From chemistry-request@server.ccl.net Sat Jun 29 09:48:20 2002 Received: from web12802.mail.yahoo.com ([216.136.174.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5TDmKu03818 for ; Sat, 29 Jun 2002 09:48:20 -0400 Message-ID: <20020629134819.66812.qmail@web12802.mail.yahoo.com> Received: from [203.87.150.242] by web12802.mail.yahoo.com via HTTP; Sat, 29 Jun 2002 06:48:19 PDT Date: Sat, 29 Jun 2002 06:48:19 -0700 (PDT) From: amor san juan Subject: Editing protein pdb To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello to all: Im now in the process of editing protein prior adding charges and solvation in docking process. Would anyone please give me basic concepts on what HOH molecules must I retain in pdb coordinates. Based on analyzing the 3ptb distribution file in AutoDock, the 2 water molecules chosen to be retained are not necessarily quite near the inhibitor benzamidine. Using the MolW protein viewer the protein backbone is being stabilized by the presence of this 2 HOH molecules. Your comments and suggestions is very helpful to me. Thanks, Amor __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com