From chemistry-request@server.ccl.net Mon Oct 25 06:41:17 1999 Received: from gwdu12.gwdg.de (gwdu42.gwdg.de [134.76.10.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA31013 for ; Mon, 25 Oct 1999 06:41:16 -0400 Received: from taurus.uni-oc.gwdg.de ([134.76.66.164] helo=gwdg.de) by gwdu12.gwdg.de with esmtp (Exim 2.12 #1) id 11fhQg-0004PA-00 for chemistry@ccl.net; Mon, 25 Oct 1999 12:32:42 +0200 Sender: crinders@gwdg.de Message-ID: <381431AA.F9005E28@gwdg.de> Date: Mon, 25 Oct 1999 12:32:10 +0200 From: Christopher Rinderspacher X-Mailer: Mozilla 4.6 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Normalization in G98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Sirs, I have following problems with Gaussian98. It seems (to me) G98 does not normalise its functions correctly. $RunGauss %chk=H2.chk # B3LYP/Gen Opt Pop=Full #P GFPrint GFInput H2 opt 0 1 H H 1 hh hh 1.1 H 0 S 1 1.0 1.0 **** This renders 1 1 H 1S 0.568448 1.0510017 2 2 H 1S 0.568448 -1.0510017 and the coordinates 0,0,+-0.2904860295 in the output file. My own calculations (using e^(-r^2) at the respective coordinates) show that the coefficients should be 0.5206 in the first orbital and about +-1.7 for the second Orbital. I purposefully chose easy functions so I could solve the integrals myself with pencil and paper. How can this be? What am I missing? Christopher -- Christopher Rinderspacher Institut fuer Organische Chemie Georg-August-Universitaet Goettingen Tammannstr. 2 37077 Goettingen E-Mail: crinder1@gwdg.de PGP-Key: http://www.gwdg.de/~crinder1/pgp.pub From chemistry-request@server.ccl.net Mon Oct 25 07:04:47 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA32025 for ; Mon, 25 Oct 1999 07:04:46 -0400 Received: from p300 (ligquim.ffclrp.usp.br [143.107.194.89]) by swan2.uspnet.usp.br (8.9.3/8.9.3) with SMTP id IAA09987 for ; Mon, 25 Oct 1999 08:50:00 -0200 (EDT) Message-ID: <014601bf1ed7$6b17ff80$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: G98: DFT and population analysis Date: Mon, 25 Oct 1999 08:55:10 -0200 Organization: Laboratorio de Modelagem Molecular - FFCLRP-USP 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear CCLers, I am trying to calculate population analysis using DFT density in G98. When I use density=current the program indicates that SCF density was used for population analysis. Is this the KS-DFT density? Or how can I obtain true DFT density. Thanks Sergio From chemistry-request@server.ccl.net Mon Oct 25 08:34:10 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.222.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA32379 for ; Mon, 25 Oct 1999 08:34:10 -0400 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 20541 invoked from network); 25 Oct 1999 12:25:35 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 25 Oct 1999 12:25:35 -0000 Received: (qmail 6538 invoked by uid 10283); 25 Oct 1999 12:25:11 -0000 Message-ID: <19991025122511.6537.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:Normalization in G98 To: crinder1@gwdg.de (Christopher Rinderspacher) Date: Mon, 25 Oct 1999 14:25:11 +0200 (MSZ) Cc: chemistry@ccl.net In-Reply-To: <381431AA.F9005E28@gwdg.de> from "Christopher Rinderspacher" at Oct 25, 99 12:32:10 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > > Dear Sirs, > > > My own calculations (using e^(-r^2) at the respective coordinates) show > that the coefficients should be 0.5206 in the first orbital and about > +-1.7 for the second Orbital. I purposefully chose easy functions so I > could solve the integrals myself with pencil and paper. How can this be? > What am I missing? > > Christopher > I can see no error. The overlap integral is exp(-0.5(r1-r2)**2), 0.5473. (Do not forget to convert the coordinates to atomic units!). Hence, the coefficient, 1/sqrt(2+2*S), is 0.5685. I suggest you sharpen your pencil once more. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Mon Oct 25 09:35:50 1999 Received: from unix2.it-datacntr.louisville.edu (unix2.it-datacntr.louisville.edu [136.165.4.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA32686 for ; Mon, 25 Oct 1999 09:35:49 -0400 Received: from athena.louisville.edu (athena.louisville.edu [136.165.4.37]) by unix2.it-datacntr.louisville.edu (8.8.8/8.8.8) with ESMTP id JAA35246; Mon, 25 Oct 1999 09:26:56 -0400 Received: from localhost (n0srin01@localhost) by athena.louisville.edu (8.8.8/8.8.8) with SMTP id JAA61586; Mon, 25 Oct 1999 09:26:46 -0400 Date: Mon, 25 Oct 1999 09:26:45 -0400 (EDT) From: Nithya Srinivasan To: chemistry@server.ccl.net cc: Nithya Subject: Charges in G94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to know how to assign charges and coordinations to individual atoms in Gaussian 94. Thanks in advance. Regards, Nithya -- NITHYA SRINIVASAN Dept. of Chemical Engineering Ph : (502) 852-1557/6347 University of Louisville Fax: (502) 852-1577/6355 Louisville, KY 40292 ns@louisville.edu http://mecca.spd.louisville.edu/~nithya From chemistry-request@server.ccl.net Mon Oct 25 11:46:51 1999 Received: from mail1-gui.server.ntli.net (mail1-gui.server.ntli.net [194.168.222.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA00519 for ; Mon, 25 Oct 1999 11:46:49 -0400 Received: from strath.ac.uk ([212.250.143.131]) by mail1-gui.server.ntli.net (Post.Office MTA v3.1 release PO203a ID# 0-33929U70000L2S50) with ESMTP id AAA25253; Mon, 25 Oct 1999 16:23:27 +0100 Sender: cbas25@ccl.net Message-ID: <38148766.383006FA@strath.ac.uk> Date: Mon, 25 Oct 1999 17:37:59 +0100 From: "Dr. Peter Bladon" Organization: Interprobe Chemical Services X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net CC: ACSMEDI@LISTS.WAYNE.EDU, cbas25@strath.ac.uk, wendy@WARR.CO, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU Subject: INTERCHEM Software and Databases Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit This is to announce the availability of the latest version of INTERCHEM Molecular Modelling Software. This includes databases containing 450,000 small molecule structures. For details see the URL: http://interchem.chem.strath.ac.uk/inter/interprobe.html I have aimed this message at several bulletins, so please accept my apologies if you receive several copies! Peter Bladon From chemistry-request@server.ccl.net Mon Oct 25 02:49:42 1999 Received: from stark.udg.es (stark.udg.es [130.206.128.61]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA30105 for ; Mon, 25 Oct 1999 02:49:41 -0400 Received: from stark.udg.es (phoenix.udg.es [130.206.128.117]) by stark.udg.es (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id IAA17313 for ; Mon, 25 Oct 1999 08:43:20 +0200 Message-ID: <3813FD2F.6191944F@stark.udg.es> Date: Mon, 25 Oct 1999 08:48:15 +0200 From: Xavier =?iso-8859-1?Q?Giron=E9s?= X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: SMILES software References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hello all, I wonder if there exists some software, freeware if possible, able to convert a SMILES string into a conventional molecular file format, e.g. .mol, .xyz, .zmt ... Any references will be much appreciated Xavier Gironés Torrent Institute of Computational Chemistry Girona, Spain From chemistry-request@server.ccl.net Mon Oct 25 18:59:55 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA02734 for ; Mon, 25 Oct 1999 18:59:55 -0400 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id RAA01293 for ; Mon, 25 Oct 1999 17:51:14 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id RAA22290 for ; Mon, 25 Oct 1999 17:51:13 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Mon, 25 Oct 1999 17:51:13 -0500 (CDT) From: Jim Phillips To: chemistry@server.ccl.net Subject: ANNOUNCE: NAMD 2.1b3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.1b3 Release Announcement | | | +--------------------------------------------------------------------+ October 25, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.1b3 is more stable than NAMD 2.0 and adds several new features: - Tcl scripting language interface and config file parsing. - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software!