From chemistry-request@server.ccl.net Mon Mar 6 03:49:37 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA25222 for ; Mon, 6 Mar 2000 03:49:33 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Mon, 6 Mar 2000 08:46:13 +0100 Message-ID: <004701bf873f$ffc12280$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <10756.000303@mnc.md> Subject: Re: CCL:XRay -> Cartesian coordinates Date: Mon, 6 Mar 2000 08:45:52 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 There are several utilities to convert fractional coordinates to Cartesian ones. The input needs beyond the coordinates the crystal cell data alpha, beta, gamma, a, b, and c. You may want to use Mol2Mol or Babel for the conversion, both supports a few standard formats and user-made free format. Several true modeling softwares can also made the conversion. Tamas Gunda > | Dear chemistry, > I found XRay data in journal in following format. How could I > convert'em into cartesian coordinates? > > --- cut --- > Atomic coordinates (x10^4)... > Atom X/a Y/b Z/c Ueq > Ni 10000 2964(1) 3500 422(4) > >... and >Hi All, >I have also same question like Mike . >How to convert X-ray coordiantes to conventional >Cartesian coordinates or Internal coordiantes? >Sincerely, >Tapan Ghanty Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- From: Mike Peleah To: Sent: Friday, March 03, 2000 5:09 PM Subject: CCL:XRay -> Cartesian coordinates > +======================---------------- --- -- - - - - . > | Dear chemistry, > : > >. > > I found XRay data in journal in following format. How could I > convert'em into cartesian coordinates? > > --- cut --- > Atomic coordinates (x10^4)... > Atom X/a Y/b Z/c Ueq > Ni 10000 2964(1) 3500 422(4) > >... > --- cut --- > > Best regards, > Mike mailto:mike@mnc.md > . > : > | > >. - - - - -- --- ----------------======================+ > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Mar 6 10:32:56 2000 Received: from SEMOVM.SEMO.EDU (semovm.semo.edu [150.201.1.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA27806 for ; Mon, 6 Mar 2000 10:32:55 -0500 Received: from tony [150.201.19.145] by SEMOVM.SEMO.EDU (IBM VM SMTP Level 310) via TCP with SMTP ; Mon, 06 Mar 2000 08:24:01 CST Message-Id: <3.0.5.32.20000306082739.007f4330@semovm.semo.edu> X-Sender: ajduben@semovm.semo.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 06 Mar 2000 08:27:39 -0600 To: chemistry@ccl.net From: "Anthony J. Duben" Subject: Re: CCL:authorship In-Reply-To: <20000305121655.92981.qmail@hotmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 12:16 PM 3/5/00 GMT, C. Yang wrote: >Yesterday, I happen to have a dinner with some biology people. >Someone showed the first draft of her paper and I noticed for the >first time that there was an astrix on two authors with a footnote >saying equal contributors. Then there was an argument that mentioning >equal contributors is common in publishing papers. But I do not >remember seeing as equal contributiors in computational chemistry >papers. I tried to tell that it might be common in biology, but someone >vehemently disagreed with me and arguing that it is common in science and >nature as well, so it is common in all the areas. Is there someone to make >comment on this. Thanks. >Parthi > >PS: if two authors have equal contribution, will it be considered both >as primary authors and can the second author who is also an equal >contributor can write his name as first author of the paper in his CV. >______________________________________________________ > > > Sounds to me like the authors are working in fairly hostile environment for tenure and promotion. Anthony J. Duben (ajduben@semovm.semo.edu) ******************************************************** Anthony J. Duben Professor and Chairman Computer Science Dept., MS 5950 Southeast Missouri State University 1 University Plaza Cape Girardeau MO 63701-4799 phone: 573-651-2194 fax: 573-651-2791 e-mail: ajduben@semovm.semo.edu or c867buc@semovm.semo.edu "Education is not the filling of a pail but the lighting of a fire." -- William Butler Yeats From chemistry-request@server.ccl.net Mon Mar 6 11:51:02 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA28374 for ; Mon, 6 Mar 2000 11:51:02 -0500 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JMPKDTZB44002HPZ@trentu.ca> for