From chemistry-request@server.ccl.net Wed Nov 27 18:22:02 2002 Received: from web12805.mail.yahoo.com ([216.136.174.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gARNM1i22595 for ; Wed, 27 Nov 2002 18:22:01 -0500 Message-ID: <20021127232201.24017.qmail@web12805.mail.yahoo.com> Received: from [61.9.74.249] by web12805.mail.yahoo.com via HTTP; Wed, 27 Nov 2002 15:22:01 PST Date: Wed, 27 Nov 2002 15:22:01 -0800 (PST) From: amor san juan Subject: Re: CCL:Autodock To: Liu zhiguo , chemistry@ccl.net In-Reply-To: <20021126012642.5775E538F7@smtp01.sohu.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Liu, Based on the manual (appendix 3:AutoDock file formats), "auto" means Autogrid will center grid maps on center of mass of molecule. Finesse, Amor San Juan, MSc candidate University of the Philippines-Diliman PHILIPPINES --- Liu zhiguo wrote: > Dear CCLers, > I have a question about "grid center" in the grid > parameter file.There are two choices for this > parameter:"xyz-coordinate" or "auto".According to > what I know,xyz-coordinate is determined by the > ligand position.Howeve,I don't know what "auto" > means exactly.There is no help about this in > autodock manual.Could anybody tell me what it > means?Any help is appreciated! > > Best Regards! > _______________________________________ > > Liu zhi-guo,Ph.D candidate, > Shanghai Institute of Materia Medica` > Phone:021-64311833-615 > Email:zgliu@sohu.com > _______________________________________ > > > > > -= 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 > > > > > __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chemistry-request@server.ccl.net Thu Nov 28 07:01:38 2002 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gASC1ci23038 for ; Thu, 28 Nov 2002 07:01:38 -0500 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr@ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id NAA03711 for ; Thu, 28 Nov 2002 13:01:37 +0100 Received: (qmail 9103 invoked by uid 525); 28 Nov 2002 12:01:37 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 28 Nov 2002 12:01:37 -0000 Date: Thu, 28 Nov 2002 13:01:37 +0100 (CET) From: To: Pornthep Sompornpisut cc: chemistry@ccl.net Subject: Ki database-summary In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thank you for the replies. In most of the replies the following link was suggested: > www.bindingdb.org Best wishes, Csaba From chemistry-request@server.ccl.net Thu Nov 28 08:42:45 2002 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gASDgji26478 for ; Thu, 28 Nov 2002 08:42:45 -0500 Received: from csuohio.edu (dialup229-229.csuohio.edu [137.148.229.229]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H6A002JNGSMCW@sims.csuohio.edu> for chemistry@ccl.net; Thu, 28 Nov 2002 08:43:36 -0500 (EST) Date: Thu, 28 Nov 2002 08:42:36 -0500 From: Valentin Gogonea Subject: Summary: CHelpG calculation for Fe To: chemistry@ccl.net Message-id: <411AB486-02D7-11D7-BD69-003065CDB448@csuohio.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.548) Content-type: text/plain; format=flowed; charset=US-ASCII; delsp=yes Content-transfer-encoding: 7BIT Dear CCLers, A couple of weeks ago I asked for advice for selecting the radius for Fe(2+) for CHelpG calculations. Thank you very much to all who answered. Valentin Gogonea Cleveland State University Here are the replies that I received: ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------ We never tried to go that far down in the periodic table when we developed some of the radii for other atoms, but I suggest that you use a (consistent) value that represents the van der Waals radius of the atom. The danger of using too large a radius is the loss of information from the other atoms in the molecule, and an underdetermined charge fitting model. Good luck with your experimentation. I suggest you try several reasonable values and then see if the charges computed for all of the atoms are reasonably consistent. Curt Breneman RPI Chemistry ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------ From gromacs list: I did gaussian 98 calculations on Fe(III). Here are my notes concerning the radii that I used. Hope it helps, Cheers, Marc For iron there are several ionic radii. Let's use radii from http://www.webelements.com/webelements/elements/text/Fe/radii.html. o Fe(III) 6-coordinate, octahedral 69 pm o Fe(III) 6-coordinate, octahedral, high spin 78.5 pm Note: The "efective ionic radii" quoted here assume that the ionic radius of F- is 133 pm and that of O2- is 140 pm. The values for iron thus correspond quite well to che tabulated Gaussian Merz-Kollman radii, and will be scaled for Francl and Breneman, with a mean factor for F- and O2-. Values depend upon the coordination number and for d-block metals on the fact whether or not the metal is in a high or low spin state. Atomnb AtTyp Merz-Kollman Francl Breneman (CHELP) (CHELPG) ............. ............. ............. ............. ............. 