From chemistry-request@server.ccl.net Mon Mar 24 08:46:50 2003 Received: from laplace.quimica.ufpr.br ([200.17.215.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2ODknr26478 for ; Mon, 24 Mar 2003 08:46:49 -0500 Received: from bohr.quimica.ufpr.br (localhost.quimica.ufpr.br [127.0.0.1]) by laplace.quimica.ufpr.br (Postfix) with ESMTP id 87553506 for ; Mon, 24 Mar 2003 10:46:36 -0300 (BRT) Message-ID: <3E7F0C3C.4070803@bohr.quimica.ufpr.br> Date: Mon, 24 Mar 2003 10:46:36 -0300 From: Eduardo User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:1.0.1) Gecko/20021005 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: About Geometry optimization while a electrical field is being applied Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Sirs I would be very gratefull if someone pointed to me some softs (preferible free and running under unix-pc plataforms) that can performed organic molecules geometry optimization (AM1 and PM3 or PM5) while an electrical field is being applied. I will sumarize the responses Thanks a lot in advance yours Eduardo -- Eduardo Lemos de Sa - edulsa@quimica.ufpr.br Dep. Quimica - Universidade Federal do Parana Curitiba - PR - Brazil Box: 19081 - Zip: 81531-990 - Phone: +55(41)361-3300 From chemistry-request@server.ccl.net Mon Mar 24 17:29:47 2003 Received: from mxout5.cac.washington.edu ([140.142.32.135]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2OMTlr04193 for ; Mon, 24 Mar 2003 17:29:47 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout5.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2OMTfEk021715; Mon, 24 Mar 2003 14:29:41 -0800 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2OMTVaL031845 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Mon, 24 Mar 2003 14:29:41 -0800 Message-ID: <3E7F86CC.6060305@u.washington.edu> Date: Mon, 24 Mar 2003 14:29:32 -0800 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net, autodock@scripps.edu Subject: autogrid/dock + segmentation fault on Redhat8 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi fellow AutoDockers and CClers, Unfortunately I still couldn't fix the problem of AutoDock not being able to take more than ten atom types, although I think I did everything according to the guidance. I used the autocomm.h-extra-maps as autocomm.h, and at least I didn't have trouble compiling both programs. I changed the Makefile according to the Linux AutoDock HOWTO. But everytime I call autogrid, I get a segmentation fault, even if I use less than ten atom types. I think the problem arises when the program starts to calculate the grids, since the gpf file was read in without problems (according to glg). I also set the stacksize to unlimited, so this cannot cause the problem either (I use bash, so I have ulimit -s unlimited). Is there anyone who experienced similar problems and could help me with this? I honestly don't know why this doen't work. Thanks a lot in advance, Carsten -- Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665 From chemistry-request@server.ccl.net Mon Mar 24 20:24:44 2003 Received: from gvlallk ([68.45.219.101]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2P1Ofr09915 for ; Mon, 24 Mar 2003 20:24:43 -0500 From: Jama Pdesupport To: Subject: Equal results just cheaper Date: Mon, 24 Mar 2003 17:26:54 -0800 Mime-Version: 1.0 Content-Type: text/html Message-Id:
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From chemistry-request@server.ccl.net Mon Mar 24 22:10:10 2003 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2P3AAr17206 for ; Mon, 24 Mar 2003 22:10:10 -0500 Received: from auto0.summerhill (syr-24-58-0-128.twcny.rr.com [24.58.0.128]) by cornell.edu (8.9.3/8.9.3) with ESMTP id WAA01080 for ; Mon, 24 Mar 2003 22:10:06 -0500 (EST) Subject: Problems with GAMESS convergence From: Connie Chang To: chemistry@ccl.net Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.8 (1.0.8-10) Date: 24 Mar 2003 22:10:05 -0500 Message-Id: <1048561807.11270.5.camel@auto0.summerhill> Mime-Version: 1.0 Hi -- I am trying to do a geometric optimization on a molecule with 140 atoms. But my process ends abnormally because SCF convergence hasn't been achieved. I'm using GBASIS = PM3 and SCFTYP=RHF. I've increased the MAXIT to 1000 (recompiling the source code) and I have made the convergence criterion less stringent with the line $SCF CONV=2d-3 DAMP=.TRUE. $END I've also made the geometric optimization less stringent (although I don't think this is the problem since it's failing at the SCF convergence level) with the line $STATPT OPTTOL=.0001 $END Does anyone know of any other ways to get my molecule to converge? I've also tried restarting the job using GUESS=MOREAD and the VECTOR frm the .dat file; but I'm not sure what to put down for number of orbitals -- NORB. Would it be 280 since I have 140 atoms? Or something else? Any other advice or recommendations would be appreciated. I'm at a loss! THanks, Connie From dmiller@sageinformatics.com Mon Mar 24 19:17:48 2003 -0500 Return-Path: From: "David Miller" To: Subject: ChemTK cheminformatics software Date: Mon, 24 Mar 2003 13:57:58 -0600 Message-ID: ChemTK evaluation software is available for download at www.chemtk.com ChemTK is a Windows based cheminformatics toolkit providing chemists the ability to visualize, organize, query, and analyze chemical screening data. It functions both as a simple and convenient SD file browser and as a powerful decision-support platform, offering intuitive clustering and property-calculation capabilities, QSAR model generation and virtual screening, rapid similarity analyses, and many additional features. Visit www.chemtk.com for a free ChemTK evaluation, and to download the ChemTK product sheet, release notes, and full documentation. For a more thorough scientific discussion of ChemTK's features, see the following article in the most recent issue of JCICS (a link to the article is available from www.chemtk.com): Miller, D.W. A Chemical Class-Based Approach to Predictive Model Generation. J. Chem. Inf. Comput. Sci. 2003, 43, 568-578. Comments and feedback are welcome. Please feel free to send me an email at the address below. Best regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller@sageinformatics.com