From toukie@zui.unizh.ch Mon Jan 5 10:13:09 1998 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id KAA09216; Mon, 5 Jan 1998 10:01:30 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA31743; Mon, 5 Jan 1998 16:01:29 +0100 Message-Id: <3.0.3.32.19980105160436.00688948@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Mon, 05 Jan 1998 16:04:36 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: ? re WebLab 2.0 partial atomic charges Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; Does anyone know how the partial atomic charges are calculated using MSI's WebLab 2.0? s it the Gasteiger-Marsili procedure, or is some other method used? For a given molecule the WebLab 2.0 partial atomic charges are quite different from the corresponding AM1 partial atomic charges. Any relevant literature references are appreciated. (My e-letters to MSI on this matter have gone unanswered, so I now bring this question to the attention of the whole CCL community.) Thanks in advance to all responders, and to all CCL members a very happy, healthy, and successful 1998! Sincerely, S. Shapiro toukie@zui.unizh.ch From chipot@host7.lctn.u-nancy.fr Tue Jan 6 14:13:18 1998 Received: from host7.lctn.u-nancy.fr for chipot@host7.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id NAA16657; Tue, 6 Jan 1998 13:47:10 -0500 (EST) From: Received: (from chipot@localhost) by host7.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id TAA24632; Tue, 6 Jan 1998 19:35:33 +0100 (NFT) Message-Id: <199801061835.TAA24632@host7.lctn.u-nancy.fr> Subject: Chambery Meeting - 2nd Circular To: CHEMISTRY@www.ccl.net Date: Tue, 6 Jan 1998 19:35:33 +0100 (NFT) Cc: jeremy.smith@cea.fr, 106561.1400@compuserve.com, garnier@biotec.jouy.inra.fr, brick@pc.chemie.tu-darmstadt.de X-Mailer: ELM [version 2.4 PL23] Content-Type: text _______________________________________________________________________ _______________________________________________________________________ European Conference on COMPUTATIONAL CHEMISTRY AND THE LIVING WORLD: FROM SEQUENCE TO FUNCTION. Chambery (French Alps), 20-24 April, 1998 Organised by the Physical Chemistry Division, French Chemical Society (SFC) Bunsen-Gesellschafft fur Physikalische-Chemie, Faraday Division of the Royal Society of Chemistry (RSC), Division di Chimica Fisica (SCI), French Biophysical Society. International Scientific Committee: J.C. Smith (CEA-Saclay, Chairman); R. Botter (DCP Paris), secretary; J. Brickmann (TH Darmstadt); J.E. Dubois (U. Paris VII); J. Garnier (INRA-Jouy); M. Karplus (U. Strasbourg); R. Lavery (IBPC, Paris); B. Maigret (U. Nancy); C. Chipot (U.Nancy); G. Richards (U. Oxford); E. Soulie (CEA-Saclay); J. Tomasi (U. Pisa); C. Troyanowsky (DCP Paris). _______________________________________________________________________ SECOND CIRCULAR _______________________________________________________________________ A - SCOPE OF THE MEETING ____________________ The results of the genome projects are expected to lead to a scien- tific revolution in the beginning of the next century. The complete gene sequences of organisms of several different levels of develop- ment, including Homo Sapiens, will be available. This enormous amount of genetic information will be in the form of nucleotide se- quences. The information present in a gene sequence is translated in the cell into a protein sequence. This sequence determines the way the protein folds into a three-dimensional architecture, which confers biological function (catalysis, recognition, etc.). The question arises as to how to exploit the genetic information as effectively as possible. To do this will require an understanding of the processes of translation of the genetic information from se- quence to structure and function. Both theory and experiment are expected to play major roles in obtaining this understanding. The meeting in Chambery will focus on the role of computational chemis- try in the activity that will be sparked by the genome results. How can numerical calculation help us to understand and exploit genome sequences ? How can modelling and simulation help in understanding how amino-acid sequence is translated into three-dimensional bio- logical structure, the functional interactions of these structures and the effect of engineered modifications ? The meeting will be covering the following topics, organised into three themes: sequence analysis, biomolecular structure and folding and biomolecular function. Research into the chemistry of biologi- cal macromolecules requires close cooperation between theorists and experimentalists. In the present meeting we hope to attract scien- tists from both fields. We have invited a number of leading experi- mentalists to give lectures, and hope to emphasize the broad com- plementarity between theory and experiment in the lectures rather than specialized discussion of theoretical methodology. The meeting is expected to be of interest to researchers in all branches of computational chemistry, as well as structural and mo- lecular biologists and biochemists. The consequences for industry of success in the endeavours discussed above are enormous, and this has been realised in several drug companies that have set up inte- grated computational/experimental groups on sequence-structure- function relationships. B - PROVISIONAL PROGRAMME _____________________ MONDAY APRIL 20-th __________________ 8.45-9.15 Welcome. THEME 1: SEQUENCES __________________ 9.15-10.00 Jean-Michel Claverie (Marseille) "Analysis of gene sequences" 10.00-10.30 Pause + Exhibition. 