From laaksone@csc.fi Fri Mar 26 05:08:44 1993 Date: Fri, 26 Mar 1993 07:08:44 -0200 (EET) From: Leif Laaksonen Subject: Re: amber/insight To: Bill Ross Message-Id: On Thu, 25 Mar 1993, Bill Ross wrote: > For those who want to display Amber trajectories, there are two > programs I know of in QCPE that do this: > > MD Display by Terry Lybrand and coworkers [SGI only] > mdXvu by Mark Forster [xwindows in general] > > Also, for people who want to import Amber output files to other > programs we (distributor of Amber) will supply a routine to read > the "parm" file that defines identity and connectivity of the atoms > in coordinate dumps. > > Bill Ross There is also the SCARECROW program which can show trajectories from CHARMM, DISCOVER, YASP, MUMOD and AMBER. Currently SCARECROW works only on SGI boxes but I'm slowly working on a Motif port. -leif laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Telefax: 358 0 4572302 FIN-02101 Espoo | Voice Mail: 358 486257407 FINLAND | Mail: Leif.Laaksonen@csc.fi One of these days I'm going to sit down and write a long letter To all the good friends I've known One of these days by Neil Young ------------------------------------------------------------------- From radomski@mond1.ccrc.uga.edu Fri Mar 26 04:11:49 1993 Message-Id: <9303261411.AA29223@mond1.ccrc.uga.edu> To: chemistry@ccl.net Subject: Neural Networks in Spectroscopy Date: Fri, 26 Mar 93 09:11:49 -0500 From: radomski@mond1.ccrc.uga.edu Hi Netters, for all of you who while attending next week ACS meeting in Denver are going to drop by the DEC's booth to see their newest line of alpha workstations I've the following. If you are interested in applications of neural nets to spectro- scopy try to be there when Jan Thomsen of CCRC would be giving a demonstration of his program - ANCHOVY (on DEC's alpha). To my best knowledge this is first time ever when neural nets are effectively used for a very quick database searches. Unfortunately, I won't be present. However, as most of the examples, spectra, network architectures, their training and so on, which Jan will be using to demo his program, are taken directly from my ongoing projects - I'd be very curious and glad to hear all your comments and opinions. Please write to me direct or use the list, whatever you prefer. Jan Radomski Complex Carbohydrate Research Center, University of Georgia, Athens, US. From 100012.1163@compuserve.com Fri Mar 26 09:47:52 1993 Date: 26 Mar 93 14:47:52 EST From: "100012.1163@compuserve.com" <100012.1163@compuserve.com> To: Subject: Molecular Modelling on a PC Message-Id: <930326194752_100012.1163_BHB35-3@CompuServe.COM> To: >internet:CHEMISTRY@oscsunb.ccl.net Dear Fellow Netters, Molecular Modelers and Computational Chemists, The molecular modelling program MOBY 1.5 is now ready for shipping. A *free* demonstration version is available. MOBY VIA ANONYMOUS FTP The demonstration version of MOBY, version 1.5 may be obtained via anonymous FTP from benny.bsc.mass.edu (or 134.241.41.5). If you have access to a computer on the Internet which supports FTP (file transfer protocol), log on to the computer and use the following sequence of commands (use lower case throughout): ftp benny-bsc.mass.edu anonymous your-email-address cd pub cd moby binary get mobyread.me get mobydemo.exe get manualps.exe quit At this point you will have the binary version of the files in your directory on the computer that is connected to the Internet. Your local information Services folk can advise you on the best way to transfer these files to your microcomputer. MOBY version 1.5 runs best on a 486 or 386. The 386 will require a math coprocessor. If you have a problem with the local file transfer, it will probably be that the files are not being transferred as binary files. mobydemo.exe is a self-extracting archive file that contains the demo version. manualps.exe is a self-extracting file that contains a postscript version of the demo manual. Make a directory called MOBY and copy the files to it. Theo run the files and they will self-extract. If you have Problems with