From jtgolab@amoco.com Tue Feb 16 04:30:24 1993 Date: Tue, 16 Feb 1993 10:30:24 -0600 From: jtgolab@amoco.com Message-Id: <9302161630.AA15081@vacc47.nap.amoco.com> To: chemistry@ccl.net Subject: Conference Announcement -------------------------------------------------------------------- Theoretical and Computational Approaches to Interface Phenomena August 2-4, 1993 South Dakota State University Amoco Chemical Company _______________________________________________________ South Dakota State University and Amoco Chemical Company will host a three day conference on Theoretical and Computational Approaches to Interface Phenomena August 2-4 1993 at South Dakota State Univeristy in Brookings, South Dakota. Speakers from academia and industry will discuss topics at the forefront of this field such as modeling catalysis, thin organic films, metals, and surfaces, surface diffusion, metal/electrolytic solution interfaces, and interactions with biological surfaces. The presentations will relate new software methodologies and theoretical techniques, present comparisons between methods or parameterization schemes, and share computational strategies. The conference will provide ample time for participants to interact with the speakers and talk to third party software vendors. A reception and registraton will be held Sunday evening, August 1 between 7 and 10 pm at the Holiday Inn of Brookings. Presentations will begin Monday morning August 2 at 8:30 am. All participants are encouraged to present a paper during the poster session on the night of August 2. Negotiations are currently underway for the publication of the conference proceedings as a hardback book. Speakers will contribute a chapter to the conference book and participants presenting posters can contribute a research summary. All presenters will be invited to contribute an abstract of their presentation for inclusion in a book of abstracts that will be distributed at the start of the conference. The conference will adjourn at 4:30 pm on Wednesday August 4. The current list of invited and/or confirmed speakers is: Max Berkowitz, University of North Carolina, Chapel Hill Jimmie Doll, Brown University Michael Klein, University of Pennsylvania Ezequiel Leiva, Universidad Nacional de Cordoba, Argentina Michael N. Liebman, Amoco Technology Company Michael Philpott, IBM, San Jose Dennis Salahub, Universidad de Montreal, Canada Harrell Sellers, South Dakota State University Yitzhak Shnidman, Eastman-Kodak Evgeny Shustorovich, Eastman-Kodak Donald Truhlar, University of Minnesota Registration is required. Sponsors for this conference are South Dakota State University, Amoco Chemical Company, Cray Research, Inc., Eastman-Kodak, and IBM. -------------------------- CUT HERE --------------------------- Registration Form To register to attend the conference and/or give an oral or poster presentation please complete this form. Please type or print. Give your name as you would like it to appear on your name badge. Dr.___ Mr.___ Ms.___ ______________________________________________ Address: ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ Telephone: ________________________ FAX: ________________________ Electronic Mail Address: ____________________________________________ I will __attend the conference __give an oral presentation __give a poster. Title of presentation: __________________________________________________ _________________________________________________________________________ _________________________________________________________________________ Abstracts received after July 2, 1993 cannot be in the book of abstracts. Registration Fee: The conference registration fee is $40 for undergraduate and graduate students and postdocs; $175 for academic staff (faculty or scientific); $370 for industrial scientists. This fee includes a reception the evening of August 1 at the Brookings Holiday Inn, a reception the evening of August 2 during the poster session, a conference banquet the evening of August 3, and the abstract booklet. Please note: Reserving a hardbound copy of the conference book will require an additional fee that will depend on the total number of books reserved and the length of the book. We anticipate that the hardbound conference book will cost about $50. I am __an undergradate student __a graduate student __a postdoc __a university faculty member __a scientific staff member __an industrial scientist and enclose a check made payable to South Dakota State University in the amount of $_______. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Return completed registration forms and abstracts to either: Dr. Harrell Sellers or Dr. Joseph T. Golab Department of Chemistry Amoco Chemical Company South Dakota State University PO Box 3011 M/C C-6 Brookings, SD 57007 Naperville, IL 60566 Tel: (605) 688-6374 (708) 961-7878 Fax: (605) 688-5822 (708) 420-4678 Email: hsellers@ncsa.uiuc.edu jtgolab@nap.amoco.com Space is limited. Please register before July 2, 1993. -------------------------- CUT HERE --------------------------- Theoretical and Computational Approaches to Interface Phenomena Conference General Information August 2-4, 1993 Hotel Information A block of rooms has been reserved at the Holiday Inn of Brookings. The special conference rate is $46.00 single and $50.00 double to quad occupancy plus tax of 6%. The phone number for the Holiday Inn of Brookings is (605) 692-9471. A Best Western, which is across the highway from the Holiday Inn, is within easy walking distance. The Best Western phone number is (605) 692-9421. To assure availability and special rates rooms should be reserved by July 2, 1993. Travel Information The Brookings Airport has commercial airline commuter service from Minneapolis operated by the G P Express Airline Company, (605) 692-6818. Flights directly into Brookings are easy to obtain, but they must connect through Minneapolis. If this is not convenient, commercial air service to Sioux Falls, South Dakota is recommended. Conveyance Vans operates a shuttle service that runs between Sioux Falls and Brookings with 'door-to-door' service. The shuttle service runs according to passengers' flight schedules. Conveyance Vans can be reached at (605) 692-2236. Cars can also be rented at the Sioux Falls airport. Flying into Brookings via Minneapolis is usually more economical than flying into Sioux Falls and driving to Brookings by car if your point of origin is southeast of Brookings. From wrinn@iris104.biosym.com Tue Feb 16 02:04:11 1993 Date: Tue, 16 Feb 93 10:04:11 -0800 From: wrinn@biosym.com Message-Id: <9302161804.AA01375@iris104.biosym.com> To: CHEMISTRY@ccl.net Subject: dmol electrostatic potentials There is a bug in DMol version 2.2 in the calculation of electrostatic potentials, as reported by Grzegorz Bakalarski. This has been corrected in version 2.3, which is (as of this week) the current version. DMol users may report bugs directly to rcenter@biosym.com. Michael Wrinn From william@chemres.tn.cornell.edu Tue Feb 16 08:28:40 1993 Message-Id: <199302161830.AA22126@oscsunb.ccl.net> From: William Shirley Subject: MPW Fortran? To: CHEMISTRY@ccl.net Date: Tue, 16 Feb 93 13:28:40 EST Which is best? I am about to enter the world of MPW by porting a large amount of Fortran code to the Macintosh. The code needs to stay in FORTRAN (rather than be converted to C) so that it can be easily supported. I know that the the question of which is the best FORTRAN compiler? has come up before. I would like to find out which is currently generally considered to be the best. Of the two MPW FORTRAN Compilers (Language Systems and Absoft), which: 1. is less bugie? 2. is easier to use? 3. has the better support tools (debugger)? 4. has the better manuals? 5. has the better telephone support? 6. has more language extensions? 7. is faster at compiling? 8. produces faster more optimized code? 9. supports math coprocessors in line? 10. has special features? Please include the version numbers of the compilers that you are familiar with so that we are not comparing old apples and new oranges. Thank you very much. Please respond to me and I will summerize. William Shirley ws15@cornell.edu From kgreevy@hpldas1.sid.hp.com Tue Feb 16 03:29:01 1993 From: Kenneth McGreevy Message-Id: <9302161929.AA29527@hpldas1.sid.hp.com> Subject: Re: X Windows for PC .. To: chemistry@ccl.net Date: Tue, 16 Feb 93 11:29:01 PST > ....................................................................... > > hi, > I know that this subject was discussed before in this forum, but i dont have > any hardcopy information with me right now. We have a 486 machine and a IBM -R > S6000. We have ethernet card on the PC also. We would like the PC to 'talk' to > the RS6000 in the X windows environment. I have few names of the commercial ve > ndors whose software could simulataneously run X, MS-DOs and MS windows applica > tions. Is there any other 'free' software available from ftp sources??? Any inp > ut on this subject is appreciated. Thanks in advance. We've had good experiences with Hummingbird Communications' EXCEED Ver 3.1 underMS Windows 3.1 on PCs of 386/20 or better. All had 8 Megabytes of memory and fast IDE hard drives with circa 24 Megabyte permanent swap. You can cut and paste from the X-window to other MS Windows apps. I believe US$ list price is $ 385.