From chemistry-request@server.ccl.net Fri Feb 28 03:34:46 2003 Received: from mail4.bluewin.ch ([195.186.4.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1S8Yja02927 for ; Fri, 28 Feb 2003 03:34:46 -0500 Received: from bluewin.ch (213.3.110.169) by mail4.bluewin.ch (Bluewin AG 6.7.015) id 3E1046D9005B3A10; Fri, 28 Feb 2003 08:33:50 +0000 Message-ID: <3E5F1E21.DE77FC8@bluewin.ch> Date: Fri, 28 Feb 2003 09:30:25 +0100 From: Borosy Andras Organization: free lance X-Mailer: Mozilla 4.77C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: Su Wu CC: David Livingstone , "Adel Abbas Ali Elazhary Sci. College" , chemistry@ccl.net Subject: Re: CCL:Drug design and QSAR books References: <3E5A3946.7982.1589C8E@localhost> <3E5B8FAC.8000002@ele.uri.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Colleagues, You may have a look on: http://www.qsar.org/resource/books.htm Regards, Andras Borosy > Having read it, I would highly recommend Livingstone's book as well. > > Su > > David Livingstone wrote: > > > Hi, > > > > > >>Dear ccl folks: > >> > >>I would gratly appreciate it if someone would recommend a book or > >>books about drug design and QSAR to read for someone who does not know > >>much about. > >> > > > > Well I would recommend mine, wouldn't I ? "Data Analysis for > > Chemists; Application to QSAR and chemical product design" Oxford > > University Press,1995, ISBN 0 19 855728 0. > > > > I can e-mail a contents list if you're interested. > > > > Cheers, > > > > Dave. > > > > > > > > ------------------------------------------------------------------ > > D.J. Livingstone ChemQuest > > Delamere House, 1 Royal Crescent, > > Sandown. Isle of Wight UK PO36 8LZ > > > > Phone & Fax: +44 (0)1983 401793 > > e-mail davel@chmqst.demon.co.uk http://www.chmqst.demon.co.uk > > ------------------------------------------------------------------ > > > > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Feb 28 02:10:42 2003 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1S7Afa28725 for ; Fri, 28 Feb 2003 02:10:41 -0500 Received: from cosmologic.de (xdsl-195-14-220-29.netcologne.de [195.14.220.29]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id AAO64503 (AUTH klamt@cosmologic.de); Fri, 28 Feb 2003 08:10:37 +0100 (CET) Message-ID: <3E5F0B6B.10300@cosmologic.de> Date: Fri, 28 Feb 2003 08:10:35 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,pdf MIME-Version: 1.0 To: Ian Hovell CC: "'chemistry@ccl.net'" Subject: Re: CCL:Solvation method References: <216FE3CA3D4DD611AE2600105AD16BDFD56AC5@correio.cetem.gov.br> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Ian, I am afraid that none of your suggested methods is really leading you to a good description of solvation in nitrobenzene. - All semiempirical methods (at least the well distributed ones that I know)have a large error in the dipole moments of the nitro group and of other nitrogen containing functional groups. Hence you cannot expect a realistic desription of solvation from them. - I am not aware that the explicit simulation of solvent molecules like nitrobenzene has really led to a good systematic description of solvation differences of solutes and it is also quite cumbersome to guarantee a good explicit solvation of different molecules. You would definitely need samplig over lots of configurations to get unbiased results. My suggestion is to use COSMO-RS in form of our program COSMOtherm. It is a combination of continuum solvation and statistical thermodynamics, and it is proven to be well abloe to handle almost all kinds of solvents and mixtures, even at variable temperature. In November we won the "First Industrial Fluid Properties Simulation Challenge on VLE Prediction" organized by NIST and AICHE, and one of the solvent occuring in that challenge was nitroethane. So I am extremely confident that COSMOtherm will give very reliable results for solvation in nitrobenzene. The underlying quantum chemical level is DFT, e.g. using the program TURBOMOLE. But Gaussian98_A11 can also be used. Be sure, such DFT/COSMO calculations do not take much time. For a Naphthalene TURBOMOLE would require about an hour or less on a LINUX PC (about 1.5 MHz). Probably they are much faster than doing lots of explicit solvent calculations. For more information see our web-site. Regards Andreas Ian Hovell wrote: > I am planning on carrying out an AM1 analysis on the solvation of aromatic > compounds in nitrobenzene. > Which method would be best? > 1. Using explicit solvent molecules in a cage around the solute in vacuo or > period box > 2. Or using an implicit solvent and minimising the molecule with AMBER > before using AM1 > The first method as I see it would take a lot longer to compute but I am not > sure yet about how to go about the second method. > Any help would be greatly welcome > Thanks > Ian > > Ian Hovell - Ph.D. > NUCLEO DE MODELAGEM MOLECULAR-NMM > Centro de Tecnologia Mineral - CETEM > Ministerio da Ciência e da Tecnologia- MCT > Avenida Ipê, No 900 - Cidade Universitaria > Ilha do Fundão Rio de Janeiro RJ Brasil > CEP 21941-590 > tel 00 55 (xx) 3865 7344 ou 3865 - 7216 > Fax 00 55 (xx) 22602837 ou 2290-4286 > e-mail hovell@cetem.gov.br > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Feb 28 05:25:54 2003 Received: from antivirus.unimo.it ([155.185.