From kraha@medinst.ernet.in Wed Jan 28 08:09 EST 1998 Received: from vivek.doe.ernet.in for kraha@medinst.ernet.in by www.ccl.net (8.8.3/950822.1) id IAA14228; Wed, 28 Jan 1998 08:09:52 -0500 (EST) Received: from vikram.doe.ernet.in by vivek.doe.ernet.in (SMI-8.6/SMI-4.1-MHS-7.0) id SAA27936; Wed, 28 Jan 1998 18:41:29 -0500 Received: from medinst.UUCP by vikram.doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA13488; Wed, 28 Jan 98 18:48:00+050 From: MR KAUSHIK RAHA X-Mailer: SCO OpenServer Mail Release 5.0 To: chemistry@www.ccl.net Subject: Sequence Alignment matrix map. Date: Wed, 28 Jan 98 18:24:52 IST Message-Id: <9801281824.aa21894@medinst.medinst.ernet.in> Content-Type: text Content-Length: 607 Status: RO Hello everyone, I am looking for a sequence alignment matrix map generating program for Windows 95 or Irix (running on a Silicon Graphics Indigo 2) on the public domain. It should read in two protein sequences and generate a matrix map which shows the homology between the two. It will spare me some coding. Thank you. Kaushik Raha. ---------------------------------------------------------------------- KAUSHIK RAHA M.Biotechnology AIIMS New Delhi 110029. INDIA. e-mail : kraha@medinst.ernet.in kaushik@aiime.ernet.in ----------------------------------------------------------------------- From hartmann@ccc.uni-erlangen.de Wed Jan 28 11:08:20 1998 Received: from faui45.informatik.uni-erlangen.de for hartmann@ccc.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id KAA14984; Wed, 28 Jan 1998 10:58:54 -0500 (EST) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by faui45.informatik.uni-erlangen.de (8.8.8/8.1.16-FAU) with ESMTP id QAA23413 for ; Wed, 28 Jan 1998 16:58:51 +0100 (MET) Received: from ccc.uni-erlangen.de (picard.organik.uni-erlangen.de [131.188.128.100]) by derioc1.organik.uni-erlangen.de (8.8.7/8.1.30-FAU) with ESMTP id QAA03567 for ; Wed, 28 Jan 1998 16:58:49 +0100 (GMT-1:00) Message-ID: <34CF54E4.D7C8B39D@ccc.uni-erlangen.de> Date: Wed, 28 Jan 1998 16:55:16 +0100 From: Michael Hartmann Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: DFT_on_PCs_Summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit My original question was: > > Dear Netters, > > does anybody know something about ab-initio and/or > DFT programs running on WinNT/Win95 - PCs. > > I will post a list of all replies. I want to thank all of you who gave me a reply... Micha and now the answers: ------------------------ TURBOMOLE (with various DFT schemes: S-VWN, B-VWN, B-LYP, B3-LYP, etc. ) is running under LINUX on PCs. Ask people at BASF (Horst Weiss) or at Karlsruhe or visit the TURBOMOLE home page. -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com ------------------------- Sure ! GoTO : http://www.theochem.uni-hannover.de/AllChem We are working on the current release 0.11. The WindosNT/Win95 (32 Bit) Version will be released soon after, but I highly recommand to use Linux as operating system, because of much better memory performance and file handling. In the current release 0.11 we have : variational coulomb integral expansion, adaptive numerical integration of the xc energy and potential, the Minmax SCF procedure for Hartree calculations, full geometry optimization (Z-Matrix and cartesian), frequency analysis, property package (see visualization with VU). Best regards, Bernd ------------------------------------------------------------------------------- ___ EMail: berni@theochem.uni-hannover.de / / _______ / /_/ ____/ REAL : Dipl. Chem. Bernd Zimmermann \___ __/ Theoretische Chemie, Universtit"at Hannover ==== \_/ ====== Am Kleinen Felde 30 LOGOUT FASCISM! D-30167 Hannover, Germany WWW : http://www.theochem.uni-hannover.de/ Phone: (int. acc.)