From ccl@www.ccl.net Tue Oct 29 01:32:43 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id AAA25253; Tue, 29 Oct 1996 00:35:12 -0500 (EST) Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by bedrock.ccl.net (8.8.0/950822.1) id AAA03078; Tue, 29 Oct 1996 00:35:09 -0500 (EST) Received: from [138.194.40.204] (mac-40204.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA11369 (5.67b/IDA-1.5 for chemistry@ccl.net); Tue, 29 Oct 1996 16:31:17 +1100 From: "Dr. Dave Winkler" Date: Tue, 29 Oct 1996 16:31:17 +1100 Message-Id: To: chemistry@ccl.net Subject: RACI Med Chem & Pharma Conf - Australia Papers for RACI medicinal chemistry and pharmacology conference Please excuse cross postings. If anyone wants to register there is still time if they email me back in the next week or so or check URL for registration forms and first circular: http://www.chem.swin.edu.au/ma/mconf.html ROYAL AUSTRALIAN CHEMICAL INSTITUTE MEDICINAL & AGRICULTURAL DIVISION 13TH NATIONAL CONFERENCE "UP AND COMING RESEARCH IN AUSTRALIA" 8-11 DECEMBER, 1996, Monash University, Clayton 3168, Victoria, Australia Sunday 8 December ----------------- Research/Industry Interface Hands on Workshop Monday 9 December ----------------- New Paradigms in Drug Discovery (Chair: Prof Peter Andrews) Mark Gallop Combinatorial Chemistry: New Technologies for Drug Discovery Joe Maeji Parallel solid phase organic synthesis. Ron Quinn High throughput screening in natural product drug discovery New Directions in Drug Development (Chair: Prof. Graham Johnston) Nick Nicola Use of the CytoSensor to study cytokine signal transduction pathways Lew Defining the pharmacophore of omega conotoxin G6a - different results between biochemical and binding assays by alanine scan Paul Rolan Use of models and surrogates to expedite exploratory development. Leighton Medal Lecture (Prof. Graham Johnston) (Chair. Prof. Colin Raston) Workshop on Chemical Databases (Damon Ridley) Combined poster session. Tuesday 10 December ------------------- Biota Medal lecture Emerging disease threats (Chair: Dr. Andrea Robinson) Colin Masters Prions and dementia Seb Marcuccio Synthesis and Evaluation of Selected Acyclic Nucleoside Analogues as Antiviral Agents Colin Barrow Exploring the Chemical basis of Amyloid Formation in Alzheimer's Disease DNA and Cancer (Chair: Prof. Bob Brownlee) Bill Denny The Design of Tumour-Activated Prodrugs for Cancer Chemotherapy Venkataraman Novel Therapeutic Principal: Antisense Paradigm and Role of Computational Chemistry Marg't Harding Organometallic Anticancer Agents Sutherland A Combinatorial Approach to the Base Sequence Selectivity of DNA Binding Molecules McFadyen Prointercalators Based on the Co(III)/Co(II) Redox Couple as Potential Hypoxia-selective Cytotoxins 1400-1530 Agrochemistry (Chair: Dr. Kevin Winzenberg) Jim Peacock Gene shears and gene Technology in Agribusiness Max Tate Monitoring Vetch Toxins in Feed and Food (Keeping "Them" Honest) Delaere Needle in a Haystack. The Chemistry of in situ quantitation Whitelaw Solubilization of Inorganic Soil Phosphates by the Soil Fungus Penicillium radicm (sp. nov.) Parallels between agrochemical and drug discovery (Chair: Dr. Andy Liepa) George Fleet Sugar Mimics: From Hydantocidin to a new Class of Amino Acids Shiela Unkles The Potential of Biosynthetic Pathways as Targets for Novel Antifungal Agents Winzenberg Strategies for Discovering New Crop Protection Chemicals Johnson Use of Natural Products Sinharine and Strobilurin A, as Lead Structures for Crop Protection Chemicals Wednesday 11 December --------------------- Adrien Albert lecture - Dr. Keith Watson (Chair: Dr. Margaret Wong) Glycomimetic chemistry (Chair: Dr. Dave Winkler) George Fleet Sugar Mimics: Bicyclic and other Nitrogen Analogues of Sugars von Itzstein Synthesis of Functionalized Sialic Acids as Biological Probes Ooi An Investigation of Silaic Acid Lyase from E. coli Novel medicinal approaches (Chair: Dr. Tracy Nero) Dave Manallack Matrix Metalloproteinases in Inflammation Lia Addadi Protein Control Over Formation of Mineral Phases in Biomineralization Breuer A Peptidyl Prodrug of a Bisphosphonate for Improved Oral Absorption Coghlan Nitro Amino Acids as Masked Dehydroamino Acid Residues in Peptides McCluskey Novel Protein Phosphatase 1 and 2A Inhibitors: Analogues of Cantharidin Kuiper Molecular Modelling and Synthesis of Antifreeze Peptides Therapeutic leads from Natural Products (Chair: Dr. Seb Marcuccio) Roufogalis Development of Drug Leads from Plants Against Specific Biological Targets Paul Alewood Conatoxins as Molecular Templates for Drug Design Hood Preliminary Studies into a New Class of Non-nucleoside Inhibitors of Reverse Transcriptase Jones Host-Dependent and Independent Consituents of Mistletoes Learning and Cognition (Chair: Dr. Ted Lloyd) John Bremner Training of Medicinal Chemists: Opportunities to Lead Marg Wong A Year before The Mast: Developing Computational Chemistry Teaching Packages for use via the Internet Maddalena Prediction of Isoreceptor Binding Affinity with Neural Nets Soloviev Molecular Properties of a Unitary NMDA/Non-NMDA Glutamate Receptor Griffith What Makes a Ligand Selective for the Dopamine D4 Receptor Subtype? Jamie Design and Synthesis of Potent Inhibitors of Indoleamine 2, 3-Dioxygenase Cheers, Dave Dr. David A. Winkler Voice: 61-3-9542-2477 Principal Research Scientist Fax: 61-3-9543-8160 CSIRO Division of Chemicals and Polymers http://www.csiro.au Private Bag 10,Clayton South MDC, http://www.wark.csiro.au Clayton 3169, Australia From John_Beckerle@quickmail.clemson.edu Mon Oct 28 11:32:35 1996 Received: from CLEMSON.EDU for John_Beckerle@quickmail.clemson.edu by www.ccl.net (8.8.0/950822.1) id LAA20756; Mon, 28 Oct 1996 11:09:19 -0500 (EST) Received: from quickmail.clemson.edu (quickmail.clemson.edu [130.127.8.57]) by CLEMSON.EDU (8.7.5/8.7.3) with SMTP id LAA02368 for ; Mon, 28 Oct 1996 11:09:11 -0500 (EST) Message-ID: Date: 28 Oct 1996 11:57:33 -0500 From: "John Beckerle" Subject: G94- Calculations with redu To: "List CCL" I would like advice on the best and easiest way to perform a calculation in G94 at a lower symmetry than the full symmetry of the molecule, but still above the NOSYMMETRY level. The only method I have come up with is to distort the molecular coordinates slightly such that the molecule retains only the amount of symmetry I want, and then perform a calculation as usual. Is there a better way? Thanks in advance. John Beckerle beckerj@clemson.edu From ccl@www.ccl.net Tue Oct 29 23:17:29 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id XAA01738; Tue, 29 Oct 1996 23:00:10 -0500 (EST) Received: from pasteur.sc.ucl.ac.be for drossart@cico.ucl.ac.be by bedrock.ccl.net (8.8.2/950822.1) id XAA27046; Tue, 29 Oct 1996 23:00:08 -0500 (EST) Received: from drossart.cico.ucl.ac.be by pasteur.sc.ucl.ac.be (5.x/SMI-SVR4) id AA29089; Wed, 30 Oct 1996 05:01:41 +0100 Message-Id: <3276D24E.62A@cico.ucl.ac.be> Date: Wed, 30 Oct 1996 04:58:06 +0100 From: DROSSART Claude Reply-To: drossart@cico.ucl.ac.be Organization: U.C.L. - CICO - Chop To: chemistry@ccl.net Subject: ESOR-VI - 6th Euro Symp. on Organic React ESOR-VI 6th European Symposium on Organic reactivity Louvain-la-Neuve 24 - 29 July 1997 _______________________________________First Circular The Catholic University of Louvain, located in the Belgian city of Louvain-la-Neuve, will host the next conference entitled "European Symposium on Organic Reactivity". This will be the sixth edition of a series of successful meetings held in Paris (1987), Padova (1989), Goteborg (1991), Newcastle-upon-Tyne (1993) and Santiago de Compostela (1995). The conference will be held during the period Thursday 24 to Tuesday 29 July 1997. The scientific sessions will start on Thursday afternoon and the meeting will end at lunchtime on Tuesday. Location ________ Louvain-la-Neuve is located about 30 km South of Brussels in the french-speaking part of Belgium. The city is connected with Brussels by rail and is readily accessible by road (Motorway E411) from everywhere in Europe. Brussels National Airport is linked to all major and most medium-size European cities. The Conference site will be part of the academic facilities of the Catholic University of Louvain (U.C.L.). This University was founded in the old Belgian city of Leuven in 1425 as one of the oldest universities in Europe. In the early 1970's, the french-speaking part of the University moved to a completely new city which was called Louvain-la-Neuve, on the territory of a town named Ottignies. The University population amounts to more than 20,000 students. Courses are organized in all disciplines of human knowledge by ten Faculties : Theology, Philosophy, Law, Economic and Social Sciences, Philology and Arts, Psychology and Educational Sciences, Sciences, Applied Sciences, Medicine and Agronomy. Scientific Programme ____________________ The meeting will be devoted to all aspects of physical organic chemistry. The conference programme will focus on three main topics : 1. Mechanisms and reactivity in organic, bioorganic and organometallic chemistry, including theoretical approaches 2. Photochemical and electron transfer activation processes 3. Molecular recognition and enzyme mechanism. The programme will include 12 plenary lectures, two parallel sessions with their own invited lectures. A limited number of oral presentations will be selected among the submitted contributions. Two separate poster sessions are planned on Friday afternoon and Monday afternoon with comfortable discussion times. Persons wishing to present an oral or poster contribution should submit a one-page abstract according to the format detailed below not later than February 15, 1997 and send it to Prof. M. Devillers ESOR-VI Conference Secretary Catholic University of Louvain Laboratory of Inorganic and Analytical Chemistry 1 place Louis Pasteur B-1348 Louvain-la-Neuve , Belgium Tel. : 