The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab
I am new to Haddock and want to dock a DNA-Protein complex(A) with another protein(B). I read handbooks and several tutorial, but are still confused. Both A and B are dimers, I know the hypothetical motif that B would bind to A, but I have not yet performs NMR.
Could I just use a.a in motif as active residue?
The other question is how to perform the re-numbering. For dimer A there two sequences with title XXXX(pdb number)_0001 XXXX(pdb number)_0002, both with chain A, and possess a lot of 0 in the sequence, I am not sure about the trimming. Do I still perform the pdb_selchain.py? if so how do I call the sequences? I use the output of pymol for renumbering ( I trim a bit with pymol), would that be okay?
Also, how to determine the residue number of active residues after the renumber, when entering the residue number, could I use the format as 1-10?