From chemistry-request@ccl.net Tue Feb 10 04:16:36 2004 Received: from smtpsrv2.hrz.uni-oldenburg.de (smtpsrv2.hrz.uni-oldenburg.de [134.106.87.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1A9GWU6015397 for ; Tue, 10 Feb 2004 04:16:33 -0500 Received: from smtpsrv2.hrz.uni-oldenburg.de (localhost.localdomain [127.0.0.1]) by smtpsrv2.hrz.uni-oldenburg.de (8.12.8/8.12.8) with ESMTP id i1A9Gfia023496 for ; Tue, 10 Feb 2004 10:16:41 +0100 Received: from loadb02.uni-oldenburg.de ([134.106.87.17]) by smtpsrv2.hrz.uni-oldenburg.de (MailMonitor for SMTP v1.2.2 ) ; Tue, 10 Feb 2004 10:16:41 +0100 (CET) Received: from rainer.uni-oldenburg.de (rainer.chemie.uni-oldenburg.de [134.106.213.32]) (authenticated bits=0) by mailgate.uni-oldenburg.de (8.12.8/8.12.8) with ESMTP id i1A9GeNX018826 for ; Tue, 10 Feb 2004 10:16:41 +0100 Message-Id: <6.0.0.22.2.20040210101127.01f00d10=at=mailsrv1.uni-oldenburg.de> X-Sender: rkoch=at=mailsrv1.uni-oldenburg.de X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Tue, 10 Feb 2004 10:18:00 +0100 To: CHEMISTRY=at=ccl.net From: Rainer Koch Subject: CCL:G03 and opteron Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, with regard to the ongoing opteron discussion: does anyone know if Gaussian plans to optimize G03 for the 64-bit cpus in the (near) future? Any information would be helpful. TIA, Rainer Koch. From chemistry-request@ccl.net Tue Feb 10 15:10:14 2004 Received: from send.it.helsinki.fi (send.it.helsinki.fi [128.214.205.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1AKACU6004456 for ; Tue, 10 Feb 2004 15:10:13 -0500 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by send.it.helsinki.fi (8.12.11/8.12.11) with ESMTP id i1AKAK57005806 for ; Tue, 10 Feb 2004 22:10:24 +0200 (EET) Received: from soul.helsinki.fi (localhost [127.0.0.1]) by soul.helsinki.fi (8.12.10/8.12.10) with ESMTP id i1AKAKjG251801 for ; Tue, 10 Feb 2004 22:10:20 +0200 (EET) Received: from localhost (sundius@localhost) by soul.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id i1AKAGkL251863 for ; Tue, 10 Feb 2004 22:10:20 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: sundius owned process doing -bs Date: Tue, 10 Feb 2004 22:10:15 +0200 (EET) From: Tom Sundius X-X-Sender: sundius!at!soul.helsinki.fi To: CHEMISTRY!at!ccl.net Subject: Re: CCL:Why the Z-matrix is called thus? In-Reply-To: <20040209232138.GB3299!at!monster.ntu.edu.au> Message-ID: References: <40279E3F.1030302!at!uvigo.es> <20040209232138.GB3299!at!monster.ntu.edu.au> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Concerning the history of the Z-matrix: It seems that Z-matrix originated with J.A. Pople and his graduate student M. S. Gordon, who wrote a Fortran program that calculated the cartesian coordinates of all the atoms in a molecule from standard values of bond lengths, angles and dihedral angles (MBLD: QCPE program number 135, see M.S. Gordon and J.A. Pople, QCPE 11, 135 (1969)). A Z-matrix has also been used in force field calculations: F = Zf, where f denotes a vector containing all the non-zero force constants, and Z is a matrix indicating their positions in the F-matrix (see, eg. J. Overend and J.R. Scherer, J. Chem. Phys. 32 (1960) 1289). However, I cannot tell if the Z-matrix in the Gaussian program got its name from this matrix... Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophesy in part +++ From chemistry-request@ccl.net Tue Feb 10 09:36:43 2004 Received: from server.theo.chemie.tu-muenchen.de (server.theo.chemie.tu-muenchen.de [129.187.122.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1AEagU6024478 for ; Tue, 10 Feb 2004 09:36:42 -0500 Received: by crease.theo.chemie.tu-muenchen.de (Postfix, from userid 547) id C444ABAC2; Tue, 10 Feb 2004 15:36:53 +0100 (CET) Date: Tue, 10 Feb 2004 15:36:53 +0100 (CET) From: Mehdi Bounouar To: CHEMISTRY.-at-.ccl.net Subject: G03 test jobs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, I'm trying to run the Gaussian test jobs, but apparently some jobs (see list) just stops without any error messages. Any clue? has somebody experienced that before ? Thanks test017.log test024.log test028.log test036.log test042.log test050.log test052.log test081.log test082.log test090.log test098.log test117.log test118.log test119.log test124.log test130.log test131.log test133.log test138.log test211.log test212.log test213.log test219.log test224.log test236.log test242.log test243.log test244.log test245.log test246.log test281.log test283.log test317.log test323.log test324.log test334.log test344.log test364.log test429.log test440.log From chemistry-request@ccl.net Mon Feb 9 20:55:28 2004 Received: from vidar.scs.uiuc.edu (vidar.scs.uiuc.edu [130.126.231.227]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1A1tRU6002900 for ; Mon, 9 Feb 2004 20:55:27 -0500 Received: from uiuc.edu (bragi.scs.uiuc.edu [130.126.226.81]) by vidar.scs.uiuc.edu (SGI-8.12.5/8.12.5) with ESMTP id i1A1tcaJ183835 for ; Mon, 9 Feb 2004 19:55:38 -0600 (CST) Sender: pogorelo[at]vidar.scs.uiuc.edu Message-ID: <40284074.7121C614[at]uiuc.edu> Date: Mon, 09 Feb 2004 20:22:44 -0600 From: "Taras V. Pogorelov" Organization: Chemical Physics, University of Illinois at Urbana-Champaign X-Mailer: Mozilla 4.77C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: Russian, ru, en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: CCL:J.Comp.Chem. Style File Needed Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, We are in need of the LaTeX style file for the Journal of Computationl Chemistry. Your help will be greatly appreciated. Best, Taras _______________________________________________________________ Taras V. Pogorelov, Chemical Physics, University of Illinois, _______________________________________________________________ From chemistry-request@ccl.net Tue Feb 10 14:29:39 2004 Received: from mprelay.uc.edu (mprelay.uc.edu [129.137.3.48]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1AJTcU6003225 for ; Tue, 10 Feb 2004 14:29:38 -0500 Received: from mirapoint.uc.edu (mirapoint.uc.edu [10.23.4.254]) by mprelay.uc.edu (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id AQJ47385; Tue, 10 Feb 2004 14:29:41 -0500 (EST) Received: from dhcp-539-820.geop.uc.edu (dhcp-539-820.geop.uc.edu [10.44.3.95]) by mirapoint.uc.edu (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id AOH43024; Tue, 10 Feb 2004 14:29:39 -0500 (EST) Subject: One question about protein-ligand binding From: Baoqiang Cao Reply-To: caobg~at~email.uc.edu To: chemistry~at~ccl.net Content-Type: text/plain Message-Id: <1076441699.25582.112.camel~at~dhcp-539-820.geop.uc.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.4-8mdk Date: Tue, 10 Feb 2004 14:35:01 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, Are there any ways to quantitatively describe how well a ligand fits a protein cavity? Any clues will be welcome! Thanks. Best, Cao From chemistry-request@ccl.net Tue Feb 10 01:14:22 2004 Received: from physunc.phy.uc.edu (physunc.phy.uc.edu [129.137.4.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1A6ELU6010271 for ; Tue, 10 Feb 2004 01:14:21 -0500 Received: from bethe.phy.uc.edu (bethe.geop.uc.edu [10.44.6.245]) by physunc.phy.uc.edu (8.9.3p2/8.9.3) with ESMTP id BAA18363 for ; Tue, 10 Feb 2004 01:14:30 -0500 (EST) Received: from dhcp-539-820.geop.uc.edu ([10.44.3.95]) by bethe.phy.uc.edu (8.9.3p2/8.9.3) with ESMTP id BAA19482 for ; Tue, 10 Feb 2004 01:14:31 -0500 (EST) Subject: One question about protein-ligand binding From: Baoqiang Cao Reply-To: bqcao~at~physics.uc.edu To: chemistry~at~ccl.net Content-Type: text/plain Message-Id: <1076393992.12844.2.camel~at~dhcp-539-820.geop.uc.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.4-8mdk Date: Tue, 10 Feb 2004 01:19:55 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, Are there any ways to quantitatively describe how well a ligand fits a protein cavity? Any clues will be welcome! Thanks. Best, Cao From chemistry-request@ccl.net Tue Feb 10 20:39:43 2004 Received: from spearnet.net (mail.spearnet.net [65.219.158.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1B1dgU6017170 for ; Tue, 10 Feb 2004 20:39:42 -0500 Received: from cornell.edu [67.193.134.227] by spearnet.net with ESMTP (SMTPD32-6.06) id A058DEF014C; Tue, 10 Feb 2004 20:15:52 -0600 Date: Tue, 10 Feb 2004 20:39:49 -0500 Subject: Re: CCL:J.Comp.Chem. Style File Needed Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v552) Cc: chemistry_at_ccl.net To: "Taras V. Pogorelov" From: Richard Gillilan In-Reply-To: <40284074.7121C614_at_uiuc.edu> Message-Id: <2DF29162-5C33-11D8-83BA-003065963E2C_at_cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=3.3 required=7.0 tests=RCVD_IN_DYNABLOCK, RCVD_IN_NJABL,RCVD_IN_NJABL_DIALUP,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I use a bibliographic style file called achemso.bst (achemso = American Chemical Society) that I found on the net. Note that J. Comput. Chem. does not like bold face and italics etc., just plain text, so I had to comment out a couple of lines. The only thing I can't do so far is get it to insert a dash in place of sequential citation numbers: [10,11,12,13] -> [10-13]. I would love to know a trick for this. Anyhow, you are welcome to the file if you can't find something better out there. Richard Gillilan MacCHESS, Cornell On Monday, February 9, 2004, at 09:22 PM, Taras V. Pogorelov wrote: > Dear All, > > We are in need of the LaTeX style file for the Journal of Computationl > Chemistry. > Your help will be greatly appreciated. > > Best, > > Taras > > _______________________________________________________________ > > Taras V. Pogorelov, Chemical Physics, University of Illinois, > _______________________________________________________________