From chemistry-request@ccl.net Tue Mar 2 01:39:44 2004 Received: from europa.pnl.gov (europa.pnl.gov [130.20.248.195]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i226dhd4006212 for ; Tue, 2 Mar 2004 01:39:44 -0500 Received: from emailfilter1.pnl.gov (emailfilter1.pnl.gov [130.20.248.23]) by pnl.gov (PMDF V6.2-X17 #30796) with ESMTP id <0HTX00A5X6F2X5_at_pnl.gov> for chemistry_at_ccl.net; Mon, 01 Mar 2004 14:57:02 -0800 (PST) Received: from pnlmse21.pnl.gov (Not Verified[130.20.128.55]) by emailfilter1.pnl.gov with NetIQ MailMarshal (v5.5.5.8) id ; Mon, 01 Mar 2004 14:57:02 -0800 Received: from pnlmse26.pnl.gov ([130.20.128.51]) by pnlmse21.pnl.gov with Microsoft SMTPSVC(5.0.2195.6713); Mon, 01 Mar 2004 14:57:02 -0800 Date: Mon, 01 Mar 2004 14:57:02 -0800 From: ^PNNL EMSL MSCF Subject: MSCF 2005 Call-for-Proposals in Environmental Molecular Science Computational Grand Challenge Applications To: chemistry_at_ccl.net Message-id: <49F10672DADC2C4F9F6C8BBD1384FFC602B60027_at_pnlmse26.pnl.gov> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.6375.0 Content-type: text/plain; charset=us-ascii Thread-Topic: MSCF 2005 Call-for-Proposals in Environmental Molecular Science Computational Grand Challenge Applications Thread-Index: AcP9gkbRGAOzfSM8REqSrVLm6TKrqgCXYLXQ Content-Class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 01 Mar 2004 22:57:02.0838 (UTC) FILETIME=[82C79160:01C3FFE0] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i226did4006213 > Richland, WA - The Molecular Science Computing Facility (MSCF) in the > William R. Wiley Environmental Molecular Sciences Laboratory at the > Pacific Northwest National Laboratory announces the 2005 > Call-for-Proposals (for allocations of computer time) for > Computational Grand Challenge Applications (CGCA) in environmental > molecular science research areas that address the environmental > problems and research needs facing the U.S. Department of Energy (DOE) > and the Nation. This call includes research applications in biology, > chemistry, climate and subsurface science and is open to all research > entities regardless of research funding source. Computer allocations > for CGCAs are for three years, with the computer allocation > appropriate for the scope of research to be performed. > Letter-of-Intent is due April 16, 2004 with final proposals due May > 31, 2004. Announcement of awards are expected September 1, 2004. > Further information on the CGCA Call-for-Proposals is available at > http://mscf.emsl.pnl.gov . The MSCF houses an 11.8 Teraflop HP Linux > Itanium2 Cluster with 980 nodes/1960 processors. The MSCF also has a > suite of computational chemistry software (Molecular Science Software > Suite) designed to take advantage of the new HP. We seek research > applications that will use a significant portion of this computational > resource. > The William R. Wiley Environmental Molecular Sciences Laboratory > (EMSL) http://www.emsl.pnl.gov is a user research facility funded by > the Office of Biological and Environmental Research in the U.S. > Department of Energy. As a National Scientific User Facility, the > mission of the EMSL is to provide advanced and unique resources to > scientists engaged in research in the environmental molecular sciences > and educate young scientists in the molecular sciences to meet the > demanding environmental challenges of the future. As a research > organization, the EMSL provides scientific recourses to attain a > molecular-level understanding of the physical, chemical and biological > processes needed to solve critical environmental problems and advance > molecular science in support of the long-term environmental missions > of DOE and the Nation. Both computational and experimental resources > are available to users at "no cost". > > Donald R. Jones, Ph.D. > Technical Leader > MSCF - Visualization and User Services > Environmental Molecular Science Laboratory > Pacific Northwest National Laboratory > 906 Battelle Blvd, MS K8-91 > Richland, WA 99352 > Phone: 509-376-3013 Email: dr.jones_at_pnl.gov > Fax: 509-376-0420 Web: http://mscf.emsl.pnl.gov > "Try not to be a man of success, but try to be a man of value." > Albert Einstein > > From chemistry-request@ccl.net Mon Mar 1 22:10:25 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i223APd4025823 for ; Mon, 1 Mar 2004 22:10:25 -0500 Received: from uci.edu (dhcp-204233.bio.uci.edu [128.200.204.233]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i223BkO1029615 for ; Mon, 1 Mar 2004 19:11:48 -0800 Message-ID: <4043FB6E.8010708_at_uci.edu> Date: Mon, 01 Mar 2004 19:11:42 -0800 From: Qiang Lu Reply-To: qiangl_at_uci.edu Organization: Biology and Biochemistry Department User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: zh-cn, en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: Is there a scale factor for dipole moment? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found Hi CCLers I know there are scales factors for frequencies and ZPE/Thermal. But is there scale factor for dipole moment in the gaussian simulations? Qiang From chemistry-request@ccl.net Tue Mar 2 02:13:54 2004 Received: from kuzey.cc.boun.edu.tr (kuzey.cc.boun.edu.tr [193.140.192.30]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i227Dld4007673 for ; Tue, 2 Mar 2004 02:13:52 -0500 Received: (qmail 80104 invoked from network); 2 Mar 2004 07:12:17 -0000 Received: from unknown (HELO guardian2.cc.boun.edu.tr) (193.140.192.10) by 0 with SMTP; 2 Mar 2004 07:12:17 -0000 Received: from saritepe.cc.boun.edu.tr ([193.140.192.31]) by guardian2.cc.boun.edu.tr (SAVSMTP 3.1.2.35) with SMTP id M2004030209121731435 for ; Tue, 02 Mar 2004 09:12:17 +0200 Received: (qmail 44028 invoked by uid 80); 2 Mar 2004 10:25:50 -0000 Received: from 193.140.78.22 ([193.140.78.22]) by webmail.boun.edu.tr (IMP) with HTTP for ; Tue, 2 Mar 2004 10:25:50 +0000 Message-ID: <1078223150.4044612eec74d:at:webmail.boun.edu.tr> Date: Tue, 2 Mar 2004 10:25:50 +0000 From: Kevser Gocmen Topal To: "chemistry:at:ccl.net" Subject: CCL:Locating transition structures MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 Hi all, I am trying to locate an transition structure. I have a single point run with the probable geometry of ts and it includes the expected imaginary frequency as the lowest eigen value. However the full optimization of the ts have failed to locate this frequency. With the check point file on hand how can i locate this transition structure? I would like to learn also about the EF option of the opt keyword. I have run a `opt=ts,ef...` calculation but it has failed with the following error after readin the guess from the check file. --- Recover connectivity data from disk. EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF- EIGENVECTOR FOLLOWING TRANSITION STATE SEARCH INITIALIZATION PASS FileIO operation on non-existent file. ileIO: IOper= 2 IFilNo(1)= -507 Len= 170002 IPos= 0 Q= ...... --------- and my input file is ------- %mem=256MB %chk=FoneMe.chk %nosave #b3lyp/6-31g* opt=(ts,readfc,EF) freq Guess=read geom=allcheck FoneMe -1 1 ------ Thanks in advance Yours. -- Kevser Gocmen Topal Bogazici University Department of Chemistry 34342 Bebek ISTANBUL Phone: +90 2123581540#2379 Knowledge speaks, but wisdom listens From chemistry-request@ccl.net Mon Mar 1 20:19:19 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i221JJd4021666 for ; Mon, 1 Mar 2004 20:19:19 -0500 Received: from cornell.edu (67-41-169-107.slkc.qwest.net [67.41.169.107]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i221KWt8020515; Mon, 1 Mar 2004 20:20:47 -0500 (EST) Message-ID: <4043E15E.5040209/at/cornell.edu> Date: Mon, 01 Mar 2004 18:20:30 -0700 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry/at/ccl.net" Subject: SDF files Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.5.0.90627, Antispam-Core: 4.0.4.92622, Antispam-Data: 2004.3.1.93161 Hi all I'm trying to glean the structures out of some SDF files that I have. I have 3 databases that have structures in them, and I'm trying to get the structures out of them. I've downloaded the SDF toolkit and the program CACTUS, but neither of those are helping me. I can get both programs to read the first structure, but I can't get any further than that. Any suggestions on how to do this, including any other programs that could be of help (free would be the best) would be most welcome. Thanks in advance, Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Tue Mar 2 02:31:06 2004 Received: from sohumx05.sohu.com ([61.135.145.