From chemistry-request@ccl.net Mon Dec 29 04:35:05 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBT9YXTC023155 for ; Mon, 29 Dec 2003 04:34:34 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id hBT9YUCI062588 for ; Mon, 29 Dec 2003 10:34:30 +0100 (CET) X-Ids: 167 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id hBT9YUEv019788; Mon, 29 Dec 2003 10:34:30 +0100 (MET) Date: Mon, 29 Dec 2003 10:34:30 +0100 (MET) From: Michel Petitjean Message-Id: <200312290934.hBT9YUEv019788.-at-.ds10.itodys.jussieu.fr> To: chemistry.-at-.ccl.net Subject: CCL: Re: calculate chi angle, surface area X-Miltered: at shiva.jussieu.fr by Joe's j-chkmail ("http://j-chkmail.ensmp.fr")! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.4 required=7.0 tests=MAILTO_TO_SPAM_ADDR version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) To: chemistry.-at-.ccl.net Subj: CCL: Re: calculate chi angle, surface area For surface area, download the ASV freeware from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html (includes ref. and documentation). For torsional angles, usual 3D geometry formulas are easy to program in fortran or C. Michel Petitjean, Email: petitjean.-at-.itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean.-at-.ccr.jussieu.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html ................................................................ From: Sivanesan Dakshanamurthy Message-ID: <187835185658.185658187835.-at-.imap.georgetown.edu> Date: Fri, 26 Dec 2003 21:31:19 -0500 Dear All: I looking for a program to calculate the following: surface area of a protein, 'chi' angle of a given sidechain, to generate 3D graph of a given data apart from excel. Could anybody help me out, thanks in advance, sincerely, sivanesan D.Sivanesan, Ph.D. Dept. of Oncology, Lombardi Cancer Center (NCI Comprehensive Cancer Center), Georgetown University, DC 20057 Phone: 202-687-6338 From chemistry-request@ccl.net Mon Dec 29 11:28:00 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBTGRSTC000947 for ; Mon, 29 Dec 2003 11:27:29 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Mon, 29 Dec 2003 14:29:27 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF36B11B~at~correio.cetem.gov.br> From: Ian Hovell To: "'chemistry~at~ccl.net'" Subject: ccl:the intergral over heat capacities Date: Mon, 29 Dec 2003 14:29:26 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello CCLers, I have been looking at this problem for some time. I think I am too close to the problem to see the answer. I would therefore like some help please. Let me quote from a paper "The C-H Bond Energy of Benzene" J.Am. Chem. Soc. vol 117, No.9, 1995 page 2595 ..... The heat of formation for c6h6 at zero K can be estimated if one knows the heat capacities of benzene, C atom, and H2. Delta f H298(C6H6) = Delta f H0(C6H6) + intergral between 0 and 298 dT[ Cp(C6H6) - 6Cp(C) - 3Cp(h2)] In the equation above the intergral over the heat capacities is evaluated as [+3.407 - 7.578] = -4.2 kcal mol-1. end of quote I have been trying to work out how the writers (Davico, Bierbaum, Depuy, Ellison and Squires) used this equation to arrive at the value for the intergal over the heat capacities as - 4.2 kcal mol-1. Any help would be extremely welcome. Thanks and am sorry as this seems to be a simple task though a can not see the wood for the trees. Ian From chemistry-request@ccl.net Mon Dec 29 11:35:13 2003 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBTGYgTC001144 for ; Mon, 29 Dec 2003 11:34:42 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id hBTGY7EW009557; Mon, 29 Dec 2003 11:34:08 -0500 Date: Mon, 29 Dec 2003 11:34:07 -0500 (EST) From: Jan Labanowski To: chemistry~at~ccl.net cc: Jan Labanowski , orlov~at~bionet.nsc.ru Subject: Bioinformatics Conf BGRS'2004, July 25-30, 2004, Novosibirsk-Russia Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=0.4 required=7.0 tests=MAILTO_TO_SPAM_ADDR,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ---------- Forwarded message ---------- Date: Mon, 29 Dec 2003 16:50:00 +0600 From: Orlov Y.L. To: jkl~at~ccl.net Subject: Conference BGRS'2004 The Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004) CALL FOR PARTICIPATION Dear Colleagues: Program and Organizing Committees have honor to announce the traditional biennial event-The Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004)-to be held on July 25-30, 2004, in Akademgorodok, Novosibirsk, Russia. Do put it in your diaries, please! BGRS'2004 is a multidisciplinary conference, and we are pleased to invite scientists with an interest in bioinformatics, mathematical, theoretical, or computational biology to attend the meeting. Its scope includes development and application of advanced methods of computational and theoretical analysis to structure-function genome organization, proteomics, and evolutionary and system biology. The event addresses the latest research in these fields, and will be a great opportunity for attendees to showcase their works. BGRS'2004 provides a general forum for disseminating and facilitating the latest developments in bioinformatics in molecular biology, and we also invite scientists participating in experimental research and using theoretical and/or computational methods in their practice and/or researchers supported by INTAS grants to come. We will be delighted to see industry representatives from biotechnology and pharmaceutical companies as BGRS'2004 conferees, too. BGRS'2004 topics of interest include: COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS Large-scale genome analysis and comparison; genome functional annotation, gene finding and prediction; genome knowledge bases and ontologies; mobile genetic elements and repeated DNA sequences, DNA nucleosomal organization. Regulatory genomic sequences: databases and knowledge bases, computer analysis, modeling and simulation, comparative genomics of regulatory regions; gene expression (models of transcription, splicing, and translation control); COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS RNA structure-function organization (analysis and prediction); protein structure and function analysis, modeling, and prediction; classification of folds and structural motifs in proteins; functional sites and active centers in 3D protein structure (recognition and modeling of function); large-scale analysis of proteomes and protein-protein interactions; COMPUTATIONAL SYSTEM BIOLOGY Gene networks, regulatory networks, signal transduction pathways, metabolic pathways, gene expression pathways (databases and knowledge bases, computer analysis, modeling, and simulation); In silico reconstruction of gene networks by computational analysis of microarray data; description and modeling of intracellular dynamics; intercellular communication modeling; virtual cell; networks and development; systems biology and biotechnology, epigenetics; COMPUTATIONAL EVOLUTIONARY BIOLOGY Genetic variation (SNPs, haplotypes, etc.); large scale genome rearrangements; genome polymorphism; molecular evolution, regulatory systems and metabolic pathways; comparative genomics; evolution of protein structure and function; phylogenetic trees reconstruction; horizontal transmission of genetic information; METHODS TO ANALYZE AND SIMULATE BIOMOLECULAR SYSTEMS AND PROCESSES Integrating genetic, functional, and molecular pathways with genetic networks from complex genetic trait analysis; interactive links between bioinformatics and experimental research on functional genomics (gene expression array analysis and other new technologies and methods); data warehousing, knowledge discovery, data mining, and machine learning in genomics and proteomics; superlarge computer systems in molecular biology and molecular genetics, high performance computing in functional and structural genomics and proteomics; data management methods and systems; database integration; data visualization; string and graph algorithms; stochastic modeling; BIOINFORMATICS AND EDUCATION As at previous conferences, the BGRS'2004 program will be composed of plenary lectures, oral reports, specialized poster sessions, computer demonstrations, software demonstrations, round table discussions, and tutorials. International Program Committee is co-chaired by Nikolay Kolchanov (Institute of Cytology and Genetics, Novosibirsk, Russia) and Ralf Hofestaedt (University of Bielefeld, Germany). Local Organizing Committee is chaired by Dagmara Furman (Institute of Cytology and Genetics, Novosibirsk, Russia). DEADLINES March 30, 2004: Four-page abstracts due May 01, 2004: Acceptance/rejection notifications sent out and the abstracts are included into the program June 15, 2004: Registration of participants at the site of the Conference To get detailed and up-to-date information, visit please our website at http://www.bionet.nsc.ru/meeting/bgrs2004/ or you can also send email to the conference coordinator bgrs2004~at~bionet.nsc.ru ============================================================================ From chemistry-request@ccl.net Sat Dec 27 12:06:23 2003 Received: from web42002.mail.yahoo.com (web42002.mail.yahoo.com [66.218.93.170]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hBRH5qTC001343 for ; Sat, 27 Dec 2003 12:05:52 -0500 Message-ID: <20031227170552.74836.qmail-.at.-web42002.mail.yahoo.com> Received: from [202.141.24.2] by web42002.mail.yahoo.com via HTTP; Sat, 27 Dec 2003 09:05:52 PST Date: Sat, 27 Dec 2003 09:05:52 -0800 (PST) From: Kaliappan Muthukumar Subject: Contour maps To: chemistry-.at.-ccl.net Cc: muthukumar2k3-.at.-yahoo.com MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1719111176-1072544752=:74610" X-Spam-Status: No, hits=1.3 required=7.0 tests=HTML_20_30,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --0-1719111176-1072544752=:74610 Content-Type: text/plain; charset=us-ascii Dear all, I am dealing with metal porphyrin complexes. I am in need of contour maps for the orbitals calculated by gaussian-98 in order to view the electron density arond each atom present in the complex. Could anyone suggest me how to get it and what are the softwares available to get it. preferably free software. I have gopenmol and Molden, But I dont know the procedure how to get the contour maps from it. Any pointers or reprints suggested will be greatefully acknowledged and I will summarize all at the end. I wish you all Happy New Year - 2004 Thank you, With regards, M.k., --------------------------------- Do you Yahoo!? Yahoo! Photos - Get your photo on the big screen in Times Square --0-1719111176-1072544752=:74610 Content-Type: text/html; charset=us-ascii
Dear all,
 
