From chemistry-request@ccl.net Tue Nov 25 08:11:27 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPDAuNL031667 for ; Tue, 25 Nov 2003 08:10:56 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id D6930181CCA8; Tue, 25 Nov 2003 14:10:54 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 4083B181CCA4; Tue, 25 Nov 2003 14:10:51 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 25 Nov 03 14:10:51 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 25 Nov 03 14:10:47 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Kwanyong Seo" Date: Tue, 25 Nov 2003 14:10:29 +0100 Subject: Re: CCL:transition dipole moment Reply-To: spanget.-at-.ruc.dk Cc: chemistry.-at-.ccl.net Message-ID: <3FC362DA.29461.64E9C45@localhost> Priority: normal In-reply-to: <00bb01c3b295$0ea1c5a0$e325f88f@ilsun> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-Spam-Report: X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Level: Dear Kwanyong Seo: the X, Y, and Z components of the transition moment vector printed by Gaussian refer to the molecular coordinate system indicated under the heading 'Standard orientation:'. If you wish to express the transition moment vector in a different coordinate system you must rotate the vector into this system. The oscillator strength (Osc.) is independent of this tranformation. Jens >--< > Dear all, > > I have performed the calculation to obtain a value of transition > dipole moment (mu(A), mu(B), mu(C)) using G03 program. The method and > basis set which I have used are CIS/6-31G**. A part of result(*.log) > is as follow: ..... =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget.-at-.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Tue Nov 25 09:28:54 2003 Received: from compton.acpub.duke.edu (compton.acpub.duke.edu [152.3.233.74]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPESMNL001178 for ; Tue, 25 Nov 2003 09:28:22 -0500 Received: from localhost (friedman.acpub.duke.edu [152.3.232.60]) by compton.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with ESMTP id hAPESL2b020492; Tue, 25 Nov 2003 09:28:21 -0500 (EST) Received: from adsl-18-3-134.rdu.bellsouth.net (adsl-18-3-134.rdu.bellsouth.net [68.18.3.134]) by webmail.duke.edu (IMP) with HTTP for ; Tue, 25 Nov 2003 09:28:21 -0500 Message-ID: <1069770501.3fc367057aad8..at..webmail.duke.edu> Date: Tue, 25 Nov 2003 09:28:21 -0500 From: Jieru Zheng To: chemistry..at..ccl.net Subject: how to read HyperChem HCS file MIME-Version: 1.0 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Spam-Status: No, hits=-0.3 required=7.0 tests=USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I have been using HyperChem7 to do conformation search. The output was saved in a default file format (.HCS) But I don't know how to open the file and read those structures generated from the conformation search. Would anybody please help? Thanks a lot! From chemistry-request@ccl.net Tue Nov 25 09:56:23 2003 Received: from sainfoin.saclay.cea.fr (sainfoin.saclay.cea.fr [132.166.192.126]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPEtpNL002409 for ; Tue, 25 Nov 2003 09:55:52 -0500 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.saclay.cea.fr (8.12.10/8.12.9/CEAnet-Internet.2.0) with ESMTP id hAPEtobf006053 for ; Tue, 25 Nov 2003 15:55:50 +0100 (MET) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.10) with ESMTP id ; Tue, 25 Nov 2003 15:52:17 +0100 Received: from penelope.saclay.cea.fr (penelope.saclay.cea.fr [132.166.189.102]) by nenuphar.saclay.cea.fr (8.12.10/8.12.9/CEAnet-Internet.2.0) with ESMTP id hAPEtoNk024645; Tue, 25 Nov 2003 15:55:50 +0100 (MET) Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2657.72) id ; Tue, 25 Nov 2003 16:02:12 +0100 Message-ID: <3808A7D2DCEAD6118B63009027287265014A20..at..azurite.saclay.cea.fr> From: VITORGE Pierre 094605 To: "'Telkuni'" , chemistry..at..ccl.net Subject: RE: "%mem" trouble of Gaussian Date: Tue, 25 Nov 2003 15:55:44 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) 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 hAPEuNNL002434 I had similar problems. I run tests with different values for %mem, it seems there is an optimum %mem value to obtain the shortest CPU time, this optimum value is usually far from the maximum reasonable value (i.e the amount of physical memory minus 150to300Mb for the system). This probably depends (among other reasons) on the size of the exchange file memory, and whether this file is at the begining of the disk. I asked help to Gaussian, but did not get any answer. Pierre Vitorge CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-Universite d'Evry-CNRS) Bat.391 Pe.40a 91191 Gif sur Yvette cedex France tel.(+33) 169-08-32-65, secr.: (+33)169-08-32-50, fax:(+33)169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre -----Message d'origine----- De : Telkuni [mailto:telkuni..at..venus.dti.ne.jp] Envoyi : mardi 25 novembre 2003 00:22 @ : chemistry..at..ccl.net Objet : CCL:"%mem" trouble of Gaussian Hello, CCLers. I like to ask the effect of "%mem=xxx" on Gaussian98W. I've met curios phenomenon with G98W_ver.A7. However I modified the PC's memory "%mem=128MB" to "%mem=512MB" on same calculation, there was very little calc time difference between them(57min and 64 min!) If anyone met same phenomenon, please let me know. All responses, I will appreciate. And I will summarize them. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni..at..venus.dti.ne.jp -= 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Nov 25 11:35:30 2003 Received: from web21202.mail.yahoo.com (web21202.mail.yahoo.com [216.136.130.18]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAPGYvNL006486 for >ccl.net>; Tue, 25 Nov 2003 11:34:58 -0500 Message-ID: <20031125163457.11518.qmail<>web21202.mail.yahoo.com> Received: from [129.109.59.107] by web21202.mail.yahoo.com via HTTP; Tue, 25 Nov 2003 08:34:57 PST Date: Tue, 25 Nov 2003 08:34:57 -0800 (PST) From: IEJMD >yahoo.com> Subject: CCL: IECMD 2003 - Program for the second day, November 25, 2003 To: chemistry<>ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii 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) Internet Electronic Conference of Molecular Design 2003, IECMD 2003, November 23 - December 6, http://www.biochempress.com All accepted papers are posted on the Web and can be downloaded as PDF files from http://www.biochempress.com All discussions of the IECMD 2003 papers will take place on the Web, using the Yahoo! group iecmd2003, http://groups.yahoo.com/group/iecmd2003 Please visit the IECMD 2003 discussion site at http://groups.yahoo.com/group/iecmd2003 to sign-up and send comments to the group. Program for the second day, November 25, 2003 1. IECMD 2003, paper 22 On the Existence of the Butterfly Isomer of Al2H2: Ab Initio Coupled-Cluster Study Jerzy Moc and Maria Wierzejewska 2. IECMD 2003, paper 44 Convergence Improvement Of Two-electron Four-center Coulomb And Exchange Integrals Over Slater-Type Orbitals Hassan Safouhi and Lilian Berlu 3. IECMD 2003, paper 23 Reaction Constants Derived from Activation Parameters for the Evaluation of Substituent and Solvent Effects Ferenc Ruff 4. IECMD 2003, paper 52 A graphical similarity function to help ligand docking to proteins based on the Molecular Lipophilicity Potential. The case of the D2 dopamine receptor Pierre-Alain Carrupt, Isabelle Raynaud, David McLoughlin, Geraldine Bouchard, Patrick Gaillard, Frederic Billois, Patrizia Crivori, Philip G. Strange, and Bernard Testa 5. IECMD 2003, paper 2 TOPS-MODE Versus DRAGON Descriptors in QSAR. 1. Skin Permeation Maykel Perez Gonzalez and Aliuska Morales Helguera 6. IECMD 2003, paper 58 An application of Multi-variate adaptive regression splines (MARS) in QSRR R. Put, D.L. Massart, and Y. Vander Heyden ===== Dr. Ovidiu Ivanciuc Sealy Center for Structural Biology Department of Human Biological Chemistry & Genetics University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-1157 USA __________________________________ Do you Yahoo!? Free Pop-Up Blocker - Get it now http://companion.yahoo.com/ From chemistry-request@ccl.net Tue Nov 25 11:18:41 2003 Received: from real.cyf-kr.edu.pl (real.cyf-kr.edu.pl [149.156.2.