From yosimori@translell.tutkie.tut.ac.jp Mon Feb 26 01:30:44 1996 Received: from translell.translell.tutkie.tut.ac.jp for yosimori@translell.tutkie.tut.ac.jp by www.ccl.net (8.7.1/950822.1) id AAA03359; Mon, 26 Feb 1996 00:51:39 -0500 (EST) Received: (from yosimori@localhost) by translell.translell.tutkie.tut.ac.jp (8.7+2.6Wbeta/3.3W9) id OAA06432; Mon, 26 Feb 1996 14:38:35 +0900 (JST) Date: Mon, 26 Feb 1996 14:38:35 +0900 (JST) Message-Id: <199602260538.OAA06432@translell.translell.tutkie.tut.ac.jp> To: CHEMISTRY@www.ccl.net Subject: unsubscribe From: yosimori@translell.tutkie.tut.ac.jp (Atsushi Yoshimori) X-Mailer: mnews [version 1.19] 1995-07/21(Fri) Please unsubscribe Atushi Yoshimori yosimori@translell.tutkie.tut.ac.jp From jankazim@aquila.ichp.waw.pl Mon Feb 26 05:30:46 1996 Received: from aquila.ichp.waw.pl for jankazim@aquila.ichp.waw.pl by www.ccl.net (8.7.1/950822.1) id FAA05204; Mon, 26 Feb 1996 05:07:28 -0500 (EST) Received: by aquila.ichp.waw.pl (5.65/1.2-eef) id AA26443; Mon, 26 Feb 96 11:04:29 +0100 Date: Mon, 26 Feb 1996 11:04:27 +0100 (CET) From: Jan Kazimirski To: chemistry@www.ccl.net Subject: Question: calc. of PED (potential energy distrib.) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters One of my friends (not subscribed to CCL - yet(:-()) asked me to send his question to the list. The question is: "Can you recommend any program (commercial or academic) which calculates PED (potential energy distribution) based on Gaussian 94 - calculated vibrational normal modes?" We both (me and my friend) would be grateful for any information. Thanks in advance. Jan Kazimirski e-mail: jankazim@aquila.ichp.waw.pl From SUBRAPS@texaco.com Mon Feb 26 13:37:36 1996 Received: from gate.texaco.com for SUBRAPS@texaco.com by www.ccl.net (8.7.1/950822.1) id NAA10088; Mon, 26 Feb 1996 13:29:22 -0500 (EST) Received: by gate.texaco.com id AA23598 (Mail SMTP Gateway 3.0 for chemistry@www.ccl.net); Mon, 26 Feb 1996 12:29:13 -0600 Message-Id: Date: 26 Feb 1996 12:19:12 GMT From: "MSBEA01.SUBRAPS" Subject: Summary : Dipole-Dipole Interaction in D To: chemistry@www.ccl.net Comment: MEMO 1996/02/26 12:26 ---------------------------------------------------------------------- THIS MAIL MESSAGE IS FROM THE INTERNET AND MAY HAVE BEEN READ, COPIED, OR MODIFIED BY USERS OTHER THAN INTENDED RECIPIENTS. ---------------------------------------------------------------------- Dear CCL members, A while ago I posted a query on dipole-dipole interactions , the following is a summary of responses that I received. Thanking you all for your time --Mani-- Dr. P. S. Subramanian Fuels and Lubrication Division Texaco Inc. P. O. Box 509 Beacon, NY 12508 email: SUBRAPS@texaco.com vmail: 914-838-7561 Response 1. You have a very strange header above your mail. It sounds almost as if you expect your mail to be tainted by the filth of the transport through internet :-) What does it mean? It was this text that aroused my curiosity, i don't know of any MD packages that do dipole-dipole interaction. Maybe Gromos does it, it seems to be quite advanced. Greetings, Frits Daalmans Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 Response 2. Dear Dr. P. S. Subramanian Could you summarize responses for your querry on CCL ? Grzegorz Bakalarski ICM Warsaw University Response 3. Hi Mani, To my knowledge only MM3 incorporates such a entity. It uses bond dipoles for such a purpose. Everyone else uses point charges (monopole approximation) to reproduce these properties. If you have a good reason to need the electrostatics (which is probably why you asked the net...) and cannot use a bond dipole scheme, then I would strongly suggest that you perform ab initio calculations, say at the HF/6-31G(d,p) level (or 6-31+G(d,p) if you have anions) and compute the monopole charges from a fit of the electrostatic potential. This method reproduces the molecular dipole moment pretty well; I'm not so sure about the molecular quadrupole moment, though. Use of Mulliken and Natural Bond Order methods is not recommended for this purpose. Be sure that you use a large enough basis set to suitably reproduce the electron density of the systems you are interested in. (As an aside, I stumbled upon this many years ago in grad school by trying to use Mulliken-based charges to reproduce the dipole moments in simple lipids. I