From kneth@chem.ruc.dk Wed Jul 9 05:50:51 1997 Received: from koala.ruc.dk for kneth@chem.ruc.dk by www.ccl.net (8.8.3/950822.1) id FAA20397; Wed, 9 Jul 1997 05:39:45 -0400 (EDT) Received: from localhost (kneth@localhost) by koala.ruc.dk (8.8.5/8.8.5) with SMTP id LAA12851; Wed, 9 Jul 1997 11:38:22 +0200 Date: Wed, 9 Jul 1997 11:38:22 +0200 (CEST) From: Kenneth Geisshirt X-Sender: kneth@koala.ruc.dk To: "B. Kallies" cc: chemistry@www.ccl.net Subject: Re: CCL:Definition of van Hove function (MD) In-Reply-To: <9707070715.AA22026@serv.chem.uni-potsdam.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, > I'm wondering if anyone knows the definition of the van Hove function. The van Hove correlation function is defined as: N N 1 / --- --- / \ G(r, t) = --- < > > |(delta(r'+r-r(i,t))*delta(r-r(j,0))dr' > N \ --- --- / / i=1 j=1 where delta is Dirac's delta function and the bracket is the (ensemble) average. > Any information would be helpful. Thanks in advance. Reference: Theory of Simple Liquids by J.P. Hansen and I.R McDonald. Best wishes Kenneth +-------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Dept. of Life Sciences and Chemistry Roskilde University | +-------------------------------------------------------------+ | E-mail: kneth@chem.ruc.dk Phone: +45 4675 7711, ext 2785 | +-------------------------------------------------------------+ From ccl@www.ccl.net Wed Jul 9 10:50:53 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA21392; Wed, 9 Jul 1997 10:25:24 -0400 (EDT) Received: from london.ks.uiuc.edu for ilya@ks.uiuc.edu by bedrock.ccl.net (8.8.6/950822.1) id KAA16129; Wed, 9 Jul 1997 10:25:23 -0400 (EDT) Received: from roma.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.20/16.2 [TBG Mods]) id AA212628323; Wed, 9 Jul 1997 09:25:23 -0500 Message-Id: <199707091425.AA212628323@london.ks.uiuc.edu> Received: by roma.ks.uiuc.edu (NX5.67d/NX3.0X) id AA02339; Wed, 9 Jul 97 09:25:22 -0500 Content-Type: text/plain Mime-Version: 1.0 (NeXT Mail 3.3 v118.2) X-Nextstep-Mailer: Mail 3.3 (Enhance 1.2) Received: by NeXT.Mailer (1.118.2) From: Ilya Logunov Date: Wed, 9 Jul 97 09:25:20 -0500 To: chemistry@ccl.net Subject: Subscribe me to the Comp-Chem-List Reply-To: ilya@ks.uiuc.edu Please suscribe me to the Computational Chemistry List. Ilya Logunov From ccl@www.ccl.net Wed Jul 9 12:50:57 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA21795; Wed, 9 Jul 1997 12:00:20 -0400 (EDT) Received: from gtc05f for reddy@gensia.com by bedrock.ccl.net (8.8.6/950822.1) id LAA20086; Wed, 9 Jul 1997 11:57:43 -0400 (EDT) Received: from genny (genny.res.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA20616; Wed, 9 Jul 1997 08:58:42 -0700 Received: by genny (940816.SGI.8.6.9/930416.SGI.AUTO) id MAA22620; Wed, 9 Jul 1997 12:19:47 GMT Date: Wed, 9 Jul 1997 05:19:46 +48000 From: Rami Reddy To: CHEMISTRY@ccl.net Subject: Re: CCL:Re: CCL:FEP binding energy In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On 7 Jul 1997, Arne Elofsson wrote: > Soaring Bear writes: > > > Greetings: > > > > > > I have noticed that published studies of FEP energy calculations > > of inhibitor binding are largely on a pairwise basis, comparing > > small numbers of inhibitors (presumably due to computational cost). > > I am interested in locating studies which have compared at least > > a dozen. I would appreciate any references. Also, any > > examples with structure based affinity calculation (especially > > linear response approximation)? > > > Dear Dr. Bear, Reddy et al evaluated a large set of related analogs using computer-assisted drug design methods that combine molecular mechanics, dynamics, FEP calculations, inhibitor design, synthesis, biochemical testing, and crystallographic structure determination of the protein-inhibitor complexes. The calculated relative binding free energies were successfully incorporated into the design of novel HIV1 protese inhibitors. This study involved a large set of molecules whose relative binding affinities were predicted using FEP method prior to synthesis, and were later confirmed by experimental measurements. Reddy et al. J. Med. Chem. 37 (1994), 1145-1152 If you have any questions or comments please let know. M. Rami Reddy Metabasis Therapeutics, Inc