From mathieu@ripault.cea.fr Fri Oct 31 04:34:43 1997 Received: from nenuphar.saclay.cea.fr for mathieu@ripault.cea.fr by www.ccl.net (8.8.3/950822.1) id DAA26662; Fri, 31 Oct 1997 03:50:19 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.8.5/ CEANET-ROUTER-3.0) with ESMTP id JAA08035 for ; Fri, 31 Oct 1997 09:49:42 +0100 (MET) Received: from cerbere.limeil.cea.fr (cerbere.bruyeres.cea.fr [132.165.76.1]) by muguet.saclay.cea.fr (8.8.5/ CEANET-ROUTER-3.0) with SMTP id JAA21909 for ; Fri, 31 Oct 1997 09:49:41 +0100 (MET) Received: by cerbere.limeil.cea.fr (CEANET-1.1+) id AA04330; Fri, 31 Oct 1997 09:49:22 +0100 Received: from vienne.ripault.cea.fr(132.165.32.4) by cerbere via smap id sma004317; Fri Oct 31 09:49:00 1997 Received: from vienne.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.4/8.7.3) with SMTP id KAA00857 for ; Fri, 31 Oct 1997 10:44:20 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <3459A874.20E3ADB4@ripault.cea.fr> Date: Fri, 31 Oct 1997 10:44:20 +0100 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.0 (X11; I; Linux 2.0.27 i586) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: averages over molecular surfaces Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL readers, recently an inquiry was made on CCL concerning molecular volumes. In the simple case where the molecule is considered as overlapping spheres, I would need to compute some quantities (e.g. electrostatic potential) averaged over the molecular surface. Is there any clever way to do that, avoiding a brute force purely numeric scheme ? Some references about this problem would be welcome. Thanks -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From raf.bruyndonckx@unifr.ch Fri Oct 31 04:47:00 1997 Received: from swifr9 for raf.bruyndonckx@unifr.ch by www.ccl.net (8.8.3/950822.1) id DAA26610; Fri, 31 Oct 1997 03:37:15 -0500 (EST) Received: from UFPER6.UNIFR.CH by swifr9 with SMTP (PP); Fri, 31 Oct 1997 09:36:23 +0100 Received: from unifr.ch by UFPER6.UNIFR.CH via Pony Express SMTP with TCP (v8.1.1-dmr001); Fri, 31 Oct 97 09:36:16 MET Sender: rbruyn@unifr.ch Message-ID: <34599A19.4BF216A5@unifr.ch> Date: Fri, 31 Oct 1997 00:43:17 -0800 From: Raf Bruyndonckx Organization: University of Fribourg X-Mailer: Mozilla 4.02 [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Ir and Rh containing clusters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, does anybody know of calculations or experimental data or calculations on small (organometallic) clusters containing at least 1 Ir-Ir, Ir-Rh or Rh-Rh bond? Information about calculations including relativistic effects on these elements are also welcome. And further more, is there any data available dealing with the softness of Ir and Rh? Please reply to : Raf.Bruyndonckx@unifr.ch . Thanks in advance Raf -- Raf Bruyndonckx Department of Inorganic Chemistry Univ Fribourg (Suisse) Perolles Tel: ++41 26 300 87 49 Fax: ++41 26 300 97 38 mailto:Raf.Bruyndonckx@unifr.ch http://sgich1.unifr.ch/ac/phd/rbruyn/ From peha@sgiclu.chemie.uni-konstanz.de Fri Oct 31 08:34:18 1997 Received: from sg7.chemie.uni-konstanz.de for peha@sgiclu.chemie.uni-konstanz.de by www.ccl.net (8.8.3/950822.1) id HAA27659; Fri, 31 Oct 1997 07:43:13 -0500 (EST) Received: from sgiclu.chemie.uni-konstanz.de (sg17.chemie.uni-konstanz.de [134.34.7.91]) by sg7.chemie.uni-konstanz.de (8.8.6/8.8.2) with SMTP id NAA17520 for <@sg7.chemie.uni-konstanz.de:chemistry@www.ccl.net>; Fri, 31 Oct 1997 13:43:42 +0100 (MET) Received: by sgiclu.chemie.uni-konstanz.de (950413.SGI.8.6.12/940406.SGI) for chemistry@www.ccl.net id NAA12630; Fri, 31 Oct 1997 13:44:29 +0100 From: peha@sg17.chemie.uni-konstanz.de (Peter Happersberger) Message-Id: <9710311344.ZM12628@sg17.chemie.uni-konstanz.de> Date: Fri, 31 Oct 1997 13:44:27 +0100 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: Win95 Macromolecular Rendering Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii >Nathan Baker wrote (23.10.97): >I was wondering if anyone knew of any programs >(besides RasMol) for rendering molecules with >large numbers (~10000) of atoms for Windows 95 >or NT. Thanks in advance! Look at: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ 'MolMol' is a nice tool for visualization of