32-10 47 28 27 Fax : 32-10 47 28 36 e-mail : devillers@inan.ucl.ac.be Plenary lectures ________________ Twelve recognized experts have already agreed to give Plenary Lectures on the following topics : V. Balzani,University of Bologna, Italy, Supramolecular photochemistry. S.J. Benkovic,The Pennsylvania State University, USA, Perspective on biocatalysis. F. Diederich,Swiss Federal Institute of Technology, Zurich, From supramolecular chemistry to medicinal chemistry. J.B. Engberts,University of Groningen, The Netherlands, Vesicles formed from synthetic amphiphiles. Fusogenic behavior and applications as drug carrier systems. J. Frechet,Cornell University, USA, Designing for novel macromolecular architectures:from concept to applications. B.Giese,University of Basel, Switzerland, Reactivity of DNA radicals. Y. Kishi,Harvard University, USA, Synthetic studies in the field of natural product chemistry. H. Mayr,Technische Hochschule Darmstadt, Germany, Linear free enthalpy relationship : a powerful tool for the design of organic or organometallic syntheses. R. Noyori,Nagoya University, Japan, Asymmetric hydrogenation : mechanistic aspects. M. Poliakoff,University of Nottingham, U.K., Intermediates in organometallic chemistry. P. von Rague Schleyer,University of Erlangen-Nuernberg, Germany, Organic reactivity and computational chemistry. I. Willner,The Hebrew University of Jerusalem, Israel, Electroenzymes, photoenzymes and command surfaces - Tailored assemblies for optobioelectronic devices. Abstracts _________ Full one-page abstracts will be reproduced directly from authors'original documents. They should be typed or printed in English using double line spacing on A4 formatted white paper. The whole of the abstract must be contained within a rectangle of size 242 x 165 mm. It will be reduced to 79%. The headings should be presented in the format given below, including the full line separating text and heading. References should be indicated within square brackets in the text and listed at the bottom of the abstract using standard Chemical Abstracts Source Service Index terminology followed by volume,(year within brackets) , first page. Example: DECOMPOSITION OF NITROSOUREAS IN THE PRESENCE OF DIFFERENT NUCLEOPHILES S. Amado*, A. Andrade, L. Garcia-Rio, J.R. Leis and A.M. Rios, Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Santiago, 15706 Santiago de Compostela, Spain. The reactivity of different nucleophiles toward the ambident electrophile N-nitroso-N,N'-dimethylurea (NDMU) has been investigated. The experimental results... The Book of Abstracts including all lectures and oral or poster contributions will be handed out to all registered participants upon arrival. Social Events _____________ The provisional social programme for Conference participants includes the following events : Thursday : Welcome drink and get-together sandwich buffet at lunchtime Thursday evening : Concert Friday evening : Belgian Cheese and Beer party at the end of the poster session Sunday afternoon : Excursion Monday evening : Conference Dinner An Accompanying Persons' Programme will be arranged for the whole conference period. Further details will be included in the Second Circular. Registration fees _________________ -Normal pre-registration fee before March 31, 1997 BEF 10 000 Registration fee after March 31, 1997 BEF 12 500 -Students before March 31, 1997 BEF 5 000 after March 31, 1997 BEF 6 000 -Participants from Industry before March 31, 1997 BEF 15 000 after March 31, 1997 BEF 18 000 -Accompanying Persons BEF 2 000 Organizing Committees _____________________ Local Organizing committee -------------------------- Chairmen :Prof. J. Fastrez and Prof. L. Ghosez (U.C.L., Louvain-la-Neuve) Conference Secretary :Prof. M. Devillers (U.C.L., Louvain-la-Neuve) Members : Dr. O. B Nagy (U.C.L., Louvain-la-Neuve) Prof. P. De Clercq (R.U.G., Gent) Prof. F. De Schrijver (K.U.L., Leuven) Prof. L. Hevesi, (F.U.N.D.P., Namur) Prof. F. Kirsch-Demesmaeker (U.L.B., Brussels) Prof. A. Laschewsky (U.C.L., Louvain-la-Neuve) Prof. J. Marchand-Brynaert (U.C.L., Louvain-la-Neuve) Prof. J.-P. Soumillion (U.C.L., Louvain-la-Neuve) International Advisory Committee -------------------------------- Prof. P. Ahlberg (Chairman, Goteborg, Sweden) Dr. M. Eckert-Maksic (Zagreb, Croatia) Prof. J. Engberts (Groningen, Netherlands) Dr. R. Leis (Santiago de Compostela, Spain) Dr. H. Maskill (Newcastle-upon-Tyne, England) Prof. R. More O'Ferrall (Dublin, Ireland) Prof. P. Mueller (Geneve, Switzerland) Prof. M. Page (Huddersfield, England) Prof. Z. Rappoport (Jerusalem, Israel) Prof. M.-F. Ruasse (Paris, France) Prof. G. Scorrano (Padova, Italy) Prof. U. Siehl (Ulm, Germany) For further information, please refer to the Scientific Secretariat of the Conference : Prof. M. Devillers ESOR-VI Conference Secretary Catholic University of Louvain Laboratory of Inorganic and Analytical Chemistry 1 place Louis Pasteur B-1348 Louvain-la-Neuve , Belgium Tel. : 32-10 47 28 27 Fax : 32-10 47 28 36 e-mail : devillers@inan.ucl.ac.be or get a moment to see our page maintained by Claude Drossart at: http://www.chim.ucl.ac.be/CHIM/esor.html To receive the Second Circular/Application Form for this Symposium (January 1997), please print and fill in the following form, send it to the Conference Secretary ( or an Email with the same information). DO NOT SEND YOUR REPLY TO THE LIST ! _______________________________________________________________ Title : Prof. - Dr. - Mr. - Mrs. (circle when applicable) Name : ____________________________________________________________ First Name : ____________________________________________________________ Institution : ____________________________________________________________ Address : ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ tel:_________________ fax:_____________________ e-mail:__________________________________________ I intend to present a short contribution preferably as oral presentation preferably as a poster I have no preference between oral and poster presentation [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] ==================================================================== Avec les meilleurs sentiments de Claude Drossart, Universite catholique de Louvain-CICO-Chop 1, place Pasteur, 1348-Louvain la Neuve (Wallonie-Belgique) tel: 32-10-472714/ fax: 32-10-473074 From jeanne@tc.cornell.edu Mon Oct 28 09:32:36 1996 Received: from theory.tc.cornell.edu for jeanne@tc.cornell.edu by www.ccl.net (8.8.0/950822.1) id JAA20105; Mon, 28 Oct 1996 09:31:26 -0500 (EST) Received: from [128.84.181.75] (JEANNE.TC.CORNELL.EDU [128.84.181.75]) by theory.tc.cornell.edu (8.6.9/8.6.6) with ESMTP id JAA45521; Mon, 28 Oct 1996 09:24:54 -0500 Message-Id: Date: Mon, 28 Oct 1996 09:35:46 -0500 To: chemistry@www.ccl.net From: "Jeanne C. Butler" Subject: Cornell Theory Center Virtual Workshop Cornell Theory Center Virtual Workshop Parallel Programming with MPI and HPF ..... January 8 to March 7, 1997 Registration deadline November 27, 1996 ..... The Virtual Workshop is an entirely over-the-network program for studying high performance computing. You work at your own pace from your home machine, with access to Web-based course materials, the CTC's world-class IBM RS/6000 SP, and dedicated e-mail consulting. This workshop covers two different approaches to developing parallel programs for a distributed memory environment: the MPI message-passing library (January 8 - February 7) and the HPF extensions to the Fortran 90 language (February 10 - March 7). You may choose to study one or both. Additional registration and course information is available at: http://www.tc.cornell.edu/Edu/VW/ From ragno@serifos.caspur.it Mon Oct 28 03:32:33 1996 Received: from serifos.caspur.it for ragno@serifos.caspur.it by www.ccl.net (8.8.0/950822.1) id CAA15437; Mon, 28 Oct 1996 02:57:08 -0500 (EST) Received: by serifos.caspur.it; id AA21982; Mon, 28 Oct 1996 08:52:53 +0100 Date: Mon, 28 Oct 1996 08:52:53 +0100 (MET) From: Gianluca Sbardella To: Tong Peng Cc: chemistry@www.ccl.net Subject: Re: CCL:Data of amino acids? In-Reply-To: Message-Id: On Fri, 25 Oct 1996, Tong Peng wrote: > Hi, everybody, > > I'd like to know where can I find data of amino acids, such their > geometry, bond length and angle of peptide bonds etc. And is there an > online resource of such kind of informations? > > Much thanks. > > Tong Peng peng@risc.nyu.edu > > Dear Dr. Peng, among the several mailing lists there's a Structural Biology List which may fit your purpose. Here is how the welcome message sounds like: > From owner@csb0.IPC.PKU.EDU.CN Mon Oct 28 08:45:39 1996 Date: Wed, 25 Sep 1996 08:56:31 -0700 (PDT) From: Lists Owner To: ragno@serifos.caspur.it Subject: welcome ********* Welcome to the Structural Biology Mailing List! ********* You have been added to this list. Welcome on board! Hope you would enjoy this list. The following text is a brief introduction to the structural biology list. Keeping it will be certainly helpful. ___________________________________________________________________ A Brief Introduction to the Structural Biology Mailing List ___________________________________________________________________ Contents: 1. About the structural biology list 2. How to subscribe/unsubscribe 3. General rules 4. About the list owner ------------------------------------------------------------------- 1. About the structural biology list This mailing list is organized for structural biologists. All the concerned researchers are encouraged to take part in. The supposed topics include: o Macromolecular crystallography o NMR and other spectroscopies o Molecular modeling and design o Structure-based drug design and QSAR o Bioinformatics o Theoretical and computational biology To send your mail to everyone in the list, please mail to: sbl@ipc.pku.edu.cn If you have any problem or special request, please mail to: owner@ipc.pku.edu.cn 2. How to subscribe/unsubscribe To subscribe, just send a short mail to owner@ipc.pku.edu.cn like this, "Please add me to the SBL ...". (This list is not maintained by a cool program but a kind young person.) Please state clearly your name, title, address, country, e-mail and academic interests. These information will be summarized in a certain database. To leave this list, please send a mail to owner@ipc.pku.edu.cn, saying "Mmm, I am tired ..." or "I am leaving on vacation ..." or anything that can make it clear. 