From chemistry-request@ccl.net Wed Feb 11 03:45:29 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1B8jSU6004763 for ; Wed, 11 Feb 2004 03:45:29 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id i1B8jhcD096958 for ; Wed, 11 Feb 2004 09:45:43 +0100 (CET) X-Ids: 166 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i1B8jZKE060784; Wed, 11 Feb 2004 09:45:35 +0100 (MET) Date: Wed, 11 Feb 2004 09:45:35 +0100 (MET) From: Michel Petitjean Message-Id: <200402110845.i1B8jZKE060784~at~ds10.itodys.jussieu.fr> To: chemistry~at~ccl.net Subject: CCL: Re:One question about protein-ligand binding X-Miltered: at shiva.jussieu.fr with ID 4029EBB7.002 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: chemistry~at~ccl.net Subject: CCL: Re:One question about protein-ligand binding >Baoqiang Cao wrote: >Dear all, > >Are there any ways to quantitatively describe how well a ligand fits a >protein cavity? Any clues will be welcome! >Thanks. > >Best, > Cao If you have the atom-pairs (e.g. H bonds, vdw bonds), a simple criterion is the variance: M.Petitjean, Internet Electron J. Mol. Des., 2002,1[4],185-192. http://www.biochempress.com Note: a rigorous definition of what is a cavity is difficult. The ALVIS software offer a simple approach, but it is parametrized by the radius of the probe. Michel Petitjean, Email: petitjean~at~itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean~at~ccr.jussieu.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html From chemistry-request@ccl.net Wed Feb 11 06:43:04 2004 Received: from oceanite.ens-lyon.fr (oceanite.ens-lyon.fr [140.77.1.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BBh3U6010904 for ; Wed, 11 Feb 2004 06:43:04 -0500 Received: from localhost (oceanite.ens-lyon.fr [127.0.0.1]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id DB34B3203C1; Wed, 11 Feb 2004 12:43:05 +0100 (CET) Received: from oceanite.ens-lyon.fr ([127.0.0.1]) by localhost (oceanite [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 28667-09; Wed, 11 Feb 2004 12:43:05 +0100 (CET) Received: from ens-lyon.fr (unknown [140.77.2.15]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id A461C32039D; Wed, 11 Feb 2004 12:43:05 +0100 (CET) Message-ID: <402A2464.8080005|at|ens-lyon.fr> Date: Wed, 11 Feb 2004 12:47:32 +0000 From: Paul Fleurat-Lessard Reply-To: Paul.Fleurat-Lessard|at|ens-lyon.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.3.1) Gecko/20030428 X-Accept-Language: fr, en MIME-Version: 1.0 To: Richard Gillilan Cc: "Taras V. Pogorelov" , chemistry|at|ccl.net Subject: Re: CCL:J.Comp.Chem. Style File Needed References: <2DF29162-5C33-11D8-83BA-003065963E2C|at|cornell.edu> In-Reply-To: <2DF29162-5C33-11D8-83BA-003065963E2C|at|cornell.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new-20030616-p5 (Debian) at ens-lyon.fr X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, > The only thing I can't do so far is get it to insert a > dash in place of sequential citation numbers: > [10,11,12,13] -> [10-13]. I would love to know > a trick for this. Anyhow, you are welcome to the file > if you can't find something better out there. I am using the package 'cite' (\usepackage{cite}) to do this with latex. You can also use the package 'overcite' depending on the way you want the call to your references to appear in the text. Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard|at|ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 84 83 69364 Lyon Cedex 07 From chemistry-request@ccl.net Wed Feb 11 04:30:55 2004 Received: from irsun275.ifp.fr ([156.118.220.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1B9UrU6006417 for ; Wed, 11 Feb 2004 04:30:54 -0500 Received: from smtp.ifp.fr by irsun275.ifp.fr (V35.12) with ESMTP Received: from irnts21.ifp.fr (irnts21.ifp.fr [156.118.15.51]) by irsun165.ifp.fr (8.8.5/8.8.5) with ESMTP id KAA21670 for ; Wed, 11 Feb 2004 10:30:12 +0100 (MET) Received: by irnts21.ifp.fr with Internet Mail Service (5.5.2657.72) id <1M6NNX02>; Wed, 11 Feb 2004 10:30:12 +0100 Message-ID: <3AA99E087354D61185E4002048403CFC02145B11_at_irnts23.ifp.fr> From: DE BRUIN theodorus To: "'chemistry_at_ccl.net'" Subject: calculation of pka valuse by ab initio methods Date: Wed, 11 Feb 2004 10:30:11 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3F081.A5B277D0" X-Spam-Status: No, hits=0.8 