From chemistry-request@ccl.net Mon Dec 15 15:43:52 2003 Received: from mail.mans.edu.eg ([193.227.50.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBFKhI8a025396 for ; Mon, 15 Dec 2003 15:43:20 -0500 Subject: CCL:'Molecular Orbital Computations on Molecular Complexes' MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Date: Mon, 15 Dec 2003 22:39:28 +0200 Content-class: urn:content-classes:message X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Message-ID: <095F5EDC6A006F41AFF7804586108ACF38E4F9..at..mail.mans.edu.eg> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL:'Molecular Orbital Computations on Molecular Complexes' thread-index: AcPDS4kDK2JAZypHS8+DfXH+iV8jcg== From: "Tarek M. El-Gogary" To: X-Spam-Status: No, hits=1.6 required=7.0 tests=BASE64_ENC_TEXT version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id hBFKhq8a025410 Hi CCLers I very much appreciate if anyone pointed me to some reviews and/or books (or even websites) appeared in the last 20 years on the subject of 'Molecular Orbital Computations on Molecular Complexes'. I'll summarize. Regards Tarek From chemistry-request@ccl.net Tue Dec 16 00:39:35 2003 Received: from brass.metals.hope.edu (brass.metals.hope.edu [198.110.98.36]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hBG5d48b006528 for ; Tue, 16 Dec 2003 00:39:04 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (SAVSMTP 3.1.1.32) with SMTP id M2003121600372316541 ; Tue, 16 Dec 2003 00:37:23 -0500 Received: from [198.110.101.2] (polik=at=hope.edu) by hope.edu; Tue, 16 Dec 2003 00:37:49 -0500 X-WM-Posted-At: hope.edu; Tue, 16 Dec 03 00:37:49 -0500 Message-Id: <5.2.0.9.2.20031216003442.00b9cb00=at=webmail.hope.edu> X-Sender: polik=at=webmail.hope.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Tue, 16 Dec 2003 00:37:00 -0500 To: CHEMISTRY=at=ccl.net From: "William F. Polik" Subject: CCL: WebMO 4.0: WWW-Based Interface for Computational Chemistry Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 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) WebMO version 4.0 has been officially released and is available for download at the WebMO website. A tour of screenshots, a working demo server, a detailed features list, and free download information can be found at http://www.webmo.net WebMO is a FREE web-based interface to popular computational chemistry programs including Gaussian, MOPAC, GAMESS, and Molpro. WebMO permits users to build 3-D molecular structures, submit multiple jobs, monitor job progress, and view text and graphical results all from within a standard web-browser. WebMO is ideal both for research and for classroom use. Features of WebMO new to version 4.0 include: * Support for Gaussian 03 * Support for Molpro 2002 * Support for Mac OS X (both server and client) * Enhanced web browser support (Windows, Mac OS X, Linux) * Support for PBS and NQS batch queuing systems (Pro) * Visualization of Natural Orbitals (Pro) * Many user interface enhancements and bug fixes The full feature list of WebMO is available at http://www.webmo.net/features.html WebMO has been adopted by hundreds of academic and professional users because it lowers the cost and greatly simplifies the implementation of computational chemistry Try out WebMO for free by visiting the WebMO Working Demo at http://www.webmo.net/demo Since WebMO is a web-based product, there is no need to install any software on your computer. Just point, click, and compute! Enjoy! The WebMO Team From chemistry-request@ccl.net Tue Dec 16 09:16:16 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGEFi8a019119 for ; Tue, 16 Dec 2003 09:15:44 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id hBGEFijm012990 for ; Tue, 16 Dec 2003 09:15:44 -0500 Date: Tue, 16 Dec 2003 09:15:44 -0500 (EST) From: Jan Labanowski To: chemistry/at/ccl.net Subject: 04.02.12 3rd SM Conference on Drug Design, The Hatton, London Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=1.4 required=7.0 tests=EXCUSE_14,OPPORTUNITY_2,USER_AGENT_PINE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ------------ Date: Tue, 16 Dec 2003 10:19:49 -0000 From: Tracey Huggett To: Ms Jan Labanowski Subject: Drug Design Don't miss SMi's 3rd annual Conference on... Drug Design 23rd & 24th February 2004 The Hatton, London Sponsored by: Chemical Computing Group Openeye Scientific Software Accelrys ** PLUS A FULL DAY POST-CONFERENCE WORKSHOP ** High-Throughput Molecular Docking - Led by: Wyeth, Pharmacia, Structural GenomiX & CCDC 25th February 2004, The Hatton London DRINKS RECEPTION SPONSORED BY: CHEMICAL COMPUTING GROUP http://www.smi-online.co.uk/goto/drugd8.asp?emref=M36ER85000254 ** DISCOUNTS AVAILABLE** 1) Save #100 when booking on to both Conference and Post-Conference Workshop 2) Academics receive a discount of 50% off Conference price Proof of status to be sent with registration. 3) Group Booking discounts are available. Contact Lucy Potucek on tel: +44 (0) 20 7827 6168 or mailto:lpotucek/at/smi-online.co.uk for further details Please quote your unique contact code: Dear , SMi has received ongoing feedback over the last two years from those at the very forefront of this challenging field, and this enables us to bring you this Conference to keep you on the cutting edge of drug design developments. At this key stage in the revolution of the drug design industry, SMi have recognised the need to evaluate these advances and provide a stepping stone for further developments. This Conference aims to include presentations on the latest developments in protein drug design and dealing with flexible structures, fragment-based drug design, integrative processes for drug design and the latest update on computational and combinatorial techniques. We will also look at how drug design fits into the drug discovery process. A unique opportunity to learn from leading industry experts including: * Dr Alexander Alex, Head, Computational Chemistry, Pfizer * Dr Pieter Stouten, Senior Research Advisor & Head, Computational Sciences, Pharmacia * Dr Richard Lewis, Head, European Computer-Aided Drug Design, Eli Lilly * Dr Steven Muchmore, Group Leader, Abbott Laboratories * Dr Jonathan Mason, Group Director, Molecular Informatics, Structure & Design, Pfizer * Dr Andrew Davis, Associate Director, Physical & Metabolic Science, Senior Principal Scientist, AstraZeneca * Dr Wolfgang Sauer, Head, Computational Chemistry, Serono * Dr Jeff Blaney, Vice President, Computational Chemistry, Structural GenomiX * Dr Keith Wilson, Vice President, Structural Chemistry & Business Development, Syrrx BENEFITS OF ATTENDING: FUNDAMENTAL ISSUES IN DESIGN: Explore the key issues, trends and technologies in drug design VIRTUAL SCREENING: Discover how new in silico techniques are helping to meet the needs of a lead-hungry industry STRUCTURE-BASED DRUG DESIGN: Examine how the cutting edge techniques are being used to advance drug discovery EXPLOITING PROTEIN STRUCTURES: Learn how to make good use of all available structural information INTEGRATED DESIGN: Assess how the various processes