3. General rules As a member of this list, please feel free to forward any question or propose any discussion concerning with structural biology. If you have received enough answers to your question, please summarize it and send it back to the list so that everybody can learn from it. You have the right to forward questions and you have the responsibility to offer what you know when you see a question. Conference announcements or product advertisements are proper for the list too. Please bear in mind that the SBL is unsupervised, which means ANY mail sent to the list will be automatically forwarded to everyone. So please do not send junk mail to the list. The owner of the SBL will keep an eye on this and get rid of those trouble-makers. Try to be ACTIVE. An active mailing list will be really helpful. Or this can be understood in a thermodynamic view: We, all the members of SBL, form a close system. Information (negative entropy) is generated continuously inside this system. Therefore according to the Second Law, energy must be put into this system to keep it and develope it. The energy comes from you, from me, from the love heart of everyone. :-) 4. About the list owner The structural biology list is sponsored by Prof. Luhua Lai and Mr. Arthur Wang. It is maintained by Mr. Arthur Wang, who is an energetic doctoral student. (arthur@ipc.pku.edu.cn). Any comments on this list will be welcome. The mail server locates at the Institute of Physical Chemistry, Peking University, Beijing, China. We have maintained an on-line bioinformatics server here: http://162.105.177.12/mirror/mirror.html At present, we are the formal mirror site of PDB and SCOP in China. Some other important databases, such as PIR, SWISSPROT, ENZYME, PROSITE and BLOCKS, are available too. Maybe you can save your network resources by visiting our server. ---------------------------- The End ------------------------------- As you read, you may subscribe sending a message such as "Please subscribe me to this list..." to owner@ipc.pku.edu.cn. Hope this helps. Bye, Gianluca Sbardella *************************************************************** * * * Dr. Gianluca Sbardella E-mail: ragno@kea.caspur.it * * Dip. Studi Farmaceutici ragno@serifos.caspur.it * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * * * * !!The electronic address is going to be changed into!! * * * * -->r.ragno@caspur.it<-- * * * *************************************************************** From ccl@www.ccl.net Wed Oct 30 15:17:39 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id OAA06756; Wed, 30 Oct 1996 14:25:11 -0500 (EST) Received: from cliff.bms.com for david@viper.bms.com by bedrock.ccl.net (8.8.2/950822.1) id OAA08875; Wed, 30 Oct 1996 14:24:55 -0500 (EST) Received: from viper (viper.wf.bms.com) by cliff.bms.com (PMDF V5.0-7 #15142) id <01IB9BPEBEGG00O7R7@cliff.bms.com> for chemistry@ccl.net; Wed, 30 Oct 1996 15:24:33 -0500 (EST) Received: by viper (950413.SGI.8.6.12/930416.SGI) for chemistry@ccl.net id OAA28579; Wed, 30 Oct 1996 14:23:36 -0500 Date: Wed, 30 Oct 1996 14:23:36 -0500 From: "David R. Langley" Subject: Counterion Distribution To: chemistry@ccl.net Message-id: <9610301423.ZM28577@viper.wf.bms.com> Dear All, I am looking for a program or CHARMM script to analize the most populated counterion positions around a biomolecule from a MD simulation. In (M.A.L. Eriksson, T. Hard and L. Nilsson, Biophysical Journal, 1995, 68, 402-426) a 3-d histogram density map was constructed from an analysis of the MD run. Is this program avalible? David R. Langley From ccl@www.ccl.net Wed Oct 30 13:17:38 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id MAA06157; Wed, 30 Oct 1996 12:29:41 -0500 (EST) Received: from sapphire.tau.ac.il for becker@sapphire.tau.ac.il by bedrock.ccl.net (8.8.2/950822.1) id MAA06515; Wed, 30 Oct 1996 12:29:35 -0500 (EST) Received: by sapphire.tau.ac.il; id AA19894; Wed, 30 Oct 1996 19:29:19 +0200 Date: Wed, 30 Oct 1996 19:29:19 +0200 (IST) From: "Oren M. Becker" To: chemistry@ccl.net, drug.dna@sci.prot.ac.uk, pdb-l@pdb.pdb.bnl.gov, bioforum@net.bio.net, biophys@net.bio.net, microbio@net.bio.net, molmodel@net.bio.net, comp-bio@net.bio.net Cc: Yechiel Becker , Oren Becker Subject: Computation in Molecular Biology Workshop, 2-11 Feb 1997 Message-Id: --------------------------------------------------------------------- UNESCO - Hebrew University of Jerusalem International School for Molecular Biology and Microbiology (ISMBM) --------------------------------------------------------------------- International Workshop on Computation in Molecular Biology 2-11 February, 1997 at The Silicon Graphics Laboratory The Hebrew University of Jerusalem Sponsored by UNESCO Paris and The Hebrew University of Jerusalem --------------------------------------------------------------------- Aims: Computation in Molecular Biology at the Silicon Graphics Lab. The course is designed for graduate students and researchers in molecular biology who are interested in studying and practicing computational methods. Number of Participants: 20 Scientific Program: Sequence analysis, modeling of biomolecules and molecular graphics, advanced topics in computational molecular biology. Teaching Staff: H. Margalit (HUJ, Jerusalem) O. M. Becker (Tel Aviv U) M. Berman (Silicon Graphics Biomedical, Ltd) C. Sander (EMBL, Heidelberg) R. Elber (HUJ, Jerusalem) A. Goldblum (HUJ, Jerusalem) Housing: All participants will be housed in a hotel (at a reduced rate) near the University Givat Ram Campus (walking distance), two participants per room. Single room should be requested. Fellowships: A limited number of fellowships to cover part of the expenses will be available. (Participants are advised to request travel fellowships from national or international scientific organizations). Registration: Please send your application by fax: name, address, fax number, telephone number, e-mail address, information on your research studies (PhD students should attach a letter of recommendation from instructor) to: FAX: 972-2-6784010 ("Computation in Molecular Biology") Registration deadline: 1 December, 1996 Acceptance letters by: 1 January, 1997 Prof. Yechiel Becker Director UNESCO-HUJ ISMBM e-mail: becker@md2.huji.ac.il --------------------------------------------------------------------- From ccl@www.ccl.net Sun Oct 27 13:32:24 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id NAA12434; Sun, 27 Oct 1996 13:30:58 -0500 (EST) Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by bedrock.ccl.net (8.8.0/950822.1) id NAA17451; Sun, 27 Oct 1996 13:30:56 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Sun, 27 Oct 1996 18:30:54 +0000 Date: Sun, 27 Oct 1996 18:30:49 +0000 (GMT) From: A J Turner To: E.Tajkhorshid@dkfz-heidelberg.de cc: Computational Chemistry List Subject: Re: CCL:Quantom Chemical Molecular Dynamics In-Reply-To: <9610251417.ZM11218@mbp-sgi7.inet.dkfz-heidelberg.de> Message-ID: Hi! Charmm will do just that. Charmm 24b2 should do the ab-initio stuff - but I found a bunch of routines missing when I tried to compile. The am1 method is quite stable now. There are numberous others - but that one is availible commercially (for the am1 at least) and straight forward. Good luck Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From ccl@www.ccl.net Wed Oct 30 12:17:59 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id MAA06032; Wed, 30 Oct 1996 12:13:01 -0500 (EST) Received: from hil-img-1.compuserve.com for 100317.2656@CompuServe.COM by bedrock.ccl.net (8.8.2/950822.1) id MAA06239; Wed, 30 Oct 1996 12:12:34 -0500 (EST) Received: by hil-img-1.compuserve.com (8.6.10/5.950515) id MAA18457; Wed, 30 Oct 1996 12:11:56 -0500 Date: 30 Oct 96 12:09:05 EST From: Herbert Koeppen <100317.2656@CompuServe.COM> To: "Comput. Chem. List CCL" Subject: RE: YAK Program Message-ID: <961030170904_100317.2656_JHF45-1@CompuServe.COM> Alexandros, contact Angelo Vedani who developed the program YAK: Dr. Angelo Vedani SIAT Biographics Laboratory Missionsstr. 60 CH-4055 Basel Schweiz Tel: ++41-61-321-0533 Fax: ++41-61-321-0540 e-mail: siat@dial.eunet.ch regards Herbert -- Dr. Herbert Koeppen, Boehringer Ingelheim KG, Medicinal Chemistry Department -- -- D-55216 Ingelheim, Germany -- phone: ++49-6132-776845 -- fax: ++49-6132-773418 -- e-mail: 100317.2656@compuserve.com From wagenert@Mailer.Uni-Marburg.DE Wed Oct 30 08:30:43 1996 Received: from Mailer.Uni-Marburg.DE for wagenert@Mailer.Uni-Marburg.DE by www.ccl.net (8.8.2/950822.1) id HAA03878; Wed, 30 Oct 1996 07:17:10 -0500 (EST) Received: by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA88376; Wed, 30 Oct 1996 13:16:36 +0100 From: wagenert@Mailer.Uni-Marburg.DE (Wagener Thomas) Message-Id: <9610301216.AA88376@Mailer.Uni-Marburg.DE> Subject: Compiling Gaussian for R10k and IRIX 6.2 To: CHEMISTRY@www.ccl.net Date: Wed, 30 Oct 1996 13:16:35 +0100 (CET) Hi everyone, last week I made a request on compiling Gaussian94 for the SGI PC with R10000 processors. Many thanks to all who answered especially Roberto Gomperts from SGI. **************************************************************************** From: "Roberto Gomperts" Hi Thomas, Gaussian was certified for the r10k based machines only starting with rev. D.3 Please contact Gaussian Inc. to get a new source and makefile. -- -- Roberto Roberto Gomperts "Gracias a la vida, roberto@boston.sgi.com que me ha dado tanto ..." phone: (508) 567 2251 Violeta Parra Fax: (508) 562 4755 **************************************************************************** However, the mails I received may be of general interest for the people using Gaussian on SGI computers so I am including all the responses I have received. Thank you very much, Thomas - "You are wrong! 