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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 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?


When I upload my file, it says “Your PDB contains multiple residues with number 1 in chain A or duplicated atom names.” How shall I correct that?

Remove the duplications :slight_smile:

Search the forum - this question has been answered many times.
Probably due to overlap in numbering.

An example of shifting the number of chains is given in our local HADDOCK installation tutorial.
You should be able to perform the same using our PDB-Tools web server.