input to visualize molecular orbitals, electrostatic distributions, electron densities, and density gradients. It runs external to both Gaussian and Data Explorer. The user is prompted for an input file name in either binary or ASCII format. The filter generates both the molecular structure file and the corresponding property files in the Data Explorer format for direct Import. Mopac2DX: This filter is in test and will be available shortly: *For more information on Visualization Data Explorer, the NEW DEC alpha version and NEW PARALLEL SMP versions for SGI and Sun multiprocessors Contact: Rich Sefecka IBM Watson Research Center Hawthorne, New York email: rsefeck@watson.ibm.com telephone: 914 784-5089 From o.casher@ic.ac.uk Fri Sep 9 12:48:11 1994 Received: from punch.ic.ac.uk for o.casher@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id LAA11236; Fri, 9 Sep 1994 11:53:33 -0400 From: Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <09239-0@punch.ic.ac.uk>; Fri, 9 Sep 1994 16:51:27 +0100 Received: by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA10041; Fri, 9 Sep 94 16:56:03 +0100 Message-Id: <9409091556.AA10041@cscmgb.cc.ic.ac.uk> Subject: Re: CCL:Q:Explorer Modules To: steve@carbo.cc.binghamton.edu (Steven Schafer) Date: Fri, 9 Sep 94 16:56:03 bst Cc: chemistry@ccl.net In-Reply-To: ; from "Steven Schafer" at Sep 8, 94 7:42 pm > Does anyone know of any Explorer modules, for use with the SGI > version, that allow you to visualize data from the ab initio package > GAMESS or dynamics files generated by the SYBYL package? Yes. Any information > on such topics would be of great help. > Check 'em out: **************************************************************************** NAME ReadGAMESS DESCRIPTION This module inputs a GAMESS input or output file, determines the connectivity using a covalent radius test, and outputs an Explorer Chemistry Pyramid. **************************************************************************** NAME WriteGAMESS DESCRIPTION This module inputs an Explorer Chemistry Pyramid and writes a GAMMES input file. The appropriate keyword and header information is extracted from a specified file, i.e., another GAMESS input or even an output. If no such file is specified the module will not work. It is a first attempt at interconverting molecular file formats such as MOPAC -> GAMESS in Explorer. **************************************************************************** NAME EyeSybyl DESCRIPTION This module reads the molecular data of a Sybly mol file and builds a Chemistry Pyramid. It is basically an implementation of the InterCon program written by Dr. Stuart Greene. **************************************************************************** EyeSybyl is included with the other Eye* modules on the IRIX 5.2 CD. IRIX 4.0.5 versions are available by ftp: argon.ch.ic.ac.uk/pub/eyechem. I havn't shipped the GAMESS modules so if you want your copies, just send me some e-mail. Salute! Omer -- Omer Casher o.casher@ic.ac.uk c/o Departmant of Chemistry Or +44 171-589-5111 (ex 55779 or 55843) Imperial College, London "If it's painful, it's incorrect." SW7 2AZ From AHOLDER@VAX1.UMKC.EDU Fri Sep 9 16:48:13 1994 Received: from vax1.umkc.edu for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.9/930601.1506) id QAA16505; Fri, 9 Sep 1994 16:37:36 -0400 Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01HGWUU4JF28ED0T3V@VAX1.UMKC.EDU>; Fri, 9 Sep 1994 14:56:59 CST Date: Fri, 09 Sep 1994 14:56:59 -0600 (CST) From: Andy Holder Subject: Sun Chemistry contact To: CHEMISTRY@ccl.net Message-id: <01HGWUU4JOPEED0T3V@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Does anyone know of a contact for Sun Microsystems that manages the Chemistry market? It seems that the old one is gone. Andy =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || Internet Addr: aholder@vax1.umkc.edu Univ. of Missouri - Kansas City || Phone Number: (816) 235-2293 Spencer Chemistry, Room 315 || FAX Number: (816) 235-5502 Kansas City, Missouri 64110 || =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From theochem@ctc.com Fri Sep 9 17:48:14 1994 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.9/930601.1506) id RAA17127; Fri, 9 Sep 1994 17:08:48 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA03140; Fri, 9 Sep 1994 17:11:14 -0400 Received: by eed02.ctc.com (920330.SGI/921111.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA05042; Fri, 9 Sep 94 17:08:31 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9409092108.AA05042@eed02.ctc.com> Subject: allotropic sulfur question To: chemistry@ccl.net (Computational Chemistry List) Date: Fri, 9 Sep 1994 17:08:30 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1493 Can someone give me some information on the allotropic form of sulfur when heated to 500 oC at ambient pressure? At this temperature the element is molten. What temperature is necessary in order to cause sulfur to combine with carbon? My Merck Index only says "cobines with carbon at high temperatures". Thanks in advance. Doug -- Douglas A. Smith Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com !!!NEW!!! Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. and still: Douglas A. Smith voice: N/A Associate Professor fax: N/A Department of Chemistry email: dsmith@uoft02.utoledo.edu and Center for Drug Design and Development The University of Toledo Toledo, OH 43606-3390 +---------------------------------+---------------------------------+ | "The juvenile sea squirt wanders through the sea searching for | | a suitable rock or hunk of coral to cling to and make its home | | for life. For this task it has a rudimentary nervous system. | | When it finds its spot and takes root, it doesn't need its | | brain any more so it eats it. It's rather like getting tenure." | | --source unknown | +-------------------------------------------------------------------+ From san@mbu.iisc.ernet.in Fri Sep 9 18:48:12 1994 Received: from sangam.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id SAA18224; Fri, 9 Sep 1994 18:22:18 -0400 From: Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with SMTP id DAA02713 for ; Sat, 10 Sep 1994 03:51:28 +0530 Received: by iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA16090; Fri, 9 Sep 94 18:27:36 EDT Date: Fri, 9 Sep 94 18:27:36 EDT Message-Id: <9409092227.AA16090@iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA22287; 9 Sep 94 18:14:55 EST (Fri) To: vigyan!chemistry@ccl.net Subject: helix formation dear friends, hallo! As you know the mechanism for helix formations in proteins (of all kinds globular or membrane ) is a subject of immense theoretical & experimental research. I request you to send me reference (recent ones prefered ) for this kind of work. this may include mathematical & statistical analysis of protein crystal strucures containing the alpha helices. The studies on the propensities of different amino acids to occurr in helical conformations, the inherent tendencies of a.a. to adopt helical conformation over the random coil or beta sheet conformation. The prediction of protein conformations for sequence. Analysis of helices in proteins e.g. geomatrical shape of the helix viz curved, linear or irregular. Methods for such analysis. theorectical methodes to study the helices in general. the amino acid propensities for membrane helices. please post your reply to CCL or directly to me at san@mbu.iisc.ernet.in I will post a summary of the references on this important topic to the CCL if i get enough response. Application of ab initio & semi empirical methods to study this problem is something not very visible in litrature. I will be thankful to any body who sends me references on this topic. yours' cordially Sandeep Kumar, MBU, IISc. Bangalore, INDIA.