Protein-Ligand docking error

[chris]

Good evening and sorry for the inconvenience,

I am trying to dock a protein and a ligand with HADDOCK 2.4, but when I put the pdb file of the ligand, I get the following error:

Error in PDB file.
Issue when parsing the PDB file at line 1 .
Residue number must be an integer (is ’ ')

Here’s a sample of the starting point of the aformentioned pdb file:

[amjjbonvin]

All atom names must be unique…

I.e. either generate your ligand with some other software (e.g. RDKit - check our shape-restraint ligand docking protocol on bonvinlab.org/education) or manually edit the PDB file and add for example a number to each atom type (C1, C2, C3…) to make them unique.