From owner-hyperchem@hyper.com Mon Apr 1 15:27:20 1996 Date: Mon, 01 Apr 1996 18:49:29 +0100 From: Frank Hoffmann Organization: Universitdt Hamburg To: hyperchem@hyper.com Subject: script command query-value Dear Hyperchemists, Does anyone know how I have to handle the script-command query-value oordinates, so that it works correct? If I run a scipt, in which this command is included, a window appears that always shows only the first twenty coordinates of the current molecule. Thanks a lot, Frank _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 1 18:03:34 1996 Date: Mon, 1 Apr 96 14:52:44 -0500 From: polowin (Joel Polowin) To: Massimo Trotta Subject: Re: PM3 parameters for sodium Cc: hyperchem@hyper.com > Date: Thu, 28 Mar 1996 16:02:55 +0100 (MET) > From: Massimo Trotta > > I am trying to use PM3 semiempirical method for calculation of system > containing Sodium+, but Hyperchem does not have parameters for that element > in that method. > Can anybody help me out with those number or should I change method? We do not have any PM3 parameters for Na; if any have been published, we would like to hear about them. Depending on what other atoms are in your system, you may need to use a different method. Our parameter sets include Na for CNDO, INDO, and ZINDO/1 (and Extended Huckel). Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 1 18:48:08 1996 Date: Mon, 1 Apr 96 16:14:02 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com, chemistry@osc.edu Subject: Info request: HyperChem add-ons Cc: scivision@delphi.com, schmitz@docadchem.com We are trying to put together information about software modules which other people have written for use with HyperChem -- DDE-linked applications, Visual Basic utilities, etc. We would like to make this sort of information readily available for distribution to anyone who asks. We would appreciate any information, hints or leads that could be sent to us at 'info@hyper.com'. Thanks very much! 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/ _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 1 21:01:33 1996 Date: Mon, 1 Apr 96 15:49:32 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: Re: script command query-value > Date: Mon, 01 Apr 1996 18:49:29 +0100 > From: Frank Hoffmann > > Does anyone know how I have to handle the script-command query-value > oordinates, so that it works correct? If I run a scipt, in which this > command is included, a window appears that always shows only the first > twenty coordinates of the current molecule. Sometimes I think that people do not believe me when I say that sometimes a simple bug will remain hidden for a *very* long time. This is one of those bugs -- it seems to have been with us for a long time, but never noticed until now. As far as I can see from my testing, only the first 512 characters of data are sent to a screen message box, in response to a 'query-value' command. This happens for every version of HyperChem from release 3 onwards, both Windows and SGI; I do not have a copy of release 2 readily accessible to check. There is no problem in using the 'omsgs-to-file' command to send the complete data set to a file; the problem appears to involve a buffer of fixed size used to display data to the screen. If you know how much data you should expect, you could display it to the screen a piece at a time with a script command. If you are running HyperChem by external software rather than from a script, you can probably set it up to display the data in pieces -- and there should be no trouble in getting the complete data set transferred through the DDE at once if you wish. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 1 21:45:35 1996 Date: Mon, 1 Apr 96 13:31 +0200 From: To: amber@cgl.ucsf.edu, anneal@chaco.com, c2-l@msi.com, CAChe@pacificu.edu, charmm-bbs@emperor.harvard.edu, chem-comp@mailbase.ac.uk, watoc@ic.ac.uk, chemistry@infomeister.osc.edu, chem-mod@mailbase.ac.uk, dibug@comp.bioz.unibas.ch, hyperchem@hyper.com, isisforum-l@mdli.com, pmd@cumbnd.bioc.columbia.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, anchodd@cc.utas.edu.au, mmodlist@chem.iupui.edu Subject: WATOC96 IMPORTANT: EXTENSION OF DEAD LINE FOR WATOC '96 ! The following is a short version of the "call for papers" brochure for WATOC '96. Those who wish to receive the brochure should write to watoc96@vms.huji.ac.il ASAP. However, the time is quite short and we suggest that you employ the home-page for the congress, as detailed below. The registration forms may be filled on the WATOC server- URL is - http:/www.ch.ic.ac.uk/watoc/watoc_israel.html You may also print the appropriate forms from this text, fill them and mail to the Secretariat. FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 JERUSALEM, ISRAEL, JULY 7 - 12, 1996 DEADLINE FOR THE SUBMISSION OF ABSTRACTS: MAY 15, 1996 ------------------------------------------------- PRELIMINARY TIMETABLE SUNDAY, JULY 7, 1996 Afternoon: Registration and distribution of Congress material General WATOC Meeting Evening: Informal Welcome Reception MONDAY, JULY 8, 1996 Morning: Opening Ceremony and Award of WATOC Prizes All day: Congress Sessions Evening: Poster Session TUESDAY, JULY 9, 1996 Morning and afternoon: Congress Sessions Late Afternoon and Evening: Tour of Jerusalem and Visit to the Israel Museum WEDNESDAY, JULY 10, 1996 Morning: Congress Sessions Afternoon: Tour of Jerusalem Evening: Poster Session THURSDAY, JULY 11, 1996 All day: Congress Sessions Evening: Banquet (optional) FRIDAY, JULY 12, 1995 Morning: Congress Sessions and Closing Ceremony Afternoon: Optional Post-Congress Tours ------------------------------------------------------------------------ CONGRESS TOPICS Research on all aspects of computational chemistry is appropriate for presentation at the Congress. The Program will consist of Plenary Lectures, Invited Talks, Oral Presentations and Poster Sessions (including an electronic Poster Session). Congress Sessions will be roughly divided according to the three main topics below: * DEVELOPMENT OF THEORETICAL METHODS: AB INITIO, SEMIEMPIRICAL, FORCE FIELDS, DENSITY FUNCTIONAL, PSEUDOPOTENTIALS, VALENCE-BOND, ELECTRON CORRELATION, PERTURBATION THEORY, ETC. * APPLICATIONS IN ORGANIC, INORGANIC, AND ORGANOMETALLIC CHEMISTRY: ELECTRONIC STRUCTURE, REACTION MECHANISMS, CATALYSIS, SOLVENT EFFECTS, PHYSICO-CHEMICAL MEASUREMENTS (NMR, IR, UV, ETC.), MOLECULAR PROPERTIES, FRONTIER ORBITALS, CONFORMATIONAL ANALYSIS, THERMODYNAMICS AND KINETICS, ETC. * BIOCHEMICAL/BIOMEDICINAL THEORY AND APPLICATIONS: PROTEIN STRUCTURE/FUNCTION, ENZYME ACTIVITY AND MECHANISMS, NUCLEIC ACIDS, MEMBRANES, RECEPTOR STRUCTURE/FUNCTION, PROTEIN- DNA INTERACTIONS, CARBOHYDRATES, MOLECULAR DYNAMICS, MONTE- CARLO, QUANTUM MECHANICAL/MOLECULAR MECHANICS CALCULATIONS, SOLVATION, DRUG DESIGN, ETC. PLENARY LECTURERS T. Blundell D. Cremer W. F. van Gunsteren K.N. Houk P. Kollman W. Kutzelnigg K. Morokuma J.A. Pople H. Schwarz S. Shaik W. Thiel F. Weinhold H. Weinstein INVITED SPEAKERS D. Avnir T. Bally M.V. Basilevsky M. Berman F. Bernardi J. Bertran J. Brickmann W.T. Borden C. Cohen T. Clark D.S. Dudis R. Elber G. Frenking J. Gauss J. Gerrat P.M.W. Gill R. Grev W.J. Hehre P.C. Hiberty S. Hoz A. Itai U. Kaldor M. Karni W. Koch D. Kost P. Lam R. Lavery G.H. Loew J.P. Malrieu K. Merz V. Minkin K. Muller S. Nagase E. Osawa A. Perczel A. Pross P. Pyykko L. Radom G. Richards H. Rzepa A. Sali J. Sauer H.F. Schaefer III H.B. Schlegel P.v.R. Schleyer B. Schoichet P. Schwerdtfeger G. Scuseria J. Skolnick R. Sustmann A. Warshel ------------------------------------------------------------- GENERAL INFORMATION An internet site for the Congress is at URL: http://www.ch.ic.ac.uk/watoc/watoc_israel.html. Please examine it regularly for updates. VENUE The Holiday Inn Crowne Plaza, Jerusalem 91130, Israel Tel: 972 2 6588888; Fax: 972 2 6514555. DATES Sunday, July 7 - Friday, July 12, 1996. LANGUAGE The official language of the Congress is English. REGISTRATION FEES until May 15, 1996 after May 16, 1996 Participant US$400 US$450 WATOC Member US$370 US$420 Student US$100 US$120 Accompanying Person US$150 US$150 Fees for PARTICIPANTS and STUDENTS include: participation in scientific sessions, Congress program and book of abstracts, invitations to the Congress tours and social events (excluding the Banquet on Thursday, July 11). Fees for ACCOMPANYING PERSONS include: two half-day tours and invitations to the Congress tours (two afternoons) and social events (excluding the Banquet on Thursday, July 11). You may register for the Congress using the enclosed form, or with the appropriate form on the WATOC Internet server. CANCELLATION POLICY Refund of registration fees will be made as follows: Airmail post-marked* before May 15, 1996 - full refund less US$40 (for handling expenses). Airmail post-marked* after May 15 until June 7 - 75% refund. Airmail post-marked* after June 8 - 50% refund. * or faxed, or electronically mailed VISAS Visas are guaranteed to all bona fide scientists. A visa to Israel is not necessary for participants from most countries (e.g., USA, Western Europe), but we suggest that you consult your travel agent. For participants from countries without diplomatic relations with Israel, please write directly to the Secretariat no later than TWO MONTHS prior to the Congress giving the following details: full name, date and place of birth, passport number and date and place of issue and expiry date, flight details (arrival date and flight number). The Secretariat will arrange for a visa to await you at Ben-Gurion Internatioanl Airport. LETTER OF INVITATION On request the Secretariat of the Congress will be happy to send a personal invitation