From rameshg@umich.edu Fri Feb 24 00:52:20 1995 Received: from seawolf.rs.itd.umich.edu for rameshg@umich.edu by www.ccl.net (8.6.9/930601.1506) id AAA18957; Fri, 24 Feb 1995 00:45:23 -0500 Received: by seawolf.rs.itd.umich.edu (8.6.9/2.2) id AAA29314; Fri, 24 Feb 1995 00:45:19 -0500 Date: Fri, 24 Feb 1995 00:45:17 -0500 (EST) From: Ramesh Gopalaswamy X-Sender: rameshg@seawolf.rs.itd.umich.edu To: chemistry@ccl.net Subject: Conformational Analysis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have been working with steroid conformational analysis in connection with receptor modeling. I have generated several (typically 100) structures (conformers) for each steroid using DGEOM program. Now I need to pick out those conformers that are unique. (DGEOM generated structures might converge to same minimum upon minimization). Any ideas on how to do that using commercial modeling software or other shareware programs? Also, how to run minimizations (for 100 or so structures) as a background job, instead of having to read in each structure on to the graphics interface? I have access to Quanta, Cerius2 and Sybyl. Thanks a lot. Ramesh (rameshg@umich.edu) From hcj@mazda.wavefun.com Fri Feb 24 01:52:22 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.9/930601.1506) id BAA19619; Fri, 24 Feb 1995 01:31:01 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA26554; Thu, 23 Feb 95 22:30:59 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA10310; Thu, 23 Feb 95 22:31:00 -0800 Date: Thu, 23 Feb 95 22:31:00 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9502240631.AA10310@mazda.wavefun.com> To: rameshg@umich.edu Cc: chemistry@ccl.net In-Reply-To: (message from Ramesh Gopalaswamy on Fri, 24 Feb 1995 00:45:17 -0500 (EST)) Subject: Re: CCL:Conformational Analysis Reply-To: hcj@wavefun.com >>>>> "Ramesh" == Ramesh Gopalaswamy writes: Ramesh> I have been working with steroid conformational analysis Ramesh> in connection with receptor modeling. I have generated Ramesh> several (typically 100) structures (conformers) for each Ramesh> steroid using DGEOM program. Now I need to pick out those Ramesh> conformers that are unique. (DGEOM generated structures Ramesh> might converge to same minimum upon minimization). Any Ramesh> ideas on how to do that using commercial modeling software Ramesh> or other shareware programs? Also, how to run Ramesh> minimizations (for 100 or so structures) as a background Ramesh> job, instead of having to read in each structure on to the Ramesh> graphics interface? I have access to Quanta, Cerius2 and Ramesh> Sybyl. Thanks a lot. Ramesh (rameshg@umich.edu) I have recently finished enhancing Spartan's conformational analysis methods. I have implemented four new methods, including an interface to DGEOM which automates the process of generating conformers, running the appropriate optimizations, removing duplicates that may result >from the optimization, and finally calculating boltzman populations based on the final conformers. The other new methods that are available, and are just as simple to use, are a simple systematic search, a Monte Carlo search, and a Genetic Algorithm based search. If you would like more information, send mail to sales@wavefun.com, or directly to me. -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From jkong@is.dal.ca Fri Feb 24 08:52:28 1995 Received: from is.dal.ca for jkong@is.dal.ca by www.ccl.net (8.6.9/930601.1506) id IAA23584; Fri, 24 Feb 1995 08:39:21 -0500 Received: by is.dal.ca (AIX 3.2/UCB 5.64/4.03) id AA63038; Fri, 24 Feb 1995 09:38:55 -0400 Date: Fri, 24 Feb 1995 09:38:55 -0400 (AST) From: Jing Kong Subject: Isomers with different ground states To: CCL Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I am doing eletronic structure studies of a small molecule. It has two conformers. The ground states of them have different symmetries. One is pi-state, the other is sigma. I suppose this happens to other molecules too. Can anyone direct me to the