From chemistry-request@ccl.net Mon May 30 14:09:20 2005 Received: from rly06e.srv.mailcontrol.com (cluster-e.mailcontrol.com [217.79.216.190]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UI9G7Y022264 for ; Mon, 30 May 2005 14:09:16 -0400 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by rly06e.srv.mailcontrol.com (MailControl) with ESMTP id j4UI9BMG007000 for ; Mon, 30 May 2005 19:09:14 +0100 Importance: Normal X-Priority: 3 (Normal) Expiry-Date: Sun, 31 Jul 2005 -1:-1:-1 +0000 Reply-To: workshops () accelrys.com To: CHEMISTRY () ccl.net Subject: CCL: Accelrys Customer Training for July MIME-Version: 1.0 Sensitivity: X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 From: Jeff Nauss Message-ID: Date: Mon, 30 May 2005 11:09:09 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 05/30/2005 11:09:14 AM, Serialize complete at 05/30/2005 11:09:14 AM Content-Type: text/plain; charset="US-ASCII" X-Scanned-By: MailControl A-04-00-00-235 (www.mailcontrol.com) X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_RCVD_HELO autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Accelrys Inc. are holding the following training workshops during July. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. MODELING Intro to Life Science Modeling with Insight II 12-13 July San Diego, CA Homology-Based Protein Design 14-15 July San Diego, CA CHARMm 18-19 July San Diego, CA Structure Based Drug Design with InsightII 20-21 July San Diego, CA Protein-Protein Docking 26 July Online Introduction to DS Modeling 1.1 27-28 July San Diego, CA For course details and registration see: http://www.accelrys.com/services/training/macro/schedule.html RATIONAL DRUG DESIGN Structure Based Design with DS Modeling 1.2 29 July San Diego, CA For course details and registration see: http://www.accelrys.com/services/training/rdd/schedule.html Questions regarding scheduling and content should be directed to workshops () accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From chemistry-request@ccl.net Mon May 30 15:10:30 2005 Received: from hotmail.com (bay15-f30.bay15.hotmail.com [65.54.185.30]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UJAO5P024695 for ; Mon, 30 May 2005 15:10:24 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 30 May 2005 12:10:23 -0700 Message-ID: Received: from 62.135.70.67 by by15fd.bay15.hotmail.msn.com with HTTP; Mon, 30 May 2005 19:10:23 GMT X-Originating-IP: [62.135.70.67] X-Originating-Email: [rhhilal () hotmail.com] X-Sender: rhhilal () hotmail.com From: "R. Hilal" To: molecular-dynamics-news () jiscmail.ac.uk Cc: chemistry () ccl.net Subject: conference, Cairo March 5 Date: Mon, 30 May 2005 19:10:23 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed X-OriginalArrivalTime: 30 May 2005 19:10:23.0959 (UTC) FILETIME=[3B2B8E70:01C5654B] X-Spam-Status: No, score=2.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,MSGID_FROM_MTA_HEADER,RCVD_IN_NJABL_PROXY autolearn=no version=3.0.3 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear All Attached please find the call for paper announcement for the chemistry conference chem04 in cairo Egypt March 5-8th, 2006. The conference devotes a special session for femto second chemistry and molecular dynamics and another on Computational chemistry. Chem04 features a workshop infemtosecond chemistry and wave packet simulation on computer. The workshop will be kindly delivered by Prof. J. Manz, O. Kuehn and M.F.Shibl of the Free-university of Berlin Germany. You all are encoureged to contribute and join the conference. Hope to see you all in Cairo. Rifaat Hilal Conference Coordinator N.B. Note that the present announcement corrects the few mistakes appeared in an earler version submit by M.Shibl. Note in particular the titles of the Femtosecond invited lectures and the e-mail address of the conference. Invitation The Department of Chemistry, Faculty of Science, Cairo University is pleased to extend a cordial invitation to attend the Biannual Conference on Chemistry Chem.04. The venue for the Conference is the University of Cairo, and the scientific program will take place during the period from 5-8 March, 2006. This event provides a forum for fostering scientific exchange and collaboration. All interested chemists are encouraged to attend and contribute to the program. The conference will focus on new and emerging trends in chemistry. Original relevant aspects of biological, medicinal, stereochemistry, natural products and industrial chemistry will feature in a program which seeks to cater for a wide range of interests in contemporary chemistry and offers a visionary perspective on future challenges and opportunities in the subject. Special Sessions on Femtosecond chemistry Invited international lectures confirmed so far are: G. Gerber (Wuerzburg) Analysis and optimal control of chemical reactions H. Kauffmann (Vienna) EXPERIMENTAL FEMTOSECOND COHERENCE AND QUANTUM-STOCHASTIC OPTICAL DYNAMICS IN CONJUGATED POLYMERS J.-L. Martin ( Paris) Femtosecond dynamics in proteins A.D. Bandrauk ( Sherbrook) Quantum theory for femto- and attosecond chemistry O. Kuehn ( Berlin) Ultra fast quantum dynamics of hydrogen bonds: from gas to condensed phase K. Takatsuka ( Tokyo) Quantum electron dynamics in hydrogen bonds Workshops A one-day workshop will be conducted in each of the following areas: Thermal Analysis Mass Spectrometry NMR Techniques HPLC Techniques The registration in any of these workshops should be indicated in the conference application form. Conference registration entitles applicants to a 50% discount in the workshop registration fee. Informal Tutorial Pre-conference tutorial and workshop will be held on Saturday March 4th on Simulation of wave packet dynamics on the computer . It will address basic concepts for laser pulse analysis and control in femtosecond chemistry. The workshop will be delivered by J. Manz, O. Kuehn and M. F. Shibl of the Free University of Berlin, Germany. duration: 8 hrs..in addition to 2+2 hrs of follow-ups on March 6th and 7th . Exhibition Exhibitors are accepted on a first come first service basis. The Exhibition features are Publishers, Journals, Software, Laboratories Equipments, Computers and Chemical Industries. Accommodation Hotel reservation for participants will be available on request in various areas and rates, in addition to a limited number of rooms in the University Guesthouse. Request for reservation should be made as early as possible. Conference Fee The registration fee for Egyptians: L.E. 500 for participants. For Non-Egyptians the registration fee in $ 350. The registration fees for any of the workshops: L.E. 200. The registration fee for any of the tutorials: L.E. 100. The registration fee covers the scientific meetings, Lunches, Closing Banquet, Excursions or a City Tour. The proceedings of the conference and accommodation at the university guest house for non-Egyptrians. Payment of registration fee is made on site upon arrival or via The National Bank of Egypt, Cairo University Branch, Ac. No. 710517 Post conference Social Activity A one-day tripe will be organized to one of the resorts including comprehensive entertainment program. Reservation should be made as early as possible. For more information please visit our web site: www.chem-conference.org.eg Correspondence All inquiries should be addressed to Prof. Dr. Rifaat H. Hilal Department of Chemistry, Faculty of Science, Cairo University, Giza, A. R. Egypt. chem4-conf () chem_sci.cu.edu.eg The conference is under the patronage of the Islamic Educational, Scientific and Cultural Organization.(ISESCO) Scientific Program English will be the official language of the conference. Abstracts of all contributions will be published in a book, which will be distributed to all registrants upon arrival. The scientific program includes plenary, invited, keynotes, oral and poster presentations, panel discussions, tutorial and workshops which cover all aspects of chemistry, industrial chemistry and chemical education. Instructions for Authors The abstracts should be written camera-ready according to the following instructions: Titles in font size 16 bold, capitals in typeface. The name(s) of authors(s) and addresses in font size 14 bold. Left justified in Times New Roman, font size 12 using doc files. A4 size papers, single space. A margin of 3 cm should be left on the top and bottom and 3 cm on both right and left sides. Literature citations should follow the ACS style. Two original copies and a diskette of the full paper (win98 or higher) should be submitted. Cairo University Faculty of Science Biannual Conference on Chemistry Chem. 04 5-8 March 2006 Organized by The Department of Chemistry Under the Patronage of Prof. Amr Ezzat Salama Minister of Higher Education and Scientific Research Prof. Ali Abdulrahman President of Cairo University Chairman Prof. Hamdi M. Hassaneen