- You'll almost certainly need a 1024 x 768 display. If your host software expects a 256 color display you will need a VGA card with 1 Megabyte of memory. A 17" or better display size is best. NOTE: The opinions are those of the submitter and do not constitute endorsement or support of any mentioned product by Hewlett Packard. ------------------------------------------------------------------ ___ Ken McGreevy /_ __ / / kgreevy@hpldas1.sid.hp.com / / /_/ HEWLETT/hp/PACKARD Scientific Instruments Div. / / /__/ TN or (415)-857-2743 From fora@iris59.biosym.com Tue Feb 16 03:38:05 1993 Date: Tue, 16 Feb 93 11:38:05 -0800 From: fora@biosym.com Message-Id: <9302161938.AA03364@iris59.biosym.com> To: chemistry@ccl.net Subject: DIBUG RE : > Do you know the mail reflector address or the newsgroup name for users > of Biosym packages ? Included is the introduction to DIBUG, the Biosym Users' Group Mailing List prepared by Dr. Reinhard Doelz. Fora Chan Technical Support BIOSYM Response Center ==================================================================== Contents: 1. Welcome to DIBUG! 2. REPORTING BIOSYM BUGS 3. How to access DIBUG archives ------------------------------------------------------------------------------- Welcome to DIBUG! dibug@comp.bioz.unibas.ch [[ You will receive this notice either upon subscribing or upon requesting a change of email address. Sending this message is, for me, a good way of checking that mail gets through -- or at least does not bounce. ]] Welcome to DIBUG ("Discovery, Insight, Biosym Users' Group"), an unmoderated mailing list for discussion of Biosym products. Expected topics of discussion include, but are not limited to, queries about how to use features of the software, and how to solve scientific problems using the software. Although this list is administered by and for Biosym users, we expect Biosym Technologies, Inc. to monitor the list, and perhaps to respond to issues that may arise. Mail sent to: dibug@comp.bioz.unibas.ch will be immediately resent to all current DIBUG subscribers. When responding to a query posted to the list, please reply to the list, unless there is a reason you prefer to limit your response to the poster, only. To reply to the list, rather than the poster, you may have to do something special, since the poster's path appears on the "From:" line, and the dibug path appears on the "To:" line. To request to be added or deleted from the subscriber list, send electronic mail to: dibug-request@comp.bioz.unibas.ch The return path will usually be taken from the From: line of your electronic mail, unless you specify an alternative path. Right now, list maintenance is being done manually, so there is no set format for specifying things; just use English. To send mail directly to the administrator of the list, send mail to dibug-admin@comp.bioz.unibas.ch The administrator is currently +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142051::embnet | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 2078 | | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- All mail sent to DIBUG will be archived at bioftp (see below). ------------------------------------------------------------------------------- REPORTING BIOSYM BUGS (Information provided by Biosym Response Center.) > For any future bugs, you can use one of many avenues to report them to > Biosym: > > 1. This forum. > 2. Email to : rcenter@biosym.com > 3. FAX a report of the bug to the Response Center at 619-458-0431 > 4. Phone in a report to the Response Center at 619-546-5509 > > Please include in your report the following information: > > Biosym Product and release number > Hardware Manufacturer and model number > Special Hardware (like stereo) > Operating system and release number > Detailed description of the bug, with the specific steps you took, so > that the bug can be reproduced. > > When Biosym receive the bug report, they will reproduce it, and > enter it into the bug tracking data base. In the event it's not > a bug, they will let you know how to proceed. > ------------------------------------------------------------------------------- How to access DIBUG archives. 1) anonymous fto to bioftp.unibas.ch (131.152.8.1) 230 Guest login ok, access restrictions apply. Remote system type is UNIX. ftp> cd DIBUG-mailinglist ftp> ls total 1118 -rw-r--r-- 1 boss manager 120 Apr 20 19:33 .hostdata -rwxrwxrwx 2 2911 embnet 8474 Apr 19 20:54 current -rw-r--r-- 1 2911 manager 131332 Apr 20 09:29 dibug-18apr92 -rw-r--r-- 1 2911 manager 214476 Apr 20 09:29 dibug-21feb92 -rw-r--r-- 1 2911 manager 216757 Apr 20 09:30 dibug-6jul91 (this list is slightly outdated; and has more up-to-date archives now). 