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1SAPra24684 for ; Fri, 28 Feb 2003 05:25:53 -0500 Received: from mail.unimo.it (mail.unimo.it [155.185.1.1]) by antivirus.unimo.it (8.12.5/8.12.5) with ESMTP id h1SAPonc020533 for ; Fri, 28 Feb 2003 11:25:50 +0100 Received: (from nobody@localhost) by mail.unimo.it (2.1.2/8.9.1/Execmail 2.1) id LAA1160147; Fri, 28 Feb 2003 11:25:50 +0100 (CET) To: chemistry@ccl.net Subject: Database screening with Autodock Message-ID: <1046427950.3e5f392e06c3d@mail.unimo.it> Date: Fri, 28 Feb 2003 11:25:50 +0100 (CET) From: 5516@mail.unimo.it MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.4 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Hi, my question is about database screening with AUTODOCK3.0.5; If possible i would like to screen entire ACD database with autodock, but i'm still looking for someone who did it... I know there is no a "standard" method to do this, but i think it's possible with some shell scripts... Have you some information about this question? Thanks in advance for your help. Marco Marco Parenti Universita' di Modena e Reggio Emilia Dipartimento di Scienze farmaceutiche 41100 Modena Italy e-mail 5516@unimo.it From chemistry-request@server.ccl.net Fri Feb 28 09:40:13 2003 Received: from interscan ([195.172.92.249]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1SEeCa14920 for ; Fri, 28 Feb 2003 09:40:13 -0500 Received: by MAIL01 with Internet Mail Service (5.5.2653.19) id <1Y4RCPK1>; Fri, 28 Feb 2003 15:31:00 -1200 Message-ID: <018F838C6F87D611B129000347AEA59FD9DCCE@UKSMA01> From: "Charlton, Michael" To: "'chemistry@ccl.net'" Subject: Scanned image -> molecular structure Date: Fri, 28 Feb 2003 02:40:49 -1200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, Does anybody know of software that will convert scanned images of 2D structures into something like a MOL file ? Thanks in advance, Michael Charlton. From chemistry-request@server.ccl.net Fri Feb 28 10:55:29 2003 Received: from c001.snv.cp.net ([209.228.32.127]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1SFtTa22424 for ; Fri, 28 Feb 2003 10:55:29 -0500 Received: (cpmta 26556 invoked from network); 28 Feb 2003 07:55:28 -0800 Received: from 209.228.32.129 (HELO mail.roberttopper.com.criticalpath.net) by smtp.register-admin.com (209.228.32.127) with SMTP; 28 Feb 2003 07:55:28 -0800 X-Sent: 28 Feb 2003 15:55:28 GMT Received: from [12.89.67.100] by mail.roberttopper.com with HTTP; Fri, 28 Feb 2003 07:55:28 -0800 (PST) Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 To: chemistry@ccl.net Cc: topper@cooper.edu From: topper@cooper.edu Subject: ECCC9 Online Conference Now Open To All X-Sent-From: roberttopper@roberttopper.com Date: Fri, 28 Feb 2003 07:55:28 -0800 (PST) X-Mailer: Web Mail 5.2.3-0_sol28 Message-Id: <20030228075528.1044.h015.c001.wm@mail.roberttopper.com.criticalpath.net> Dear colleagues, The 9th Electronic Computational Chemistry Conference is now underway! Please visit http://eccc9.cooper.edu to view any of 40 presentations and participate in the online discussions. ECCC9 will end on Monday, March 31. With best regards, Robert Topper ECCC9 Principal Organizer ***************************************************************************** 9th ELECTRONIC COMPUTATIONAL CHEMISTRY CONFERENCE MARCH 2003 http://eccc9.cooper.edu ***************************************************************************** Robert Q. Topper, Ph.D. Associate Professor of Chemistry School of Engineering The Cooper Union for the Advancement of Science and Art 51 Astor Place New York, NY 10003 phone: (212) 353-4378 fax: (212) 353-4341 ***************************************************************************** http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** From chemistry-request@server.ccl.net Fri Feb 28 13:43:26 2003 Received: from adenine.cgl.ucsf.edu ([169.230.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1SIhQa07674 for ; Fri, 28 Feb 2003 13:43:26 -0500 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.3/8.12.3/GSC1.16) with ESMTP id h1SIhQPo935463 for ; Fri, 28 Feb 2003 10:43:26 -0800 (PST) Date: Fri, 28 Feb 2003 10:43:26 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry@ccl.net Subject: sofwares for non-linear fitting!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, What are the best softwares (free and for UNIX) to do non-linear fitting for a very large amount of data? Thanks. Pradipta