Dean of the Faculty of Science Co-Chairmen Prof. M. M. Fathi Vice Dean Prof. Hamdi Hamouda Head of the Chemistry Department _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ _________________________________________________________________ Don't just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/ From chemistry-request@ccl.net Mon May 30 13:03:58 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UH3wJg019304 for ; Mon, 30 May 2005 13:03:58 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j4UH3wtv019303 for chemistry %a% ccl.net; Mon, 30 May 2005 13:03:58 -0400 Date: Mon, 30 May 2005 13:03:58 -0400 Message-Id: <200505301703.j4UH3wtv019303 %a% server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request %a% ccl.net using -f From: "Peter, , Politzer" To: chemistry %a% ccl.net X-Web-Message-Number: 050530130237-19209 Subject: W:Question for CCL members X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Can anyone suggest or direct me to a procedure for simulating the movements of nanoparticles under an external force in a viscous medium that contains obstacles (protein fibers)? Any assistance would be greatly appreciated. Peter Politzer ppolitze %a% uno.edu From chemistry-request@ccl.net Tue May 31 04:48:57 2005 Received: from poincare.ciril.fr (persmail.uhp-nancy.fr [194.214.217.19]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4V8mqkV005256 for ; Tue, 31 May 2005 04:48:53 -0400 Received: from ptxavier (pt-xav.lctn.uhp-nancy.fr [193.50.239.125]) by poincare.ciril.fr (8.13.4/8.13.4/Guy-30-12-2004) with SMTP id j4V7xiL0006582; Tue, 31 May 2005 09:59:45 +0200 (METDST) From: "Xavier ASSFELD" To: "Paul Fleurat-Lessard" , Subject: RE: Energy decomposition with G03 Date: Tue, 31 May 2005 09:59:44 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 In-Reply-To: <429B03D1.3050206 |a| ens-lyon.fr> Importance: Normal X-Spam-Score: 0 () X-Scanned-By: poincare.ciril.fr on 194.214.217.19 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Paul, have you ever heard about CECA from Pr. Mayer? Have a look at this URL: http://occam.chemres.hu you'll easily find and install the program APOST which enables you to run a "Chemical Energy Component Analysis". Yours. ...Xav Pr. Xavier Assfeld Xavier.Assfeld |a| cbt.uhp-nancy.fr Chimie et Biochimie thioriques T: (33) 3 83 68 43 82 Faculti des Sciences F: (33) 3 83 68 43 71 54506 Vandoeuvre, France http://www.lctn.uhp-nancy.fr X> -----Message d'origine----- X> De : Computational Chemistry List [mailto:chemistry-request |a| ccl.net]De X> la part de Paul Fleurat-Lessard X> Envoyi : lundi 30 mai 2005 14:15 X> @ : chemistry |a| ccl.net X> Objet : CCL:Energy decomposition with G03 X> X> X> Dear CCLers, X> X> I am using Gaussian03 to analyse a molecule consisting of two fragments X> linked by a weak bond (kind of H-bond). I would like to analyse the X> energetical origin of this bond with some kind of energy decomposition X> scheme. i thought that the Morokuma scheme was available in G03 but I X> cannot find the right keyword, can you help me ? X> Do you know some other tools that can provide such an analysis ? X> X> On the same topic, I would also like to analyse this complexe using a X> fragment approach (because in some cases, the two fragment are in fact X> part of a larger molecule that adopts a cyclic geometry). I was using X> such a tool within the exthuc program (FMO option), and I know that X> there is something similar in ADF... but I cannot find anything in X> G03... do you know a tool for this ? X> X> Thanks in advance, X> Paul. X> X> -- X> Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard |a| ens-lyon.fr X> Laboratoire de Chimie X> Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 X> 46, Allie d'Italie Fax: + 33 (0)4 72 72 88 60 X> 69364 Lyon Cedex 07 X> X> Si vous ne pouvez expliquer un concept ` un enfant de six ans, X> c'est que vous ne le comprenez pas complhtement. X> Albert Einstein X> X> X> X> X> -= This is automatically added to each message by the mailing script =- X> To send e-mail to subscribers of CCL put the string CCL: on your X> Subject: line X> and send your message to: CHEMISTRY |a| ccl.net X> X> Send your subscription/unsubscription requests to: X> CHEMISTRY-REQUEST |a| ccl.net X> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs X> X> If your is mail bouncing from ccl.net domain due to spam filters, please X> use the Web based form from CCL Home Page X> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ X> X> X> X> X> From chemistry-request@ccl.net Tue May 31 08:09:13 2005 Received: from dorado.vub.ac.be (dorado.vub.ac.be [134.184.129.10]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VC9AEE015751 for ; Tue, 31 May 2005 08:09:10 -0400 Received: from web1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by dorado.vub.ac.be (Postfix) with ESMTP id 2439423C for ; Tue, 31 May 2005 13:18:33 +0200 (CEST) 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 NAA07571; Tue, 31 May 2005 13:18:32 +0200 (MEST) for chemistry |a| ccl.net Date: Tue, 31 May 2005 13:18:32 +0200 (MEST) Message-Id: <200505311118.NAA07571 |a| web1.ulb.ac.be> From: Christophe Biot To: chemistry |a| ccl.net X-sender-IP: 194.167.99.112 Subject: X3LYP and G03 X-Mailer: Webmail ULB v2.1 MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4VC9DEE015758 Dear CCL members, In order to study non covalent interactions, we would like to use the newly defined hybrid functional named X3LYP. X3LYP is the extended hybrid functional combined with Lee Yang Parr correlation functional. Please could you tell us how to parameterised Gaussian 03 to do that? Regards. Christophe **************************************** BIOT Christophe ENSCL - Ecole Nationale Supirieure de Chimie de Lille Citi Scientifique, Bbtiment C7 - BP 108 59652 Villeneuve d'Ascq Cedex France Phone: +33 (0)32043 4893 fax: +33 (0)32043 6585 **************************************** From chemistry-request@ccl.net Tue May 31 06:07:22 2005 Received: from gvedoh01.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VA7KwX008815 for ; Tue, 31 May 2005 06:07:20 -0400 To: CCL Subject: a secure Xterm emulator MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy () givaudan.com Date: Tue, 31 May 2005 11:22:22 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 6.5.3|September 14, 2004) at 31/05/2005 12:07:19, Serialize complete at 31/05/2005 12:07:20, Serialize by Router on gvedoh01/H/Givaudan(Release 6.5.3|September 14, 2004) at 31/05/2005 12:07:20 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4VA7MwX008821 Dear Colleagues, What do you suggest as a secure Xterm emulator (with ssh ans sftp etc) for XP which enables me to use my XP desktop as an X window terminal of our linux machine? I know Reflection from WRQ. Many thanks, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy () givaudan.com From chemistry-request@ccl.net Tue May 31 08:42:43 2005 Received: from thumbler.kulnet.kuleuven.ac.be (thumbler.kulnet.kuleuven.ac.be [134.58.240.45]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VCgblY017267 for ; Tue, 31 May 2005 08:42:38 -0400 Received: from localhost (localhost [127.0.0.1]) by thumbler.kulnet.kuleuven.ac.be (Postfix) with ESMTP id CDBD11379BB for ; Tue, 31 May 2005 13:38:45 +0200 (CEST) Received: from lepidus.kulnet.kuleuven.ac.be (lepidus.kulnet.kuleuven.ac.be [134.58.240.72]) by thumbler.kulnet.kuleuven.ac.be (Postfix) with ESMTP id 340801378E5 for ; Tue, 31 May 2005 13:38:45 +0200 (CEST) Received: from bohr.quantchem.kuleuven.ac.be (bohr.quantchem.kuleuven.ac.be [134.58.49.6]) by lepidus.kulnet.kuleuven.ac.be (Postfix) with SMTP id F112C38007E for ; Tue, 31 May 2005 13:38:39 +0200 (CEST) Received: (qmail 1751 invoked by uid 276); 31 May 2005 11:38:39 -0000 Date: Tue, 31 May 2005 13:38:39 +0200 (CEST) From: Pham Cam Nam X-Sender: nam () localhost.localdomain To: chemistry () ccl.net Subject: Problem: O3LYP keyword on Gaussian03 C01 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by KULeuven Antivirus Cluster X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Please send your message to subscribers of CCL (chemistry () ccl.net) Jan ---------------------------- Original Message ---------------------------- Subject: W:O3LYP keyword on Gaussian03 C01 From: "NAM, CAM, PHAM" Date: Thu, May 26, 2005 5:44 am To: chemistry-request () ccl.net -------------------------------------------------------------------------- Dear all, I have a problem on C01 version as following: - I ran optimization job using keyword IOP(3/74=-24) for O3LYP in B03 version: OK! - In the meanwhile, I run it with keyword O3LYP as well as IOP(3/74=-24), jobs are always terminated with Error termination via lnkle: /usr/local/chem/g03C01/l9999.exe Now, if I take the optimation geometry from output file of the job on Gaussian03 version B03 from the keyword: IOP(3/74=-24) and run single point calculation on Gaussian03 