Protonating structures programmatically

GROMACS version: 21.5
GROMACS modification: No

I would like to ask for some advice on protonating residues when running simulations at pH values that are substantially different than neutral. Pdb2gmx has the -inter (and also -his, -lys, etc.) flags to set the protonation status of lysine, histidine, and other residues manually. (Say, one can “deprotonate” LYS, and set it to LYN, or set HIS to HID.) I wonder that if I use a pdb structure with pdb2gmx where the right residues are already set to LYN, (or HID, etc), will pdb2gmx add the correct hydrogen bonds to the structure, or one simply has to do this step manually?

(In the case of cysteines in disulfide bridges, setting them to Amber-style CYX results in erroneous dynamics, the disulfide bridges are not recognized, even though the number of hydrogens is correct after pdb2gmx, and I use amber force fields.)

Thank you.