+511+762-5448 ------------------------------------------------------------------------------- Hallo, ich glaube mit NT siehts nicht ganz so gut aus obwohl: fuer ab initio gibt es Gamess/NT (kostenlos, nur ab initio & MP2) Gaussian-94W (ab initio, MP2-n, DFT, $750) PC-Spartan-Plus (ab initio, nur Organik, langsam) Hyperchem (ab initio, geruechteweise sehr langsam) zusaetzlich meines Wissens demnaechst Crays/Oxford Moleculars Unichem (habe ich schon als Demo gesehen) Fuer Linux gibt es obengenannte Programme sowie Turbomole (DFT, ab initio, MP2, 1200 DM, sehr schneller Code) DEFT (DFT-code von St. Amand, kostenlos - bin mir nur nicht ganz sicher ob das auch unter Linux laeuft) Jaguar-3.0 (Schroedinger Inc., $1200) Qchem (angekuendigt) welches ich im wesentlichen benutze. Letzteres soll es irgendwann auch mal als NT Version geben. Viele Gruesse Peter --------------------------------- Dr. Peter Burger Anorg.-Chem. Institut Uni Zuerich Winterthurerstr. 190 8057 Zuerich chburger@aci.unizh.ch ---------------------------------- I am sure you know about Gaussian 94 for Windows 95/NT. If not, just look at their home page, http://www.gaussian.com. Hope this helps. Oscar ......................................................................... Prof. Dr. Oscar N. Ventura Head, MTC-Lab, Avda. Gral. Flores 2124, P.O.Box 1157, 11800 Montevideo, Uruguay Tel:+598-2-9248396 Fax:+598-2-9241906 E-Mail:oscar@bilbo.edu.uy Web:http://bilbo.edu.uy/MTC-Labs/ TMMeC:http://bilbo.edu.uy/tmmec/ ......................................................................... ---------------------------------- Hi, Michael! You have group of programs running on Windows, the most popular is Gaussian, Hyperchem, Spartan, ... ---------------------------------- Gaussian 94W does both ab initio and DFT calculations under Windows 95 and NT 4.0. More details on the G94W package are available on our web site www.gaussian.com. Douglas J. Fox Director of Technical Support help@gaussian.com ------------------------- If you have a source license, Gaussian compiles on Linux using f2c/gcc. It does not compile using g77 or eg77 (which would be faster) due to some very ugly and invalid equivalences done in some of the utility functions. ( I gave up when I say a routine with ~100 arguments, some of which had been unsafely equivalenced. ) I have a patch file to convert the source tree into a Debian/hamm package for installation on our PC's, but can't distribute the .debs due to the commercial nature of Gaussian. Some versions of the C libraries were incompatible with the Gaussian code. Earlier Libc5's and the current libc6 work though - later libc5's had an incompatibility. Specifying alignment flags might also boost it's performance, but I haven't experimented there (it's difficult enough to compile Gaussian without playing with optional flags). WinNT/win95 ... if you can't get precompiled binaries, you could do it yourself from your source code. Some fortran compilers will object to the gaussian code- so you may need to try multiple compilers or use f2c/wingcc to get it to work. If it were me, I'd just put Linux on a small extra disk and set up the machine to dual boot, since you won't be able to use Word while gaussian is running anyway. By specifying an upper memory limit in either the job file or the site configuration file, you can leave Linux enough memory to continue using the machine interactively. -Drake -- Dr. Drake Diedrich, Research Officer - Computing, (02)6279-8302 John Curtin School of Medical Research, Australian National University 0200 Replies to other than Drake.Diedrich@anu.edu.au will be routed off-planet --------------------------- Hallo! Warum installierst Du nicht ein Betriebssystem (z.B. Linux), dann kannst Du ALLES (z.B. Gaussian, oder, wenn es beliebt, DFT wie deMon, ADF etc.) benutzen. Thomas ch glaube, es gibt eine Spartan-Version, wo soetwas drin ist. Zumindestens HF-MP2. Ich kenne die Windows nicht, aber wenn Du einen vernuenftigen Fortran-Compiler hast, koenntest Du damit auch deMon (oder das 'neue' Cache) installieren. Kostet beides 1000 Dollar, wenn ich nicht irre, koennte ich mich sogar drum kuemmern, ich kenne beide Gruppen. Ciao Thomas -------------------------- Dear Sir, In first of all, I'd like know if you can run ab-intio or DFT programs on UNIX or LINUX. On the other hand, Do you have a group in DFT or no?, if the answer is yes, What's the main purpose of your DFT's group?. I realize you this questions because we want contact with some grups in DFT. Regards. MANUEL. Dear Michael: With respect to question about packages in DFT available for PCs, my first suggestion is a comertial package of D.R. Salahub. His address is: Departement de chimie, Universite de Montreal, C.P. 6210, Succ. A, Montreal, Quebec H3C 3V1, Canada. I don't know his e-mail but if you need it, please send me a e-mail and i'd find out it. Regards. Manuel Pereiro. ---------------------------- From chipot@host7.lctn.u-nancy.fr Wed Jan 28 11:08:38 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 KAA14806; Wed, 28 Jan 1998 10:29:48 -0500 (EST) From: Received: (from chipot@localhost) by host7.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id QAA02594 for chemistry@www.ccl.net; Wed, 28 Jan 1998 16:17:12 +0100 (NFT) Message-Id: <199801281517.QAA02594@host7.lctn.u-nancy.fr> Subject: 98.04.20 Comp.Chem & Living World -- Chambery Meeting To: chemistry@www.ccl.net Date: Wed, 28 Jan 1998 16:17:12 +0100 (NFT) *** [Modified by Jan Labanowski -- jkl@ccl.net *** Registration forms and detailed information available *** in CCL Conference List: *** http://www.ccl.net/cca/info/conferencelist.html *** under 98.04.20 *** ] 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 AS SOON AS POSSIBLE. _______________________________________________________________________ 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. [JKL -- Additional information in CCL archives in Conferences section: http://www.ccl.net/cca/info/conferencelist.html REGISTRATION AND WHEREABOUTS, ETC. http://www.ccl.net/cca/info/conferencelist/mess0205.html ] _______________________________________________________________________ Chris Chipot Laboratoire de Chimie Theorique Phone: (33) 3-83-91-25-96 U.M.R. C.N.R.S. No 7565 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 laaksone@csc.fi Thu Jan 29 04:11:47 1998 Received: from pobox.csc.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id DAA19242; Thu, 29 Jan 1998 03:42:13 -0500 (EST) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with SMTP id KAA15678 for ; Thu, 29 Jan 1998 10:42:01 +0200 (EET) Date: Thu, 29 Jan 1998 10:42:06 +0200 (GFT Standard Time) From: Leif Laaksonen To: chemistry@www.ccl.net Subject: Version 1.1 of gOpenMol available Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, Version 1.1 of the gOpenMol program is now available for Intel Windows 95/NT (I don't have any Alpha with Windows NT available). URL: http://laaksonen.csc.fi/gopenmol/ Lots of bugs have been corrected and some new features have been added. * Possibility to display AutoDock trajectories * Mapping of grid data info on the isocontour surface * Possible to read atom partial charges from MOPAC and GAUSSIAN output files. * Possibility to use either orthogonal or perspective projection. Please have a look at the Gallery at: http://laaksonen.csc.fi/gopenmol/gallery/ I will make Unix versions available as soon as I have time... Please observe that gOpenMol is NOT in the public domain. I will retain the Copyright to gOpenMol but I provide the possibility to use the program to anybody interested in using it free of charge. 