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i227V0d4008367 for ; Tue, 2 Mar 2004 02:31:05 -0500 Received: from mx33.mail.sohu.com (unknown [192.168.41.183]) by sohumx05.sohu.com (Postfix) with ESMTP id 44B2757E8D for ; Tue, 2 Mar 2004 15:32:29 +0800 (CST) Message-ID: <4795240.1078212748602.JavaMail.postfix^at^mx33.mail.sohu.com> Date: Tue, 2 Mar 2004 15:32:28 +0800 (CST) From: To: Subject: Can you give me some papers about aim2000? Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-Mailer: Sohu Web Mail 2.0.13 X-SHIP: 221.137.8.118 X-Priority: 3 X-SHMOBILE: 0 X-SHBIND: 0 Dear CCLer, Can you give me some papers about AIM2000? Thank you for advance! Li Qiang Shanghai Institute of Organic Chemistry Chinese Academy of Science No. 354, Road Fenglin Shanghai, 200032, China Tel: 0862164163300-2753 Fax: 0862164166128 E-mail: liqiang^at^pub.sioc.ac.cn From chemistry-request@ccl.net Tue Mar 2 07:17:15 2004 Received: from linus.imcm.cas.cz (Linus.imcm.cas.cz [147.231.77.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i22CHEd4024610 for ; Tue, 2 Mar 2004 07:17:14 -0500 Received: from localhost (ccl@localhost) by linus.imcm.cas.cz (8.9.3/8.9.3) with ESMTP id NAA05981 for ; Tue, 2 Mar 2004 13:18:40 +0100 Date: Tue, 2 Mar 2004 13:18:40 +0100 (CET) From: Petr Toman To: CHEMISTRY-.at.-ccl.net Subject: CCL: IRC in Gaussian 98 stops at false minimum Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, I would like to calculate the reaction path from a transition structure of a merocyanine molecule (37 atoms). Transition point was verified by a Freq calculation, imaginary frequency is 43 cm-1. The problem is that IRC calculation stops after very few points reporting "Minimum found on this side of the potential". However, usual geometry optimization (OPT) starting at this point finds the actual minimum far away. My question is what is the criterion for a minimum in Gaussian IRC calculation? Thank you for your help. Best regards, Petr Toman From chemistry-request@ccl.net Tue Mar 2 05:56:27 2004 Received: from mx.physto.se (syslx11.physto.se [130.237.208.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i22AuQd4019488 for ; Tue, 2 Mar 2004 05:56:27 -0500 Received: from localhost (localhost [127.0.0.1]) by mx.physto.se (Postfix) with ESMTP id 796222FA40 for ; Tue, 2 Mar 2004 11:57:55 +0100 (CET) Received: from mx.physto.se ([127.0.0.1]) by localhost (syslx11.physto.se [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 29591-10 for ; Tue, 2 Mar 2004 11:57:55 +0100 (CET) Received: from qcplx04.physto.se (qcplx04.physto.se [130.242.128.83]) by mx.physto.se (Postfix) with ESMTP id 495FC2FA2C for ; Tue, 2 Mar 2004 11:57:55 +0100 (CET) Date: Tue, 2 Mar 2004 11:57:55 +0100 (CET) From: Tomasz Borowski To: chemistry!at!ccl.net Subject: SCI-PCM in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new at physto.se Dear CCL Users, I'm looking for an explanation of the input format for the SCRF=SCIPCM method in Gaussian98/03. To be more specific, I'd like a description of the last three entries in the following line, which can be placed after the geometry section in the input: 78.39 0.0004 74 37 2 with best regards, Tomasz Borowski (borowski!at!physto.se) From chemistry-request@ccl.net Tue Mar 2 08:35:07 2004 Received: from irsun275.ifp.fr (ns2.ifp.fr [81.255.42.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i22DZ6d4029344 for ; Tue, 2 Mar 2004 08:35:07 -0500 Received: from smtp.ifp.fr by irsun275.ifp.fr (V35.12) with ESMTP Received: from irnts21.ifp.fr (irnts21 [156.118.15.51]) by irsun165.ifp.fr (8.8.5/8.8.5) with ESMTP id OAA06619 for ; Tue, 2 Mar 2004 14:36:34 +0100 (MET) Received: by irnts21.ifp.fr with Internet Mail Service (5.5.2657.72) id <1M6NZTRR>; Tue, 2 Mar 2004 14:36:33 +0100 Message-ID: <3AA99E087354D61185E4002048403CFC02145B55!at!irnts23.ifp.fr> From: DE BRUIN theodorus To: "'chemistry!at!ccl.net'" Subject: summary : calculation of pka valuse by ab initio methods Date: Tue, 2 Mar 2004 14:36:32 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i22DZ7d4029345 Dear CCLers, Recently, I've asked a question about calculation pKa values using ab initio methods (see below). For the moment I've received 3 replies: COSMO-RS is the only code I know that will deal with real solvents, beyond the zeroth order dielectric continuum... John McKelvey I am very skeptical of the ability of any