Applying a post transational modification to a protein structure

GROMACS version: ND
GROMACS modification: Yes/No
Hello everyone, I hope I can find someone who guides me about how to apply a PTM for a specific protein… I already tried via PyMol then I minimized the energy via YASARA but once I run MDs … the modified residue was flipped out.
So I wonder if I can run PTMs via gromacs or not?
have a nice day

Can you please elaborate on what type of PTM you are trying. Glycosylation, fatty acid conjugation, phosphorylation, etc…