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How to Prepare PDB Files for Running HADDOCK Manually

In order to run HADDOCK you need to have the structures of the molecules (or fragments thereof) in PDB format. There are a few points to pay attention to when preparing the PDBs for HADDOCK.

  • Make sure that all PDB files end with an END statement.
  • HADDOCK can deal with chain breaks (e.g. missing density in crystal structures or between the two strands of a DNA molecules). In the case of multiple chains within one molecule (e.g. DNA) or in the presence of co-factors, it is however necessary to add a TER statement in between the chains/sub-molecules.
  • Remove the SEGIDs if present (the SEGID is a four character long string at columns 73-76 in the PDB format). This is particularly important for docking from an ensemble of starting conformations. If the strings for SEGIDs are not blanked, you will face with some problems at the topology and structure generation step. For removing the SEGIDs an awk script called pdb_blank_segid is provided in the tools directory. In order to use it, type in to command window:

pdb_blank_segid input.pdb > output.pdb

  • When starting from an ensemble of structures like, for example, from an NMR PDB entry, split structures into single PDB files. Again make sure that each structure file ends with an END statement and does not contain any SEGID.
  • HADDOCK can deal with ions, in the case that the ion naming is consistent with the ion topologies provided in HADDOCK (check for this the ion.top file in the toppar directory). For example, a CA heteroatom with residue name CA2 will be interpreted as a neutral calcium atom. For creating a doubly charged calcium ion, you should name the residue after CA+2. In this way, the doubly charged ion will be properly recognized by HADDOCK (See also the FAQ for docking in the presence of ions).
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