DNA-Protein Interaction


I’m trying to dock DNA-protein using easy interface but it showing this error

There was an inconsistency in your data

Error message

Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.
Directory of the run: http://alcazar.science.uu.nl/serviceresults/HADDOCK2.2/5028507797/case14

The PDB format is strict with respect to column alignments.
So check your PDB. Where did you get it from.

Sometime reading it in for example PyMol and exporting it as PDB again solves the problem.

You can also use our PDB-tools to validate your file, e.g using our new online portal at


And you can use the pdf_validate tool to check your file