I am dealing with  metal porphyrin complexes. I am in need of contour maps for the orbitals calculated by gaussian-98 in order to view the electron density arond each atom present in the complex.
 
Could anyone suggest me how to get it and what are the softwares available to get it. preferably free software.
 
I have gopenmol and Molden, But I dont know the procedure how to get the contour maps from it. 
 
Any pointers or reprints suggested will be greatefully acknowledged and I will summarize all at the end.  
 
I wish you all  Happy New Year - 2004
 
Thank you,
With regards,
M.k.,

Do you Yahoo!?
Yahoo! Photos - Get your photo on the big screen in Times Square --0-1719111176-1072544752=:74610-- From chemistry-request@ccl.net Mon Dec 29 10:05:30 2003 Received: from wrzx35.rz.uni-wuerzburg.de (wrzx35.rz.uni-wuerzburg.de [132.187.3.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBTF4xTC031578 for ; Mon, 29 Dec 2003 10:04:59 -0500 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx35.rz.uni-wuerzburg.de (Postfix) with ESMTP id 84C22A5FEF for ; Mon, 29 Dec 2003 16:04:56 +0100 (CET) Received: from virusscan (localhost [127.0.0.1]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id 39B351D409 for ; Mon, 29 Dec 2003 16:04:56 +0100 (CET) Received: from wrzx28.rz.uni-wuerzburg.de (wrzx28.rz.uni-wuerzburg.de [132.187.3.28]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id 1ACCB18EB3 for ; Mon, 29 Dec 2003 16:04:56 +0100 (CET) Received: from WAC1136 (wac1136.chemie.uni-wuerzburg.de [132.187.69.136]) by mailmaster.uni-wuerzburg.de (Postfix) with ESMTP id BCF0693DB3 for ; Mon, 29 Dec 2003 16:04:55 +0100 (CET) From: dominik.auer|at|mail.uni-wuerzburg.de To: chemistry|at|ccl.net Date: Mon, 29 Dec 2003 16:06:45 +0100 MIME-Version: 1.0 Subject: Compilation Problems with NBO 5.0 Message-ID: <3FF05115.3950.103C61B@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.12a) Content-type: text/plain; charset=ISO-8859-1 Content-description: Mail message body X-Virus-Scanned: by amavisd-new (Rechenzentrum Universitaet Wuerzburg) X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id hBTF5UTC031601 Dear All, during the last couple of day I am trying to compile NBO 5.0 for Gaussian 98 by creating a new link l607.exe. My problem is that, the compilation breaks with an error message I can not resolve. Has anybody an idea that helps me. Here is part of the building log file: pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:524288 -o l607.exe ml607.o l607.a util.so util.so: the use of `tmpnam' is dangerous, better use `mkstemp' l607.a(ncsmat.o): In function `ncsmat_': ncsmat.o(.text+0x109): undefined reference to `gauerr_' l607.a(nbhalt.o): In function `nbhalt_': nbhalt.o(.text+0x9b): undefined reference to `gauerr_' util.so: undefined reference to `gdate_' util.so: undefined reference to `nudffx_' util.so: undefined reference to `gbgixm_' util.so: undefined reference to `ntrclo_' util.so: undefined reference to `numer_' util.so: undefined reference to `ntrrd_' util.so: undefined reference to `ntrpos_' util.so: undefined reference to `numerc_' util.so: undefined reference to `gbtrn0_' util.so: undefined reference to `ntrasy_' util.so: undefined reference to `ntrio_' util.so: undefined reference to `ntrext_' util.so: undefined reference to `gbcmog_' util.so: undefined reference to `gbtrnx_' util.so: undefined reference to `ntropn_' util.so: undefined reference to `nucdip_' util.so: undefined reference to `nwform_' util.so: undefined reference to `ntrwat_' util.so: undefined reference to `gcfact_' util.so: undefined reference to `ntstat_' util.so: undefined reference to `nucmom_' util.so: undefined reference to `numin3_' util.so: undefined reference to `ntrrew_' util.so: undefined reference to `ntrerr_' util.so: undefined reference to `gdimer_' util.so: undefined reference to `gbgixx_' util.so: undefined reference to `ntrwrt_' util.so: undefined reference to `gdiis_' util.so: undefined reference to `gbtrn4_' util.so: undefined reference to `ntrprt_' util.so: undefined reference to `gcos_' util.so: undefined reference to `gcona_' make: *** [l607.exe] Error 1 endif Thank you in advance. Merry X-Mas Dominik ---------------------------------------------------------- +++++++++++++++ Dipl. - Chem. Dominik Auer +++++++++++++++ +++ Inst. f. Anorganische Chemie, Universitdt W|rzburg +++ ++++++++++ Am Hubland, 97074 W|rzburg, Germany +++++++++++ +++++++ e-Mail: dominik.auer|at|mail.uni-wuerzburg.de +++++++ ---------------------------------------------------------- From chemistry-request@ccl.net Mon Dec 29 07:58:28 2003 Received: from mail3.cc.huji.ac.il (real-outmail.cc.huji.ac.il [132.64.1.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBTCvuTC028517 for ; Mon, 29 Dec 2003 07:57:57 -0500 Received: by mail3.cc.huji.ac.il (Postfix, from userid 31998) id A309068205; Mon, 29 Dec 2003 14:57:55 +0200 (IST) Received: from webmail.cc.huji.ac.il (webmail.cc.huji.ac.il [132.64.1.3]) by mail3.cc.huji.ac.il (Postfix) with ESMTP id 6EBA0681A0 for ; Mon, 29 Dec 2003 14:57:55 +0200 (IST) Received: (from nobody@localhost) by webmail.cc.huji.ac.il (8.11.6/8.11.6) id hBTCvtX25400 for CHEMISTRY*at*ccl.net; Mon, 29 Dec 2003 14:57:55 +0200 Received: from angeles-4.ch.huji.ac.il (angeles-4.ch.huji.ac.il [132.64.90.90]) by webmail.huji.ac.il (IMP) with HTTP for ; Mon, 29 Dec 2003 14:57:55 +0200 X-Authentication-Warning: webmail.cc.huji.ac.il: nobody set sender to avitals*at*chem.ch.huji.ac.il using -f Message-ID: <1072702675.3ff024d3c262d*at*webmail.huji.ac.il> Date: Mon, 29 Dec 2003 14:57:55 +0200 From: avitals*at*chem.ch.huji.ac.il To: CHEMISTRY*at*ccl.net Subject: localized orbitals MIME-Version: 1.0 Content-Type: text/plain; charset=windows-1255 User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Originating-IP: 132.64.90.90 X-Spam-Level: X-Spam-Status: No, hits=0.1 required=7.0 tests=NO_REAL_NAME,USER_AGENT_IMP,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hBTCwSTC028536 Hello, I am looking for a computer program for viewing localized orbitals (3D), from a Gaussian98 or Gamess output file. I am looking for a program which is distributed freely on the web. Thank you, Avital Steinberg Hebrew University graduate student ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/