From chemistry-request@server.ccl.net Tue Sep 12 06:44:47 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA04062 for ; Tue, 12 Sep 2000 06:44:44 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 12 Sep 2000 12:46:46 +0200 Sender: zhang@ccl.net Message-ID: <39BE0811.F8592BFE@mail.biokemi.su.se> Date: Tue, 12 Sep 2000 12:40:18 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: Trevor Kramer CC: chemistry@ccl.net Subject: Re: CCL:Reusing autogrid maps in autodock References: <968711513_PM_BeOS.tkramer@hampshire.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Trevor, If you run autogrid for your ligands against one macromolecule separately, you will get different map files for different ligands. As I understand, the map files should be ligand specific, otherwise the program may not discriminate good and bad ligand. Sincerely, Xiao-Ping Zhang > > Hello, > > I am currently using autodock3 for a research project and have a > question regarding its relation to autogrid. I have setup autodock to > automatically screen a large library of molecules by seting up the > parameter files for each ligand and then running autogrid3 and then > autodock3. Since autogrid takes a significant period of time I was > wandering of it was possible to reuse the grid maps it generates for all > the runs. The same macomolecule is used in each case and the size and > position of the grid is the same. I know I would have to run autogrid > once so it would generate grid maps for all supported atom types but > would this work? The dpf file also mentions the maps.fld file which may > need to be created for each run. Any help would be appreciated. Thank > you. > > Trevor Kramer > Hampshire College > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se