in drug design are being integrated to increase efficiency NETWORK WITH KEY EXPERTS: Discuss and exchange ideas with leaders in the field Please scroll down to view the full Conference Agenda. Day One 23rd February 2004 8.30 Registration & Coffee 9.00 Chairman's Opening Remarks Dr Harren Jhoti, Chief Scientific Officer, Astex Technology FUNDAMENTAL ISSUES IN DRUG DESIGN 9.10 What are the developments in the drug design industry? * The number of drug targets continues to increase: identifying which are the most promising * Meeting all the requirements of a successful drug: a difficult task * The need to reduce the rate of failure, particularly at the clinical stages * The move towards an integrated approach to drug design * What are the future prospects for drug design? Dr Alexander Alex, Head, Computational Chemistry & Dr Jonathan Mason, Group Director, Molecular Informatics, Structure & Design, Pfizer DECISION SUPPORT FOR DRUG DESIGN 9.40 Learning from the past, living in the future * The need for good decisions: the cost of bad ones * Learning from the history of drug discovery * What makes a good target? * What makes a good lead? * Datamining the pharmaceutical industries experience of medicinal chemistry * What is the role of protein structure? Dr John Overington, Senior Vice President, Drug Discovery, Inpharmatica RATIONAL DRUG DESIGN - REALITY OR SCIENCE FICTION? 10.20 Can CADD finally live up to its name? * Medicinal chemistry programmes start with target selection * Computationally-driven lead discovery: what matters most? * Are virtual drugs better than real ones? * Just good or good enough? * Getting the balance right Dr Wolfgang Sauer, Head, Computational Chemistry, Serono 11.00 Morning Coffee LEAD GENERATION AND VIRTUAL SCREENING TECHNOLOGIES STRUCTURE-BASED SCREENING IN LEAD DISCOVERY 11.40 Scaffold-Based Drug DiscoveryTM * Large capacity co-crystallography * Optimising scaffold discovery for chemistry * Structure-based library design with optimal scaffolds * Structure-based optimisation of PK * In vivo studies with scaffold-based leads Michael Milburn, Senior Vice President, Research, Plexxikon ACCELERATING THE PROCESS FROM IN SILICO IDEAS TOWARDS LEAD MOLECULES 12.20 Or how to create value * Overview: the number of promising in silico screening methods has increased significantly * The efficiency and proof of an in silico screening method from real compounds tested in biology * The transition from in silico to wet chemistry: what is critical? * The fuel of in silico screening: chemical spaces that are available or can be synthesised * The implementation of a seamless and efficient idea to compound process Dr Lutz Weber, Chief Executive Officer, Morphochem 1.00 Networking Lunch AUTOMATED DE NOVO DESIGN 2.20 Structure-based and ligand-based design formats * SkelGen: a universal engine for de novo chemical structure generation * Strategies and constraints for de novo design * De novo structure-based design * De novo ligand-based design * De novo chemotype switching and synthetic sense Dr Philip Dean, Chief Scientific Officer, De Novo Pharmaceuticals NOVEL STRUCTURE-BASED LEAD GENERATION 3.00 Structure-based fragment screening against protein kinases and proteases * High-throughput x-ray crystallography for fragment screening * Choosing the right fragments to screen * Large-scale docking of fragment libraries * Progress to date Dr Chris Murray, Director, Computational Chemistry & Informatics, Astex Technology 3.40 Afternoon Tea APPLICATION OF LIGAND DOCKING PROGRAMS IN DRUG DISCOVERY 4.00 Sensitive dependence on program, search algorithm, scoring function and data set * Evaluation and side-by-side comparison of 6 commercial programs: FlexX, GOLD, ICM, LigandFit, NWU-Dock and QXP * RMS deviations from the crystal structure, not a good measure of docking quality * To improve pose prediction: focus on scoring functions rather than search algorithms * Protein flexibility and water molecules are important * Targeting protein-protein interactions by combining virtual and biophysical screening Dr Pieter Stouten, Senior Research Advisor & Head, Computational Sciences, Pharmacia Italia, Pfizer Group SUCCESSFUL LIGAND DOCKING RELIES ON KNOWLEDGE OF THE BINDING SITE 4.40 Assessment of protein ligand docking parameters based on the classification of binding site * Binding site shape and volume determine the extent of the docking search problem * Why do we need control ligands and what do they predict? * How do you pull out the right poses with the right scoring function * The trade off between accuracy and time * The false positive problem Dr Scott Kahn, Chief Scientific Officer, Accelrys 5.20 EVALUATING SCORING FUNCTIONS WITH FRED * Physics base scoring functions : PB, MMFF * Heuristic scoring functions : Chemscore, ScreenScore, PLP * Smooth scoring functions based on gaussian functions Dr Mark McGann, Principal Developer, Docking Software, OpenEye Scientific Software 6.00 Chairman s Closing Remarks and Close of Day One 6.10 DRINKS RECEPTION: In association with Chemical Computing Group Day Two 24th February 2004 8.30 Re-registration & Coffee 9.00 Chairman's Opening Remarks Dr Vincent Mikol, Head, Structural Biology & Molecular Modelling, Aventis DOES VIRTUAL SCREENING ACTUALLY WORK? 9.10 The struggle with proof of principal * Is the virtual screening experiment properly validated? * Do we get the results due to the program working as we hope? * Why are there so few validated results published? Dr Steven Muchmore, Group Leader, Abbott Laboratories ISSUES AND CASE STUDIES IN STRUCTURE-BASED DRUG DESIGN FASTTM STRUCTURE-DRIVEN LEAD DISCOVERY AND OPTIMIZATION 9.40 Structure-based drug discovery for protein kinases * Gene to protein technology platform * Kinase structure pipeline * Parallel lead generation and optimisation * Structure-biased library design * Designing for selectivity, not just affinity Dr Jeff Blaney, Vice President, Computational Chemistry, Structural GenomiX HOW TO HIT A MOVING TARGET 10.20 Practical considerations for the structure-based design of kinase inhibitors * Kinases as targets for structure-based drug design * Virtual screening for P38 kinase inhibitors * Conformational flexibility and the discovery of selective P38 kinase inhibitors * Conformational flexibility in Aurora kinase * The use of non-classical hydrogen bonds in designing kinase inhibitors Dr Ronald Knegtel, Group Leader, Molecular Modelling, Vertex 11.00 Morning Coffee PHARMACOPHORE DOCKING 11.40 An example of applications development in the Molecular Operating Environment (MOE) * Protein-ligand docking using MOE * Requirements to increase the speed and efficiency of ligand docking * Use of matching pharmacophore features on the ligand and in the receptor site * MOE as a development environment for this new tool Dr Steve Maginn, Director, Scientific Services, Chemical Computing Group STRUCTURE BASED-DRUG DESIGN OF DPP4 INHIBITORS 12.20 From gene to multiple, diverse and clinical candidates in 15 months * Target selection and drug