2) via gopher. GOPHER is a very interesting browsing tool which enables you to read in archives, do database searches, and more. The gopher server at bioftp has been established a few months ago, and is now making the dibug archives available as well. I reindex the archive each day. If you have questions or comments on the GOPHER software, you can get in contact with the Gopher development team by sending e-mail to: gopher@boombox.micro.umn.edu If you are interested in news about new gopher servers and software you can subscribe to the gopher-news mailing list by sending e-mail to: gopher-news-request@boombox.micro.umn.edu If you want to get the most recent releases of the gopher software, you can get these via anonymous ftp from boombox.micro.umn.edu in the /pub/gopher directory. I keep a binary depository for gopher executables preconfigured for accessing bioftp in the directory programs/gopher-binaries/old: 3 -r-xr-xr-x 1 boss manager 1248 Mar 13 11:33 README 368 -rw-r--r-- 1 boss manager 188416 Mar 13 11:25 gopher.Convex 541 -rwxr-xr-x 1 boss manager 276708 Mar 13 11:25 gopher.IRIX4.0 256 -rw-r--r-- 1 boss manager 131072 Mar 13 11:22 gopher.SUN 202 -rw-r--r-- 1 boss manager 103424 Mar 13 11:14 gopher.ULTRIX-32 320 -rw-r--r-- 1 boss manager 163840 Mar 13 11:23 gopher.ULTRIX4.1 All you need is to binary ftp the correct image, and then % setenv TERM vt100 % gopher Internet Gopher Information Client v0.7 Root Directory 1. About Gopher, and this bioftp site/ --> 2. DIBUG [Discover Insight Biosym User Group] Mailing list/ 3. EMBnet Services/ 4. Molecular Biology Archive List. 5. and if you have suggestions or problems.... 6. bioftp server: READ ME FIRST. 7. bioftp server: data on EMBL CD-ROM/ 8. bioftp server: small databases/ 9. more GOPHERs (biological and others)/ You select option 2 by typing 2 and get Internet Gopher Information Client v0.7 DIBUG [Discover Insight Biosym User Group] Mailing list --> 1. Search the mailing list archives for a keyword 2. current/ 3. dibug-18apr92/ 4. dibug-21feb92/ 5. dibug-6jul91/ If you hit again you can search for a keyword. E.g., searching indigo, gives us Internet Gopher Information Client v0.7 Search the mailing list archives for a keyword : indigo --> 1. gene@iris4 Re: Re: Indigo support by Biosym?. 2. shenkin (P Re: Indigo support by Biosym?. 3. CAMBPRMS@u Re: Re: Indigo support by Biosym?. 4. Reinhard D Re: Last call for new list admin in the US. and the first hit would be the mail from Gene Plagge... After lots of questions from various people, I have tried to collect BCL macros which have been posted or entioned by researchesr of BIOSYM staff. This includes the famous 'lipid' macros, and the interesting discussion on the animation business. The following files are currently available which are NOT in the gifts directory of the software distribution: README.some_remarks Don Mackay Quote from the header: " Some words of wisdom for BCL macro users/developers: There are a few known bugs in the version 2.0 release of BCL that macro developers should be aware of. These bugs will be fixed in a maintenance release due out this summer. "... animation.suggestion Robert P. Milius Quote from the header: " I wanted to make a movie of a dynamics run and dump the images to video (an abekas unit). I had initially tried (and failed) to write a macro and came up with the following ... " build_bilayer.bcl Don Mackay build_lipid.bcl Don Mackay build_macro.README Don Mackay fragment_file.psv Don Mackay (!!! BINARY !!!) frags.def Quote from the header: (README file is build_macro.README) build_lipid.bcl Builds a phospholipid from a menu of possible head and tail groups (the user must choose one and only one from the H, R1, and R2 group). build_bilayer.bcl A BCL macro that takes an object (which may contain more than one molecule) and arrays it in the current orientation into a 2D array of molecules reminiscent of a mono- or bilayer. fragment_file.psv An extended fragment file with the lipid fragments added to the standard distributed library. The build_lipid macro requires this library (...) frags.def The labels and fragment assignment tags associated with the new fragment_file.psv above. from_1_letter_code.macro Don Mackay Quote from the header: " I have interfaced an awk script which will read an external file containing 1 letter amino acid abbreviations and build the corresponding structure using Insight commands. The format of the sequence file is arbitrary. The sequence need not have any particular delimiting character between letters (indeed, the letters can run together) and they can be either upper or lower case. Any characters encountered that do not correspond to the standard 20 amino acid abbreviations are ignored. " ram.bcl Russ Helfand Quote from the header: " # This is a BCL macro called ram. Its purpose is to produce Ramachandran # graphs where the phi and psi angles are plotted against each other for # residues in a single conformation of a protein. It is assumed that each # residue's backbone atoms conform to the normal naming convention of # N, CA, C. ... HOW TO GET THESE FILES PER FTP: ================================ Anonymous ftp is available to bioftp.unibas.ch (131.152.8.1). In the directory DIBUG/mailinglist, the subdirectory BCL contains the files as mentioned above. PLEASE NOTE THAT YOU MUST TRANSFER THE *PSV FILE IN BINARY MODE. ftp> pwd 257 "/DIBUG-mailinglist/BCL" is current directory. ftp> ls 200 PORT command successful. 