required=7.0 tests=HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C3F081.A5B277D0 Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, According to you, what is the best method to calculate absolute pKa values, i.e. without first deriving some linear semi-empirical equation for a training set, but to calculate pKa directly from the Delta G of the dissociation reaction. I would like to calculate pKa values for some medium sized molecules, NOT just in water, but in mixtures of water with alcohols for which experimental data are very sparse. I am aware that the calculated solvation energy for charged species can contain relatively big errors, affecting Delta G and finally resulting in errors of several units in the pKa value. According to some people, this problem can partially be overcome by applying continuum models in which explicitly some solvent molecules are taken up. Is DFT accurate enough, which continuum model is best, etc... I'll summarize the results. Thanks in advance, Theo de BRUIN ------_=_NextPart_001_01C3F081.A5B277D0 Content-Type: text/html; charset="iso-8859-1"
Dear CCLers,
 
According to you, what is the best method to calculate absolute pKa values, i.e. without first deriving some linear semi-empirical equation for a training set, but to calculate pKa directly from the Delta G of the dissociation reaction. I would like to calculate pKa values for some medium sized molecules, NOT just in water, but in mixtures of water with alcohols for which experimental data are very sparse.

I am aware that the calculated solvation energy for charged species can contain relatively big errors, affecting Delta G and finally resulting in errors of several units in the pKa value.
According to some people, this problem can partially be overcome by applying continuum models in which explicitly some solvent molecules are taken up.
Is DFT accurate enough, which continuum model is best, etc...
 
I'll summarize the results.
 
Thanks in advance,
Theo de BRUIN
------_=_NextPart_001_01C3F081.A5B277D0-- From chemistry-request@ccl.net Wed Feb 11 03:37:57 2004 Received: from fitch3.uni2.net (fitch3.uni2.net [130.227.52.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1B8btU6004534 for ; Wed, 11 Feb 2004 03:37:56 -0500 Received: from HLUSF26A.lundbeck.com ([130.227.160.123]) by fitch3.uni2.net (8.12.6/8.11.6) with SMTP id i1B8c2JY014940 for ; Wed, 11 Feb 2004 09:38:10 +0100 Received: from ([172.16.0.163]) by HLUSF26A.lundbeck.com; Wed, 11 Feb 2004 09:37:33 +0100 (CET) Received: FROM ludk0006.lundbeck.com BY ludk0163.lundbeck.com ; Wed Feb 11 09:37:57 2004 +0100 Received: by ludk0006.lundbeck.com with Internet Mail Service (5.5.2657.72) id <1HB5CDKF>; Wed, 11 Feb 2004 09:37:58 +0100 Message-ID: From: Jan Torleif Pedersen To: "'chemistry_at_ccl.net'" Subject: Snake plot program - round 2 Date: Wed, 11 Feb 2004 09:37:53 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Greetings again, And thanks for all the input on the snake plotting program. So three options fell out of the survey, none of which were really satisfying so it appears that there is scope for a nice tool here. The result of the query was: 1) Viseur by Champagne http://icbtools.med.cornell.edu/viseur/overview.html Development of this seems to have stopped - am I right ? Does not appear to make snake plots in an intelligent way, long intracellular loops result in a three page postscript file with the insert. Also does not remove alignment gaps when making the snake plot. 2) The SOSUI tool http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html This is a web-based tool and can not be used for proprietary sequences. 3) Use a molecular modelling program and make a nice ribbon drawing. Ahhh well that is an option but the cartoons do have some pedagogical advantages. Any other ideas are welcome. Or if anybody has a few lines of code that generate a PostScript that would be appreciated. Regards -- Jan Dr. Jan Torleif Pedersen Section head, Bioinformatics Department of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 DK-Valby Denmark phone: +45 36 43 28 87 FAX: +45 36 43 82 53 email: jatp_at_lundbeck.com From chemistry-request@ccl.net Wed Feb 11 11:06:13 2004 Received: from correo1.us.es (correo1.us.es [150.214.9.229]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BG6CU6021470 