Subject: Editing protein pdb

From: amor san juan <[email-masked]>
Date: Sat, 29 Jun 2002 06:48:19 -0700 (PDT)

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

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