From JEREMYW@num-alg-grp.co.uk Thu Mar 31 06:02:23 1994 Received: from ben.britain.eu.net for JEREMYW@num-alg-grp.co.uk by www.ccl.net (8.6.4/930601.1506) id FAA07829; Thu, 31 Mar 1994 05:23:29 -0500 Received: from num-alg-grp.co.uk by ben.britain.eu.net via JANET with NIFTP (PP) id ; Thu, 31 Mar 1994 11:23:07 +0100 Message-Id: <6979.9403311019@nags2.nag.co.uk> Received: from vax.nag.co.uk (nagvax) by nags2.nag.co.uk (4.1/UK-2.1) id AA06979; Thu, 31 Mar 94 11:19:05 BST Date: 31 Mar 94 11:18:00 WET From: JEREMY WALTON Subject: Re: Using SGI's IRIS Explorer in Computational Chemistry To: CHEMISTRY >> I would suggest that AVS and its Molecule Data Type are much better >> for chemistry, since the data type was an integral part of the initial >> design of AVS. It is very flexible and as such there are many ways in which >> data can be stored in its various components, which are hierarchical lists. >> I have a nine+ page description of how the MDT is structured if anyone is >> interested (at least, how it is structured and used in the Chemistry Viewer). >> In general, the MDT is an organized collection of atom-based substructure >> and quantum chemical information. Hi Doug, My copy of the "AVS Technical Overview" shows the Molecule Data Type being added to AVS as a new feature at version 3 in March 1991. By contrast, the molecular pyramid datatype was a feature of version 1.0 of IRIS Explorer, announced the same year. However, this is really of little relevance to this group (I'm sure we don't want an AVS vs IRIS Explorer discussion along the lines of the recent FORTRAN vs C flame wars ;-) ). One problem that some users have had with the pyramid datatype is its complexity - partly because it was designed so that the same heirarchical structure can be used to store both molecular data and unstructured grids. However, once mastered, the molecular pyramid can indeed be used powerfully - e.g. the EyeChem suite of chemistry modules developed by Omer Casher and his colleagues, which are part of version 2.2 of IRIS Explorer. Malcolm and I have been having (somewhat fitful) exchanges on ways in which this can be improved, possibly by making use of IRIS Explorer's functionality for creating user-defined types. Either way, it'd be nice to hear more about the AVS MDT, so if there was any more information which could be shared with the group, I'm sure I'm not the only one who'd be interested. 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 thys@schs.uia.ac.be Thu Mar 31 08:02:24 1994 Received: from sch2.uia.ac.be for thys@schs.uia.ac.be by www.ccl.net (8.6.4/930601.1506) id HAA08614; Thu, 31 Mar 1994 07:45:10 -0500 Received: from localhost by sch2.uia.ac.be (8.6.4/Ultrix3.0-C) id OAA11120; Thu, 31 Mar 1994 14:43:42 +0200 Date: Thu, 31 Mar 1994 14:43:35 +0200 (MET DST) From: Gerd Thys Subject: IP and EA in semi-empirical methods To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I'm looking for articles comparing ionisation-potentials and electron-affinities, obtained by using MINDO/3, MNDO, AM1 and PM3 and experimental data (or ab-initio calculations). I'm especially interested in molecules containing phenyl-, furane-, pyrrole- and thiophene-groups. I already have the articles of M.J.S. Dewar and M.L. Mckee (J.Comp.Chem., p.84 (1983)) and M.J.S. Dewar and W. Thiel (J.Am.Chem.Soc. p.4907 (1977)) on the MNDO results for H,C,N,O en S-containing molecules. I wonder if there are similar articles for the other three methods. Greetings, Gerd ------------------------------------------------------------------------ Gerd Thys Dienst voor structuurchemie Universiteitsplein B-3610 wilrijk BELGIUM E-mail: thys@uia.ac.be ------------------------------------------------------------------------ From PHYSPLMP@MIZZOU1.missouri.edu Thu Mar 31 09:02:25 1994 Received: from MIZZOU1.missouri.edu for PHYSPLMP@MIZZOU1.missouri.edu