2+2=5.8354! Please adjust your equipment accordingly." The Computer (your friend) ***************************************************************************** * Thomas Wagener * Tel: ++49-(0)6421-285561 * * FB Chemie * * * Phillips-Universitaet Marburg * Email: wagenert@mailer.uni-marburg.de * * * * * 35032 Marburg * * * Germany * * ***************************************************************************** From: Danne R Rasmussen Hello Thomas, We have G94 running here at the Australian National University Supercomputer Facility on an SGI PC with R10000 chips. I suggest you need to get a more current release of G94. From recollection we had troubles with versions prior to D.2 I believe the current version is D.4 I think there are also many valuable bug fixes between versions C.2 and D.4 Cheers, Danne From: Michael A McAllister Thomas, we also have a few R10K machines -- word from Gaussian directly is that they do NOT have a verified working version of G94 for the R10K processor (IP 28). That was as of about a month ago when I talkedto them. They were working on it, so i think there is hope that it will work eventually. I got around the problem by using R8K optimized binaries on the R10K. They seem to run fine and give correct test results. Interestingly, the R4400 based binaries do NOT give correst answers when run on the R10K. They do give correct answers when used on the R5K, however. Go figure. As I said, wedo have a few of these R10K's and would love to know if you do find someone who has a successful Makefile. Good luck. Mike McAllister ************************************************************************** Assistant Professor of Chemistry voice: 817-565-4584 University of North Texas fax: 817-565-4318 P.O. Box 5068 email: mam0008@jove.acs.unt.edu Denton, TX 76203 www: http://www.unt.edu/~mam0008 ************************************************************************** From: "Dr. Daniel L. Severance" Hi, I have done it. I picked up the latest version of G94 which had the updated Makefile. The people at Gaussian also said there were some program changes involved so you might want to call them. Dan From: "Brent H. Besler" I was only able to get G94 rev D4 working correctly by compiling it in R8000 mode. I just modified the g94 makefile so that the processor type was set to R8000. G94 gives correct results. In R10000 mode it dies usually in MP2 gradients or in HF gradients. From: Jeremy R Greenwood Dear Thomas, We had no end of trouble with G94 on R10000 until we ordered the D.3 revision, which worked first time. I highly recommend spending the $$$ on the update and not wasting more time. Hope this helps, Jeremy From: young@argus.cem.msu.edu Hi, We had problems getting g94 to run under 6.2 on 4400's and will be trying 10000's this week. We did finally get it to run under the 6.2. It required installing two patches to the BLAS libraries, one that came out a few months ago and one from a week or two ago. Hope this helps. Dave Young young@slater.cem.msu.edu -------------------------------------------------------------------------- Computational chemistry, teaching, visualization and programming. -------------------------------------------------------------------------- From: "C. S. Page" Dear Thomas, We have had a lot of fun trying to compile G94 on an R5000 under Irix 6.2, and, basically, the problem has not yet been resolved. The only fully working version that I have was compiled with the Mips 3 compiler option using a number of patches to eg. the BLAS routines. These will also help matters in the majority of cases (all of the test jobs will run, for example) for the Mips 4 version. The ones we have are: Patch SG0001262: libblas autoblock problem Patch SG0001378: Complex Arithmetic Broken in 6.2 libftn Patch SG0001436: fix for branch in branch delay slot in libfastm Patch SG0001496: libblas generates incorrect answers on R5000/R10000 An alternative is to use the Challenge Complib libraries instead BLAS: the BLAS patches are quite large (~50Mb in total) and you may wish to forget about them. If you have any trouble getting hold of the patches, please let me know and I will e-mail the distribution. I will also see if I can find the input deck that runs on an R4400, but gives nan's in l502 on an R5/10k using the Mips 4 libraries: if you can get this one to run, your problems are over! We have been in touch with SGI and they have been looking into the matter for some time. There will be a posting to CCL when there is a solution. I hope that this is of some help to you. Chris Page __________ Department of Chemistry Tel: +44 (0)171 594 5795 Imperial College GB-LONDON SW7 2AY From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Dear Dr Weagner To compile g94 on R10000 you could probably use -mips4 -64 and -r10000 flags. Probably you also should specify 64 bit pointers: -DP64. As I know there are more specific options (e.g. rounding off, IEEE aritmethics ....) Moreover I am not sure if rev C.2 has been prepared to run on R10000. Even for Rev. D.1 I can see support for R8000 PC. So probably you will have more problems Best regards, G Bakalarski ( grzesb@icm.edu.pl) From: Johan Landin Hello Thomas, Maybe you need a later revision of Gaussian 94 in order to succeed? I believe that the first revision certified for IRIX 6.2 and R10000 is Gaussian 94 Revision D.3. However, since I have not checked this explicitly myself I suggest that you contact Gaussian Inc. directly in these matters. If your university already has a licence for Gaussian 94 the cost for a new tape, with the latest revision, will be only $200. Regards, /Johan Landin -- ___________________________________________________________________ Johan Landin Tel: +46 31 773 3767 Dept. of Medical Biochemistry Fax: +46 31 41 6108 Medicinaregatan 9 Home: +46 31 14 7554 S-413 90 Goteborg, Sweden Email: landin@mednet.gu.se From: "Jean Francois Marquis" hi Thomas and Dorothee, It seems like you have some problems to re-compile GAUSSIAN on our machine. Did you ever compile this code on SGI with IRIX 5.3 ? What cc command line did you use ? Could you verify what versions of compiler is installed on your SGI by the command "versions -b | grep compiler" Some suggestions described in few steps : First if you use Kernigham and Richie C put -cckr option in the cc invocation line, in other case ANSI C is the default. Second As you know IRIX 6.2 and R10000 are fully 64 bits stuff... so if this code is 32 bit (i mean addresses, pointers...) you could begun to re-compile it with these options "cc -32 ...." If it's OK, go ahead with "cc -n32 .." which translate "old 32 bits code" in "new 32 bits one" and will be more efficient on the R10K. And at last you can if needed take advantage of the 64 bits addressing (pointers,tabs, and files greater than 2Go in memory) but be careful on the code. Some cast like (int) p where p is a pointer (consquently 64 bits) will give a false or non sense result... Hope this helps, jef. -- ================================================================ = Jean-Francois MARQUIS = Pre-sales engineer = SGI France AIX-EN PROVENCE Office = Parc club du golf, bat 20 = Av. Guillibert de la Lauziere = BP 107000 Aix-en-Provence cedex 3 = FRANCE ( ) ____ ( ) _/__|__\___ ( -- (_ _|__ __] AIX -- () () TOULOUSE = Tel : (33) 04 42 39 77 79 = Fax : (33) 04 42 39 77 50 = E-Mail : jef@aix.sgi.com ================================================================ From wwrich@ddix7.monsanto.com Tue Oct 29 09:32:57 1996 Received: from gatekeeper.monsanto.com for wwrich@ddix7.monsanto.com by www.ccl.net (8.8.0/950822.1) id JAA28490; Tue, 29 Oct 1996 09:25:49 -0500 (EST) Received: by gatekeeper.monsanto.com; id AA02250; Tue, 29 Oct 96 08:25:49 CST Received: from ddix7.monsanto.com(137.35.8.5) by gatekeeper.monsanto.com. via smap (V3.1.1) id xma002131; Tue, 29 Oct 96 08:25:38 -0600 Received: by ddix7.monsanto.com (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id IAA06217; Tue, 29 Oct 1996 08:25:17 -0600 From: wwrich@ddix7.monsanto.com (Wendy W. Richardson) Message-Id: <199610291425.IAA06217@ddix7.monsanto.com> Subject: IRIX 6.2 and R10000 To: CHEMISTRY@www.ccl.net Date: Tue, 29 Oct 96 8:25:13 CST We are about to upgrade one of our workstations to an R10000 processor, with the corresponding upgrade to IRIX 6.2. The guy from SGI said the 6.2 release was fairly stable, and the systems related stuff should all work fine, but we could have some problems with applications software (he is not familiar with modeling software). Has anyone else done this? Does your modeling software still work? Is it faster? Were there any special things you had to do to get things to work? Will I need to get/create another set of executables? I am most concerned about: Sybyl, Daylight, Gaussian94, Macromodel, Catalyst, Spartan I will summarize any responses I receive... ------------------------------------------------------------- ("`-/")_.-'"``-._ Wendy W. Richardson, Ph.D. (. . `) -._ )-;-,_() Sr. Research Investigator (v_,)' _ )`-.\ ``-' Searle _;- _,-_/ / ((,' 4901 Searle Parkway ((,.