The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
Im trying to dock protein chains from PDB with aptamers PDB file generated via Vfold3D. The HADDOCK server is giving me an error: Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.
The second PDB file was the one generated by Vfold3D. Please guide me. I’m new to this. 
Hello,
One quick fix would be to open your PDB with an external tool (PyMol for instance) and save it again as PDB. The columns will be rewritten by PyMol and well-aligned.
Good luck!
Mikael