From chemistry-request@ccl.net Thu Nov 27 01:14:40 2003 Received: from avmx.iitkgp.ernet.in ([203.197.98.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAR6DxNL032150 for ; Thu, 27 Nov 2003 01:14:08 -0500 Received: from avmx.iitkgp.ernet.in (avmx [203.197.98.4]) by avmx.iitkgp.ernet.in (8.12.5/8.12.5) with ESMTP id hAR6WXgH015176 for ; Thu, 27 Nov 2003 12:02:34 +0530 Received: from iitkgp.iitkgp.ernet.in (iitkgp.iitkgp.ernet.in [203.197.98.10]) by avmx.iitkgp.ernet.in (8.12.5/8.12.5) with ESMTP id hAR6WVbb015171; Thu, 27 Nov 2003 12:02:31 +0530 Received: from cts.iitkgp.ernet.in (localhost [127.0.0.1]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id LAA20372; Thu, 27 Nov 2003 11:34:31 -0500 (GMT) X-Authentication-Warning: iitkgp.iitkgp.ernet.in: iscan owned process doing -bs Received: from localhost (utpal@localhost) by cts.iitkgp.ernet.in (8.11.6/8.11.6) with ESMTP id hAR5qPu32154; Thu, 27 Nov 2003 11:22:27 +0530 Date: Thu, 27 Nov 2003 11:22:25 +0530 (IST) From: utpal sarkar To: Mark Thompson cc: chemistry=at=ccl.net Subject: Re: CCL:ArgusLab 4.0 beta #2: critical bug fix available. In-Reply-To: <000801c3b449$cff1abc0$0200a8c0@planaria> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.5 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,RCVD_IN_RFCI, RCVD_IN_UNCONFIRMED_DSBL,USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCL users, I have downloaded ArgusLab 4.0 Beta and installed it. But it is not working. When clicking on the icon, it gives "ArgusLab 4.0 beta1 is expred and will nolonger function. License is expired or invalid." Can anybody give me suggestion to get rid of this problem. Thnaks. with regards Utpal Sarkar Chemistry Department (SRF) Indian Institute of Technology Kharagpur-721302 INDIA On Wed, 26 Nov 2003, Mark Thompson wrote: > > I've fixed a critical bug in ArgusLab (available in 4.0) and made a > new installer available on the ArgusLab website. > > > The bug: > -------- > Occasionally, bonds would simply disappear from a molecule during > editing. Furthermore, you could not remake the bond once it > disappeared. This bug happened under rare conditions and was hard to > reproduce. > > If you already have installed ArgusLab beta #2, you can simply > reinstall over it, or uninstall/reinstall. > > Thanks for the help from several users on this and apologies for the > annoying bug! > > Sincerely, > Mark Thompson > > *************************** > Mark Thompson, PhD > Planaria Software LLC > PO Box 55207 > Seattle, WA 98155 > > mark=at=arguslab.com > http://www.arguslab.com > *************************** > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl=at=ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- There are living systems, there is no "living matter". From chemistry-request@ccl.net Thu Nov 27 05:10:47 2003 Received: from web1.ulb.ac.be (interface.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARAAFNL014131 for ; Thu, 27 Nov 2003 05:10:15 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id LAA18850; Thu, 27 Nov 2003 11:10:14 +0100 (MET) for chemistry$at$ccl.net Date: Thu, 27 Nov 2003 11:10:14 +0100 (MET) Message-Id: <200311271010.LAA18850$at$web1.ulb.ac.be> From: Giju Kalathingal To: chemistry$at$ccl.net Subject: Summary:Geometry optimization with BSSE correction X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCl-all, Thanks to all for providing the information. It could be summarized as follows. Gaussian98 A10/A11, Gaussian 03, Gamess(US), and MOLPRO are capable of doing it. We have tested it with Argon dimer using Gaussian03. The optimization succeeded only under non-symmetry (NOSYMMETRY keyword). Very useful webpage on this is, http://iqc.udg.es/~perico/bbopt.html Giju Kalathingal Department of General Chemistry (ALGC) Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium. Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 E-mail: Giju.Kalathingal$at$vub.ac.be ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Thu Nov 27 06:50:48 2003 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARBoGNL017661 for ; Thu, 27 Nov 2003 06:50:17 -0500 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id hARBoAnE043276; Thu, 27 Nov 2003 09:50:10 -0200 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id hARBo5IC043274; Thu, 27 Nov 2003 09:50:09 -0200 Date: Thu, 27 Nov 2003 09:50:05 -0200 (BDB) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Matthias Ullmann cc: chemistry~at~ccl.net Subject: Re: CCL:Free software on ComFA In-Reply-To: <3FC4F4C2.1050400~at~iwr.uni-heidelberg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Dr Ullman, Try SOMFA2 (http://bellatrix.pcl.ox.ac.uk/). Input files in .cssr format may be generated in Mol2mol (http://freeweb.interware.hu/frenzy/mol2mol/). Best wishes. -Andre On Wed, 26 Nov 2003, Matthias Ullmann wrote: > Dear all, > > I am looking for free software that can be used for ComFA (comparative > field analysis) of small molecules. I am very greatful for any > informations. I will make a list and send it to CCL. > > Best regards, > > Matthias Ullmann > > -- > ======================================== > Prof. Dr. G. Matthias Ullmann > Structural Biology/Bioinformatics > University of Bayreuth > Universitdtsstr. 