From chemistry-request |-at-| server.ccl.net Mon Jun 24 11:47:49 2002 Received: from cse.nd.edu (root[ AT ][129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OFlnQ01133 for ; Mon, 24 Jun 2002 11:47:49 -0400 Received: from dylan.cse.nd.edu (ako&$at$&dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g5OFlkS08774 for ; Mon, 24 Jun 2002 10:47:46 -0500 (EST) Received: from localhost (ako&$at$&localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g5OFliT05777 for ; Mon, 24 Jun 2002 10:47:44 -0500 (EST) Date: Mon, 24 Jun 2002 10:47:44 -0500 (EST) From: Alice NgarKit Ko To: chemistry;at;ccl.net Subject: charmm problems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I have a few questions on running charmm simulations. 1) I have this protein pdb file from protein data bank. It has a -9 charge. Do I need to add 9 Na+ to balance the charge? If yes, how and where do I add them? 2) After taking care of the charge and solvation, how long do I need to minimize the system? Or how do I know if the system is minimized? 3) After minimization and heating the system back to 300K, how kind of output files do I need to anaylsis the dyanmics? Unformatted trj? What will be the other options of output file? Thanks in advance for your time and help. Alice