Dockit DG dock engine

• After the ligand is inside all site spheres, the spheres are removed and conjugate gradient minimization continues in 4 dimensions vs. the distance geometry intramolecular error function and an intermolecular steric and electrostatic function:
  
• United atoms with no explicit hydrogens are used; charges are assigned by analogy to AMBER using SMARTS rule-based assignment.
   
• Docking is scored initially by the final, optimized intermolecular energy.