A worldwide e-Infrastructure for NMR and structural biology

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).
Your rating: None

Cite WeNMR/WestLife

Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.


The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858