DOCK is a separate program that calculates possible binding orientations, given the structures of ligand and receptor molecules. Some uses are to examine a particular binding interaction or to search a database for ligands of a target receptor.
Dock Prep can perform several tasks to prepare structures as input to the DOCK suite of programs:
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 Surface/Binding Analysis category.
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:
W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules" J Am Chem Soc 117:5179 (1995).Water charges correspond to the TIP3P model:
W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura, "Comparison of simple potential functions for simulating liquid water" J Chem Phys 79:926 (1983).The values are assigned as an atom attribute named charge and will be included in Mol2 output. The files used for charge assignment are in the share/DockPrep/ directory of a Chimera installation:
A related tool is ViewDock, which facilitates interactive screening of DOCK output.
Does not add missing heavy atoms. Even when all residues are present in a structure, atoms may be missing from sidechains or the termini (for example, there may be no OXT atom on the C-terminal residue). Chimera does not build in any missing residues or parts of residues. The only atoms added are hydrogens, and when a residue is partly missing, an additional hydrogen will be added to fill the valence of the existing portion. Because it is not part of the standard residue, there will be a warning about the extra, unrecognized hydrogen during the charge assignment step.
Charges only added to atoms in standard residues. Charges are only added to atoms in water, standard amino acids, standard nucleic acids, and a few common variants and capping groups (as in the Amber all*94.lib files). However, Amber's Antechamber module generates parameters for arbitrary organic molecules, and Dock Prep may use this program in the future.
Possible ways to resolve null charge assignments: