From chemistry-request@ccl.net Wed May 11 07:52:33 2005 Received: from web60213.mail.yahoo.com (web60213.mail.yahoo.com [209.73.178.116]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4BBqTEc016441 for ; Wed, 11 May 2005 07:52:30 -0400 Received: (qmail 96480 invoked by uid 60001); 11 May 2005 10:52:27 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=6A4NAKJXysmJ7hX8FNA0GiRI0cmQtsIwmOHz8UQ8uIANN1EM6da/rfttZSXMpDBcb7wG8ruFdwcgTxmUPpJA9pKO0ZJkajygQTuJgNtKHdzvSBs7CpmKiDj8eVvcK9wCdTB+r+nHCsfHeOowSyoum+/2ohhPl1vG3Fj2iEVUGec= ; Message-ID: <20050511105227.96478.qmail..at..web60213.mail.yahoo.com> Received: from [139.19.34.3] by web60213.mail.yahoo.com via HTTP; Wed, 11 May 2005 03:52:27 PDT Date: Wed, 11 May 2005 03:52:27 -0700 (PDT) From: Its August Subject: Beginner's question on docking To: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, I've two question on ligand docking. Excuse me for asking such very basic questions: 1. Docking methods calculate Binding Free Energy differences( or Delta G) as a measure of binding Affinity.(Please correct me if I'm wrong). Is there any other Thermodynamic function that can replace Delta G as a measure of binding affinity for ? 2. On Docking in a Grid: Docking programs like AUTODOCK evalutae the Energy of a molecule on a GRID. I beleive the a GRID point is nothing but a point in a 3d Space for which u know the binding affinity of a particular chemical group precomputed at that GRID point. However in some pose of the ligands one particular chemical group MAY NOT EXACTLY fall in one of such GRID point(Whatever fine resolution the grid may have ) How to calcualte energy in that case? I've came across a term like GRID INTERPOLATION. Is that anything to do with in such a case? Moreover I would like to know how additive are these interactions. That means the energy computed for an isolated chemical group in a GRID , is it equal for the same group in a ligand or in a set of different ligands? Do the other neighbouring chemical groups exert some effect? Are there any literature references for this? Thanks in advance Discover Yahoo! Find restaurants, movies, travel and more fun for the weekend. Check it out! http://discover.yahoo.com/weekend.html From chemistry-request@ccl.net Wed May 11 09:39:43 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BDddM5022206 for ; Wed, 11 May 2005 09:39:39 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j4BDdd1H022205 for chemistry|at|ccl.net; Wed, 11 May 2005 09:39:39 -0400 Date: Wed, 11 May 2005 09:39:39 -0400 Message-Id: <200505111339.j4BDdd1H022205|at|server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request|at|ccl.net using -f From: "Juan, , Elezgaray" To: chemistry|at|ccl.net X-Web-Message-Number: 050511093813-22153 Subject: W:Biomolecular Simulations Meeting Bordeaux, 2&3 Sept. 2005 (2nd anct) X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net ===================== SECOND ANNOUNCEMENT ===================== BIOMOLECULAR SIMULATIONS - Satellite meeting to the International Biophysics Congress, Montpellier 2005 BORDEAUX-FRANCE: 2 & 3 SEPTEMBER 2003 http://www.iecb.u-bordeaux.fr/satellite2005/ ============================================================== Dear colleague, We are organizing a satellite meeting dedicated to Biomolecular Simulations in Bordeaux on September 2nd and 3rd 2005 The following speakers have already confirmed their participation: Paolo Carloni (Sissa, Italy) Christophe Chipot (Nancy, France) Jonathan Essex (Southampton, UK) Angel Garcia (Los Alamos, USA) Helmut Grubmller (Gttingen, Germany) Siewert-Jan Marrink (Groningen, The Netherlands) Pascal Auffinger (Strasbourg, France) Franca Fraternalli (London, UK) We kindly invite you to log on to our website for further information: http://www.iecb.u-bordeaux.fr/satellite2005/ You can also download a flyer describing this Summer School by following this link: http://www.iecb.u-bordeaux.fr/satellite2005/biomolsim.pdf Yours sincerely, The organisers Marc Baaden (IBPC, Paris) Juan Elezgaray (IECB, Bordeaux) Michel Laguerre (IECB, Bordeaux) Mark Sansom (LMB, Oxford) From chemistry-request@ccl.net Wed May 11 10:32:00 2005 