I am sorry for the late reply but I was out of country from 10 to 26.07.

In our tests six copolymers samples were selected and have been used to test the hybrid algorithm.  The coordinates of the probe molecule and the target molecule as well as their surface are randomly rotated and translated. The surface dot coordinates have also been moved with the probe and target molecules. Then an initial solution is randomly generated containing six variables, three translational degrees of freedom and three rotational degrees of freedom. The position of the target molecule is fixed and six variables define the orientation of the probe molecule. The evaluation score is composed of two parts: the matching score and penalty score of atomic overlapping. The position of the target molecule is also fixed and some changeable variables are defined for the probe molecule. Only a local search was performed near these binding sites. Considering the fast convergence of GA near the best solution, we usually only use GA in the local search. A set of `chromosomes' are randomly generated and each one represents an orientation. The fitness score of each `chromosome' is the interaction energy between the probe and target molecules. Only van der Walls energy, electrostatic energy and hydrogen-bond energy are considered. Our purpose was mainly to purge the high-energy conformations, and in the mean time to calculate the interaction energy precisely. When the unbonded interaction energy remains stable in a user-defined region after 20–30 iterations, `convergence' is achieved.