From chemistry-request@server.ccl.net Thu Oct 19 06:20:45 2000 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA01516 for ; Thu, 19 Oct 2000 06:20:44 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id NAA19391; Thu, 19 Oct 2000 13:15:26 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Thu, 19 Oct 2000 13:15:26 +0300 (EET DST) From: Mikael Johansson X-Sender: mpjohans@soul.helsinki.fi To: Danilo Gonzalez cc: chemistry@ccl.net Subject: Re: CCL:Trajectory analisys in Hyperchem In-Reply-To: <39EE120E.3FB8B1F@lauca.usach.cl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! On Wed, 18 Oct 2000, Danilo Gonzalez wrote: > I'm working with Hyperchem 5.2 in a PC (Athlon 800 MHz), using AMBER > force field. I 'm runing a Molecular Dynamics calculation, and saving > the trayectory file. Anybody know how can I measure the distance between > two atoms during the trayectory? You first must select the two atoms you are interested in, and then name the selection. When starting the MD-run, click on the "Averages..." tab and move your named selection over to either the "Average only" or "Avg. & Graph" field. After the simulation run you should find a *.csv file with the same base name that you gave the trajectory file. This should include the distance between the atoms for each saved time step. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi From chemistry-request@server.ccl.net Thu Oct 19 06:50:33 2000 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA02320 for ; Thu, 19 Oct 2000 06:50:30 -0400 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer); Thu, 19 Oct 2000 11:45:28 +0100 Reply-To: "a.oganov" From: "Artem R. Oganov" To: chemistry Subject: CCL:critical point Date: Thu, 19 Oct 2000 11:45:33 +0100 Message-ID: BlankDear CCLers, I wonder if it is possible to say that in a fluid system there is a unique value of the critical density, above which the system is necessarily liquid, and below which it is gaseous - at temperatures below the critical, and arbitrary pressure. This seems to be the case, but is there any mathematical proof that this critical density will be the same at all pressures and all subcritical temperatures? I'll summarise if requested. Thanks a lot, Artem ----------------------------------------------------- Artem Oganov Department of Geological Sciences University College London Gower Street London WC1E 6BT tel: +44 (020)-7679-3449 fax: +44 (020)-7387-1612 email: a.oganov@ucl.ac.uk http://slamdunk.geol.ucl.ac.uk --------------------------------------------------- From chemistry-request@server.ccl.net Thu Oct 19 08:41:27 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA02925 for ; Thu, 19 Oct 2000 08:41:27 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id PAA18954 for ; Thu, 19 Oct 2000 15:01:38 +0200 (CEST) Date: Thu, 19 Oct 2000 15:01:38 +0200 From: Christian Pilger To: chemistry@ccl.net Subject: ligand binding In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl'ers, I am performing docking studies employing AUTODOCK 3. Due to its size and conformational flexibility, I ususally get more then one suggestion for meaningful orientation/conformation within the proposed binding site of the enzyme for a given inhibior structure. These are subsequentely ranked by AUTODOCK's implemented empirical free energy function. However when using a different empirical scoring scheme (e.g. SCORE by Wang et al.) on the suggested inhibitor/enzyme complexes, frequently the order is altered, leading to a different hypothesis for the active conformation of the considered inhibitor. In order to make the "correct" selection (the Xray structure of the complex of the lead compound/enzyme is known) out of the proposed binding modes for a single inhibitor, I would like to employ other methods for ranking these. I'm aware of such methods like FEP, but I don't have much experience in running molecular dynamics calculations. I would like to extend the results obtained for the lead compound to a dataset of structurally related compounds to get an hypothesis for the active conformation for each. Finally, I'd like to compare the binding affinities among the candidates of my dataset. My request to the members of this list: Can somebody provied me with useful hints, webpages, books, howto's, or other references to methods suitable for the relative ranking of proposed binding modes of a single inhibitor ? Would it be possible to extend this somehow to the dataset (about 20 compounds) ? I have access to AMBER 6. Regards, Christian ----------------------------------------------------------------- Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de Word Wide Web: http://oc30.uni-paderborn.de/~cpilger ----------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Oct 19 12:20:43 2000 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04037 for ; Thu, 19 Oct 2000 12:20:43 -0400 Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by ccshst09.cs.uoguelph.ca (8.9.3/8.9.3) with ESMTP id MAA22687 for ; Thu, 19 Oct 2000 12:15:38 -0400 (EDT) Message-Id: <200010191615.MAA22687@ccshst09.cs.uoguelph.ca> Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.48); 19 Oct 00 12:15:35 -0500 Received: from SpoolDir by MSNET (Mercury 1.48); 19 Oct 00 12:15:20 -0500 From: "Bill Smith" Organization: Math & Stats, University of Guelph To: chemistry Date: Thu, 19 Oct 2000 12:15:15 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:critical point Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.12b) Critical points for pure fluids and binaries are discussed in most chemical engineering thermodynamics texts. In a fluid system consisting of a single component, there is a unique critical POINT. That means that the critical T, P, and density are unique values for that fluid. For T>Tc, the substance is called a "fluid", since it has both gas-like and liquid-like properties. (In the culture of the field, a "supercritical fluid" often means that T>Tc AND P>Pc.) For T > BlankDear CCLers, > > I wonder if it is possible to say that in a fluid system there is a > unique value of the critical density, above which the system is > necessarily liquid, and below which it is gaseous - at temperatures > below the critical, and arbitrary pressure. This seems to be the case, > but is there any mathematical proof that this critical density will be > the same at all pressures and all subcritical temperatures? I'll > summarise if requested. Thanks a lot, > > Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics and School of Engineering Room 546 MacNaughton Building University of Guelph Stone Road and Gordon Streets Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; http://www.mathstat.uoguelph.ca/faculty/smith/