references to the studies of the similar phenomina including the dynamics of the isomerization? Many thanks! Jing From jaouad@ugr.es Fri Feb 24 09:04:58 1995 Received: from ocelote.cica.es for jaouad@ugr.es by www.ccl.net (8.6.9/930601.1506) id IAA23710; Fri, 24 Feb 1995 08:51:11 -0500 Received: (from ean@localhost) by ocelote.cica.es (8.6.9/8.6.9) id OAA25017 for CHEMISTRY@ccl.net; Fri, 24 Feb 1995 14:44:50 +0100 X400-Received: by mta rica in /PRMD=/ADMD=/C=/; Relayed; Fri, 24 Feb 1995 14:24:02 UTC+0100 X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Fri, 24 Feb 1995 14:24:02 UTC+0100 X400-Received: by /PRMD=es/ADMD=/C=/; Relayed; Thu, 23 Feb 1995 22:13:55 UTC+0200 Date: Thu, 23 Feb 1995 22:13:55 UTC+0200 X400-Originator: jaouad@ugr.es X400-Recipients: non-disclosure:; X400-Content-Type: P2-1984 (2) X400-MTS-Identifier: [/PRMD=es/ADMD=/C=/;950223221355] Content-Identifier: 39 Conversion: Prohibited From: Jaouad el bahraoui To: CHEMISTRY@ccl.net (confirm) Message-ID: <39*/S=jaouad/O=ugr/PRMD=iris/ADMD=mensatex/C=es/@MHS> Subject: DGAUS BASIS ? Return-Receipt-To: Jaouad el bahraoui MIME-Version: 1.0 (Generated by Ean X.400 to MIME gateway) Dear Net-chemists I'm thinking about treating my molecules with density functional calculation, and I'm interisting too to perform my DFT calculation by the basis set used by DGAUS, but I'dont know how to do it, the introduction of this basis it not so clear. Does anyone know how to do this, plase share your knowledge with me!. thanks in advance. jaouad ******************************************************************************** EL BAHRAOUI JAOUAD Ph.D.STUDENT Instituto de Biotecnologia Grupo de Modelizacion y Diseno Molecular Universidad de GRANADA,Facultad de Ciencias, GRANADA 18071,Spain TEL: 34-58-243186. FAX: 34-58-243186 EMAIL: jaouad@ugr.es ******************************************************************************** From wdi@ccl.net Fri Feb 24 14:52:38 1995 Received: from schiele for wdi@ccl.net by www.ccl.net (8.6.9/930601.1506) id OAA02457; Fri, 24 Feb 1995 14:36:47 -0500 Received: by schiele (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@ccl.net id UAA22666; Fri, 24 Feb 1995 20:33:06 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9502242033.ZM22664@schiele> Date: Fri, 24 Feb 1995 20:33:03 +0100 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Announce: New Mailing List of German Chemical Assocation Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii We are proud to announce a new mailing list of the 'Computer-Information-Chemistry' (CIC) specialist group of the German Chemical Association (GDCh). Subscribe by sending mail to majordomo@eros.ccc.uni-erlangen.de with subscribe gdch-cic in the mail BODY. The purpose of this list is to provide a discussion forum for German chemists especially in connection with the upcoming scientific information project in collaboration with the German physical, mathemathical and informatics societies. The basic character of this list is national (but nobody will be excluded) and the language German. The new list does not intend to substitute or compete with the OSC chemistry list. We recommend that questions and discussions of a general nature are handled via the OSC list in order to benefit from the much larger knowledgeable audience and to underscore the international character of science. The following is the info file from the gdch-cic list: *************************************************************************** Diese Mailing-Liste mit dem Namen 'gdch-cic' befindet sich unter der Adresse 'eros.ccc.uni-erlangen.de' im Computer-Chemie-Centrum der Universitaet Erlangen-Nuernberg. Sie ist ein elektronisches Diskusssionsforum der Fachgruppe 'Chemie Information Computer' (CIC) in der GDCh, der Gesellschaft Deutscher Chemiker. Die Liste dient zur Zeit primaer als Koordinierungs- und Austauschstelle zur Projektierung des Informationsprojektes, das gemeinsam mit den Verbaenden der Physiker, Mathematiker und Informatiker konzipiert wird. Im Moment ist die Liste unmoderiert, d.h. jeder Bezieher der Liste kann ungefiltert Beitraege hineingeben, die sofort an alle Subskribenten weitergegeben werden. Auch die Mitgliedschaft ist frei. Es nicht nicht zwingend notwendig, Mitglied der GDCh oder der CIC zu sein, obwohl wir beides empfehlen. 