version C01 by using available keyword O3LYP, the energies in both cases are quite different. Here is an example: Molecule HCCH 1a. with IOP(3/74=-24)/6-311G(d,p) opt (Gaussian03 B03) result: SCF Done: E(ROPTX+HF-V5+LYP) = -77.1651016059 A.U. after 6 cycles Convg = 0.2402D-08 -V/T = 2.0034 S**2 = 0.0000 Version=x86-Linux-G03RevB.03\State=1-SGG\HF=-77.1651016 1b. With O3LYP/6-311G(d,p) Test (gaussian03 C01) result: E(RO+HF-V5+LYP) = -77.3227635563 A.U. "Version=IA32L-G03RevC.01\State=1-SGG\HF=-77.3227636" My questions are: - Could be IOP(3/74=-24) used to refer to 03LYP? - If the answer is Ok then why are two energies in version B03 and C01 different? - How can I solve this problem? I am looking forward to hear from you soon. Yours regards PHAM CAM NAM -- Computational Chemistry List http://www.ccl.net E-mail: chemistry-request () ccl.net or ccl () ccl.net From chemistry-request@ccl.net Tue May 31 10:25:23 2005 Received: from web26807.mail.ukl.yahoo.com (web26807.mail.ukl.yahoo.com [217.146.176.83]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4VEPH9A024238 for ; Tue, 31 May 2005 10:25:17 -0400 Received: (qmail 79510 invoked by uid 60001); 31 May 2005 14:25:15 -0000 Message-ID: <20050531142515.79508.qmail$at$web26807.mail.ukl.yahoo.com> Received: from [213.140.56.83] by web26807.mail.ukl.yahoo.com via HTTP; Tue, 31 May 2005 16:25:15 CEST Date: Tue, 31 May 2005 16:25:15 +0200 (CEST) From: may abdelghani Subject: Radical Dimerization To: chemistry$at$ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello,CCLers I want to study theoretically the Radical Dimerization of some monomers; I would like to know, in particularly, why some dimizations is not acceble (we can not build the polymer from this monomers). My question is: what are the properties (total energy, spin density, charge density ), that I should calculate, in order to answer on this problem? Best regard may abdelghani _____________________________________________________________________________ Dicouvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vidios ! Criez votre Yahoo! Mail sur http://fr.mail.yahoo.com From chemistry-request@ccl.net Tue May 31 12:41:27 2005 Received: from marge.uochb.cas.cz (marge.uochb.cas.cz [147.231.129.3]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VGfNeG001263 for < ccl.net>; Tue, 31 May 2005 12:41:24 -0400 Received: by marge.uochb.cas.cz (Postfix, from userid 8) id AB0357AC0; Tue, 31 May 2005 17:38:19 +0200 (CEST) Received: from [147.231.129.187] (sisa.uochb.cas.cz [147.231.129.187]) by marge.uochb.cas.cz (Postfix) with ESMTP id 079317A90; Tue, 31 May 2005 17:38:19 +0200 (CEST) Message-ID: <429C84E6.5030903 >< uochb.cas.cz> Date: Tue, 31 May 2005 17:38:14 +0200 From: "Mgr. Lubos Vrbka" < uochb.cas.cz> Reply-To: lubos.vrbka >< uochb.cas.cz Organization: IOCB User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: andras.borosy >< givaudan.com Cc: CCL < ccl.net> Subject: Re: CCL:a secure Xterm emulator References: < givaudan.com> In-Reply-To: < givaudan.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 hello, > What do you suggest as a secure Xterm emulator (with ssh ans sftp etc) for > XP which enables me to use my XP desktop as an X window terminal of our > linux machine? I know Reflection from WRQ. i'd recommend putty for this purpose. other possibility is to install cygwin and use xterm that is part of this package. both are for free. however, if you need only terminal emulator (no X-windows application output to your windows box), cygwin (more or less complete linux environment running under windows) is an overkill. regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic ..................................................... From chemistry-request@ccl.net Tue May 31 11:51:38 2005 Received: from vscano-a.ucl.ac.uk (vscano-a.ucl.ac.uk [144.82.100.152]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VFpY2i031429 for ; Tue, 31 May 2005 11:51:34 -0400 Received: from socrates-a.ucl.ac.uk ([144.82.100.160]) by vscano-a.ucl.ac.uk with esmtp (Exim 4.34) id 1Dd8Lm-0006Rt-Pl; Tue, 31 May 2005 16:08:14 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.7p1+Sun/8.9.3) id j4VF8EH03023; Tue, 31 May 2005 16:08:14 +0100 (BST) Message-Id: <200505311508.j4VF8EH03023 %x% socrates-a.ucl.ac.uk> Subject: helium density with Gaussian To: chemistry %x% ccl.net (CCL) Date: Tue, 31 May 2005 16:08:14 +0100 (BST) Cc: T.vanMourik %x% ucl.ac.uk (Tanja van Mourik) From: Tanja van Mourik X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCL-MailScanner-Information: Please contact the UCL Helpdesk, helpdesk %x% ucl.ac.uk for more information X-UCL-MailScanner: Found to be clean X-UCL-MailScanner-SpamCheck: X-MailScanner-From: uccatvm %x% ucl.ac.uk X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCL'ers, I am trying to calculate the CISD density for a He atom using Gaussian: #CISD/GEN Density=Current I manage this without problems for basis sets up to aug-cc-pV5Z. However, when using aug-cc-pV6Z, I get the error message: Not enough memory in GToLag: JobTyp=1 LenV= 104425222 NeedRS= 441 LenG= 16653 MaxRS= 300 short by 2421675 words. Error termination via Lnk1e in /export/home/disk1/tvm/G03/g03/l1111.exe at Tue Apr 26 17:02:25 2005. I increased the requested memory from 800Mb to as much as 7000Mb, but I keep getting the same error message (with exactly the same amount of "missing" words - 2421675 words). Has anyone encountered similar problems when calculating densities? I am using Gaussian03, Revision B.04. The same error happens on a Sun V880 server and an Intel Xeon cluster. I also tried Gaussian 98 on a Pentium 4/Xeon cluster, but I get the same error message, with the same amount of missing words (2494995) irrespective of whether I request 800Mb or 1800Mb memory. Does anyone have any idea how to solve this problem? Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik %x% ucl.ac.uk London WC1H 0AJ, UK home: tanja %x% van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ================================================================= From chemistry-request@ccl.net Tue May 31 11:54:14 2005 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VFsAuu031558 for ; Tue, 31 May 2005 11:54:10 -0400 Received: from [129.74.81.11] (verdi.chem.nd.edu [129.74.81.11]) (authenticated bits=0) by pickering.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id j4VFs7dF019529 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NO) for ; Tue, 31 May 2005 10:54:08 -0500 (EST) Message-ID: <429C87BB.9040204 (a) nd.edu> Date: Tue, 31 May 2005 10:50:19 -0500 From: "Lauren O'Neil" User-Agent: Mozilla Thunderbird 1.0 (X11/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry (a) ccl.net Subject: DNA Base-Flipping: TI vs PMF Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-ND-MTA-Date: Tue, 31 May 2005 10:54:09 -0500 (EST) X-ND-Virus-Scan: engine v4.4.00; dat v4502 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I would like to calculate the free energy change for the process of base-flipping in DNA using Amber. I have been working with the online tutorial of thermodynamic integration in Amber and have a few questions as to how I could implement this for the base-flipping of damaged DNA. Along the lines of the tutorial I was thinking of a cycle in which DNA (flipped-in)-->water and DNA (flipped-out)--> water using dummy atoms. Can Amber handle using that many dummy atoms (DNA = duplex 16-mer)? How could I ensure that the two "water" states are the same, or can I? To get around the waters being the same I was also thinking of starting with a water box that contained both the flipped-in and flipped-out DNA (as dummy atoms) and then going both the flipped-in and flipped-out directions to get the free energy difference. The larger question is - How do you determine that the reference state (water) is the same for any cycle? Also, could this be done directly (without a common reference state)? If yes, can Amber do this? I am interested in using thermodynamic integration rather than potential of mean force for this calculation because of the choice of path for the flipping process. Any thoughts?? Lauren L O'Neil lhunter2 (a) nd.edu From chemistry-request@ccl.net Tue May 31 16:53:23 2005 Received: from mxsf04.cluster1.charter.net (mxsf04.cluster1.charter.net [209.225.28.204]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VKrHxO013533 for ; Tue, 31 May 2005 16:53:17 -0400 Received: from mxip14a.cluster1.charter.net (mxip14a.cluster1.charter.net [209.225.28.144]) by mxsf04.