From krys.radacki@ac.rwth-aachen.de Fri May 8 03:29:36 1998 Received: from mail.rwth-aachen.de for krys.radacki@ac.rwth-aachen.de by www.ccl.net (8.8.3/950822.1) id DAA25371; Fri, 8 May 1998 03:25:12 -0400 (EDT) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #23726) with ESMTP id <01IWSARW5V8A0003RX@mail.rwth-aachen.de> for chemistry@www.ccl.net; Fri, 8 May 1998 09:21:28 +0200 Date: Fri, 08 May 1998 07:20:26 +0000 From: Krzysztof Radacki Subject: GaussView error Sender: root@mail.rwth-aachen.de To: Comutating Chemistry List Message-id: <3552B239.D2F25387@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.1.99 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hi CCL-ers In last par days GaussViev makes my hairs grey. Every time when Gaussian job is broken with error-link due to reaching of maximal optimalization steps GaussView by try to read molecule from log-data and after "warning : no archive entry produce error" produce new error dialog: "Activietes: " -Reading Gaussian Out file " -Parsing Gaussian LOG file " -Reading Gaussian Charge Data " "Error Message: " Invalid Charge Data (Line 11460) where line 11460 of logfile is: "Sum of Mulliken charges= 0.00000 In correctly terminated file one can find: "Sum of Mulliken charges= .00000 but of course this one '0' makes no difference in error-dialog. Any sugestions how can I quick view my last geometry (quick means that I don't want to copy last cartesian from log-file and formate it to gaussian input). -- Krzys Radacki krys.radacki@ac.rwth-aachen.de From darrena@chem.leeds.ac.uk Fri May 8 07:29:38 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA13192; Fri, 8 May 1998 06:50:41 -0400 (EDT) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id LAA17942 for ; Fri, 8 May 1998 11:49:24 +0100 (BST) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: Date: Fri, 8 May 1998 11:45:10 +0100 To: chemistry@www.ccl.net From: Darren Andrews Subject: 3D orbitals/electron densities from GAMESS I am trying to find a way of generating high-quality electron densities coloured with electrostatic potentials from GAMESS, or possibly gaussian, output. It would be good to be able to do orbitals as well. POV-ray and POV-chem give good quality ray traced images but the input needs to be of the right form. MacMolplt does something similar but is INCREDIBLY slow and gives very chunky results, and I can't get it to colour the electron density with the EP. If possible I would like to get SPARTAN quality output. Does anyone know of a way I can get these images from a free-of-charge package? Cheers, Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From brupalf@umich.edu Fri May 8 11:29:41 1998 Received: from donkeykong.rs.itd.umich.edu for brupalf@umich.edu by www.ccl.net (8.8.3/950822.1) id KAA04815; Fri, 8 May 1998 10:51:15 -0400 (EDT) Received: from choplifter.rs.itd.umich.edu (smtp@choplifter.rs.itd.umich.edu [141.211.63.90]) by donkeykong.rs.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id KAA28057 for ; Fri, 8 May 1998 10:51:15 -0400 (EDT) Received: from localhost (brupalf@localhost) by choplifter.rs.itd.umich.edu (8.8.8/5.1-client) with SMTP id KAA07260 for ; Fri, 8 May 1998 10:51:14 -0400 (EDT) Precedence: first-class Date: Fri, 8 May 1998 10:51:14 -0400 (EDT) From: Bruce Allan Palfey X-Sender: brupalf@choplifter.rs.itd.umich.edu Reply-To: Bruce Allan Palfey To: chemistry@www.ccl.net Subject: low barrier hydrogen bonds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Over the past few years, low barrier hydrogen bonds (LBHB for short) have received a fair amount of attention in enzymology. They are characterized by being short, having low isotopic fractionation factors, and very large proton NMR chemical shifts. Some say that they are extremely favorable energetically and hence an important "tool" used by enzymes in catalysis, while others disagree. I was wondering if anyone could tell me whether the common molecular mechanics force fields could be expected to properly model LBHB. Can one expect AMBER, CHARMm, etc., to accurately predict the LBHB lengths and frequencies? Or are these bonds unusual enough that new terms need to be included? Bruce Palfey Department of Biological Chemistry University of Michigan Ann Arbor, MI 48109-0606 From nakiya@engin.umich.edu Fri May 8 15:29:43 1998 Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by www.ccl.net (8.8.3/950822.1) id PAA27390; Fri, 8 May 1998 15:09:49 -0400 (EDT) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id PAA28354 for ; Fri, 8 May 1998 15:09:49 -0400 (EDT) Date: Fri, 8 May 1998 15:09:48 -0400 (EDT) From: Naoko Akiya To: chemistry@www.ccl.net Subject: CCL: intermolecular potential In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I have a very basic question -- please bear with me. I am still trying to learn the basics, and unfortunately, there is no one around me who can answer this question. I plan to do a simulation of a solution, with one solute molecule surrounded by solvent molecules. Before I do the simulation, I need to obtain parameters