From BISETTYK@wpogate.mlsultan.ac.za Mon Apr 14 03:36:07 1997 Received: from Raven.und.ac.za for BISETTYK@wpogate.mlsultan.ac.za by www.ccl.net (8.8.3/950822.1) id DAA18841; Mon, 14 Apr 1997 03:25:11 -0400 (EDT) Received: from wpogate.mlsultan.ac.za (wpogate.mlsultan.ac.za [196.13.102.11]) by Raven.und.ac.za (8.8.3/8.7.3) with SMTP id JAA25503 for ; Mon, 14 Apr 1997 09:24:16 +0200 (SAT) From: "KRISHNA BISETTY" To: Chemistry@www.ccl.net Date: Mon, 14 Apr 1997 09:12:00 +200 Subject: Query X-Gateway: iGate, (WP Office) vers 4.04c - 1009 MIME-Version: 1.0 Message-Id: <3351D910.04B3.0000@wpogate.mlsultan.ac.za> Content-Type: TEXT/PLAIN; Charset=US-ASCII Content-Transfer-Encoding: 7BIT Dear computational chemists, I successfully optimised two small peptide molecules separately using G92W, installed on a 486DX computer used specifically to run the Nicolet Impact series FT-IR. After each optimization, the settings on the OMNIC software, used to run the FT-IR change. Is this probably due to the computation itself? "Is it a good idea to run any computational software packages, which are installed on a PC dedicated to a particular Analytical instrument?" Any suggestions would be greatly appreciated. Best wishes ------------------------------------------------------------------------------------- Vincent Bisetty Department of Chemistry ML Sulatn Technikon Durban South Africa Bisettyk@wpo.mlsultan.ac.za ----------------------------------------------------------------------------------------- From JARP@WCHUWR.CHEM.UNI.WROC.PL Mon Apr 14 06:36:08 1997 Received: from indigo2 for JARP@WCHUWR.CHEM.UNI.WROC.PL by www.ccl.net (8.8.3/950822.1) id GAA22345; Mon, 14 Apr 1997 06:07:07 -0400 (EDT) Received: from wchuwr.chem.uni.wroc.pl by indigo2 via SMTP (940816.SGI.8.6.9/930416.SGI) for id MAA05540; Mon, 14 Apr 1997 12:04:42 GMT Received: from ICHUWR/SMTPQueue by wchuwr.chem.uni.wroc.pl (Mercury 1.11); Mon, 14 Apr 97 12:07:21 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Mon, 14 Apr 97 12:07:03 +0100 From: "Jaroslaw Panek" Organization: University of Wroclaw (Chemistry) To: chemistry@www.ccl.net Date: Mon, 14 Apr 1997 12:07:01 GMT+1 Subject: CCL: Can I get ESR spectra from ab-initio calculs? Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <258B9A93442@wchuwr.chem.uni.wroc.pl> Hello CCL-ers: Does anyone of you know, how to obtain ESR hyperfine tensors from ab- initio results (e.g. Gaussian94 .wfn file). I know that isotropical hyperfine splittings are calculated from Fermi contact analysis, but what about anisotropic part? Thanks for any help Jaroslaw Panek Faculty of Chemistry Univ. Wroclaw, Poland jarp@wchuwr.chem.uni.wroc.pl From hinsen@lmspc1.ibs.fr Mon Apr 14 06:45:35 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id GAA22386; Mon, 14 Apr 1997 06:14:21 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id MAA23065; Mon, 14 Apr 1997 12:11:29 +0200 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id MAA24981; Mon, 14 Apr 1997 12:10:18 +0200 Date: Mon, 14 Apr 1997 12:10:18 +0200 Message-Id: <199704141010.MAA24981@lmspc1.ibs.fr> From: Konrad Hinsen To: chemistry@www.ccl.net Subject: Announcement: The Molecular Modeling Toolkit Now available: The Molecular Modeling Toolkit ============================================= The Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling. MMTK is developed in and around Python, a high-level object-oriented general-purpose programming language (see http://www.python.org for more information). Python was chosen because it allows rapid code development and testing, while providing a very convenient C interface for dealing with time-critical calculations. Like Python, MMTK is copyrighted but free software. MMTK is based on an object-oriented model of molecular systems. A system is made up of molecules, complexes, and atoms, all of which are defined in a central database of definition files, which themselves are (very simple) Python programs. A molecule, for example, is defined in terms of atoms, functional groups, bonds, force field parameters etc. It is possible to introduce specialized versions of these objects; for example, MMTK has special support for proteins, which are basically chemical complexes, but can be handled in terms of peptide chains, residues, sidechains etc. Among the operations that are currently implemented you can find: - construction of molecular systems - standard geometrical operations on coordinates - rigid-body fits - visualization using external PDB and VRML viewers - the AMBER 94 force field - energy minimization (steepest descent and conjugate gradient) - molecular dynamics (velocity Verlet) - normal mode calculation Compared to standard modelling code written in Fortran, MMTK is much easier to understand, extend, and modify. For example, new force fields can be added without touching any existing code, i.e. without any risk of breaking it. The following example gives some idea of what MMTK applications look like. It generates a representation of the protein crambin from a PDB file, performs an energy minimization using the conjugate gradient algorithm until the forces are sufficiently small, calculates the normal modes, prints the vibrational frequencies, and shows an animation of the lowest non-zero mode. --------------------------------------------------------------------------- from mmtk import * world = InfiniteUniverse(AmberForceField()) world.protein = Protein('crambin') minimizer = ConjugateGradientMinimizer(world, log = (0, None, 50, stdout, ("energy",))) minimizer(convergence = 1.e-3, steps = 10000) modes = NormalModes(world) for mode in modes: print mode.frequency view(modes[6]) --------------------------------------------------------------------------- For more information and to download MMTK, point your Web browser at http://www.yi.com/home/HinsenKonrad/mmtk.html -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From genghis@darkwing.uoregon.edu Mon Apr 14 10:36:09 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id KAA23681; Mon, 14 Apr 1997 10:27:06 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.5/8.8.5) with SMTP id HAA20676; Mon, 14 Apr 1997 07:26:47 -0700 (PDT) Date: Mon, 14 Apr 1997 07:26:47 -0700 (PDT) From: Dale Andrew Braden To: Jaroslaw Panek cc: chemistry@www.ccl.net Subject: Re: CCL:G:Can I get ESR spectra from ab-initio calculs? In-Reply-To: <258B9A93442@wchuwr.chem.uni.wroc.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Jaroslaw, Vincenzo Barone posted a modification to the Gaussian code a few weeks ago which will produce a nicely formatted, complete ESR analysis. Check the CCL archives. Even without the modification, you can get the anisotropic hfc components for each atom by specifying "Prop=EFG IOp(6/17=2,6/26=4)" and the appropriate option to the Density keyword, if necessary, in the route section. This tells Gaussian to calculate only the electronic component of the electric field gradient integrals for the nuclei, using the spin density matrix. You'll see a section in the output called "Electric Field Gradient -- (tensor representation) -- Eigenvalues" that will contain the values for the nuclei. All the best, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From s197216@ccs.sogang.ac.kr Mon Apr 14 13:36:12 1997 Received: from ccs.sogang.ac.kr for s197216@ccs.sogang.ac.kr by www.ccl.net (8.8.3/950822.1) id MAA25308; Mon, 14 Apr 1997 12:44:33 -0400 (EDT) Received: from localhost by ccs.sogang.ac.kr (8.8.5/Sogang) id BAA15925; Tue, 15 Apr 1997 01:43:21 +0900 (KST) Date: Tue, 15 Apr 1997 01:43:19 +0900 (KST) From: Kang Jin Koo X-Sender: s197216@ccs To: chemistry@www.ccl.net Subject: SCIPCM + Potential Energy Surface Scan in G-94W Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I've done potential surface scan in SCIPCM environment. But, in doing calculation in G-94W, the following messages are, "Density matrix breaks symmetry, pCut 1.00D-07 Density matrix has no symmetry -- integrals replicated." ...... ...... ...... repeated. I would like to know the meaning of these messages. Any Comment are helpful to me. Kang, Jin-Koo Dept. of Chem. Eng. Sogang University Seoul, Korea. From castejon@kbw350.chem.yale.edu Mon Apr 14 14:36:12 1997 Received: from kbw350.chem.yale.edu for castejon@kbw350.chem.yale.edu by www.ccl.net (8.8.3/950822.1) id OAA25854; Mon, 14 Apr 1997 14:08:22 -0400 (EDT) From: Received: by kbw350.chem.yale.edu (AIX 3.2/UCB 5.64/4.03) id AA17125; Mon, 14 Apr 1997 14:07:47 -0400 Date: Mon, 14 Apr 1997 14:07:47 -0400 Message-Id: <9704141807.AA17125@kbw350.chem.yale.edu> To: chemistry@www.ccl.net, s197216@ccs.sogang.ac.kr Subject: Re: CCL:SCIPCM + Potential Energy Surface Scan in G-94W Hi Jin. Don't worry about these messages. This means that the numerical integration done by gaussian is given two integral that should be equal by symmetry, different. You can disable this by putting the keyword: nosymm in the route card. Henry., From soperpd@nylon.es.dupont.com Mon Apr 14 16:36:14 1997 Received: from gatekeeper.es.dupont.com for soperpd@nylon.es.dupont.com by www.ccl.net (8.8.3/950822.1) id QAA26785; Mon, 14 Apr 1997 16:29:40 -0400 (EDT) Received: by gatekeeper.es.dupont.com; id QAA01309; Mon, 14 Apr 1997 16:29:40 -0400 Received: by esds01.es.dupont.com; id AA17511; Mon, 14 Apr 97 16:29:38 -0400 Received: (from soperpd@localhost) by nylon.es.dupont.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id QAA15208; Mon, 14 Apr 1997 16:30:17 -0400 Date: Mon, 14 Apr 1997 16:30:17 -0400 Message-Id: <199704142030.QAA15208@nylon.es.dupont.com> From: Paul Soper To: chemistry@www.ccl.net Subject: CCL: Batch Substructure Searching Reply-To: soperpd@esvax.dnet.dupont.com A colleage of mine is looking for a non-interactive program which will take two 2D structures, compare them, and say whether one is present as a substructure in the other. He wants to do a large number of pair-wise comparisons, so batch operation is a must. He'd obviously prefer that the program be available without cost. Thanks, Paul Soper ----------------------------------------------------------------- Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-2112 ----------------------------------------------------------------- From jsb2@camsoft.com Mon Apr 14 22:36:16 1997 Received: from camsoft.com for jsb2@camsoft.com by www.ccl.net (8.8.3/950822.1) id WAA27978; Mon, 14 Apr 1997 22:01:48 -0400 (EDT) From: Date: Mon, 14 Apr 97 22:01:48 EDT Received: by camsoft.com (4.1/3.1.090690-CambridgeSoft Corp.) id AA10934; Mon, 14 Apr 97 22:01:48 EDT Message-Id: <9704150201.AA10934@camsoft.com> To: chemistry@www.ccl.net, soperpd@esvax.dnet.dupont.com Subject: Re: CCL:Batch Substructure Searching > A colleage of mine is looking for a non-interactive program >which will take two 2D structures, compare them, and say whether >one is present as a substructure in the other. He wants to do a >large number of pair-wise comparisons, so batch operation is a >must. He'd obviously prefer that the program be available >without cost. Can't help you with the "without cost" part, but this is definitely possible with CS ChemFinder for Windows and a smidgen of Visual Basic. I've done it. You should have no problem doing several thousand to several tens of thousands of pairs an hour, depending on how fast a machine you're using. More information about ChemFinder is available from http://www.camsoft.com, or from me in a pinch. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com