l - People

ligand) is then put into standard orientation. This is the convention that X L
r coincide
with the origin, S Xr lie along the z-axis, and X M
r
5.2).
246
lie in the –y part of the yz plane (Figure
The coordinates of the ligand are required in PDB format, as is the GROMACS .itp
(include topology) and the AutoDock .pdbq (structure + charges + bond mobility) files.
The latter two can be generated from the first using the PRODRG program[123].
Definition of Rotations
The three euler rotations mentioned earlier are the rotation of the M domain about the x-
axis, σx, also referred to as a “pitch” rotation, σy, the “yaw” rotation, and σz, the “roll”
rotation (Figure 5.2). The ligand is conventionally not rotated, i.e. remains stationary
with respect to S.
One must keep in mind that the magnitude of the displacement of X M
r
due to a yaw
rotation depends on the pitch coordinate. Also, while yaw and roll rotations result in
orthogonal displacements of domain M at pitch = 0°, the displacements become
progressively more parallel as pitch approaches ±90°. For these reasons if phase space is
explored at equal angular intervals, regions approaching pitch = ±90° are explored more
densely than regions near pitch = 0°. Finally, when pitch is exactly ±90°, yaw and roll
rotations are exactly equivalent up to a sign and it is impossible to control either