From chemistry-request@server.ccl.net Mon Sep 16 09:20:01 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GDK0w05161 for ; Mon, 16 Sep 2002 09:20:01 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g8GDK0q28599 for ; Mon, 16 Sep 2002 06:20:00 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 4650; Mon, 16 Sep 2002 06:20:15 -0700 (PDT) Received: from renoir.scripps.edu (renoir.scripps.edu [137.131.252.25]) by relay2.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g8GDJnO27004; Mon, 16 Sep 2002 06:19:49 -0700 (PDT) Received: from localhost (crowley@localhost) by renoir.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id GAA1234269; Mon, 16 Sep 2002 06:19:48 -0700 (PDT) Date: Mon, 16 Sep 2002 06:19:47 -0700 From: Michael Crowley To: Richard Wood cc: "chemistry@ccl.net" Subject: Re: CCL:CHARMM coordinates In-Reply-To: <3D8358A9.F0023052@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Richard, The following will write a pdb of the current coordinates in the MAIN coordinate vector. open unit 1 write form name last.pdb write coor pdb unit 1 close unit 1 Take a look at the doc for io (io.doc) for more about what choices you have for the form of the output from write coor. Cheers, Mike ----------------------------------------------------------------- Physical mail: Dr. Michael F. Crowley Department of Molecular Biology, TPC6 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037 Electronic mail: crowley@scripps.edu Telephone: 858/784-9290 Fax: 858/784-8688 ----------------------------------------------------------------- On Sat, 14 Sep 2002, Richard Wood wrote: > Hi all > > I should probably know this, but how can I save the coordinates from a > single step of a CHARMM dynamics trajectory? More specifically, I want > to save the last frame of a 200000 step dynamics run. I have used COOR > DYNA and set the begin and stop values the same as in > > OPEN READ UNIT 15 FILE NAME "newattestverlet24.5.dcd" > COOR DYNA FIRSTU 15 NUNIT 1 BEGIN 200000 STOP 200000 > > This works, as it writes out a set of coordinates. But is it really the > frame that I wanted? Or is there another way to do this? > > Thanks to all in advance. > > Richard > > > > -= 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 Mon Sep 16 10:27:14 2002 Received: from ms1.uibk.ac.at ([138.232.1.201]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GERDw06480 for ; Mon, 16 Sep 2002 10:27:13 -0400 Received: from localhost (web-mail2.uibk.ac.at [138.232.1.226] Hannes.Loeffler@uibk.ac.at) by ms1.uibk.ac.at (8.11.3/E2) with ESMTP id g8GERAr69626330 for ; Mon, 16 Sep 2002 16:27:11 +0200 (CEST) Received: from 62.47.210.203 ( [62.47.210.203]) as user c72409@mail1.uibk.ac.at by web-mail2.uibk.ac.at with HTTP; Mon, 16 Sep 2002 16:27:10 +0200 Message-ID: <1032186430.3d85ea3e55867@web-mail2.uibk.ac.at> Date: Mon, 16 Sep 2002 16:27:10 +0200 From: Hannes Loeffler To: chemistry@ccl.net Subject: CHARMM: How to manipulate the coordinate set? MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 62.47.210.203 Hello CCLers, I'm trying to compute an energy surface by varying two distances: an internal coordinate of a given molecule and one between the molecule and a chloride ion. I tried to set the two distances by editing the IC table (param, edit, build) but I was unable to make CHARMM aware of the new coordinate set. How do I fill the internal coordinate arrays with data from ICs in each step of the double loop? Thanks in advance, Hannes. -- Hannes Loeffler | tel: +43-(0)512-507-5166 | fax: +43-(0)512-507-2714 http://www-c724.uibk.ac.at/staff/loeffler/ | mailto:Hannes.Loeffler@uibk.ac.at Institute for General, Inorganic and Theoretical Chemistry University of Innsbruck, Austria From chemistry-request@server.ccl.net Mon Sep 16 17:08:23 2002 Received: from rockridge.uits.indiana.edu ([129.79.1.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GL8Nw12938 for ; Mon, 16 Sep 2002 17:08:23 -0400 Received: from jade.iupui.edu (jade.iupui.edu [134.68.220.114]) by rockridge.uits.indiana.edu (8.12.1/8.12.1/IUPO) with ESMTP id g8GL8Ln1009476 for ; Mon, 16 Sep 2002 16:08:21 -0500 (EST) Received: from localhost (qzou@localhost) by jade.iupui.edu (8.10.1/8.10.1/jade.20020708) with SMTP id g8GL8MX13423 for ; Mon, 16 Sep 2002 16:08:22 -0500 (EST) X-Authentication-Warning: jade.iupui.edu: qzou owned process doing -bs Date: Mon, 16 Sep 2002 16:08:22 -0500 (EST) From: Qin Zou To: chemistry@ccl.net Subject: increase GA runs in ADT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know how to increase the number of the runs in ADT? I know in regular Autodock3 one can change in "constant.h" and recompile it. But where should I change in ADT? Thanks. Q From chemistry-request@server.ccl.net Mon Sep 16 18:43:49 2002 Received: from medusa.wo.utoledo.edu (IDENT:kmMvsJHz/lCZZ+odQNOIwcbHBhp0FejO@[131.183.69.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GMhnw14573 for ; Mon, 16 Sep 2002 18:43:49 -0400 Received: from there (IDENT:eD140leCeVi7xxS8/Ye8FU0lsUnbN68L@localhost.localdomain [127.0.0.1]) by medusa.wo.utoledo.edu (8.11.6/8.11.6) with SMTP id g8GMlD504373 for ; Mon, 16 Sep 2002 18:47:13 -0400 Message-Id: <200209162247.g8GMlD504373@medusa.wo.utoledo.edu> Content-Type: text/plain; charset="iso-8859-1" From: Venkataraman Kabaleeswaran Reply-To: vkabale@uoft02.utoledo.edu Organization: univ of toledo To: chemistry@ccl.net Subject: autodock Date: Mon, 16 Sep 2002 18:47:13 -0400 X-Mailer: KMail [version 1.3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit I am new user to autodock. I have difficulities in converting from pdb to mol2 ...to pdbqs. Finally I made those with long way, assumeing there is some easy way to do that. I have problem in making grid parameter file , while doing mkgpf3 lig.pdbq macro.pdbqs I got an error message " autogrid is too large"etc Is there any easy way or script to convert the pdb files to autodock pbq or pdbqs etc......and also step by step way to dock the ligand by user friendly. thanks in advance venkataraman