From chemistry-request@www.ccl.net Fri Apr 9 08:08:12 1999 Received: from ntsvexch.albmolecular.com (mail.albmolecular.com [205.247.153.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA19012 Fri, 9 Apr 1999 08:08:11 -0400 (EDT) Received: by Ntsvexch with Internet Mail Service (5.0.1457.3) id <1WP5HDR7>; Fri, 9 Apr 1999 08:10:35 -0400 Message-ID: <80F79FF3ECD6D1119D9000805FCC602A309C5C@Ntsvexch> From: "Andruski, Stephen W." To: "'CCL'" Subject: MIF summary Date: Fri, 9 Apr 1999 08:10:33 -0400 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain About a month ago I posted a question regarding the MIF format and its status. I only received one response from David E. Bernholdt suggesting CML as a better way to achieve the same goal. See the CML Web site at http://www.xml-cml.org/ for more information. For an example of the use of the MIF format for computational chemistry see Mark Favas' posting to CCL on 91/10/15 titled "Comput. chemistry archive/data exchange file format" in the CCL archives. I am not convinced that CML is a better solution. In my mind MIF and CML each have advantages and disadvantages, and may both be appropriate for different applications. In either case, it seems there is little active interest in developing standards. Software support is also needed in order to clearly show the utility of these formats and to work out the problems and limitations. My original question and the response are listed below. *************************************************** Original post: Does anyone out there know the status of the MIF (Molecular Information File) format. Searching the CCL archives, the most recent message on this topic I found was ~1993. I have searched the Internet and cannot find any information out there, though a number of years ago the format specification and preliminary data dictionary were available (I have copies, but no longer remember whose Web site they were on). This file format seems like such a good idea for the archiving and transmittal of molecular data (MO calculations, MM calculations, multiple conformations, X-ray data, etc.) in a single file. Much like the CIF format now widely used for crystallographic data, the content is extensible using data dictionaries and could accommodate a large amount of different data for different uses. My gut feeling is that no group or Society has taken the lead in promoting this file format and interest has therefor waned. Perhaps the ACS Division of Computers in Chemistry would be an appropriate group to do this. I hope that there is some interest out there. I will gladly summarize the responses I get. Thank you. Steve Andruski *********************************** Dr. Stephen W. Andruski Senior Research Chemist II Albany Molecular Research, Inc. 21 Corporate Circle Albany, New York 12203 USA Tel. (518) 464-0279, Ext. 3303 Fax (518) 464-0289 http://www.albmolecular.com E-mail: stephena@albmolecular.com ************************************ ******************************************************************* Response from David E. Bernholdt: It strikes me that the "right" way to do something like this these days is to use XML. Chemical Markup Language (CML) was one of the very first XML applications (having started development before XML itself. It is certainly not as complete as CIF or (what I recall of) MIF, but it could be a useful starting point or at least a source of ideas. I think XML offers a huge potential to standardize the input and output of many comp. chem. applications -- if people think it is useful enough to agree to/help develop the standards. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu ************************************************************************ ***** From chemistry-request@www.ccl.net Fri Apr 9 08:21:09 1999 Received: from ntsvexch.albmolecular.com (mail.albmolecular.com [205.247.153.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA19092 Fri, 9 Apr 1999 08:21:08 -0400 (EDT) Received: by Ntsvexch with Internet Mail Service (5.0.1457.3) id <1WP5HDSB>; Fri, 9 Apr 1999 08:23:32 -0400 Message-ID: <80F79FF3ECD6D1119D9000805FCC602A309C5D@Ntsvexch> From: "Andruski, Stephen W." To: "'CCL'" Subject: Marching Cubes on a PC Date: Fri, 9 Apr 1999 08:23:31 -0400 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain Several years ago Stuart Green at the University of Leeds made available code using the "marching cubes" algorithm to generate surfaces for the visualization of orbitals, etc. in Rasmol and Chime (see http:/www.chem.leeds.ac.uk/stuartg/marching/surface.html). Has anyone implemented this code on a PC under DOS, Windows 95/98 or NT? Thanks in advance for any responses. I'll summarize if there is enough interest. Steve Andruski > *********************************** > Dr. Stephen W. Andruski > Senior Research Chemist II > Albany Molecular Research, Inc. > 21 Corporate Circle > Albany, New York 12203 USA > Tel. (518) 464-0279, Ext. 3303 > Fax (518) 464-0289 > http://www.albmolecular.com > E-mail: stephena@albmolecular.com > ************************************ > > From chemistry-request@www.ccl.net Fri Apr 9 09:33:45 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA20227 Fri, 9 Apr 1999 09:33:43 -0400 (EDT) Received: from voxopm-e.csc.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id QAA25194 for ; Fri, 9 Apr 1999 16:33:42 +0300 (EET DST) Date: Fri, 9 Apr 1999 16:33:42 +0300 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@www.ccl.net Subject: Material for teaching comp.chem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers, I have searched some material of computational chemistry (mainly molecular modeling teaching material and self-learning material) from internet. I have find some material, but if you know a good source, please give me a hint, I really appreciate it. I would like which kind of material courses, exercises, interactive exercises etc. is provided and it would be available for everyone. Thanks in advance. Sincerely Yours, Maija Lahtela-Kakkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing Tekniikantie 15 a D P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi *************************************** From chemistry-request@www.ccl.net Fri Apr 9 10:48:26 1999 Received: from titus.u-strasbg.fr (titus.u-strasbg.fr [130.79.79.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA21087 Fri, 9 Apr 1999 10:48:25 -0400 (EDT) Received: from igbmc.u-strasbg.fr (zinfandel [130.79.79.230]) by titus.u-strasbg.fr (8.9.0/8.9.0) with ESMTP id QAA22774; Fri, 9 Apr 1999 16:54:32 +0200 (MET DST) Sender: calimet@titus.u-strasbg.fr Message-ID: <370E676E.67B11905@igbmc.u-strasbg.fr> Date: Fri, 09 Apr 1999 20:47:42 +0000 From: Nicolas Calimet X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: What's the latest UHBD version ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I started to use UHBD ver 6.1.exp about two months ago to perform PB molecular dynamics. I got the distribution from somebody in my lab, and I'm wondering whether it's the latest release or not. Mainly, I'd like to know if the surface forces (hydrophobic contribution) have been actually implemented, as written in the docs but seemingly not in the source code. Furthermore, as any experimental version, this one reveals some problems concerning several options of the 'md' command, sometimes leading to crash -- again in the distribution I have. I guess I've fixed some of them, say the ones usefull for me. But it's worthless if there is a new version available... Any information/help would be greatly appreciate ! Thanks, Nicolas Calimet, PhD student IGBMC - University of Strasbourg - France calimet@igbmc.u-strasbg.fr