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id j4VHxEUi022456 for ; Tue, 31 May 2005 13:59:15 -0400 Received: from 24-247-172-122.dhcp.bycy.mi.charter.com (HELO inspiron9100) (24.247.172.122) by mxip14a.cluster1.charter.net with ESMTP; 31 May 2005 13:59:14 -0400 Message-Id: <440397$a1h4am_at_mxip14a.cluster1.charter.net> X-IronPort-AV: i="3.93,153,1115006400"; d="scan'208"; a="337154390:sNHT18744632" From: "Jim Kress" To: "'Christophe Biot'" Cc: Subject: RE: X3LYP and G03 Date: Tue, 31 May 2005 13:59:14 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 In-Reply-To: <200505311118.NAA07571_at_web1.ulb.ac.be> Thread-Index: AcVl7pcB5n9dgaZMTJKw7/KdDFIexgAG33NA X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net PC GAMESS already supports X3LYP and is much faster than Gaussian 03. You can get PC GAMESS at: http://www.msg.ameslab.gov/GAMESS/pcgamess.shtml Or contact Alex Granovsky ( gran_at_classic.chem.msu.su ) Jim > -----Original Message----- > From: Christophe Biot [mailto:cbiot_at_ulb.ac.be] > Sent: Tuesday, May 31, 2005 7:19 AM > To: chemistry_at_ccl.net > Subject: CCL:X3LYP and G03 > > Dear CCL members, > > In order to study non covalent interactions, we would like to > use the newly defined hybrid functional named X3LYP. X3LYP is > the extended hybrid functional combined with Lee Yang Parr > correlation functional. > > Please could you tell us how to parameterised Gaussian 03 to do that? > > Regards. > > Christophe > > **************************************** > BIOT Christophe > ENSCL - Ecole Nationale Supirieure de Chimie de Lille Citi > Scientifique, Bbtiment C7 - BP 108 > 59652 Villeneuve d'Ascq Cedex > France > Phone: +33 (0)32043 4893 > fax: +33 (0)32043 6585 > **************************************** > > > > > > > > > > > -= 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 is mail bouncing from ccl.net domain due to spam > filters, please use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Tue May 31 18:40:21 2005 Received: from web31506.mail.mud.yahoo.com (web31506.mail.mud.yahoo.com [68.142.198.135]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4VMeHjh019306 for ; Tue, 31 May 2005 18:40:17 -0400 Received: (qmail 52917 invoked by uid 60001); 31 May 2005 21:40:17 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=TiPgeZAxsIQbmCo+Cbg60sSIa94SbBPDjI1huCvVVylM1wHGTTkhfxX6D+TPanBaQeNTiZ6kVI7YJSZy7PJTSFKVmbEreS1/1Tur6LenQSluxR55tanr2FbPKxYgoG8eE2LImzKDx2yTaweMj2c0QTG/psg40B2ZzmD69FFcGV4= ; Message-ID: <20050531214017.52915.qmail *o* web31506.mail.mud.yahoo.com> Received: from [165.106.23.135] by web31506.mail.mud.yahoo.com via HTTP; Tue, 31 May 2005 14:40:17 PDT Date: Tue, 31 May 2005 14:40:17 -0700 (PDT) From: Vincent Xianlong Wang Subject: CCL:a secure Xterm emulator To: "Mgr. Lubos Vrbka" , andras.borosy *o* givaudan.com Cc: CCL In-Reply-To: 6667 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=3.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FORGED_YAHOO_RCVD autolearn=no version=3.0.3 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net You may try VNC(Virtual Network Computing) at http://www.realvnc.com. It has a free edition and the size is very small and very convenient to use. It provides cross-platform connection for all sorts of operating system. Best, Vincent --- "Mgr. Lubos Vrbka" wrote: > hello, > > > What do you suggest as a secure Xterm emulator > (with ssh ans sftp etc) for > > XP which enables me to use my XP desktop as an X > window terminal of our > > linux machine? I know Reflection from WRQ. > i'd recommend putty for this purpose. other > possibility is to install > cygwin and use xterm that is part of this package. > both are for free. > however, if you need only terminal emulator (no > X-windows application > output to your windows box), cygwin (more or less > complete linux > environment running under windows) is an overkill. > > regards, > lubos > > -- > >..................................................... > Mgr. Lubos Vrbka > > Center for Biomolecules and Complex Molecular > Systems > Institute of Organic Chemistry and Biochemistry > Academy of Sciences of the Czech Republic > Prague, Czech Republic > >..................................................... > > -= 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 *o* ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST *o* ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to > spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > __________________________________ Do you Yahoo!? Yahoo! Small Business - Try our new Resources site http://smallbusiness.yahoo.com/resources/ From chemistry-request@ccl.net Tue May 31 19:58:39 2005 Received: from fujitsu0.fujitsu.com (fujitsu0.fujitsu.com [192.240.0.