this process, you can email to CHIPMAN@TOPCAT.bsc.mass.edu MOBY VIA E-MAIL The demonstration version of MOBY, version 1.5 may be obtained via e-mail from InterNet:SVSERV@DHDSPRI6.BITNET. To receive the files, send the following commands in the body of your message: get /chemistry/mobydemo.exe get /chemistry/manualps.exe MANUALPS.EXE is a self-extracting archive with the manual for the demo in encapsulated postscript format (the printing area is A5, so it should print on letter or legal format paper). If you encounter problems, please send a message to: stumpe@spint.compuserve.com Dr. Chipman has kindly advised Springer-Verlag in improving the English language version of MOBY 1.5. He has extensively tested MOBY in classes and he has agreed to answer any questions you may have. USING MOBY WITH OTHER PROGRAMS Version 1.5 of MOBY can be used as a "front end" to draw structures for input into other programs, such as MOPAC. MOBY can output a structure that can be used directly in MOPAC. This file format, called a Z-matrix, can be used by many molecular modeling and quantum mechanics programs. MOBY will also save structures in the form of molfiles for use in the MACCS-II data base. Molefiles contain the structure in the form of cartesian coordinates and can be used by many other programs. MOBY will also read MOPAC output files, either from MOPAC or from the many other programs which write MOPAC output files. All you have to know to use a MOPAC file with MOBY is that the first three lines of the file are reserved for information about the MOPAC calculation (keywords) and the name of the molecule. When you read a MOPAC file into MOBY, MOBY prompts you for the number (3) of lines to be skipped. Therefore, MOBY can be used to visualize structures resulting from the MOPAC calculation directly. A software routine QC4MOBY is available to MOBY users to extract geometry, IR- and UV spectral data and molecular orbital data from files generated with the Quantum Chemistry programs MOPAC 6.0, SCAMP 4.2 or GAUSSIAN 82/90. The converted files can be read by MOBY version 1.5. MOBY offers an extensive range of modelling functions: - Display of up to 2000 centers - Fast 3D graphics - Independent manipulation of freely-definable fragments - Structure comparison - Property comparison - Force field calculations on up to 150 centers interacting with up to 2000 other centers - Geometry optimization - Conformational analysis - Molecular dynamics simulation - Extensive tools for the energy analysis of structures - Quantum chemical calculations based on the semi-empirical MNDO and AM1 methods - Display of: - IR spectra and normal coordinates - UV/Visible spectra - Molecular orbitals - Isopotential surfaces for electrostatic potentials - Freely-definable format for reading non-MOBY geometry data - Library of important structures and their geometries - Construction and maintenance of an individual structure library - On-line help - PROTOCOL mode for recording a program session - DEMO mode for re-running a previously recorded program session This latest version, MOBY 1.5, is for IBM-PC-compatible personal computers with the following minimum specifications: - 640 kb random access memory (530 kb free) - 80x87 arithmetic coprocessor - graphics adapter: Hercules, EGA, or VGA (1024x768 maximum) - a mouse and - a hard disk are strongly recommended running under MS-DOS version 2.0 or later. Since MOBY requires 530 kB of random access memory to be free, MS-DOS Version 4.0 is not a good choice; MS-DOS 5.0 is strongly preferred. MOBY 1.5 will be demonstrated at the Spring ACS Meeting. Look for the Springer-Verlag booth. For more information write to: In North America: Springer-Verlag New York Electronic Media Services c/o Ms. Raye Hazan 175, Fifth Avenue New York, NY 10010 USA Phone: (212) 460-1653 Fax: (212) 473-6272 InterNet: Hazan@SPINT.CompuServe.com Sincerely yours Dr. Rainer Stumpe Chemistry Editorial Springer-Verlag Tiergartenstr. 17 D(W)-6900 Heidelberg Phone: +49-(0)6221-48 73 10 Fax: +49-(0)6221-41 39 82 INTERNET:stumpe@spint.compuserve.com