From chemistry-request@server.ccl.net Thu Apr 13 06:41:37 2000 Received: from mjco-s2.ice.mpg.de (mjco-s2.ice.mpg.de [195.37.47.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA17555 for ; Thu, 13 Apr 2000 06:41:22 -0400 Received: from ice.mpg.de (unverified [195.37.47.130]) by mjco-s2.ice.mpg.de (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 13 Apr 2000 12:40:48 +0200 Message-ID: <38F5A3EB.BE2FA551@ice.mpg.de> Date: Thu, 13 Apr 2000 12:39:39 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: CML at the CIC meeting, was: CML is dead Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA17556 Hi everybody, this is a brief summary of my impressions on the discussions about CML at the CIC meeting. CIC stands for Computers, Information, Chemistry and is the name if the working group of the German Chemical Society dealing with these issues. This years workshop has been held during the Analytica trade fair in Munich. 9.30-10.00 W. Koch, Frankfurt/D, Dissemination of Chemical Information 10.00-10.30 G. Kaupp, Oldenburg/D, Exchange Formats for Chemical Information - State of Art and Perspectives 10.30-11.00 A. Dransfeld, Leuven/B, Data in between Databases - What we need to make CML Work for all Chemists 11.30-12.00 W.-D. Ihlenfeldt/D, New Developments in the Field of Structure Representation 12.00-12.30 Th. Fröhlich, Köln/D, From the Exchange of Spectral Data to an Independent Analytical Data Interchange Except for W.-D. Ihlenfeldts extremely interesting talk on his latest developments on 2D structure diagram generation and related topics of visualizing chemical data, all of the talks had at least some references to CML. W. Koch is coordinator of the "Global Info" project, funded by the Germany ministry for Education and Research. This projects aims at providing suggestions and solutions for dealing with the challenges of the internet age for the dissemination of chemical data. G. Kaupp's important point was that we throw away an incredible amount of extremely valuable scientific material by discarding the original analytical data and just displaying 2D or pseudo-3D pictures in our scientific publications (http://kaupp.chemie.uni-oldenburg.de/global-info/plea/plea_end.html). He presented his groups approach of using VRML as an exchange format, which was questioned by a number of people in the audience, because VRML was not designed for this purpose and lacks for example support for physical units. Thus, one has to keep additional information outside the VRML data, which makes the approach inherently error prone. Kaupp's justification was the well known argument (from the ongoing discussion on the list), that VRML does have functional tools, in contrast to CML, which does not but would at least theoretically be much better suited for coding chemical documents. I do not agree with this view and so do many others on this list, but because the lack of tools and support for CML by major companies was a common argument in the discussions it emphasizes the need for the CML community to produces as many working applications as possible and to efficiently advertise these. Alk Dransfelds talk was completely dedicated to the topic of CML, giving some overview about the latest developments in the field. Alk mentioned our latest endeavour to encode calculated as well as experimental NMR in a CML 1.0 compliant way. He made some statements on potential improvements, well aware of the fact changes to a standard are an extremely sensitive topic. Th. Froehlich gave a very interesting overview of the use of JCAMP-DX and -CS for independent analytical data exchange. He stated that JCAMP does already feature many advantages of CML like mixing and crosslinking of different data types in one document. He presented a set of nicely done java applets that are able to display JCAMP files for IR, NMR, MS in a web browser and to save these data to the local harddisk of the user. The applets will be freely available soon. Dr. Froehlich also stated that his company will open-source the java classes for reading and writing JCAMP-DX, which is very good news. He also expressed his commitment to CML as the future, potentially better way for exchanging chemical data on the web. As conclusion on could say that many people in the field are aware of CML and its potential but hesitate to invest time and effort in development and implementation of CML, certainly partly because there is the feeling that they can not do things with CML that can't be achieved with the well established formats. Greetings, Christoph Steinbeck -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Thu Apr 13 08:41:38 2000 Received: from org.chem.msu.su (org.chem.msu.su [158.250.32.94]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA18882 for ; Thu, 13 Apr 2000 08:36:15 -0400 Received: from org.chem.msu.su (acylium.chem.msu.su [158.250.32.71]) by org.chem.msu.su (8.9.3/8.9.3) with ESMTP id QAA89269; Thu, 13 Apr 2000 16:34:47 +0400 (MSD) Message-ID: <38F5BF2B.F16E04A7@org.chem.msu.su> Date: Thu, 13 Apr 2000 16:35:56 +0400 From: "Serge A.Pissarev" X-Mailer: Mozilla 4.72 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chmigorn@nus.edu.sg, chemistry@ccl.net Subject: Re: CCL:isomer software References: <3.0.6.32.20000411151216.00796100@alfa.chem.uw.edu.pl> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Try: ftp://org.chem.msu.su/pub/software/SMOG/ hope it will be helpful -- Serge Andrzej Leniewski wrote: > I encountered one at the site > http://www.mathe2.uni-bayreuth.de/molgen4/start.html, > although it is not freeware. > Andrzej Leniewski > > At 3:36 PM 4/4/00 +0800, you wrote: > > >Dear Netters, > >could someone please tell me what software > >(preferably freeware) is available for > >drawing structures of isomers upon entering > >a given bruto molecular formula!? > >Many thanks!! > >Yours sincerely > >I.Novak > >Dept.of Chemistry > >National University of Singapore > >Singapore 117543 > >chmigorn@nus.edu.sg From chemistry-request@server.ccl.net Thu Apr 13 11:38:57 2000 Received: from catios.udea.edu.co (catios.udea.edu.co [200.24.20.180]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA19995 for ; Thu, 13 Apr 2000 11:38:48 -0400 Received: from localhost (alemoe@localhost) by catios.udea.edu.co (8.9.3/8.9.3) with ESMTP id JAA19721 for ; Thu, 13 Apr 2000 09:51:00 -0500 Date: Thu, 13 Apr 2000 09:51:00 -0500 (COT) From: Alejandro Montoya Escobar To: CCL group Subject: Honololu meeting! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccl, A week ago someone posted an e-mail concerning a computational conference in Honolulu. Unfortunately, I do not have this e-mail and I want to know about it. Could someone forward me this information. Thanks a lot. Alejandro. From chemistry-request@server.ccl.net Thu Apr 13 14:30:56 2000 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22590 for ; Thu, 13 Apr 2000 14:30:44 -0400 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id e3DISMU06043 for ; Thu, 13 Apr 2000 14:28:22 -0400 (CST) Date: Thu, 13 Apr 2000 14:28:22 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: chemistry@ccl.net Subject: Blends Polymer Simulations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! I'm looking for some reference about Blends Polymer simulations, I'm using BLENDS/Cerius2, I will appreciate some reference in that Belnds/C2 is used. I will summarise the answers. Thanks a lot! Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Thu Apr 13 21:34:51 2000 Received: from ripspost.aist.go.jp (ripspost.aist.go.jp [150.29.251.