to participate. It should be understood that such an invitation is only meant to help participants to raise travel funds or obtain a visa. It is not a commitment on the part of the organizers to provide any financial support. CALL FOR PAPERS The Scientific Committee welcomes scientific contributions dealing with any of the Congress main or related topics. Participants who wish to present papers are requested to submit an abstract to the Secretariat no later than May 15, 1996. Submittal of more than one abstract is wellcome. Abstracts submitted after this date may be scheduled for poster presentation, but their inclusion in the Abstract Book cannot be guaranteed. Scheduling and publication in the Congress publications is dependent on the payment of Registration Fees. For guidelines regarding the preparation of Abstracts please see the appropriate page. WATOC ELECTRONIC POSTERS An electronic poster session will be part of WATOC '96 and will begin one month before the Congress. The Chairman of the poster session is Professor Henry Rzepa of Imperial College, London. Professor Rzepa maintains and updates the WATOC server, and all abstracts for the electronic posters should be submitted through the appropriate form on that server. The URL of the server is http://www.ch.ic.ac.uk/watoc For abstracts submission, the URL is http://www.ch.ic.ac.uk/watoc/abstracts/abstract-form.html Help for submitting an electronic poster may be found under http://www.ch.ic.ac.uk/watoc/posters.html All abstracts for the electronic poster session should be submitted not later than May 15, 1996. They will undergo regular refereeing before being mounted for the electronic Conference. Abstracts to the electronic conference that are submitted by non-registered participants will not appear in full form in the book of abstracts of WATOC '96. However, abstract titles, authors and URL addresses of the electronic posters will be included in the Congress Book of Abstracts. PROCEEDINGS All oral presentations will be published, following regular journal refereeing, in a special issue of the Journal of Molecular Structure (Theochem) which publishes regularly all the plenary and invited lectures of WATOC conferences. Please indicate on the registration form if you are interested in purchasing the Proceedings. The proposed price for participants is DFl. 175,- (approx. US$120). SCHOLARSHIPS A limited amount of funding may be available for young scientists. Applications should be made directly to the Chairman. They should include a CV and, preferably, letters of recommendation from scientists in the field. The support for young students will not include travel expenses. CLIMATE The weather in Jerusalem in July is warm and dry during the day, and cooler at night. Rain in July is a miracle! Temperatures range between 27 C (81 F) during the day and 17 C (63 F) at night. CLOTHING Informal for all occasions. We suggest that you bring sunglasses, a hat, comfortable walking shoes and a swimsuit. A light jacket may be useful for the evening. OFFICIAL CARRIER El Al Israel Airlines is the official carrier for the Congress. ------------------------------------------------------------------------------ TRAVEL AND ACCOMMODATION KENES TOURS P.O. Box 50006, Tel Aviv 61500, Israel Tel : 972 3 5140014 Fax : 972 3 5140044 / 5175674 Kenes Tours is the official travel agent for the Fourth World Congress of Theoretically Oriented Chemists and will be offering specially reduced rates for accommodation and Congress Tours. Hotel space has been reserved by Kenes Tours at the following hotels: Per person in a Single Room double room one person DELUXE CLASS Holiday Inn Crowne Plaza* Regular Room US$ 91 US$166 Crowne Club Room** US$117 US$216 SUPERIOR CLASS Park Plaza Hotel US$ 46 US$ 86 TOURIST CLASS Jerusalem Gate US$ 45 US$ 84 Tirat Bat-Sheva US$ 41 US$ 76 * Congress venue ** Crowne Plaza Club rooms include access to the Executive Floor Lounge. All above hotels are located within walking distance of the Congress venue except the Tirat Bat-Sheva hotel which is located in the city center with a regular bus service to the Congress venue. Rates are per night, per person including a large Israeli buffet style breakfast and service charge. STUDENT DORMITORIES A limited number of rooms has been reserved at the Hebrew University student dormitories, approximately 4 km from the Congress venue. Regular bus service to the Congress venue is available. Prices are US$20 per person in a double room, US$25 per person in a single room. Prices do not include breakfast. Applications should be made to the Secretariat. YOUTH HOSTELS Prices are between US$18-US$28.00 per person, per night, including breakfast. For reservations, please write directly to: 1. Israel Youth Hostels Association Convention Center, 1 Shazar St., Jerusalem 91060, Israel. Tel: 972 2 6558400; Fax: 972 2 6558432 2. Beth Shemuel Hostel. 6 Shamah St., Beth Shemuel, Jerusalem 94101, Israel Tel: 972 2 203456; Fax: 972 2 203467 Regular bus service to the Congress venue is available. HOW TO BOOK In order to benefit from the special congress rates, kindly send the enclosed Accommodation Form with the required deposit (see below) by AIRMAIL at your earliest convenience. You may also reserve accommodation for the Congress using the appropriate form on the WATOC Internet server. Reservations will be confirmed on a 'first come first served' basis. PAYMENT Payment of services (less deposit) should be made at the Kenes Tours Hospitality Desk upon registration. Kenes Tours accepts Travelers' cheques and Eurocheques (in the currency of the issuing country), Visa, MasterCard, American Express and Diners Club credit cards. Payment in Israeli currency is subject to Value-Added Tax which is currently 17%. IMPORTANT NOTES * Participants requiring single rooms will be accommodated in double rooms for single occupancy, without additional charge. * Kenes Tours reserves the right to change the requested hotels to those of a similar grade or better. * Kenes Tours and their agents shall not be responsible for, and shall be exempt from, all liability in respect of any loss, damage, injury, accident, delay or inconvenience to any person, or his/her luggage or any other property, for any reason whatsoever, for any tourist services provided. * Personal travel and health insurance is highly recommended. * Official check-in time for hotels is 14:00 and check-out time is noon. CANCELLATION POLICY Up to May 15, 1996 - full refund less bank charges Up to July 1, 1996 - cancellation charge of $ 50.00 per room After July 1 - cancellation charge of one night accommodation at your selected hotel. AIRPORT ASSISTANCE All participants advising Kenes Tours of their flight details will be met by a Kenes representative and assisted inside the arrival hall at the Ben-Gurion terminal, upon arrival on Sunday, July 7, 1996. Transfers from the Airport to the Congress hotels can be arrranged on Sunday, July 7, 1996 or any other day at an additional cost of US$30.00 per person, on a car sharing basis. Please forward exact flight information at least three weeks prior to arrival if transfer is required. TRANSPORTATION TO JERUSALEM FROM BEN-GURION INTERNATIONAL AIRPORT For participants arriving at Ben-Gurion International Airport who have not booked their transfer in advance, the following transportation alternatives to Jerusalem are available: "Egged" buses leave the airport regularly for Jerusalem Central Bus Station, from 07.00 to 21.30. Buses run until 15.30 on Friday and service resumes at 18.15 on Saturday (payment in local currency, approximately US$5). "Nesher"(sherut) taxis leave the airport for Jerusalem hotels, 24 hours a day. Taxis are shared with other passengers and they leave only when all places are taken, and cost approximately US$15 per person (payment in local currency). Private taxis (24 hours a day). The fare is fixed and the price list is posted at the taxi station in the airport as well as with the drivers. The price is approximately US$50 per taxi (payment in foreign or local currency). ------------------------------------------------------------------------------ FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 JERUSALEM, ISRAEL, JULY 7-12, 1996 REGISTRATION FORM Please complete and return this form, together with your payment, to: Secretariat WATOC '96 P.O.Box 50006, Tel-Aviv 61500 Israel Tel: 972-3-5140000 or 972-3-5140014 Fax: 972-3-5175674 or 972-3-5140077 Identification -------------- -------------- Please complete this section accurately; the information you provide will allow us to correspond with you efficiently, and it will also be used for your delegate badge at the Congress. Participant (Please TYPE or PRINT IN BLOCK LETTERS) Surname______________________________________________________________________ Initials_____________________ First name __________________________________________________________________ Title [ ] Prof. [ ] Dr. [ ] Mr. [ ] Mrs. [ ] Ms. Department___________________________________________________________________ Institution _________________________________________________________________ Mailing Address [ ] Office [ ] Residence ------------------------------------------------- ------------------------------------------------- No.___________Street___________________________________Suite/Apt.____________ City____________________________State/Province_______________________________ Country_________________________Postal Code__________________________________ Telephone (office hours) Country/city/number_________________________________ Fax Country/city/number_________________________________ E-Mail Address_______________________________________________________________ Accompanying persons -------------------- -------------------- List only those individuals registering for the Accompanying Persons' Program: Surname______________________________First name_________________Title_________ Surname______________________________First name_________________Title_________ Surname______________________________First name_________________Title_________ Surname______________________________First name_________________Title_________ Registration Fees ----------------- ----------------- Please check the appropriate box/s Until May 15, 1996 After May 16, 1996 Participant [ ] US $400 [ ] US $ 450 WATOC Member [ ] US $370 [ ] US $ 420 Student [ ] US $100 [ ] US $ 120 Accompaning Person/s x____ [ ] US $150 [ ] US $ 150 Banquet [ ] US $ 50 [ ] US $ 50 Payment ------- ------- Please indicate amount enclosed and ensure that you send your fully completed registration form together with your payment: Total Fees: $_______________US Method of Payment ----------------- ----------------- Option 1: Credit Card - Payments will be charged in US $ [ ] Visa [ ] MasterCard [ ] Diners [ ] American Express Number_____________________________Expiry Date (month/year)___________________ Name as shown on card: Surname__________________________________First name___________________________ Signature________________________________Date (day/month/year)________________ For payment by Visa, please indicate home address if other than mailing No._____________Street_________________________________Suite/Apt._____________ City____________________________State/Province________________________________ Country_________________________Postal Code___________________________________ Option 2: Bank Transfer - with your name and address indicated on the reverse. If payment is made for more than one person or by a company - please make sure that all names are indicated and send fully completed regsitration forms together with a copy of the bank transfer. Please make drafts payable to: "WATOC '96" and send them to Bank Leumi Le'Israel, Gan Hair Branch, Tel Aviv, Israel, Account number 816-56027/73 Patam. Bank charges are the responsibility of the payee and should be paid in addition to the registration fees. Option 3: Cheque made payable to "WATOC '96" Enclosed cheque number__________________ Bank________________________________ _______________________________________________________________________________ Please include fully completed registration form Cancellation policy ------------------- ------------------- Refund of Registration fees will be made as follows: Post-marked* prior to May 15, 1996 - full refund less US$ 40 handling fee Post-marked from May 15 until June 7 - 75% refund Post-marked after June 8 - 50% refund * or faxed, or electronically mailed [ ] I am interested in ordering the Congress Proceedings (Dfl. 175 ~ US$ 120) DATE__________________ SIGNATURE________________________________________ ----------------------------------------------------------------------------- COMPLIMENTARY CONGRESS TOURS OF JERUSALEM All tour descriptions may be found on the WATOC server. All Congress participants and registered accompanying persons are invited to join the following half-day tours: TUESDAY, JULY 9, 1996 JERUSALEM LEGENDS BY NIGHT WEDNESDAY, JULY 10, 1996 JERUSALEM THROUGH THE AGES ACCOMPANYING PERSONS' TOURS Registered accompanying persons are invited to join the following two half-day tours: MONDAY, JULY 8, 1996 TEL MARESHA AND KIBBUTZ BET GUVRIN THURSDAY, JULY 9, 1996 IN THE FOOTSTEPS OF JESUS ---------------------------------------------------------------------------- PRE- AND POST-CONGRESS TOURS The following tours are being offered exclusively to Congress participants PRE-CONGRESS DAY TOURS A. SATURDAY, JULY 6, 1996 BETH SHEAN, NAZARETH, TIBERIAS including the Church of the Anunciation and Sea of Galilee Price per person: US$60.00 Includes entrance fees. B. SUNDAY, JULY 7, 1996 DEAD SEA AND MASADA Price per person: US$65.00 Includes entrance fees and visit to Ein Gedi Spa Pick-up and drop off for day tours will be from Congress Hotels C. WEDNESDAY, JULY 3 - SUNDAY, JULY 7, 1996 EGYPT TOUR - 4 NIGHTS/3 DAYS POST-CONGRESS TOURS (TOURS D AND E CAN BE COMBINED) D. FRIDAY, JULY 12 - SUNDAY JULY 14, 1996 GALILEE TOUR - 2 NIGHTS E. SUNDAY, JULY 14 - TUESDAY, JULY 16, 1996 JORDAN TOUR - 3 days/2 nights IMPORTANT NOTE: A valid entry visa to Jordan should be obtained at the Jordanian embassy/consulate in your home country prior to your arrival to Israel. It is your responsibility to obtain this Jordanian visa, and a re-entry visa (if applicable) to Israel. TOUR RATES ARE BASED ON A MINIMUM OF 15 PARTICIPANTS PER TOUR ----------------------------------------------------------------------------- FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 Jerusalem, Israel, July 7 - 12, 1996 ACCOMMODATION, TOURS AND ARRIVAL TRANSFER FORM Please TYPE or PRINT in BLOCK LETTERS and AIRMAIL to: KENES TOURS P.O.Box 50006, Tel Aviv 61500, Israel Tel : 972 3 5140004, Fax: 972 3 5140044/5175674 SURNAME __________________ FIRST NAME __________________________ ADDRESS _________________________________________________________ _________________________________________________________________ _________________________________________________________________ COUNTRY __________________ TEL NO. ____________________ FAX NO. ____________________________ E-MAIL ADDRESS_________________________________________________ TYPE OF ROOM REQUIRED: [ ] double [ ] single [ ] other __________________ * I will share my accommodation with __________________________________ I/We require hotel accommodation as follows: First choice: -------------------------------------- Second choice: ------------------------------------ Check-in date:__________Check-out date:_________ No. of Nights__________ TOURS : NO. OF SEATS [ ] A. Beth Shean, Nazareth, Tiberias, Saturday, July 6, 1996 ____________ [ ] B. Dead Sea and Masada, Sunday, July 7, 1996 ____________ [ ] C. Egypt Tour, July 3-7,1996 oSingle oDouble*____________ [ ] D. Galilee Tour,Fri-Sun, July 12-14, 1996 oSingle oDouble*____________ [ ] E. Jordan Tour,Sun-Tues, July 14-16, 1996 oSingle oDouble*____________ * I will share my accommodation with _______________________________ ARRIVAL TRANSFER : Arrival on _______________________ Airline/Flight _________________ at ____________ hours. [ ] Please arrange arrival transfer to Jerusalem Congress hotels at an additional cost of US$30.00 per person on a car sharing basis. HOTEL DEPOSIT : All requests for accommodation must be accompanied by a deposit of one night accommodation of your selected hotel per room. Please make cheque payable to Kenes Tours or charge deposit to credit card, as per below: [ ] Cheque enclosed [ ] Credit card __________________________________ Number _____________________________ Expiration Date________________ SIGNATURE __________________________ DATE ____________________ --------------------------------------------------------------------- ABSTRACTS INFORMATION FORM DEADLINE FOR THE RECEIPT OF ABSTRACTS: MAY 15, 1996 Please state below the name, address and title of presenting author: FAMILY NAME___________________________________________________ FIRST NAME______________________________________________________ TITLE____________________________________________________________ ADDRESS_________________________________________________________ _________________________________________________________________ ________________________________________________________________ COUNTRY________________________ FAX____________________________ TELEPHONE NUMBER_______________________________________________ E-MAIL ADDRESS__________________________________________________ I wish to submit the enclosed abstract for [ ] oral [ ] oral and video [ ] poster presentation 1. Abstracts should be typed on plain white paper in a rectangle 17cm x 23cm. The entire abstract, including title, author(s), institution(s), country and acknowledgments must fit within the rectangle. 2. Abstracts will be printed exactly as submitted. Font size should be equal or larger than 10 pts. Abstracts should be typed on an electric typewriter or be of print quality out-put. A dot-matrix printout is not acceptable. 3. Capitalize and do NOT indent title. Title should be followed by author(s)' name(s) on a separate line and, on the following line - institution, city and country. First names or initials must precede last name. Leave one line between the title and the author's names. Underline the name of the presenting author. Begin body of the abstract on a new line and indent five spaces. 4. PLEASE DO NOT FOLD OR FAX YOUR ABSTRACTS 5. Abstracts should be sent with five (original and four copies) copies to: Secretariat WATOC '96, P.O. Box 50006, Tel Aviv 61500, Israel _______________________________________________________________ Prof. Amiram Goldblum Chairman of WATOC '96 Phone 972-2-758701 Hebrew University of Jerusalem FAX 972-2-410740 School of Pharmacy email watoc96@vms.huji.ac.il Jerusalem 91120 ISRAEL ________________________________________________________________ _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 2 16:33:46 1996 Sender: From: "tamasgunda@tigris.klte.hu" To: chemistry@infomeister.osc.edu Date: Tue, 2 Apr 1996 08:37:30 +1 Subject: 5th ICSA - conference Cc: amber@cgl.ucsf.edu, anneal@chaco.com, c2-l@msi.com, CAChe@pacificu.edu, charmm-bbs@emperor.harvard.edu, chem-comp@mailbase.ac.uk, watoc@ic.ac.uk, chem-mod@mailbase.ac.uk, dibug@comp.bioz.unibas.ch, hyperchem@hyper.com, isisforum-l@mdli.com, pmd@cumbnd.bioc.columbia.