discovery strategy * Proven high-throughput crystallisation technology * Atomic structures of DPP4 and DPP4 family members * X-ray crystallography for lead optimisation * Fragment based design * Future prospects Dr Keith Wilson, Vice President, Structural Chemistry & Business Development, Syrrx 1.00 Networking Lunch APPLICATION AND LIMITATIONS OF X-RAY CRYSTALLOGRAPHIC DATA IN STRUCTURE-BASED LIGAND AND DRUG DESIGN 2.20 The distinction between ligand design and drug design * Case studies of successful, yet to be successful and not so successful structure-based drug design projects * Uncertainties in x-ray crystallographic models and the impact on structure-based design * Uncertainties and opportunities caused by flexibility of proteins * The complementarity of high-throughput screening and structure-based design Dr Andrew Davis, Associate Director, Physical & Metabolic Science, Senior Principal Scientist, AstraZeneca STRUCTURE-BASED DESIGN CONUNDRUMS 3.00 Targets with multiple possible active sites * Native x-ray structures where complexes are difficult to obtain * Using NMR, fluorescence, point mutations and other methods to provide clues * Evaluation of multiple docking strategies * Application to several therapeutic areas Dr Alan Katz, Principal Research Scientist, Computational Chemistry, Wyeth 3.40 Afternoon Tea THE ROLE OF PROPERTY MODELLING AUTOMATED ITERATIVE DESIGN 4.00 How can we best use QSAR to drive drug discovery? * Combining de novo design, QSAR and medicinal chemistry * Translating established powerful models into novel chemical structures * How can we make all our models generally more interpretable and useful to the bench chemist? * What are the issues involved in extrapolating outside the training set? * How do we try to keep the proposed structures chemically sensible? Dr Richard Lewis, Head, European Computer-Aided Drug Design, Eli Lilly TOWARDS ACCURATE PREDICTION OF KEY ADMET PROPERTIES 4.40 An assessment of the current state-of-the-art * The rise of early ADMET in drug discovery * Progress in developing in silico models for key ADMET properties * Examples of the application of models in drug discovery * Current obstacles to better predictions * Future directions Dr David Clark, Director, Computer-Aided Drug Design & Knowledge Management, Argenta Discovery 5.20 Chairman's Closing Remarks and Close of Conference ** PLUS A FULL DAY POST-CONFERENCE WORKSHOP ** High-Throughput Molecular Docking - Led by: Wyeth, Pharmacia, Structural GenomiX & CCDC 25th February 2004, The Hatton London Workshop Leaders: Dr Juan Alvarez (Organizer), Associate Director, Computational Chemistry, Wyeth Research Dr Jeff Blaney, Vice President, Computational Chemistry, Structural GenomiX Dr Romano Kroemer, Senior Scientist, Molecular Modeling & Design, Pharmacia Dr Robin Taylor, Development Director, CCDC About the Workshop: Virtual Screening, in particular high-throughput molecular docking, has emerged as a complementary strategy to high-throughput screening as a means for identifying novel drug leads. The increased robustness of computational algorithms and scoring functions, the availability of affordable, massive computational power, and the potential for timely structural elucidation of target molecules have provided unprecedented opportunities for this technology. Combinatorial chemistry and genomics have created a compound and target rich environment whereby even the tremendous advances in assay automation, analytical sensitivity, and miniaturisation, which have enabled for the high-throughput screening (HTS) of huge chemical libraries, will not be sufficient to address the industry s needs. Consequently, virtual screening has become a staple strategy in all major pharmaceutical companies and in many emerging pharmaceutical companies. The primary purpose of this interactive workshop is the identification and discussion of the critical issues related to using high-throughput molecular docking (HTMD) as a source for novel lead molecules. Delegates will receive an overview of different algorithms and processes for effectively carrying out HTMD and gain a better understanding of: * Opportunities and limitations what are realistic expectations for the type of molecules that can be identified? What will I miss? How does HTMD compare to HTS? * Ligand-related issues selection, processing, perception * Target processing waters, metals, cofactors * Docking schemes and scoring functions speed vs accuracy, how should they be balanced? * Measuring performance how should algorithms be validated? How do I know if my virtual screen was successful ? * Emerging technologies - target flexibility A full itinerary will be available shortly on our website www.smi-online.co.uk/drugd.asp About Your Workshop Leaders: Dr John Alvarez holds the position of Associate Director of Computational Chemistry in the Chemical and Screening Sciences Department of Wyeth Research, overseeing groups in Cambridge, MA; Pearl River, NY; Princeton, NJ; and Collegeville, PA. He received his SB from MIT in Chemistry in 1986 and his PhD from UCSF in Pharmaceutical Chemistry in 1992. His graduate research focused on oxidative mechanisms of haemoproteins as well as the structure-based identification and optimisation of HIV-1 protease inhibitors. He joined Genetics Institute in 1992, and after its acquisition by American Home Products became the Head of the Computational Group at Wyeth. His current research efforts are focused around molecular docking and automated structure-based optimisation algorithms. Dr Jeff Blaney is the Vice President of Computational Chemistry. Jeff has 19 years of experience in industrial drug discovery research, focusing on structure-based design, high-throughput docking, combinatorial library design, and chemical informatics. For the two years prior to joining SGX, Jeff was Executive Director, Chemical and Physical Sciences R&D at DuPont Pharmaceuticals Research Laboratories. From October 1997 until February 2000 he was Vice President, Computational Chemistry at Metaphorics. From 1992 until October 1997 Jeff was Director of Computational Chemistry and Biophysical Chemistry at Chiron Corporation. Jeff received a PhD in Pharmaceutical Chemistry from UCSF and a BA in Chemistry-Zoology from Pomona College. Dr Romano Kroemer is a Principal Research Scientist in Computational Chemistry at Pharmacia (Pfizer Group) in Milan, Italy. In 1993 he received his PhD in Chemistry from the University of Innsbruck, Austria, while he was working at the Sandoz (now Novartis) Research Institute in Vienna, Austria. After two years as a computational chemist with Sandoz he took up a position as Postdoctoral Research Assistant at the Physical and Theoretical Chemistry Laboratory at Oxford University, UK. In 1998 he became a Lecturer in Computational Chemistry at the University of London, UK, where he was in charge of his own research group. In 2001 he joined Pharmacia as a Computational Chemist. Currently his research efforts are focussed on evaluation and