From MUEM@iuct.fhg.de Fri Apr 12 04:46:06 1996 Received: from fhg.de for MUEM@iuct.fhg.de by www.ccl.net (8.7.1/950822.1) id EAA04285; Fri, 12 Apr 1996 04:04:35 -0400 (EDT) From: Received: by fhg (fhg.de) with PRESMTP; Fri, 12 Apr 96 10:04:24 +0200 from FHG-GATEWAY X-Env: MUEM@iuct.fhg.de -> chemistry@www.ccl.net Date: Fri, 12 Apr 96 10:04:10 +0200 Received: by fhg (fhg.de) with PSI; Fri, 12 Apr 96 10:04:10 +0200 from 45297290070 Message-Id: <9604120804.AA14905@fhg.de> To: Subject: MOPAC-Charges: Summary Dear CCLers some weeks ago I asked for the charges calculated in MOPAC: > MOPAC calculates "NET ATOMIC CHARGES" in a really simple manner: > atom electron densities are calculated as a sum of the diagonal elements of > the density matrix, and net atomic charges are then calculated by subtracting > this value from the core charge. > I know, there are much better methods for charge calculation (ESP...), however, > can anybody tell me, whether this method has a special name, or can give me a > literature reference ? I got several different answers, however, the MOPAC charges are of Coulson type. Thanks to: Darko Babic, Dave Giesen, Bill Ross, Jimmy Stewart, Brian Teppen, Lee Wilson Martin *----------------------------------------------------------------------------- * Dr. Martin Mueller * Fraunhofer-Institute for Environmental Chemistry and Ecotoxicology * (Dep.: Environmental Information and Evaluation Systems) * Postfach 1260 * D-57377 Schmallenberg * Germany * Phone : *49-2972-302 227 * FAX : *49-2972-302 319 * email : muem@iuct.fhg.de *----------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Apr 12 05:46:06 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id FAA04573; Fri, 12 Apr 1996 05:10:38 -0400 (EDT) Received: from kvlvax.kvl.dk for lasse@kvlvax.kvl.dk by bedrock.ccl.net (8.7.1/950822.1) id FAA14990; Fri, 12 Apr 1996 05:10:35 -0400 (EDT) From: Received: by kvlvax.kvl.dk (MX V4.2 AXP) id 3; Fri, 12 Apr 1996 11:11:20 +0100 Date: Fri, 12 Apr 1996 11:11:19 +0100 To: chemistry@ccl.net Message-ID: <009A0BE9.3D5B6428.3@kvlvax.kvl.dk> Subject: CCL:G: Orbital contrib. to molecular prop.'s Hi ! I am calculating electric field gradients (in cadmium complexes) using Gaussian94 (and MolCas). It is, of course, possible to get this molecular property once the total wavefunction is known, but I would like to get a bit more detailed information, and my question is : "Is it possible to split the total electric field gradient into individual molecular orbital contributions using Gaussian94 ?" (I am using this in a context where it is sufficient to use to SCF orbitals). Thanks in advance, Lars Hemmingsen email: lasse@mafy.kvl.dk From S.R.Kilvington@soton.ac.uk Fri Apr 12 06:46:46 1996 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.7.1/950822.1) id GAA06059; Fri, 12 Apr 1996 06:27:29 -0400 (EDT) Received: from willow.soton.ac.uk (willow.soton.ac.uk [152.78.128.20]) by beech.soton.ac.uk (8.6.12/hub-8.5a) with ESMTP id LAA14567 for ; Fri, 12 Apr 1996 11:27:21 +0100 Received: (from srk@localhost) by willow.soton.ac.uk (8.6.10/client-8.8) id LAA10162 for CHEMISTRY@www.ccl.net; Fri, 12 Apr 1996 11:23:13 +0100 Message-Id: <199604121023.LAA10162@willow.soton.ac.uk> Subject: rigid receptor models To: CHEMISTRY@www.ccl.net Date: Fri, 12 Apr 1996 11:23:13 +0100 (BST) From: "Simon Kilvington" X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hia, does anyone know where I can find a good discusion about the use of rigid vs flexible receptor models in computer-aided drug design? --- Simon Kilvington, srk@soton.ac.uk From MASS@sauron.quimica.uniovi.es Fri Apr 12 10:46:09 1996 Received: from opalo.etsiig.uniovi.es for MASS@sauron.quimica.uniovi.es by www.ccl.net (8.7.1/950822.1) id KAA09614; Fri, 12 Apr 1996 10:19:10 -0400 (EDT) From: Received: from sauron.quimica.uniovi.es (sauron.quimica.uniovi.es) by etsiig.uniovi.es (PMDF V5.0-7 #4541) id <01I3GEIU70R0984I72@etsiig.uniovi.es> for chemistry@www.ccl.net; Fri, 12 Apr 1996 13:12:17 +0100 (GMT) Received: from sauron.quimica.uniovi.es by sauron.quimica.uniovi.es (PMDF V5.0-3 #4543) id <01I3GEIC7VW0B9SOL8@sauron.quimica.uniovi.es> for chemistry@www.ccl.net; Fri, 12 Apr 1996 13:15:30 +0000 (WE) Date: Fri, 12 Apr 1996 13:15:30 +0000 (WE) Subject: CCL:Summary: Clusters containing octahedral Ti To: chemistry@www.ccl.net Message-id: <01I3GEIC7ZNMB9SOL8@sauron.quimica.uniovi.es> X-VMS-To: AIN"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCL'ers, A while back I asked this question: I am trying to model the interactions of intercalated molecules in lamellar phosphates