From kevin@rose.chem.wesleyan.edu Tue Jan 18 00:51:00 1994 Received: from rose.chem.wesleyan.edu for kevin@rose.chem.wesleyan.edu by www.ccl.net (8.6.4/930601.1506) id AAA01759; Tue, 18 Jan 1994 00:03:28 -0500 Received: by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA13862; Mon, 17 Jan 1994 23:32:33 -0500 Date: Mon, 17 Jan 1994 23:32:33 -0500 Message-Id: <9401180432.AA13862@rose.chem.wesleyan.edu> From: Kevin.McConnell@rose.chem.wesleyan.edu (kevin@rose.wesleyan.edu) To: landman@hal.physics.wayne.edu Cc: CHEMISTRY@ccl.net In-Reply-To: Joe Landman's message of Mon, 17 Jan 94 21:13:30 EST <9401180213.AA02023@hal.physics.wayne.edu> Subject: Hyperchem 3.0 Hi Joe, I am some what familuar with the problem you are having. If you intend to animate your trajectory you might want to just write out the coordinates to a file. You can do this by writing a script to run the simulation and specify the option: notify-on-update coordinates there is a sample script in the hyperchem directory react.scr or this this script I've used in class might help. -------cut here--------- start-logging hcl_md.log no append-omsgs-to-file hcl_mdvel.log open-file hcl_1.hin render-method spheres select-atom 1 1 select-atom 2 1 color-selection red ; react.scr ; ; this script is for MD of ; H-Cl ; ; velocity in HIN file is 300 Ansgstroms/picosecond ; select-none select-atom 1 1 calculation-method molecularmechanics molecular-mechanics-method mm+ mechanics-print-level 9 dynamics-restart false dynamics-run-time 0.2 dynamics-heat-time 0.2 dynamics-cool-time 0 dynamics-time-step 0.0005 dynamics-starting-temp 0.0 dynamics-simulation-temp 300.0 dynamics-temp-step 25 dynamics-constant-temp true dynamics-snapshot-filename hcl_md.snp dynamics-snapshot-period 1 dynamics-average-period 20 dynamics-collection-period 20 ;velocities 1 1 notify-on-update coordinates do-molecular-dynamics query-value velocities stop-logging omsgs-not-to-file exit-script ------------end here------------------- good luck Kevin Kevin McConnell kevin@rose.chem.wesleyan.edu Dept. of MB&B Molecular Biophysics Program Wesleyan University Middletown CT. From smb@smb.chem.niu.edu Tue Jan 18 10:51:49 1994 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.4/930601.1506) id KAA06036; Tue, 18 Jan 1994 10:42:21 -0500 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA16779 (5.67a/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net>); Tue, 18 Jan 1994 09:42:18 -0600 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net) id AA06234; Tue, 18 Jan 94 09:34:26 -0600 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:chemistry@ccl.net) id AA09585; Tue, 18 Jan 94 09:34:24 -0600 Date: Tue, 18 Jan 94 09:34:24 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9401181534.AA09585@smb.chem.niu.edu> To: chemistry@ccl.net Subject: New Chemistry Gopher Site in Operation Hello Chem-Netters, I recently received a Camille and Henry Dreyfus Chemical Informatics Award to study the possibility of using a gopher site on the Internet to distribute chemical information. I would like to announce that the Northern Illinois University Chemical Gopher Site is now in operation. For those of you not familiar with gopher, it is a front-end program to the internet that makes access to the Internet particularly painless. Addresses and ftp protocols are handled transparently so that the user does not need to understand much, if anything about the Internet. The gopher client is available on a variety of platforms from boombox.micro.umn.edu in the /pub/gopher directory. Access to the NIU Chemistry Gopher is obtained by pointing your client at hackberry.chem.niu.edu port 70 or through the listing of all gophers maintained at the University of Minnesota. Please feel free to poke around our site. We have placed some information on the gopher, including conference information, software information, and access site to other chemistry information on the Internet. If you have information you would like to add, such as an announcment of an upcoming meeting or new software, please email the announcement to me at admin@hackberry.chem.niu.edu. If you have any suggestions, complaints, or problems, send me a note at the same address. This is an experimental site, meaning that we will be adding new features in the future. Some plans include a chemistry email phone book, MSDS databases, electronic conferencing, and a preprint archive. I will post new features of the Gopher Site to this list as needed. Thanks for your interest. Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 smb@smb.chem.niu.edu From herbert.homeier@rchs1.chemie.uni-regensburg.de Tue Jan 18 11:07:51 1994 Received: from rrzs1.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id JAA05550; Tue, 18 Jan 1994 09:57:01 -0500 Received: from rchs1.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA08044; Tue, 18 Jan 94 15:56:45 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.31)) id AA13810; Tue, 18 Jan 94 15:56:58 +0100 Date: Tue, 18 Jan 94 15:56:58 +0100 From: Herbert Homeier (t4720) Message-Id: <9401181456.AA13810@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: JCP Express Hi all, perhaps the following service of JCP is interesting for some of you. Best regards Herbert -------------------------------------------------------------- Dr. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: homeier@rchs1.chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de -------------------------------------------------------------- ----- Begin Included Message ----- J C P E X P R E S S An experimental project in electronic manuscript distribution of the Journal of Chemical Physics and the AIP. The JCPExpress is a free trial service for electronic distribution of preprints of manuscripts between acceptance and publication in the Journal of Chemical Physics. Manuscripts are voluntarily submitted by authors in some electronic format. Each manuscript in the database is then made available in PostScript format and in the original Tex, WordPerfect, or Microsoft Word format if available. Each manuscript is identified by the AIP ID number with the format "nnnyii" where "nnn" is the manuscript identifier, and "yii" is the issue number ("y" is the last digit of the year and "ii" is the issue (01-24)). There are some 25 manuscripts available as of 9/23/93. JCPExpress can be accessed by e-mail or by anonymous ftp. By e-mail to: express@jcp.uchicago.edu Responses are determined by the "Subject:" line. If the "Subject:" line contains the following words, the e-mail responses are: Subject: Information returned: help -- This file is returned by e-mail authorinfo -- Instructions on submitting electronic copies of accepted manuscripts to JCPExpress. ftpinfo -- Instructions on obtaining electronic copies of manuscripts from JCPExpress via FTP. index -- Records for manuscripts in the Express data base for the latest two issues are returned. Records contain the AIP ID number, title, authors, and formats of files available for the given manuscript. fullindex -- Records for all manuscripts available in the Express database are returned. jcptitles yii -- Returns a list of all articles scheduled for publication, in issue yii with titles, authors, and the AIP numbers. If no issue number is specified, the information for the latest two issues' contents are returned. express yii -- Returns a list of all articles appearing in JCP Express. scheduled for publication in issue yii with titles, authors, and the AIP numbers. If no issue number is specified, the Express information for the latest two issues' contents are returned. jcptitles and express return only the title of each article, the author, and the AIP manuscript number. Further information, including authors' addresses, can be found in the index (.ix) files for individual manuscripts and in the main index files. These can be obtained via e-mail as explained below using Subject: get nnnyii.ix with the appropriate AIP ID number. get help -- Identical to "help" get authorinfo -- Identical to "authorinfo" get ftpinfo -- Identical to "ftpinfo" get index -- Identical to "index" send xxxx -- Identical to "get xxxx" join -- adds your address to the "express" mailing list leave -- removes your address from the mailing list. get fn1.d1 fn2.d2 fn3.d3 ... -- fn1, fn2, are FILE NUMBERS (AIP ID numbers) of manuscripts in JCPExpress. For each, a DESCRIPTOR is required (d1 would be the descriptor for file fn1). Descriptors are: ix -- index ( abs -- abstract ) ps -- PostScript file tex -- TeX file dvi -- dvi file mw -- Microsoft Word ( wp -- Word Perfect ) NOTE: MANY FILES WILL BE TOO LARGE TO RETRIEVE SUCCESSFULLY BY E-MAIL. WE RECOMMEND FTP TRANSFER, AS DESCRIBED IN THE FILE "FTPINFO" LISTED ABOVE. NOTE -- All manuscripts will exist in PostScript format, and many will exist other formats. Formats are listed in the Index for each file. Note also that we limit e-mail messages