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HADDOCK 2.4
Frequently Asked Questions

Below you will find a list of frequently asked questions about HADDOCK 2.4. If you have a question that is not listed here, please contact us at the ask.bioexcel.eu forum.


This might happen in high resolution crystal structures where possibly different conformations of a side-chain are seen. These conformations are indicated by A,B,C,... next to the residue name and will have partial occupancies. If this error is raised, you will have to remove the duplicated residues/side-chains. This can be done for example with our PDB-tools pdb_selaltloc command.

This error means you have selected the wrong molecule type for your PDB. Please go back to the input page and select the correct molecule type.

When using Ions, you need to specify the charge of the ion by modifying both the residue and atom names in the PDB file. Please check the supported ions section of the HADDOCK library for the correct format.

This error is raised when you input a molecule with multiple chains that have overlapping numbering. To fix this error you need to renumber your input PDB (or shift the numbering of the chains) so that the numbering is non-overlapping across all chains. This can be done for example with our PDB-tools pdb_reres (or pdb_shiftres) command.

HADDOCK expects that each residue in a chain has a unique number. This error is raised when you input a molecule with multiple residues that have the same number in the same chain. To fix this error you need to renumber your input PDB so that the numbering is unique across all residues in a chain. This can be done for example with our PDB-tools pdb_reres command. Note that this problem can occur in the numbering of residues in the hypervariable loops of antibodies, where sometime insertion codes are used (e.g. 100, 100A, 100B). In that case you can use the PDB-tools pdb_fixinsert command.

When selecting residues for the active and passive residues, you need to select at least one residue for the active residues - this is the residue that will be used to drive the docking.

This error is raised if active (and passive) residues are defined for one molecule but nothing is defined for the other molecule(s).

This error is raised when for example defining only passive residues for one molecule but no active residues for the other molecule. I.e. it only makes sense to define passive residues for a molecule if the other molecule has active residues defined.

This error means that some issue occurred on your end, there is nothing you can do to fix it, except may-be trying again after cleaning your cache. If the error persist, please contact the HADDOCK team at ask.bioexcel.eu and provide information about the service/interface your were using, what were the input files and any other relevant information. We can not support you without proper information.
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This work is co-funded by the Horizon 2020 projects EOSC-hub and EGI-ACE (grant numbers 777536 and 101017567), BioExcel (grant numbers 823830 and 675728)
and by a computing grant from NWO-ENW (project number 2019.053).