failed miserably. In my thinking during that time, I was sure that I could reproduce the molecular dipole from point charges--after all, we all learned it could be done in our fields courses. But of course I was not aware that Mulliken population analysis was not based on trying to reproduce the molecular dipole. It took me a while to realize that it was the method, not the idea, that was at fault.) Hope this helps, Craig -- ----------------------------------+----------------------------------------- Papernet: Craig W. Burkhart | *** GO TRIBE!! *** WORLD SERIES '96 *** Goodyear Research | 142 Goodyear Blvd | 1995 American League Central Div. Champs Akron, OH 44305 | 1995 American League Champion Mouthnet: 216.796.3163 | Faxnet: .3304 | TSN MVP -Albert Belle (50HR,52DB,126RBI) Internet: cburkhart@goodyear.com | TSN Fireman of the Year - Jose Mesa ----------------------------------+----------------------------------------- SPRING TRAINING IS HERE*** SPRING TRAINING IS HERE***SPRING TRAINING IS HERE WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! ---------------------------------------------------------------------------- Response 4. Any package that does molecular dynamics with an MM2-derived force field should include interactions of bond dipoles. (HyperChem does; please contact me for details.) I don't know of any that explicitly include effects of molecular dipoles, but I'm not sure if that's what you were asking about. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ Response 5 Orient 3.2 by Anthony Stone of Cambridge University calculates all sorts of things using electrostatic expansions i.e., charges, dipoles, quadrupoles etc. The new version has basic molecular dynamics in it. If you want a copy you'll have to Email him directly on ajs1@cam.ac.uk and explain who you are and why you want to use it. Darren Andrews. University of Manchester, Department of Chemistry, Oxford road, Manchester. M13 9PL. Darren.Andrews@man.ac.uk PGP: 512/A971A9 Tel: 0161 275 4699. Fax: 0161 275 4598. From Lysakowski@aol.com Mon Feb 26 16:30:52 1996 Received: from emout10.mail.aol.com for Lysakowski@aol.com by www.ccl.net (8.7.1/950822.1) id QAA11774; Mon, 26 Feb 1996 16:23:05 -0500 (EST) From: Received: by emout10.mail.aol.com (8.6.12/8.6.12) id QAA25613; Mon, 26 Feb 1996 16:22:45 -0500 Date: Mon, 26 Feb 1996 16:22:45 -0500 Message-ID: <960226162244_432088794@emout10.mail.aol.com> To: MOL-DIVERSITY@listserv.arizona.edu cc: ISISFORUM-L@mdli.com, chemistry@www.ccl.net, CHMINF-L@iubvm.ucs.indiana.edu, ISISFORUM-L-EXPAND@mdli.com Subject: The Electronic Lab Notebooks Consortium (The R&D Team Computing Consortium) This press release is simultaneously submitted to CHMINF-L, CHEMIND-L, CCL, ISISforum-l, and Mol-Diversity lists. If you have subscriptions to more than one of these lists, we apologize for the multiple posting. =========================================================== Subj: Re: The Electronic Lab Notebooks Consortium From: Lysakowski@AOL.COM (Rich Lysakowski) Lorrin, There are no full solutions on the market for collaborative electronic laboratory notebooks now. Vendors who had the best "software notebook" products have withdrawn them from the market, at least temporarily. This is a complex area with difficult requirements to meet because of the extensive legal and regulatory contraints, and the appropriate technology components. However, all required pieces exist today, including the technology and full understanding of the legal and regulatory requirements. They just must be fitted together in the appropriate combinations and processes to support recordkeeping for patent and regulatory litigation in regulated R&D processes. We spent several years researching requirements and working with vendors as a vendor-independent scientific software product research information and consulting service. We have very extensively researched all commercial products that come even close to meeting the needs of scientists for electronic notebooks. We are willing to share the results with your requestors. We created the vendor-independent consortium to drive the open forum and open process required to create electronic notebooks and the larger systems into which they must fit. This is called "The R&D Team Computing Consortium" (a.k.a. The Electronic Laboratory Notebooks