30, BGI > 95447 Bayreuth > Germany > > Telephone: +49-921-55-3545 > Fax: +49-921-55-3544 > e-mail: Matthias.Ullmann~at~uni-bayreuth.de > http://www.bp.uni-bayreuth.de/bisb/ > ======================================== > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY~at~ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST~at~ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl~at~ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@ccl.net Thu Nov 27 07:48:43 2003 Received: from mail2.cc.huji.ac.il (mail2.cc.huji.ac.il [132.64.1.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARCmANL020330 for ; Thu, 27 Nov 2003 07:48:11 -0500 Received: by mail2.cc.huji.ac.il (Postfix, from userid 31998) id 2C6433FEB7; Thu, 27 Nov 2003 14:48:07 +0200 (IST) Received: from baikal (baikal.ch.huji.ac.il [132.64.98.42]) by mail2.cc.huji.ac.il (Postfix) with SMTP id 64ACE400A9 for ; Thu, 27 Nov 2003 14:47:54 +0200 (IST) Message-ID: <017a01c3b4e4$ac9a1c70$2a624084~at~ch.huji.ac.il> From: "David Danovich" To: Subject: CCL:g98 Date: Thu, 27 Nov 2003 14:47:45 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1255" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Level: X-Spam-Status: No, hits=0.5 required=7.0 tests=PRIORITY_NO_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, In the Gaussian output file there is information which related to dipole moment Dipole moment (Debye): X= 0.0000 Y= 0.0000 Z= -2.8469 Tot= 2.8469 as well as some information in the end of output file 1\1\GINC-PAULI\SP\RHF\6-31G(d)\C1H2O1\DODIK\27-Nov-2003\0\\# HF/6-31G* TEST\\form\\0,1\C\O,1,1.22\H,1,1.08,2,120.\H,1,1.08,2,120.,3,180.,0\\ Version=DEC-AXP-OSF/1-G98RevA.7\State=1-A1\HF=-113.8636997\RMSD=8.275e -05\Dipole=0.,0.,-1.1200326\PG=C02V [C2(C1O1),SGV(H2)]\\@ with some information about dipole. What this last dipole means? Thank you in advance David ________________________________________________________________ Dr. David Danovich, Department of Organic Chemistry, The Hebrew University, Edmond J. Safra Campus - Givat Ram, 91904 Jerusalem, Israel http://yfaat.ch.huji.ac.il/david.html, David.Danovich~at~huji.ac.il FAX:(+972)-2-6585345, Phone:(+972)-2-6586934(w), (+972)-2-9995935(h) From chemistry-request@ccl.net Thu Nov 27 09:49:39 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAREn8NL025714 for ; Thu, 27 Nov 2003 09:49:08 -0500 Received: from [136.206.117.195] by hawk.dcu.ie with HTTP; Thu, 27 Nov 2003 14:49:07 +0000 Date: Thu, 27 Nov 2003 14:49:07 +0000 Message-ID: <3F6B7AEB0006910C*at*hawk.dcu.ie> From: "Noel O'Boyle" Subject: SQM programs To: chemistry*at*ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hAREndNL025740 Hello CCLers, Can someone tell me what programs are available to perform Pulay's scaled quantum mechanical (SQM) method, and to carry out any necessary rotation of the input coordinates from Gaussian03 output. Thanks, Noel O'Boyle From chemistry-request@ccl.net Thu Nov 27 10:49:57 2003 Received: from mail.univ-reims.fr (mail.univ-reims.fr [193.50.208.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARFnPNL029862 for ; Thu, 27 Nov 2003 10:49:25 -0500 Received: from smtp.univ-reims.fr (smtp.univ-reims.fr [193.50.208.24]) by mail.univ-reims.fr (8.12.10/8.12.9) with ESMTP id hARFoLsE007776 for ; Thu, 27 Nov 2003 16:50:22 +0100 (MET) Received: from ([10.16.1.59]) by smtp.univ-reims.fr (MailMonitor for SMTP v1.2.2 ) ; Thu, 27 Nov 2003 16:49:21 +0100 (CET) Message-ID: <3FC61E07.3040505-.at.-univ-reims.fr> Date: Thu, 27 Nov 2003 16:53:43 +0100 From: eric.henon-.at.-univ-reims.