-' ((,/ Skokie, IL 60077 wwrich@ddix7.monsanto.com From jkl@ccl.net Thu Oct 31 05:05 EST 1996 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.2/950822.1) id FAA25460; Thu, 31 Oct 1996 05:05:01 -0500 (EST) Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id FAA11600; Thu, 31 Oct 1996 05:05:01 -0500 From: Jan Labanowski Date: Thu, 31 Oct 1996 05:05:01 -0500 Message-Id: <199610311005.FAA11600@krakow.ccl.net> To: chemistry@www.ccl.net Subject: FUTURE OF CCL Cc: jkl@ccl.net Dear CCL Subscribers, So this is another piece on the future of CCL from my perspective. The future will be a constant feature on the list, and I will be bugging you about once a week or so... Sorry... But I have to do it... But please refrain from discussing list support efforts on the CCL itself. It would add to the noise, and it is more than enough that I have to do it. Send your comments to me directly. All past messages on this topic are archived under http://www.ccl.net/ccl/future.html gopher://www.ccl.net:73/11/future ftp://www.ccl.net/pub/chemistry/future and you can also get them via e-mail by sending a message: select chemistry cd future get * quit to MAILSERV@www.ccl.net So You and me can always check the progress of this thing and learn from it. If you did not have a chance to read the previous stuff, please do... In short, I got some NSF money for developing the list and moving it into some self-funding model. Otherwise, I would have to close it. First of all let me thank the many people who replied to my previous message. I got a lot of encouragement, some criticism (actually I did not get any substantial criticism, just advice and warnings on policies), and a lot of advice. I got a lot of messages, and please be patient. I will answer them all, unless they do not call for my comments, but some of them (e.g., offers of collaboration) require more thought than others, and some others, which offer advice require analysis, i.e., time. And if you notice the time stamp on this message, you will concur that I am trying hard to get on top of things. A short progress report. I am hiring a person to help me mostly with the Web site organization and software support. I hope to have another opening if you help (yes... I will stick my hand in a moment...). I hope this person will start working by the end of November. So you will see soon some improvement. Many of you are worried about me wanting to commercialize the list fast. Let me make this clear. The FREE list as it is now, will stay as a part of Ohio Supercomputer Center (OSC) for as long as I have the grant from NSF (i.e., likely up to 3 years). Even if I was a greedy individual who wants to make big bucks on Internet fast (popular fad nowadays), I cannot do it, since I am working at OSC and OSU. While I will be trying things within constraints which are placed upon me, the list is FREE. It may also stay FREE much longer than the NSF grant. But I do not have a crystal ball, and to ensure list existence and possible growth (and extension), I have to provide the list with a path of growth, safety net, ensured future funding, and institutional stability. While you may be bored already, read on, since we can all learn from this experience, and many of us see that traditional academia is changing not necessarily according to our wishes or opinions. Some of you, as I can see from your reactions, may have similar questions, or may have them in the future. If at the latter time, I will have list run as (or also as) a for-profit organization I treat it as means, not ends. It simply may be more convenient from the operational point of view. I am old enough to know that this endeavor will not bring big income. My only worry is to keep it alive since I believe that it is a useful thing. If I just pass it to one of the Web malls in exchange for publicity, it will be there only as long as the mall exists, or as long, as it brings money directly or indirectly. On the other hand, I created the list with your help, and I really care, though some of you may think, I am playing a marketing spiel. While I cannot praise enough the organizational protection and infrastructure of OSC/OSU, I can count on it as long as they support the CCL, not as long I as live... Let me explain in more detail the CCL environment. OSC is a supercomputer center supported by the State of Ohio (we are a line in Ohio budget) and also from other sources and foundations. OSC's primary goal is to serve Ohio academia, but we also are chartered to foster other computer and communication related initiatives within the state. We also have an active research and development program, and are involved in many outreach initiatives within Ohio and beyond (e.g., we have an important involvement in the US DoD High Performance Computing Modernization Program). We are also visible on the national arena, and you can find more about it from our OSC Web page (http://www.ccl.net/), press coverage, and "rumors". On the other hand, OSC is located on the Ohio State University (OSU) campus, and uses OSU infrastructure, administration, and adheres to OSU internal rules and regulations. At the same time, OSC is not an academic department of OSU, and therefore, the employees of the OSC are not, by definition faculty members, and do not have tenure (with one exception, which does not have much to do with the OSC relation to OSU). And do not worry that I will spend money recklessly. I have to go through my OSC administration to spend every dime. And if they do not like it, they will not spend it -- we are very careful here about the publicity, and spending "taxpayer's money", since our existence depends on public support. In summary, the CCL presence in OSC is just a GOOD WILL of OSC management. And this may change if CCL is classified by my peers as burden, liability, or simply an unrelated activity for the Center. And some people complain about the resources taken by the list, so I have to fix this problem if I want to enjoy the environment and cooperation of the OSC. While it is not customary to talk dollar amounts on the list, I have to... The NSF grant, provides me with a single support type position, and a very limited budget for other things. I am very lucky that I got what I got, but even my office space line was cut. OSC pays the off-campus overhead rate and I have to pay for it from my grants -- this is however much better deal compared to the regular overhead in academic departments. The fact of GETTING SUPPORT FOR THE LIST FROM THE PRESTIGIOUS NSF IS PROBABLY MORE IMPORTANT THAN THE PRECISE AMOUNT. At least this is how I understand it. THANK YOU ALL FOR THIS OPPORTUNITY, WHICH WOULD NOT HAPPEN IF THE LIST WAS A NOISY AND LOW CONTENTS MEDIUM. But to really develop CCL resources into the state-of-the-art environment which can be useful to all of you, I need more assets than the grand provides. We all know this theme: "There is so much one could do, but there is only 24hrs/day". 1) I really need AT LEAST 2 FULL TIME PEOPLE to work on the development of the resource and getting it to the point of STEADY STATE (when it can be managed more economically) of EXCELLENCE (when it is useful and attractive to subscribers, users, and supporters). a) computer expert with practical knowledge of hardware, software, networking, electronic publishing, etc. (I am currently in the process of getting such a person using my NSF budget, though I am leveraging my CCL vision against monetary reality, which cannot work forever... I hope that optimism is contiguous...). b) an experienced, versatile chemist, with a broad background in comp.chem, and related areas, who will be willing to develop the organization for the archives, implement it, and provide the highly automatized protocol for future upkeeping and extension. c) I may need some consulting in these disciplines of Comp.Chem., which I cannot provide from within OSC. CCL is an international forum, and it gives me a real possibility to ask people who are top specialists in some specific areas, but happen to live in countries with depressed economies (or are currently out of job in leading economies) to contribute summaries, overviews, and tutorials and other work which can be done via network. Of course, I will accept FREE help and contributions ALWAYS. 2) I need a lot of legal advice, and organizational advice... 3) I need to invest in hardware, software, secure bandwidth, and a stable office/work environment for the list. 4) I need student assistants to help with mechanical, and routine tasks. Let us play the numbers then: Ad 1a) I will probably need to augment salary at some point, to be able to ensure stability of this position. Ad 1b, 1c) With benefits and other overheads we are talking $60-70k at current levels. I may try to out-source this work to retired people, or less expensive geographic areas, but it involves some risks... Ad 2) This is expensive stuff... Ask a good corporate/foundation/trademark/ copyright type lawyer how much he/she charges for an hour. My EDUCATED guess is at least $500, and I need many hours to make it through transition period, avoid legal traps, and ensure future institutional stability. I am VERY LUCKY to have excellent opportunity at OSC to work with Eclips (Electronic Commerce, Law, and Information Policy Strategies) -- check it out, http://www.ccl.net/Eclips -- you, or your organization may really want to work with this group -- they are Internationally acclaimed and extremely successful group, though do not take too much of their time since I need them too {;-)}). However, while their staff was very helpful with fast advice, to really get this going, I need to help them justify their substantial involvement. Ad 3). T1 line (and I need one to relieve OSC network traffic) is around $1,000 a month or more, depending on how far you are from Central Office, and how much competition CAP introduced in your area. You may have noticed that CCL competes on the Web/ftp Server with OSC contents. During busy hours it gets slow, and everybody knows it. It is bad for OSC and for CCL. I have to move primarily Web and ftp servers and searches out of OSC server. I also need communication hardware (router). I need a server machine to last some time. And I need gobs of fast disk space, backups, UPSs, scanner, etc. And I need software (e.g., commercial strength Web server, new goodies for Web multimedia scripting/publishing, applets, VRML, libraries, etc., etc.). To stay current, I have to