as for the input pdb file, with or withg original ligand in this new version

[MachineGUN001]

hi, @gcorso

thank your gus to provide the latest new version. I'm trying to compare the differences in the docking results between this new version and the past version.

The input pdb file, the protein file. If the file includes the original ligand, will using this pdb file including the ligand directly affect the docking results? If the ligand structure in the pdb is eliminated using pymol, etc., will the results be improved when docking using diffdock?

Many thanks,

Best, Sh-Y