for ; Wed, 11 Feb 2004 11:06:12 -0500 Received: from correo1.us.es (localhost.localdomain [127.0.0.1]) by correo1.us.es (8.11.7/8.11.1) with ESMTP id i1BG6UJ19164 for ; Wed, 11 Feb 2004 17:06:30 +0100 Received: from simulux.us.es (IDENT:root{at}simulux.us.es [150.214.145.66]) by correo1.us.es (8.11.7/8.11.1) with ESMTP id i1BG6Op19130; Wed, 11 Feb 2004 17:06:24 +0100 Received: from localhost (rafapa@localhost) by simulux.us.es (8.11.6/8.11.1) with ESMTP id i1BGBre21260; Wed, 11 Feb 2004 17:11:53 +0100 Date: Wed, 11 Feb 2004 17:11:53 +0100 (CET) From: "Rafael R. Pappalardo" To: Mehdi Bounouar cc: Subject: Re: CCL:G03 test jobs In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Tue, 10 Feb 2004, Mehdi Bounouar wrote: > > Hello, > > I'm trying to run the Gaussian test jobs, but apparently some jobs (see > list) just stops without any error messages. > > Any clue? has somebody experienced that before ? > > > Thanks > > > Which operating system, compiler and hardware are you using? Regards Rafael -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa{at}simulux.us.es From chemistry-request@ccl.net Wed Feb 11 15:28:29 2004 Received: from mail.med.cornell.edu (mail.med.cornell.edu [140.251.3.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BKSSU6001926 for ; Wed, 11 Feb 2004 15:28:28 -0500 Received: from FABIEN ([140.251.76.36]) by mail.med.cornell.edu (Netscape Messaging Server 3.6) with ESMTP id AAA53064; Wed, 11 Feb 2004 15:28:42 -0500 From: "Fabien Campagne" To: "'Jan Torleif Pedersen'" , Subject: RE: Snake plot program - round 2 Date: Wed, 11 Feb 2004 15:31:07 -0500 Message-ID: <000f01c3f0dd$ff368e70$244cfb8c@FABIEN> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal In-Reply-To: X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Greetings, The development of Viseur has stopped in 1998. I agree that the algorithm that Viseur used to build snake-plots is by today's standards a bit primitive. See [3] for a different and more flexible method. If you are interested in snake-plots, please check out the Residue-based Diagram editor: http://icb.med.cornell.edu/crt/RbDe/Rbde.xml [1] (This is a web-based application) For batch processing of snake-plots and other residue-based diagrams, please see our Residue-based Diagram Generator, RbDg: http://icb.med.cornell.edu/crt/RbDg/index.xml [2] These two tools are actively developed and maintained. Free academic licenses are offered. Nonexclusive site-licenses are available for industry through the Cornell Research Foundation. Contact me directly if you are interested. I am not a CCL subscriber. [1] Skrabanek L, Campagne F, Weinstein H. Building protein diagrams on the web with the residue-based diagram editor RbDe. Nucleic Acids Res. 2003 Jul 1;31(13):3856-8. [2] Campagne F, Bettler E, Vriend G, Weinstein H. Batch mode generation of residue-based diagrams of proteins. Bioinformatics. 2003 Sep 22;19(14):1854-5. [3] Campagne F, Weinstein H. Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins. J Mol Graph Model. 1999 Jun-Aug;17(3-4):207-13. Fabien Campagne, PhD -- http://icb.med.cornell.edu Bioinformatics Officer, Institute for Computational Biomedicine Assistant Professor, Dept. of Physiology and Biophysics Weill Medical College of Cornell University ---------------------- phone: (212)-327-8341 c/o Rockefeller University, Smith Hall 410 fax: (212)-327-7344 Box 270; 1230 York Avenue ----------------------- New York, NY 10021 ----------------------- -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request[at]ccl.net] On Behalf Of Jan Torleif Pedersen Sent: Wednesday, February 11, 2004 3:38 AM To: 'chemistry[at]ccl.net' Subject: CCL:Snake plot program - round 2 Greetings again, And thanks for all the input on the snake plotting program. So three options fell out of the survey, none of which were really satisfying so it appears that there is scope for a nice tool here. The result of the query was: 1) Viseur by Campagne http://icbtools.med.cornell.edu/viseur/overview.html Development of this seems to have stopped - am I right ? Does not appear to make snake plots in an intelligent way, long intracellular loops result in a three page postscript file with the insert. Also does not remove alignment gaps when making the snake plot. 2) The SOSUI tool http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html This is a web-based tool and can not be used for proprietary sequences. 