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.22]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BEVmsT024743 for ; Wed, 11 May 2005 10:31:48 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 1005) id 71F252380C2; Wed, 11 May 2005 15:26:58 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 13C8B2380D5 for ; Wed, 11 May 2005 15:26:52 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 11 May 05 15:26:51 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 11 May 05 15:26:42 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry|at|ccl.net Date: Wed, 11 May 2005 15:26:20 +0200 Subject: Analysis of Cartesian Force Constant Matrix Reply-To: spanget|at|ruc.dk Message-ID: <4282241D.23248.159C44B@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Level: Dear CCL! Can anyone recommend a utility program that will transform the cartesian force constant matrix from a Gaussian chk-file into a basis of 'symmetry coordinates' (corresponding to bond stretchings, bendings, etc.), enabling corresponding analysis the vibrational modes, e.g., in terms of potential energy distributions and other useful parameters? Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget|at|ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Wed May 11 04:20:11 2005 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4B8K6pi004925 for ; Wed, 11 May 2005 04:20:07 -0400 Received: from yangtze.hku.hk (localhost.localdomain [127.0.0.1]) by yangtze.hku.hk (8.13.1/8.13.1) with ESMTP id j4B8GLAh026884 for ; Wed, 11 May 2005 16:16:21 +0800 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.13.1/8.13.1/Submit) with ESMTP id j4B8GLIh026881 for ; Wed, 11 May 2005 16:16:21 +0800 Date: Wed, 11 May 2005 16:16:21 +0800 (HKT) From: lhhu ^^^ yangtze.hku.hk To: chemistry ^^^ ccl.net Subject: Tinker input file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear all CCLers, I would like to use free TINKER to calculated molecular dynamics. But the input file of tinker seems difficult to generate because the int or xyz file need to be assigned force field atom type first. Can anyone tell me about the most convenient way to generate the input xyz or int file? Is there any free program I can use? Thank you very much, Holly From chemistry-request@ccl.net Wed May 11 12:38:22 2005 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BGcID3004184 for ; Wed, 11 May 2005 12:38:18 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1DVtB5-0001UR-JL for CHEMISTRY-.at.-ccl.net; Wed, 11 May 2005 12:31:15 -0300 Received: from 138.73.24.157 ( [138.73.24.157]) as user khunter-.at.-mailserv.mta.ca by webmail.mta.ca with HTTP; Wed, 11 May 2005 12:31:15 -0300 Message-ID: <1115825475.428225438ceff-.at.-webmail.mta.ca> Date: Wed, 11 May 2005 12:31:15 -0300 From: khunter-.at.-mta.ca To: CHEMISTRY-.at.-ccl.net Subject: CCL: DE2Siz in DoE2D error MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.157 X-Spam-Status: No, score=0.2 required=5.0 tests=FORGED_RCVD_HELO,NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net The following error arises when attempting to model semi-large systems with MP2 with Gaussian 03 on a Linux cluster. Disk-based method using O(N**2) memory for 10 occupieds at a time. Estimated scratch disk usage= -1 words. Inconsistency from DE2Siz in DoE2D. Changing the memory, disk space, and %rwf appear to have no affect. Any assisstance on how to correct this error would be greatly appreaciated. Ken Hunter Mount Allison University From chemistry-request@ccl.net Wed May 11 13:47:14 2005 Received: from ion.chem.utk.edu (ion.chem.utk.edu [160.36.200.