Refinement with HADDOCK

HADDOCK final step is MD refinement in water.

  1. How can I find the MD parameters HADDOCK used?
  2. Can I only run this stage on a protein complex with small ligands instead of full docking, simply to optimize the final geometry (bonds, angles), maybe remove some clashes and adjust sidechains?


You can find more information about the MD parameters in the Docking Protocol section.

Our webserver has a dedicated Refinement Interface, you could achieve the same on the local setup using the same parameters:!