current ab initio method to accurately calculate pKa's. Consider acetic acid. Its pKa is dominated by solvent effects and is largely determined by deltas and not deltaH. Wayne E. Steinmetz we recently published a calculation scheme for pKa (pKb will follow soon, prel. results can be obtained on request). We just calculated dG_diss based on DFT/COSMO and added the statistical thermodynamics contribution from COSMO-RS. We got a single very good linear correlation of dG_diss with pKa for a very broad range of organic and inorganic acids. It is probably the most accurate "ab initio" prediction of pKa. Nevertheless there is a serious problem with the slope of the regeression line which is discussed in detail in the paper: A. Klamt, F. Eckert, M. Diedenhofen, and M.E. Beck, "First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale", J. Phys. Chem. A., 107, 9380 - 9386 (2003) Andreas Klamt Orginal question: Dear CCLers, According to you, what is the best method to calculate absolute pKa values, i.e. without first deriving some linear semi-empirical equation for a training set, but to calculate pKa directly from the Delta G of the dissociation reaction. I would like to calculate pKa values for some medium sized molecules, NOT just in water, but in mixtures of water with alcohols for which experimental data are very sparse. I am aware that the calculated solvation energy for charged species can contain relatively big errors, affecting Delta G and finally resulting in errors of several units in the pKa value. According to some people, this problem can partially be overcome by applying continuum models in which explicitly some solvent molecules are taken up. Is DFT accurate enough, which continuum model is best, etc... -------- Theodorus de Bruin Institut Frangais du Pitrole Direction Chimie et Physico-Chimie Appliquies Dipartement Thermodynamique et Modilisation Moliculaire 1 & 4 Avenue de bois Preau 92852 Rueil-Malmaison Cedex Tel: +33 (0)1.47.52.54.38 Fax: +33 (0)1.47.52.70.58 From chemistry-request@ccl.net Tue Mar 2 11:21:47 2004 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 i22GLkd4005698 for ; Tue, 2 Mar 2004 11:21:46 -0500 Expiry-Date: Mon, 31 May 2004 -1:-1:-1 +0000 Reply-To: training!at!accelrys.com To: CHEMISTRY!at!ccl.net Cc: judith.madeley!at!accelrys.com Subject: CCL: Accelrys Customer Training in May MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Jeff Nauss Date: Tue, 2 Mar 2004 08:23:15 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 03/02/2004 08:23:17, Serialize complete at 03/02/2004 08:23:17 Content-Type: text/plain; charset="US-ASCII" Accelrys Inc. are holding the following training workshops at locations in the US and Europe during May. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic. MACROMOLECULAR MODELING Introduction to InsightII for Life Sciences 11-12 May in Burlington, MA Homology-Based Protein Design 13-14 May in Burlington, MA Structure Based Drug Design 17-18 May in Burlington, MA CHARMm 19-20 May in Burlington, MA Modeling of GPCR Proteins with InsightII 21 May in Burlington, MA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html CHEMINFORMATICS DS AccordEnterprise Client 10 May in San Diego, CA DS Accord for Excel Enterprise 11 May in San Diego, CA Accord Inventory 12 May in San Diego, CA Accord HTS 13 May in San Diego, CA DIVA 14 May in San Diego, CA Accord Enterprise Informatics Database Admin. 17-18 May in San Diego, CA For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html MATERIALS SCIENCE Introduction to Materials Studio 10 May in Cambridge, UK Introduction to Polymer Modeling 11- 12 May in Cambridge, UK Introduction to Quantum Mechanics 13-14 May in Cambridge, UK Workshop on Crystal Structure Determination 17 May in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html BIOINFORMATICS Wisconsin Package and SeqLab 25-26 May in Burlington, MA SeqWeb 27 May in Burlington, MA DS Gene 28 May in Burlington, MA For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-1761 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss!at!accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Tue Mar 2 04:25:19 2004 Received: from mail.intervet.com ([212.108.12.