Protein DNA run fails


#1

Hi,
I’m trying to dock a 20 bp DNA with a Protein. I have prepared the DNA from haddock dna modelling server and trying to dock it with a multimeric protein’s crystal structure.
However, the docking fails repeatedly saying “First pdb file contains multiple chains with overlapping numbering: A5 - B5”

Is it not possible to run docking with multiple chain containing protein ?
Please help me out here. I’m keeping the protein and DNA file here https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Thank you.


#2

Hello,

This is possible to provide a PDB with multiple chains but then you need to have unique residue IDs for all residues. Meaning that your second chain (here B) should start with residue ID 202 (last residue ID from chain A + 1).

Mikael

PS: Note that this forum is searchable and the answer to your question is already provided… E.g.:


and