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, anchodd@cc.utas.edu.au, mmodlist@chem.iupui.edu Priority: normal * * * Second Announcement * * * 5th International Conference on Chemical Synthesis of Antibiotics and Related Microbial Products Debrecen (Hungary) September 1-6, 1996 The Organizing Committee has the pleasure to announce the "5th International Conference on Chemical Synthesis of Antibiotics and Related Microbial Products" which, following previous meeting in Aussois (France), Oiso (Japan), Banz (Germany) and Nashville (USA) will be held in Debrecen (Hungary) at the Lajos Kossuth University, from September 1 (Sunday) to September 6 (Friday), 1996. The conference will feature plenary lectures, invited lectures and a poster session. The purpose of the program is to bring experts together and up to date on the developments of topics including isolation, structural elucidation, total synthesis, chemical or biochemical modification and SAR of antibiotics and related natural products of bilogical importance. In order to provide you with a meaningful personal scientific atmosphere, attendance of the Symposium is limited to approximately 300 conferees. Already accepted invitation for a lecture: J.E. Baldwin (Oxford), R. Beugelmans (Gif-sur-Yvette), M. Chmielewski (Warsaw), B. Fraser-Reid (Durham), S. Hanessian (Montreal), F.W. Lichtenthaler (Darmstadt), M.J. Miller (Notre Dome) C. Monneret (Paris), W. Priebe (Houston), H. Redlich (Munster), K. Shiomi (Tokyo), K.Tatsuta (Tokyo), J. Thiem (Hamburg), A. Vasella (Zurich), J. Vilarrasa (Barcelona), A. Weis (San Antinio), D.H. Williams (Cambridge) The conference site, Lajos Kossuth University, is situated in the green belt forest area of Debrecen, the second biggest city of the country, the economic, intellectual and artistic center of Eastern Hungary. With its historical, cultural and religious relics the 631-year old Calvinist town offers plenty of sights to the visitor. Thirty kilometers away from the city the Hortobagy National Park attracts people with the ancient flora and fauna of the Great Hungarian Plain and the "puszta". The guests are also invited to the cellars of Tokaj, to taste the famous Hungarian wines. In the university campus a quiet environment is provided to the conferees for scientific discussions, and there are many opportunities for recreation on the sport grouds and in the world famous medicinal spa of the "Big Forest". Located 230 km east from Budapest, the capital of Hungary, Debrecen is easily accessible from the Budapest International Airport by train, car or in chartered buses. For more information please, write to: Prof. Ferenc Sztaricskai President of 5th ICSA Research Group of Antibiotics of the Hungarian Academy of Sciences, P.O.Box 70, H-4010 Debrecen, Hungary Telefax: (+36-52) 310 936 E-mail: antibiotics@tigris.klte.hu Second Circular is available on request. To receive further infomation and the Second Circular on the 5th International Conference on Chemical Synthesis of Antibiotics and Related Microbial Products Please, return a card to the address above with the following data: NAME:__________________________________________________ ADDRESS:_____________ FAX:___________________________________________________ I am interested in atten- I intend to I plan to bring ding the conference___ present a poster__ ___guest(s). ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 4 20:51:48 1996 From: mgmsorg@bellatrix.pcl.ox.ac.uk (mgmsorg) Subject: First Electronic Molecular Modelling & Graphics Society Conference To: hyperchem@hyper.com Date: Thu, 4 Apr 1996 23:34:30 +0000 (GMT) FIRST ELECTRONIC MOLECULAR GRAPHICS AND MODELLING SOCIETY CONFERENCE ******************************************************************** The First Electronic Molecular Graphics and Modelling Society Conference (MGMS EC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Oct 7-18, 1996. The conference is sponsored by Elsevier and the Molecular Graphics and Modelling Society and will be co-organized by Graham Richards, Art Olson, Rod Hubbard and Barry Hardy. MGMS EC-1 will be a fully international event open to all members of the scientific community and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure; Membranes and Membrane Proteins; Bioinformatics; Computational Nanotechnology; Protein Folding; Modelling of In Vivo Activity; Knowledge-based Library Design; Surface Science; Host-guest interactions; Carbohydrates; Enzyme Mechanisms; Conformational Analysis; Nucleic Acids; Quantum Chemistry; Car-Parrinello Methods and Applications; Structure-based Design; Visualization; and Perspectives. Each subject area has a section convener who will screen abstracts sent by authors for suitability. Authors can opt to submit a non-permanent presentation like a normal conference poster or a presentation which will be refereed and considered for publication in the Journal of Molecular Graphics. Referees will be appointed by the section conveners. Presentations must be prepared in Hypertext Markup Language (HTML), graphics (GIF,JPEG) and other Web-compatible formats (VRML,Java,PDF) so that participants can view the papers via the World Wide Web. Aid and consultation will be provided to participants in the months prior to the event to help them with their presentation (Email:mgmsorg@bellatrix.pcl.ox.ac.uk). Further details will be given in the authors' guide accessible via the URL: http://bellatrix.pcl.ox.ac.uk/mgms/ During the conference discussions will take place via the Internet in real-time using a virtual conference centre based on a MOO (multiple-user domain, object oriented) and via Internet-accessible electronic mailing lists. Trial sessions for those not familiar with MOOs will be held before the conference. During the conference, a timetable for MOO discussion sessions of each section will be posted. Since these realtime discussions are an integral part of the conference, authors will be expected to attend one for their subject; the right is reserved not to referee submissions by authors who do not attend one of these sessions. The Conference will feature a Virtual Trade Center where commercial vendors, software and hardware developers, consultants, and contractors will be able to display their goods and services and provide software demonstrations in return for exhibition fees to support conference activities. Any potential exhibitors should contact Barry Hardy at barry@bellatrix.pcl.ox.ac.uk ******************* DEADLINES AND DATES 1) DO NOW - The MGMS mailing list Conference-related news and announcements will be posted regularly to the MGMS mailing list (http://bellatrix.pcl.ox.ac.uk/hypermail/mgms/). If you wish to subscribe to the MGMS list send the following one line message to majordomo@bellatrix.pcl.ox.ac.uk: subscribe mgms@bellatrix.pcl.ox.ac.uk your_email@address your_name 2) DO NOW - Registration The deadline for registration is Sept 15th 1996. Early registration is strongly encouraged to aid the efficient operation of the conference including the establishment of timely access to the conference. If you intend to participate in MGMS EC-1 please use the registration form accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ which will be available for electronic registration starting April 22. The electronic registration will be used to construct a registrant database for the conference which will generate the conference mailing list and handle assignment of userids and passwords. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 35 pounds sterling (50 US dollars) with a special rate for students of 20 pounds sterling (30 US dollars). A copy of a suitable student identification or a letter from the supervisor will be required to be charged at the lower rate. Cheques or bank orders (in pounds or dollars) should be made out to Greenlea Communications and mailed to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Please supply your complete name, address, fax and phone numbers, and email address in your correspondence. A conference userid and password will be forwarded to you. It is hoped to establish a credit card clearing service in May and information will be provided at the conference site in due course. Academic registrants from economically-disadvantaged countries can write to Barry Hardy requesting an exemption to the registration fee. Exemptions will be made on a discretionary basis taking into account the reasons given for the request and will be dependent on suitable funds being available. We will consider economically disadvantaged countries to include those of Eastern Europe, Africa, Central and South America, Indian sub-continent, etc. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is July 1. Email your abstract directly to the appropriate section convener listed below. Fuller details of the scope of each section will be given in the authors' guide accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ Your abstract should be no longer than 300 words. And remember to state which category of presentation (non-permanent poster or refereed paper) you wish. If you are unsure as to which section your abstract is suitable for, please email a possible section convener or Barry Hardy (barry@bellatrix.pcl.ox.ac.uk). Section conveners do have the discretion to reject abstracts, ask for revisions to an abstract or to send the abstract to the convener of a more suitable section. 4) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is Sept 15th. You must deposit your text and graphics files at the conference ftp site for presentation at the conference. Ftp instructions are provided at the conference site. Hard copies of final refereed papers following the format of the Journal of Molecular Graphics should be sent by Dec 1 to: Graham Richards, Journal of Molecular Graphics, Physical & Theoretical Chemistry Lab, Sth Parks Rd, University of Oxford, Oxford, OX1 3QZ, UK. Journal guidelines will be posted at http://bellatrix.pcl.ox.ac.uk/mgms/ Although there is no limit to the graphics authors choose to display in their conference presentation, the editor reserves the right to limit the number of free colour figures in each printed journal article. 5) Refereeing Period The refereeing period will commence upon completion of the conference. If you have a presentation at MGMS EC-1 you may be requested to contribute a refereeing evaluation on another conference presentation. Referee reports will be due November 15. ******************* SECTIONS AND SECTION CONVENERS (Please email section conveners with questions related to your particular section and presentation. Details on the sections are accessible via http://bellatrix.pcl.ox.ac.uk/mgms/) Any general emails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, MOO queries, etc.) should be sent to: mgmsorg@bellatrix.pcl.ox.ac.uk 1. Protein Structure Rod Hubbard University of York, UK Email:rod@yorvic.york.ac.uk 2. Nucleic Acids David Beveridge Wesleyan University, USA Email:bever@rose.chem.wesleyan.edu 3. Membranes and Membrane Proteins Alan Robinson University of Oxford, UK Email:alan@bellatrix.pcl.ox.ac.uk and Terry Stouch Bristol-Myers Squibb, USA Email:stouch@dino.bms.com 4. Bioinformatics Convener to be announced Email:mgmsorg@bellatrix.pcl.ox.ac.uk 5. Computational Nanotechnology Al Globus NASA-Ames, USA Email:globus@nas.nasa.gov 6. Protein Folding Jeffrey Skolnick Scripps Institute, USA Email:skolnick@scripps.edu 7. Modelling of In Vivo Activity Edward Hodgkin Wyeth-Ayerst Research, USA Email:hodgkie@war.wyeth.com 8. Knowledge-based Library Design Mike Hann GlaxoWellcome, UK Email:mmh1203@ggr.co.uk 9. Surface Science Donald Brenner North Carolina State, USA Email:dwb@ripley.mte.ncsu.edu 10. Host-Guest interactions Jon Essex Southampton University, UK Email:J.W.Essex@soton.ac.uk 11. Carbohydrates and Protein-Carbohydrate Interactions Anne Imberty CNRS, France Email:imberty@nantes.inra.fr 12. Enzyme Mechanisms Guy Grant University College Dublin, Ireland Email:ggrant@macollamh.ucd.ie 13. Stochastic Methods for Conformational Sampling Robert Topper The Cooper Union, USA Email:topper@cooper.edu 14. Quantum Chemistry Tim Clark University of Erlangen, Germany Email:clark@organik.uni-erlangen.de 15. Structure-based Design David Winkler CSIRO, Australia Email:D.Winkler@chem.csiro.au 16. Car-Parrinello Methods and Applications Michele Parrinello Max-Planck Institute, Germany Email:prr@prr.mpi-stuttgart.mpg.de 17. Visualization Art Olson Scripps Institute, USA Email:olson@scripps.edu 18. Perspectives in Molecular Modelling Graham Richards University of Oxford, UK Email:gr@vax.ox.ac.uk _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 8 17:02:46 1996 Date: Mon, 8 Apr 1996 13:37:00 -0400 (EDT) From: "Todd J. Raeker" To: hyperchem@hyper.com Subject: MD simulation problems Hello HyperChem users' I am a new user of HyperChem and have encountered a strange problem when doing constant Temperature MD simulations. Over time my molecule drifts off the screen window and I can never get it back since I don't know where it went. I can load it into Molecule Presentations and scale to fit causes it to be centered on the screen window. Saving to file after scaling does not nothing. The real problem is that these simulations break down after a while. I calculate averages of dihedral angles and after about 300 ps they become constant. I suspect whats happening is that the molecule has drifted so far from the origin that the coordinates get extermely large. Small increments (from time step integration) added to extremely large numbers get lost in round off. Is there a way to stop the molecule from drifting? This is significant programming error in my opinion. Regards Todd Dr. Todd J. Raeker | Department of Chemistry Theoretical Chemistry Group | Kent State University raeker@saturn.kent.edu | Kent, OH 44242-0001 Phone (216)-672-2986 | _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 8 22:10:55 1996 Date: Mon, 8 Apr 1996 18:08:20 -0500 (CDT) From: Vladimir Basiuk To: hyperchem@hyper.com Subject: refs Dear HyperChemers: Could anybody point me to any articles describing the comparison of experimental IR spectra with those calculated using HyperChem semiempirical methods (PM3, AM1, etc.)? Thank you. Sincerely, Vladimir Basiuk _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 9 13:15:26 1996 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: hyperchem@hyper.com Date: Tue, 9 Apr 1996 09:39:12 +0100 Subject: Evaluation of Vibrational Force Fields Cc: Vladimir Basiuk > Date: Mon, 8 Apr 1996 18:08:20 -0500 (CDT) > From: Vladimir Basiuk > To: hyperchem@hyper.com > Subject: refs > Dear HyperChemers: > Could anybody point me to any articles describing the comparison of > experimental IR spectra with those calculated using HyperChem > semiempirical methods (PM3, AM1, etc.)? > Thank you. > Sincerely, > Vladimir Basiuk > > Dear Vladimir Basiuk! Try the following paper: D. M. Seeger, C. Korzeniewski, W. Kowalchyk: "Evaluation of Vibrational Force Fields Derived by Using Semiempirical and ab initio Methods" J. Phys. Chem. *95*, 6871-6879 (1991). Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark E-Mail: JSL@virgil.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 9 20:46:20 1996 Date: Tue, 9 Apr 96 12:16:19 -0400 From: polowin (Joel Polowin) To: "Todd J. Raeker" , hyperchem@hyper.com Subject: Re: MD simulation problems > Date: Mon, 8 Apr 1996 13:37:00 -0400 (EDT) > From: "Todd J. Raeker" > > I am a new user of HyperChem and have encountered a strange problem when > doing constant Temperature MD simulations. Over time my molecule drifts > off the screen window and I can never get it back since I don't know > where it went. I can load it into Molecule Presentations and scale to > fit causes it to be centered on the screen window. Saving to file > after scaling does not nothing. I think that I don't understand your question. The molecules in an MD simulation move; the point of view is fixed unless you deliberately move it; therefore the molecules can drift off-screen. You can use the translation and rotation tools to change the viewpoint; you can use the space bar to rescale the picture so that everything is in view. > The real problem is that these simulations break down after a while. I > calculate averages of dihedral angles and after about 300 ps they become > constant. I suspect whats happening is that the molecule has drifted so > far from the origin that the coordinates get extermely large. Small > increments (from time step integration) added to extremely large numbers > get lost in round off. Is there a way to stop the molecule from > drifting? This is significant programming error in my opinion. I would have to see one of these files (as a .HIN and .SNP) to check this, but it sounds unlikely. The calculations are 32-bit and the coordinates of atoms are stored internally with 15 or 16 significant figures. Even if your molecule was moving at 100 A/ps -- which is pretty fast -- in 300 ps it would travel only 30,000 A, which still leaves many significant figures of precision. On the other hand, on that time scale with molecules far apart, the atomic motions probably *would* become extremely regular. If you can send me an example (by E-mail, or uploaded to the /incoming directory of ftp.hyper.com), I can take a look at it. I do not understand what you mean by "stop the molecule from drifting". Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 11 00:43:23 1996 Date: Wed, 10 Apr 1996 17:02:57 -0500 (GMT-0500) From: Eduardo Enrique Chamorro To: hyperchem@hyper.com Dear Hyperchemist Could anybody point me to any articles describing about the calculation of electrostatic potential. HyperChem calculates and plots the electrostatic potential from the results of single point, but not show in log file numerical values. The On-line Help (and manuals...) are very short! Thanks. Eduardo E. Chamorro _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 11 09:09:58 1996 Subject: Inorganic clusters To: hyperchem@hyper.com Date: Thu, 11 Apr 1996 10:22:11 +0100 (BST) From: "I.Theaker" Sender: I.Theaker@chem.hull.ac.uk Help ! I am fairly new to HyperChem but rapidly growing more confident in its use. I need to model structures such as Os3(CO)12 and have actually started with Ru3(CO)12 since the manual suggests that HyperChem works better for the 2nd row Transition Metals (and indeed doesn't provide parameters for Os). As an exercise to investigate the relationship between method chosen and computational speed I tried a geometry optimisation on the above structure with the MM+ force field, a ZINDO/1 quantum mechanical procedure and via AB INITIO methods. The first method gave semi-realistic (?) results in a small time, the second method took ages and then had to be stopped prematurely since the Ru-C=O bonds started to develop non-linear conformations and the final method crashed whilst trying to write to a log file. Any comments would be gratefully accepted regards Ian Theaker [I.Theaker@chem.hull.ac.uk] _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 11 10:48:21 1996 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "I.Theaker" , hyperchem@hyper.com Date: Thu, 11 Apr 1996 12:15:52 +0100 Subject: Re: Inorganic clusters > Subject: Inorganic clusters > To: hyperchem@hyper.com > Date: Thu, 11 Apr 1996 10:22:11 +0100 (BST) > From: "I.Theaker" > Help ! > > I am fairly new to HyperChem but rapidly growing more confident in its > use. I need to model structures such as Os3(CO)12 and have actually > started with Ru3(CO)12 since the manual suggests that HyperChem works > better for the 2nd row Transition Metals (and indeed doesn't provide > parameters for Os). > > As an exercise to investigate the relationship between method chosen and > computational speed I tried a geometry optimisation on the above structure > with the MM+ force field, a ZINDO/1 quantum mechanical procedure and via > AB INITIO methods. > > The first method gave semi-realistic (?) results in a small time, the > second method took ages and then had to be stopped prematurely since the > Ru-C=O bonds started to develop non-linear conformations and the final > method crashed whilst trying to write to a log file. > > Any comments would be gratefully accepted > > regards > > Ian Theaker > > [I.Theaker@chem.hull.ac.uk] > Dear Ian Theaker, just two remarks: 1) Remember to select the UHF option in the "Semi-empirical Options" dialog box when working with ZINDO/1, particularly when dealing with transition metal complexes; the procedure was developed as an UHF method. See the original publications by Zerner et al., refs. are given in the "HyperChem Reference" manual. 