development of docking and scoring algorithms. Romano is the co-author of approximately 50 publications in computational chemistry. Dr Robin Taylor is currently Development Director at the Cambridge Crystallographic Data Centre, where he has responsibility for directing the development of life science and database software products. These include the well-known docking program GOLD. Prior to joining CCDC, he was leader of the Computational Chemistry Group at Zeneca Agrochemicals in the UK. He has degrees from the universities of Oxford and Cambridge. Drinks Reception Sponsor Information Chemical Computing Group provides state of the art drug discovery software. MOE delivers leading applications in protein modelling, combinatorial library design and focusing, QSAR, bio- and chemoinformatics, and structure-based drug design. Platform independent application source code and an embedded programming language are also included, making MOE the most complete and flexible solution available. ** DISCOUNTS AVAILABLE** 1) Save #100 when booking on to both Conference and Post-Conference Workshop 2) Academics receive a discount of 50% off Conference price Proof of status to be sent with registration. 3) Group Booking discounts are available. Contact Lucy Potucek on tel: +44 (0) 20 7827 6168 or mailto:lpotucek/at/smi-online.co.uk for further details Please quote your unique contact code: CONFERENCE PRICING: All Conference pricing now includes an Audio CD of the Conference (excluding those booking with a Academic Discount) Conference & Executive Briefing Fee: #1878.00 + VAT Total:#2206.65 Conference only Fee: #1279.00 + VAT Total: #1502.83 Executive Briefing only Fee: #699.00 +VAT Total: #821.33 Conference delegates not wishing to receive the Audio CD of the Conference can deduct #211.50 (inc. VAT) from the pricing option listed above, which includes the two-day Conference. ACADEMIC DISCOUNT: Proof of status to be sent with registration. Conference & Executive Briefing: #1149.00 + VAT Total: #1350.08 Conference Fee: #550.00 + VAT Total: #646.25 Executive Briefing only Fee: #699.00 +VAT Total: #821.33 SPONSORSHIP AND EXHIBITION OPPORTUNITIES: SMi offer sponsorship, exhibition, advertising and branding packages, uniquely tailored to complement your company's marketing strategy. Prime networking opportunities exist to entertain, enhance and expand your client base within the context of an independent discussion specific to your industry. Should you wish to join the increasing number of companies benefiting from sponsoring our conferences please call Trevor Day on tel: +44 (0) 20 7827 6074 or mailto:tday/at/smi-online.co.uk ACCOMMODATION SOLUTIONS: For accommodation solutions simply call our Reservations Team on tel: +44 (0) 870 9090 713 fax: +44 (0) 870 9090 714 or mailto:hotels/at/smi-online.co.uk and we will be happy to book a hotel to suit you. Yours sincerely Tracey Huggett SMi Conferences Ltd mailto:tracey.huggett/at/smiconferences.co.uk You are registered as: jkl/at/ccl.net Your unique contact code: M36 EM - RM 85000254 SMi Group Ltd gathers and manages data in accordance with the Data Protection Act 1998. If you would prefer not to receive further email messages: If you do not wish to receive further email messages from SMi Group, please go to www.smi-online.co.uk/removals.asp Alternatively, 1. Click on the Reply button 2. Replace the contents of the subject field with just the word REMOVE 3. Click the Send button Please allow approximately 5 working days for your email removal request to be applied to our database. Following your request, you may receive additional emails during the transitional period, whilst the changes are applied. From chemistry-request@ccl.net Tue Dec 16 05:07:54 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 hBGA7M8a014615 for ; Tue, 16 Dec 2003 05:07:23 -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 <0HPZ006I8G4BUA$at$mailserver.unimi.it> for chemistry$at$ccl.net; Tue, 16 Dec 2003 11:07:23 +0100 (MET) Received: from villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0HPZ00JSIG48OW$at$smtp.unimi.it> for chemistry$at$ccl.net; Tue, 16 Dec 2003 11:07:21 +0100 (MET) Date: Tue, 16 Dec 2003 11:11:12 +0100 From: Giulio Vistoli Subject: CCL:Escher NG 1.0 release To: CCL Message-id: <002101c3c3bc$eea93380$424f959f@villa> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, We are proud to announce the release of Escher NG 1.0, freely downloadable at www.ddl.unimi.it ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich. The new release, with a reengineered code, includes some new features: - Protein-protein and DNA-protein docking capability. - Fast surface calculation based on the NSC algorithm. No external software are required. - Only two PDB files are required as input. - Parallel code. ESCHER NG is one of the first docking software that take full advantages of the multiprocessor hardware. Tested on two processor systems, ESCHER runs about 1.8 time faster than an equivalent single processor workstations (same CPU and same clock). These performances can be increased optimizing the code that was not originally developed to the parallel execution. ESCHER NG can run also on single processor systems in sequential mode. - Language localization. The Win32 version is included in the latest VEGA OpenGL package and in the full package we can find the source code and the executables for Win32, Irix6.2, Linux, AmigaOS. Best regards Giulio Vistoli and Alessandro Pedretti From chemistry-request@ccl.net Tue Dec 16 10:29:07 2003 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGFSY8a020691 for ; Tue, 16 Dec 2003 10:28:34 -0500 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id hBGFSYr2029597 for ; Tue, 16 Dec 2003 09:28:34 -0600 (CST) Received: from chief (chief.chem-eng.northwestern.edu [129.105.205.171]) by casbah.it.northwestern.edu via smap (V2.0) id xma029408; Tue, 16 Dec 03 09:28:28 -0600 From: "Jim Pfaendtner" To: Subject: IA64/Rocks/Gaussian 03 - Any experience/comments? Date: Tue, 16 Dec 2003 09:28:33 -0600 Message-ID: <000701c3c3e9$43f7b790$abcd6981@chief> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0008_01C3C3B6.F95D4790" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.6 required=7.0 tests=HTML_80_90,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0008_01C3C3B6.F95D4790 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi, We are considering adding a cluster which would be based on Itanium processes running the latest Rocks distribution and Gaussian 03. Does anyone have any experience with such a cluster. I have heard that Rocks 3.0.0 is unstable with the ia64 distribution. Thanks for any comments! Jim ------=_NextPart_000_0008_01C3C3B6.F95D4790 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

 

We are considering adding a cluster which would be = based on Itanium processes running the latest Rocks distribution and Gaussian = 03.  Does anyone have any experience = with such a cluster.  = I have heard that Rocks 3.0.0 is unstable with the ia64 = distribution.