3) Use a molecular modelling program and make a nice ribbon drawing. Ahhh well that is an option but the cartoons do have some pedagogical advantages. Any other ideas are welcome. Or if anybody has a few lines of code that generate a PostScript that would be appreciated. Regards -- Jan Dr. Jan Torleif Pedersen Section head, Bioinformatics Department of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 DK-Valby Denmark phone: +45 36 43 28 87 FAX: +45 36 43 82 53 email: jatp[at]lundbeck.com -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY[at]ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Feb 11 13:37:08 2004 Received: from calmail-me.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BIb5U6029501 for ; Wed, 11 Feb 2004 13:37:06 -0500 Received: from [128.32.198.76] (account shaji[at]calmail.berkeley.edu) by calmail-me.berkeley.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 852167 for chemistry[at]ccl.net; Wed, 11 Feb 2004 10:37:20 -0800 From: "CHEMPATH, SHAJI" Subject: solvation in Gassian03 To: chemistry[at]ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Wed, 11 Feb 2004 10:37:20 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello CCLers, I am trying to do geometry-optimizations with SCRF=PCM or SCRF=SCIPCM. I can get the runs to converge only for very simple molecules like "H2O". For anything compilcated, like "H2SO4", the optimization does not converge. Here is a sample of my input file. Is there anything I can do to get the optimizations to converge? (Note: I am new to quantum computational chemistry and Gaussian 03). Thanks in advance Shaji. (shaji[at]berkeley.edu) --- input file --------------------------------- %rwf=500MB %mem=500MB #p HF/LANL2DZ Opt scrf=(pcm) scf=tight h2so4 in water-test of gaussian test 0 1 S -0.094478 -0.000002 0.119257 ... more coordinates....... From chemistry-request@ccl.net Wed Feb 11 13:09:10 2004 Received: from um-exproto5.um.umsystem.edu (um-exproto5.um.umsystem.edu [207.160.151.45]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BI9AU6028054 for ; Wed, 11 Feb 2004 13:09:10 -0500 Received: from UM-EMAIL04.um.umsystem.edu ([207.160.151.17]) by um-exproto5.um.umsystem.edu with Microsoft SMTPSVC(6.0.3790.0); Wed, 11 Feb 2004 12:09:15 -0600 Received: webmail.um.umsystem.edu 207.160.151.19 from 207.160.151.42 207.160.151.42 via HTTP with MS-WebStorage 6.5.6944 Received: 207.160.151.42 207.160.151.42 from 128.206.124.129 128.206.124.129 via HTTP with MS-WebStorage 6.5.6944 MIME-Version: 1.0 content-class: urn:content-classes:message From: "Janosi, Lorant (UMC-Student)" Content-Type: multipart/alternative; boundary="_40EF3CCA-D55D-4D8C-BAF2-146B0DADBC83_" Subject: forcefield parameters To: "chemistry|at|ccl.net" Thread-Topic: forcefield parameters Thread-Index: AcPwyf44+gGGtDfRQnqZik8hfcCdOQ== Message-ID: <92FE3800-AC0C-4652-B330-20DE149B79DD@mimectl> X-Mailer: Microsoft Outlook Web Access 6.5.6944.0 X-MimeCtl: Produced By Microsoft Exchange V6.5.6944.0 Date: Wed, 11 Feb 2004 12:08:04 -0600 X-OriginalArrivalTime: 11 Feb 2004 18:09:15.0113 (UTC) FILETIME=[28909590:01C3F0CA] X-Spam-Status: No, hits=2.2 required=7.0 tests=FORGED_OUTLOOK_TAGS, FROM_HAS_MIXED_NUMS,HTML_30_40,HTML_MESSAGE,TO_ADDRESS_EQ_REAL autolearn=no version=2.61 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --_40EF3CCA-D55D-4D8C-BAF2-146B0DADBC83_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, I am interested in a Molecular Dynamics simulation of a system using CHARMm= forcefiled. In order to do that, I need to compute the forcefield paramete= rs for some molecules. I was thinking in using gaussian (98 / 03), but I do= n't know how these forcefield parameters are computed. Any help or suggesti= on would be more than welcome. Thanks a lot. Lori. Univ. of Missouri-Columbia --_40EF3CCA-D55D-4D8C-BAF2-146B0DADBC83_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
I am interested in a Molecular Dynamics si= mulation of a system using CHARMm forcefiled. In order to do that, I need t= o compute the forcefield parameters for some molecules. I was thinking in u= sing gaussian (98 / 03), but I don't know how these forcefield parameters a= re computed. Any help or suggestion would be more than welcome.
