Article ID: 309 - Last Modified: May 9, 2011
Are water molecules flexible in IFD?
Water residues are fixed (included in the receptor grid) during the Glide docking stages, but may be moved in the Prime active site optimization, where they will be flexible, as long as they are within the distance set in 'Refine residue within [ ] Å of ligand poses' (5 by default). You may specifically set water residues to be flexible in the 'Additional residues to refine' ('Additional residues' in earlier releases) text box or you may require them not to move by using the 'Do not refine residues' text box ('Omitted residues' in earlier releases).
One other place where waters can move is during the constrained minimization of the Protein Preparation step.
Keywords: Induced fit, explicit water, flexible, frozen
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