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA24506 for ; Thu, 13 Apr 2000 21:34:50 -0400 Received: from rpsmtp1.aist.go.jp (rpdgate1.aist.go.jp [150.29.254.30]) by ripspost.aist.go.jp (8.9.3/3.7W) with ESMTP id KAA12013 for ; Fri, 14 Apr 2000 10:34:46 +0900 (JST) Received: from tnhost2.tniri.go.jp (localhost [127.0.0.1]) by rpsmtp1.aist.go.jp (8.9.3/3.7W) with ESMTP id KAA07464 for ; Fri, 14 Apr 2000 10:34:45 +0900 (JST) Received: from tniri.go.jp (tnpc33.tniri.go.jp [150.82.49.136]) by tnhost2.tniri.go.jp (8.9.3/3.7W) with ESMTP id KAA15569 for ; Fri, 14 Apr 2000 10:34:44 +0900 (JST) Message-ID: <38F67B5B.D130DDE1@tniri.go.jp> Date: Fri, 14 Apr 2000 10:58:52 +0900 From: "Dr. Abhijit Chatterjee" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: New Journal Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Call for papers for IJMS (http://www.mdpi.org/ijms/) Dear colleague: I would like to invite you to contribute a review or research paper for consideration and publication in International Journal of Molecular Sciences (ISSN 1422-0067) at the http://www.mdpi.org/ijms/ website. It was launched in March 2000. Please visit http://www.mdpi.org/ijms/list00.htm for the first issues. A "Call for Papers to the IJMS" message as a pdf can be downloaded at http://www.mdpi.org/ijms/ijmsadvert.pdf. Because it is a free online journal, papers published in IJMS will receive very high publicity. Authors who have published in MDPI's other journals (e.g., MOLECULES at http://www.mdpi.org/molecules/) have informed us that they receive many more reprint requests than for other papers. Please list IJMS (ISSN 1422-0067) the http://www.mdpi.org/ijms/ on your website. You are invited to send your manuscripts to the Editor-in-Chief, Prof. Dr.Jerzy Leszczynski by e-mail: jerzy@tiger.jsums.edu. Thank you in advance for your kind support. Looking forward to hearing >from you soon. Sincerely, Jerzy Leszczynski The Editor-in-Chief, IJMS (http://www.mdpi.org/ijms/) e-mail: jerzy@tiger.jsums.edu Shu-Kun Lin Managing Editor, lin@mdpi.org >>>>>>>>>>>>>> Sincerely yours Abhijit Chatterjee (Editorial Board Member) From chemistry-request@server.ccl.net Thu Apr 13 10:55:55 2000 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA19639 for ; Thu, 13 Apr 2000 10:55:54 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3/8.9.3) with ESMTP id QAA08235; Thu, 13 Apr 2000 16:51:40 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 13 Apr 00 17:02:10 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 13 Apr 00 17:02:03 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Brian Space Date: Thu, 13 Apr 2000 17:01:54 +0100 Subject: Re: CCL:Reduced Mass CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <2A1037412@virgil.ruc.dk> Dear Brian Space: > In Gaussian output how is the reduced mass defined? Let the r'th normal mode vector of unit length be given as _ 1/2 Q = >_ c q , q = m x r i ir i i i i where the sum is over the 3N mass-weighted atomic displacement coordinates q. m are the corresponding atomic masses in AMU, and x the cartesian displacement coordinates (in Angstrom). The "reduced mass" M in AMU may then be obtained as _ 2 -1 M = 1 / [ >_ c m ] r i ir i The "normal coordinates" printed by Gaussian apparently correspond to cartesian vectors (in Angstrom) normalized to unit length; in order to obtain the proper length of this vector, the printed coefficients d must be multiplied by the inverse square root of the reduced mass: -1/2 printed d <--- M d ir r ir The proper cartesian displacement vector is then obtained as _ X = >_ d x r i ir i The coefficients c and d are related by -1/2 d = c m ir ir i and we have the following relation -1/2 |X | = |Q | M r r r The inverse square root of the reduced mass is simply the length of the cartesian displacement vector X for unit displacement along normal mode Q. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Apr 13 13:54:47 2000 Received: from abacus.ac.BrockU.CA (abacus.ac.BrockU.CA [139.57.65.