for the intermolecular and intramolecular potential models. I plan to use the intramolecular potential models available in the literature for both the solute and the solvent. For the intermolecular potential, I will just use the Lennard-Jones and electrostatic interaction terms, but I still need to obtain the parameters. I would like to obtain those parameters by fitting the ab initio interaction energies to this intermolecular potential. This is where I have a question (finally). When I calculate the interaction energies by ab initio methods, should I keep the geometries of the solute and the solvent molecules fixed to the equilibrium geometries as specified by the intramolecular potential models that I chose? I am inclined to do so, but I wanted to get the opinions of the experts... Thank you very much for your patience. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (734) 764-7121 Ann Arbor, MI 48109-2136 fax (734) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From gbr@NPD.UFPE.BR Fri May 8 15:37:46 1998 Received: from NPD1.NPD.UFPE.BR for gbr@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id PAA28440; Fri, 8 May 1998 15:22:20 -0400 (EDT) Received: from npd.ufpe.br (Hartree.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IWSPJNHYU80016LT@NPD.UFPE.BR> for CHEMISTRY@www.ccl.net; Fri, 8 May 1998 16:24:42 GMT-3 Date: Fri, 08 May 1998 16:18:01 -0300 From: Gerd Bruno Rocha Subject: Summary: Atomic STO Program To: CHEMISTRY@www.ccl.net Message-id: <35535A69.52278ECC@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.04 [en] (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Dear Netters, Some weeks ago, I placed in CCl the following question : >I would appretiate if you could inform me of a computer program >which is able to compute SCF atomic wavefunctions using >Slater-type-orbitals and/or hydrogen-type-orbitals. >Info on how to download or get it would be of importance. Thanks for all. Answers: 1) ADF is a DFT program that uses Slater Type Orbitals as basis functions. Visit out website for more info: http://www.scm.com Best regards, --------------------------------------------------------------------- Bert te Velde SCIENTIFIC COMPUTING & MODELLING phone: +31-20-4447625 Chemistry Department, Vrije Universiteit fax: +31-20-4447643 De Boelelaan 1083 email: tevelde@scm.com 1081 HV Amsterdam; The Netherlands --------------------------------------------------------------------- 2) Dear Gerd, of course there are a lot of commercial programs like Gaussian an Spartan, availible for UNIX as well as for PC I think you will be interested in some free software. Then try GAMESS (for unix and pc-systems) Unix: http://www.msg.gameslab.gov/GAMESS/gamess.html PC: http://classic.chem.msu.su/gran/gamess/index.html Greetings Wolfgang *********************************************************************** Dr. Wolfgang Utz Institut fuer Pharmazie u. LM-Chemie Universitaet Erlangen-Nuernberg Schuhstr. 19 91052 Erlangen Tel. 09131/854100 Fax 09131/852585 E-mail:utz@pharmazie.uni-erlangen.de *********************************************************************** 3) Gerd: If you don't find anything else, I have an old AIM-type program (mainly ANSI66 FORTRAN) that contains a complete atomic GC-UHF calculation as an integral part. It's STO-based, but the basis sets are not built-in (I just keep a copy of the Clementi/Roetti tables nearby). - 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 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -- *********************************************************************** Universidade Federal de Pernambuco Centro de Ciencias Exatas e da Natureza Departamento de Quimica Fundamental http://www.dqf.ufpe.br Recife - PE - Brazil Gerd Bruno Rocha E-Mail : gbr@npd.ufpe.br : gerd@simas.dqf.ufpe.br DSc Student in Computational Chemistry *********************************************************************** From s197216@ccs.sogang.ac.kr Fri May 8 22:29:45 1998 Received: from ccs.sogang.ac.kr for s197216@ccs.sogang.ac.kr by www.ccl.net (8.8.3/950822.1) id VAA00605; Fri, 8 May 1998 21:32:55 -0400 (EDT) Received: from localhost by ccs.sogang.ac.kr (8.8.8/Sogang) id KAA08838; Sat, 9 May 1998 10:26:06 +0900 (KST) Date: Sat, 9 May 1998 10:26:05 +0900 (KST) From: Kang Jin Koo To: chemistry@www.ccl.net Subject: aqueous solvation of Fe(NO3)3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I'm a graduate student and studying Fe(NO3)3 solvation in supercritical water. But in this case, it is not clear that Fe(NO3)3 ionizes or makes clusters. And I need adequate potential functions for molecular dynamics. So, any paper, book, or comment concerned will be very helpful for me. Your replies will be summerized in ccs. thanks in advance, Jinkoo Kang -------------------------------------------------------------------------- Sogang University, Dept. of Chemical Engineering, Crystallization Laboratory, Seoul, Korea Telephone : 82-2-705-8481 E-mail : s197216@ccs.sogang.ac.kr --------------------------------------------------------------------------