Email: reddy@gensia.com From ccl@www.ccl.net Wed Jul 9 12:51:12 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA21962; Wed, 9 Jul 1997 12:23:10 -0400 (EDT) Received: from indigo14.carb.nist.gov for gilson@indigo14.carb.nist.gov by bedrock.ccl.net (8.8.6/950822.1) id MAA20775; Wed, 9 Jul 1997 12:23:08 -0400 (EDT) Received: (from gilson@localhost) by indigo14.carb.nist.gov (8.7.5/8.7.3) id MAA29342; Wed, 9 Jul 1997 12:23:08 -0400 (EDT) Date: Wed, 9 Jul 1997 12:23:08 -0400 (EDT) Message-Id: <199707091623.MAA29342@indigo14.carb.nist.gov> From: "Dr. Mike Gilson" To: chemistry@ccl.net Subject: Database for Molecular Binding and Recognition Dear Colleagues, We are interested in creating a publicly accessible database containing information on noncovalent binding affinities, with an emphasis on biomolecules. Such a database could be useful in a range of applications, including drug-discovery and the development of computational models for predicting affinities. We hope to establish a stable, expanding resource that will be helpful to many scientists over a period of years. This is a complex and somewhat ill-defined task, however. It is necessary to define the scope of the data to be included, to implement the database effectively, and to establish mechanisms for filling and maintaining it. Before taking these steps, we would like to learn of any similar efforts in the scientific community in order to avoid duplication of effort. We also would like to consult with people interested in using the database, whether as depositors or users of the data. Finally, we would like to be sure that the utility of this database will justify the effort of creating it. This message, then, is to solicit your advice and suggestions on these topics. In order to permit a general exchange of views, we have established a web-site that will allow comments and subsequent discussion to be posted publicly. The URL is http://db3.sdsc.edu/DbNcB/. We would very much appreciate your participation. With best regards, Phil Bourne Mike Gilson San Diego Supercomputer Center Center for Advanced Research in Biotechnology gilson@indigo14.carb.nist.gov Nick Hodge Craig Wilcox Computer-Aided Drug Design Group Department of Chemistry The DuPont Merck Pharmaceutical Company University of Pittsburgh From ccl@www.ccl.net Wed Jul 9 15:45:59 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA22996; Wed, 9 Jul 1997 15:02:22 -0400 (EDT) Received: from relay1.scripps.edu for pelleque@scripps.edu by bedrock.ccl.net (8.8.6/950822.1) id PAA27803; Wed, 9 Jul 1997 15:02:21 -0400 (EDT) Received: from scfv.scripps.edu (scfv.scripps.edu [137.131.240.32]) by relay1.scripps.edu (8.8.5/TSRI-1.5) with SMTP id MAA20360 for ; Wed, 9 Jul 1997 12:02:18 -0700 (PDT) Received: by scfv.scripps.edu (5.x/SMI-SVR4) id AA05165; Wed, 9 Jul 1997 12:02:18 -0700 Date: Wed, 9 Jul 1997 12:02:18 -0700 From: pelleque@scripps.edu (Jean-Luc Pellequer) Message-Id: <9707091902.AA05165@scfv.scripps.edu> To: chemistry@ccl.net Subject: Gaussian 94 optimization X-Sun-Charset: US-ASCII Hi, I am a beginner with Gaussian 94 and would like to know if it is possible to partialy optimize geometry using only cartesian coordinates. Thank you very much, Jean-Luc Pellequer pelleque@scripps.edu From ccl@www.ccl.net Wed Jul 9 15:46:05 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA23009; Wed, 9 Jul 1997 15:05:35 -0400 (EDT) Received: from voimax.voima.jkl.fi for eloranta@voimax.voima.jkl.fi by bedrock.ccl.net (8.8.6/950822.1) id PAA27898; Wed, 9 Jul 1997 15:05:33 -0400 (EDT) Received: (from eloranta@localhost) by voimax.voima.jkl.fi (8.8.5/8.8.5) id WAA06171 for chemistry@ccl.net; Wed, 9 Jul 1997 22:05:42 +0300 From: Jussi Eloranta Message-Id: <199707091905.WAA06171@voimax.voima.jkl.fi> Subject: Summary of SC-IPCM query To: chemistry@ccl.net Date: Wed, 9 Jul 1997 22:05:42 +0300 (EET DST) Content-Type: text Dear netters, Sometime ago I posted a query about references for the SC-IPCM method. Here is the summary of the replies I got - thanks to all who replied. It appears that currently there is no paper describing the SC-IPCM method exactly, altough the references for the IPCM method reveal most of the practical information. Regards, Jussi Eloranta ---- CUT ---- My original posting: Does anyone know references for the SCI-PCM solvent model as implemented in Gaussian 94? The Gaussian manual gives four references which all are under preparation and I was not able to find out if these have been published now. "Exploring Chemistry with Electronic Structure Methods (2nd ed.)" also points to one of these unpublished articles. Also a pointer to good review article on the solvent models would be very helpful. Answers: -------------------------------------- landin@mednet.gu.se wrote: An extensive review on solvation methods has been written by Tomasi et.al. [1] , if merely an overview is desired consult instead Cramer & Truhlar [2] . 1. Tomasi, J. and M. Persico, Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent. Chem. Rev., 1994. 94(7): p. 2027-2094. 2. Cramer, C.J. and D.G. Truhlar, Development and Biological Applications of Quantum Mechanical Continuum Solvation Models, in Quantitative Treatments of Solute/Solvent Interactions, P. Politzer and J.S. Murray, Editors. Vol. 1. 1994, Elsevier Science B. V.: Amsterdam. p. 9-54. --------------------------- mbdtsnm@mchhpf.ch.man.ac.uk wrote: as far as i know there have still been no 'published' accounts of the sci-pcm methods - though i assume that the theory will be very similar to the "IPCM" method which has has a couple of published references.(i don't have them handy but can get them if necessary - they should be easy enough to locate). Just out of interest i think there is a paper coming out in the Aug. 15th edition of J.Chem.Phys. from the lab of J. Tomasi which sets out a new definition of teh cavity surface in the PCM model ( i think that it will be more akin to a connolley type surface with concave parts.) -------------------------- arilahti@ra.abo.fi wrote (loosely translated text): I performed a literature search about SCIPCM about two weeks ago but it appears that the publication is still in preparation. The situation is rather strange because people are working with the model but no one can look at the method more closely. People tend to use the Gaussian manual or the "exploring chemistry with electronic structure methods" as a reference for the method. ------------------------------ albeiro@chemindy.sci.fau.edu wrote: Please check out JACS, 1996, 118, 5408 and the references cited on the methodolgy section. ----- CUT ------- From kotelyan@plmsc.psu.edu Wed Jul 9 17:50:56 1997 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id RAA24703; Wed, 9 Jul 1997 17:48:12 -0400 (EDT) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id RAA16977; Wed, 9 Jul 1997 17:47:57 -0400 (EDT) Date: Wed, 9 Jul 1997 17:47:56 -0400 (EDT) From: Mike Kotelyanskii To: "B. Kallies" cc: chemistry@www.ccl.net Subject: Re: CCL:Definition of van Hove function (MD) In-Reply-To: <9707070715.AA22026@serv.chem.uni-potsdam.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Very nice discussion of the Van Hove Function can be found in the book by J.Higgins and Benoit "Neutron Scattering from Polymers" (Title may not be very accurate, but it sounds like that) If I am not mistaken Allen & Tildesley's "Computer Simulation of Liquids" has it too Hope it helps Mike ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsylvania State University University Park, PA 16802, USA -------------------------------------------------------------------------------- On Mon, 7 Jul 1997, B. Kallies wrote: > > > > Dear Colleagues, > > I'm wondering if anyone knows the definition of the van Hove function. I > know that it is used to describe time-space correlation in MD simulations of > solutions in order to calculate relaxation times of ordered structures like > solvent shells. > > Any information would be helpful. Thanks in advance. > > > ----------------------------------------------------- > Dr. Bernd Kallies > Institut fuer Physikalische und Theoretische Chemie > Universitaet Potsdam > Am Neuen Palais 10 > 14469 Potsdam > GERMANY > e-mail: kallies@serv.chem.uni-potsdam.de > WWW : http://www.chem.uni-potsdam.de/~kallies/kallies.htm > Tel : [+49] (0)331 / 977-1313 > Fax : [+49] (0)331 / 977-1315 > ----------------------------------------------------- > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > >