I submitted a docking job (protein-ligand) by specifying a list of active residues (binding sites). The run completed successfully, but after downloading the results and inspecting the active residues, I noticed that some of the residues I originally provided are no longer present.
What do you mean exactly by no longer present?
The residues are missing in the structure? What were those residues?
They are still present in the structure, but they do not appear in the active residue list, even though I have defined them as active. In particular, one arginine is consistently missing from the active residue list for the protein I’m using.
The server will filter out by default all the buried residues.
You can turn that option off at submission time (need expert access for that)