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Wir koennen keine unbegrenzte Aufbewahrung garantierten, aber es stehen auf jeden Fall die Nachrichten der letzten Wochen fuer Spaeteinsteiger zum nachtraeglichen Studium zur Verfuegung. Um diese gespeicherten Nachrichten zu erhalten, schicken Sie bitte das Kommando 'get gdch-cic aktuell' im Hauptteil der Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. An die Liste angekoppelt ist ein Archiv aktueller Dokumente, die die CIC betreffen, zum Beispiel Protokolle und Reports. Eine Uebersicht erhalten Sie mit dem Kommando 'index gdch-cic' im Hauptteil einer Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. Auch diese Texte stehen Ihnen ueber ein 'get' Kommando zur Verfuegung. Wenn Sie techische Fragen haben oder Probleme mit dem Bezug der Liste oder der Verbreitung Ihrer Meldungen, wenden Sie sich bitte an 'gdch-cic-owner@eros.ccc.uni-erlangen.de'. Erlangen, 24.2.95 -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 From y_zheng@ccmail.pnl.gov Fri Feb 24 15:52:46 1995 Received: from pnl.gov for y_zheng@ccmail.pnl.gov by www.ccl.net (8.6.9/930601.1506) id PAA03299; Fri, 24 Feb 1995 15:25:12 -0500 From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HNFEIB2ZO000004U@pnl.gov>; Fri, 24 Feb 1995 12:24:40 -0800 (PST) Date: Fri, 24 Feb 1995 12:18 -0800 (PST) Subject: MD simulation of binary solvent mixtures To: chemistry@ccl.net Message-id: <01HNFEIB6E4200004U@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, I am looking for programs to set up molecular dynamics simulations on binary solvent mixtures. Any suggestions as to how to setup mixed solvent box and what is the best way to solvate a molecule with these binary solvent boxes will be greatly appreciated. Please reply to me directly. Thanks in advance! Yajun From A.T.Yagnik@exeter.ac.uk Fri Feb 24 16:53:50 1995 Received: from sun2.nsfnet-relay.ac.uk for A.T.Yagnik@exeter.ac.uk by www.ccl.net (8.6.9/930601.1506) id QAA04584; Fri, 24 Feb 1995 16:47:38 -0500 From: Via: uk.ac.exeter; Fri, 24 Feb 1995 16:34:59 +0000 Received: from cen.exeter.ac.uk by exub.exeter.ac.uk with SMTP (PP) id <17661-0@exub.exeter.ac.uk>; Fri, 24 Feb 1995 16:32:47 +0000 Message-Id: <26577.9502241632@cen> Subject: Important Modelling Books & Journals To: CHEMISTRY@ccl.net Date: Fri, 24 Feb 1995 16:32:01 +0000 (GMT) Reply-To: A.T.Yagnik@exeter.ac.uk Content-Type: text Content-Length: 1362 Hi everyone, Our Molecular Modelling Section is still relatively in its infancy and we are looking to purchase some journals and books on the subject. I'm writing to ask if people could give me their opinions as to what they feel are the most essential Journals that any Molecular Modelling (esp. protein modelling and drug design) group should have (the top 3-4 in terms of reputation and quality of science will do). In addition if you could also let me know of any similar books of use to the layman (explaining basic theory and practice) and also to the experienced modeller. It would be great if contact addresses of publishers etc could also be supplied. I will summarise if requested. Please Email me directly. Thanks for your help, Tosh. -- =============================================================================== Asutosh T Yagnik, Tel: (+44) 1392 263451 Protein Structure Group, Fax: (+44) 1392 263434 Department of Chemistry, Email: ATYagnik@exeter.ac.uk University of Exeter, * * Stocker Road, Exeter. EX4 4QD. UK. > \__/ {All opinions are my own!} "Nature can provide for the needs of people, but not the greeds" M.K.Gandhi ===============================================================================