Dock Prep can perform several tasks to prepare structures as input to the DOCK suite of programs (or for other types of calculations), including:
If there are extra molecules other than solvent that should not be present during docking, these should be deleted before Dock Prep is run. Dock Prep does not delete extra chains or other molecules besides solvent, because depending on the specific situation, they might be important for binding or maintaining receptor structure. Similarly, binding might require the presence of more chains than are included in the structure file; the relevant form should be generated before Dock Prep is run (see also Unit Cell).
There are several ways to start Dock Prep, a tool in the Structure Editing category (including using it via Minimize Structure).
Under Molecules to prep, the structure(s) of interest should be chosen from the list of open molecule models. Individual models or blocks of models can be chosen with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.
Several operations can be performed on the chosen structures:
The rotamer library options replace each truncated sidechain with a complete sidechain of the same residue type, as if using the command swapaa with the specified rotamer library and preserve true (default settings of other options). If different settings are desired, use swapaa separately before using Dock Prep. The mutation option changes each residue with a truncated sidechain to glycine or alanine, the latter if a CB atom is present.
Using one of these options to generate complete sidechains is recommended because in incomplete residues, the partial charges will not sum to integer values, and extra hydrogens (unrecognized in the charge addition step) will be added where the missing atoms would have been attached.
The resulting protonation states of such groups and of those with possibly perturbed pKa values (for example, in active sites or coordinating metal ions) should be checked manually and corrected as needed. Correction may consist of deleting unwanted hydrogens (for example, with Atoms/Bonds... delete in the Actions menu) or adding hydrogens that were not added automatically (for example, with Build Structure). Charge assignment should be repeated after any manual correction of protonation states.
Charges for standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are looked up using assignment files based on the Amber parameter files all*94.lib. If any atoms in standard residues are not recognized, a warning will appear and information on the atoms will be sent to the Reply Log. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved.
Charges for nonstandard residues, if any, are calculated using Amber's Antechamber module (included with Chimera; publications involving its use should cite the reference). It is necessary to specify the formal charge of each nonstandard residue and which charge calculation method should be used.
Tasks are performed in the order listed on the Dock Prep dialog. If any individual step is canceled, subsequent steps will not be performed; for example, if charge assignment is canceled, a Mol2 file will not be written. To skip a particular step, uncheck its option before initiating the Dock Prep calculation.
A related tool is ViewDock, which facilitates interactive screening of DOCK output.
Does not build missing segments. Structures may have missing residues or atoms where coordinates could not be determined because of disorder or flexibility. Dock Prep can fix truncated sidechains, but it will not build missing backbone segments.