proteins. There are binaries for SGI, DEC, Linux ... and Win95! (In the Win95-Version TIF-export doesn't work, but you can make high quality pictures using MolMol in combination with PovRay. The Linux version export graphics in various formats TGA, TIF, ... Greetings Peter -- ------------------------------------------------------------------------ Peter Happersberger Ph.D. Student Faculty of Chemistry University of Konstanz Email: Peter.Happersberger@uni-konstanz.de URL: http://sg17.chemie.uni-konstanz.de/~peha/ Voicenet: ++49-(0)7531-88-3928 or Fax: ++49-(0)7531-88-3097 Papernet: AG Przybylski, P.O. Box M 732, 78457 Konstanz, Germany ------------------------------------------------------------------------- From kotelyan@plmsc.psu.edu Fri Oct 31 10:34:33 1997 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id JAA28117; Fri, 31 Oct 1997 09:50:22 -0500 (EST) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id JAA00880; Fri, 31 Oct 1997 09:50:11 -0500 (EST) Date: Fri, 31 Oct 1997 09:50:10 -0500 (EST) From: Mike Kotelyanskii To: David Giesen cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Web-based molecule builder In-Reply-To: <34563705.41C6@mozart.rl.kodak.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Risking to start another lengthy Linux discussion, and in line of the previous postings about Spartan. I am also interested in the 3D structure builder, as my boss is not really eager to shell out extra k$ for an MSI suit of programs, as we eould probably most intersted in the visualization tools, all the rest we develop ourself. Tried to download their WebBuilder but I found it only for the Mac and Windows. I somehow had the impression that they would have a lot of potential customers among people running Linux/Unix. So, I just wonder if there is any chance for the Linux port? ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan University Park, PA 16802, USA -------------------------------------------------------------------------------- On Tue, 28 Oct 1997, David Giesen wrote: > > Has anyone out there developed a 3-D, web-based molecule builder (not > just a viewer)? > > A search of the CCL archives (thanks Jan!) turned up > Molecule_Builder_1.0.java, but that is only 2-D. I've also searched the > web extensively with no luck. > > I'd be happy to hear from any one who has undertaken or has plans to > undertake this project. > > I am familiar with WebLab Plus from the MSI people. > > If there is interest, I'll summarize any results to the list - > > Thanks - > > Dave Giesen > giesen@kodak.com > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From g-recht@chem.nwu.edu Fri Oct 31 11:34:21 1997 Received: from mercury.chem.nwu.edu for g-recht@chem.nwu.edu by www.ccl.net (8.8.3/950822.1) id KAA28620; Fri, 31 Oct 1997 10:44:30 -0500 (EST) Received: from nano (nano.chem.nwu.edu [129.105.14.190]) by mercury.chem.nwu.edu (8.8.5/8.8.5) with SMTP id JAA28336 for ; Fri, 31 Oct 1997 09:43:42 -0600 (CST) Message-Id: <3.0.3.32.19971031094714.00915820@mercury.chem.nwu.edu> X-Sender: g-recht@mercury.chem.nwu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Fri, 31 Oct 1997 09:47:14 -0600 To: chemistry@www.ccl.net From: "G. Rechtsteiner" Subject: Vibrational Visualization of Gaussian Outputs Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello: I am currently looking for a program (free or inexpensive, sorry, I am still a graduate student), that will help me to visualize the vibrational modes of a molecule from a Gaussian 94 (or 92) output file. I am aware of Re_view for MOPAC files, but of none for Gaussian. Thank you, Greg -- Greg Rechtsteiner Northwestern University g-recht@chem.nwu.edu From gran@classic.chem.msu.su Fri Oct 31 11:38:29 1997 Received: from classic.chem.msu.su for gran@classic.chem.msu.su by www.ccl.net (8.8.3/950822.1) id LAA28792; Fri, 31 Oct 1997 11:13:45 -0500 (EST) From: Received: from classic ( [158.250.32.143] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Fri, 31 Oct 1997 19:12:39 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-Id: <199709311912.3921623.7@classic.chem.msu.su> Return-receipt-to: gran@classic.chem.msu.su Date: Fri, 31 Oct 97 19:11:29 +0300 To: CHEMISTRY@www.ccl.net Subject: The PC GAMESS v. 4.3 is available X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.27c (Unregistered) Dear PC GAMESS users, I'm glad to inform you that the new version (4.3) of the PC GAMESS is released and now available from the official GAMESS www and ftp sites. Compared to the previous public PC GAMESS version 4.1, the main differences are in the the MP2, MP2 gradient, and CI gradient codes. Please see the URLs http://classic.chem.msu.su/gran/gamess/index.html http://www.msg.ameslab.gov/GAMESS/dist.pc.html for all the information concerning the new PC GAMESS version. If you use the PC GAMESS regularly, you can help us by sending me (gran@classic.chem.msu.su) an e-mail with the subject "the PC GAMESS user". We would be glad to get the statictics concerning typical PC GAMESS usage and the hardware used. Any useful suggestions are highly appreciated too. We are interested also in the benchmark comparison with other quantum chemistry packages running both on the PC, and other platforms, etc... This all will help us to estimate the number of current PC GAMESS users, as well as to make decision about future plans concerning both the whole PC GAMESS project, and the main directions of our attention, etc... Yours sincerely, Alex. A. Granovsky, Moscow State University, Laboratory of Chemical Cybernetics ----------------------------------------------------------- gran@classic.chem.msu.su Fri Oct 31 19:11:00 1997 ----------------------------------------------------------- From rkrocha@dedalus.lcc.ufmg.br Fri Oct 31 11:42:29 1997 Received: from dedalus.lcc.ufmg.br for rkrocha@dedalus.lcc.ufmg.br by www.ccl.net (8.8.3/950822.1) id KAA28674; Fri, 31 Oct 1997 10:54:06 -0500 (EST) Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA41628; Fri, 31 Oct 1997 13:55:58 -0200 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Fri, 31 Oct 1997 13:55:57 -0200 (BDB) From: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: Binding Energy by MM. Summary. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, About three weeks ago I posted a message about binding energy by molecular mechanics. I would like to thank to all of you that have replied to my help question. Here is my original post: Dear CCLers, I would appreciate any help in getting some references (comments will be very appreciated) on how to calculate the interaction (binding) energy in systems like drug-receptor by using only molecular mechanics (molecular minimization and dynamics). What kind of relationship can be make about the energy calculated by molecular mechanics (energy of forcefield) and energy of Gibbs (delta G), and what background theoretical is necessary to do that. I will sumarize. Best regards. Ramon. Here is the replies. Is included the address of all that replied my question: From: "Volkhard Helms" you might be interested in the following study : HELMS, V., E. DEPREZ, E. GILL, C. BARRET, G. HUI BON HOA, R.C. WADE (1996) Biochemistry, Vol. 35, p.1485-1499. Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket . From:"Fernando Danilo Gonzalez Nilo" Con el InsightII 950 es posible calcular la energia libre de enlace, con Discover_3/EnergyAnalyse, con este modulo puedes seleccionar dos subset y calcular la energia de interaccion. Para mas detalles teorico busca bibliografia de Johan Aqvist, una de sus publicaciones respecto a este tema esta en: Protein Engineering vol 8, no 11, pp 1137-1144, 1995, es un buen ejemplo de esta tecnica. Suerte! From: "M. Rami Reddy" The following papers would be helpful for calculating binding energies using molecular mechanics calculations. J. Med. Chem. vol 39, pages 705-712 (1996) J. Med. Chem. vol 38, pages 305-317 (1995) J. Am. Chem. Soc. Vol 118, pages 3959-3969 (1996) Good Luck, From: "Dr. Mike Gilson" The statistical-thermodynamic basis for computation of binding affinities: A critical review. Michael K. Gilson and James A. Given and Bruce L. Bush and J. Andrew McCammon, Biophys. J. 72:1047-1069,1997. Best regards, From: "Dr. Chris L. Waller" Please see: R.D. Head, M.L. Smythe, T.I. Oprea, C.L. Waller, S.M. Greene, G.R. Marshall, "VALIDATE: A New Method For The Receptor-Based Prediction Of Binding Affinities Of Novel Ligands." J. Am. Chem. Soc. 1996, 118, 3959-3969 and references cited