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i229PId4015164 for ; Tue, 2 Mar 2004 04:25:18 -0500 Received: (from root@localhost) by mail.intervet.com (8.9.3c/8.6.12) id KAA28019; Tue, 2 Mar 2004 10:26:42 +0100 (MET) Received: by mail.intervet.com (TUNIX txp2/smap) id sma025882; Tue, 2 Mar 04 10:25:10 +0100 Received: by inbexc0.inb.intra with Internet Mail Service (5.5.2653.19) id ; Tue, 2 Mar 2004 10:25:43 +0100 Message-ID: <199616BFDF195F489F36CCDC175777390ED15B@shmn04> From: "Oellien, F (Frank)" To: "'Richard Wood'" Cc: chemistry..at..ccl.net Subject: RE: SDF files Date: Tue, 2 Mar 2004 10:28:16 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i229PJd4015165 Hello Richard, you start with a SD File, right? What do you want to do with the structures? Are you searching for specific structures? If you are using CACTVS, do this: 1. Start csts 2. Write the following code set infile [molfile open your_sdfile.sdf r] molfile loop $infile ehandle { ... ... do somehting with the structure ... ... } In the body of the loop you can define various methods like Hashcode calculations, write the structures to other chemical exchange formats, modify them and so on. Bye Frank Dr. Frank Oellien Intervet Innovation GmbH | Akzo Nobel DrugDiscovery / BioChemInformatics Zur Propstei 55270 Schwabenheim Tel.: +49 (0)6130-948-365 Fax: +49 (0)6130-948-517 E-Mail: Frank.Oellien..at..intervet.com -----Original Message----- From: Richard Wood [mailto:rlw28..at..cornell.edu] Sent: Dienstag, 2. Mdrz 2004 02:21 To: chemistry..at..ccl.net Subject: CCL:SDF files Hi all I'm trying to glean the structures out of some SDF files that I have. I have 3 databases that have structures in them, and I'm trying to get the structures out of them. I've downloaded the SDF toolkit and the program CACTUS, but neither of those are helping me. I can get both programs to read the first structure, but I can't get any further than that. Any suggestions on how to do this, including any other programs that could be of help (free would be the best) would be most welcome. Thanks in advance, Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 -= 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, jlabanow..at..nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -------------------------------------- This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender. -------------------------------------- From chemistry-request@ccl.net Tue Mar 2 07:56:41 2004 Received: from pc15190.chemie.uni-marburg.de (pc15190.Chemie.Uni-Marburg.DE [137.248.152.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i22Cued4026851 for ; Tue, 2 Mar 2004 07:56:41 -0500 Received: from sg1503.chemie.uni-marburg.de (root..at..sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by pc15190.chemie.uni-marburg.de (8.12.11/8.12.9/schn) with ESMTP id i22Cw5AO006184 for ; Tue, 2 Mar 2004 13:58:06 +0100 Received: from lein.chemie.uni-marburg.de (pc15217.Chemie.Uni-Marburg.DE [137.248.152.51]) by sg1503.chemie.uni-marburg.de (8.12.10/8.12.10/schn) with ESMTP id i22Cw40l014717 for ; Tue, 2 Mar 2004 13:58:05 +0100 (MET) Received: from lein.chemie.uni-marburg.de (localhost [127.0.0.1]) by lein.chemie.uni-marburg.de (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id i22CtXdm006971 for ; Tue, 2 Mar 2004 13:55:33 +0100 Received: (from matthias@localhost) by lein.chemie.uni-marburg.de (8.12.3/8.12.3/Submit) id i22CtXrN006970 for chemistry..at..ccl.net; Tue, 2 Mar 2004 13:55:33 +0100 Date: Tue, 2 Mar 2004 13:55:33 +0100 From: Matthias Lein To: Computational Chemistry List Subject: 40th Symposium for Theoretical Chemistry Message-ID: <20040302125533.GA6936..at..chemie.uni-marburg.de> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-15 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.4.1i X-Spam-Status: No, hits=0.0 required=5.0 tests=none autolearn=no version=2.63-chemie_mr X-Spam-Checker-Version: SpamAssassin 2.63-chemie_mr (2004-01-11) on lorstein.chemie.uni-marburg.de X-Virus-Scanned: by amavisd-new Dear Colleagues, on behalf of the organisers Gernot Frenking and Max C. Holthausen, I have the pleasure and honour to announce that the 40th Symposium for Theoretical Chemistry will take place in Suhl/Germany, from September 19 to September 23. The topic will be Computational Chemistry. Further information on registration and participation can be found on: http://www.chemie.uni-marburg.de/stc2004/ The list of invited speakers includes: * Elfi Kraka: "The Central Role of the Self-Interaction Error in Density Functional Theory" * Frank Neese: "Theoretical Optical and Magnetic Spectroscopy of Open Shell Transition Metal Complexes of Relevance to Bioinorganic Chemistry" * Georg Schreckenbach: "Actinide Molecular Science - New Results" * Peter Schwerdtfeger: "From Relativity to Electroweak Interactions" * Kevin Naidoo: "Stretching Glycosidic Bonds to the Point of Breaking and Beyond" * Matthias Bickelhaupt: "Molecular Recognition in Catalysis and DNA Replication" * Georg Jansen: "Calculation and Modelling of Intermolecular Forces" * Eluthavingal Jemmis: "Electronic Structural Relationship between Boron and Carbon" * Christoph van W|llen: "Two-Component Relativistic Density Functional Calculations" * Frank Weinhold: "Unified Theory of Chemical Bonding Interactions in the Natural Bond Orbital Framework" * Robert Deeth: "Structure and Mechanism in Transition Metal Mediated Reactions" * Helge Kragh (After Dinner Lecture): "Chemical Elements, the Periodic System, and Early Quantum Chemistry" * Peter Janich (Opening Lecture, in German): "Theorie und Praxis. Zur Rolle einer alten Unterscheidung f|r die theoretische Chemie" Sincerely, Matthias Lein. -- Matthias Lein From chemistry-request@ccl.net Tue Mar 2 03:53:37 2004 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i228rUd4012359 for ; Tue, 2 Mar 2004 03:53:32 -0500 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id QAA18662 for ; Tue, 2 Mar 2004 16:41:27 +0800 Message-Id: <200403020841.QAA18662=at=mx1.ustc.edu.cn> Date: Tue, 2 Mar 2004 16:43:20 +0800 From: "6!Q8@W" Reply-To: dxl=at=mail.ustc.edu.cn To: CCL Subject: weak interaction systems with DFT Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i228rcd4012405 Dear CCL#: I have met some discussion about the calculations of the weak interaction systems with DFT(GGA) with the adsorption energy about 30 kJ/mol, such as the physical adsorption. Both the supported and unsupported opinions exist. Do anyone know the final conclusion? or recommend me some paper about this discussion. Thanks. Thank you for your help!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!Ding Xunlei !!!!!!!!!!!!!!!!!!!!!!!!!!!!2004-03-02 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl=at=mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl From chemistry-request@ccl.net Tue Mar 2 06:47:24 2004 Received: from mbu.iisc.ernet.in (mbu.iisc.ernet.in [144.16.74.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i22BlLd4022161 for ; Tue, 2 Mar 2004 06:47:23 -0500 Received: from mbu.iisc.ernet.in (localhost.localdomain [127.0.0.1]) by mbu.iisc.ernet.in (8.12.8/8.12.8) with ESMTP id i22Bmlil028634; Tue, 2 Mar 2004 17:18:47 +0530 Received: from localhost (gyan@localhost) by mbu.iisc.ernet.in (8.12.8/8.12.8/Submit) with ESMTP id i22BmjAU028630; Tue, 2 Mar 2004 17:18:46 +0530 Date: Tue, 2 Mar 2004 17:18:45 +0530 (IST) From: Gyanendra Kumar To: Richard Wood cc: "chemistry/at/ccl.net" Subject: Re: CCL:SDF files In-Reply-To: <4043E15E.5040209/at/cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Richard, You can try babel. you can seperate individual structures from a SDF database using this free program downloadable from the net. Gyan. On Mon, 1 Mar 2004, Richard Wood wrote: > Hi all > > I'm trying to glean the structures out of some SDF files that I have. I > have 3 databases that have structures in them, and I'm trying to get the > structures out of them. I've downloaded the SDF toolkit and the program > CACTUS, but neither of those are helping me. I can get both programs to > read the first structure, but I can't get any further than that. > > Any suggestions on how to do this, including any other programs that > could be of help (free would be the best) would be most welcome. > > Thanks in advance, > Richard > > -- ******************************************** Gyanendra Kumar (Research Student), Prof. A. Surolia's Lab, #204, Molecular Biophysics Unit, Indian Institute Of Science, Bangalore, PIN-560012.INDIA, Phone 91-80-22932389,22932714, 22932539(Res). http://mbu.iisc.ernet.in/~surolia/gyan.html ******************************************** Residence: R-17, Students Hostel, IISc. ********************************************