spend substantial resources on this. Ad 4) Student help is less expensive, probably in the vicinity of $10,000/yr total. I intentionally did not include figures for each item, since I do not want to undercut my negotiating position (this message is public announcement), but it may sum up EASILY to $200,000 a year. But of course, I will work with what I have to the extent I can... I cannot collect such money from the individual membership donations, though, obviously, if ALL OF YOU chipped a $100 a year, I would be FINE. But I am trying to be realistic. On the other hand, the list developed its assets in the course of its over 5 year existence. The Computational Chemistry is seen as the high growth area for the years to come, and is advertised as the job for the 21st century. Moreover, I would not even think about it, if I could not get a combined experience, help, and support of the OSC, which developed a lot of understanding and good models by providing services to many sectors of Ohio economy, education, and government. Moreover, I have a substantial period of time, when I can use the educational umbrella, and tax benefits of my organization and its infrastructure. And it is much cheaper than if I would have to build all this myself. I am now in the process of putting together a plan for seeking corporate contributions. You will learn about it soon, but I have to do more studies. While I have some idea on how much some companies pay for having their logo and link to their site in the Web site run by the academic/non-profit, any advice would be greatly appreciated. I added the odometers to some pages in CCL archives, so we all have better idea about traffic. And beside, in a few months the Web pages will be better organized and designed and at that time I may start working on more publicity for this site. So, please help with suggestions. PLEASE... So now is the reality check... Please contribute as individuals now... I will of course remind you about the CCL Drive several times. Send the checks with the amount you consider reasonable to me: Jan Labanowski Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43212-1163 and make the checks payable to: OSC Development Fund (CCL) (Not to me personally, since I will not be able to cash them!!!). You will receive a THANK YOU letter, which you need to keep for your records, since the contribution IS TAX DEDUCTIBLE and you should deduct it on your income tax return (Yes, I checked this!!!). I will create a special Web Page to thank all supporters (but if you want to be anonymous, let me know VERY EXPLICITLY, and obviously, I will not mention your name). I will be updating the Web page with amounts received so we all know how we are doing. Of course, beside thank you, you will not get any other favors from me, and your contribution is STRICTLY VOLUNTARY. On the other hand, I will soon go after corporate support. I will appreciate help from CCL subscribers working for the for profit corporations, and also for suggestions whom I should contact and how (e.g., many hardware and software vendors out-source their publicity efforts to advertising companies and I need good contacts in this respect). Thank you for your patience... Yours, Jan Labanowski jkl@ccl.net From alain.kessi@psi.ch Thu Oct 31 05:17:53 1996 Received: from psizi1.psi.ch for alain.kessi@psi.ch by www.ccl.net (8.8.2/950822.1) id EAA12532; Thu, 31 Oct 1996 04:40:49 -0500 (EST) Received: from localhost by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA17871; Thu, 31 Oct 1996 10:43:52 +0100 Sender: kessi@psizi1.psi.ch Message-Id: <327874D8.7DE1@psi.ch> Date: Thu, 31 Oct 1996 10:43:52 +0100 From: Alain Kessi Organization: Paul Scherrer Institut, Zuerich, Switzerland X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: "Dr. Bruno Manunza" , Alexandros Alexidis Cc: CCL Computational Chemistry List Subject: Re: CCL:Looking for the YAK program References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Bruno Manunza wrote: > Yeti and Yak molecular mechanics and display programs for receptor > modeling with special treatment of h-bonding. Contact: Angelo Vedani, > Biographics Laboratory, Swiss Institute for Alternatives to Animal > Testing, Aeschstrasse 14, CH-4107 Ettingen, Switzerland, E-mail: > vedani@czheth5a.bitnet I very much doubt that you'll reach Angelo Vedani by e-mail at the above address, since Bitnet has been inoperative in Switzerland for some years now. The postal address I have (from November 1995) for the laboratory is SIAT Biographics Laboratory, Missionsstr. 60, CH-4055 Basel, Switzerland Tel (061) 321 05 33 Fax (061) 321 05 40 You may want to look at the Yak page http://www.pharma.ethz.ch/text/research/cadd/yak.html and check the paper by Angelo Vedani (written when he was at the University of Kansas), YETI: An Interactive Molecular Mechanics Program for Small-Molecule Protein Complexes, Journal of Computational Chemistry, Vol. 9, No. 3, 269-280 (1988) The Yak reference is Vedani, A.; Zbinden, P.; Snyder, J.P. Pseudoreceptor modeling: A New Concept for the Three-dimensional Construction of Receptor Binding Sites. J. Receptor Res., 1993, 13, 163-177. An application of Yak is described in Snyder, J.P.; Rao, S.N.; Koehler, K.F.; Vedani, A. Minireceptors and Pseudoreceptors. In 3D QSAR in Drug Design. Theory, Methods and Applications, Kubinyi, H., Ed.; Escom: Leiden, 1993, pp. 336-354. Hope this helps ... Alain Kessi -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From hutschka@quantix.u-strasbg.fr Thu Oct 31 10:18:14 1996 Received: from quantix.u-strasbg.fr for hutschka@quantix.u-strasbg.fr by www.ccl.net (8.8.2/950822.1) id JAA14483; Thu, 31 Oct 1996 09:40:08 -0500 (EST) From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA47589; Thu, 31 Oct 1996 15:41:00 +0100 Date: Thu, 31 Oct 1996 15:41:00 +0100 Message-Id: <9610311441.AA47589@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: G92,rms rrms units in PD charges Cc: hutschka@quantix.u-strasbg.fr hello, I'm fitting atomic charges with potential derived method (MK,CHELP,CHELPG) with gaussain92. The quality of the fit is given by the rms and the rrms. I want to know in what units are given the rms and the rrms. I know that these units are KJ/mol for rms and % for rrms but I need to confirm this. More if I have a value of 0.15 for the rrms, does it mean 0.15% or 15% ?? If somebody could give me this information (about rms and rrms) it would be very helpful. Thanks a lot to everybody, answers will be sumarysed. Francois. ============================================================================= ¤ François HUTSCHKA Ph.D. Student in Quantum Chemistry ¤ ¤ ¤ ¤ Laboratoire de Chimie Quantique ¤ ¤ UPR 139 du CNRS ¤ ¤ 4, rue Blaise Pascal Phone: (33).88.41.60.32 ¤ ¤ 67000 STRASBOURG Fax: (33).88.61.20.85 ¤ ¤ FRANCE E-Mail: hutschka@quantix.u-strasbg.fr ¤ ============================================================================= From hutschka@quantix.u-strasbg.fr Thu Oct 31 10:32:32 1996 Received: from quantix.u-strasbg.fr for hutschka@quantix.u-strasbg.fr by www.ccl.net (8.8.2/950822.1) id JAA14495; Thu, 31 Oct 1996 09:41:13 -0500 (EST) From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA32506; Thu, 31 Oct 1996 15:42:15 +0100 Date: Thu, 31 Oct 1996 15:42:15 +0100 Message-Id: <9610311442.AA32506@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: G92,HF MP2 densities in CHK file Cc: hutschka@quantix.u-strasbg.fr hello, I am using gaussian92 to fit atomic charges with potential derived methods. To save computer time the electronic density can be read from the checkpoint file to avoid to calculate it several time if you want to use it for different calculations. By default, the HF density is saved in the CHK file. Since I want to use the MP2 density, could somebody tell me if there is a way to save the MP2 density in the CHK file and if so, how to do it ?? More is it possible to save both the HF and the MP2 densities in the same CHK file?? Thanks a lot for your help. I will sumaryse the answers. Francois. ============================================================================= ¤ François HUTSCHKA Ph.D. Student in Quantum Chemistry ¤ ¤ ¤ ¤ Laboratoire de Chimie Quantique ¤ ¤ UPR 139 du CNRS ¤ ¤ 4, rue Blaise Pascal Phone: (33).88.41.60.32 ¤ ¤ 67000 STRASBOURG Fax: (33).88.61.20.85 ¤ ¤ FRANCE E-Mail: hutschka@quantix.u-strasbg.fr ¤ ============================================================================= From aiz0001@jove.acs.unt.edu Thu Oct 31 12:17:53 1996 Received: from mercury.acs.unt.edu for aiz0001@jove.acs.unt.edu by www.ccl.net (8.8.2/950822.1) id MAA15713; Thu, 31 Oct 1996 12:09:01 -0500 (EST) Received: from jove.acs.unt.edu (6930@jove.acs.unt.edu [129.120.1.41]) by mercury.acs.unt.edu (8.8.2/8.8.2) with ESMTP id LAA16063; Thu, 31 Oct 1996 11:08:54 -0600 (CST) Received: from localhost (aiz0001@localhost) by jove.acs.unt.edu (8.8.2/8.8.2) with SMTP id LAA12396; Thu, 31 Oct 1996 11:08:50 -0600 (CST) Date: Thu, 31 Oct 1996 11:08:50 -0600 (CST) From: Anita Ilze Zvaigzne To: "Benny G. Johnson" cc: chemistry@www.ccl.net Subject: Re: CCL:Fortran 90 references In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 30 Oct 1996, Benny G. Johnson wrote: > Dear netters, > > Can anyone recommend a good Fortran 90 reference? I'll summarize the > answers. > > Thanks, > Benny > I have found the following book to be particularly useful in conversion from f77 to f90: T.M.R. Ellis, Ivor R. Philips, Thomas M. Lahey; Fortran 90 Programming, Addison-Wesley Publishing Company : New York, 1994. ISBN 0-201-54446-6 However, this is more of a tutorial guide than an actual programmer's reference. I am not sure if this is what you are looking for, but I hope it helps! :-) Sincerely, Anita Zvaigzne From peng@risc.nyu.edu Thu Oct 31 13:17:52 1996 Received: from risc.nyu.edu for peng@risc.nyu.edu by www.ccl.net (8.8.2/950822.1) id MAA15924; Thu, 31 Oct 1996 12:48:30 -0500 (EST) Received: by risc.nyu.edu (AIX 3.2/UCB 5.64/4.03) id AA32847; Thu, 31 Oct 1996 12:46:20 -0500 Date: Thu, 31 Oct 1996 12:46:20 -0500 (EST) From: Tong Peng To: chemistry@www.ccl.net Subject: Summary of Amino Acids Question Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Below is a summary of answers I received to my question about amino acids data. Thanks to all! Tong Peng The question: ================ > Hi, everybody, > > I'd like to know where can I find data of amino acids, such their > geometry, bond length and angle of peptide bonds etc. And is there an > online resource of such kind of informations? > Answers: =================== From: CHRISTIAN PARRY These are known as parameters and come with molecular modelling programs such as Charmm (or Xplor, for that matter), OPLS, etc. For academic charmm contact M. Karplus at Harvard, Dept of Chem or MSI. ================== From: Wayne Steinmetz Check out my Web page, MolData, which is an annotated bibliography to chemical data sources on the World Wide Web. The most useful links will data sources on the World Wide Web. The most useful links will found on the Organic Chemistry and Biochemistry pages. The URL for MolData is http://pages.pomona.edu/~wsteinmetz/moldata.html ========================= From: "[ISO-2022-JP] ^[$B@5B<^[(B" (1) For unionized amino acids, L.Schaefer group study unionized amino acid by ab initio 4-21G basis set. Please use CAS for searching them....... (2) For amino acids zwitterion forms, two papers show glycine zwitterion in the gas phase does not exist. =========================== From: "Igor V. Pletnev" & From: Konrad Hinsen Have a look at http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html From dsmith@CTCnet.Net Thu Oct 31 13:20:57 1996 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.2/950822.1) id NAA16120; Thu, 31 Oct 1996 13:16:34 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id NAA14168; Thu, 31 Oct 1996 13:14:47 -0500 Date: Thu, 31 Oct 1996 13:14:47 -0500 Message-Id: <199610311814.NAA14168@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: THF values for COSMO calculations Another summary long overdue. Doug ============================================================================ ============ My original message: We are doing some MOPAC 93/COSMO calculations and need the following information, if anyone has it. (1) Dielectric constant for THF (tetrahydrofuran) (2) Solvent radius for THF (the value used for RSOLV) Thanks in advance. ============================================================================ ============ The dielectric constant for THF is reported to be 8.2 in a paper that I was reviewing for the publication in JACS. ============================================================================ ============ 11.6 (-70 C), 7.58 (25 C). Source: John A. Dean, "Handbook of Organic Chemistry", 1987, McGraw-Hill, Inc. Radius? I don't know. Yong ============================================================================ ============ the dielectric constant for thf at 25c is 7.6 Louis Lalas Regulatory Affairs Analyst, VWR Scientific Products ============================================================================ ============ You asked about: >(1) Dielectric constant for THF (tetrahydrofuran) >(2) Solvent radius for THF (the value used for RSOLV) for use with COSMO in MOPAC. The dielectric constant for THF is 7.32 (according to my Chemist's Companion handbook), but the RSOLV value is not so readily defined. According to the article in J. Chem. Soc. Perkin Trans 2, 1993, p802 by A. Klamt and G. Schuurmann, R(solv) is an upperlimit for the minum distance to a solute atom and: "The most reliable value for each solvent has to be found empirically." I have played with this some, and actually just using a value of 1 seems to work as well as anything for the properties I was evaluating. As I understand it, R(solv) relates more to the radius of a local dipole (which may interact with the solute) of the solvent molecule, rather than the overall solvent molecule radius. Also, conventional wisdom is that when dealing with ions, a larger value for the radius is necessary, although I haven't observed this myself. I would be interested in a summary, if any of your replies outlines an appropriate way to come up with R(solv) values. Otherwise, I'd suggest you just try using 1 as the value. Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. -- Dr. Douglas A. Smith, President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: dsmith@dasgroup.com Johnstown, PA 15904-5428 | Contract R&D specialists in computational chemistry, process modeling, synthesis and design of novel compounds for chemistry, materials science, and biotechnology. From dsmith@CTCnet.Net Thu Oct 31 13:25:24 1996 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.2/950822.1) id NAA16118; Thu, 31 Oct 1996 13:16:32 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id NAA14166; Thu, 31 Oct 1996 13:14:45 -0500 Date: Thu, 31 Oct 1996 13:14:45 -0500 Message-Id: <199610311814.NAA14166@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: isocyanates: summary Quite a while back I asked a question of the list regarding the calculated non-linearity of isocyanates, i.e. R-N=C=O. I did get a reasonable response, and apologize for the summary not appearing earlier (we changed Internet access providers and were without mail access for over a month!). Anyway, here is my original posting and the edited responses. The answer, in short, is that the bond is NOT linear. I hope that those who answered that it should be linear, or thought that it should be linear, are not offended. Doug ============================================================================ =========== My original posting: However, the results are not intuitively obvious. For example, using H-N=C=O as a test case, the bond angles and distances are as given in the table. distance angle N-C C-O N-C-O ------- ------- --------- AM1 1.23 A 1.20 A 166.7 PM3 1.25 A 1.18 A 166.7 RHF/6-31G* 1.20 A 1.15 A 174.2 Similar deviations from linearity are seen in the angles of substituted isocyanates. What is the expected N-C-O angle based on experiment and/or higher levels of theory? ============================================================================ =========== Should be linear. I would suggest trying an H-N=C=O CASSCF calculation. A CCSD(T) calculation should also be feasible with a basis set of this size on an RS/6000 type of machine. This smells like artifactual symmetry breaking to me. I find it extremely interesting that RHF/6-31G* gave a non=linear N-C-O angle. Also the 6-31G* has been known to give result in bent geometries for linear carbon clusters,( such as C4-C7). I would recommend using the pVDZ basis set for exploring this aspect of the problem in a cost efficient fashion. If you do not have any access to Xray diffraction data of similar systems, and are concerned about site modeling or solid state effects, I would reccomend fixing the N-C-O angle to be linear. -Galen F. Gawboy Pinnacle Technology Resources, Inc. ============================================================================ =========== The only experimental evidence I know of for isocyanic acid, HNCO, is from spectroscopic data: Hocking, Gerry and Winnewisser, Can. J. Phys., 53, 1869 (1975) Hocking, Gerry and Winnewisser, Astrophys. J., 174, L93 (1972) as quoted by Harmony et al, J. Phys. Chem. Ref. Data, 8(3), 619 (1979). I don't have copies of the primary literature with me, but Harmony's comments is that "it was necessary to assume linearity of NCO group. The reported values of NH and HNC are most strongly affected by this assumption, but the heavy-atom distances are also affected to a smaller extent." Values quoted: NC 1.209A CO 1.166 NH 0.986 HNC 128.0 Hope this is of some help to you. Please summarise for CCL, as I'd be interested in seeing responses that you get. Prof. Helder M. Marques, Department of Chemistry University of the Witwatersrand ============================================================================ =========== I can't give you any experimental results on isocyanates, but I have optimized HNCO (Cs symmetry) at various levels (see below). The simple answers to your last question are 1) HNCO is not linear at any level of theory (including DFT and MP2), and 2) semiempirical methods do not "fail"; they actually reproduce other theoretical models reasonably well. Here are my results (they are close to, but not identical to what you reported). Theory Energy r(NC) r(CO) angle(NCO) AM1 -15.15 1.232 1.202 166.7 PM3 -15.29 1.251 1.181 168.6 HF/6-31G* -167.761384 1.200 1.145 174.2 MP2/6-31G* -168.232430 1.224 1.184 171.7 HF/6-31G** -167.766024 1.199 1.148 174.3 MP2/6-31G** -168.242279 1.225 1.183 171.7 B3LYP/6-31G** -168.681498 1.218 1.174 172.2 BP86/6-31G** -168.689231 1.230 1.186 171.3 SVWN/6-31G** -167.794926 1.216 1.177 172.3 Comments on structures: 1. Basis set has little effect on HF and MP2 structures 2. HF bond distances are much shorter than MP2 (especially CO distance) and bond angles are larger 3. Both PM3 and AM1 duplicate MP2 structure at least as well as HF 4. Agreement between MP2 and DFT is good for all types of DFT, but best agreement is between BP86 and MP2 5. Bond angle at MP2 and DFT is approx 172. The NCO unit is NOT linear. Comments on calculations: 1. All calculations used Cs symmetry 2. AM1, PM3, HF, MP2 calculations performed with Spartan 4.0.3 3. MP2 optimizations done with "unfrozen" core 4. DFT calculations performed with Gaussian 94 5. Also tried SVWN/6-31G** with PS-GVB (fine mesh) and obtained essentially identical result. If I recall correctly, sometime back in the '80s (or possibly very late '70s),HF Schaefer published an article in JACS on the structure of cumulenes like 1,2,3-butatriene (H2C=C=C=CH2) and found that these were not linear. I don't have the reference, but you should be able to find it without too much trouble. Good luck! Alan Shusterman Department of Chemistry Reed College ============================================================================ ============ We have been doing some computational research involving isocyanates, and we have found that, with the exception of silyl isocyanates, these cumulenes are not linear. This result is in agreement with experimental data. The sp-hybridized carbon atom does not yield a bond angle of 180 deg. because the lone pair of the nitrogen atom interacts with the pi*(C=O)orbital. This stabilizaing two-electron interaction is enhanced when the O-C-N atoms are not linear. Therefore, the HF results, particularly those obtained at HF/6-31G* level, reflect correctly this interaction. Fernando Cossio ============================================================================ =========== I've performed _ab initio_ calculations on .alpha.