I have recieved this warning when trying to use FlexPepDocking refinement protocol for a tyrosine phosphorylated peptide.
core.util.switchresiduetypeset: (0) [ WARNING ] When switching to centroid mode, a normal replacement type for residue TYR:phosphorylated can't be found.
core.util.switchresiduetypeset: (0) [ WARNING ] an autogenerated replacement type is being used instead.
I was curious if this warning is problematic for future downstream results as the phosphate modfiication if very important in peptide binding. I cannot seem to find the patch files requried to mediate this problem based on what i Have read online. Any insight would be appreciated.