2) With ZINDO/1 I frequently found it necessary to select the "accelerate convergence" option to obtain SCF convergence at all. And in UHF calculations, a relatively small "Convergence limit" should be specified. Good Luck! Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark E-Mail: JSL@virgil.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Apr 12 13:43:21 1996 Date: Fri, 12 Apr 1996 14:29:37 +0100 To: hyperchem@hyper.com From: Martin.McCoustra@Nottingham.AC.UK (Dr. Martin McCoustra) Subject: Ab Initio Basis Sets A student in our research group would like to do some ab initio calculations on small clusters of up to 7 platinum and/or rhodium atoms with a single attached CO molecule as a model for CO adsorbed on the surface of a Pt-Rh alloy crystal. Does anyone, or can point me in the direction of, basis sets at a reasonable level that are suitable for Pt and Rh in addition to C and O. Thanks, Martin McCoustra _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Apr 12 19:29:26 1996 Date: Fri, 12 Apr 96 15:32:13 -0400 From: polowin (Joel Polowin) To: Martin.McCoustra@Nottingham.AC.UK (Dr. Martin McCoustra) Subject: Re: Ab Initio Basis Sets Cc: hyperchem@hyper.com > Date: Fri, 12 Apr 1996 14:29:37 +0100 > From: Martin.McCoustra@Nottingham.AC.UK (Dr. Martin McCoustra) > > A student in our research group would like to do some ab initio > calculations on small clusters of up to 7 platinum and/or rhodium atoms with > a single attached CO molecule as a model for CO adsorbed on the surface of a > Pt-Rh alloy crystal. Does anyone, or can point me in the direction of, basis > sets at a reasonable level that are suitable for Pt and Rh in addition to C > and O. Although you can include any element in the basis sets for HyperChem, it can use only s, p, and d orbitals. It seems unlikely to me that you would be able to get a good basis set for Pt without including f orbitals. For Rh, of course, you can use any of the basis sets from STO-2G and -2G* to STO-6G and -6G*, which are included with HyperChem, as well as basis sets that you add yourself. 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/ _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Apr 15 22:23:00 1996 From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: hyperchem@hyper.com Date: Mon, 15 Apr 1996 16:52:17 GST Subject: conjugated systems The HyperChem Handbook on Computational Chemistry (Version April 1994) describes on page 183 a procedure that MM+ is supposed to follow in case of single bonds that are not sp3-sp3 hybridized. I am not able to verify the correction that is made to the single bond of butadiene but rather find a bond length for the conjugated double bonds and the singhle bond being very close (far from the corection of 0.6 for each sp2 carbon (MM+ with bond dipoles and no cutoff option). Only when semiempirical methods are used (AM1) the desired bond length are obtained. Am I doing something wrong or does MM+ not account for the difference? Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 16 17:17:44 1996 Date: Tue, 16 Apr 96 11:47:01 -0400 From: polowin (Joel Polowin) To: Eduardo Enrique Chamorro Subject: HyperChem electrostatic potential Cc: hyperchem@hyper.com > Date: Wed, 10 Apr 1996 17:02:57 -0500 (GMT-0500) > From: Eduardo Enrique Chamorro > > Could anybody point me to any articles describing about the calculation > of electrostatic potential. HyperChem calculates and plots the > electrostatic potential from the results of single point, but not show in > log file numerical values. The On-line Help (and manuals...) are very short! The only way to get electrostatic potential data from the current versions of HyperChem is by examining the contour plots. (With the SGI version, one can also save the 3D grid data in a .HIN file.) Our development wish-list includes a suggestion for some ability for users to determine values of QM functions at specified points. As for general information about the electrostatic-potential calculations, users should see the _Computational Chemistry_ manual. The current version of that manual for Windows has relevant information on pages 25, 48-49, 93, 107, and 214-215. (The version for SGI includes an index; I am hoping to create an index for the Windows version of the manual sometime soon, and make it available for distribution.) Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Apr 17 18:25:01 1996 Date: Wed, 17 Apr 96 13:57:34 -0400 From: polowin (Joel Polowin) To: "Gregor Fels" , hyperchem@hyper.com Subject: Re: conjugated systems > From: "Gregor Fels" > Date: Mon, 15 Apr 1996 16:52:17 GST > > The HyperChem Handbook on Computational Chemistry (Version April > 1994) describes on page 183 a procedure that MM+ is supposed to follow in > case of single bonds that are not sp3-sp3 hybridized. > I am not able to verify the correction that is made to the single > bond of butadiene but rather find a bond length for the conjugated > double bonds and the singhle bond being very close (far from the > corection of 0.6 for each sp2 carbon (MM+ with bond dipoles and no > cutoff option). > Only when semiempirical methods are used (AM1) the desired bond > length are obtained. > Am I doing something wrong or does MM+ not account for the > difference? I build butadiene with HyperChem and optimized the structure with MM+. Then I changed the inner two carbons' types to '**', and re-optimized, then changed the other carbons to '**' as well and optimized again. For trans-butadiene, my results were: Atom types lengths lengths C3=C3-C3=C3 C3=C3 1.34183 A C3-C3 1.34372 A C3=**-**=C3 C3=** 1.34432 **-** 1.47179 **=**-**=** **=** 1.34527 **-** 1.47453 which are pretty much as described in the manual. I think you may be doing something wrong. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 18 17:23:43 1996 Date: Thu, 18 Apr 1996 18:27:12 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Delta G message To: chemistry@infomeister.osc.edu Cc: hyperchem@hyper.com Hi, I received a message today from Steve Bowles (I think that's his name) of Sandoz concerning the use of EXCEL and HyperChem to calculate deltaG values. I deleted his message by accident. I don't have any earth-shattering news for him but if he wishes to write to me again I'll reply to him _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Apr 19 15:24:30 1996 Date: Thu, 18 Apr 1996 18:39:30 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Sandoz and Delta G calculations To: hyperchem@hyper.com Cc: chemistry@infomeister.osc.edu Hi, I received a message from Steven Bowles (I think that's his name) of Sandoz concerning the calculation of deltaG values using Excel and HyperChem. I deleted his message by accident. I don't have any earth-shattering information for him but if he writes to me again, I'll reply to him again asap. I apologise to those of you for whom this message is of no interest. Regards, Paddy. Paddy Kane 94970459@vax1.dcu.ie _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Apr 19 20:26:43 1996 From: "GRAHAM WILLS-JOHNSON" Organization: RMIT Applied Physics To: hyperchem@hyper.com Date: Fri, 19 Apr 1996 11:34:33 EST-10 Subject: Quick off the mark... and completely glitch-free. Priority: normal IS THIS A RECORD? 1996 seems to be the year we have reached "critical mass", with several of the research groups in our department starting to see the advantages of molecular modelling as an adjunct to their main lines of attack, and a class of fifteen Honours year students suddenly appearing, needing to be taught HyperChem. Our sturdy 486 was already choked to the gills, running 168 hours per week. So we bought a new Pentium to share the load - and our first copy of release 4.5 (having 4.0, we had planned to sit things out till 5.0 came along). Our PC/LAN manager de-boxed the Pentium, set it up and brought it into the Graphics lab. I got him to instal FTP, and tested that by transferring a lengthy .scr and the accompanying .hin's from the 486. He had the new HyperChem disks at the ready, so went ahead and installed it. The familiar interface flashed up. I reached across and moused up the .scr. I would say that within fifteen seconds of the completion of installation, we had it busy with a job that is still running three days later. True, I still don't know whether the output makes sense, though it looks OK on the screen, and a check "behind the scenes" with File Manager while it is still running shows output files accumulating at much the expected rate. Graham Wills-Johnson. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Apr 24 00:08:10 1996 Date: Tue, 23 Apr 1996 13:49:28 -0700 (PDT) From: Laurence Lavelle To: hyperchem@hyper.com Subject: Windows 95 & HyperChemn 4.0 Can I use HyperChem 4.0 with Windows 95? If so will HyperChem 4.0 run in 32 bit mode? PLease add my email address to the HyperChem Users Group. Thanks Laurence Lavelle _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Apr 24 15:59:01 1996 From: Mike Taylor To: hyperchem@hyper.com Date: Wed, 24 Apr 1996 14:43:05 +0000 Subject: selected-atom script variable Reply-To: m.taylor@pra.org.uk I'm trying to use the 'selected-atom' variable in a Hyperchem 4 script to extract the sequence number of a certain selected atom, and just get the error message "Query-value: Unknown variable 'selected-atom'. " in response to the line query-value selected-atom 2 which I intend to recover the number of the second selected atom, after first selecting three atoms in the molecule. I'm sure it's obvious, but what am I doing wrong? P.S. Does there exist somewhere a sample text file which gives an example of the use of every Hyperchem script variable and command? Thanks for any help. Mike Taylor (m.taylor@pra.org.uk) Paint Research Association PRA 8 Waldegrave Road TEDDINGTON TW11 8LD UK PRA on the Web: http://www.pra.org.uk Tel: +44 (181) 977 4427 Fax: +44 (181) 943 4705 _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 25 00:24:14 1996 Date: Thu, 25 Apr 1996 10:27:00 +0900 From: =?ISO-2022-JP?B?GyRCRiNfNzJtSVcbKEI=?= Subject: quedf To: hyperchem@hyper.com FROM:QZG07361@niftyserve.or.jp MASAO FUJISAWA Dear Sir I am Hyper chem's user.(CP10-8813-Z-0798) I want to do the following question. The description that "you should be able to calculate dynamic propaties by using only data in the CSV file " in a manual ( Computatinal Chemstry p 64). However, do can calculate dynamic propaties by using only data in the CSV file without using velocity component in the Hin file? Sincerely _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 25 00:26:36 1996 Date: Wed, 24 Apr 96 16:19:37 -0400 From: polowin (Joel Polowin) To: hyperchem@hyper.com, m.taylor@pra.org.uk Subject: Re: selected-atom script variable > From: Mike Taylor > Date: Wed, 24 Apr 1996 14:43:05 +0000 > > I'm trying to use the 'selected-atom' variable in a Hyperchem 4 script > to extract the sequence number of a certain selected atom, and just > get the error message "Query-value: Unknown variable > 'selected-atom'. " in response to the line > > query-value selected-atom 2 > > which I intend to recover the number of the second selected atom, > after first selecting three atoms in the molecule. I don't see anything wrong with the above, and it works properly for me with HyperChem 4. My best guess is that the problem is because you're using Windows 95, and your Win'95 Regional Settings are set to something other than "English (United States)". For reasons which we don't understand, some of the scripts and DDE functions work (as far as we know) only with the English(U.S.) setting; otherwise when HyperChem tries to compare the command text with all of the known commands which are built into it, none of them match. My attempts to extract information from Microsoft about possible causes have been unsuccessful. > P.S. Does there exist somewhere a sample text file which gives an > example of the use of every Hyperchem script variable and command? I am not aware of any such file. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 25 14:47:15 1996 From: hocquet@cas.lca.espci.fr Date: Thu, 25 Apr 1996 15:24:07 +0200 To: hyperchem@hyper.com Subject: a dumb question about strain energies Cc: ahocquet@micronet.fr dear hyperchemers, in a chemical education publication the author compares the reactivity of alkenes towards BH3. He calculates (using molecula r mechanics) the strain energy of several alkenes and then plots it as a function of rate constant. I suspect his comparison o f strain energies is not valid if he compares alkenes like , say, 1-hexene and 2-hexene, because the parameters of the dihedra ls wont be the same. Am i right or is his calculation valid, pointing out that the alkenes bear the same number of each atom a nd bond ty bond types ? thank you for your answers Alexandre Hocquet _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Apr 25 21:15:40 1996 Date: Thu, 25 Apr 96 17:22:30 -0400 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: Re: a dumb question about strain energies Cc: ahocquet@micronet.fr > From: hocquet@cas.lca.espci.fr > Date: Thu, 25 Apr 1996 15:24:07 +0200 > > in a chemical education publication the author compares the reactivity > of alkenes towards BH3. He calculates (using molecular mechanics) the > strain energy of several alkenes and then plots it as a function of rate > constant. I suspect his comparison of strain energies is not valid if he > compares alkenes like , say, 1-hexene and 2-hexene, because the parameters > of the dihedrals wont be the same. Am i right or is his calculation valid, > pointing out that the alkenes bear the same number of each atom and > bond types ? It seems to me that his assumptions probably are not valid. With the usual force fields, at least he is working with just rearrangments of the same atom types. But the connections are not the same; for example, 1-hexene has only one sp3 C atom bonded to an sp2 C atom, while 2-hexene has two sp3 C atoms bonded to sp2 C atoms. The bond angles are also dissimilar, and there are differing numbers of dihedral angles between the two systems! On the other hand, if he does get good correlations and they have some predictive ability, I would be willing to consider that the work may have some merit as long as the author makes it clear that there are serious limitations on his assumptions, and that he is aware of the difficulty. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Apr 26 00:05:33 1996 Date: Fri, 26 Apr 1996 09:23:00 +0900 From: =?ISO-2022-JP?B?GyRCRiNfNzJtSVcbKEI=?= Subject: dynamics To: hyperchem@hyper.com FROM:QZG07361@niftyserve.or.jp MASAO FUJISAWA Dear Sir I am Hyper chem's user.(CP10-8813-Z-0798) I want to do the following question. The description that "you should be able to calculate dynamic propaties by using only data in the CSV file " in a manual ( Computatinal Chemstry p 64). However, do can calculate dynamic propaties by using only data in the CSV file without using velocity component in the Hin file? Sincerly _______________________________________________________________________________ From owner-hyperchem@hyper.com Sun Apr 28 02:00:39 1996 Date: Sun, 28 Apr 1996 13:08:00 +0900 From: =?ISO-2022-JP?B?GyRCRiNfNzJtSVcbKEI=?= Subject: dynamics To: hyperchem@hyper.com FROM:QZG07361@niftyserve.or.jp MASAO FUJISAWA Dear Sir I am Hyper chem's user.(CP10-8813-Z-0798) I want to do the following question. The description that "you should be able to calculate dynamic propaties by using only data in the CSV file " in a manual ( Computatinal Chemstry p 64). However, do can calculate dynamic propaties by using only data in the CSV file without using velocity component in the Hin file? I look forward to hearing from you in the near future. Sincerly _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 30 15:04:31 1996 Date: Tue, 30 Apr 96 16:22 +0200 From: To: amber@cgl.ucsf.edu, anneal@chaco.com, c2-l@msi.com, CAChe@pacificu.edu, charmm-bbs@emperor.harvard.edu, chem-comp@mailbase.ac.uk, watoc@ic.ac.uk, chemistry@infomeister.osc.edu, chem-mod@mailbase.ac.uk, dibug@comp.bioz.unibas.ch, hyperchem@hyper.com, isisforum-l@mdli.com, pmd@cumbnd.bioc.columbia.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, anchodd@cc.utas.edu.au, mmodlist@chem.iupui.edu Subject: WATOC96 Message from the President Call for Scientific Contributions to WATOC '96 The extended May 15 deadline for the submission of abstracts of papers to be presented at the WATOC World Congress in Jersulalem approaches. The Scientific Contributions of the participants in the many areas represented in the Congress will augment the already rich program of Plenary and Invited lectures signifiantly. Your participation in WATOC '96 will be rewarded by exceptional science as well as magnificent culture and history. I look forward to welcoming you in Jerusalem in July. Paul Schleyer President, WATOC _______________________________________________________________ Prof. Amiram Goldblum Chairman of WATOC '96 Phone 972-2-758701 Hebrew University of Jerusalem FAX 972-2-410740 School of Pharmacy email watoc96@vms.huji.ac.il Jerusalem 91120 ISRAEL ________________________________________________________________ _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 30 16:25:04 1996 Date: Tue, 30 Apr 1996 17:29:36 +0100 To: hyperchem@hyper.com From: Martin.McCoustra@Nottingham.AC.UK (Dr. Martin McCoustra) Subject: Problem with logging ab initio calculations I've recently been carrying out some ab initio (6-31G* level) calculations on the molecule N2O5. I can happily optimise the geometry and then do a single point calculation on the optimsed system which takes of the order of 30-45 mins. If, however, I attempt to log the output of the ab initio calculation using a print-level of 9, the calculation appears to stall at ca. iteration 15 of the SCF calculation and the log file only gets as far as the final values of the MO energies and coefficients even after leaving the calculation running for ca. 12 hours (overnight). As I'm running Hyperchem under NT 3.51, I am then forced to shut down the WIN16 subsystem of NT to shutdown Hyperchem as the cancel menu item doesn't appear to free up the program by cancelling the calculation. A similar logged calculation on a slightly smaller molecule (ClONO2) worked perfectly. Any ideas? Martin McCoustra Department of Chemistry University of Nottingham Nottingham, UK. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 30 16:36:06 1996 Date: Tue, 30 Apr 1996 18:37:00 +0200 (MET DST) To: chemistry@infomeister.osc.edu From: ahocquet@micronet.fr (Alexandre HOCQUET) Subject: another dumb question about molecular mechanics Cc: hyperchem@hyper.com Dear CCLers and Hyperchemers, In their molecular mechanics principles review (J. Chem. Ed. , 59, 269-274, 1982) Boyd and Lipkowitz present the conformations of cyclohexa-1,4-diene as an example of supremacy of molecular mechanics upon hand held molecular models : the dreiding model predicts boat geometry whereas molecular mechanics calculate it planar. I do believe that this example is demonstrative, presenting molecular mechanics to students as a sophisticated hand held model. Unfortunately, as i tried to minimize cyclohexa-1,4-diene with the MM+ force field provided by Hyperchem, the results show that the minimum (9.10 kcal.mol-1) corresponds to a torsion angle between 1,2,3 and 4 carbons of 260, in a boat conformation. The constrained planar structure corresponds to 9.73 kcal.mol-1 and goes back to the former conformation when constrain is removed. Besides, An AM1 semiempirical calculation does find the minimum to be planar. So my questions are : Does the MM+ forcefield, or the parameters provided in Hyperchem, lack the accuracy needed to perform this calculation ? Does any references about molecular mechanics calculations of this molecule exist ? Does anybody know the references about calculations, Xray and NMR results that Boyd and Lipkowitz cite with no references (or, to be honnest, the reference cited was "in press" : Lipkowitz et al. in J. Org. Chem.) ? Am i doing something wrong ? Thanks in advance for any answers (if somebody is interested, i will summarize the answers) Alexandre Hocquet Laboratoire de Chimie Analytique ESPCI 10, Rue Vauquelin 75231 Paris Cedex 05 France tel : 33 1 40794420 fax : 33 1 40794425 email : ahocquet@micronet.fr ou hocquet@cas.espci.fr ou hocquet@ens-cachan.fr _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 30 17:27:10 1996 Date: Tue, 30 Apr 96 13:08:02 -0400 From: polowin (Joel Polowin) To: =?ISO-2022-JP?B?GyRCRiNfNzJtSVcbKEI=?= , hyperchem@hyper.com Subject: Re: dynamics > Date: Fri, 26 Apr 1996 09:23:00 +0900 > FROM:QZG07361@niftyserve.or.jp MASAO FUJISAWA > > The description that "you should be able to calculate dynamic > propaties by using only data in the CSV file " in a manual > ( Computatinal Chemstry p 64). > However, do can calculate dynamic propaties by using only data > in the CSV file without using velocity component in the Hin file? The manual does not say "only". But to calculate time correlation functions and diffusion constants, velocity information would indeed be needed. That information can be obtained from an .SNP (snapshot) file. Or, if you run a molecular dynamics playback and specify one particular time step for the starting and ending times, that "animation frame" will be brought into HyperChem. This will include the atomic velocities. The velocity information can then be retrieved by saving that structure in a HIN file, or by using script commands such as "velocity". Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 30 20:21:11 1996 Date: Tue, 30 Apr 96 17:01:05 -0400 From: polowin (Joel Polowin) To: Martin.McCoustra@Nottingham.AC.UK (Dr. Martin McCoustra), hyperchem@hyper.com Subject: Re: Problem with logging ab initio calculations > Date: Tue, 30 Apr 1996 17:29:36 +0100 > From: Martin.McCoustra@Nottingham.AC.UK (Dr. Martin McCoustra) > > I've recently been carrying out some ab initio (6-31G* level) > calculations on the molecule N2O5. I can happily optimise the geometry and > then do a single point calculation on the optimsed system which takes of the > order of 30-45 mins. If, however, I attempt to log the output of the ab > initio calculation using a print-level of 9, the calculation appears to > stall at ca. iteration 15 of the SCF calculation and the log file only gets > as far as the final values of the MO energies and coefficients even after > leaving the calculation running for ca. 12 hours (overnight). As I'm running > Hyperchem under NT 3.51, I am then forced to shut down the WIN16 subsystem > of NT to shutdown Hyperchem as the cancel menu item doesn't appear to free > up the program by cancelling the calculation. > > A similar logged calculation on a slightly smaller molecule (ClONO2) > worked perfectly. My best guess is that this is a variation on the known problem with NT and HyperChem, wherein there is a communications problem between the graphical display and the computational modules such that after a large amount of data has passed back and forth between the two, the calculation aborts and HyperChem reports a communication problem. At this point, one can save the structure, restart HyperChem, and continue the calculation. With earlier versions of Windows NT than 3.51 (with the third service pack), both the graphical and computational modules simply froze (and ChemPlus and HyperNMR did not work properly). None of these problems are seen with Windows or Windows 95, and the problem appears to lie in Windows NT. One user has reported that the problem appears to involve the NT system file 'pagingfile.sys', which he observed to grow with each exchange of data between front and back ends. When the file reached the maximum size specified in the NT configuration, the calculation halted. But we have not observed this effect ourselves. The problem can be at least partially avoided by reducing the frequency with which the structure is redisplayed on the screen during a calculation. For example, if the structure is redisplayed only every 10th iteration, then the calculation can run 10 times as long before it locks up. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Apr 30 22:23:54 1996 From: Gerardo Burton To: "'Alexandre HOCQUET'" Cc: "'hyperchem@hyper.com'" Subject: RE: another dumb question about molecular mechanics Date: Tue, 30 Apr 1996 19:47:41 -0300 Hi I tried this minimization with Hyperchem 4.5 using MM+: I started with = the model builder which gave a boat conformation and then with MM+ and = obtained the non planar structure as a flattened boat and Energy=3D8.977 = Kcal/mol (Gradient 0.00079). I then took that "optimized" structure and = reminimized it with PCModel for Windows 5.13 where it immediately gave = the planar structure! I went back to Hyperchem redrew the structure = "PLANAR" and added H's WITHOUT using the model builder. I minimized this = structure and now I obtained the planar conformation with Energy=3D = 3.0488 Kcal/mol (Gradient 0,00083), i.e the real minimun. I rechecked the "non planar minimun" that HyperChem found, and in both = PCModel AND Hyperchem it has a very high torsion energy component, = however for some strange reason Hyperchem does not reflect that in the = Gradient. I made some other tests and found that Hyperchem reached = another boat type minimun with Energy=3D10.94!! This structure rapidly = converged to the planar real minimun with PCModel. I never found differences between the parameters in Hyperchem and = PCModel, maybe this is a bug in Hyperchem optimizers. As I see it, = optimizers are the weakest point of Hyperchem (an implementation of BFGS = would be great!) Gerardo Gerardo Burton e-mail: burton@quimor.qo.fcen.uba.ar Departamento de Quimica Organica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Tel/FAX 54 1 788-6915 ---------- From: Alexandre HOCQUET[SMTP:ahocquet@micronet.fr] Sent: Martes 30 de Abril de 1996 15:37 To: chemistry@infomeister.osc.edu Cc: hyperchem@hyper.com Subject: another dumb question about molecular mechanics Dear CCLers and Hyperchemers,=20 In their molecular mechanics principles review (J. Chem. Ed. , 59, = 269-274, 1982) Boyd and Lipkowitz present the conformations of = cyclohexa-1,4-diene as an example of supremacy of molecular mechanics upon hand held molecular models : the dreiding model predicts boat geometry whereas molecular mechanics calculate it planar. I do believe that this example is demonstrative, presenting molecular mechanics to students as a sophisticated hand held model. Unfortunately, as i tried to minimize cyclohexa-1,4-diene with the MM+ = force field provided by Hyperchem, the results show that the minimum (9.10 kcal.mol-1) corresponds to a torsion angle between 1,2,3 and 4 carbons = of 26=B0, in a boat conformation. The constrained planar structure = corresponds to 9.73 kcal.mol-1 and goes back to the former conformation when constrain = is removed. Besides, An AM1 semiempirical calculation does find the minimum to be = planar. So my questions are :=20 Does the MM+ forcefield, or the parameters provided in Hyperchem, lack = the accuracy needed to perform this calculation ? Does any references about molecular mechanics calculations of this = molecule exist ? Does anybody know the references about calculations, Xray and NMR = results that Boyd and Lipkowitz cite with no references (or, to be honnest, the reference cited was "in press" : Lipkowitz et al. in J. Org. Chem.) ? Am i doing something wrong ?=20 Thanks in advance for any answers (if somebody is interested, i will summarize the answers) Alexandre Hocquet Laboratoire de Chimie Analytique ESPCI 10, Rue Vauquelin 75231 Paris Cedex 05 France tel : 33 1 40794420 fax : 33 1 40794425 email : ahocquet@micronet.fr ou hocquet@cas.espci.fr ou hocquet@ens-cachan.fr