10.30-11.15 Antoine Danchin (Paris) "The Genome Projects". 11.00-12.15 Three short talks 14.00-14.45 Cyrus Chothia (Cambridge) "Patterns in Protein Structure" 14.45-15.15 Charles Brooks (Scripps Institute) "Simulation of Protein Folding" 15.15-15.45 Two short talks. 15.45-16.15 Break. 16.15-17.15 Oral Poster presentations. 17.15-18.15 Poster session. 18.30 Reception by the Mayor of Chambery. TUESDAY APRIL 21-st ___________________ THEME 2: FOLDING AND STRUCTURE ______________________________ 9.00- 9.45 Mannfred Sippl (Graz) "Molecular forces in protein folding and prediction." 9.45-10.45 Three short talks 10.45-11.30 Pause + Exhibition. 11.30-12.15 Michael Hecht (Princeton) "De Novo Proteins from Designed Combinatorial Libraries." 14.00-14.45 Eugene Shakhnovitch (Harvard) "Lattice Models of Protein Folding" 14.45-15.45 Three short talks. 15.45-16.15 Break. 16.15-17.15 Oral poster presentations. 17.15-18.15 Poster session. WEDNESDAY APRIL 22-nd _____________________ 9.00- 9.45 Wilfred van Gunsteren (Zurich) "Reversible Protein Folding in Solution by MD Simulation" 9.45-10.30 Pause + Exhibition. 10.30-11.15 Three short talks. AFTERNOON FREE: - Ski trip - Wine trip - Visit of the city THURSDAY APRIL 23-rd ____________________ 9.00- 9.45 Chris Dobson (Oxford) "Nuclear Magnetic Reso- nance in Protein Folding" 9.45-10.30 Pause + Exhibition. 10.30-11.30 Three short talks. 11.15-12.15 Eric Westhof (Strasbourg) "Simulation of Nuc- leic Acid Structure" THEME 3: BIOMOLECULAR INTERACTIONS AND FUNCTION _______________________________________________ 14.00-14.45 David Chandler (Berkeley) "Statistical Mecha- nics of Biological Interest" 14.45-16.00 Pause + Exhibition. 15.30-16.30 Three short talks. 20.00 Banquet and Blues concert "The Baskerville's Blues Band" FRIDAY APRIL 24-th __________________ 9.00- 9.45 Harel Weinstein (New York) "From sequence to molecular mechanism in G-protein coupled re- ceptors: structural motifs as functional microdomains." 9.45-10.30 Pause + Exhibition. 10.30-11.30 Three short talks. 11.30-12.15 Klaus Schulten (Illinois) "Evolution of effi- cient light harvesting in photosynthesis - One goal, many solutions." (this talk will be mo- ved to eariler in the week). 14.00-14.45 Wayne C. Guida (Novartis Pharmaceutical) "Drug Design" 14.45-16.30 Oral presentations and final discussion. _______________________________________________________________________ CALL FOR PAPERS _______________________________________________________________________ Attendents who want to present a poster or make an oral presentation should send a one-page abstract. Authors who would like to make an oral presentation are asked to send their abstract BEFORE January 10-th, 1998. Oral presentations will be selected by the scientific committee at the end of January 1998, and the authors of the selected papers will be informed at the begining of February 1998. _______________________________________________________________________ PUBLICATION OF THE PROCEEDINGS _______________________________________________________________________ The proceedings of this meeting will be published as a special issue of Theoretical Chemistry Accounts (formerly Theoretica Chimica Acta), Edi- ted by R. Lavery and J. Tomasi. Principal speakers are invited to prepare full articles, that present their recent results or give an overview of their contributions. Full articles can contain up to 24 double-spaced pages of text plus figures. Short talks and posters will be published in the form of letters, which can contain up to 12 double- spaced pages. Speakers are urged to bring their manuscripts with them to the meeting to enable rapid refereeing. The ABSOLUTE DEADLINE for submissions will be March 31-st 1998. Instructions for authors can be obtained from the Web site: http://link.springer.de/link/service/journals/00214/ or from any copy of "Theoretical Chemistry Accounts". It should be noted that colour figures will be published free of charge, and that it is possible to add supplementary material in the form of web archives. _______________________________________________________________________ PRACTICAL INFORMATION _______________________________________________________________________ LOCATION: The meeting will be held at the Centre de Congres Le Manege, 331 rue de la Republique, 73000 Chambery. The center is in downtown Chambery, within easy walking dis- tance of the railway station and numerous bars, brasseries and restaurants that serve breakfast, lunch and dinner. ACCESS: Chambery can be conveniently reached by air road or rail. The high speed TGV train runs directly to Chambery in 3 hours from Paris Gare de Lyon, or Paris Charles de Gaulle airport. Railway information and reservation: SNCF: Tel. 33.8.36.35.35.35 Internal flights exist between Paris Orly and Chambery-Aix- les-Bains airports (1 hour 10 mins). N.B. Transfer between Charles de Gaulle and Orly takes up to 2 hours by train. Chambery can also be reached by train from Geneva airport (1 hour 15 mins) or bus from Lyon Satolas airport (1 hour). Access by car by toll autoroute from Lyon and Geneva (A43) and Grenoble and Italy (A41). _______________________________________________________________________ _______________________________________________________________________ Participants should fill out the REGISTRATION/EVENTS AND ACCOMODATION FORMS and send them to the SEPARATE ADDRESSES indicated. _______________________________________________________________________ _______________________________________________________________________ _______________________________________________________________________ CONFERENCE REGISTRATION _______________________________________________________________________ Please, send the completed registration form AS SOON AS POSSIBLE and by REGULAR MAIL with payment fee to the Conference address. REGISTRATION FEES(*) ____________________ ____________________________________________________________________ Before March 15-th After March 15-th ____________________________________________________________________ Regular price 2400 FF 2800 FF Members of the 1800 FF 2200 FF Organizing Societies Students 1300 FF 1700 FF ____________________________________________________________________ (*) Registration fees include the conference dinner and concert for the participants o METHOD OF PAYMENT _________________ All payments must be in FRENCH FRANCS. Bank order and bank draft payable to: DCP/SFC, Congres de Chimie Informatique BNP Saclay Account N 30004 01788 0010000693 27 N.B. We have already received a large number of preliminary inquieries. Places at the meeting are limited to 320 and will be allocated on a first come first served basis. o HOTEL ACCOMMODATION ___________________ Hotels of different price categories have been reserved for the Confe- rence period. o DAILY RATES OF HOTEL ROOMS __________________________ _____________________________________________________________ Hotel category Single room Double room 1 person 2 persons _____________________________________________________________ 3-star Hotel 400 FF 450 FF 2-star Hotel 250 FF 300 FF 1-star Hotel 180 FF 220 FF _____________________________________________________________ (Price in French Francs, taxes, services and breakfast included) o STUDENT ACCOMMODATION _____________________ Room 20 m2, 2 persons 220 FF/room Room 30 m2, 3 persons 285 FF/room Room 35 m2, 4 persons 340 FF/room (Price per room and per day, breakfast included, towel upon request) o HOTEL AND STUDENT ROOM RESERVATIONS ___________________________________ Please, reserve by completing the enclosed ACCOMMODATION FORM. All ac- commodation will be allocated in the order of receipt of registration. If rooms are unavailable at your requested choice of hotel category, the closest available rate will be assigned. You will receive written confirmation and a hotel voucher stating the name and adress of the ho- tel booked as soon as your accommodation form and deposit have been re- ceived by "BRIGITTE DEBAS, ITC". o SHARING ROOM ____________ For those, who intend to share a room with an other registrant, please indicate roommate's name in accommodation form. o BOOKING PAYMENT _______________ DEPOSIT, which include processing charges received by "BRIGITTE DEBAS, ITC" must accompany your accommodation form. This deposit (excluding the booking fees) will be deduced from your hotel bill when you check- out. NO RESERVATION will be confirmed until your payment is received. All payment must be in French Francs only: Bank transfer and bank draft payable to: BRIGITTE DEBAS, ITC Account N : 18006-00010-00606453050-57 Bank: Credit Agricole de la Savoie. and mailed with Accommodation Form to: BRIGITTE DEBAS, ITC - Cité de l'Entreprise Boulevard Barrier 73100 Aix les Bains France Note: In order to avoid any trouble in money transfer, a copy of remit- tance invoice or receipt should be sent with your Accomodation Form. o CANCELLATION AND REFUND _______________________ Deposit (minus 85 FF processing charges) will be refunded