 

Thanks for any comments!

 

Jim

 

------=_NextPart_000_0008_01C3C3B6.F95D4790-- From chemistry-request@ccl.net Tue Dec 16 07:16:47 2003 Received: from smtp.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hBGCGB8a016611 for ; Tue, 16 Dec 2003 07:16:15 -0500 Received: (qmail 46790 invoked by uid 2000); 16 Dec 2003 20:15:27 -0000 Message-ID: <20031216201527.46789.qmail(at)smtp.fescomail.net> From: "xiongying99" To: "CCL" Subject: the problem for AMBER parameter in ONIOM method of gaussian? Date: Tue, 16 Dec 2003 20:15:27 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="gb2312" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.3 required=7.0 tests=DEAR_SOMETHING,FROM_ENDS_IN_NUMS version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I know how to add AMBER force field parameters in the input file when I do a calculation with ONIOM method. However when I want to consider some atoms unbonded, how should I define them? For example, I will calculate a protein including two zinc ions. These two zinc ions are not bonded with any atom in this system, but the program will say, for example "Bondstretch undefined between atoms 1689(Zn) 4232". How should I solve this problem? Thank you for your time and help! ---------------------------------------------------------------- FESCOmail.net From chemistry-request@ccl.net Tue Dec 16 04:09:41 2003 Received: from mail.zrz.tu-berlin.de (mail.zrz.TU-Berlin.DE [130.149.4.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBG9978a012674 for ; Tue, 16 Dec 2003 04:09:08 -0500 Received: from localhost ([127.0.0.1] helo=mail.zrz.TU-Berlin.DE) by mail.zrz.tu-berlin.de with esmtp (exim-4.30-1) for id 1AWBCU-00031J-M7; Tue, 16 Dec 2003 10:09:06 +0100 Received: from mail.zrz.TU-Berlin.DE ([130.149.4.15]) by mail.zrz.TU-Berlin.DE (MailMonitor for SMTP v1.2.2 ) ; Tue, 16 Dec 2003 10:09:06 +0100 (CET) Received: from mailbox.tu-berlin.de ([130.149.4.18]) by mail.zrz.tu-berlin.de with esmtp (exim-4.30-1) for id 1AWBCU-00030b-Ku; Tue, 16 Dec 2003 10:09:06 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailbox.tu-berlin.de with esmtp (exim-4.30-1) for id 1AWBCU-0002PU-CL; Tue, 16 Dec 2003 10:09:06 +0100 Mime-Version: 1.0 X-Sender: chwu0531*at*mailbox.zrz.tu-berlin.de (Unverified) Message-Id: Date: Tue, 16 Dec 2003 10:09:41 +0100 To: chemistry*at*ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: fix for intel fortran 8.0 Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Virus-Scanned: Sophos MailMonitor on mail.zrz.tu-berlin.de; Tue, 16 Dec 2003 10:09:06 +0100 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 hBG99f8a012690 Dear all, when I tested the new Intel Fortran compiler, version 8.0, I noticed that quantum chemistry software did not pass the test suite. This could be traced down to a (sometimes) non-working FORTRAN index() function. Substituting the support function by the following C code (somewhere in your C source files) fixed the problem. Of course, one could compile this bit separately and substitute the library entry, but this is INTELs job. The fix is quick and dirty but ---- works. long for_f90_index(source,lens,target,lent,back) char *source,*target; int lens,lent,back; { long i; /* hand-made index function */ if (lent == 0) { if (!back) { return 0; } else { return lens+1; } } if (!back) { for (i=0; i<=lens-lent; i++) { if (!memcmp(source+i,target,(size_t) lent)) return (i+1); } } else { /* backward search */ for (i=lens-lent; i>=0; i--) { if (!memcmp(source+i,target,(size_t) lent)) return (i+1); } } if (!back) { return 0; } else { return lens+1; } } +---------------------------------+----------------------------------+ | Prof. Christoph van W|llen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitdt Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Stra_e des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen*at*TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@ccl.net Tue Dec 16 09:12:20 2003 Received: from web1.ulb.ac.be (fisu.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGEBm8a018967 for ; Tue, 16 Dec 2003 09:11:48 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id PAA05913; Tue, 16 Dec 2003 15:11:47 +0100 (MET) for chemistry*at*ccl.net Date: Tue, 16 Dec 2003 15:11:47 +0100 (MET) Message-Id: <200312161411.PAA05913*at*web1.ulb.ac.be> From: Giju Kalathingal To: chemistry*at*ccl.net Subject: Calculations without Born-Oppenheimer approximation "2nd Call" X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Last week I had send the following message without any success. So I am posting it again. Dear CCL-all, Could you please give me some info on programs that let me to do quantum chemical calculations (geometry optimzations and vibrational frequencies) without Born-Oppenheimer approximation? Thanks in advance. Giju Kalathingal Department of General Chemistry (ALGC) Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium. Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 E-mail: Giju.Kalathingal*at*vub.ac.be ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Tue Dec 16 05:04:15 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 hBGA3h8a014466 for ; Tue, 16 Dec 2003 05:03:43 -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 <0HPZ005MYFRA2J-.at.-mailserver.unimi.it> for chemistry-.at.-ccl.net; Tue, 16 Dec 2003 10:59:34 +0100 (MET) Received: from villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0HPZ00JJGFR8OW-.at.-smtp.unimi.it> for chemistry-.at.