-methylazo alkyl isocyanates some years ago (RT Kroemer et al., J. Chem. Soc. Perkin-II (1994) pp2129). These calculations were HF/6-31G* and MP2/6-31G*. The most remarkable geometrical change at these levels of theory was a decrease in the N-C-O bond angle from 171.5 to 167 degrees. This small angle can be partially explained by a perturbation induced by the nearby diazene group. However, as I was initially surprised by the fact that the N-C-O group is not linear, I performed calcs on CH3-N=C=O and found a bond angle of 174.9 degrees at the HF/6-31G* level. The non-linearity and the decrease in the angle comparing HF/6-31G* and MP2/6-31G* was also observed by other people (S Ellis et al., Can. J. Chem. 69 (1991) pp1000) for H2B-N=C=O and F2B-N=C=O. If you perform a search for R-N=C=O in the Cambridge Crystallographic Database, you will find at least 50 structures (either -N=C=O as a ligand in metalloorganic compounds or as part of "real" organic compounds). In none of these structures you will find absolute linearity, the N-C-O angle varying from approx. 165 to 178 degrees. Of course one can argue that the levels of theory mentioned above are not enough (one needs larger basis sets and more sophisticated schemes for taking electron correlation into account than MP2), and in the crystal structures the N-C-O angle is non-linear because of neighbour group effects and crystal packing etc. Therefore, it would be interesting for me to know where you found the "observed linearity of the N-C-O" angle (maybe spectroscopy?). Maybe you could try a really sophisticated calculation on H-N=C=O (such as QCISD(TQ) or a coupled cluster calculation with a large basis set, the system itself is not very large). Dr. Romano T. Kroemer Phys. & Theoret. Chem. Lab. University of Oxford ============================================================================ =========== -- Dr. Douglas A. Smith, President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: dsmith@dasgroup.com Johnstown, PA 15904-5428 | Contract R&D specialists in computational chemistry, process modeling, synthesis and design of novel compounds for chemistry, materials science, and biotechnology. From peng@risc.nyu.edu Thu Oct 31 14:17:59 1996 Received: from risc.nyu.edu for peng@risc.nyu.edu by www.ccl.net (8.8.2/950822.1) id NAA16339; Thu, 31 Oct 1996 13:39:29 -0500 (EST) Received: by risc.nyu.edu (AIX 3.2/UCB 5.64/4.03) id AA20693; Thu, 31 Oct 1996 13:37:20 -0500 Date: Thu, 31 Oct 1996 13:37:19 -0500 (EST) From: Tong Peng To: chemistry@www.ccl.net Subject: Note on Summary of Amino Acids Question Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Dear collegues, I just sent a summary of answers to my question about Amino acids to this list. I should have mentioned that the summary only contains replies sent directly to me. There are also many replies to the question sent to the CCL list, those I didn't repeat in my summary. And my sincere thanks are to all who gave me help. Tong Peng From peha@chemie.uni-konstanz.de Thu Oct 31 17:17:54 1996 Received: from sg7.chemie.uni-konstanz.de for peha@chemie.uni-konstanz.de by www.ccl.net (8.8.2/950822.1) id QAA17654; Thu, 31 Oct 1996 16:52:03 -0500 (EST) Received: from sgiclu.chemie.uni-konstanz.de (sg17.chemie.uni-konstanz.de [134.34.7.91]) by sg7.chemie.uni-konstanz.de (8.8.2/8.8.0) with SMTP id WAA10446 for <@sg7.chemie.uni-konstanz.de:chemistry@www.ccl.net>; Thu, 31 Oct 1996 22:52:33 +0100 (MET) Received: by sgiclu.chemie.uni-konstanz.de (950911.SGI.8.6.12.PATCH825/940406.SGI) for chemistry@www.ccl.net id WAA10939; Thu, 31 Oct 1996 22:50:58 +0100 From: "Peter Happersberger" Message-Id: <9610312250.ZM10937@sg17.chemie.uni-konstanz.de> Date: Thu, 31 Oct 1996 22:50:55 +0100 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: CCL: Summary of MOPAC question Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, below is a summary of answers I received to my question to MOPAC. Thanks to all! Peter Happersberger ____________________ My questions: So, I'm looking for 1. the source code of MOPAC7 (LINUX), because I want to calculate molecules greater than 60 atoms. 2. other programms (molecular mechanics, semiempirical) with the ability of calculating As-C, As-O ans As-S bonds. _____________________ Answers: FROM: Joel Polowin With HyperChem, you can calculate such structures using the CNDO, INDO, and PM3 semi-empirical methods. The MM+ molecular mechanics method does not have explicit parameters for such bonds, but it can interpolate the necessary parameters with its default-parameter scheme; the actual values of the interpolated parameters can be displayed in a log file. ----------------------------------------------------------------------------- FROM: "lldmpc::mrgate::a1::moralega"@lldmpc.dnet.dupont.com <"lldmpc::mrgate::a1::moralega"@lldmpc.dnet.dupont.com> check the CCL web page: http://www.ccl.net/chemistry.html It has the code for Mopac7. ------------------------------------------------------------------------------ FROM: Dr. Bruno Manunza ad 1) gopher://www.ccl.net:73/11/software/SOURCES/FORTRAN/mopac7_sources or ftp to: www.ccl.net and cd to pub/chemistry/software/SOURCES/FORTRAN ad 2) check these pages: http://latina.chem.cinvestav.mx/RLQ/mecanica_molecular.html http://tutor.oc.chemie.th-darmstadt.de/TZ/AKLindner/pimm_e.html ------------------------------------------------------------------------------ FROM: Stephen P. Molnar I attempted to compile MOPAC7 for a larger number of atoms a couple of months ago in Linux. Unfortunately, the memory management method that Jimmy Stewart uses precluded success. In plain terms, it didn't work! If you manage to do it, however, I'd appreciate details. ------------------------------------------------------------------------------- From landman@dearborn.sgi.com Thu Oct 31 18:17:54 1996 Received: from deliverator.sgi.com for landman@dearborn.sgi.com by www.ccl.net (8.8.2/950822.1) id RAA17870; Thu, 31 Oct 1996 17:26:20 -0500 (EST) Received: from aspire.dearborn.sgi.com by deliverator.sgi.com via ESMTP (950413.SGI.8.6.12/951211.SGI.AUTO) id OAA08199; Thu, 31 Oct 1996 14:26:09 -0800 Received: from phonon.dearborn.sgi.com by aspire.dearborn.sgi.com via ESMTP (950413.SGI.8.6.12/930416.SGI) id RAA01289; Thu, 31 Oct 1996 17:26:08 -0500 Received: from localhost (localhost [127.0.0.1]) by phonon.dearborn.sgi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA01114; Thu, 31 Oct 1996 14:01:41 -0800 Date: Thu, 31 Oct 1996 14:01:41 -0800 (PST) From: Joseph Landman To: "Wendy W. Richardson" cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:IRIX 6.2 and R10000 In-Reply-To: <199610291425.IAA06217@ddix7.monsanto.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Wendy: Yes my modeling programs work. The issue is a coff type binary or an elf type binary. Coff binaries are no longer supported as of 6.2. You can check to see if they are coff or elf by typing file name_of _executable This will report the binary type. Moreover, with 6.2, you have access to the better MIPSpro compilers which generate much better code than the older compilers. The R10k desktop ran my molecular dynamics code at 20 seconds per time step as compared to an older R8k desktop at 50 seconds per time step. The R10k is an extremely fast MD platform from my perspective. Joe On Tue, 29 Oct 1996, Wendy W. Richardson wrote: -> -> -> ->We are about to upgrade one of our workstations to an R10000 processor, ->with the corresponding upgrade to IRIX 6.2. The guy from SGI said the ->6.2 release was fairly stable, and the systems related stuff should all ->work fine, but we could have some problems with applications software ->(he is not familiar with modeling software). -> ->Has anyone else done this? Does your modeling software still work? Is ->it faster? Were there any special things you had to do to get things ->to work? Will I need to get/create another set of executables? -> ->I am most concerned about: Sybyl, Daylight, Gaussian94, Macromodel, -> Catalyst, Spartan -> ->I will summarize any responses I receive... ->------------------------------------------------------------- -> ("`-/")_.-'"``-._ ->Wendy W. Richardson, Ph.D. (. . `) -._ )-;-,_() ->Sr. Research Investigator (v_,)' _ )`-.\ ``-' ->Searle _;- _,-_/ / ((,' ->4901 Searle Parkway ((,.-' ((,/ ->Skokie, IL 60077 wwrich@ddix7.monsanto.com -> -> ->--- ->Administrivia: This message is automatically appended by the mail exploder: ->CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator ->MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 ->Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search -> Web: http://www.ccl.net/chemistry.html ->--- -> +-----------------------+----------------------------+ | Joe Landman | +1 810 848 4469 voice FH | | Systems Engineer | +1 313 441 2200 voice DH | | | +1 313 441 6341 fax DH | | Silicon Graphics Inc. | | | 24155 Drake Road, | landman@sgi.com | | Farmington MI 48335 | Mail stop DMR 2204 | +-----------------------+----------------------------+ http://reality.sgi.com/landman_dearborn/landman.html