Consortium") and is described below. This new consortium of 15+ chemical, pharmaceutical and biotech companies will deliver mission-critical software systems for electronic laboratory notebooks and team data management and collaboration within a short time frame, greatly accelerated by the results of our research. We expect the software notebook systems to have integrated tools for combinatorial chemistry, chemical structure databases, and biological information databases, as well as instrument interfacing and LIMS. We will be working with various vendors that make these tools already to integrate them into the solutions. Hence, this recent press release is right in line with your query. Could you please disseminate it to your requestors, and have them contact me directly? I will be able to give them accurate and up-to-date information about what is happening in this emerging software market. Rich Lysakowski, Ph.D. Director of R&D The R&D Team Computing Consortium ============================================== FOR IMMEDIATE RELEASE: Contact: Dr. Rich Lysakowski The R&D Team Computing Consortium (a.k.a. The Electronic Notebooks Consortium) phone: 508-443-4771 e-mail: lysakowski@aol.com TeamScience, Inc., 8 Pheasant Avenue Sudbury, Massachusetts USA 01776 ========================================================= Industry Consortium Recruits Members To Create Advanced Software Systems for Scientific Laboratories Vendor-Independent Initiative Uses Open Process to Replace Outmoded R&D Project Data Management Systems Collaborative Electronic Laboratory Notebooks Being Driven to Market By User-Funded Consortium ========================================================= BOSTON, MA--The R&D Team Computing Consortium (a.k.a. The Electronic Laboratory Notebook Software Consortium) is recruiting additional member companies to help define and drive the creation of broad-based industry solutions for software electronic laboratory notebooks and R&D project data management and collaboration systems. Founded in late 1995 by companies in the chemical, pharmaceutical and biotechnology industries, this 15-plus member consortium is using an open, vendor-independent process to specify design requirements and fund qualified vendors to develop advanced software systems to meet the needs of chemists, biologists, and materials scientists and engineers. "The entire current system of R&D project data management is archaic in the electronic age, because critical R&D information is too often locked away on paper" says Dr. Rich Lysakowski, a principal of TeamScience Inc, the software research and engineering project management firm that is leading and managing the consortium. "Data need to be easily searched and shared by other researchers or authorized people with a need to know." This two-year industry-wide collaborative project will deliver specifications and object-oriented software for collaborative electronic notebooks and other specialized modules for client/server computers to meet the diverse needs of these different communities. The consortium is funding vendors to rapidly develop modular and highly reusable mission-critical solutions that support recordkeeping in legally-defensible ways for regulated industries. "To meet our aggressive schedule we are building on top of well-tested industry-leading platforms already in wide use, rather than building from scratch. We are emphasizing forward-looking tools and standards such as CORBA, Java, the World Wide Web, and others that apply to laboratory and R&D applications," says Dr. Lysakowski. "We have researched the requirements and priorities for many companies over the past years, including several in the Electronic Records Consortium (ERC), to ensure that we have completely covered the needs of these industries," Dr. Lysakowski adds. The R&D Team Computing Consortium is building on the work of the ERC and other more recent research projects. The technologies of electronic recordkeeping systems, groupware, document and workflow management, LIMS and instrument interfacing tools, chemical and biological information databases, the World Wide Web, intelligent agents, and integration tools are ready to be applied to this unique set of automation problems faced by R&D teams. By pooling the resources of major end-user corporations, and