The pH of my crystal PDB is 5.5, but I would like to perform a simulation under pH=7.

I used PDB2PQR to change the protonation state, but because my structure contains a modified residue (acetylated lysine) and ZN, PDB2PQR cannot recognize it. The .pqr file generated by PDB2PQR has the acetylated lysine and ZN missed.

Is there any ways that I can figure it out?

PS: The force field I used is Amber and in the 2022 Amber manual, it said parameters for acetylated lysine can be obtained by "source leaprc.protein.ff19SB_modAA"