From jaeric@mtcamm.monsanto.com Mon Jul 26 03:00:15 1993 From: Jon A. Erickson Message-Id: <9307261300.AA15383@mtcamm.monsanto.com> Subject: Re: Transition state opt. in CADPAC To: chemistry@ccl.net (OSU Comp. Chem. List) Date: Mon, 26 Jul 93 8:00:15 CDT > Will you please inform me what are the keywords necessary > for the transition state optimisation in CADPAC ( ab inition program)? > Please send me a sample input file. > D. sengupta India. ipcakc@ipc.iisc.ernet.in There is a TS optimizer in CADPAC using the Schlegel algorithm. The keywords are: BERNY END The option to use is SADDLE, I believe. This may have changed with more recent versions of CADPAC, please correct me if this is the case. -- ################################################################ # Jon Erickson e-mail: jaeric@mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. FAX: (314) 694-1080 # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ From adit@Kodak.COM Mon Jul 26 05:30:26 1993 Date: Mon, 26 Jul 93 09:30:26 EDT From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9307261330.AA05415@bcc9.kodak.com> To: chemistry@ccl.net Subject: Scanned structures to molecule files? Folks, Maybe I was just dreaming but it seems to me some time ago that someone either had or was looking for a piece of software that would allow one to scan in 2D structures (from say a publication) and make mol files from the info. If anyone has any information on such a program I would appreciate hearing from them. The platform is not too important. In the RARE event that there is a substantial response I will summarize for the net of course. Thanks in advance for your help. Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com From pmr1716@ggr.co.uk Mon Jul 26 18:17:55 1993 Date: Mon, 26 Jul 93 18:17:55 GMT From: Peter Murray-Rust Message-Id: <9307261817.AA11991@uk6x09.ggr.co.uk> To: CHEMISTRY@ccl.net Subject: Multiple synthesis This may not be quite the right newsgroup, but I'd be interested to know what experience others have had in multiple synthesis (by which I mean the automatic synthesis of large numbers of chemicals - for example for biological screening). PS - I gave up actual synthesis many years ago - at the request of my labmates - so I'm sure computers can do better than me now. :-) Peter ------------------------------------------------------------------------------ Peter Murray-Rust | "Nothing exists except atoms and empty pmr1716@ggr.co.uk | space; all else is opinion" (Democritos). Protein Structure Group, Glaxo Group Research, Greenford, MIDDX, UB6 0HE, UK ------------------------------------------------------------------------------ From bruce@dggpi2.chem.purdue.edu Mon Jul 26 07:25:04 1993 Date: Mon, 26 Jul 93 12:25:04 -0500 From: bruce@dggpi2.chem.purdue.edu (Bruce Luxon) Message-Id: <9307261725.AA05183@dggpi2.chem.purdue.edu> To: chemistry@ccl.net Subject: MORASS Address A request was made for the numerical address for the MORASS code in ftp anonymous at DGGPI2.CHEM.PURDUE.EDU - it is 128.210.43.164 . MORASS performs a hybrid matrix analysis of 2D NOESY volumes so one can do NOESY constrained Molecular Dynamics. Hope this helps. Bruce ____________________________________________________________________________ | | | |"You can't always get what you want, | Dr. Bruce A. Luxon | | But if you try sometimes, | Chemistry Department | | You'll get what you need ..." | Purdue University | | | W. Lafayette, IN 47907 | | Mick Jagger | (317)494-5289; Fax (317)494-0239 | | | bruce@dggpi2.chem.purdue.edu | |______________________________________|___________________________________| From maloneyhuske%phvax.dnet@smithkline.com Mon Jul 26 12:48:11 1993 Date: Mon, 26 Jul 93 16:48:11 -0400 Message-Id: <9307262048.AA29121@smithkline.com> From: maloneyhuske%phvax.dnet@smithkline.com (Keith MaloneyHuss x6083) To: "chemistry@ccl.net"%inet.dnet@smithkline.com Subject: CAOS software user comments (Summary) Here is the long overdue summary of responses to my request for user comments on Computer Assisted Organic Synthesis (CAOS) software: >> First the original query: > I'm trying to find out how computational methods other than > modelling are being used to help synthetic and medicinal chemists. > I've seen a few of the synthetic chemistry software packages (e.g. CAMEO, > CHIRON, LHASA), and am wondering if and how this type of software is being > used. Wendy Warr's Directory of Chemistry Software is a good listing, but > I would really like to get comments from users out there. > If people using any software as an aid in synthesis would email me about > their experiences, I'd be happy to summarize. > Thanks. > --keith > Keith MaloneyHuss maloneyhuske@smithkline.com >> This is the info on Wendy Warr's book that should have been included in my >> original question: Wendy Warr, Peter Willett and Geoff Downs are the editors of the book: Directory of Chemistry Software 1992, Cherwell Scientific Publishing and the American Chemical Society. It lists all known software and lists functions, references, sources, hardware requirements, pricing and user support. They do not review each package. However this is a directory not a review, and as such it is very good. Ulrich Jordis has published an addendum to Warr's book: Oesterr. Chemie Zeitschrift (12) 340-343 (1992) and (1) 17-19 (1993). >> The responses: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I'd like to respond to your request for user response on the usage of software for sythetic chemists. We are running a national center for chemical software which can be accessed through the network by all Dutch universities (the CAOS/CAMM Center). So, our accounting can supply you with some statistics of the usage of those packages. Currently we offer access to four synthesis planning and related packages, LHASA, CAMEO, CHIRON, and SYNGEN. More important for organic chemists are the reaction databases, of which we currently supply ORAC, REACCS, SYNLIB, and the FCD. I gathered the number of activations for the first five months of this year. The figures concern only activations of real users. All activations by courses or CAOS/CAMM Center staff have been removed from the statistics. LHASA: ? (Only known for May: 6 activations) CAMEO: 7 CHIRON: 12 SYNGEN: 8 ORAC: 877 REACCS: 103 SYNLIB: 123 LHASA (Prof. Corey, Harvard) is used a couple of times a month. However, I know only two examples of users making up their entire sythesis plan with LHASA. In only one of these two cases, the synthesis plan is really put to reality in the lab. This case has been submitted for publication (v. Roozendaal, Scheeren et al., Can. J. Chem.). All other activations are limited to at most a few minutes cpu, meaning that only small synthetic problems can have been analyzed. My impression is that most of these activations concern curiosity activations (to see what the program looks like). CAMEO (Prof. Jorgensen, Yale) and CHIRON (Prof Hannessian, Montreal) have pretty much the same story as LHASA. The usage is limited to a couple of activations in a month. I don't have a clear insight in what users use the programs for. I was told that CAMEO was merely used to estimate pKa values, but I don't know whether that is also true for our users. SYNGEN (Prof. Hendrickson, Brandeis) has an even lower number of activations than the previous programs. In my opinion this is due to the inappropriate user interface, which makes it nearly impossible to analyse the program's results. I was told that major improvements will follow in the next release. ORAC (MDL Ltd.) is the leader in usage of our organic chemistry programs, but the usage includes the FCD (Fine Chemical Directories). REACCS (MDL Ltd.) is going to be discontinued on our site, so, the usage is decreasing, because of our policy to let them switch to ORAC. So, it cannot be concluded from the figures that ORAC is eight times more popular than REACCS. However, we have always found a preference of users towards ORAC. I think it has two reasons: REACCS is complexer in its usage for beginning users and REACCS does not support simple terminals very well. SYNLIB (Distributed Chemical Graphics, Inc.) used to be the highest in the usage lists (a couple of years ago), but usages has switched to ORAC and to some extend also to REACCS. These programs have been developed further while SYNLIB remained more or less on the same level. FCD (MDL, Ltd.) is introduced only a year ago, but has gained a high popularity already. The exact usage is not known, because the FCD is implemented in ORAC. I hope this was the kind of information you were looking for. I'm highly interested in your summary to see what the experience is from other users. Yours sincerely, Jan-Willem Boiten CAOS/CAMM-Center, Univ. of Nijmegen +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We were one of the first to use MDL's original SECCS program and have used REACCS and ORAC for quite a few years. I'm not a synthetic chemist but a modeller and comp. chemist who helped implement this. The chemists tell me they find it extremely useful. It usually shows them synthetic paths they have come up with themselves but also suggests new paths they hadn't thought of. We have had a look at Chemical Design's new reaction database and have purchased a single user license to try it out in our labs. **>> then this reply to my question about SECCS: I'm not surprised that the MDL person hadn't heard of SECCS. As I mentioned, we were one of the fledgling MDL's first customers, when Todd Wipke and Stuart Marsen founded it. SECCS was Todd's first attempt at a reaction expert system and was the forerunner of REACCS. It didn't work very well but it was the beginning of an idea. You should check out the new ChemRXS program from Chemical Design Ltd (chemdesign@applelink.apple.com) if you want to cover all possibilities. It is likely to be the cheapest option but I can't tell you how well it works yet. Dr. David A. Winkler Principal Research Scientist CSIRO Division of Chemicals and Polymers Clayton, Australia. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ The cover story planned for our December '93 should be of interest to you: Chemically Intelligent Computing Systems. Regards--Barbara F. Graham (aka BFG) Editor, Chemical Design Automation News +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thanks to everyone who responded. Further comments are welcome. --keith Dr. Keith MaloneyHuss SmithKline Beecham Pharmaceuticals maloneyhuske@smithkline.com From merkle@parc.xerox.com Mon Jul 26 09:09:22 1993 From: Ralph Merkle To: CHEMISTRY@ccl.net Subject: Nanotechnology Conference Message-Id: <93Jul26.160931pdt.12171@manarken.parc.xerox.com> Date: Mon, 26 Jul 1993 16:09:22 PDT SUMMARY: The third nanotechnology research conference will be held October 14-16 in Palo Alto. It is a multidisciplinary meeting on molecular nanotechnology, that is, thorough three-dimensional structural control of materials and devices at the molecular level. Attendees will include chemists, materials scientists, physicists, engineers, and computer scientists interested in learning about the field and possibly steering their careers toward nanotechnology today. For further information, contact foresight@cup.portal.com. ANNOUNCEMENT: Third Foresight Conference on Molecular Nanotechnology: Computer-Aided Design of Molecular Systems October 14-16, 1993 Palo Alto, California Sponsor: Foresight Institute Cosponsors: Stanford University Department of Materials Science and Engineering, Molecular Graphics Society (USA), Institute for Molecular Manufacturing This conference is a meeting of scientists and technologists working in fields leading toward molecular nanotechnology: thorough three-dimensional structural control of materials and devices at the molecular level. The conference will cover topics relevant to the pursuit of molecular control, drawing from fields such as: * computer science (e.g. molecular modeling, system design issues) * computational chemistry * physics (e.g. proximal probes such as the STM and AFM) * mechanical engineering (CAD) * many others Developments in these fields are converging, opening opportunities for fruitful collaboration in developing new instruments, devices, and capabilities. Topics and invited speakers include: * Introduction to the Design of Molecular Systems Eric Drexler, Institute for Molecular Manufacturing * Computational Nanotechnology Ralph Merkle, Xerox Palo Alto Research Center * Design of Macromolecular Objects Manfred Mutter, Institut de Chimie Organique * Molecular Modeling William Goddard III, California Institute of Technology * Crystal-Based Molecular CAD Geoff Leach,Royal Melbourne Institute of Technology * Packing Molecular Building Blocks Markus Krummenacker, Institute for Molecular Manufacturing * Visualization with Molecular Graphics Michael Pique, Scripps Research Institute * Mechanical Engineering CAD Joel Orr, Autodesk, Inc. * Molecular Building Blocks Ted Kaehler, Apple Computer, Inc. * Modeling Mechanochemical Processes Charles Musgrave, California Institute of Technology * Modeling Diamond CVD with Density Functional Theory Warren Pickett, Naval Research Laboratory * Atom Manipulation by Proximal Probes: Experiment and Theory Makoto Sawamura, Aono Atomcraft Project, Japan * Nanomanipulator: Scientific Visualization for Scanning Tunneling Microscopy (STM) Russell Taylor, Univ. of North Carolina at Chapel Hill * Ab Initio Methods and Software Charles Bauschlicher, NASA Ames * Nanocomputers and Reversible Computation J. Storrs Hall, Rutgers University The first Nanotechnology Award (and accompanying cash prize) will be presented at the meeting. Nomination information will be available from Foresight Institute. DEMONSTRATIONS Leading vendors will demonstrate products useful in the pursuit of molecular control, including molecular modeling software and hardware, and proximal probe systems (e.g. STM). CALL FOR PAPERS Contributions on relevant topics are solicited for presentation in lecture or poster format. Potential contributors are asked to submit an abstract (200-400 words), including names, addresses, telephone and fax numbers of the author(s), and an indication of whether oral or poster presentation is preferred. Papers of both kinds will be reviewed for publication. In choosing papers, priority will be given to (1) cogent descriptions of the state of the art in techniques relevant to the construction of complex molecular systems, (2) well-grounded proposals for multidisciplinary efforts which, if funded and pursued, could substantially advance the state of the art, and (3) reports of recent relevant research. JOURNAL & BOOK PUBLICATION OF PROCEEDINGS Proceedings of the conference will be refereed and published in a special issue of the international journal Nanotechnology, and later in book form. Abstracts due August 16, 1993 Notification of acceptance September 1, 1993 Manuscripts due October 14, 1993 Abstracts should be directed to the Foresight Institute, Box 61058, Palo Alto, CA 94306, USA; fax 415-324-2497. PRE-CONFERENCE TUTORIAL A full-day tutorial on molecular modeling and computational chemistry will be held on October 13. This tutorial is designed for computer scientists and programmers interested in using their computer skills to become active in the field of nanotechnology. The workshop will be taught by Bill Goddard, Ralph Merkle, Eric Drexler and others. More detailed information, including registration materials, will be sent to all conference registrants. SITE AND ACCOMMODATIONS Conference sessions will be held at the Hyatt Rickeys Hotel in Palo Alto. Accommodation arrangements should be made directly with the hotel. Reservations should be made by September 29; when making reservations, mention that you are attending the "Foresight Nanotechnology Conference" to obtain the lower conference room rate. Deposits in the amount of the first night's stay plus tax are required to guarantee reservations; these are refundable up to 6 PM on the date of arrival. Room rate: $89, single or double occupancy, plus 10% local tax. Hyatt Rickeys 4219 El Camino Real Palo Alto, CA 94306 (415) 493-8000 tel (415) 424-0836 fax TRANSPORTATION The conference site is easily reached from San Francisco International Airport and San Jose International Airport. Information on ground transportation services will be mailed to registrants. REGISTRATION FORM (please print and mail or fax) Name: Title: Dr. Prof. Ms. Mr. Address: Tel.: Fax: Email: Position (programmer, professor, director, etc.): Organizational affiliation (for your badge): The registration fee includes the scientific program, Wednesday evening reception, Thursday and Friday luncheons, and a copy of the proceedings journal issue. (Student and one-day rates do not include proceedings.) postmarked: by Sept. 1 after Sept. 1 Regular $350 $400 Academic, nonprofit, governmental $275 $325 Student $100 $125 One day (specify day) $135 $160 Add $200 for Pre-conference Tutorial registration. Total amount: $ Payment may be made by VISA, MasterCard, check, or international money order valid in the U.S. Make checks payable to "Foresight Conferences"; checks and bank drafts must be in U.S. dollars drawn on a U.S. bank. Refunds of registration fees can only be made on receipt of a written request which must be postmarked no later than September 15, and are subject to a $50 administrative fee. Credit card registrations may be faxed; please do not send credit card information over the Internet. Card #: Exp. date: Signature (required for credit card registrations): Mail or fax registration to: Foresight Institute Box 61058, Palo Alto CA 94306 USA Tel. 415-324-2490 Fax 415-324-2497 Internet: foresight@cup.portal.com PLEASE FORWARD THIS ANNOUNCEMENT TO APPROPRIATE NEWS GROUPS AND MAILING LISTS