utilizing the core competencies and best-of-breed technologies from qualified vendors, the consortium will deliver open, integrated software platforms and intelligent tools to significantly enhance scientific R&D and testing laboratory project data management productivity and global collaboration>while addressing the legal and regulatory needs to create and preserve reliable and trustworthy electronic records. Scientists have long felt the need for electronic laboratory notebooks as a way to minimize the tedium of laboratory work. Currently, researchers often spend many hours per week capturing data in paper notebooks to document their work. Paper notebooks are just one part of a much larger system for managing records, data and documents in research and development projects. Scientists require flexible, open and interoperable software solutions for electronic laboratory notebooks, project data management, and collaboration. These tools must come from several software markets simultaneously. A major technical goal of the consortium is to pull together all necessary pieces, which exist already, and use them in the right combinations to satisfy all major requirements, and at the same time establish some software standards for open, integrated systems for R&D and testing laboratories. Progress on these inevitable electronic laboratory software notebook systems had been impeded by the immaturity of software technology and standards, and by rampant ignorance of existing technology and procedures to address the legal and regulatory concerns. However, software, legal, and regulatory experts in the top Fortune 500 companies now agree that practical and prudent electronic ways are available to address each of these concerns. Software and standards have matured to the point where global electronic laboratory notebooks and project data management systems are really just a logical next step beyond the current the World Wide Web and various commercial groupware and document management systems on the market today. The vendor selection process will begin within the next few months. Qualified vendors of electronic laboratory notebooks, groupware, document and workflow management, LIMS and instrument interfacing systems, scientific information databases, and integration tools will be awarded contracts to develop and support various scientific software clients, middleware, and base platform enhancements. The user-driven consortium will provide the necessary open process to ensure that the emerging products fit end users' needs well. End user companies and software vendors interested in participating should contact: Director of R&D The R&D Team Computing Consortium TeamScience, Inc. 8 Pheasant Avenue Sudbury, MA 01776. E-mail: lysakowski@aol.com Tel: 508-443-4771 Fax: 508-879-8120 From osawa@cochem.tutkie.tut.ac.jp Mon Feb 26 18:30:53 1996 Received: from cochem2.cochem2.tutkie.tut.ac.jp for osawa@cochem.tutkie.tut.ac.jp by www.ccl.net (8.7.1/950822.1) id SAA12752; Mon, 26 Feb 1996 18:06:40 -0500 (EST) Received: from [133.15.160.31] (cochem3.tutkie.tut.ac.jp [133.15.160.31]) by cochem2.cochem2.tutkie.tut.ac.jp (8.6.12+2.4W/3.3W9) with SMTP id IAA22913 for ; Tue, 27 Feb 1996 08:10:08 +0900 Message-Id: <199602262310.IAA22913@cochem2.cochem2.tutkie.tut.ac.jp> Date: Tue, 27 Feb 1996 08:06:11 +0900 To: chemistry@www.ccl.net From: osawa@cochem.tutkie.tut.ac.jp (Eiji Osawa) X-Sender: osawa@cochem2.cochem2.tutkie.tut.ac.jp Subject: WATOC96 2nd circular Return-Receipt-To: osawa@cochem.tutkie.tut.ac.jp MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8-J13) To the list members of Japan, Taiwan, Korea, China and other Asian countries: I have a stock of the 2nd circular for WATOC96, World Congress of Comutational Chemists, to be held in Jerusalem, Israel, July 7 to 12, 1996. Deadline of abstract is April 15, 1996. Those who are interested should send me e-mail for a copy or take a look at its homepage, http://www.ch.ic.ac.uk/watoc/watoc_israel.html. Eiji Osawa /************************************************* * Eiji Osawa * Department of Knowledge-based Information Engineering * Toyohashi University of Technology * Aichi 441, Japan * Phone: x-81-532-47-0111(ex. 853) * FAX: x-81-532-48-5588 * E-mail: osawa@cochem.tutkie.tut.ac.jp *************************************************/