We will collect here problems and solutions. The following topics are currently available:
What about missing atoms or point mutations?
Missing atoms will be automatically generated by HADDOCK when
generating the topologies and PDB files
of the molecules in the begin directory. This is done when running the generate_A.inp
and generate_B.inp CNS scripts (these are based on the generate_easy.inp script from
the CNS distribution). HADDOCK uses the PDB files defined in the
new.html file. In case of missing residues, chain breaks will be introduced.
When setting up the docking from an ensemble of structures it can happen that single point mutants coordinates files
are available. These can be used as well provided you do the following:
- edit the PDB file and rename the mutated residue to the proper amino acid name
- keep or rename appropriately the matching side-chain atoms
The missing atoms will be generated automatically. It is important to have at least the backbone atoms defined
since their average position will be used as starting point to "grow" the missing atoms.
Always check that the sequence of the various PDB files match!
What about ions?
Some proteins contains ions such as for example calcium. Their inclusion might be important for docking
purposes, in particular for proper electrostatics! In principle, they should be recognized in the
topology generation step provided their name in the PDB file
matches the ion names defined in the ion.top file in the toppar directory. To avoid that a
N- or C-terminal patch be applied to them, they should also be defined in the topallhdg5.3.pep
file (look for the "first IONS" and "last IONS" statements).
Another problem occurs with ions in torsion angle dynamics since they are unconnected single atoms.
A workaround, provided they are only present in one of the molecules, is to fix them during the
torsion angle simulated annealing step. For this, edit the
refine.inp CNS script in the protocols directory and uncomment the following line:
fix sele=(resname CA2) end
Change the ion residue name as needed (this above example is for a calcium 2+ ion).
It is also recommended to define distance restraints between the ligands and the ions to maintain
a proper coordination geometry.
Domain definition for docking
In general, it is recommended to remove any part of your system such as flexible linkers
that are not involved in the interaction with the partner for docking. Keeping these might
give trouble in the sorting of solutions. For example, such a linker can make contacts with the
partner molecule, resulting in a lower total energy and, in that way, "bad" solutions could still be kept.
When choosing which of the two molecules will be in the first segid (e.g. "A"), it is recommended to
choose the largest and/or most rigid one of the two. This should give better clustering results since
in the rmsd calculation for clustering (rmsd.inp CNS script) the
structures are first fitted on the backbone of the first molecule and then the rmsds are calculated for
the backbone of the entire complex.
Defining the largest and best defined (most rigid) molecule first should thus result in a better fitting.
In case where highly flexible segments are present, it might be a good idea to also limit the regions for
fitting and rmsd calculations by modifying the rmsd.inp CNS script
and adding explicit residue range selections, e.g.: