Scoring the ligand

The energy scoring component of DOCK [55-57] is also based on the implementation of force field scoring. The program offers the possibility of precomputing the van der Waals and electrostatic potentials for the receptor and 

Given a suitable potential energy function [69], the straightforward method to relax the enzyme-ligand structure, and to reach a local minimum in the complex potential energy surface, would be a simple MM energy 

From the generated MD trajectory one can obtain average motions of atoms over time, average interaction energy values for the bound structure, time correlations for atomic positions and velocities, and RMS geometric fluctuations to be compared with any available experimental data. A particular intermolecular distance, or the interaction energy between two functional groups 

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