of Ti. I am looking for molecular mechanics parameters (van der Waals parameters at least) for this compounds. Does anybody know where I could obtain these parameters or a method to calculate them ? I had these two answers, thanks a lot for spent some of your time in answering my question. From: IN%"guerlin@FHI-Berlin.MPG.DE" "Thomas Guerlin" Electron energy Loss near edge Structures at Oxygen K edges of Titanium IV oxygen compounds R.Brydson H.Sauer W.Engel F.Hofer, Phys Cond Matt 4 3429 (1992) Electron Energy Loss near Edge Structure X. Weng Dissertation at arizone State university Xray Absorption of transition metal oxides F.M.F. de Groot Proefshrift University of Nijmeng X-ray absorption and dichroism of transition metals and their compopunds FMF de Groot, J of Electron Spectroscopy and Relat Phenomena 67 529 (1994) From: IN%"pletnev@analyt.chem.msu.su" "Igor V. Pletnev" Hi, Miguel, There was a paper by Peter Comba on mol. mech. for (octahedral naturally) Ti(IV) diketonates: Inorg Chem 1994, 33, 3396-3400 Best wishes, Igor ________________________________________________________________________ Miguel A. Salvado Dpto. Quimica Fisica y Analitica Universidad de Oviedo E-mail: mass@dwarf1.quimica.uniovi.es ________________________________________________________________________ From huang@mazda.wavefun.com Fri Apr 12 11:46:11 1996 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.7.1/950822.1) id LAA10923; Fri, 12 Apr 1996 11:32:18 -0400 (EDT) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA17999; Fri, 12 Apr 96 08:32:34 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma017997; Fri Apr 12 08:32:22 1996 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:CHEMISTRY@www.ccl.net id AA27863; Fri, 12 Apr 96 08:31:23 -0700 From: "Wayne Huang" Message-Id: <9604120831.ZM27861@mazda.wavefun.com> Date: Fri, 12 Apr 1996 08:31:21 -0700 In-Reply-To: "Wayne Huang" "CCL:96.06.12 Computational Chemistry Workshops" (Apr 10, 5:23pm) References: <9604101723.ZM8150@mazda.wavefun.com> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@www.ccl.net, sparlist@mazda.wavefun.com Subject: A short note to CC Workshops Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hello again, A short note adding to the announcement of Computational Chemistry Workshops offered by Wavefunction. The June 12-14 workshop is full now. For those who wish to come in June, please consider our newly scheduled 2nd June workshop - June 26-28, 1996. Thanks for your time. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From D.Turner@sheffield.ac.uk Fri Apr 12 12:37:34 1996 Received: from pp2.shef.ac.uk for D.Turner@sheffield.ac.uk by www.ccl.net (8.7.1/950822.1) id LAA10913; Fri, 12 Apr 1996 11:30:57 -0400 (EDT) Received: from sunc.shef.ac.uk by pp2.shef.ac.uk with local SMTP (PP); Fri, 12 Apr 1996 16:29:42 +0100 Received: (from li2dbt@localhost) by sunc.shef.ac.uk (8.7.1/8.7.1) id QAA16217; Fri, 12 Apr 1996 16:29:38 +0100 (BST) Date: Fri, 12 Apr 1996 16:29:38 +0100 (BST) From: D Turner Message-Id: <199604121529.QAA16217@sunc.shef.ac.uk> To: chemistry@www.ccl.net Subject: IR-Range Vibrational frequency calculations Cc: D.Turner@sheffield.ac.uk Hello I trying to find out general opinion as to which molecular mechanics/ force-field software provides the most reliable IR-range vibrational frequencies. I am interested in MM-based methods since I am looking to do rapid calculations on sets of small organic molecules, as typically encountered in pharmaceutical/agrochemical applications. I am NOT interested in proteins, polyscaccharides or other large polymers. Due to the nature of the application (QSAR studies) I am more concerned with relative rather than absolute accuracy of the calculated frequencies. Thus far MM3(94) has been suggested to me. Thanks in advance for any help Dave Turner ======================================================================== | Dept of Information Studies | Sheffield University, UK | Tel.: 0114 2825 093 Fax.: 0114 780 300 | E-mail: D.Turner@sheffield.ac.uk ======================================================================== From jose@zeus.uncor.edu Fri Apr 12 13:46:11 1996 Received: from zeus.uncor.edu for jose@zeus.uncor.edu by www.ccl.net (8.7.1/950822.1) id NAA12987; Fri, 12 Apr 1996 13:13:21 -0400 (EDT) Received: by zeus.uncor.edu; id AA11668; Fri, 12 Apr 1996 14:16:26 -0300 Sender: jose@zeus.uncor.edu Message-Id: <316E8FE9.6488@zeus.uncor.edu> Date: Fri, 12 Apr 1996 14:16:25 -0300 From: "Jose Santiago Duca (h)" X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: jose@zeus.uncor.edu Subject: about HyperChem and Mopac Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I have just a little question about HyperChem, since I am not too much familiarized with this package, but with Ampac and Mopac. Is there any possibility of reading the Am(Mo)pac density matrix with HyperChem in order to avoid a single point calculation each time I need to work with spin or charge surfaces plots? I suspect the answer is affirmative (via using a script file, maybe), but I don't know how to handle it, so could anybody help me, please? Thanking in advance, Jose -- Dr. Jose Santiago Duca (h) jose@zeus.uncor.edu http://zeus.uncor.edu/jsd/jsd.htm From Jeffrey.Nauss@UC.EDU Fri Apr 12 15:46:11 1996 Received: from jazz.san.uc.edu for Jeffrey.Nauss@UC.EDU by www.ccl.net (8.7.1/950822.1) id PAA14928; Fri, 12 Apr 1996 15:02:17 -0400 (EDT) Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-6 #7238) id <01I3GIAOZS9YA736PK@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Fri, 12 Apr 1996 15:00:08 -0500 (EST) Received: from ucmod2.che.uc.edu by ucmod2.che.uc.edu via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) id OAA24155; Fri, 12 Apr 1996 14:56:06 -0400 Date: Fri, 12 Apr 1996 14:56:01 -0400 From: "Jeffrey L. Nauss" Subject: Heating before Molecular Dynamics Sender: nauss@UC.EDU Cc: chemistry@www.ccl.net, DIBUG@sunsite.icm.edu.pl Message-id: <316EA741.167E@UC.Edu> Organization: Dept. Chem., University of Cincinnati MIME-version: 1.0 X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP12) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Newsgroups: bionet.molec-model When using CHARMM or AMBER for molecular dynamics, the system is usually heated to the required temperature, ran in an equilibration period, and only then is the actual production run. However, in Discover, there is no heating phase. The system is instanteously heated to the required temperature and equilibrated before the production phase. Why the difference in the two approaches? What is Discover doing differently from CHARMM and AMBER so that a heating phase is not required? -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From h.rzepa@ic.ac.uk Fri Apr 12 16:16:43 1996 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.7.1/950822.1) id PAA15015; Fri, 12 Apr 1996 15:23:53 -0400 (EDT) Received: from judy.ic.ac.uk by punch.ic.ac.uk with SMTP (PP); Fri, 12 Apr 1996 20:23:42 +0100 Received: from cscmgb.cc.ic.ac.uk (sg1.cc.ic.ac.uk [155.198.63.8]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id UAA04573 for ; Fri, 12 Apr 1996 20:23:19 +0100 (BST) Received: from [155.198.63.14] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id UAA06701; Fri, 12 Apr 1996 20:23:14 +0100 X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 12 Apr 1996 19:32:08 +0000 To: chemistry@www.ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: Re: CCL:Java and other WWW developments Paul Weber writes >A common vision is to think of the Browser as the new desktop, or GUI to >your work. You might, in the not too distant future, get a chemistry >version of "plug and play" where a molecule sketched in a Tripos applet is >used to pull out compounds from an MDL database, some of which are then >minimized using the Merck FF, all on the same page (which could then be >stored or "registered" as a notebook page that could be searched later). The Web as a new operating system metaphor is also the objective of the X-Window consortium, and perhaps even Apple OpenDoc/Cyberdog. Thus what Paul Weber writes seems pretty much on the ball! >I think that it is a good time for the community to search for acceptable >standards, such as SGI's Molecular Inventor, Tripos's SLN, DayLight's >SMILES, or the PDB (yuck). The chemistry community could then promote the >use of these standard formats by all software producers, whether garage-shop, >grad student, or public company. Somehow I doubt we will end up with only one. But I fully endorse the need to search for standards. Perhaps I should note that IUPAC is convening a new committee, CPEP (printed and electronic publications) which takes Internet standards as one of its major briefs. It will only respond to what the community wants (I hope). If people want to go "off-line" from this forum to discuss these issues, do post to chemime@ic.ac.uk >Watch the Web for more big developments soon! Do I take this to mean that with conventional chemistry software markets perhaps stagnant or certainly not expanding as fast as in the past, the "Internet" is viewed by all as the great new white hope? We can all only benefit it this is so!