Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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HADDOCK2.2 manual

Changes with respect to version 2.1

HADDOCK2.2 has been made compatible with CNS version 1.3. Because of changes in CNS1.3, the linkage files in the toppar directory do no longer contain wild cards. All linkages are specified explicitely.

Also, only three character residue names are now used:

  • WAT and HOH added as water residues (same param as TIP3P)
  • GLUH changed to GLH
  • ASPH changed to ASH
Accordingly, all protocol files have been modified to make use of WAT, HOH and TIP3.

For use with CNS version 1.3, the 5.4 version of the protein topology and parameter files MUST be used:

  • topallhdg5.4.pro
  • parallhdg5.4.pro
  • topallhdg5.4.pep
  • topallhdg5.4.pep-noCter
  • topallhdg5.4.pep-noNter
  • topallhdg5.4.pep-noter
  • topallhdg5.4.sol
  • parallhdg5.4.sol
And for DNA:
  • dna-rna-allatom-hj-opls-1.3.param
  • dna-rna-allatom-hj-opls-1.3.top
  • dna-rna-1.3.link
  • dna-rna-pho-1.3.link

A CNS version check has been build in the parameter files.

Other main changes with respect to version 2.1 are listed in the following:

  • It is now possible to mix molecule types within one molecule as long as there is no overlap in residue numbering. This this enables for example the docking of a protein onto a protein-DNA complex.
  • New S3 and C4 symmetry restraints
  • Radius of gyration restraint
  • Option to automatically define dihedral angle restraints from the input structures
  • Pseudo contact shift restraints
  • Interaction matrix to scale down or turn off interactions between specific molecules
  • Water-mediated contact probabilities option based on Kyte-Doolittle hydrophobic scale
  • DNA-specific fraction of water to keep for solvated docking
  • Fraction of common contact (FCC) clustering option
  • Default setup (parameters/topology files) for CNS1.3
  • Removed analysis options (procheck, prosa)
  • Added examples for various docking scenarios (see the example directory)

Please send any suggestions or enquiries to Alexandre Bonvin