Optimal rigid-body orientation

D. A. Gschwend and I. D. Kuntz. Orientational sampling and rigid-body minimization in molecular docking revisited On-the-fly optimization and degeneracy removal. Journal of Computer-Aided Molecular Design, 10 123-132, 1996. 

A sequential optimization procedure, which considers only non bonding interactions and which treats the molecules as rigid bodies, was used to locate stable orientations of the seiector and selectand the procedure is applied only to the minima obtained by the selecting routine... 

Analysis) works by using a Monte Carlo procedure to randomly orient a given number of molecules in a trial unit cell. To accomplish this stochastic approach to sampling trial unit cells, the energy of the cell is minimized with a rigid body optimizer, Although this procedure imposes no space group symmetry, symmetry may be present in the minimized structures as permitted by the number of molecules in the cell. 

Certain special features to be imposed on a model may be expressed by more complicated constraint equations. We note as an example the assumption of a rigid molecule with prescribed dimensions whose position and orientation are to be refined. The position may be described by the coordinates of the centre of mass and the orientation by three Euler angles with respect to a unitary coordinate system. The atomic coordinates and thus the structure factor. Equation [1], are expressed as functions of these six parameters. The latter may then be adjusted to optimize the deviance. A similar procedure can be used to constrain the atomic displacement parameters of a molecule to rigid-body movements described by a translation tensor, a libration tensor and a transla-tion/libration-correlation tensor (TLS model). This model neglects intramolecular vibrations. 

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