26 Fe 0.69 0.75 0.85 6-coordinate, octahedral 26 Fe 0.785 0.85 0.97 6-coordinate, octahedral, high spin ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------ you could try a number of different radii and see where the charges are approximately constant. I would guess a radius of 2.0 A. Please, see our article, where we determine a radius for Cu2+: E. Sigfridsson & U. Ryde (1998) "A comparison of methods for deriving atomic charges from the electrostatic potential and moments". J. Comp. Chem. 19, 377-395. Best regards, Ulf ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------ We typically use Fe radius of 1.5A, sometimes even 1.3A, but the Fe(3+) or Fe(2+) is nearly always surrounded by ligands and the whole complex is treated by quantum calc's (DFT), so the Fe radius is not important. Use of the bare ion alone will lead to poor properties, as we showed in an Inorg. Chem. paper on metal cations in water in 1996. Best Regards, Lou Noodleman ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------ To read in a radius for Fe, use the option "pop=(chelpg,ReadAtRadii)". These values are usually not the textbook van der Waals radii, but radii that have been chosen by the authors of a given charge scheme. The choice of a radius for an element that was not in the original parameter set is a judgment call and depends somewhat on the task at hand (whether the atom is ionic, for example). Below is an example input file in which I arbitrarily chose to use the metallic radius of Fe. #p rhf/sto-3g scf=tight symm=loose pop=(chelpg,readradii) test ferrocene example 0 1 Fe -0.000000 -0.000000 0.000000 X -0.000000 0.000000 -2.160000 C -0.000000 1.250000 -2.160000 C 1.188821 0.386271 -2.160000 C -1.188821 0.386271 -2.160000 H 0.113936 2.334029 -2.160000 C 0.734732 -1.011271 -2.160000 H 2.255002 0.612895 -2.160000 C -0.734732 -1.011271 -2.160000 H -2.184585 0.829614 -2.160000 H 1.279732 -1.955239 -2.160000 H -1.464084 -1.821299 -2.160000 X 0.000000 0.000000 2.160000 C 0.000000 1.250000 2.160000 C -1.188821 0.386271 2.160000 C 1.188821 0.386271 2.160000 H -0.113936 2.334029 2.160000 C -0.734732 -1.011271 2.160000 H -2.255002 0.612895 2.160000 C 0.734732 -1.011271 2.160000 H 2.184585 0.829614 2.160000 H -1.279732 -1.955239 2.160000 H 1.464084 -1.821299 2.160000 Fe 1.24 Regards, Jim Hess From chemistry-request@server.ccl.net Thu Nov 28 02:51:24 2002 Received: from pallas_ex003.pallas_uk ([195.167.133.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAS7pNi08716 for ; Thu, 28 Nov 2002 02:51:23 -0500 Received: by pallas_ex003.pallas_uk with Internet Mail Service (5.5.2653.19) id ; Thu, 28 Nov 2002 07:54:46 -0000 Message-ID: <2A5044E3B5F36440814C888668E9D6A564E9AF@pallas_ex003.pallas_uk> From: David Clark To: "'chemistry@ccl.net'" Subject: Tools for HTS Data Analysis Date: Thu, 28 Nov 2002 07:54:45 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi Does anyone have any experience that they would be willing to share of tools for HTS data analysis, particularly those that aim to help in the analysis of (qualitative) SAR? I will summarise any responses for the list. Many thanks David E. Clark, PhD. Project Leader (Computer-Aided Drug Design) Argenta Discovery Ltd. 8/9 Spire Green Centre Harlow Essex CM19 5TR United Kingdom Telephone Direct: +44 (0) 1279 645 611 Telephone Switchboard: +44 (0) 1279 645 645 Fax: +44 (0) 1279 645 646 E-mail: david.clark@argentadiscovery.com Web site: www.argentadiscovery.com Legal Notice Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this e-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this e-mail or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you are not an addressee, please inform the sender immediately. Further, Argenta Discovery makes every effort to keep its network free from viruses including the scanning of incoming and outgoing mail. However, you do need to check this e-mail and any attachments to it for viruses, as Argenta Discovery can take no responsibility for any computer virus that might be transferred by way of this e-mail. Argenta Discovery Limited is registered in England: No. 3671653 with its registered office at 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, CM19 5TR, UK VAT registration number GB 736 3943 12 From chemistry-request@server.ccl.net Thu Nov 28 17:20:02 2002 Received: from mail1.ceniai.inf.cu ([169.158.128.142]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gASMJwi00649 for ; Thu, 28 Nov 2002 17:19:59 -0500 Received: from uucp.ceniai.inf.cu (uucp.ceniai.inf.cu [169.158.128.157]) by mail1.ceniai.inf.cu (8.11.0/8.11.0) with ESMTP id gASMJjZ21945 for ; Thu, 28 Nov 2002 17:19:45 -0500 (CST) Received: (from uucp@localhost) by uucp.ceniai.inf.cu (8.11.6/8.11.6) with UUCP id gASMMw027274 for chemistry@ccl.net; Thu, 28 Nov 2002 17:22:58 -0500 (CST) (envelope-from amesa@info.isctn.edu.cu) Received: from ctn.isctn.edu.cu by isctn.edu.cu with smtp (Smail3.1.29.1 #312) id m18HWRD-000oDEC; Thu, 28 Nov 2002 16:43 CST Received: from localhost by ctn.isctn.edu.cu with bsmtp (Smail3.1.29.1 #229) id m1Vm24o-000X0nC; Thu, 28 Nov 2013 08:56 CST Message-Id: From: "Ariel Mesa Ibirico" To: chemistry@ccl.net Date: Thu, 28 Nov 2002 17:36:07 -0500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Paralelized MOPAC Priority: normal X-mailer: Pegasus Mail for Windows (v2.31) Hello! I am a MOPAC user and I have been recently provided with a Linux cluster. Since that point everything is happy but, there is always a but, I have no any paralelized version of MOPAC. Could anyone tell me how can I get it? Best regards! Ariel ___________________________________ Ariel Mesa Ibirico Estudiante de Radioquimica Instituto de Ciencias y Tecnologia Nucleares