From chemistry-request@www.ccl.net Tue Aug 11 07:12:22 1998 Received: from cammsg1.caos.kun.nl (cammsg1.caos.kun.nl [131.174.88.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA19714 Tue, 11 Aug 1998 07:12:21 -0400 (EDT) Received: from schaft by cammsg1.caos.kun.nl with local id 0z6CLl-0007PP-00; Tue, 11 Aug 1998 13:12:21 +0200 Subject: Is there a need for a Calculated Structures Database ? To: chemistry@www.ccl.net Date: Tue, 11 Aug 1998 13:12:21 +0200 (MDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Message-Id: From: Gijs Schaftenaar A Calculated Structures Database. --------------------------------- Not more than perhaps a decade ago, Computational Chemistry used to be the realm of Quantum Chemists with access to a supercomputer. Computer resources usually restricted calculations to small molecules. Nowadays this situation has changed drastically. With the continuous speedup of computer hardware, calculations on chemically interesting systems have become tractable to the bench chemist and the study of short lived intermediates and transition states, often inaccessible to experiment, have become common practice. The Computational Chemistry community has steadily grown and broadened and does no longer exist of pure specialists only. The Computational Chemistry List (CCL; URL: http://www.ccl.net/ccl/welcome.html), a Web site and an e-mail exploder which allows computational chemistry researchers from around the world to exchange information and experiences is an important commucation channel. With so many structures being calculated, the need for a (comprehensive) database of calculated structures has been voiced a number of times on the Computational Chemistry List. The Carnegie-Mellon Quantum Chemistry Archive, created by Prof. Pople's group for users of the Gaussian package, has been an attempt to set up such a database. However, for a number of reasons this database has never been very successful. Gaussian users could (can) contribute to this database by sending a routinely created archive file by surface mail to the curators of the database, the Chemistry Publishing Unit of Carnegie-Mellon University. Access to the database can only be obtained by purchasing it together with its dedicated software. But for a database to be successful, ease of contributing to it and ease of data retrieval are determing factors. The CAOS/CAMM Center, the Dutch national academic Center for the Application of Information Technology in Chemistry, is exploring the possibility to create, curate and maintain a comprehensive archive of calculated structures at both the ab-initio and semi-empirical level with emphasis on co-ordinate data. Contributions to this database should be submitable via e-mail and/or the World Wide Web. We intend to automate submission by incorporating a submission form into our popular quantum chemistry visualisation tool MOLDEN, which interfaces not only to Gaussian but to a range of other Ab Initio and semi-empirical codes. MOLDEN currently has a distribution of over 800 copies world wide and is freely available to academic researchers making (coordinate) data contibution an easy task. Access to the database will be given via the World Wide Web and added value is intended by linking it to other chemically oriented databases, in particular to the Quantum Chemistry Literature Database (QCLDB). The Gaussian archive file format might serve as a starting point for the definition of a new and richer format which would include semi-empirical calculations and links to literature and other chemical databases. Because the Center maintains the MOLDEN software, adaptions to deal with a new data format can easily be implemented and distributed. With this message we try to measure the potential (mental) support for such an initiative and to determine the willingness among computational chemists to contribute data to the intended database of calculated structures. This will help us to determine if the allocation of computational and human resources to this effort can meet with sufficient enthousiasm to start. For the database to reach the critical mass needed to become a successful operation, in addition to the processing of existing data sources, the active contribution of data from many private sources is necessary. Therefor your answer to the following questions is very much appreciated. 1. Do you think that the proposed initiative is advisable and/or needed ? 2. Would you be willing to contribute data to the proposed database, using either a MOLDEN form or a WEB based form? Your answers are welcomed at the e-mail addresses: schaft@caos.kun.nl (Gijs Schaftenaar, Computational Chemist and MOLDEN author CAOS/CAMM Center.) or noordik@caos.kun.nl (Jan Noordik, Director CAOS/CAMM Center) ------------------+-----------------------+------------------------------ CAOS/CAMM Center Phone: +31(0)24-3653386 University of Nijmegen +31(0)24-3653391(secr.) Toernooiveld 1 Fax: +31(0)24-3652977 6525 ED Nijmegen e-mail: post@caos.kun.nl The Netherlands URL: http://www.caos.kun.nl ------------------+-----------------------+------------------------------ The CAOS/CAMM Center is the Dutch Academic Facility for the Application of Information Technology in: Organic Chemistry: CAOS Computational Chemistry, Molecular Modeling, 3D Databases: CAMM Bioinformatics: CAMMSA It is also the Dutch National Node in EMBnet and GDB. ------------------+-----------------------+------------------------------