Hi, all. A few months ago, I am grateful to got a batch peptide generator protocol releaseed by @JS in the community. LibDock and CDOCKER perform well for docking small peptides (such as dipeptides and tetrapeptides) and proteins, but have difficulty in docking proteins with large peptides (such as heptapeptides to dodecapeptides). This should be the reason why the binding site cannot accommodate large peptides due to the large volume of peptides. Therefore, I thought of ZDOCK , but the ligands of ZDOCK can only be selected one by one. Therefore, I wanted to know how to modify ZDOCK protocol in Pipeline Pilot so that the input ligand protein can select ligand-all like CDOCKER.