Docking cyclic peptides using Ligand PDBs

[jannled]

Hello,

I want to dock a cyclic peptide on a target, with the cyclic peptide chain being defined as UNL in the PDB. When using the online Haddock tool, I define the cyclic peptide PDB as Ligand, and turn on the cyclic peptide button (as shown in the picture below). Question: Is the cyclic peptide protocol running, even though I defined the peptide PDB as Ligand and not as Peptide?

Many thanks

[amjjbonvin]

). Question: Is the cyclic peptide protocol running, even though I defined the peptide PDB as Ligand and not as Peptide?

No it won’t. This only works with amino acids, i.e. standard supported ones defined as ATOM