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA21362 for ; Thu, 13 Apr 2000 13:54:46 -0400 Received: from localhost (srothste@localhost) by abacus.ac.BrockU.CA (8.9.3/8.9.3) with SMTP id NAA403082; Thu, 13 Apr 2000 13:53:47 -0400 (EDT) Date: Thu, 13 Apr 2000 13:53:46 -0400 (EDT) From: "Stuart M. Rothstein" To: Alejandro Montoya Escobar cc: CCL group Subject: Re: CCL:Honololu meeting! In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Alejandro: For a list of symposia with some descriptions try http://www.chembio.uoguelph.ca/pac2000/syposia.htm The deadline to contribute abstracts to the ACS webpage is tomorrow (April 14th)! Stuart M. Rothstein, Professor of Chemistry and Physics, Brock University, St. Catharines, Ontario, L2S 3A1 CANADA srothste@abacus.ac.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ On Thu, 13 Apr 2000, Alejandro Montoya Escobar wrote: > > Dear ccl, > > A week ago someone posted an e-mail concerning a computational conference > in Honolulu. Unfortunately, I do not have this e-mail and I want to know > about it. Could someone forward me this information. > > Thanks a lot. > > Alejandro. > > From chemistry-request@server.ccl.net Thu Apr 13 20:34:15 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA24311 for ; Thu, 13 Apr 2000 20:34:14 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id RAA03273 for ; Thu, 13 Apr 2000 17:33:46 -0700 Resent-From: Eugene Leitl Resent-Message-ID: <14582.26473.353477.654289@lrz.uni-muenchen.de> Resent-Date: Thu, 13 Apr 2000 17:33:45 -0700 (PDT) Resent-To: MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Message-Id: Reply-To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST From: "Slutsky, Bruce" To: CHMINF-L@LISTSERV.INDIANA.EDU Subject: Computers in Chemistry event in New York City 4/28/00 Date: Thu, 13 Apr 2000 17:59:42 -0400 The New York Section of the American Chemical Society Computers in Chemistry Topical Group DATE: Friday, April 28, 2000 TIMES: Dinner - 4:00 PM Social hour - 5:30 PM Seminar - 6:00 PM PLACE: New York University Room 1003 Main Building 31 Washington Place New York, N.Y. 10003 SPEAKER: Dr. Carlos Simmerling Department of Chemistry SUNY at Stony Brook Stony Brook, New York 11794 "BRIDGING THE GAP BETWEEN LOW AND HIGH RESOLUTION BIOMOLECULAR STRUCTURES WITH MOLECULAR DYNAMICS SIMULATIONS" ABSTRACT: Genome projects are rapidly providing vast numbers of DNA sequences. The value of these sequences would be greatly enhanced by detailed three-dimensional structures for the proteins that they encode. Rapid methods for predicting structures will therefore become increasingly important in the near future. Such predictions, however, are likely to have regions of poor quality even in the best cases. Our research focuses on developing computer simulation techniques to improve the accuracy in these models to the level required for insight into function and design of compounds to modify that function. This seminar will describe our recent progress in method development and application to protein loops as well as entire protein structures. Dr. Carlos Simmerling began his undergraduate work at St Xavier College in Chicago and completed his bachelor's degree in 1991 at the Univ. of Illinois at Chicago. He remained at UIC for graduate study under Ron Elber and received his Ph.D. in Chemistry from UIC in 1994. This was followed by postdoctoral study with Peter Kollman in the Department of Pharmaceutical Chemistry at UCSF from 1994-1998. He is currently an assistant professor in the Department of Chemistry at SUNY Stony Brook, and is also a member of Stony Brook's Center for Structural Biology. Dr. Simmerling recently received an AMDeC Tartikoff/Perelman/EIF Young Investigator Award for breast cancer research. RESERVATION: For dinner, please contact Dr. John M. Halpin 212-998-8418 john.halpin@nyu.edu Indoor parking is available on Broadway (between E 8th St. and Waverly) and on E 8th St. (between 5th Ave. and University Place). Both locations are within easy walking distance of NYU. ________________________________________________________________________ __ John M. Halpin Clinical Asst. Professor Department of Chemistry New York University Room 1018A 100 Washington Square East New York, New York 10003 (212) 998-8418 john.halpin@nyu.edu