only by "Bri- gitte Debas, ITC" on receipt of a written cancellation sent only to "Brigitte Debas, ITC" (by fax N 33 79 88 11 36 or letter) and not di- rectly to the hotel before March 20-th, 1998. Any cancellation after this date will not be refunded. o EVENTS, EXCURSIONS AND TOURS ____________________________ * Evening events ______________ Reception by the Mayor of Chambery Participants are invited to attend a free reception, organized by the Mayor of Chambery on Monday evening, April 20-th, at 6.30 PM. * Conference dinner _________________ The official Conference Dinner will be held at the Conference site "Le Manège" on Thursday, April 23rd. A concert of CHICAGO BLUES will be given by THE BASKERVILLES BLUES BAND - winners of Polyphonie Ile- de-France Blues contest. Dinner and Concert are included in the fees for the participants and will be 280 FF per accompanying person. * Excursions and Tours ____________________ WEDNESDAY AFTERNOON (22-nd April) will be reserved for trips. We are planning five types of trip. Accompanying persons are welcome to come. Tour tickets can be paid with room reservation or will be available at the registration desk in "Le Manège". 1 - HIGH-ALTITUDE ALPINE SKI TRIP TO COURCHEVEL ___________________________________________ 300 FF per person Price includes transport and afternoon ski pass. Ski boots can be rented in Chambery. 2 - WINE ROAD _________ 160 FF 3 - VISIT OF CHAMBERY _________________ 55 FF 4 - LAC DU BOURGET ______________ 165 FF 5 - CHAMONIX - MER DE GLACE _______________________ 450 FF _______________________________________________________________________ REGISTRATION FORM _______________________________________________________________________ Computational Chemistry and the Living World, from Sequence to Function Chambery, april 20-24, 1998 To be returned to: Mr. Rene Botter, Computational Chemistry and the Living World, Laboratoire de Chimie Physique, 11 rue P. et M. Curie, 75005 PARIS France .................................................................>8.... REGISTRATION FORM _________________ NAME: _________________________________________________________________ ADDRESS: ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ TELEPHONE: ____________________________________________________________ FAX: __________________________________________________________________ E-MAIL: _______________________________________________________________ REGISTRATION FEES _________________ (Conference Dinner and Concert included) ____________________________________________________________________ Before March 15-th After March 15-th ____________________________________________________________________ Regular price 2400 FF 2800 FF Members of the 1800 FF 2200 FF Organizing Societies Students 1300 FF 1700 FF ____________________________________________________________________ METHOD OF PAYMENT _________________ All payments must be in FRENCH FRANCS. Bank order and bank draft payable to: DCP/SFC, Congres de Chimie Informatique BNP Saclay Account N 30004 01788 0010000693 27 I WISH/DO NOT WISH TO PRESENT A POSTER ________________________________ Participants wishing to present a poster should send a hard copy of a one-page abstract to Rene Botter, at the above address, before January 10-th 1998. I WISH/DO NOT WISH TO MAKE A 20 MINUTE ORAL PRESENTATION ______________ Authors of all posters presented will be invited to make very short oral introductions to their posters. If you wish to be considered for a longer presentation, please indicate this above. .................................................................>8.... .................................................................>8.... ACCOMMODATION, EVENTS AND TOUR FORM ___________________________________ To be completed and returned with payment to: ITC-Cité de l'Entreprise Boulevard Robert Barrier, 73100 Aix les Bains - France NAME (Mr, Ms) _________________________________________________________ FIRST NAME ____________________________________________________________ TITLE _________________________________________________________________ COMPANY/INSTITUTION ___________________________________________________ ___________________________________________________ ADRESSS _______________________________________________________________ _______________________________________________________________ _______________________________________________________________ POSTAL/ZIP CODE ___________________ CITY ______________________________ COUNTRY ___________________________ TELEPHONE _________________________ FAX ______________________________ E-MAIL ________________________________________________________________ ACCOMPANIED BY: NAME __________________________________________________________________ FIRST NAME ____________________________________________________________ DATE OF ARRIVAL _______________________________________________________ TIME __________________________________________________________________ DATE OF DEPARTURE _____________________________________________________ TIME __________________________________________________________________ MEANS OF TRANSPORTATION: Car _________ Train __________ Air _________ ACCOMMODATION REQUIRED: 1 person _________ 2 persons(*) ___________ Double bed _________ 2 single beds ___________ Rates per Room and per Night. Deposit includes 85 FF processing charges received by "ITC": ____________________________________________________________ Category Price Deposit ____________________________________________________________ 3-star hotel 350 FF to 500 FF 485 FF 2-star hotel 250 FF to 330 FF 335 FF 1-star hotel 180 FF to 220 FF 265 FF 2-bed room 220 FF/ room 305 FF 3-bed room 285 FF/ room 370 FF 4-bed room 340 FF/ room 425 FF ____________________________________________________________ (*) If you wish to share a room with another (other) registrant(s), please indicate: Name: Mr / Ms _________________________________________________________ Mr / Ms _________________________________________________________ Mr / Ms _________________________________________________________ Mr / Ms _________________________________________________________ TOTAL HOTEL DEPOSIT __________________________________ FF EVENT AND TOUR FORM ___________________ EVENING EVENT: Conference Dinner: Thursday, April 23-rd 280 FF x _________ acompanying person(s) _____________________________________ FF EXCURSIONS AND TOURS: ___________________________________________________________________ Ref. Name Price Number of Persons Total ___________________________________________________________________ T1 Chambery 55 FF x ________________ _______ FF T2 Lac du Bourget 165 FF x ________________ _______ FF T3 Ski-Courchevel 300 FF x ________________ _______ FF T4 Wine road 160 FF x ________________ _______ FF T5 Chamonix-Mont Blanc 420 FF x ________________ _______ FF ___________________________________________________________________ TOTAL ACCOMMODATION ______________ FF TOTAL CONFERENCE DINNER ______________ FF TOTAL EXCURSIONS ______________ FF ____________________________________________ TOTAL AMOUNT ______________ FF PAYMENT (in French Francs only) _______________________________ o CREDIT CARD: NAME __________________________________________________________________ EXPIRATION DATE _______________________________________________________ CARD NO. ______________________________________________________________ DATE AND SIGNATURE ____________________________________________________ o BANK CHEQUE AT THE ORDER OF "ITC - Congrès": Bank Order or Bank Draft payable to: ITC-Congrès Account No: 86 06 59 80 051 Bank: CREDIT AGRICOLE DE LA SAVOIE Code: 18106 - 00810/44 Only application received with this accommodation and tour form toge- ther with the payment of the amount will be considered. DATE ____________________________________ NAME AND SIGNATURE OF PERSON RESPONSIBLE ______________________________ ______________________________ .................................................................>8.... _______________________________________________________________________ _______________________________________________________________________ _______________________________________________________________________ Chris Chipot Laboratoire de Chimie Theorique Phone: (33) 3-83-91-25-96 U.R.A. C.N.R.S. No 510 Fax: (33) 3-83-91-25-30 Universite Henri Poincare - Nancy I B.P. 239 54506 Vandoeuvre-les-Nancy Cedex E-mail: chipot@lctn.u-nancy.fr `The light shines through the darkness and the darkness has not overcome it' _______________________________________________________________________ From hinsen@lmspc1.ibs.fr Thu Jan 8 08:13:42 1998 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id HAA27125; Thu, 8 Jan 1998 07:54:06 -0500 (EST) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id NAA17502; Thu, 8 Jan 1998 13:53:04 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id NAA17036; Thu, 8 Jan 1998 13:50:36 +0100 Date: Thu, 8 Jan 1998 13:50:36 +0100 Message-Id: <199801081250.NAA17036@lmspc1.ibs.fr> From: Konrad Hinsen To: root@liposome.genebee.msu.su CC: chemistry@www.ccl.net In-reply-to: (message from root on Thu, 25 Dec 1997 22:55:13 +0300 (MSK)) Subject: Re: CCL:md rookie update > The dcd trajectory format is machine-dependant; there is a other-endian > filter out there which I haven't been able to get to work, however. The Molecular Modelling Toolkit (MMTK), available at http://starship.skyport.net/crew/hinsen/mmtk.html, allows conversion of DCD files into machine-independent netCDF files. The inverse conversion is not yet implemented, but MMTK contains plenty of analysis functions to do whatever you want with the netCDF trajectory files. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From laaksone@csc.fi Thu Jan 8 09:13:42 1998 Received: from pobox.csc.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id JAA27452; Thu, 8 Jan 1998 09:03:45 -0500 (EST) Received: from voxopm.minedu.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with ESMTP id QAA20263; Thu, 8 Jan 1998 16:03:26 +0200 (EET) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by voxopm.minedu.fi (8.8.8/8.8.8/CSC/Svrs-3.18) with SMTP id QAA19365; Thu, 8 Jan 1998 16:03:25 +0200 (EET) Date: Thu, 8 Jan 1998 16:04:17 +0200 (GFT Standard Time) From: Leif Laaksonen To: Konrad Hinsen cc: root@liposome.genebee.msu.su, chemistry@www.ccl.net Subject: Re: CCL:md rookie update In-Reply-To: <199801081250.NAA17036@lmspc1.ibs.fr> Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, If you aren't worried about loosing the last decimal of the accuracy you can use my small FORTRAN program for CHARMM trajectories for the formatting/unformatting at: http://laaksonen.csc.fi/gopenmol/distribute/linux/charmmtrj.f I mostly use the program to move the trajectories between different types of machines. Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- On Thu, 8 Jan 1998, Konrad Hinsen wrote: > > The dcd trajectory format is machine-dependant; there is a other-endian > > filter out there which I haven't been able to get to work, however. > > The Molecular Modelling Toolkit (MMTK), available at > http://starship.skyport.net/crew/hinsen/mmtk.html, allows conversion > of DCD files into machine-independent netCDF files. The inverse > conversion is not yet implemented, but MMTK contains plenty of > analysis functions to do whatever you want with the netCDF trajectory > files. > -- > ------------------------------------------------------------------------------- > Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr > Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 > Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 > 41, av. des Martyrs | Deutsch/Esperanto/English/ > 38027 Grenoble Cedex 1, France | Nederlands/Francais > ------------------------------------------------------------------------------- > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: hinsen@lmspc1.ibs.fr > -- Original Sender From: Address: hinsen@ibs.ibs.fr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From david@viper.wf.bms.com Thu Jan 8 11:13:42 1998 Received: from cliff.bms.com for david@viper.wf.bms.com by www.ccl.net (8.8.3/950822.1) id KAA28578; Thu, 8 Jan 1998 10:32:21 -0500 (EST) Received: from viper.wf.bms.com by cliff.bms.com (PMDF V5.1-10 #22413) with SMTP id <01IS4Q8SO39O004PXC@cliff.bms.com> for chemistry@www.ccl.net; Thu, 8 Jan 1998 10:31:06 EST Received: by viper.wf.bms.com (950413.SGI.8.6.12/930416.SGI) id KAA26553; Thu, 08 Jan 1998 10:30:16 -0500 Date: Thu, 08 Jan 1998 10:30:16 -0500 From: "David R. Langley" Subject: CCL:md rookie update To: root@liposome.genebee.msu.su Cc: chemistry@www.ccl.net Message-id: <9801081030.ZM26551@viper.wf.bms.com> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) Content-type: text/plain; charset=us-ascii Hi, The best wat to go from a charmm DCD formate (machine-dependent) to a machine-independent formate and then back to the DCD formate is to use charmm. The following is a charmm input file for such conversions. * d(ccaacgttgg)2 + 18 NA + 1335 waters. D.R. Langley 2-12-97 * ! Startup script for CHARMm ! UPPER ! case for files to write !open write card unit 7 name DNA.LOG !outu 7 banner bomblevel -2 wrnlev 5 prnlev 5 open read card unit 21 name "DNAPRM/BMS.RTF" read rtf card unit 21 close unit 21 open read card unit 22 name "DNAPRM/BMS.prm" read param card unit 22 close unit 22 DELE ATOM SELECT ALL END read sequ card * d(ccaacgttgg) strand A * 10 C C A A C G T T G G generate A setup FIRS 5TER LAST 3TER read sequ card * d(ccaacgttgg) strand B * 10 C C A A C G T T G G generate B setup FIRS 5TER LAST 3TER read sequ NA 18 generate C setup noang nodihe open read unit 21 card name DNA_2.CRD !canonical B-DNA read coor unit 21 card close unit 21 !To convert charmm DCD files to a machine-independent formate use next 3 lines. OPEN READ UNIT 99 FILE NAME DNANA.DCD OPEN WRITE UNIT 98 CARD NAME DNANA.DHX DYNA FORM FIRST 99 NUNIT 1 BEGIN 250 SKIP 250 OUTPUT 98 !To convert charmm DHX files back into DCD formate use next 3 lines. OPEN READ UNIT 99 CARD NAME DNANA.DHX OPEN WRITE UNIT 98 FILE NAME DNANA.DCD DYNA UNFORM INPUT 99 OUTPUT 98 STOP -- David R. Langley, Ph.D. Bristol Myers Squibb Pharma. Res. Inst. Department of Macromolecular Structure P.O. Box 5100 Room 458B Wallingford, CT 06492 email: david@viper.wf.bms.com phone: (203) 284-6656 fax: (203) 284-7702 From sabrash@richmond.edu Thu Jan 8 13:13:44 1998 Received: from pinstripe.richmond.edu for sabrash@richmond.edu by www.ccl.net (8.8.3/950822.1) id NAA29390; Thu, 8 Jan 1998 13:02:19 -0500 (EST) Received: from [128.135.85.63] (photon.uchicago.edu [128.135.85.63]) by pinstripe.richmond.edu (8.8.5/8.7.3) with ESMTP id NAA18696 for ; Thu, 8 Jan 1998 13:02:20 -0500 (EST) X-Sender: sabrash@facstaff.richmond.