Why did my structure split into pieces using ZDock?

24 December 2021 1 5K Report

Hi I'm trying to perform protein-protein docking via ZDock but the results are weird as shown in the figure.

Specifically, the ligand is a homology model of the variable region of an antibody, generated by Swiss-Model, and the receptor is DLL4 (PDB ID: 5MVX) with no water molecules and other nonfunctional atoms. Is there something I should do before uploading these files to ZDock?

Interestingly, the output of HDock looks good, but I still wonder what happened when using ZDock.

Yilin Zhu

Chain names replicated.

Try the code: alter chain A, chain='B'

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