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 --------- From Dominik.Horinek@chemie.uni-regensburg.de Thu Jan 29 05:08:35 1998 Received: from rrzs2.rz.uni-regensburg.de for Dominik.Horinek@chemie.uni-regensburg.de by www.ccl.net (8.8.3/950822.1) id EAA19648; Thu, 29 Jan 1998 04:21:53 -0500 (EST) Received: from rchsg38.chemie.uni-regensburg.de (rchsg38.chemie.uni-regensburg.de [132.199.48.138]) by rrzs2.rz.uni-regensburg.de (8.8.8/8.8.8) with SMTP id KAA29431; Thu, 29 Jan 1998 10:21:03 +0100 (MET) Received: from rchsg38 by rchsg38.chemie.uni-regensburg.de via SMTP (940816.SGI.8.6.9/URRZ-Sub-1.5-irix5) (for ) id JAA07407; Thu, 29 Jan 1998 09:18:57 GMT Sender: hod01123@chemie.uni-regensburg.de Message-ID: <34D04981.FF6@chemie.uni-regensburg.de> Date: Thu, 29 Jan 1998 10:18:57 +0100 From: Dominik Horinek Organization: Universitaet Regensburg X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: sum:G94 Mp2 problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Two days ago I reported a MP2 problem under Gaussian94. Jobs crashed with the error message 'PickT4: no shell combinations can fit!'. Thanks for the replies from: Carlos P. Sosa Michael A McAllister Frank Jensen Craig Wilson Jochen Buehler Giovanni Scalmani It is a memory problem. It can be solved by increasing %Mem, MaxDisk and specifying MP2=Direct. Greetings, Dominik -- ------------------------------------------------------------------ Dominik Horinek Institut fuer physikalische und theoretische Chemie Universitaet Regensburg Universitaetsstr. 31, 93053 Regensburg, Deutschland email: Dominik.Horinek@chemie.uni-regensburg.de ------------------------------------------------------------------ From vero@malabar.cad.cea.fr Thu Jan 29 06:08:29 1998 Received: from nenuphar.saclay.cea.fr for vero@malabar.cad.cea.fr by www.ccl.net (8.8.3/950822.1) id FAA19926; Thu, 29 Jan 1998 05:44:14 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.8.8/CEAnet-relay-4.0.3) with ESMTP id LAA01210 for ; Thu, 29 Jan 1998 11:43:07 +0100 (MET) Received: from malabar.cad.cea.fr (malabar.cad.cea.fr [132.169.56.128]) by muguet.saclay.cea.fr (8.8.8/CEAnet-relay-4.0.3) with SMTP id LAA26495 ; Thu, 29 Jan 1998 11:39:57 +0100 (MET) Received: by malabar.cad.cea.fr (950413.SGI.8.6.12/SGI+CEANET.2.0.1) (for ) id KAA23812; Thu, 29 Jan 1998 10:38:28 GMT From: "Veronique Lamare" Message-Id: <9801291138.ZM23810@malabar.cad.cea.fr> Date: Thu, 29 Jan 1998 11:38:27 +0100 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: AM1 parameters for Cs Cc: jer@malabar.cad.cea.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters Does anyone have AM1 parameters for Cs+ ion? Thanks a lot to answer. -- Veronique LAMARE CEA email vero@malabar.cad.cea.fr From lanig@organik.uni-erlangen.de Thu Jan 29 09:08:32 1998 Received: from faui45.informatik.uni-erlangen.de for lanig@organik.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id IAA20509; Thu, 29 Jan 1998 08:53:37 -0500 (EST) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by faui45.informatik.uni-erlangen.de (8.8.8/8.1.16-FAU) with ESMTP id OAA24514 for ; Thu, 29 Jan 1998 14:53:33 +0100 (MET) Received: from indigo11 (indigo11.organik.uni-erlangen.de [131.188.128.69]) by derioc1.organik.uni-erlangen.de (8.8.7/8.1.30-FAU) with SMTP id OAA08876 for ; Thu, 29 Jan 1998 14:53:31 +0100 (GMT-1:00) Sender: lanig@organik.uni-erlangen.de Message-ID: <34D089E7.167E@organik.uni-erlangen.de> Date: Thu, 29 Jan 1998 14:53:43 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum Uni Erlangen/Nbg. X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Zeolite coordinates Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear readers, within a project calculating the adsorption energy of small organic molecules in zeolites, I need cartesian coordinates of a few zeolites in various dimensions (to check the size dependence of the model). Can somebody point me e.g. to a database of unit cells for zeolites and useful software to convert such a cell into cartesian coordinates? I searched already the CCDB and the Web with no luck. Any help is higly appreciated! Regards H Lanig -- --------------------------------------------------------------------- Dr. Harald Lanig Computer Chemie Centrum der Universitaet Erlangen/Nuernberg Institut fuer Organische Chemie I Naegelsbachstr. 