Point deletion mutation

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.4
I want to create a point deletion mutation? Can I delete that residue on the PDB file? The peptide interation also will be deleted. Do that effect to docking result by Haddock? Thank you.

That will introduce a gap… Probably not the best way to look at this.
I would rather try to model first the protein after the deletion, which can cause all kinds of structural rearrangements.
Could be done by MD for example. And only then try potentially some docking