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPGI9NL005775 for >ccl.net>; Tue, 25 Nov 2003 11:18:10 -0500 Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by real.cyf-kr.edu.pl (8.11.6/8.11.6) with ESMTP id hAPGHgg26105 for >ccl.net>; Tue, 25 Nov 2003 17:17:42 +0100 X-RAV-AntiVirus: This e-mail has been scanned for viruses on host: real.cyf-kr.edu.pl Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id RAA10907; Tue, 25 Nov 2003 17:17:41 +0100 (MET) Date: Tue, 25 Nov 2003 17:17:41 +0100 (MET) From: Marcin Krol >cyf-kr.edu.pl> To: chemistry<>ccl.net Subject: Polarization in proteins Message-ID: >kinga.cyf-kr.edu.pl> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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) Dear All, I am interested in calculating polarization effects (changes in partial charges) on conformational changes in proteins. I know that there are many potentials for polarizable water (and other small molecules) models but I am looking for a (preferably free) program/forcefield that uses electonegativity equalization method and is parametrized for proteins. I would also be grateful for any links to relevant papers. Thank you in advance marcin From chemistry-request@ccl.net Tue Nov 25 12:38:08 2003 Received: from gothmog.gpcc.itd.umich.edu (gothmog.gpcc.itd.umich.edu [141.211.2.180]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPHbbNL008948 for ; Tue, 25 Nov 2003 12:37:37 -0500 Received: from rygar.gpcc.itd.umich.edu (rygar.gpcc.itd.umich.edu [141.211.2.202]) by gothmog.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id MAA07728 for ; Tue, 25 Nov 2003 12:37:36 -0500 (EST) Received: from localhost (jyudenfr@localhost) by rygar.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id MAA02212 for ; Tue, 25 Nov 2003 12:37:36 -0500 (EST) Precedence: first-class Date: Tue, 25 Nov 2003 12:37:36 -0500 (EST) From: Joslyn Y Kravitz X-X-Sender: jyudenfr:at:rygar.gpcc.itd.umich.edu To: CHEMISTRY:at:ccl.net Subject: Re: CCL:D orbitals in Gaussian In-Reply-To: <000c01c3b06d$db989680$0901a8c0@mmserver> Message-ID: References: <001101c3b061$881f8830$80e12844@Garfield> <000c01c3b06d$db989680$0901a8c0@mmserver> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,REFERENCES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I have received some helpful responses to my question about orienting orbitals in Gaussian. The main suggestions had to do with symmetry, but since my molecules are C1, that doesn't come into play. What does come into play is the "NoSymmetry" keyword. This is not the same as "GUESS=NoSymm" which has to do with the symmetry of the initial guess. This "NoSymmetry" command tells Gaussian, "I don't care what you think the major symmetry element is, I want my molecule to stay just the way I entered it!" Or more formally, it prevents gaussian from putting the coordinates into the standard orientation, so it uses the input coordinates all the way through. Thanks all, Joslyn Kravitz >===== Original Message From Joslyn Kravitz ===== >Hello, > >For some time I have been trying to use Gaussian to calculate the >molecular orbitals for some vanadyl compounds. I want to see which atomic >orbitals from the V are contributing to the homo, somo and lumo. I have >obtained lovely pictures of the MO's but I want to be able to quantify >the atomic orbital contributions. According to an e-mail I received from >the help line at Gaussian the orbitals are numbered like this: > >d0 = z^2 (really 3z^2-r^2) >d+1 = xz >d-1 = yz >d+2 = x^2 - y^2 >d-2 = xy > >Unfortunately, since Gaussian puts the molecules into the standard >orientation the atomic orbital names in the output no longer correspond >to the ones you normally think of based on symmetry. That is, you would >expect the dz^2 to be oriented along the V=O bond and all the others to >fall in place around it, but that doesn't seem to be true. The dz^2 >orbital is oriented along whatever random direction is designated the z >axis in the "standard orientation" and then the other orbitals fall in >around that. Unfortunately, that makes interpreting the results a little >difficult, especially when different compounds are oriented differently, >so that the atomic orbitals are not named consistently between compounds. > >I