25 D-91052 Erlangen, Germany Phone +49(0)9131-85 6581 Fax -85 6565 mailto:lanig@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/lanig --------------------------------------------------------------------- From xyn@ornl.gov Thu Jan 29 13:08:34 1998 Received: from aspen.lsd.ornl.gov for xyn@ornl.gov by www.ccl.net (8.8.3/950822.1) id MAA21649; Thu, 29 Jan 1998 12:09:46 -0500 (EST) From: Received: (qmail 16396 invoked by uid 29178); 29 Jan 1998 17:04:36 -0000 Date: 29 Jan 1998 17:04:36 -0000 Message-ID: <19980129170436.16395.qmail@aspen.lsd.ornl.gov> To: chemistry@www.ccl.net Subject: Special Issue on computational molecular biology CALL FOR PAPERS =============== Journal of Combinatorial Optimization Special Issue on Computational Molecular Biology Guest Editors: Ying Xu, Satoru Miyano, Tom Head. Submission Deadline: August 15, 1998. The past ten years have witnessed the rapid development of a new discipline, computational molecular biology. Combinatorial optimization and algorithms have played a significant role in advancing this new discipline. The partnership between mathematics, in particular combinatorial optimization and algorithms, and molecular biology has greatly enriched both fields, leading to new ways of thinking and greater challenges to meet. The scope of this Special Issue includes all aspects of combinatorial optimization and algorithms in computational molecular biology. Original papers are solicited that describe research on combinatorial methods for problems arising from the following areas (nonexhaustive) of molecular biology: -- DNA sequencing -- DNA mapping -- recognition of genes and regulatory elements -- RNA/protein structure prediction -- molecular evolution -- combinatorial libraries and drug design -- bio-sequence analysis and comparison -- computing with biomolecules. Six hard copies of each submitted manuscript should be sent to one of the guest editors by August 15, 1998. Manuscripts must be prepared according to the normal submission requirements of the Journal of Combinatorial Optimization (see ). Each manuscript will be refereed by at least three anonymous reviewers. Notification of acceptance will be sent to the authors before November 30, 1998. The Special Issue is expected to be published by mid-1999. Addresses of the guest editors: Ying Xu Computational Biosciences Section Building 1060 COM Oak Ridge National Laboratory Oak Ridge, TN 37831-6480, USA Tel: 423-574-3783 Fax: 423-241-1965 Email: xyn@ornl.gov Web: Satoru Miyano Human Genome Center Institute of Medical Science University of Tokyo Shirokanedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan. Tel.: +81-3-5449-5615 Fax: +81-3-5449-5442 Email: miyano@ims.u-tokyo.ac.jp Tom Head Department of Mathematics Binghamton University Binghamton, NY 13902-6000, USA Tel: 607-777-2278 Email: tom@math.binghamton.edu Web: From bruno@antas.agraria.uniss.it Thu Jan 29 15:08:36 1998 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id OAA22111; Thu, 29 Jan 1998 14:22:07 -0500 (EST) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA035411521; Thu, 29 Jan 1998 20:18:41 +0100 Date: Thu, 29 Jan 1998 20:18:35 +0100 (NFT) From: "Dr. Bruno Manunza" To: Harald Lanig Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Zeolite coordinates In-Reply-To: <34D089E7.167E@organik.uni-erlangen.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 29 Jan 1998, Harald Lanig wrote: > Dear readers, > > within a project calculating the adsorption energy of small organic > molecules in zeolites, I need cartesian coordinates of a few zeolites > in various dimensions (to check the size dependence of the model). > Can somebody point me e.g. to a database of unit cells for zeolites > and useful software to convert such a cell into cartesian coordinates? > I searched already the CCDB and the Web with no luck. > > Any help is higly appreciated! > > > Regards > H Lanig > Dear Harald, you may check the 'zeolite web' at http://trigger.ch.umist.ac.uk:8081/zeolites/web/intro.htm it has a database of structures which may be helpful to you. Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it