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BHlBJ0009098 for ; Wed, 11 May 2005 13:47:12 -0400 Received: from localhost ([127.0.0.1] helo=ion.chem.utk.edu) by ion.chem.utk.edu with esmtp (Exim 4.32) id 1DVuJg-000307-19 for chemistry () ccl.net; Wed, 11 May 2005 12:44:12 -0400 Received: from 66.32.92.115 (SquirrelMail authenticated user setca) by ion.chem.utk.edu with HTTP; Wed, 11 May 2005 12:44:12 -0400 (EDT) Message-ID: <35234.66.32.92.115.1115829852.squirrel () ion.chem.utk.edu> Date: Wed, 11 May 2005 12:44:12 -0400 (EDT) Subject: CCL: SETCA 2005 -- June 17-19 From: "SETCA 2005" To: chemistry () ccl.net Reply-To: setca () ion.chem.utk.edu User-Agent: SquirrelMail/1.4.4 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net The 34th meeting of the Southeast Theoretical Chemistry Association will take place in Knoxville, TN on June 17-19, 2005. More details can be found on the Web at http://www.chem.utk.edu/SETCA/ Please forward this message to others who may be interested. We look forward to seeing you in Knoxville this summer! -- Robert Harrison and Robert Hinde Co-Chairs, SETCA 2005 http://www.chem.utk.edu/SETCA/ e-mail setca () mail.chem.utk.edu or FAX 865-974-3454 From chemistry-request@ccl.net Wed May 11 15:44:28 2005 Received: from proxy2.uh.cu (smtp2.uh.cu [200.55.139.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BJiJO7016762 for ; Wed, 11 May 2005 15:44:23 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by proxy2.uh.cu (Postfix) with ESMTP id D87B12FDC7; Wed, 11 May 2005 14:55:16 -0400 (CDT) Received: from fq.uh.cu (unknown [192.168.3.4]) by proxy2.uh.cu (Postfix) with ESMTP id A491E2FDC2; Wed, 11 May 2005 14:55:16 -0400 (CDT) Received: from fq.uh.cu (IDENT:1565@localhost [127.0.0.1]) by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id j4BEm4JZ025965; Wed, 11 May 2005 10:48:04 -0400 Received: from localhost (david@localhost) by fq.uh.cu (8.12.4/8.12.4/Submit) with ESMTP id j4BEm4tq025962; Wed, 11 May 2005 10:48:04 -0400 Date: Wed, 11 May 2005 10:48:04 -0400 (CDT) From: David Santos Carballal To: lhhu ## yangtze.hku.hk Cc: chemistry ## ccl.net Subject: Re: CCL:Tinker input file 2 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I forgot: You would find the pdbxyz.exe in the bin directory of TINKER, if you run it from Windows David Santos Carballal On Wed, 11 May 2005 lhhu ## yangtze.hku.hk wrote: > > Dear all CCLers, > > I would like to use free TINKER to calculated molecular dynamics. But the > input file of tinker seems difficult to generate because the int or xyz > file need to be assigned force field atom type first. Can anyone tell me > about the most convenient way to generate the input xyz or int file? Is > there any free program I can use? > > Thank you very much, > > Holly > > > -= 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 ## ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST ## ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed May 11 12:24:47 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BGOjDA003033 for ; Wed, 11 May 2005 12:24:45 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j4BGOjJa003032 for chemistry ## ccl.net; Wed, 11 May 2005 12:24:45 -0400 Date: Wed, 11 May 2005 12:24:45 -0400 Message-Id: <200505111624.j4BGOjJa003032 ## server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request ## ccl.net using -f From: "Perez, Nueno, Violeta" To: chemistry ## ccl.net X-Web-Message-Number: 050511122201-2851 Subject: W:Evaluating programs of conformational search X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I'm doing ab initio loop modeling for a protein whith Congen program and I would like to evaluate my results. I have heard about programs like PROCHECK or WHATCHECK, what is better? Is there any other program better for this? I have another question. Could you tell me a good program for scanning a ligand binding site in a protein? I have used Autodock, is there other program more interesting for these purpose? Thank you very much. Violeta Isabel Prez Nueno Instituto Qumico de Sarri Barcelona vio_de_chocolate ## yahoo.es From chemistry-request@ccl.net Wed May 11 15:27:56 2005 Received: from proxy2.uh.cu (smtp2.uh.cu [200.55.139.