therein. Regards, From: "John Marelius" you may want to take a look at the linear interaction energy (LIE) method introduced by Aqvist et al., 1994 for calculating absolute free energies of binding. It is a semi-empirical method which is computationally less expensive than FEP. It is still similar to FEP in that it is based on thermodynamic cycles and includes thermal conformational sampling. However, the method involves only simulations of the two physical states (bound and free ligand) and requires no transformation processes. The method and some applications are described in: Aqvist, J., Medina, C. and Samuelsson, J.E., Protein Eng., 7 (1994) 385. Aqvist, J. and Mowbray, S.L., J. Biol. Chem., 270 (1995) 9978. Aqvist, J., J. Comp. Chem., 17 (1996) 1587. Hulten, J., Bonham, N.M., Nillroth, U., Hansson, T., Zuccarello, G., Bouzide, A., Aqvist, J., Classon, B., Danielsson, H., Karlen, A., Kvarnstrom, I., Samuelsson, B. and Hallberg, A., J. Med. Chem., 40 (1997) 885. Hansson, T. and Aqvist, J., Protein Eng., 8 (1995) 1137. Hansson, T., Marelius, J. and Aqvist, J., J. Comput.-Aided Mol. Design, 1998, in press. regards, ____________________________________________________________________________ Ramon Kleber da Rocha VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de Espectroscopia e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil ____________________________________________________________________________ From freunsch@pctc.chemie.uni-erlangen.de Fri Oct 31 13:34:20 1997 Received: from faui40.informatik.uni-erlangen.de for freunsch@pctc.chemie.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id MAA29370; Fri, 31 Oct 1997 12:38:06 -0500 (EST) Received: from pctc.chemie.uni-erlangen.de (pctc.chemie.uni-erlangen.de [131.188.120.2]) by faui40.informatik.uni-erlangen.de (8.8.7/8.1.4-FAU) with SMTP id SAA25136 for ; Fri, 31 Oct 1997 18:37:56 +0100 (MET) Received: from gaston.chemie.uni-erlangen.de by pctc.chemie.uni-erlangen.de (AIX 3.2/UCB 5.64/4.03) id AA17514; Fri, 31 Oct 1997 18:36:56 +0100 Received: from localhost by gaston.chemie.uni-erlangen.de (5.65v3.2/1.1.10.5/14Jul97-1224PM) id AA09388; Fri, 31 Oct 1997 18:37:55 +0100 Date: Fri, 31 Oct 1997 18:37:55 +0100 (MET) From: Peter Freunscht X-Sender: freunsch@gaston.chemie.uni-erlangen.de Cc: chemistry@www.ccl.net Subject: Re: CCL:G:Vibrational Visualization of Gaussian Outputs In-Reply-To: <3.0.3.32.19971031094714.00915820@mercury.chem.nwu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 31 Oct 1997, G. Rechtsteiner wrote: > Hello: > > I am currently looking for a program (free or inexpensive, sorry, I am > still a graduate student), that will help me to visualize the vibrational > modes of a molecule from a Gaussian 94 (or 92) output file. I am aware > of Re_view for MOPAC files, but of none for Gaussian. > > Thank you, > > Greg > Hello Greg: xvibs (in the CCL archives) will read G94 output and produce files readable by xmol (both vectors and animations). We are currently working on a more comfortable interface based on Tcl/Tk - let me know if you are interested in details. Ciao Peter ----------------------------- Dipl. Chem. Peter Freunscht Inst. f. Physikalische Chemie I der Universitaet Erlangen Egerlandstr.3 - 91058 Erlangen - Deutschland/Germany Tel:09131/85-7335 Fax:09131/85-8307 eMail:freunsch@pctc.chemie.uni-erlangen "...when men were men and wrote their own device drivers." Linus Torvalds From case@scripps.edu Fri Oct 31 13:47:50 1997 Received: from relay1.scripps.edu for case@scripps.edu by www.ccl.net (8.8.3/950822.1) id NAA29471; Fri, 31 Oct 1997 13:04:14 -0500 (EST) Received: from cauchy (cauchy.scripps.edu [137.131.252.32]) by relay1.scripps.edu (8.8.7/TSRI-1.8rn) with SMTP id KAA20737; Fri, 31 Oct 1997 10:03:59 -0800 (PST) Message-Id: <199710311803.KAA20737@relay1.scripps.edu> Received: by cauchy (1.38.193.4/16.2) id AA03457; Fri, 31 Oct 1997 10:03:48 -0800 Date: Fri, 31 Oct 1997 10:03:48 -0800 From: David Case To: amber@cgl.ucsf.edu, chemistry@www.ccl.net Subject: Announce: Amber 5.0 is available It gives us great pleasure to announce the release of AMBER 5.0. This code is a joint effort of the Kollman group at UCSF, the Case group at The Scripps Research Institute, David Pearlman at Vertex, the