Dealing with elemental ions

HADDOCK
2

The way to define ions for HADDOCK is explained in Box 3 of our Nature Protocols 2010 server paper:
The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897 (2010). Download the final author version here.

In short:

  1. the residue name should contain the absolute charge state
  2. the atom name should have the exact charge

E.g. for a zinc atom:

  • residue name: ZN2
  • atom name: ZN+2 (atom name with four characters should be shifted by one column to the left)
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