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: fr-fr, fr MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: new release of KISTHEP software Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.7 required=7.0 tests=NO_REAL_NAME,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Computational Chemistry List, A new release of the KISTHEP Package, version 1.0 is available from the web site at http://www.univ-reims.fr/Labos/GSMA/siteKisthep . KISTHEP is a free chemical software for the calculation of thermodynamical and kinetical properties > from quantum chemical data. The graphical interface has been improved. RRKM calculations ("Tight TS" case) are now available. KISTHEP is a java application, thus KISTHEP can be run under Windows or Linux or ... platform. Comments, questions and suggestions for future improvements should be sent to eric.henon-.at.-univ-reims.fr Best wishes, Eric Henon, Frederic Bohr From chemistry-request@ccl.net Thu Nov 27 07:58:29 2003 Received: from mx03.uni-tuebingen.de (mx03.uni-tuebingen.de [134.2.3.13]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARCvvNL020860 for ; Thu, 27 Nov 2003 07:57:57 -0500 Received: from Telemachos.pharm.chemie.uni-tuebingen.de (telemachos.pharm.chemie.uni-tuebingen.de [134.2.68.234]) by mx03.uni-tuebingen.de (8.12.3/8.12.3) with ESMTP id hARCvsSZ005032 for ; Thu, 27 Nov 2003 13:57:54 +0100 From: Christoph Nimptsch Organization: Uni =?iso-8859-1?q?T=FCbingen?= To: chemistry-.at.-ccl.net Subject: CCL:Free software on ComFA Date: Thu, 27 Nov 2003 14:00:19 +0100 User-Agent: KMail/1.5.3 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Message-Id: <200311271400.19548.christoph.nimptsch-.at.-uni-tuebingen.de> X-AntiVirus: checked by AntiVir Milter 1.0.4; AVE 6.22.0.1; VDF 6.22.0.50 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hARCwTNL020876 Hello, as far as I know, Tripos has a patent for using GRID-maps (www.moldiscovery.com) with general PLS regression techniques. Am I right? So be careful not to violate this patent with free software. Christoph ------------------------------------------ Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universitdt T|bingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071 / 29 73047 Fax.: 07071 / 29 2470 mailto:christoph.nimptsch-.at.-uni-tuebingen.de ------------------------------------------ From chemistry-request@ccl.net Thu Nov 27 08:40:18 2003 Received: from vspw2074.nikem.xoffice.getracenter.it ([213.140.25.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARDdkNL022680 for ; Thu, 27 Nov 2003 08:39:46 -0500 Received: by vspw2074.nikem.xoffice.getracenter.it with Internet Mail Service (5.5.2656.59) id ; Thu, 27 Nov 2003 14:39:45 +0100 Message-ID: From: Forlani Roberto To: chemistry-.at.-ccl.net Cc: "Matteo Floris (E-mail)" Subject: Italian Chemoinformatic's newsletter Date: Thu, 27 Nov 2003 14:39:44 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I'm glad to let you know that Italian Chemoinformatic's newsletter is now available from Matteo Floris. If you're interested to subscribe or to share(#) informations follow this link: http://www.cheminfo.it/mlist/index.php HTH, Roberto Forlani (#) in this case please contact directly the author at the provided address NiKem Research S.r.l. via Zambeletti, 25 20021 Baranzate di Bollate (MI) Italy tel. (+39) 02-35694-7496/7573 fax. (+39) 02-35694-7606 e-mail: roberto.forlani-.at.-NOSPAMnikemresearch.com (GnuPG key available) web-site: http://www.nikemresearch.com From chemistry-request@ccl.net Thu Nov 27 05:39:51 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hARAdJNL015156 for ; Thu, 27 Nov 2003 05:39:20 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HP00070KAXJXD.-at-.mailserver.unimi.it> for chemistry.-at-.ccl.net; Thu, 27 Nov 2003 11:39:20 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HP00032BAXHBW.-at-.smtp.unimi.it> for chemistry.-at-.ccl.net; Thu, 27 Nov 2003 11:39:17 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 3ED7314792; Thu, 27 Nov 2003 11:52:07 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 33ABB1478F for ; Thu, 27 Nov 2003 11:52:07 +0100 (CET) Date: Thu, 27 Nov 2003 11:52:04 +0100 (CET) From: Alessandro Contini Subject: sp PCM calculation on a H transfer TS To: chemistry.-at-.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hARAdqNL015179 Hi, I'm trying to use g03 to compute SP energies on H transfer TS previously located. I would like to include solvent effect by PCM. However the calculation stops immediatly with the following error: United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 26 is unbound. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Error termination via Lnk1e in /usr/local/g03/l301.exe It's clear that Hydrogen 26 is unbound, being the H implicated in the transfer. Does anybody knows how to fix such error? Any suggestion will be appreciated Thanks Alessandro Contini Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini.-at-.unimi.it