From msj@fskru5.hre.hydro.com Fri Jan 16 04:15:59 1998 Received: from fskru5.hre.hydro.com for msj@fskru5.hre.hydro.com by www.ccl.net (8.8.3/950822.1) id EAA16308; Fri, 16 Jan 1998 04:09:00 -0500 (EST) Received: by fskru5.hre.hydro.com (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id LAA17736; Fri, 16 Jan 1998 11:06:13 +0100 From: "Merethe Sjovoll" Message-Id: <9801161106.ZM17734@fskru5.hre.hydro.com> Date: Fri, 16 Jan 1998 11:06:13 +0100 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Different extended Huckel Parameters for Ni Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello everyone, I wondered if any of you were familiar with extended Huckel parameters for Ni. I found that two rather different sets are used in the programs Yaehmop by Greg Landrum and the QCPE program No. 571. According to Greg the Yaehmop parameters are particularly suited for cases where Ni is in a cation state. Does anybody recognize and know the origin of the other parameter set. I only show the IP's here: IP 4s 4p 3d Yaehmop -10.95 -6.27 -14.2 QCPE 571 -9.17 -5.15 -13.49 The electrons are "tighter" in the Yaehmop parameters, consistent with the situation in a positively charged atom. I am doing calculations on perowskites like La2NiO4 and wonder which parameter set is the best to use in this case. Best regards, Merethe -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 27 22 * * ******************************************************** From Henryette.Roth@rzmail.uni-erlangen.de Fri Jan 16 04:38:08 1998 Received: from max4.rrze.uni-erlangen.de for Henryette.Roth@rzmail.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id DAA16253; Fri, 16 Jan 1998 03:50:03 -0500 (EST) Received: from cssun.rrze.uni-erlangen.de by max4.rrze.uni-erlangen.de; Fri, 16 Jan 1998 09:49:50 +0100 Received: from local by cssun (SMI-8.6/cl-RRZE) id IAA16622; Fri, 16 Jan 1998 08:49:50 GMT From: Henryette Roth Subject: J.Mol.Model.: Review open for discussion To: chemistry@www.ccl.net Date: Fri, 16 Jan 1998 09:49:50 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Message-Id: <34bf1f2e61fb002@max4.rrze.uni-erlangen.de> OFFICE MEMO Date: 15/1/1998 J.Mol.Model.: Review open for discussion Dear colleague, we are pleased to announce the publication of the second Journal of Molecular Modeling Review entitled "Three-Dimensional Models of Immune Cell Surface Proteins and Identification of Binding Sites" by Juergen Bajorath The review is accessible free of charge at the journals WWW-sites, http://link.springer.de/journals/jmm/ and http://www.ccc.uni-erlangen.de/info/JMOLMOD/ We encourage you to take part in the Open Discussion. The following abstract gives you a taste of the subject reviewed. ________________________________________________________________________________ ABSTRACT The extracellular regions of many cell surface proteins of the immune system contain distinct modules that may be linked in many different ways and are often only loosely tethered to a transmembrane segment. To identify important regions for binding in these molecules, molecular models are used to select residues for mutagenesis and to map binding sites. Many immune cell surface proteins belong to protein super- families and display only limited sequence identity compared to proteins with known three-dimensional (3D) structure, often 30% or less. Therefore, their detailed 3D structures are difficult to predict, and structure-based sequence analysis and model assessment are particularly important components of the model building process. In some cases, experimentally determined structures have made it possible to assess the accuracy of the predictions, which illustrates the opportunities and shortcomings of the approach. Herein the model-based identification of binding sites is described and representative examples are discussed. Tim Clark Henryette Roth (editor) (assistant editor) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Editorial Office ^ ^ ^ Computer-Chemie-Centrum ^ [+49](0)9131 / 85-6567 ^ ^ Universitaet Erlangen-Nuernberg ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ http://www.ccc.uni-erlangen.de ^ http://link.springer.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From illien@chimie.univ-nantes.fr Fri Jan 16 05:15:23 1998 Received: from nasta2.sciences.univ-nantes.fr for illien@chimie.univ-nantes.fr by www.ccl.net (8.8.3/950822.1) id FAA16613; Fri, 16 Jan 1998 05:01:16 -0500 (EST) Received: from callisto.chimie.univ-nantes.fr (callisto.chimie.sciences.univ-nantes.fr [193.52.103.2]) by nasta2.sciences.univ-nantes.fr (8.8.5/8.8.5) with SMTP id KAA04252 for ; Fri, 16 Jan 1998 10:59:52 +0100 Received: from [193.52.103.103] (McSpectro1) by callisto.chimie.univ-nantes.fr, Fri, 16 Jan 98 10:45:54 +0100 Date: Fri, 16 Jan 98 10:45:53 +0100 Message-Id: <9801160945.AA11413@callisto.chimie.univ-nantes.fr> X-Sender: illien@193.52.103.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: illien@chimie.univ-nantes.fr (Bertrand Illien) Subject: GAUSSIAN94 for Pentium II Dear CCL readers Gaussian Inc. distributes GAUSSIAN 94 for 486,pentium and pentium pro under FRee BSD or Linux (RedHat). We would like to Know if someone has already run Gaussian 94 on pentium II with single or 2-processors under Free BSD or RedHat ? It is possible and stable ? I''ll Summarize. Bertrand ________________________________________________ Bertrand ILLIEN Laboratoire de Spectrochimie Universite de Nantes Faculte des Sciences et Techniques 2, rue de la Houssiniere BP 92208 44322 Nantes Cedex 3 FRANCE Tel: (+33) (0)2 40 37 30 44 Fax: (+33) (0)2 40 74 50 00 E-Mail: illien@chimie.univ-nantes.fr _________________________________________________ From goeller@pc04.chemie.uni-jena.de Fri Jan 16 10:15:25 1998 Received: from pc04.chemie.uni-jena.de for goeller@pc04.chemie.uni-jena.de by www.ccl.net (8.8.3/950822.1) id JAA17875; Fri, 16 Jan 1998 09:31:30 -0500 (EST) Received: by pc04.chemie.uni-jena.de; id AA23428; Fri, 16 Jan 1998 15:31:52 +0100 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <34BF6F58.41C6@pc04.chemie.uni-jena.de> Date: Fri, 16 Jan 1998 15:31:52 +0100 From: Andreas Goeller Organization: Institut fuer Physikalische Chemie X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.2 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: goeller@pc04.chemie.uni-jena.de Subject: NLO; SOS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I've got some questions regarding Nonlinear optics Sum over States The 3rd order polarisability (2nd order hyperpolarisability) gamma for one molecule is regarding to Butcher, Cotter, The Elements of Nonlinear Optics, Academic Press, defined as gamma(ijkl)(-oms,om1,om2,om3) = e**4/(3! * h/2pi)**-3 * Perm-Op * sum ( (rgm(i)*rmn(j)*rno(k)*rog(l))/(mg-oms)(ng-om2-om3)(og-om3) + (rgm(j)*rmn(i)*rno(k)*rog(l))/(mg+om1)(ng-om2-om3)(og-om3) + (rgm(j)*rmn(k)*rno(i)*rog(l))/(mg+om1)(ng+om1+om2)(og-om3) + ( rgm(j)*rmn(k)*rno(l)*rog(i))/(mg+om1)(ng+om1+om2)(og+oms) ) with oms=om1+om2+om3 g, m, n, o are ground and exc. steates mg, ng, og are E(exc.)-E(ground) r are transition dipole moments i, j, k, l are cartesian coordinates and the pairs (om1, j), (om2, k), (om3, l) are permuted by Perm-Op 1) there are some similar formulae in literature which I can't directly deduce to this formula. Is this the right definition? 2) gm is the transition 1-2, 1-3 and so on. Analogously og is 2-1, 3-1 ... Has one to take rgm(i) = -rog(i) for m = o? There should be a difference between the transition dipole moment "upstairs" and "downstairs". 3) Is it allowed to reach the ground state with the transition rmn(i) or rno(i)? Is it allowed to stay in one state, e.g. rmn(i) with m=n would be the dipole moment of that state (corrected by the dipole moment of the ground state)? 4) According to finite field NLO: There the field is always defined in atomic units. What is 1au of the electric field in V/m (SI)? I will post a summary of (hopefully many) answers to the list. Thanks in advance. -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From s.hogg@ic.ac.uk Fri Jan 16 13:15:26 1998 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id MAA19036; Fri, 16 Jan 1998 12:26:22 -0500 (EST) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 1.62 #1) id 0xtFX9-0003pJ-00; Fri, 16 Jan 1998 17:26:19 +0000 Received: from mtcmsa.mt.ic.ac.uk (root@mtcmsag1.mt.ic.ac.uk [155.198.96.22]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id RAA10438 for ; Fri, 16 Jan 1998 17:26:11 GMT Received: from mtcse.mt.ic.ac.uk by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA23687; Fri, 16 Jan 1998 17:26:08 GMT X-Received: from helen.mt.ic.ac.uk by mtcse.mt.ic.ac.uk; Fri, 16 Jan 1998 17:26:07 GMT Message-Id: <3.0.5.32.19980116172141.007ff890@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Fri, 16 Jan 1998 17:21:41 +0000 To: chemistry@www.ccl.net From: Simon Hogg Subject: VChem from VirtualChemistry Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Does anyone know where I can get a copy (demo or otherwise) of VChem (apparently from www.virtualchemistry.com, but the website is empty (but working)). An Archie search turned up just a CGA program for 'learning what an atom is' but the vchem I am looking for is apparently a little modelling program Any pointers? -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk From alex.klinsky@scientist.com Fri Jan 16 16:15:37 1998 Received: from unet.univie.ac.at for alex.klinsky@scientist.com by www.ccl.net (8.8.3/950822.1) id PAA19842; Fri, 16 Jan 1998 15:50:41 -0500 (EST) Received: from cardenolid (uvo-75.univie.ac.at [131.130.230.175]) by unet.univie.ac.at (8.7.1/8.7.1) with SMTP id VAA123518 for ; Fri, 16 Jan 1998 21:50:29 +0100 From: "Alexander Klinsky" To: Subject: Isosurface visualisation library ? Date: Thu, 15 Jan 1998 21:21:12 +0100 Message-ID: <01bd21f3$1fc18e30$0100007f@cardenolid> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Dear Colleagues! Does anybody know of a free isosurface visualisation library or package which allows to color individual parts of the generated isosurface ( from a 3D gridded data set ) based on another 3D data set. I would like to display ab-initio calculated ESPs (Cube=Potential) on an electron density isosurface from a Gaussian94 calculation using the Cube=Density keyword. It should be callabe from C/C++ and/or Fortran77 and running under Unix(Linux) or NT. Best regards, Alexander Klinsky Inst. of pharm. chemistry Dep. of odour research University of Vienna From smithja@ucarb.com Fri Jan 16 16:23:09 1998 Received: from sctmg02.sct.ucarb.com for smithja@ucarb.com by www.ccl.net (8.8.3/950822.1) id PAA19858; Fri, 16 Jan 1998 15:53:44 -0500 (EST) Received: by sctmg02.sct.ucarb.com with Internet Mail Service (5.0.1458.49) id ; Fri, 16 Jan 1998 15:50:30 -0500 Message-ID: From: "Smith JA (Jack)" To: "'Didier MATHIEU'" , "'CCL'" Subject: RE: Qeq & others charge equilibration method Date: Fri, 16 Jan 1998 15:54:57 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Content-Type: text/plain > I currently need a very fast method to estimate the molecular > electrostatic potential outside de Van der Waals surface, preferably > avoiding QM calculations, and turn to empirical charge equilibrations > methods. Finally I consider using the QEq scheme, but maybe I could > benefit from the experience of some of us, especially if s.O. already > studied MEP built from QEq charges ?? > A simple idea I've been toying with is the use of Rappe's QEq scheme (perhaps coupled with Landis' VALBOND scheme) together with a variationally derived analytical Thomas-Fermi expression for the charge density of charged atoms. This generates a very quick, crude, but surprisingly good electron density (a superposition of charged atom densities) and a full electrostatic potential (in analytical form) corresponding to the QEq charges. It's fast enough to perform at an MD timescale. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From atiller@vishnu.msicam.co.uk Fri Jan 16 17:15:29 1998 Received: from msicam.co.uk for atiller@vishnu.msicam.co.uk by www.ccl.net (8.8.3/950822.1) id QAA20009; Fri, 16 Jan 1998 16:23:27 -0500 (EST) Received: from garuda.msicam.co.uk by msicam.co.uk (940816.SGI.8.6.9/SMI-4.1 (MSI-Cambridge)) id VAA09230; Fri, 16 Jan 1998 21:19:17 GMT Message-Id: <3.0.32.19980116212740.006a7c04@192.190.183.28> X-Sender: andrew_tiller@192.190.183.28 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Fri, 16 Jan 1998 21:27:44 +0000 To: chemistry@www.ccl.net From: Andrew Tiller Subject: CCL:? re WebLab 2.0 partial atomic charges Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues Apparently there has been some confusion about the charge assignment method used by MSI's WebLab Viewer; in fact the Gasteiger method is used, as indicated in the program's integral help text. QEq is one of the methods available in our Cerius2 product, but not in WebLab Viewer. (If a molecule is read from one of the file formats supported by WebLab Viewer, any partial charges included in the file are, of course, retained on the molecule.) Sincere apologies to Dr Shapiro, Dr Goto and the CCL community for the confusion over this issue. Best wishes Andy Tiller *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* * Andrew Tiller, PhD. * * Director, Market Development, Molecular Simulations Inc * * The Quorum, Barnwell Road, Cambridge, CB5 8RE, UK * * Tel: +44 1223 413 300, Fax: +44 1223 413 301 * *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*