by www.ccl.net (8.6.4/930601.1506) id JAA09074; Thu, 31 Mar 1994 09:00:33 -0500 From: Message-Id: <199403311400.JAA09074@www.ccl.net> Received: from MIZZOU1 by MIZZOU1.missouri.edu (IBM VM SMTP V2R2) with BSMTP id 8314; Thu, 31 Mar 94 08:01:31 CST Received: by MIZZOU1 (Mailer R2.10 ptf000) id 3323; Thu, 31 Mar 94 08:01:31 CST Date: Thu, 31 Mar 94 07:57:10 CST To: thys@sch2.uia.ac.be cc: chemistry@ccl.net Subject: Re: CCL:IP and EA in semi-empirical methods In-Reply-To: thys@sch2.uia.ac.be -- Thu, 31 Mar 1994 14:43:35 +0200 (MET DST) In 1990 J.J.P.Stewart, the author of MOPAC, prepared an extensive comparison of PM3, AM1 and MNDO. It is published as Vol. 4, No.1, of J. of Computer-aided Mol ecular Design, ESCOM, Mar. 1990 (a special issue). Hope this is a help. Pat Plummer, Univ. of Missouri-Columbia From SBOESCH@aardvark.ucs.uoknor.edu Thu Mar 31 12:02:27 1994 Received: from aardvark.ucs.uoknor.edu for SBOESCH@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id LAA10719; Thu, 31 Mar 1994 11:26:51 -0500 From: Message-Id: <199403311626.LAA10719@www.ccl.net> Date: Thu, 31 Mar 94 10:27 CST Subject: mpLockfile on g92/dft To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters, We recently put g92/dft on a silicon graphics workstation. Everytime we run a gaussian job a file called mpLockFile is written to the temporary portion of the disk (/tmp). Has anyone encountered this before? Thank for the help. Scott Boesch Department of Chemistry & Biochemistry University of Oklahoma From ravishan@swan.wcc.wesleyan.edu Thu Mar 31 12:15:28 1994 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.4/930601.1506) id LAA10973; Thu, 31 Mar 1994 11:46:54 -0500 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA23666; Thu, 31 Mar 1994 11:44:13 -0500 Date: Thu, 31 Mar 1994 11:44:13 -0500 Message-Id: <9403311644.AA23666@swan.wcc.wesleyan.edu> From: "G. Ravishanker" To: chemistry@ccl.net Subject: Unrolled helix diagrams Hi I am trying to generate the unrolled-helix diagrams that you see in some of the DNA papers, especially the ones from Dickerson's lab. It is basically a cylindrical projection of the backbone (or even the bases, if one wants) whereby one projects all DNA atoms to a cylinder of particular radius and then cut open the cylinder. The 2-D projection typically has the polar coordinates (the angle phi and the z-coordinate) plotted against one another. I am having problems carrying this out: 1. After the projection, when I draw the unrolled structure (in 2-D), some parts of the backbone are phase-shifted. That is, the backbone does not appear as a single line, but as a line of some n-bases and then the next contiguous bases on the same helix appear as another line shifted by 180. I have managed to correct this by some "ugly" piece of code. 2. The distance in the 2-D diagram between the phosphates of the two helics do not correspond to the 3-D distances. This is of course a major problem. Since one of the axes is an angle and the other a distance, what exactly should be done to reflect the 3-space geometry correctly in 2-space? I would appreciate any help I can get and Thanks in advance. Ravi **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06457. * **************************************************************************** From jkl@ccl.net Thu Mar 31 16:02:40 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id PAA14871; Thu, 31 Mar 1994 15:44:17 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id PAA00241; Thu, 31 Mar 1994 15:44:17 -0500 Date: Thu, 31 Mar 1994 15:44:17 -0500 Message-Id: <199403312044.PAA00241@krakow.ccl.net> To: chemistry@ccl.net Subject: Florida Shortcourse on Applied Molecular Orbital Theory Cc: jkl@ccl.net I am forwarding this message to the list on request from Karen (Janiszewski) Yanke (yanke@qtp.ufl.edu). ATTENTION! This is your last chance! The Ninth