to 160 Kbytes and many manuscript files exceed this. In these cases and when downloading non-ASCII formats, the files should be transferred using ftp. Please send comments and suggestions via e-mail to "admin@jcp.uchicago.edu". Complaints will be grudgingly accepted also. ---------------------- End of Help File -------------------------------- More Information on JCP Express: Why distribute electronically? Manuscripts submitted to the Journal of Chemical Physics are accepted quickly, but the delays inherent in publishing a journal result in several months' delay between the acceptance of a manuscript and its publication in the Journal of Chemical Physics. Even after publication, slow mail delivery to many parts of the world results in still longer delays for many subscribers. Electronic distribution, though, has none of these delays. It takes only a few minutes after acceptance of a manuscript to prepare it to be distributed electronically. The world-wide Internet and Bitnet networks can transfer large amounts of text anywhere on the planet almost instantly, either through electronic mail or direct File Transfer Protocol access. The Journal of Chemical Physics Express is designed to take advantage of this great speed by allowing anyone in the world to retrieve electronic copies of manuscripts by electronic mail and FTP. The JCP Express does not replace the Journal of Chemical Physics; it only makes it easier to obtain text not yet available through the conventional means. What manuscripts will be available? The JCP Express will only provide manuscripts which are not yet easily available in published form, i.e. papers "In press". This means that manuscripts will be added to the system as soon as they have been accepted and are made available to the JCP in electronic form, and removed once it can be assured that all subscribers should have received their copies, a few months after the publication date. Who may use the JCP Express? Initially anyone with an Internet- or Bitnet-connected computer may use the JCP Express. For the initial trial period, there are no fees and no access restrictions. Anyone with e-mail access can use the mail server, and anyone with FTP access can use the anonymous FTP server. Information on obtaining files via ftp is available in the "ftpinfo" file from the Express mail server. What are the file formats? Manuscripts available via JCP Express will be in several formats. The JCP Express offices will translate all manuscripts to Adobe Postscript format; thus all manuscripts will be available as PostScript files. Manuscripts submitted as Tex or RevTex files will also be available in tex and dvi formats. Manuscripts submitted as Microsoft Word or other formats will be available in the original format as well as in postscript format. Use of RevTex is recommended. How do I submit a manuscript? Your manuscript must have been accepted for publication in the Journal of Chemical Physics. If you did not provided a copy in electronic form at time of acceptance, you may do so later by FTP. Information on how to do this is available in the "authorinfo" file available from the JCP FTP or mail server. The easiest way to submit a manuscript to the JCP Express is to include a 3.5" disk and a statement of permission for electronic publication with the final version of your manuscript after it has been accepted for publication in the Journal of Chemical Physics. No manuscript will be made available by JCP Express which has not been accepted and scheduled for publication in the Journal of Chemical Physics. How can I get more information? More information on JCP Express is available from the FTP and mail servers. To get information from the mail server, send electronic mail To: express@jcp.uchicago.edu Subject: help and a file giving more specific details about using the mail server will be sent to you. The server also has information files on other subject: Subject: authorinfo [ for information on submitting manuscripts ] and Subject: ftpinfo [ to learn how to use the FTP server ] To obtain these or other files by FTP, open an FTP connection to jcp.uchicago.edu, with a user-name of "ftp" or "anonymous" and your e-mail address as the password. All the JCP Express files are found in the /pub directory. Are there human beings there too? If you have a problem with the JCP Express mail or FTP server, or have a question or suggestion about the system, you can send e-mail To: admin@jcp.uchicago.edu and it will be read by the Journal of Chemical Physics staff. Please don't hesitate to write if there's a way we can make the system work better for you. ----- End Included Message ----- From adit@Kodak.COM Tue Jan 18 12:51:11 1994 Received: from Kodak.COM for adit@Kodak.COM by www.ccl.net (8.6.4/930601.1506) id LAA07068; Tue, 18 Jan 1994 11:52:37 -0500 Received: from bcc9.