Merz group at Pennsylvania State University, Tom Darden at NIEHS, and David Ferguson at the University of Minnesota. As in the past, this version of AMBER will be jointly supported by Oxford Molecular (OM) as well as by the various authors. Oxford Molecular will offer commercial-level support and update services and the option of bundling AMBER with their other complementary software. AMBER 5.0 (1997) represents a significant change from the most recent previous version, 4.1, which was released in 1995. Briefly, the major differences include: (1) an updated and parallelized implementation of the particle-mesh Ewald routine, and its incorporation into the free energy module; (2) "locally-enhanced sampling" (LES) code that allows parts of the system to be present as multiple copies; (3) an alternate version of Sander (ROAR) that includes the ability to define part of the system as a quantum-mechanical section (QM/MM), and includes alternate integrators; (4) PROFEC (pictorial representation of free energy changes), a set of tools for carrying out and displaying extrapolative free energy changes; (5) new and parallelized methods for NMR refinement; incorporation of penalites based on pseudocontact shifts. (6) updates to the functionality and stability of LEaP. If you are interested in obtaining a copy of AMBER 5.0, please contact Oxford Molecular at one of the following sites: USA: Toll Free: 1-800-876-9994 phone (408) 879-6300 fax (408) 879-6302 e-mail: products@oxmol.com UK: phone +44 1865 784600 fax +44 1865 784601 e-mail: products@oxmol.co.uk Thank you for your interest and continued support. From bruno@antas.agraria.uniss.it Fri Oct 31 14:34:20 1997 Received: from ICINECA.CINECA.IT for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id OAA29849; Fri, 31 Oct 1997 14:16:26 -0500 (EST) Received: from cinymp.cineca.it by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Fri, 31 Oct 97 20:16:32 ITA Received: from antas.agraria.uniss.it by cinymp.cineca.it with SMTP (5.61/CRI-80.1) id AA62147; Fri, 31 Oct 97 20:16:39 +0100 Date: Fri, 31 Oct 1997 20:14:49 +0100 (NFT) From: "Dr. Bruno Manunza" To: "G. Rechtsteiner" Cc: chemistry@www.ccl.net Subject: Re: CCL:G:Vibrational Visualization of Gaussian Outputs In-Reply-To: <3.0.3.32.19971031094714.00915820@mercury.chem.nwu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 31 Oct 1997, G. Rechtsteiner wrote: > Hello: > > I am currently looking for a program (free or inexpensive, sorry, I am > still a graduate student), that will help me to visualize the vibrational > modes of a molecule from a Gaussian 94 (or 92) output file. I am aware > of Re_view for MOPAC files, but of none for Gaussian. > > Thank you, > > Greg Dear Greg, molden would probably do what you are looking for, as well as TransFreq. You may also check for RamVib. You'll find links to them and other package on our web site at: http://antas.agraria.uniss.it/software.html Hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From daizadeh@indigo.ucdavis.edu Fri Oct 31 17:34:24 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id QAA02007; Fri, 31 Oct 1997 16:40:30 -0500 (EST) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id NAA10221; Fri, 31 Oct 1997 13:42:24 -0800 From: "Iraj Daizadeh" Message-Id: <9710311342.ZM10219@indigo.ucdavis.edu> Date: Fri, 31 Oct 1997 13:42:03 -0800 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Doug Fox , chemistry@www.ccl.net Subject: Solution. Print out of MOs from two different sets: Cc: fink@indigo.ucdavis.edu, Ahmed Bouferguene , John McKelvey , Stephan Irle Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. The overall project was to simply construct an overlap matrix of MO's from different sets. I have summarized replies to the previous message I submitted (utter nonsense!). The problem was to save the MO's from an initial run of Gaussian. Then during a second run read these in and project onto them atomic overlaps and the MOs of the current calculation. Lets take a closer look at the problem: Example: trivial model system H-H+ run 1 H -- H+ -- > coefficients of expansion of MO's print out from G94 run2 H+--H -- > read in MO's from checkpoint file and construct: (Smo)ij = sum_{mu,nu} Cmu,i * (Sao)mu,nu * Cnu,j Now to do this I did the following: First I printed out the coefficients of Mo's from the first run by introducing a link into G94 called l612.F. The line is shown below: Call FileIO (2,-IRwCa,NBSq,V,0) do 200 i=1,NBsq 200 write (IUnitA,2010) V(i) 2010 format (E40.30) Also I print out Overlap matrix over atomic orbitals: NTT = Nbasis*(NBasis+1)/2 Call FileIO(2,-IRwSao,NTT,V,0) do 211 i=1,NTT 211 write (IOvlp,2010) V(i) Now I rerun G94 and print out the IRwCa again for the new molecule. (BE WARNED: Fortran is the transpose of C/C++; that is: F(i,j) = C[j][i];) In my C code I construct the overlap matrix myself. This is a very cumbersome method for doing this but it works!!! Now for the C_{pho,k}'s from the same calculation, of course, the Smo Matrix should be unitary. But for different combinations of MO set this is not the case *yet some symmetry should be there ** it depends on your system of course ** *. This is my no means the best possible methodology I would appreciate any other solutions. Any comments, questions, or suggestions would be appreciated. Iraj. Hi Iraj, Use the option IOP(3/33=1). *********************************************************************** * Lorsque la chance s'envole, * * Lorsque la raison decole, * * Il nous reste la picole. * *********************************************************************** Ahmed Bouferguene --- Hi Iraj, Yes the matrix you get is the matrix S_{\mu , \nu} which is the overlap between atomic orbitals. Now, the overlap between molecular orbitals, if my memory is still good should be zero since this is one of the constraint in the derivation of the Hartree-Fock equation. Ahmed Bouferguene -- Add IOP(3/33=1) to get all of the one electron operator matrices in the log file. Doug Fox -- Hi Iraj, as far as I know there is no such option. However, the overlap between different sets of orbitals during an SCF calculation is evaluated if you set iop(5/14=1) and scf=dm which will activate the conventional (and very slow) direct minimization technique proposed by Seeger and Pople (J. Chem. Phys., 65 (1976), 265-271) in L503. You may want to cut out the responsible part of the code (mainly subroutine BESSRT) and wrap your own code (reading of MO input, overlap matrix etc.) around it. I would very much appreciate if you could post a summary if you get more replies on this topic. Stephan Irle -- G9x does exactly this automatically (default,) I believe. John If the intention is to use this as an initial guess it is done by default. Doug Fox -- Iraj, If the point is to get this into the checkpoint file you can use, %chk=mychk # ... Guess=(Read,Save,Only) which will pick up the previous MO's, project onto the new basis set, save them to the checkpoint file and then only do properties before quiting. Then you could pick them up from the checkpoint file for visualizing etc. -- -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu From daizadeh@indigo.ucdavis.edu Fri Oct 31 17:43:39 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id RAA06341; Fri, 31 Oct 1997 17:16:35 -0500 (EST) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA13324; Fri, 31 Oct 1997 14:17:53 -0800 From: "Iraj Daizadeh" Message-Id: <9710311417.ZM13322@indigo.ucdavis.edu> Date: Fri, 31 Oct 1997 14:17:40 -0800 In-Reply-To: Stephan Irle "Re: Solution. Print out of MOs from two different sets:" (Oct 31, 5:02pm) References: <9710311342.ZM10219@indigo.ucdavis.edu> <345A557E.AAEF879C@emory.edu> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Doug Fox , daizadeh@indigo.ucdavis.edu, Stephan Irle Subject: Apolgy. Print out of MOs from two different sets: Cc: Ahmed Bouferguene , John McKelvey , chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii The "utter nonsense" part of this letter was not meant to be offensive in any way to you!!! It was meant to be offensive to ME since the original question was misleading, erroneous and down-right poorly thought out and stated! Thank you again to those people who have given me suggestions and to those that are reading these email messages. Iraj. > Iraj Daizadeh wrote: > > > Hello. > > > > The overall project was to simply construct an overlap matrix of MO's > > from > > different sets. I have summarized replies