13. Ligand Flexibility and Constraints

To allow flexibility in the ligand, it is necessary to assign the rotatable bonds. It is a good idea to have handy a plot of the ligand, labelled by atom name, and a second labelled by atom serial number (atom ID). AutoDock can handle up to MAX_TORS rotatable bonds: this parameter is defined in "autodock.h", and is ordinarily set to 32. If this value is changed, AutoDock must be recompiled.

Torsions are defined in the PDBQ file using the following tokens or keywords:

 
		ROOT / ENDROOT
		BRANCH / ENDBRANCH
		TORSION / ENDTORSION

These keywords use the metaphor of a tree. See the diagram below for an example. The "root" is defined as the fixed portion of the ligand, from which rotatable `branches' sprout. Branches within branches are possible, and torsions are a special case of branches, where the two atoms at either end of the rotatable bond have only two nearest neighbors (unlike branches which can have three or more). Nested rotatable bonds are rotated in order from the "leaves" to the "root".

The PDBQ keywords must be carefully placed, and the order of the ATOM or HETATM records may need to be changed in order to fit into the correct branches. The PDBQ keywords can be abbreviated to no less than the first 4 letters. To assist the user in placing these keywords correctly, and in re-ordering the ATOM or HETATM records in the ligand PDBQ file, it is best to use the interactive program AutoTors (see below).

Note: AutoTors , AutoGrid and AutoDock do not recognize PDB "CONECT" records, neither do they output them.

"CONSTRAIN" defines a single, optional distance constraint, between two flexible parts of the ligand. It is not normally used in docking. This retains only those conformations where this distance is within a certain range of values. In docking, a conformation which violates this constraint is instantly rejected; it does not increment the rejections-counter in simulated annealing, its energy is not evaluated, nor is the steps-counter incremented. This PDBQ keyword has the following syntax:

 
CONSTRAIN atom1 atom2 lower upper

The first two parameters are the atom serial numbers of the two atoms to be constrained, and the last two are the lower and upper bounds for this distance, in Angstroms. This can be particularly useful when docking say two proteins: a loop from one protein can be cut out and the ends constrained to have roughly the same value as in the original protein.

The next sections describe the input files needed for AutoTors , and how to run it.