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 8 Jan 1998 12:01:50 -0600 To: CHEMISTRY@www.ccl.net From: sam abrash Subject: CCL: Gaussian vs QChem CCL'ers: I have a grant to buy a quantum chemistry program. Does anyone out there have experience with both Gaussian and QChem and can you tell me something about the strengths and weaknesses of each. It would be most helpful. Thanks in advance. Sam Abrash Visiting Scientist, James Franck Institute And Associate Professor, University of Richmond sabrash@richmond.edu From smb@smb.chem.niu.edu Thu Jan 8 13:24:10 1998 Received: from cz2.chem.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id MAA29256; Thu, 8 Jan 1998 12:25:47 -0500 (EST) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA18568; Thu, 8 Jan 98 10:58:39 -0600 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA13457; Thu, 8 Jan 98 11:22:23 -0600 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) id LAA26777; Thu, 8 Jan 1998 11:23:34 -0600 Sender: smb@smb.chem.niu.edu Message-Id: <34B50B95.15FB@smb.chem.niu.edu> Date: Thu, 08 Jan 1998 11:23:33 -0600 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Cc: "Bachrach, Steven" Subject: Internet Journal of Chemistry now available Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Internet Journal of Chemistry (IJC), an electronic journal, is now available at http://www.ijc.com/ IJC features peer-reviewed original research in all areas of chemistry, and allows authors to enhance their article by making use of publication features available only on electronic media. The journal will be covered by Chemical Abstracts. IJC will be available at no cost for 1998. Information on submitting to IJC can be found at the IJC home page. Steven Bachrach, Editor Internet Journal of Chemistry -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From rvenable@deimos.cber.nih.gov Thu Jan 8 13:31:43 1998 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id MAA29354; Thu, 8 Jan 1998 12:56:01 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA108831748; Thu, 8 Jan 1998 12:49:08 -0500 Date: Thu, 8 Jan 1998 12:49:08 -0500 (EST) From: Rick Venable To: Leif Laaksonen Cc: Konrad Hinsen , root@liposome.genebee.msu.su, chemistry@www.ccl.net Subject: Re: CCL:md rookie update In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 8 Jan 1998, Leif Laaksonen wrote: > If you aren't worried about loosing the last decimal of the accuracy you > can use my small FORTRAN program for CHARMM trajectories for the > formatting/unformatting at: > http://laaksonen.csc.fi/gopenmol/distribute/linux/charmmtrj.f > I mostly use the program to move the trajectories between different > types of machines. Of course, if you're actually using CHARMM, you can use the built-in FORMAT and UNFORMAT commands to move CHARMM trajectories across machines types (whether you call them .dcd or .trj files). It's a feature that's been available for well over a decade, since the differences in machine dependent floating point representations were even greater in the past. It allows the user some control over the precision, by changing some of the scaling and the Z format specs (Fortran zoned-hexadeciamal format). I should add that, besides big-endian and little-endian IEEE f.p. representations, there can be file structure differences between platforms as well. The Fortran standard does not define the structure of a binary file on disk, only the results of READ and WRITE operations; the details can be machine dependent. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable From wolfskil@MIT.EDU Thu Jan 8 14:13:45 1998 Received: from MIT.EDU for wolfskil@MIT.EDU by www.ccl.net (8.8.3/950822.1) id NAA29842; Thu, 8 Jan 1998 13:59:01 -0500 (EST) Received: from MIT.MIT.EDU by MIT.EDU with SMTP id AA27468; Thu, 8 Jan 98 13:59:04 EST Received: from FOOTNOTE.MIT.EDU by MIT.MIT.EDU (5.61/4.7) id AA25467; Thu, 8 Jan 98 13:59:00 EST Date: Thu, 8 Jan 98 13:59:00 EST X-Sender: wolfskil@po8.mit.edu Message-Id: To: chemistry@www.ccl.net From: wolfskil@MIT.EDU (Jud Wolfskill) Subject: New book on Fortran 95 available The following is a book which readers of this list might find of interest. For more information please visit http://mitpress.mit.edu/promotions/books/ADAFPF97 Fortran 95 Handbook: Complete ISO/ANSI Reference by Jeanne C. Adams, Walter S. Brainerd, Jeanne T. Martin, Brian T. Smith, and Jerrold L. Wagener The Fortran 95 Handbook is a comprehensive reference work for the Fortran programmer and implementor. It contains a complete description of the Fortran 95 programming language. February 1998 ISBN 0-262-51096-0 MIT Press * 5 Cambridge Center * Cambridge, MA 02142 * (617) 625-8569 From qoajnv@usc.es Thu Jan 8 15:13:45 1998 Received: from uscmail.usc.es for qoajnv@usc.es by www.ccl.net (8.8.3/950822.1) id OAA00324; Thu, 8 Jan 1998 14:30:02 -0500 (EST) Received: from localhost (qoajnv@localhost) by uscmail.usc.es (8.8.5/8.8.5) with SMTP id UAA26534 for ; Thu, 8 Jan 1998 20:29:03 +0100 (MET) Date: Thu, 8 Jan 1998 20:29:03 +0100 (MET) From: Armando Juan Navarro Vazquez To: CHEMISTRY@www.ccl.net Subject: question on irc Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I have tried to perform a irc calculation on a system with a very flat potential surface, but it could be only completed sucessfully on one side of the potential, but only one point is located in the other side (program considers is as a minimum). How can I calculate further points on this side of the potential?. Thanks in advance Armando Navarro Departamento de quimica Organica. Facultade de quimica. Universidade de Santiago de Compostela. e-mail:qoajnv@uscmail.usc.es From qoajnv@usc.es Thu Jan 8 15:24:53 1998 Received: from uscmail.usc.es for qoajnv@usc.es by www.ccl.net (8.8.3/950822.1) id PAA00563; Thu, 8 Jan 1998 15:03:28 -0500 (EST) Received: from localhost (qoajnv@localhost) by uscmail.usc.es (8.8.5/8.8.5) with SMTP id VAA29077 for ; Thu, 8 Jan 1998 21:03:04 +0100 (MET) Date: Thu, 8 Jan 1998 21:03:04 +0100 (MET) From: Armando Juan Navarro Vazquez To: chemistry@www.ccl.net Subject: A question on irc Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I have posted a question on irc calculations but I made a mistake. I post now the complete message. I have tried to perform a irc calculation on a system with a very flat potential surface, using the b3lyp functional in g94, but it could be only completed sucessfully on one side of the potential,however only one point is located in the other side (program considers is as a minimum). How can I calculate further points on this side of the potential?. Thanks in advance Armando Navarro Departamento de quimica Organica. Facultade de quimica. Universidade de Santiago de Compostela. e-mail:qoajnv@uscmail.usc.es From chem8@york.ac.uk Thu Jan 8 16:13:46 1998 Received: from pump2.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA00833; Thu, 8 Jan 1998 15:40:45 -0500 (EST) Received: from ebor.york.ac.uk (chem8@ebor.york.ac.uk [144.32.129.242]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id UAA19635 for ; Thu, 8 Jan 1998 20:40:32 GMT Date: Thu, 8 Jan 1998 20:40:29 +0000 (GMT) From: John Waite To: chemistry@www.ccl.net Subject: Pd(CO)n, n=1 to 4, samples wanted Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A Happy New Year to all CCLers. Does anyone out there know of either a commercial supplier or has (any) samples of Pd(CO)n, n=1 to 4? Myself and a collaborator are just completing some computations on these compounds and would like to run some spectra to confirm our findings. John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7229811-5 X 1-810 Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6503131 c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece From sabarker@nwlink.com Thu Jan 8 18:13:47 1998 Received: from alabama.nwlink.com for sabarker@nwlink.com by www.ccl.net (8.8.3/950822.1) id RAA01495; Thu, 8 Jan 1998 17:20:49 -0500 (EST) Received: from utah (sabarker@nwlink.com [199.242.23.2]) by alabama.nwlink.com (8.8.8/8.8.8) with SMTP id OAA11875 for ; Thu, 8 Jan 1998 14:20:49 -0800 (PST) Date: Thu, 8 Jan 1998 14:15:20 -0800 (PST) From: "Scott A. Barker" X-Sender: sabarker@utah To: chemistry@www.ccl.net Subject: I have two Multias that must go... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please reply OFF-LIST. This is a complete package and I must sell everything at once. I want $2000, or best offer, for EVERYTHING. This system has been used for about 6 months and operated (Win NT 4.0 Server :( ) problem free; shortly after their purchase I did replace one motherboard though. All components are new (~6mos). There is a great deal of value here, I simply need to purchase (or trade for?) a Win95 laptop computer. These are DEC Multias (aka UDB) complete with ram and internally mounted scsi hard drives. For great information on these systems, look at some of the links Starship has to offer: http://www.starshipcorp.com/onlinereference.html#links CPUs 2-DEC Multia with 64bit Alpha 166MHz processor RAM 6-16Mb 72pin Parity HDs (all SCSI) 1-2.3 Gb 3 =' internal to one 166MHz 1-1.2 Gb 3 =' internal to one 166MHz Keyboards 1-DEC extended with 10 key 1-Reveal extended with 10 key, speakers and microphone Misc 2-RedHat Linux (Alpha v4.0) Cd-ROM 1-RedHat Linux (Alpha v4.1) Cd-ROM Boxed with Manual 1-AB Data Transfer Switch (for 2 CPU's using 1 keyboard/monitor) 2-DEC 3-button Mouse 2-3.5' SCSI Internal HD/External SCSI-2 kit 2-External SCSI-2 kit (replaced by Internal kit, above) 1-SCSI2/SCSI Cable TOTAL COST $2000 Scott A. Barker pokeyd@nwlink.com