Refinement with HADDOCK

HADDOCK
1

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?

Thanks.

2

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: https://wenmr.science.uu.nl/haddock2.4/settings#refinement!