Question about webserver

HADDOCK
1

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?

Thanks!

2

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?

3

Remove the duplications :slight_smile:

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

4

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.

Check:

https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#dealing-with-multi-chain-proteins