C4 zinc finger protein

[amjjbonvin]

Hi Sarah

Remember that the HADDOCK forum is searchable. You will need to restrain your zinc coordination. See

Dealing with elemental ions

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: the residue name should contain the absolute charge state 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)

And the way to define distance restraint to the Zinc is explained in the following thread:

Zinc finger protein

Which kind of restraints did you define to maintain the geometry of the zinc finger? To get proper results make sure to define distance restraints between: all atoms coordinating the zinc (basically define the tetrahedron connecting them each coordinating atom and the zinc atom. Note that the distance restraints must have the zinc atom name between double quotes because of the + in the name. The correct nomenclature for HADDOCK for the zinc is: residue name: ZN2 atom name: ZN+2 (shifted …