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This is the UCSF DOCK problem page. There are other problem pages too:

Docking problems in general

  • treatment of entropy
  • treatment of receptor desolvation
  • treatment of induced-fit effects
  • ligand internal energy

DOCK 3.5.54

  • prepare new distribution
  • "collisions"
  • inline out of box detection
  • ligand internal energy
  • write out multiple structures for PLOP