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA10215; Tue, 18 Jan 94 11:54:04 -0500 Reply-To: adit@Kodak.COM Received: by bcc9.kodak.com (4.1/SMI-4.1) id AA10217; Tue, 18 Jan 94 11:48:54 EST Date: Tue, 18 Jan 94 11:48:54 EST From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9401181648.AA10217@bcc9.kodak.com> To: chemistry@ccl.net Subject: Final Notice of MM/MD workshop. Folks, I have agreed to post this reminder to the net on behalf of the organizers of the Workshop. Hope that you decide to come. Adi. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > From detar@mailer.fsu.edu Mon Jan 10 14:43:47 1994 > Date: Mon, 10 Jan 94 12:02:10 EST > From: (Del Detar) @mailer.cc.fsu.edu > To: adit@kodak.com > Subject: mmmd > Content-Length: 6448 > January 6, 1994 > > Enclosed you will find the preliminary version of the program for the 4th Biennial Workshop on > Molecular Mechanics and Molecular Dynamics. We are fortunate to have Jack Dunitz among the > outstanding speakers. The topics include a number of very important current research areas, including > drug design, biomolecules, and polymers. There will be several talks about describing new proposals for > improved force fields. Warren Hehre will present a workshop on use of ab initio methods. There are new > applications of molecular mechanics to structures and to reactions, and new applications of molecular > dynamics. This promises to be an excellent program. If you plan to attend, please forward the enclosed > registration form by January 28. > > > Arrangements have been made with the Cabot Lodge Motel, 2735 N. Monroe > Street, Tallahassee, FL 32303, telephone 904-386-8880. The rate quoted by the > motel is $58 single or double. The motel has a shuttle that picks up guests > at the airport and a shuttle to the conference center. There will be a > reception at the hotel on February 21, Monday, from 6 to 8 pm. The motel is > about 3 miles from the conference center. > > > > Tentative Program > (as of December 30, 1993) > Fourth Biennial Workshop on > Molecular Mechanics and Molecular Dynamics > February 22-25, 1994 > > Sponsored by the Supercomputer Computations Research Institute > Florida State University, Tallahassee, Florida > > FEB 21 Monday > 6:00 to 8:00 pm Reception at Cabot Lodge Motel 2735 N. Monroe St. > > FEB 22 Tuesday > 8:00 Continental Breakfast > 9:00 Welcome > 9:10 Preliminary Comments: DeLos F. DeTar > 9:15 Jack Dunitz > 10:15 Coffee > 10:30 J.E.Anderson Measuring Attractive van der Waals > Interactions within Molecules > 11:00 J.Phillip Bowen > 11:30 Helena Dodziuk > 12:00 Lunch > 1:15 Thomas Halgren > 2:15 Curt M. Breneman > 2:45 Frank J.J.Leusen Ab initio prediction of possible > crystal structures > 3:15 Coffee > 3:30 Hubert Bodot Vibrational analysis and identification > of organic transients issued from > photoisomerization and photolysis experiments > performed on molecules isolated in > cryogenic matrices > 4:00 David M. Gange Robust fit: a novel method for > molecular superposition > 4:30 contributed talks Daniel P. Vercauteren, C. Giessner-Prettre > S. Vijayakumar > > FEB 23 Wednesday > 8:00 Continental Breakfast > 9:00 D. L. Beveridge > 10:00 Coffee > 10:15 Douglas A. Smith Modeling the hydrogen bond > 10:45 Bastiaan van de Graaf > 11:15 S. Swaminathan Molecular dynamics of novel DNA structures > 11:45 David C. Doherty Molecular dynamics simulation and > analysis of cooperative motions in chain > molecules > 12:15 Lunch > 1:30 Dora M. Schnur ERROR: MISSING PARAMETERS - What do I do now? > 2:00 John Wendoloski > 3:00 Coffee > 3:15 posters > Warren Hehre - mini workshop on computational techniques > 5:00 > > FEB 24 Thursday > 8:00 Continental Breakfast > 9:00 Warren Hehre Elucidation of product distributions > in organic reactions > 10:00 Coffee > 10:15 Terry R. Stouch > 10:45 Jan Dillen An empirical force field for alkenes. > A comparison with MM3 > 11:15 Samuel Krimm > 12:15 Lunch > 1:30 Adi Treasurywala > 2:30 Wayne Mattice > > 3:00 Load buses for trip to Wakulla Springs, boat trip and dinner > 6:30 Dinner at Wakulla Springs > > FEB 25 Friday > 8:00 Continental Breakfast > 9:00 Kendall N. Houk > 10:00 Coffee > 10:15 Henk C. van der Plas Intramolecular Diels-Alder > reactions of pyrimidines: a synthetic and > computational study > 10:45 Hagai Meirovitch New methods for simulating the > free energy of bio-macromolecules > 11:15 Eva Meirovitch Structure determination of flexible > biological macromolecules from NMR data > 11:45 Workshop ends > > > > > Here's the Registration Form in case you need it > > > MOLECULAR MECHANICS AND MOLECULAR DYNAMICS 1994 > Program # 1902994 > > To register, please complete this electronic form and return it with your credit > card information noted below. If you prefer, print out a hard copy of the form, > and send it when completed, with your check, to Conference Registrar, CPDPS, > Florida State University, Tallahassee FL 32306-2027. For registration > information, call (904) 644-3806. > > Name_____________________________________ SS# _______________________ > Organization __________________________________________________________ > Phone: _____________________ Address ________________________________ > _______________________________________________________________________ > _______________________________________________________________________ > > I prefer to pay my fee of $__________ by: > __ Check enclosed (payable to Florida State University) > __ Mastercard __VISA (Mastercard or Visa ONLY please) > Acct.#_________________________________Exp.date ________________ > Signature: _______________________________________ > > Registration fees: $350 after Jan 15, 1994; $325 before Jan 15, 1994; > $250 for those whose posters or talks are accepted; $150 for students > > The registration fee includes the cost of most meals. > > Can send it to: slampman@mailer.fsu.edu > FAX 904-644-2589 > > > Arrangements have been made with the Cabot Lodge Motel, 2735 N. Monroe > Street, Tallahassee, FL 32303, telephone 904-386-8880. The rate quoted by the > motel is $58 single or double. The motel has a shuttle that picks up guests > at the airport and a shuttle to the conference center. There will be a > reception at the hotel on February 21, Monday, from 6 to 8 pm. The motel is > about 3 miles from the conference center. > > > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From nish@cv1.chem.purdue.edu Tue Jan 18 15:51:08 1994 Received: from mentor.cc.purdue.edu for nish@cv1.chem.purdue.edu by www.ccl.net (8.6.4/930601.1506) id PAA09625; Tue, 18 Jan 1994 15:51:00 -0500 Received: from cv1.chem.purdue.edu by mentor.cc.purdue.edu (5.61/Purdue_CC) id AA09706; Tue, 18 Jan 94 15:50:52 -0500 Received: by cv1.chem.purdue.edu (931110.SGI.ANONFTP/931108.SGI.ANONFTP) for @mentor.cc.purdue.edu:chemistry@ccl.net id AA06221; Tue, 18 Jan 94 15:59:48 -0500 From: nish@cv1.chem.purdue.edu (Nishantha ) Message-Id: <9401182059.AA06221@cv1.chem.purdue.edu> Subject: Tektronix graphics packages To: chemistry@ccl.net Date: Tue, 18 Jan 1994 15:59:47 -0500 (EST) Content-Type: text Content-Length: 502 Hi I am looking for a moleculer graphics package that runs on a Tektronix graphics terminal.I have seen many packages (PD and otherwise) that support X-windows but I am specifically interested in a Tektronix package .The reason for Tektronix emulation is basically due to my inability to support X-windows on my home PC . ( unless of course I start running Linux ). Is there such a package in existance out there. Any help , suggestions would be much appreciated. Thanks Nishantha Illangasekare From ravishan@swan.wcc.wesleyan.edu Tue Jan 18 15:52:59 1994 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.4/930601.1506) id OAA09251; Tue, 18 Jan 1994 14:59:16 -0500 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA22934; Tue, 18 Jan 1994 14:56:41 -0500 Date: Tue, 18 Jan 1994 14:56:41 -0500 Message-Id: <9401181956.AA22934@swan.wcc.wesleyan.edu> From: "G. Ravishanker" To: chemistry@ccl.net Subject: GROMOS Trajectory file... Hi I would like to confirm that the trajectory files written out by GROMOS (GROMOS87 and afterwards...) is still a title line followed by 3*natoms coordinates in (10f8.3) format for constant volume simulations. I also would like to make sure that this is the case with AMBER trajectory files also. Thanks for the help in advance. **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06457. * ****************************************************************************