We are trying to dock a protein with phosphorylated ARG residues; I have seen that the only supported residues are ADE, CYT, GUA, THY, and URI.
The issue we have is that after docking the phosphorylated ARG residue, it becomes a normal ARG residue.
Is there any protocol for this that we are messing? How can we solve this issue?
Sharing any example commend or PDB file is highly appreciated.