Water: my target crystal structure has some waters in the active site, what should I do with them?Up to table of contents
This FAQ applies to: Any version.
Often, inclusion of an important water can improve the docked results. We have also developed a new method for including multiple sites of hydration--please see (reference) for more information. Some of the automated scripts will remove water and other non-protein components, but you can use the GUI to process coordinates to create a PDBQT file. The coordinates are input, hydrogens added, and charges calculated using the menus in the PMV portion of the GUI. This process is described in more detail in the tutorial. Note that the current Babel-based method for adding hydrogens will not optimize the position of the hydrogens--it is often better to add these hydrogens manually using an external molecular modeling program. Alternatively, a new method has been developed for predicting position of waters and their displacement with AutoDock 4.x (Forli and Olson 2012, see User Manual referrences)