to the previous message I > > submitted > > (utter nonsense!). > > > > The problem was to save the MO's from an initial run of Gaussian. > > Then during > > a second run read these in and project onto them atomic overlaps and > > the MOs of > > the current calculation. Lets take a closer look at the problem: > > > > Example: > > > > trivial model system H-H+ > > run 1 > > H -- H+ -- > coefficients of expansion of MO's print out from G94 > > > > run2 > > H+--H -- > read in MO's from checkpoint file and construct: > > > > (Smo)ij = sum_{mu,nu} Cmu,i * (Sao)mu,nu * Cnu,j > > > > Now to do this I did the following: > > > > First I printed out the coefficients of Mo's from the > > first run > > by introducing a link into G94 called l612.F. The line is shown > > below: > > > > Call FileIO (2,-IRwCa,NBSq,V,0) > > do 200 i=1,NBsq > > 200 write (IUnitA,2010) V(i) > > > > 2010 format (E40.30) > > > > Also I print out Overlap matrix over atomic orbitals: > > > > NTT = Nbasis*(NBasis+1)/2 > > Call FileIO(2,-IRwSao,NTT,V,0) > > do 211 i=1,NTT > > 211 write (IOvlp,2010) V(i) > > > > Now I rerun G94 and print out the IRwCa again for the new molecule. > > > > (BE WARNED: Fortran is the transpose of C/C++; that is: F(i,j) = > > C[j][i];) > > > > In my C code I construct the overlap matrix myself. This is a very > > cumbersome > > method for doing this but it works!!! Now for the C_{pho,k}'s from > > the same > > calculation, of course, the Smo Matrix should be unitary. But for > > different > > combinations of MO set this is not the case *yet some symmetry should > > be there > > ** it depends on your system of course ** *. > > > > This is my no means the best possible methodology I would appreciate > > any other > > solutions. Any comments, questions, or suggestions would be > > appreciated. > > > > Iraj. > > > > Hi Iraj, > > > > Use the option IOP(3/33=1). > > > > *************************** > > ******************************************* > > * Lorsque la chance s'envole, > > * > > * Lorsque la raison decole, > > * > > * Il nous reste la picole. > > * > > * > > ********************************************************************* > > > > Ahmed > > Bouferguene > > > > --- > > Hi Iraj, > > > > Yes the matrix you get is the matrix S_{\mu , \nu} which is the > > overlap > > between atomic orbitals. Now, the overlap between molecular orbitals, > > if > > my memory is still good should be zero since this is one of the > > constraint in the derivation of the Hartree-Fock equation. > > > > Ahmed > > Bouferguene > > > > -- > > > > Add IOP(3/33=1) to get all of the one electron operator matrices in > > > > the log file. > > > > Doug Fox > > -- > > Hi Iraj, > > > > as far as I know there is no such option. However, the overlap > > between different sets of orbitals during an SCF calculation is > > evaluated if you set iop(5/14=1) and scf=dm which will activate > > the conventional (and very slow) direct minimization technique > > proposed by Seeger and Pople (J. Chem. Phys., 65 (1976), 265-271) > > in L503. > > > > You may want to cut out the responsible part of the code (mainly > > subroutine BESSRT) and wrap your own code (reading of MO input, > > overlap matrix etc.) around it. > > > > I would very much appreciate if you could post a summary if you > > get more replies on this topic. > > > > Stephan Irle > > -- > > > > G9x does exactly this automatically (default,) I believe. > > > > John > > > > If the intention is to use this as an initial guess it is done by > > default. > > > > Doug Fox > > -- > > > > Iraj, > > > > If the point is to get this into the checkpoint file you can use, > > > > %chk=mychk > > # ... Guess=(Read,Save,Only) > > > > which will pick up the previous MO's, project onto the new basis set, > > save them to the checkpoint file and then only do properties before > > quiting. Then you could pick them up from the checkpoint file for > > visualizing > > etc. > > -- > > > > -- > > Iraj Daizadeh > > Department of Chemistry > > University of California > > One Shields Ave. > > Davis, CA 95616-5295 > > Phone: 916.754.8695 > > Fax: 916.752.8995 > > email: daizadeh@indigo.ucdavis.edu > > >-- End of excerpt from Stephan Irle -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu