From chemistry-request@server.ccl.net Fri Mar 15 09:03:28 2002 Received: from cube.univ-lemans.fr ([193.52.31.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FE3Rp11294 for ; Fri, 15 Mar 2002 09:03:28 -0500 Received: by cube with Internet Mail Service (5.5.2653.19) id ; Fri, 15 Mar 2002 15:03:20 +0100 Message-ID: <14518E66DD9DD3118312009027C3EEA31498AB@cube> From: Minisini Benoit To: "'chemistry@ccl.net'" Subject: CCL: Difficulty in Optimisation of Cell with pseudopotential cod e. Date: Fri, 15 Mar 2002 15:03:17 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hello everybody, I would like to perform an optimisation cell with a planewave pseudopotential code. I see it could be dangerous because of the pulay stress. But how can I see the importance of this stress on my result, knowing that my initial cell parameters were 5.28*5.28*10.13 angstroms cube (volume=282 angstrom cube) and the final parameters are 5.15*5.15*10.45 angstroms cube (volume=277 angstrom cube). Could you give me the reference of some articles about this problem? waiting for your kind reply, with regards Benoit ___________________________________ Benoit Minisini ISMANS (Institut Superieur des Materiaux du Mans) 44, Avenue F.A. Bartholdi 72000 Le Mans Tel.: +33 (0)2 43 21 40 14 Fax : +33 (0)2 43 21 40 39 E-Mail : bminisini@ismans.univ-lemans.fr Web : From chemistry-request@server.ccl.net Fri Mar 15 09:45:38 2002 Received: from tele-post-20.mail.demon.net ([194.217.242.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FEjcp12097 for ; Fri, 15 Mar 2002 09:45:38 -0500 Received: from chmqst.demon.co.uk ([158.152.83.101] helo=chmqst) by tele-post-20.mail.demon.net with esmtp (Exim 3.35 #1) id 16lsxb-0005Qu-0K for chemistry@ccl.net; Fri, 15 Mar 2002 14:45:36 +0000 From: "David Livingstone" Organization: ChemQuest To: chemistry@ccl.net Date: Fri, 8 Mar 2002 14:43:43 +0100 MIME-Version: 1.0 Subject: CCL: QSAR and Molecular Modelling Conference Reply-to: davel@chmqst.demon.co.uk Message-ID: <3C88CE1F.19045.C9617A@localhost> X-Confirm-Reading-To: davel@chmqst.demon.co.uk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v4.01) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Apologies if you receive multiple copies of this. -------------------------------------------------------------- The next European conference on QSAR and Molecular Modelling will be held in the UK in Bournemouth from the 8th to the 13th of September, 2002. The session titles are: Expanding the Knowledge Base High Throughput Processes Modelling the Organism Modelling the Chemistry Modelling the Data Informatics 1: Bioinformatics Web based Dissemination, Integration and Quality Assurance Informatics 2: Cheminformatics Registration is now open and abstracts are invited for both poster and oral presentations. Visit our website ate www.euro-qsar.org. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Delamere House, 1 Royal Crescent, Sandown. Isle of Wight UK PO36 8LZ Phone & Fax: +44 (0)1983 401793 e-mail davel@chmqst.demon.co.uk http://www.chmqst.demon.co.uk ------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Mar 15 11:04:31 2002 Received: from alcides.host4u.net ([216.71.64.98]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FG4Vp13316 for ; Fri, 15 Mar 2002 11:04:31 -0500 Received: from saturn.simbiosys.ca (CPE0020af6deab6.cpe.net.cable.rogers.com [24.156.62.119]) by alcides.host4u.net (8.11.6/8.11.6) with ESMTP id g2FFw5O26616 for ; Fri, 15 Mar 2002 09:58:05 -0600 Received: from there (pluto.simbiosys.ca [192.168.213.1]) by saturn.simbiosys.ca (Postfix) with SMTP id A78B1AEF for ; Fri, 15 Mar 2002 11:04:18 -0500 (EST) Content-Type: text/plain; charset="iso-8859-1" From: Owen Lewis To: CCL Subject: H-bond acceptor strengths Date: Fri, 15 Mar 2002 11:04:18 -0500 X-Mailer: KMail [version 1.3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <20020315160418.A78B1AEF@saturn.simbiosys.ca> Hi CCLers, Does anyone have a idea on where I could find tabulated data on the acceptor strength of atoms in small fragments? I've read an article by Berthelot et al in 'Perspectives in Drug Discovery and Design' Vol 18., and that was a good start, but I would like to find further information. Many thanks - all responses appreciated. Owen Lewis From chemistry-request@server.ccl.net Fri Mar 15 13:00:50 2002 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FI0op15418 for ; Fri, 15 Mar 2002 13:00:50 -0500 Received: from wk39.asc.hpc.mil (wk39.asc.hpc.mil [129.48.245.39]) by sas.asc.hpc.mil (8.11.6/8.11.6) with ESMTP id g2FI0iL6119883 for ; Fri, 15 Mar 2002 13:00:44 -0500 (EST) Received: from localhost (blaudejp@localhost) by wk39.asc.hpc.mil (SGI-8.9.3/8.9.3) with ESMTP id NAA01474 for ; Fri, 15 Mar 2002 13:00:40 -0500 (EST) Date: Fri, 15 Mar 2002 13:00:39 -0500 From: "JEAN P. BLAUDEAU" To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am wondering if anyone would know of any programs that can calculate pKa's quantum mechanically. I think ChemCad calculates them semi-empirically, but I would prefer a QM method. Thank you, Jean --------------------------------------------------------------------------- Jean-Philippe Blaudeau ASC/HP, 2435 5th Street, Bldg. 676 Director of Computational Wright-Patterson Air Force Base Chemistry and Materials Ohio, 45433-7802 PET ASC MSRC & Phone: 937-904-5145 HPTi FAX: 937-255-4585 Email: blaudejp@asc.hpc.mil URL: http://www.asc.hpc.mil/PET/CCM --------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Mar 15 12:03:55 2002 Received: from electra.cc.umanitoba.ca ([130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FH3tp14738 for ; Fri, 15 Mar 2002 12:03:55 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.12.0/8.12.0) with SMTP id g2FH3kOd020103 for ; Fri, 15 Mar 2002 11:03:46 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: One more Gaussian Front End Item Date: Fri, 15 Mar 2002 11:03:45 -0600 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Just an addition to the question of "front ends" for Gaussian. Since G98 does all of its calculations in redundant internal coordinates, no matter what input format the structure is in (unless instructed otherwise), there is no need to construct Z-matrices at all. ANY program that can generate a file containing Cartesian coordinates from a drawn structure can be used to create input files, along with a text editor to add the necessary route commands etc. I suppose there are specific cases where a Z-matrix is superior, especially if you want to guide a geometry optimization in some ways, but you must specify that the optimization be done in Z-matrix coordinates or G98 will simply create redundant internals from your Z-matrix. So, for most purposes we just input Cartesians. Of course, this approach still means you have to use the G98 input syntax with all of its idiosyncrasies and inconsistencies - and those of you who were reading CCL in the recent past know my opinions about that. But it does give you complete control, and is much cheaper than Gaussview (i.e. basically free). For a "back end" we have been using Molekel because it makes such lovely pictures. Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ From chemistry-request@server.ccl.net Fri Mar 15 14:52:20 2002 Received: from hartree.ccqc.uga.edu ([128.192.2.57]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FJqJp16992 for ; Fri, 15 Mar 2002 14:52:19 -0500 Received: from localhost (hlwood@localhost) by hartree.ccqc.uga.edu (8.9.1/8.9.1) with SMTP id OAA13800 for ; Fri, 15 Mar 2002 14:51:55 -0500 Date: Fri, 15 Mar 2002 14:51:55 -0500 (EST) From: Lee Woodcock To: Computational Chemistry List Subject: Re: CCL:One more Gaussian Front End Item In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, There is another good front end for linux users: ghemical is a good (free) molecule buider that allows users to build rough stuctures and clean them up with MM and Semi-empirical calculations. There is rpm and source available for download at the following website: http://www.uku.fi/~thassine/ghemical/ good luck Lee --------------------------------------------------------------------------- H. Lee Woodcock III | Phone: 706 542-7374 Ctr. for Comp. Quantum Chem. | Fax: 706 542-0406 University of Georgia | E-mail: hlwood@ccqc.uga.edu Athens, GA 30602-2556 | http://zopyros.ccqc.uga.edu/~hlwood --------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Mar 15 19:15:03 2002 Received: from postal.sdsc.edu (IDENT:9wDGbt3QqzFvseRf7D1ekRHVydpKNafd@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2G0F2p22431 for ; Fri, 15 Mar 2002 19:15:02 -0500 Received: from koa.sdsc.edu (IDENT:sEfWy+qDQiTgriO3dvqjYbKxLcXccUMO@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/server/32b1) with ESMTP id g2G0ExY22466; Fri, 15 Mar 2002 16:14:59 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id QAA06848; Fri, 15 Mar 2002 16:14:58 -0800 (PST) Date: Fri, 15 Mar 2002 16:14:58 -0800 From: Wibke Sudholt To: "JEAN P. BLAUDEAU" cc: Subject: Quantum mechanical pKa's In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Schroedinger's quantum chemical code Jaguar has a pKa prediction module. See http://www.schrodinger.com/Products/pka.html. Best regards, Wibke Sudholt University of California, San Diego On Fri, 15 Mar 2002, JEAN P. BLAUDEAU wrote: > > Hello, > I am wondering if anyone would know of any programs that can calculate > pKa's quantum mechanically. I think ChemCad calculates them > semi-empirically, but I would prefer a QM method. > Thank you, > Jean > > --------------------------------------------------------------------------- > Jean-Philippe Blaudeau ASC/HP, 2435 5th Street, Bldg. 676 > Director of Computational Wright-Patterson Air Force Base > Chemistry and Materials Ohio, 45433-7802 > PET ASC MSRC & Phone: 937-904-5145 > HPTi FAX: 937-255-4585 > Email: blaudejp@asc.hpc.mil URL: http://www.asc.hpc.mil/PET/CCM > --------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Mar 15 16:34:28 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2FLYRp18295 for ; Fri, 15 Mar 2002 16:34:27 -0500 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g2FLYFg26651; Fri, 15 Mar 2002 13:34:15 -0800 (PST) Message-Id: <200203152134.g2FLYFg26651@mx.seanet.com> To: , From: Mark Thompson Subject: Re: CCL:One more Gaussian Front End Item Date: Fri, 15 Mar 2002 13:34:19 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 > For a "back end" we have been using Molekel because it makes such lovely > pictures. > > Dr. Philip G. Hultin > Associate Department Head and > Associate Professor of Chemistry An alternative back end for reading Gaussian structures and making beautiful pictures of surfaces is ArgusLab (http://www.arguslab.com) Not free, but exceedingly inexpensive for academics. Mark ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com =======================================