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4VNwYrQ022375 for ; Tue, 31 May 2005 19:58:35 -0400 Received: from fujitsu0.fujitsu.com (localhost [127.0.0.1]) by fujitsu0.fujitsu.com (8.13.1/8.13.1) with ESMTP id j4VLbxXb008734; Tue, 31 May 2005 14:37:59 -0700 (PDT) Received: from fujitsu7i.fnanic.fujitsu.com ([133.164.253.7]) by fujitsu0.fujitsu.com (8.13.1/8.13.1) with ESMTP id j4VLbs9c008649; Tue, 31 May 2005 14:37:54 -0700 (PDT) Received: from cachemai2.fnanic.fujitsu.com (localhost [127.0.0.1]) by fujitsu7i.fnanic.fujitsu.com (8.13.2/8.13.2) with ESMTP id j4VLbqAo002750; Tue, 31 May 2005 14:37:52 -0700 (PDT) Received: from daveg-lifebook.cachesoftware.com (localhost [127.0.0.1]) by cachemai2.fnanic.fujitsu.com (8.13.2/8.13.2) with ESMTP id j4VLmdhn029220; Tue, 31 May 2005 14:48:47 -0700 (PDT) Message-Id: <6.2.1.2.0.20050531095142.040430a8@133.164.253.31> X-Mailer: QUALCOMM Windows Eudora Version 6.2.1.2 Date: Tue, 31 May 2005 14:37:42 -0700 To: may abdelghani , chemistry #%# ccl.net From: David Gallagher Subject: Re: CCL:Radical Dimerization In-Reply-To: <20050531142515.79508.qmail #%# web26807.mail.ukl.yahoo.com> References: <20050531142515.79508.qmail #%# web26807.mail.ukl.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi May, One property to consider is "susceptibility to radical attack" computed > from Fukui's frontier density theory after a quantum mechanics calculation. This property can be tabulated quantitatively by atom, or displayed by color on the van der Waals surface of the molecule. Programs such as CAChe can calculate and display this property in just a few seconds for small molecules. It provides a fast qualitative indication of which parts of the monomer or radical are most susceptible to radical attack, although it does not consider sterics or energetics of the reaction. A more quantitative approach is to use a quantum mechanics method to model all the possible reaction paths and then compare the activation energies (kinetics) and heats of reaction (thermodynamics). Regards, David Gallagher Fujitsu, Portland, Oregon At 07:25 AM 5/31/2005, may abdelghani wrote: >Hello,CCLers >I want to study theoretically the Radical Dimerization >of some monomers; I would like to know, in >particularly, why some dimizations is not acceble (we >can not build the polymer from this monomers). My >question is: what are the properties (total energy, >spin density, charge density ), that I should >calculate, in order to answer on this problem? >Best regard >may abdelghani > > > > > > >_____________________________________________________________________________ >Dicouvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos >mails, photos et vidios ! >Criez votre Yahoo! Mail sur http://fr.mail.yahoo.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 #%# ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST #%# ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue May 31 22:05:15 2005 Received: from ion.chem.utk.edu (ion.chem.utk.edu [160.36.200.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j51258AE028075 for >ccl.net>; Tue, 31 May 2005 22:05:09 -0400 Received: from localhost ([127.0.0.1] helo=ion.chem.utk.edu) by ion.chem.utk.edu with esmtp (Exim 4.32) id 1DdIbM-0000K9-4v for chemistry<>ccl.net; Tue, 31 May 2005 22:05:00 -0400 Received: from 66.32.5.224 (SquirrelMail authenticated user setca) by ion.chem.utk.edu with HTTP; Tue, 31 May 2005 22:05:00 -0400 (EDT) Message-ID: <47344.66.32.5.224.1117591500.squirrel<>ion.chem.utk.edu> Date: Tue, 31 May 2005 22:05:00 -0400 (EDT) Subject: CCL: SETCA 2005 -- June 17-19 From: "SETCA 2005" >ion.chem.utk.edu> To: chemistry<>ccl.net Reply-To: setca<>ion.chem.utk.edu User-Agent: SquirrelMail/1.4.4 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net The 34th meeting of the Southeast Theoretical Chemistry Association is approaching quickly! Deadline for hotel reservations is JUNE 1, 2005! SETCA 2005 will take place in Knoxville, TN on June 17-19, 2005. Visit our Web page for more information: http://www.chem.utk.edu/SETCA/ We look forward to seeing you in Knoxville this summer! -- Robert Harrison and Robert Hinde Co-Chairs, SETCA 2005 http://www.chem.utk.edu/SETCA/ e-mail setca<>mail.chem.utk.edu or FAX 865-974-3454 -- Robert Harrison and Robert Hinde Co-Chairs, SETCA 2005 http://www.chem.utk.edu/SETCA/ e-mail setca<>mail.chem.utk.edu or FAX 865-974-3454 -- Robert Harrison and Robert Hinde Co-Chairs, SETCA 2005 http://www.chem.utk.edu/SETCA/ e-mail setca<>mail.chem.utk.edu or FAX 865-974-3454