Thanks a lot.
Lori.
 
Univ. of Missouri-Columbia
 
--_40EF3CCA-D55D-4D8C-BAF2-146B0DADBC83_-- From chemistry-request@ccl.net Wed Feb 11 13:48:55 2004 Received: from ns1.scripps.edu (ns1.scripps.edu [192.42.82.59]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BImpU6030054 for ; Wed, 11 Feb 2004 13:48:52 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id i1BIn6U12305 for ; Wed, 11 Feb 2004 10:49:06 -0800 (PST) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id e199d722_5cc2_11d8_8a92_00304811a0c8_902; Wed, 11 Feb 2004 18:48:28 +0000 (UTC) Received: from chagall.scripps.edu (chagall [137.131.252.60]) by relay1.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id i1BImS002768; Wed, 11 Feb 2004 10:48:28 -0800 (PST) Received: from titan.scripps.edu (titan [137.131.252.36]) by chagall.scripps.edu (SGI-8.9.3/TSRI-3.2.1) with ESMTP id KAA08317; Wed, 11 Feb 2004 10:48:27 -0800 (PST) Date: Wed, 11 Feb 2004 10:50:04 -0800 Subject: Re: CCL:J.Comp.Chem. Style File Needed Content-Type: multipart/alternative; boundary=Apple-Mail-4--566043685 Mime-Version: 1.0 (Apple Message framework v481) Cc: Richard Gillilan , "Taras V. Pogorelov" , chemistry_at_ccl.net To: Paul Fleurat-Lessard From: Antitsa Stoycheva In-Reply-To: <402A2464.8080005_at_ens-lyon.fr> Message-Id: <1A858B72-5CC3-11D8-8DA6-000393A45DEC_at_scripps.edu> X-Mailer: Apple Mail (2.481) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-4--566043685 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Continuing the discussion: \usepackage{citesort} will also do the trick. Antitsa --------------------------------------- Antitsa D. Stoycheva, Ph. D. Postdoctoral Associate The Scripps Research Institute and Center for Theoretical Biological Physics and Department of Physics University of California at San Diego antitsa_at_scripps.edu On Wednesday, February 11, 2004, at 04:47 AM, Paul Fleurat-Lessard wrote: > Dear CCLers, >> The only thing I can't do so far is get it to insert a >> dash in place of sequential citation numbers: >> [10,11,12,13] -> [10-13]. I would love to know >> a trick for this. Anyhow, you are welcome to the file >> if you can't find something better out there. > > I am using the package 'cite' (\usepackage{cite}) to do this with > latex. You can also use the package 'overcite' depending on the way you > want the call to your references to appear in the text. > > > Paul. > > -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat- > Lessard_at_ens-lyon.fr > Laboratoire de Chimie > Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 > 46, Allie d'Italie Fax: + 33 (0)4 72 72 84 83 > 69364 Lyon Cedex 07 > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST_at_ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow_at_nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > --Apple-Mail-4--566043685 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Continuing the discussion: \usepackage{citesort} will also do the trick. Antitsa --------------------------------------- Antitsa D. Stoycheva, Ph. D. Postdoctoral Associate The Scripps Research Institute and Center for Theoretical Biological Physics and Department of Physics University of California at San Diego antitsa_at_scripps.edu On Wednesday, February 11, 2004, at 04:47 AM, Paul Fleurat-Lessard wrote: Dear CCLers, The only thing I can't do so far is get it to insert a dash in place of sequential citation numbers: [10,11,12,13] -> [10-13]. I would love to know a trick for this. Anyhow, you are welcome to the file if you can't find something better out there. I am using the package 'cite' (\usepackage{cite}) to do this with latex. You can also use the package 'overcite' depending on the way you want the call to your references to appear in the text. Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard_at_ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 84 83 69364 Lyon Cedex 07 -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY_at_ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow_at_nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --Apple-Mail-4--566043685-- From chemistry-request@ccl.net Wed Feb 11 18:37:35 2004 Received: from antivirus2.its.rochester.edu (antivirus2.its.rochester.edu [128.151.57.