chemistry@ccl.net; Mon, 6 Mar 2000 10:45:32 EST Date: Mon, 06 Mar 2000 10:49:18 -0500 From: elewars Subject: SEMIEMPIRICAL REVIEWS--SOME ADDITIONS To: chemistry@ccl.net Message-id: <38C3D37D.4400C0E2@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Mon 2000 March 6 Hello, here are 4 additions to my summary of semiempirical reviews; again, thanks very much. QUESTION If anyone knows of a *recent* (1995 or later) review of semiempirical> In case u r interested, methods, including or devoted to AM1 and PM3, I would appreciate receiving the reference. (I looked in the CCL archives first; no luck). Thanks very much ============ 4 more answers: #1 Qiang Cui I'd recommend the following review: > Perspectives on semi-empirical molecular orbital theory, W. Thiel, Adv. Chem. > Phys. Vol, XCIII, 1996. ======== #2 > Although regarded by many as unqualified to offer a review of AM1 > and PM3, by reason of presumed bias, I nevertheless feel that some > factual input on this topic would be useful. > > For a list of known faults, average errors in heats of formation, > geometries, etc. in MNDO, AM1, and PM3, please look in > > http://www.schrodinger.com/Mopac/html/node656.html > > or > > http://home.att.net/~mopacmanual/node656.html > > My objective in writing AM1 and PM3 was to reduce the error in > computed quantities, including hydrogen bonds. This was partly > successful in AM1 - the geometry of the water dimer was incorrect, > and partly successful in PM3 - the shape of the PES was incorrect. > > Jimmy Stewart > > ( @ @ ) > .-------------oOOo----(_)----oOOo-------------------------------------. > | James J. P. Stewart | | > | Stewart Computational Chemistry | E-mail: jstewart@fujitsu.com | > | 15210 Paddington Circle | WWW: http://home.att.net/~MrMOPAC | > | Colorado Springs CO 80921-2512 | | > | USA .ooo0 | Phone: USA +(719) 488-9416 | > | ( ) Oooo. | | > .--------------------\ (----( )-------------------------------------. > \_) ) / > (_/ ========= #3 David Gallagher In case anyone is interested, Jimmy Stewart, author of MOPAC, will be talking about the evolution of semi-empirical codes and the latest developments in MOPAC at the MOPAC User Group meeting at the ACS, Saturday 25th March 1.30pm, Argent Hotel, 50 Third Street, San Francisco. Details are available at http://www.schrodinger.com/Forms/mopac_ugm.html David Gallagher Fujitsu =========== #4 AM Hi! Saw your posting on CCL Hope this hepls. Artem Here is a ref: Hydrogen bonds: a comparison of semiempirical and ab initio treatments Dannenberg, J. J. THEOCHEM (1997), 401(3), 279-286 H-bonding interactions calcd. using the AM1, PM3 and SAM1 semiempirical MO methods are compared with the best available ab initio calcns. for several intermol. interactions of interest: AcOH dimers, H2O-C2H2, H2O-HCN, HCHO-C2H2, HCHO-HCN, O3-C2H2, O3-HCN, (MeCO)2CH2, melamine-cyanuric acid, and MeNO2-NH3. Exptl. values are also presented where available. The energetic comparisons are based upon enthalpies of interaction from the ab initio calcns. after counterpoise and vibrational corrections are applied. Overall, AM1 seems to do best, except for O-H.cntdot..cntdot..cntdot.O interactions, where none of the 3 methods excel. ============ From chemistry-request@server.ccl.net Mon Mar 6 14:11:05 2000 Received: from mserv3.dl.ac.uk (root@mserv3.dl.ac.uk [148.79.80.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29061 for ; Mon, 6 Mar 2000 14:11:04 -0500 Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by mserv3.dl.ac.uk (8.9.3/8.9.3/[ref postmaster@dl.ac.uk]) with ESMTP id SAA15175 for ; Mon, 6 Mar 2000 18:06:30 GMT Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv1.dl.ac.uk with ESMTP id SAA16063 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from h.j.j.vandam@dl.ac.uk); Mon, 6 Mar 2000 18:05:35 GMT Precedence: first-class Sender: H.J.J.VanDam@dl.ac.uk Message-ID: <38C3F08A.F16C3E7@dl.ac.uk> Date: Mon, 06 Mar 2000 17:53:14 +0000 From: Huub van Dam Organization: CCLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary Datamanagement Question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, Recently I asked the question below and I would like to summarize the one answer I got with many thanks to Ferenc Csizmadia. Best regards, Huub Question: ======= I have been asked to give a talk on scientific data management to bring forward the requirements of the chemical community. So I would like to invite any comments or references on topics like: - Datastorage: What data do we need to store, how much of it and for how long? - Interoperability: Different data formats and programs and to make everything (not) work together. - Visualisation: What and how to visualise (and what does it show)? - Analysis: Storing tons of data is one thing but how to extract meaningful information from all that? What kind of analysis do we want to do? - Any other aspect that comes to mind. Reply: ===== Dear Huub, We apply the following principles at ChemAxon: - the data management system should work in every OS - the all data should be stored in (one or more) SQL capable relational database(s) - the system should communicate with the database engine through a standard interface. - (if possible) the data should be displayed in HTML format, so the queries could be handled from browsers. These requirements can be satisfied using the Java programming language. The standard interface to the databases can be JDBC. HTML pages can be generated by JSP (Java Server Pages) scripts. We created JChem, a Java development tool for creating custom systems that handle chemical structures (http://www.jchem.com). Similar solutions can also be applied to other types of scientific data. -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ======================================================================== From chemistry-request@server.ccl.net Mon Mar 6 14:53:09 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29251 for ; Mon, 6 Mar 2000 14:53:08 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id NAA18973 for ; Mon, 6 Mar 2000 13:47:48 -0500 (EST) Message-ID: Date: 6 Mar 2000 13:59:46 -0500 From: "Boyd" Subject: Gordon Conference announcement! To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi CCLers, The Gordon Research Conference on Computational Chemistry will be held this year at Queen's College, Oxford, England, 2-7 July 2000. Attendance is limited, and the conference is always oversubscribed. Apply early. Presentation of a contributed poster paper counts heavily toward acceptance. Apply online at http://www.grc.uri.edu/ The Chair of this year's conference is Dr. Terry R. Stouch, Computer-Assisted Drug Design, Bristol-Myers Squibb Pharmaceutical Research Institute P.O. Box 5400, Princeton, NJ 08543-5400 USA Email Stouch@bms.com Tel: (609)818-5442 Fax: (609)252-6030 or (609)818-3560 The Vice-Chair is Dr. Bernard R. Brooks, Bldg 12A, Room 2041, NIH, Bethesda, MD 20892-5626, USA Tel. 301-496-0148 Office, 301-496-6889 Lab, Fax 301-496-2172 Email: brbrooks@helix.nih.gov Topics: Bioinformatics, Chemoinformatics, Computational Advances, Drug Design, Force Fields, Free Energy Simulations, Hardware and Systems, Mesoscale Modeling, Molecular Simulations, Quantum Chemistry, Quantum Mechanics/Molecular Mechanics, Solvation, Structural Biology Invited speakers and participants include: John A. Pople, Nobel Laureate, Northwestern University Walter Kohn, Nobel Laureate, University of California, Santa Barbara Martin Karplus, Harvard University Charles L. Brooks, The Scripps Research Institute Peter A. Kollman, University of California, San Francisco Peter Goodford, Oxford University, UK James J. P. Stewart, author of MOPAC and MOZYME Liem X. Dang, Pacific Northwest National Lab Dominic J. Tildesley, Unilever Research, UK Dennis J. Underwood, DuPont Pharmaceuticals Martyn Guest, Daresbury Laboratory, UK Michael K. Gilson, Center for Advanced Research in Biotechnology Ron Elber, Cornell University Thomas Halgren, Schroedinger, Inc. Ursula Rothlisberger, ETH Zentrum, Switzerland Herman Berendsen, University of Groningen Jeffrey Madura, Duquesne University Jiali Gao, University of Minnesota Julia Goodfellow, School of Crystallography, University of London Martin Head-Gordon, University of California, Berkeley Michael Levitt, Stanford University School of Medicine Nohad Gresh, Faculte de Pharmacie de Paris Wilfred F. van Gunsteren, ETH Zentrum, Switzerland For further information, see http://www.grc.uri.edu/programs/2000/compchem.htm Thanks and see you in Oxford, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis E-mail boyd@chem.iupui.edu