Dimer dissolved / splited during docking

I was docking a homolog model dimer protein (swissmodel) with peptide ligand and the dimer splitted apart. Previously when i was using the exprimental xray crystallography structure to screen for optimal parameters, they never split into discrete chains. Anyone encountered similar issues? Please help thanks.

This is my homolog model

DRA00201_DRB00101_renumbered.pdb (236.4 KB)

Could you please share the link of the HADDOCK run?

THanks for the prompt reply, please refer to below for the link


Since your dimer is a model, it could well be there are clashes that cause the models to separate. You could try refining it first using the refinement interface and defining each monomer as one molecule

thanks for the respond. may i know how to define each monomer as one molecule? And please recommend any structure refinement interface. thanks

Split the file into two (one file per monomer)

And submit it to the HADDOCK refinement interface:


(you do need expert access for this - request it online in your registration page)

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The server simply doesn’t support refinement of a single molecule - it is meant for complexes

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