My docking_prepack application is incorrectly patching the hydroxyproline residues. Although the log file indicates that the full-atom patch is correctly read from the fa_standard/patches and also successfully patched, the output prepacked file contains a bond between the CD as well as CG to the OD1 of the HYP residue.
The original pdb file had HYP residues annotated as HETATM with appropriate CONECT coordinates. I have tried to use both the original pdb as well changing HETATM to ATOM and deleting CONECT coordinates but no change in the output.
The pro_hydroxylated_case1.txt file in the fa_standard/patches contains the following line,
NAME3 PRO DPR
Shouldn't the DPR be HYP? In any case, I changed it to HYP but the output was identical!
Any advice is deeply appreciated.