Annual Florida Shortcourse on Applied Molecular Orbital Theory is scheduled for May 1-8, 1994. A few spots remain. If interested, contact Rodney J. Bartlett right away! Telephone: (904) 392-6974 or (904) 392-1597 Fax: (904) 392-8722 E-Mail: bartlett@qtp.ufl.edu From JARZECAA@ctrvax.Vanderbilt.Edu Thu Mar 31 18:02:47 1994 Received: from ctrvx1.Vanderbilt.Edu for JARZECAA@ctrvax.Vanderbilt.Edu by www.ccl.net (8.6.4/930601.1506) id RAA16363; Thu, 31 Mar 1994 17:24:28 -0500 From: Received: from ctrvax.Vanderbilt.Edu by ctrvax.Vanderbilt.Edu (PMDF V4.2-15 #3899) id <01HAMMMMYVOG8XOO1U@ctrvax.Vanderbilt.Edu>; Thu, 31 Mar 1994 16:22:18 CST Date: Thu, 31 Mar 1994 16:22:18 -0600 (CST) Subject: CI in Gaussian 92 To: chemistry@ccl.net Message-id: <01HAMMMN1AHE8XOO1U@ctrvax.Vanderbilt.Edu> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, Does anyone know what the "Energy(CI, Size)" value is in the Gaussian 92 output for CI calculations ? How is this diffrent from Energy(CI) value ? Happy Easter, Thank You for your time and help. A.A.J. ***************************************** Andrzej A. Jarzecki Vanderbilt University Department of Chemistry Nashville, TN 37235. Telenone: 615-322-7324 e-mail: Jarzecaa@Ctrvax.Vanderbilt.Edu ***************************************** From rjaeger@marvin.chem.utoronto.ca Thu Mar 31 19:02:33 1994 Received: from alchemy.chem.utoronto.ca for rjaeger@marvin.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id SAA17146; Thu, 31 Mar 1994 18:25:15 -0500 Received: from marvin.chem.utoronto.ca (marvin.chem.utoronto.ca [128.100.81.52]) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) with SMTP id SAA20789 for <@ALCHEMY.CHEM.UTORONTO.CA:CHEMISTRY@ccl.net>; Thu, 31 Mar 1994 18:24:25 -0500 Received: by marvin.chem.utoronto.ca (931110.SGI/931108.SGI.ANONFTP) for @ALCHEMY.CHEM.UTORONTO.CA:CHEMISTRY@ccl.net id AA14092; Thu, 31 Mar 94 18:24:24 -0500 Date: Thu, 31 Mar 94 18:24:24 -0500 From: rjaeger@marvin.chem.utoronto.ca (Raimund Jaeger) Message-Id: <9403312324.AA14092@marvin.chem.utoronto.ca> To: CHEMISTRY@ccl.net Subject: CCL: Request for a code for Stone's distributed multipole analysis Hello, I am working on the calculation of the rotational flexibility of polymer backbones. I determined several torsional potentials of the backbone - bonds with ab initio calculations (Gaussian '92). Currently, I'm trying to describe the ab initio torsional potentials with van der Waals - and electrostatic interaction, where I use the MM2 parametrization for the vdW terms and electrostatic point charges derived from Mulliken's population analysis or natural population analysis. When I tried to fit the ab initio torsional potentials with vdW - and electrostatic (monopole) interactions, I got the impression that the results could be improved, if I include higher multipole momenta (dipole, quadrupole, etc.) into the electrostatic interaction. Stone's 'distributed multipole analysis' (DMA) calculates the higher electrostatic multipole momenta from the charge density obtained from ab initio calculations. Stone's DMA seems to implemented in some ab initio packages, but I didn't come across a code which has an interface to the Gaussian '92 package. Therefore my questions: - Does anyone has some experience with modeling non bonded interactions with electrostatic interactions including higher multipole momenta (derived from ab initio results)? - Does anyone know about a program which can use Gaussian '92 results as input for a distributed multipole analysis? Thanks, R. Jaeger. *************************************************************************** R. Jaeger phone: (416) 978 1697 Chemistry Dept., University of Toronto fax : (416) 978 8775 80 St. George St. e-mail: rjaeger@marvin.chem.utoronto.ca Toronto, Ont. M5S 1A1 Canada ***************************************************************************