-ccl.net; Tue, 16 Dec 2003 10:59:32 +0100 (MET) Date: Tue, 16 Dec 2003 11:03:23 +0100 From: Giulio Vistoli Subject: CCL:VEGA 1.5.1 release To: CCL Message-id: <001701c3c3bb$d750c000$424f959f@villa> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, We are proud to announce the release of VEGA1.5.1 release that is freely downloadable at www.ddl.unimi.it. Between the several new function we would like to focus your attention on the capability to add the hydrogens, on the complete 3D molecular editor with fragment libraries and on the database engine. New features: - Chem3D loader. - Accelrys archive file (.arc) support in the trajectory analysis. - Capability to add the hydrogens. - RMSD calculation in the trajectory analysis. - CHARMM lipid and GRID force field templates. - POPC lipid bilayer cluster in crystal and solid phase. New OpenGL features: - ESCHER NG and ESCHER NG Plugin: protein-protein and DNA-protein docking system. - Database engine for directory, sdf and zip files. - Complete 3D molecular editor with fragment libraries. - Multiple workspaces. - Remove residue/s dialog box. - Molecule place dialog box. - Fix/merge molecules. - Multiple Mini Editor and Graph Editor windows. - Now the centroids can be updated dynamically or kept fixed. - The residue renumbering is now available for all atoms and for the selected atoms only. Best regards Giulio Vistoli & Alessandro Pedretti From chemistry-request@ccl.net Tue Dec 16 06:42:03 2003 Received: from mail.zrz.tu-berlin.de (mail.zrz.TU-Berlin.DE [130.149.4.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGBfU8a016113 for ; Tue, 16 Dec 2003 06:41:31 -0500 Received: from localhost ([127.0.0.1] helo=mail.zrz.TU-Berlin.DE) by mail.zrz.tu-berlin.de with esmtp (exim-4.30-1) for id 1AWDZy-0003JU-Kz; Tue, 16 Dec 2003 12:41:30 +0100 Received: from mail.zrz.TU-Berlin.DE ([130.149.4.15]) by mail.zrz.TU-Berlin.DE (MailMonitor for SMTP v1.2.2 ) ; Tue, 16 Dec 2003 12:41:30 +0100 (CET) Received: from mailbox.tu-berlin.de ([130.149.4.18]) by mail.zrz.tu-berlin.de with esmtp (exim-4.30-1) for id 1AWDZy-0003Ir-JU; Tue, 16 Dec 2003 12:41:30 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailbox.tu-berlin.de with esmtp (exim-4.30-1) for id 1AWDZx-0001UO-NN; Tue, 16 Dec 2003 12:41:29 +0100 Mime-Version: 1.0 X-Sender: chwu0531-.at.-mailbox.zrz.tu-berlin.de Message-Id: Date: Tue, 16 Dec 2003 12:42:05 +0100 To: chemistry-.at.-ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Intel Fortran 8.0 bug Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Virus-Scanned: Sophos MailMonitor on mail.zrz.tu-berlin.de; Tue, 16 Dec 2003 12:41:30 +0100 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 hBGBg38a016135 Meanwhile I have analyzed the error in the FORTRAN support library and constructed a small test case. Try this with ifort version 8: program test character*48 str(2) str(1)=' 1. this is some junk' str(2)=' 2. here is the target' do i=1,2 write (6,*) index(str(i), ' the') end do end and you will see what's going wrong (I got the answers 61 and 13). The error is in the support function for_string_index. It is not unreasonable to assume a problem in the quality control. +---------------------------------+----------------------------------+ | Prof. Christoph van W|llen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitdt Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Stra_e des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen-.at.-TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@ccl.net Tue Dec 16 11:38:38 2003 Received: from mail1.engr.sc.edu (mail1.engr.sc.edu [129.252.21.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGGc68a022951 for ; Tue, 16 Dec 2003 11:38:06 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Problems installing Gaussian 03 Rev B.05 Date: Tue, 16 Dec 2003 11:38:06 -0500 Message-ID: <99296F29E0A01A40A0503EB30507ECF91E9AAE.-at-.mail1.engr.sc.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Problems installing Gaussian 03 Rev B.05 Thread-Index: AcPD8vtjnnOZBaGsTTCbnzgxFGWd/g== From: "WANG, YIXUAN " To: 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 hBGGcc8a022980 Dear List Members we are having problems installing Gaussian Rev B.05 in our alpha Compaq Tru64 UNIX V5.1A (Rev. 1885) machines (revision B.04 works without problems) We think that the problem is due to a missing library. Can somebody help us with this ? % g03 resolve_symbols: loader error: dlopen: util.so: symbol "__tls_allocate_v2" unresolved % Thanks for your help, Eduardo --------------------------------------------------------- Eduardo J. Lamas Department of Chemical Engineering University of South Carolina Swearingen Engineering Center Columbia, SC 29208 Phone: (803) 777-8584 e-mail: lamas.-at-.engr.sc.edu ------------------------------------------------------- From chemistry-request@ccl.net Tue Dec 16 15:39:25 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGKcs8a027681 for ; Tue, 16 Dec 2003 15:38:54 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id hBGKcsEW028481 for ; Tue, 16 Dec 2003 15:38:54 -0500 Date: Tue, 16 Dec 2003 15:38:53 -0500 (EST) From: Jan Labanowski To: chemistry!at!ccl.net Subject: First Announcement: 4th Indo-US Workshop, Jan. 8-12, 2005 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=0.1 required=7.0 tests=EXCUSE_3,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ---------- Forwarded message ---------- Date: Tue, 16 Dec 2003 13:57:27 -0600 From: Indo-US Workshop Series To: Jan K Labanowski Subject: First Announcement: 4th Indo-US Workshop, Jan. 8-12, 2005 Fourth Indo-US Workshop on Mathematical Chemistry January 8 12, 2005 Pune, India The Fourth Indo-US Workshop on Mathematical Chemistry with applications to drug design, risk assessment of chemicals, chemoinformatics, bioinformatics, computational biology and toxicology will be held during January 8 12, 2005, in Pune, India. The conference is being sponsored jointly by the University of Pune, Pune, Maharashtra (India), the Natural Resources Research Institute of the University of Minnesota Duluth, (USA) and the International Society of Mathematical Chemistry. Dilip K. Sinha, University of Calcutta (India) and Subhash C. Basak, Natural Resources Research Institute, University of Minnesota Duluth (USA), are the Co-Chairpersons of the Indo-US Workshop on Mathematical Chemistry Series from India and the United States, respectively. The First Indo-US Workshop was held during January 9-13, 1998, at Visva Bharati University, Santiniketan, West Bengal, India. The Second Indo-US Workshop was held at the University of Minnesota Duluth, USA, during May 30-June 3, 2000. Over one hundred scientists from four continents participated in both the First and Second Indo-US Workshops. The Third Indo-US Workshop was held this past August (2 7, 2003) at the University of Minnesota Duluth, USA. The Fourth Indo-US Workshop will bring together leading researchers in the field of Mathematical and Computational Chemistry. The results of the latest research in the field will be presented along with important applications of mathematical and computational approaches to chemistry, drug discovery, environmental toxicology, quantitative structure-activity relationships (QSAR), quantitative molecular similarity analysis (QMSA), chemoinformatics and bioinformatics, including genomics and proteomics. Tentative titles for presentations are now being accepted for the Fourth Indo-US Workshop. If you are interested in participating in this workshop please send the title of your presentation along with your name and contact information by email (preferred), fax or mail to: Fourth Indo-US Workshop co/Brian Gute Natural Resources Research Institute University of Minnesota Duluth 5013 Miller Trunk Highway Duluth, MN 55811 Fax: +1-218-720-4328 mathchem!at!nrri.umn.edu For further information please contact Drs. Subhash C. Basak or Indira Ghosh Subhash C. Basak Workshop Series Co-Chairperson (USA) Natural Resources Research Institute University of Minnesota Duluth 5013 Miller Trunk Highway Duluth, MN 55811, USA Tel: (218) 720-4230 Fax: (218) 720-4328 sbasak!at!nrri.umn.eduIndira Ghosh Bioinformatics Center Institute of Bioinformatics & Biotechnology University of Pune, Ganeshkhind Pune, 411 007 Tel: +91 20 569 0195 indira!at!bioinfo.ernert.in This announcement has also been posted on the Workshop website and further details will be forthcoming: http://www.nrri.umn.edu/indousworkshop/ Thanks again for your interest in the Indo-US Workshop series. If you find this information useful, be sure to share it with a friend! To subscribe or cancel a subscription: If this workshop newsletter was forwarded to you by a friend and you would like to receive future mailings, please send an email with Subscribe in the Subject header to mathchem!at!nrri.umn.edu To be removed from this workshop newsletter subscription list, send an email with Unsubscribe in the Subject header to mathchem!at!nrri.umn.edu The University of Minnesota is an equal opportunity educator and employer. From chemistry-request@ccl.net Tue Dec 16 20:09:22 2003 Received: from smtp.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hBH18m8a030854 for ; Tue, 16 Dec 2003 20:08:49 -0500 Received: (qmail 78431 invoked by uid 2000); 17 Dec 2003 09:08:08 -0000 Message-ID: <20031217090808.78430.qmail..at..smtp.fescomail.net> References: <20031216201527.46789.qmail..at..smtp.fescomail.net> <3FDF723B.2080000..at..jh-inst.cas.cz> In-Reply-To: <3FDF723B.2080000..at..jh-inst.cas.cz> From: "xiongying99" To: lubos.vrbka..at..jh-inst.cas.cz, "CCL" Subject: Re: CCL:the problem for AMBER parameter in ONIOM method of gaussian? Date: Wed, 17 Dec 2003 09:08:08 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="gb2312" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=1.3 required=7.0 tests=DEAR_SOMETHING,FROM_ENDS_IN_NUMS,IN_REP_TO, QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Lubos Vrbka You can add force field parameter in G03. Please see the manual of G03: the section" Molecular Mechanics Methods". You can also see the example file" test528.gjf" in G03. !!!!!!!!!!!!!!!!xiongying !!!!!!!!!!!!!!!!yxiong..at..mail.ccnu.edu.cn !!!!!!!! !!!!!!!!!!!!2003-12-16 > dear sir, > >> I know how to add AMBER force field parameters in the input file when I >> do a calculation with ONIOM method. However when I want to consider some >> atoms unbonded, how should I define them? For example, I will calculate >> a protein including two zinc ions. These two zinc ions are not bonded >> with any atom in this system, but the program will say, for example >> "Bondstretch undefined between atoms 1689(Zn) 4232". How should I solve >> this problem? > i was running some simulation using ONIOM and amber forcefield in > gaussian03. there was mg cation solvated by water molecules... i had no > problems using the amber force field, and i didn't see any such error > messages... part of my input file follows, you could find some relevant > info... > > #p oniom(b3lyp/gen:amber) opt freq maxdisk=1gb > > name > > 2 1 > ! "inner shell"; amber atom types are necessary > Mg-Mg2+ 0.00000 0.00000 0.00000 > O-OW -2.11300 0.00000 0.00000 > H-HW -2.69100 -0.77600 0.00000 > H-HW -2.69100 0.77600 0.00000 > O-OW 2.11300 0.00000 0.00000 > H-HW 2.69100 -0.77600 0.00000 > H-HW 2.69100 0.77600 0.00000 > O-OW 0.00000 -2.11300 0.00000 > H-HW 0.00000 -2.69100 -0.77600 > H-HW 0.00000 -2.69100 0.77600 > O-OW 0.00000 2.11300 0.00000 > H-HW 0.00000 2.69100 -0.77600 > H-HW 0.00000 2.69100 0.77600 > O-OW 0.00000 0.00000 -2.11300 > H-HW -0.77600 0.00000 -2.69100 > H-HW 0.77600 0.00000 -2.69100 > O-OW 0.00000 0.00000 2.11300 > H-HW -0.77600 0.00000 2.69100 > H-HW 0.77600 0.00000 2.69100 > ! "outer shell"; amber atom types are necessary > O-OW -0.92900 -5.66100 -2.36200 medium > H-HW -1.74200 -6.03500 -2.70300 medium > ... > > could i have one question, too, please? i recall recent post at ccl > concerning getting non-standard amber types to amber. there was no > response to the author. you mention in the beginning of your mail that > you know how to include such parameters in the calculation. as i don't > know how, could you please tell me? i would be very grateful for any > information (i.e. useful links on web or just sample input file...) > > hope my information help... kind regards, > l.v. > > -- > ..................................................... > Mgr. Lubos Vrbka > > Center for Complex Molecular Systems and Biomolecules > J. Heyrovsky Institute of Physical Chemistry > Academy of Sciences of the Czech Republic > Prague, Czech Republic > > http://www.jh-inst.cas.cz/~vrbka > ..................................................... > ---------------------------------------------------------------- FESCOmail.net From chemistry-request@ccl.net Tue Dec 16 18:03:58 2003 Received: from smtp4.server.rpi.edu (smtp4.server.rpi.edu [128.113.2.