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BNbXU6010210 for ; Wed, 11 Feb 2004 18:37:34 -0500 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with ESMTP id i1BNbpLM003518 for ; Wed, 11 Feb 2004 18:37:51 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with SMTP id i1BNboMW003514 for ; Wed, 11 Feb 2004 18:37:51 -0500 (EST) Received: from mail.rochester.edu (mail.rochester.edu [128.151.224.17]) by mail.rochester.edu (8.12.10/8.12.1) with SMTP id i1BNblUE009737 for ; Wed, 11 Feb 2004 18:37:50 -0500 (EST) Sender: weiz:at:mail.rochester.edu From: "weiz" Reply-to: weiz:at:mail.rochester.edu To: chemistry:at:ccl.net Subject: help about gaussian X-Mailer: Quality Web Email v3.0q, http://netwinsite.com/refw.htm Date: Wed, 11 Feb 2004 18:37:47 -0500 Priority: normal Message-id: <402abccb.2608.26554:at:mail.rochester.edu> X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi,all: If I have a long peptide strand,let say,21 residue poly-alanine. and I want to do a geometry optimization and freq calculation for the alanine in the middle of the chain,I want to treat this residue quantum mechanically and the left part of the strand molecular mechanically. if I use Gview03 to set up the job file,I need to decide the charge of both the low layer and high layer.since I only chose the C,O,N,H,CA atoms of the central residue to be the high layer,then the charges of both layers are not zero.can someone tell me how to find out the charges for each layer? regards Wei zhuang From chemistry-request@ccl.net Wed Feb 11 15:55:06 2004 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BKt3U6003429 for ; Wed, 11 Feb 2004 15:55:03 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id i1BKtJ8L016696 for ; Wed, 11 Feb 2004 15:55:19 -0500 (EST) Message-Id: <200402112055.i1BKtJ8L016696:at:copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Wed, 11 Feb 2004 15:45:47 -0500 Subject: Z-matrix input for Gamess-US wanted From: "Olga Dmitrenko" To: CHEMISTRY:at:ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Score: 2.1 SPAM_PHRASE_00_01,UPPERCASE_25_50 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.3 required=7.0 tests=UPPERCASE_25_50 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I would much appreciate if somebody of you will kindly send me an example of the Gamess-US input with the Z-matrix which really works for GAMESS VERSION = 20 JUN 2002 (R2). Somehow... I have troubles to run simple example on methylene molecule (I copied it > from http://www.npaci.edu/Resources/SciComp/Applications/GAMESS/gamess_sect3.html : $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END $SYSTEM TIMLIM=2 MEMORY=100000 $END $STATPT OPTTOL=1.0E-5 $END $BASIS GBASIS=STO NGAUSS=2 $END $GUESS GUESS=HUCKEL $END $DATA Methylene...1-A-1 state...RHF/STO-2G Cnv 2 C H 1 rCH H 1 rCH 2 aHCH rCH=1.09 aHCH=110.0 $END I am getting "**** ERROR, NO $DATA GROUP WAS FOUND". From chemistry-request@ccl.net Wed Feb 11 16:47:12 2004 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1BLlAU6005299 for ; Wed, 11 Feb 2004 16:47:10 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id i1BLlRcD028733; Wed, 11 Feb 2004 16:47:27 -0500 (EST) Date: Wed, 11 Feb 2004 16:30:55 -0500 From: Rick Venable To: "Janosi, Lorant (UMC-Student)" cc: "chemistry$at$ccl.net" Subject: Re: CCL:forcefield parameters In-Reply-To: <92FE3800-AC0C-4652-B330-20DE149B79DD@mimectl> Message-ID: References: <92FE3800-AC0C-4652-B330-20DE149B79DD@mimectl> ReplyTo: Rick_Venable$at$nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.4 required=7.0 tests=RCVD_IN_NJABL, RCVD_IN_NJABL_RELAY autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 11 Feb 2004, Janosi, Lorant (UMC-Student) wrote: > I am interested in a Molecular Dynamics simulation of a system using > CHARMm forcefiled. In order to do that, I need to compute the > forcefield parameters for some molecules. I was thinking in using > gaussian (98 / 03), but I don't know how these forcefield parameters > are computed. Any help or suggestion would be more than welcome. There's CHARMm, and then there's CHARMM. You can find info on the current academic CHARMM force field development by Alex MacKerell at URL http://www.pharmacy.umaryland.edu/~alex/research.html The commercial CHARMm force field was developed independently; see Momany, F.A., and Rone, R., Validation of the General Purpose QUANTA 3.2/CHARMm Force Field. J. Comp. Chem. 13, 888-900, 1992 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable$at$nih.gov ALT email: rvenable$at$speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=