From chemistry-request@ccl.net Tue Nov 2 11:27:30 2004 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA2GRTjA021533 for >ccl.net>; Tue, 2 Nov 2004 11:27:29 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.13.1/8.13.1) with SMTP id iA2Ga4Ee004319 for >ccl.net>; Tue, 2 Nov 2004 11:40:30 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SMSSMTP 4.0.0.59) with SMTP id M2004110211403006375 for >ccl.net>; Tue, 02 Nov 2004 11:40:30 -0500 Received: from sparky.ic.sunysb.edu (daemon<>sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.13.1/8.13.1) with ESMTP id iA2GeUMK008193 for >ccl.net>; Tue, 2 Nov 2004 11:40:30 -0500 (EST) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id iA2GeQqU019966 for >ccl.net>; Tue, 2 Nov 2004 11:40:30 -0500 (EST) Date: Tue, 2 Nov 2004 11:40:26 -0500 (EST) From: Yong Liang Yang >ic.sunysb.edu> To: chemistry<>ccl.net Subject: kinetic time in docking process Message-ID: >sparky.ic.sunysb.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 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 CCL users: I have a question regarding the kinetic time in the docking process using LGA method.(I am using Autodock) How do I collect the information of kinetic times? In another words, the time step that each final configuration is reached from the initial state. Another quesiton is that how could I change the temperature in LGA method? In another words, I want to run the docking process for a specific ligand under different constant temperatures. It seems that the default temperature for LGA method is 300k. Any input will be highly appreciated! Have a wonderful day. Cheers Yong