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGN3P8a029487 for ; Tue, 16 Dec 2003 18:03:26 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp4.server.rpi.edu (8.12.10/8.12.9) with ESMTP id hBGN3Qto018674; Tue, 16 Dec 2003 18:03:26 -0500 Message-Id: <200312162303.hBGN3Qto018674..at..smtp4.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: gkalathi..at..vub.ac.be From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry..at..ccl.net X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Tue, 16 Dec 2003 18:03:25 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:Calculations without Born-Oppenheimer approximation "2nd Call" X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=-0.5 required=7.0 tests=EMAIL_ATTRIBUTION version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Tue, 16 Dec 2003 15:11:47 +0100 (MET) Giju Kalathingal wrote: > Last week I had send the following message without > any success. So I am posting it again. > > Dear CCL-all, > > Could you please give me some info on programs > that let me to do quantum chemical calculations > (geometry optimzations and vibrational frequencies) > without Born-Oppenheimer approximation? > > Thanks in advance. > > Giju Kalathingal > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Perhaps the reason you did not get any response was because your question specifically dealt with programs for geometry optimzations and vibrational frequencies. These concepts (molecular geometry and molecular vibrations) are normally understood within the Born-Oppenheimer approximation. I do not know of any readily available programs that deal with these outside of BO. However quantities such as bond lengths and vibrational frequencies are derivable from experiment and thus these concepts ARE defined beyond the Born-Oppenheimer approximation: equilibrium bond lengths, for instance, would be defined as the peaks in the two-particle radial distribution functions for the two bonded nuclei. See the special issue of Israel Journal of Chemistry, vol.19 (1980) for many papers (and much debate), e.g. those of R.G.Woolley, pp.30-46 and of Carl Trindle, pp.47-53. L. Lathouwers and P. Van Leuven (CPL 52, 439, 1977; PRA 18, 2150, 1978; IJQC S12, 371, 1978) demonstrated that the generator coordinate method could be employed to avoid the BO separation and develop a non-adiabatic formulation of molecular quantum theory. In a series of pioneering papers on hydrides (CPL 3, 705, 1969; PS 185, 90, 1969; PRA 2, 728, 1200, 1675, 1970; PRA 3, 565, 1022, 1971; PRA 4, 457, 1971; PRA 5, 1104, 1972), I.L.Thomas put electrons into electronic orbitals and protons into protonic orbitals (thereby avoiding the BO approximation), antisymmetrized the two kinds of orbitals separately, performed SCF computations and obtained molecular structures and spectra that corresponded to experiment. For instance, the microwave transition frequency of ammonia (conventionally explained by "umbrella flipping" between two structures) is now obtained as the transition frequency between protonic orbitals. Subsequently Thomas went on to become vice-president of Occidental Petroleum and did not continue his protonic structure studies. I wrote some programs to do similar computations as part of my candidacy work at Stony Brook in the early 80s, but those are now lost on some magnetic tape somewhere. There are now several computations and programs that go beyond the BO approximation by calculating the nonadiabatic coupling terms or performing a diabatic transformation in multi-reference CI or CASSCF spaces (see e.g. D.R.Yarkony in "Modern Electronic Structure Theory" Part I, World Scientific, Singapore, 1995, pp.642-721; W.Domcke, et al. CPL 216,362, 1993; 226, 257, 1994; Neuheuser, Sukumar and Peyerimhoff, Chem.Phys., 194, 45-64, 1995; Mol.Phys. 95, 61-70, 1998) but none of these can be considered as truly "without Born-Oppenheimer approximation" (PRA=Phys.Rev A; CPL=Chem.Phys.Lett.; IJQC=Int.J.Quantum Chem) N. Sukumar RPI Department of Chemistry From chemistry-request@ccl.net Tue Dec 16 12:19:51 2003 Received: from postal.sdsc.edu (postal.sdsc.edu [132.249.20.114]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBGHJK8a024046 for ; Tue, 16 Dec 2003 12:19:20 -0500 Received: from tick.sdsc.edu (IDENT:wd4vHgplOTFgTFy3I4MP6n22gOAEdmEa..at..tick.sdsc.edu [132.249.20.95]) by postal.sdsc.edu (8.11.7/8.11.7/server/62) with ESMTP id hBGHJHJ01295; Tue, 16 Dec 2003 09:19:17 -0800 (PST) Received: from localhost by tick.sdsc.edu (SGI-8.9.3p2/1.11-IRIXclient) with ESMTP id JAA53880; Tue, 16 Dec 2003 09:19:17 -0800 (PST) Date: Tue, 16 Dec 2003 09:19:17 -0800 From: Laura Brovold To: Jim Pfaendtner cc: Subject: Re: CCL:IA64/Rocks/Gaussian 03 - Any experience/comments? In-Reply-To: <000701c3c3e9$43f7b790$abcd6981@chief> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Greetings I've run GAMESS (US) computations on several x86-based Rocks clusters and have been extremely pleased with the systems. With that said, I don't have any direct experience with itanium-based rocks clusters, but their 'Rocks register' web page indicates there are a handful of itanium-based Rocks clusters up and running: http://www.rocksclusters.org/rocks-register/index.php?sortby=CPUType&sortorder=up Additionally, from their discussion list, I have not read any messages that indicate the above clusters are unstable. It appears there will be a new release of Rocks soon (I believe by the beginning of next week) for x86, itanium and opteron clusters that will be based on Red Hat Enterprise Linux 3. Best Regards, Laura Gregerson On Tue, 16 Dec 2003, Jim Pfaendtner wrote: > Hi, > > We are considering adding a cluster which would be based on Itanium > processes running the latest Rocks distribution and Gaussian 03. Does > anyone have any experience with such a cluster. I have heard that Rocks > 3.0.0 is unstable with the ia64 distribution. > > Thanks for any comments! > > Jim > > ----------------------------------------- Laura Gregerson (Brovold) UCSD/SDSC MC-0505 9500 Gilman Dr. La Jolla, CA 92093-0505 phone:(858)534-5007 http://www.sdsc.edu/~lgregers/laura.html -----------------------------------------