150 Opening ASCII mode data connection for '/bin/ls'. total 2522 -rw-r--r-- 1 boss manager 2372 Sep 4 11:01 README.some_remarks -rw-r--r-- 1 boss manager 5226 Sep 4 11:36 animation.suggestion -rw-r--r-- 1 boss manager 3069 Sep 4 11:01 build_bilayer.bcl -rw-r--r-- 1 boss manager 2923 Sep 4 11:01 build_lipid.bcl -rw-r--r-- 1 boss manager 2037 Sep 4 11:02 build_macro.README -rw-r--r-- 1 boss manager 1249761 Sep 4 11:01 fragment_file.psv -rw-r--r-- 1 boss manager 8118 Sep 4 11:01 frags.def -rw-r--r-- 1 boss manager 8457 Sep 4 11:01 from_1_letter_code.macro -rw-r--r-- 1 boss manager 7842 Sep 4 11:01 ram.bcl 226 Transfer complete. HOW TO GET THESE FILES PER EMAIL: ================================== There is a very elementary email service running on bioftp@comp.bioz.unibas.ch in order to get you the files per email if you do not have internet access. This mailer is meant to do other jobs usually and is not prepared to send help and instructions. the only instructions are the following: (1) ONLY 1 request per mail message. (2) AUTOMATIC WILD CARD EXPANSION of the last word. (3) The command to be sent is get software bcl where can be any of the following: README.some_remarks animation.suggestion build_bilayer.bcl build_lipid.bcl build_macro.README fragment_file.psv_uuencode fragment_file.psv_uuencode_check frags.def from_1_letter_code.macro ram.bcl The following commands, therefore, are valid: get software bcl (gets you all) get software bcl ram.bcl (gets you only the ramachandran macro) get software bcl build (gets you all build* files) ######## W A R N I N G ########## The fragment_file.psv_uuencode file is huge (22000 lines) and therefore might not pass through all mailers. If you really need the file, check with the data given in fragment_file.psv_uuencode_check to see whether you received all data in full length. If so, run uudecode on your IRIS to recover the original psv file. Please note that, depending on the traffic, it can take several hours (up to 2 days) if such large files are to be transferred. ==================================================================== From doherty@msc.edu Tue Feb 16 09:52:53 1993 Message-Id: <9302162152.AA04779@uh.msc.edu> Date: Tue, 16 Feb 1993 15:52:53 -0600 To: CHEMISTRY@ccl.net, William Shirley From: doherty@msc.edu (David C. Doherty) Subject: Re: MPW Fortran? At 1:28 PM 2/16/93 -0500, William Shirley wrote: >Of the two MPW FORTRAN Compilers (Language Systems and Absoft), >which: > >1. is less bugie? >2. is easier to use? >3. has the better support tools (debugger)? >4. has the better manuals? >5. has the better telephone support? >6. has more language extensions? >7. is faster at compiling? >8. produces faster more optimized code? >9. supports math coprocessors in line? >10. has special features? > I have no experience with the Absoft product. I have extensive experience with Language Systems product. I am very pleased with the latter; have no desire for the former. My response to each of your 10 questions is favorable for the Language Systems product. -- David Doherty --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From OLIVER@psipsy.uct.ac.za Tue Feb 16 19:26:35 1993 Message-Id: To: chemistry@ccl.net From: "Oliver Hill" Date: 17 Feb 93 01:23:03 SAST-2 Subject: Mass Spec programs Dear All A collegue of mine is working on Organometallic complexes and polymers and needs a program to help him interpret his mass spec. Does anyone know of any programs for this sort of thing? Ideally the software should be academic, run on a PC and be available by anonymous FTP, although he'd be interested in everything available. We do have ChemWindow which comes with a molecular mass calculater but he would like something a bit mor advanced and specifically for mass. spec. Please E-Mail responses and if there are enough I'll summerize to the list. Thanks in advance Oliver ______________________________________________________________________ Oliver Hill Department of Chemistry University of Cape Town Rondebosch, 7700 SOUTH AFRICA OLIVER@PSIPSY.UCT.AC.ZA (internet) Tel. +27-21-650-2527 Fax. +27-21-650-3788 ______________________________________________________________________