have tried using input coordinates that place the V=O bond along a >z-axis and setup the equatorial plane in an appropriate way and then >running a "NoSymm" calc, but that doesn't seem to help at all. Does >anyone know how I can convert my calculated orbitals to more "chemically >intuitive" ones, or at the very least, force Gaussian to not reorient the >molecule? > >Thank you, >Joslyn Kravitz >Depart. Of Chem. >University of Michigan From chemistry-request@ccl.net Tue Nov 25 12:47:13 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 hAPHkfNL009356 for ; Tue, 25 Nov 2003 12:46:42 -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 <0HOX00D785DUZM!at!mailserver.unimi.it> for chemistry!at!ccl.net; Tue, 25 Nov 2003 18:46:42 +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 <0HOX00CSV5DQDX!at!smtp.unimi.it> for chemistry!at!ccl.net; Tue, 25 Nov 2003 18:46:38 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 933E114792; Tue, 25 Nov 2003 18:59:31 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 632A81478F; Tue, 25 Nov 2003 18:59:31 +0100 (CET) Date: Tue, 25 Nov 2003 18:59:29 +0100 (CET) From: Alessandro Contini Subject: Re: CCL:how to read HyperChem HCS file In-reply-to: <1069770501.3fc367057aad8!at!webmail.duke.edu> To: Jieru Zheng Cc: chemistry!at!ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=GB2312 References: <1069770501.3fc367057aad8!at!webmail.duke.edu> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,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 hAPHlDNL009370 Hi, you can open the *.HCS files from the same Conformational Search Box where you launched the calculation: > From the Hyper7 "Compute" menu choose "Conformational Search" -> the box opens -> from the box "File" menu choose "Open" and search your .HCS file Reguards Alessandro Contini On Tue, 25 Nov 2003, Jieru Zheng wrote: > Dear all, > > I have been using HyperChem7 to do conformation search. The output was saved > in a default file format (.HCS) But I don't know how to open the file and read > those structures generated from the conformation search. Would anybody please > help? > > Thanks a lot! > > > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > 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 From chemistry-request@ccl.net Tue Nov 25 13:46:20 2003 Received: from hellmouth2.gatech.edu (hellmouth2.gatech.edu [130.207.165.162]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPIjmNL011412 for ; Tue, 25 Nov 2003 13:45:49 -0500 Received: from hellmouth2.gatech.edu (localhost [127.0.0.1]) by hellmouth2.gatech.edu (Postfix) with SMTP id 29DA6A8CD for ; Tue, 25 Nov 2003 13:45:48 -0500 (EST) (envelope-from ok16!at!mail.gatech.edu) Received: from acmey.gatech.edu (acmey.prism.gatech.edu [130.207.171.27]) by hellmouth2.gatech.edu (Postfix) with ESMTP id B1F16A6FB for ; Tue, 25 Nov 2003 13:44:30 -0500 (EST) (envelope-from ok16!at!mail.gatech.edu) Received: by acmey.gatech.edu (Postfix, from userid 11564) id 7248631F25; Tue, 25 Nov 2003 13:44:30 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by acmey.gatech.edu (Postfix) with ESMTP id 69D4A330FB for ; Tue, 25 Nov 2003 13:44:30 -0500 (EST) (envelope-from ok16!at!mail.gatech.edu) Date: Tue, 25 Nov 2003 13:44:30 -0500 (EST) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Subject: summary of energy decomposition method Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.1 required=7.0 tests=FROM_ENDS_IN_NUMS,MAILTO_TO_SPAM_ADDR,USER_AGENT_PINE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers; The summary of the answers for my question about energy decomposition methods is as follows. ----------------------------------------------------------------------- Date: Tue, 18 Nov 2003 13:47:54 -0700 From: Tapas Kar To: Ohyun Kwon , chemistry!at!ccl.net Subject: RE: energy decomposition method Hi, One such possibility is Gamess(USA) for Morokuma energy decomposition scheme. Thanks, Tapas --------------------------------------------------------------------------- Date: Tue, 18 Nov 2003 23:49:24 +0100 From: Fabrice Leclerc To: Ohyun Kwon Subject: Re: CCL:energy decomposition method The NBO package (NBO 5.0, http://www.chem.wisc.edu/~nbo5) allows to run natural energy decomposition analysis (NEDA). The energy decomposition is calculated in a different way with respect to Morokuma analyses (see bibliography from GlendeningTimes New Roman). It does often converge easier and faster. I recommend the method particularly for big or complex systems. The program can be interfaced to GAMESS(US), GAUSSIAN and other QM packages. -------------------------------------------------------------------------- Date: Wed, 19 Nov 2003 08:54:07 +0100 From: Stan van Gisbergen To: Ohyun Kwon Cc: chemistry!at!ccl.net Subject: Re: CCL:energy decomposition method Dear Dr. Kwon, The Amsterdam Density Functional (ADF) program (http://www.scm.com) uses an adaptation of Morokuma's bond energy decomposition to the Kohn-Sham molecular orbital method, which works also for unrestricted calculations. This leads to a split up of the bond energy in electrostatic energy, steric repulsion, Pauli repulsion, and orbital interactions. The latter are symmetry decomposed according to the Ziegler transition state method. Best regards, Stan van Gisbergen, Scientific Computing & Modelling ----------------------------------------------------------------------------- Date: Wed, 19 Nov 2003 09:38:28 +0100 From: "Gerd [iso-8859-1] Rther" To: Ohyun Kwon Subject: Re: CCL:energy decomposition method Hi, you can use the Program Apost by Istvan Mayer a posteriori if you have http://occam.chemres.hu/programs/ see the readme files there and an accepted paper "An exact chemical decomposition scheme for the molecular energy" by Istvan Mayer, which will appear in Chem. Phys. Letters. Gerd ------------------------------------------------------------------------------- Date: Wed, 19 Nov 2003 10:23:14 +0100 From: Marcel Swart To: Ohyun Kwon Cc: chemistry!at!ccl.net Subject: Re: CCL:energy decomposition method One of the strong points of ADF (http://www.scm.com) is its energy decomposition analysis, see also: F.M. Bickelhaupt and E.J. Baerends, "Kohn-Sham Density Functional Theory: Predicting and Understanding Chemistry" In: Rev. Comput. Chem.; Lipkowitz, K. B. and Boyd, D. B., Eds.; Wiley-VCH: New York, 2000, Vol. 15, 1-86. ----------------------------------------------------------------------------- Date: Thu, 20 Nov 2003 14:27:00 +0100 From: marquez!at!us.es To: ohyun.kwon!at!chemistry.gatech.edu Subject: CCL: energy decomposition analysis Hi, Besides the Morokuma analysis there is also the CSOV (Constrainded Space Orbital Variations) energy decomposition analysis from Paul Bagus. It allows you to decompose the interaction energy between two fragments in terms of polarization of each fragment an charge transfer from one fragment to the other one. It is currently implemented in the HONDO program and currently I'm working in extending the analysis to allow one of the fragments to be described by a multireference wavefunction. If you are interested let me know. Yours, -- Dr. Antonio M. Marquez Dpt. of Physical Chemistry Dpto. de Quimica Fisica University of Seville Universidad de Sevilla E-41012 Seville (SPAIN) 41012-Sevilla Phone: 34-95-4557177 FAX: 34-95-4557174 -- Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon!at!chemistry.gatech.edu From chemistry-request@ccl.net Tue Nov 25 12:49:27 2003 Received: from gate002.lsu.edu (gate002.ocs.lsu.edu [130.39.184.137]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAPHmuNL009448 for ; Tue, 25 Nov 2003 12:48:56 -0500 From: Lacramioara Negureanu To: chemistry..at..ccl.net Subject: thermochemistry with NwChem Sensitivity: Date: Tue, 25 Nov 2003 11:48:52 -0600 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 version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello I would like to use NwChem to calculate ( ab initio) thermochemical data ( enthalpy, entropy, electronic energy) ; There is any way to get these energyes , besides vibrational frequencies, with NwChem??? I would really appreciate any help lacra From chemistry-request@ccl.net Tue Nov 25 20:02:09 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQ11aNL006209 for ; Tue, 25 Nov 2003 20:01:37 -0500 To: chminf-l:at:listserv.indiana.edu, chemistry:at:server.ccl.net, qsar_society:at:accelrys.com Subject: 2nd call for papers - CINF program - ACS 227th at Anaheim MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 From: Osman F Guner Message-ID: Date: Tue, 25 Nov 2003 17:01:34 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 11/25/2003 17:01:38, Serialize complete at 11/25/2003 17:01:38 Content-Type: multipart/alternative; boundary="=_alternative 00054AA588256DEA_=" X-Spam-Status: No, hits=2.1 required=7.0 tests=HTML_10_20,HTML_FONT_BIG,HTML_FONT_FACE_ODD,HTML_MESSAGE version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 00054AA588256DEA_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable There are still several openings for papers and the submission deadline is = approaching rapidly!=20 We invite you to submit a paper at the chemical information division at=20 227th ACS National Meeting at Anaheim, California. The symposia in the=20 CINF program are listed below. Contact the session organizer for any=20 questions. Please use the OASYS to submit your abstract. The system will = be closed for external submissions after December 1st 2003. 1. Enter the author submittal site at http://oasys.acs.org/oasys.htm. 2. Click the link to the CINF division, and select the appropriate=20 symposium 3. Follow the prompts to submit an abstract. Anaheim, March 28-April 1, 2004 Division of Chemical Information Program Chair: O. F. G=FCner, Accelrys Inc, 9685 Scranton Road, San Diego, = CA 92121-3752, 858-799-5341, fax 858-799-5100, e-mail: osman:at:accelrys.com=20 Advances in pharmacophores and 3D searching (Cosponsored with comp and=20 medi). O. F. G=FCner Chemical information needs for industrial and engineering chemistry=20 (Cosponsored with iec). T. Wright, MDL Information Systems, Inc, 14600=20 Catalina Street, San Leandro, CA 94577, 510-357-2222, fax 510-614-3652,=20 e-mail: terryw:at:mdli.com CINF serves SCHB: Patent information for small chemical businesses=20 (Cosponsored with chal, schb and bmgt). A. Engel, Paterra, Inc, 526 N=20 Spring Mill Road, Villanova, PA 19085-1928, 610-527-4500, fax=20 610-527-2041, e-mail: aengel:at:paterra.com Electronic Lab Notebooks R. Lysakowski Jr., Executive Director,=20 Collaborative Electronic Notebook Systems Association, 800 West Cummings=20 Park, Suite 5400, Woburn, MA 01801, 781-935-9600, fax 781-935-3113,=20 e-mail: rich:at:censa.org Environmental Chemistry: Where to find your information (Cosponsored with=20 envr and toxi). E. Kajosalo, Libraries, Massachusetts Institute of=20 Technology, 77 Masschusetts Avenue, Room 14S-134, Cambridge, MA 02155,=20 617-253-9795, fax 617-253-6365, e-mail: kajosalo:at:mit.edu General papers O. F. G=FCner How do the changes in 21-CFR part 11 affect you? (Cosponsored with anyl,=20 chas, laba and medi). D. A. Evans, MDL Information Systems, 14600 Catalina = Street, San Leandro, CA 94577, 510-357-2222 x1145, fax 510-614-3651,=20 e-mail: davide:at:mdli.com Informatics challenges in Nanotechnology (Cosponsored with pres, comp and=20 inor). S. C. McGrother, Accelrys Inc, 9685 Scranton Rd, San Diego, CA=20 92121, 858-799-5355, fax 858-799-5100, e-mail: smcgrother:at:accelrys.com Poster session O. F. G=FCner Research collaboratories, virtual laboratories, and Grid computing=20 (Cosponsored with CSA Trust) G. Grethe, Consultant, 352 Channing Way,=20 Alameda, CA 94502-7409, 510-333-7526, fax 510-865-5152, e-mail:=20 ggrethe:at:comcast.net; W. A. Warr, Wendy Warr & Associates, 6 Berwick Court, = Holmes Chapel, Cheshire, CW4 7HZ, United Kingdom, 011 44 1477 533837, fax=20 +44-1477-533837, e-mail: wendy:at:warr.com The bigger picture: linking bioinformatics to cheminformatics (Cosponsored = with biot, medi and comp). M. A. Miller, Consultant, 955 Ridge Hill Lane,=20 Suite 30, Midvale, UT 84047, 801 569 1390, fax 801 365 3949, e-mail:=20 ChemMitch:at:yahoo.com Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman:at:accelrys.com, http://www.accelrys.com --=_alternative 00054AA588256DEA_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
There are still several openings for pape= rs and the submission deadline is approaching rapidly!

We invite you to submit a paper at the ch= emical information division at 227th ACS National Meeting at Anaheim, California.  The symposia in the CINF program are listed below.  Contact the session organizer for any questions.  Please use the OASYS to submit your abstract.  The system will be closed for external submissi= ons after December 1st 2003.

1. Enter the author submittal site at http= ://oasys.acs.org/oasys.htm.
2. Click the link to the CINF division, and select the appropriate symposiu= m
3. Follow the prompts to submit an abstract.

Anaheim,

March 28-April 1, 2004

Division of Chemical Informa= tion


Program Chair: O. F. G=FCner, A= ccelrys Inc, 9685 Scranton Road, San Diego, CA 92121-3752, 858-799-5341, fax 858-79= 9-5100, e-mail: osman:at:accelrys.com

Advances in pharmacophores and 3D searching (Cosponsored with comp and medi). O. F. G=FCner

Chemical information needs for industrial and engineering chemistry (Cosponsored with iec). T. Wright, MDL Information Systems, Inc, 14600 Catalina Street, San Leandro, CA 94577, 510-357-2222, fax 510-614-3652, e-mail: terryw:at:mdli.com

CINF serves SCHB: Patent in= formation for small chemical businesses (Cosponsored with chal, schb and bmgt). A. Engel, Paterra, Inc, 526 N Spring Mill Road, Villanova, PA 19085-1928, 610-527-4500, fax 610-527-2041, e-mail: aengel:at:paterra.com

Electronic Lab Notebooks R. Lysakowski Jr., Executive Director, Collaborative Electronic Notebook Systems Association, 800 West Cummings Park, Suite 5400, Woburn, MA 01801, 781-935-9600, fax 781-935-3113, e-mail: rich:at:censa.org

Environmental Chemistry: Wh= ere to find your information (Cosponsored with envr and toxi). E. Kajosalo, Libraries, Massachusetts Institute of Technology, 77 Masschusetts Avenue, Room 14S-134, Cambridge, MA 02155, 617-253-9795, fax 617-253-6365, e-mail: kajosalo:at:mit.edu

General papers O. F. G=FCner

How do the changes in 21-CFR part 11 affect you? (Cosponsored with anyl, chas, laba and medi). D. A. Evans, MDL Information Systems, 14600 Catalina Street, San Leandro, CA 94577, 510-357-2222 x1145, fax 510-614-3651, e-mail: davide:at:mdli.com

Informatics challenges in N= anotechnology (Cosponsored with pres, comp and inor). S. C. McGrother, Accelrys Inc, 9685 Scranton Rd, San Diego, CA 92121, 858-799-5355, fax 858-799-5100, e-mail: smcgrother:at:accelrys.com

Poster session O. F. G=FCner

Research collaboratories, v= irtual laboratories, and Grid computing (Cosponsored with CSA Trust) G. Grethe, Consultant, 352 Channing Way, Alameda, CA 94502-7409, 510-333-7526, fax 510-865-5152, e-mail: ggrethe:at:comcast.net; W. A. Warr, Wendy Warr & Associates, 6 Berwick Court, Holmes Chapel, Cheshire, CW4 7HZ, United Kingd= om, 011 44 1477 533837, fax +44-1477-533837, e-mail: wendy:at:warr.com

The bigger picture: linking bioinformatics to cheminformatics (Cosponsored with biot, medi and comp). M. A. Miller, Consultant, 955 Ridge Hill Lane, Suite 30, Midvale, UT 84047, 801 569 1390, fax 801 365 3949, e-mail: ChemMitch:at:yahoo.com




Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman:at:accelrys.com, http://www.accelrys.com --=_alternative 00054AA588256DEA_=--