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BJRpUD015641 for ; Wed, 11 May 2005 15:27:53 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by proxy2.uh.cu (Postfix) with ESMTP id 648302FD4D; Wed, 11 May 2005 14:26:55 -0400 (CDT) Received: from fq.uh.cu (unknown [192.168.3.4]) by proxy2.uh.cu (Postfix) with ESMTP id 337642FD48; Wed, 11 May 2005 14:26:55 -0400 (CDT) Received: from fq.uh.cu (IDENT:1565@localhost [127.0.0.1]) by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id j4BEJhJZ024432; Wed, 11 May 2005 10:19:43 -0400 Received: from localhost (david@localhost) by fq.uh.cu (8.12.4/8.12.4/Submit) with ESMTP id j4BEJgIU024429; Wed, 11 May 2005 10:19:42 -0400 Date: Wed, 11 May 2005 10:19:42 -0400 (CDT) From: David Santos Carballal To: lhhu ## yangtze.hku.hk Cc: chemistry ## ccl.net Subject: Re: CCL:Tinker input file In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Holly: If you want to generate the xyz file for TINKER to calculate a molecular dynamics: *first, you must create the molecule in hyperchem, gaussview, etc..., then save it as protein data bank (*.pdb or *.ent). *second you must run pdbxyz.exe included in the TINKER package via MS-DOS, write the name of the file saved in the format *.pdb or *.ent and it will create the file *.xyz *third you must open the *.xyz with a word processing and assign manually the force field atom type in the sixth column (after the cartesian coordinates and before the connectivities), the place of the force field atom type is filled with zeros by pdbxyz.exe. David Santos Carballal On Wed, 11 May 2005 lhhu ## yangtze.hku.hk wrote: > > Dear all CCLers, > > I would like to use free TINKER to calculated molecular dynamics. But the > input file of tinker seems difficult to generate because the int or xyz > file need to be assigned force field atom type first. Can anyone tell me > about the most convenient way to generate the input xyz or int file? Is > there any free program I can use? > > Thank you very much, > > Holly From chemistry-request@ccl.net Wed May 11 19:09:22 2005 Received: from postoffice10.mail.cornell.edu (postoffice10.mail.cornell.edu [132.236.56.14]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BN9IUq032296 for ; Wed, 11 May 2005 19:09:18 -0400 Received: from [192.168.0.139] (ip.253.34.140-dhcp.chem.cornell.edu [128.253.34.140]) by postoffice10.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id j4BLxxqZ012086; Wed, 11 May 2005 18:00:04 -0400 (EDT) In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v728) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: Cc: chemistry %a% ccl.net From: Geoff Hutchison Subject: Re: CCL:Tinker input file Date: Wed, 11 May 2005 17:59:57 -0400 To: lhhu %a% yangtze.hku.hk X-Mailer: Apple Mail (2.728) X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4BN9MUq032300 On May 11, 2005, at 4:16 AM, lhhu %a% yangtze.hku.hk wrote: > I would like to use free TINKER to calculated molecular dynamics. > But the input file of tinker seems difficult to generate because > the int or xyz file need to be assigned force field atom type > first. Can anyone tell me about the most convenient way to generate > the input xyz or int file? Is there any free program I can use? Use Open Babel (or the original Babel): Open Babel: http://openbabel.sf.net/ Babel 1.6 (and older): http://www.ccl.net/cca/software/UNIX/babel/ Some atom types may or may not be assigned automatically depending on which force field you wish to use and what format you used originally. However, it's a great time-saver. Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruqa Group http://abruna.chem.cornell.edu/ From chemistry-request@ccl.net Wed May 11 18:02:26 2005 Received: from mx.seanet.com (mx.seanet.com [199.181.164.10] (may be forged)) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BM2Jgp027318 for ; Wed, 11 May 2005 18:02:22 -0400 Received: from planaria (c-24-18-186-63.hsd1.wa.comcast.net [24.18.186.63]) (authenticated bits=0) by milkyway.seanet.com (8.13.2/8.13.2) with ESMTP id j4BM2ACK018806; Wed, 11 May 2005 15:02:18 -0700 (PDT) (envelope-from mark %a% arguslab.com) Reply-To: From: "Mark Thompson" To: "Its August" , Subject: RE: Beginner's question on docking Date: Wed, 11 May 2005 15:02:13 -0700 Message-ID: <000401c55675$16725080$0200a8c0@planaria> 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 IMO, Build 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 In-Reply-To: <20050511105227.96478.qmail %a% web60213.mail.yahoo.com> Importance: Normal X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net You should read "Automated docking using a Lamarckian Genetic Algorithm,....." by Morris, Goodsell, Olson, et. al. J. Comp. Chem. 19, 1639-1662, (1998) It will answer several of your questions. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request %a% ccl.net]On Behalf Of Its August Sent: Wednesday, May 11, 2005 3:52 AM To: chemistry %a% ccl.net Subject: CCL:Beginner's question on docking Hello, I've two question on ligand docking. Excuse me for asking such very basic questions: 1. Docking methods calculate Binding Free Energy differences( or Delta G) as a measure of binding Affinity.(Please correct me if I'm wrong). Is there any other Thermodynamic function that can replace Delta G as a measure of binding affinity for ? 2. On Docking in a Grid: Docking programs like AUTODOCK evalutae the Energy of a molecule on a GRID. I beleive the a GRID point is nothing but a point in a 3d Space for which u know the binding affinity of a particular chemical group precomputed at that GRID point. However in some pose of the ligands one particular chemical group MAY NOT EXACTLY fall in one of such GRID point(Whatever fine resolution the grid may have ) How to calcualte energy in that case? I've came across a term like GRID INTERPOLATION. Is that anything to do with in such a case? Moreover I would like to know how additive are these interactions. That means the energy computed for an isolated chemical group in a GRID , is it equal for the same group in a ligand or in a set of different ligands? Do the other neighbouring chemical groups exert some effect? Are there any literature references for this? Thanks in advance Discover Yahoo! Find restaurants, movies, travel and more fun for the weekend. Check it out! http://discover.yahoo.com/weekend.html -= 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 %a% ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST %a% ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed May 11 16:31:12 2005 Received: from zproxy.gmail.com (zproxy.gmail.com [64.233.162.199]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BKV7xl019700 for ; Wed, 11 May 2005 16:31:07 -0400 Received: by zproxy.gmail.com with SMTP id 13so423748nzp for ; Wed, 11 May 2005 13:31:07 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=kXFk5/BUsE+8tNU3UqqSBcHNoOfcVD2zGhtDrLgO6fjdAaGSRJCBnV77nWl7S0dC673iQ4NViP8swm0JO+b2kYxfHIbi43xAYVFNRBeUb711UO8DXDiaK1JlA3QU+rWxQfOe5ZKnDtmUYDlwKXpg0q/D7EMJrg6XcwvEsCafR50= Received: by 10.36.154.6 with SMTP id b6mr339343nze; Wed, 11 May 2005 12:31:06 -0700 (PDT) Received: by 10.36.9.16 with HTTP; Wed, 11 May 2005 12:31:06 -0700 (PDT) Message-ID: Date: Wed, 11 May 2005 14:31:06 -0500 From: Gustavo Seabra Reply-To: To: chemistry %a% ccl.net Subject: Re: CCL:Opteron or Nocona ? In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline References: X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE,RCVD_BY_IP, REPLY_TO_EMPTY autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4BKVCxl019710 On 5/7/05, Luigi Cavallo wrote: > > Hi, > > we are going to invest some money for a few computers, and we have to > make a decision between the AMD-Opterons and the Intel-Nocona. What's > better ? We are experienced with the Opterons, but we have no idea about > the Noconas... > > Major codes to run on them will be classical QM packages as ADF, G03, TM, > some AIMD as CPMD, and possibly some classical MD as gromacs. > > Thanks, > Luigi > > -= 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 %a% ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST %a% ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > Notice that AMD has recently launched the Dual Core Opteron processors. There you can basically get the equivalent of twice as much processors, for about the same price. Check: http://www.infoworld.com/infoworld/article/05/04/21/17TCamd_1.html http://www.d-silence.com/story.php?headline_id=21036&comment=1 -- --------------------------------------------------------------------------------------------- Gustavo Seabra Graduate Student Chemistry Dept. Kansas State University Registered Linux user number 381680 Say NO! to software patents: http://www.nosoftwarepatents.com --------------------------------------------------------------------------------------------- If at first you don't succeed... ...skydiving is not for you. From chemistry-request@ccl.net Wed May 11 20:10:11 2005 