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.
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