Received: from relay12-159.bu.edu (relay12-159.bu.edu [128.197.159.81]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4C0A57U005996 for ; Wed, 11 May 2005 20:10:06 -0400 Received: from vajdalaptop (vajdalap.bu.edu [128.197.126.65]) by relay12-159.bu.edu (8.12.8/8.12.8) with ESMTP id j4BNFQTX024897 for ; Wed, 11 May 2005 19:15:26 -0400 Message-Id: <200505112315.j4BNFQTX024897 :a: relay12-159.bu.edu> From: "Sandor Vajda" To: Subject: 3rd Conference on MODELING OF PROTEIN INTERACTIONS IN GENOMES Date: Wed, 11 May 2005 19:15:31 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01C5565D.CCA06C60" X-Mailer: Microsoft Office Outlook, Build 11.0.6353 Thread-Index: AcVWfvSDERGbHtblR16qzqZVen2g9g== X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE, HTML_NONELEMENT_30_40 autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C5565D.CCA06C60 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit 3rd Conference on MODELING OF PROTEIN INTERACTIONS IN GENOMES June 26-28, 2005, Lawrence, KS http://www.bioinformatics.ku.edu/conferences/mpi2005 *** CALL FOR PAPERS *** The biannual conference (Charleston 2001, Stony Brook 2003, http://www.bioinformatics.ku.edu/conferences) plays an important role in shaping the community of protein interaction modelers, discussing current progress in the field and setting new goals in this key area of Computational Biology and Bioinformatics. As in the previous meetings, we intend to keep the focus on theoretical foundations of the field and its interface with the experimental studies. The Conference is sponsored by the Center for Bioinformatics at the University of Kansas. organizers Ilya Vakser, The University of Kansas Sandor Vajda, Boston University Program interactome Protein structure-function macromolecular assemblies docking and binding binding sites and more... Speakers Ruben Abagyan, Scripps Institute Patrick Aloy, EMBL Charles Brooks, Scripps Institute Carlos Camacho, Boston University Dmitrij Frishman, Technische Universitat Munchen Adam Godzik, Burnham Institute Jeffrey Gray, Johns Hopkins University Barry Honig, Columbia University Joel Janin, Centre National de la Recherche Scientifique Robert Jernigan, Iowa Sate University Krzysztof Kuczera, University of Kansas Ronald Levy, Rutgers University Jie Liang, University of Illinois Chicago Garland Marshall, Washington University Ruth Nussinov, National Cancer Institute Arthur Olson, Scripps Institute Andrej Sali, UCSF Harold Scheraga, Cornell University Jeffrey Skolnick, University at Buffalo Michael Sternberg, Imperial College London Lynn Ten Eyck, San Diego Supercomputer Center Sandor Vajda, Boston University Ilya Vakser, University of Kansas Alfonso Valencia, Centro Nacional de Biotecnologia Spain Gennady Verkhivker, Pfizer Michael Washburn, Stowers Institute Zhiping Weng, Boston University Shoshana Wodak, University of Toronto Willy Wriggers, University of Texas Health Science Center Location The meeting will take place in the Eldridge Hotel in downtown Lawrence, KS. Eldridge is a historic hotel in the heart of a charming district with art galleries, boutique shopping, outdoor dining and live music. PARTICIPATION The number of participants is limited to 100. In selecting participants, the preference will be given to those who have a poster presentation on the subject of the conference. If you would like to attend the conference, please submit a request as soon as possible, by e-mail only, to Ilya Vakser (vakser :a: ku.edu) or Sandor Vajda (vajda :a: bu.edu). Include a brief (a few sentences) description of your research, your full affiliation, position (faculty, postdoc, student, etc.), address (email and regular), and the day-time phone number. If you would like to present a poster, please include a half-page abstract. If your application is accepted, we will communicate with you regarding the details of registration, accommodation, and travel. The early registration fee for the participants of the conference is $250 ($150 for postdocs and students). After June 5, the fee will be $300 ($200 for postdocs and students). ------=_NextPart_000_0000_01C5565D.CCA06C60 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

3rd Conference on MODELING OF PROTEIN INTERACTIONS IN = GENOMES

June 26-28, 2005, Lawrence, KS =

http://www.bioinformatics.ku.edu/conferences/mpi2005

 

*** CALL FOR PAPERS ***

 

The biannual conference (Charleston 2001, Stony Brook 2003, http://www.bioinformatics.ku.edu/conferences) plays an important role in shaping the community of protein interaction modelers, discussing = current progress in the field and setting new goals in this key area of = Computational Biology and Bioinformatics. As in the previous meetings, we intend to = keep the focus on theoretical foundations of the field and its interface with the experimental studies. The Conference is sponsored by the Center for Bioinformatics at the University of Kansas.<= /p>

 

organizers

 

Ilya Vakser, The University of Kansas

Sandor Vajda, Boston University

 

Program

 

interactome

=

Protein structure-function =

macromolecular = assemblies

docking and = binding

binding sites and = more...

 

Speakers

 

Ruben Abagyan, Scripps Institute
Patrick Aloy, EMBL

Charles Brooks, Scripps = Institute

Carlos Camacho, Boston University
Dmitrij Frishman, Technische Universitat Munchen
Adam Godzik, Burnham Institute
Jeffrey Gray, Johns Hopkins University

Barry Honig, Columbia University
Joel Janin, Centre National de la Recherche Scientifique
Robert Jernigan, Iowa Sate University

Krzysztof Kuczera, University of Kansas
Ronald Levy, Rutgers University

Jie Liang, University of Illinois = Chicago

Garland Marshall, Washington = University
Ruth Nussinov, National Cancer Institute
Arthur Olson, Scripps Institute
Andrej Sali, UCSF

Harold Scheraga, Cornell University

Jeffrey Skolnick, University at = Buffalo
Michael Sternberg, Imperial College London
Lynn Ten Eyck, San Diego Supercomputer Center
Sandor Vajda, Boston University
Ilya Vakser, University of Kansas
Alfonso Valencia, Centro Nacional de Biotecnologia Spain
Gennady Verkhivker, Pfizer

Michael Washburn, Stowers = Institute

Zhiping Weng, Boston University
Shoshana Wodak, University of Toronto
Willy Wriggers, University of Texas Health Science Center

 

Location

 

The meeting will take place in the Eldridge Hotel in downtown = Lawrence, KS. Eldridge is a historic hotel in the heart of a charming district with = art galleries, boutique shopping, outdoor dining and live music. =

 

PARTICIPATION

 

The number of participants is limited to 100. In selecting participants, the preference will be given to those who have a poster presentation on the subject of the conference. If you would like to = attend the conference, please submit a request as soon as possible, by e-mail only, = to Ilya Vakser (vakser :a: ku.edu) or Sandor Vajda (vajda :a: bu.edu). Include a = brief (a few sentences) description of your research, your full affiliation, = position (faculty, postdoc, student, etc.), address (email and regular), and the day-time phone number. If you would like to present a poster, please = include a half-page abstract. If your application is accepted, we will communicate = with you regarding the details of registration, accommodation, and travel. = The early registration fee for the participants of the conference is $250 ($150 = for postdocs and students). After June 5, the fee will be $300 ($200 for = postdocs and students).

 

 

 

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