Newest CHARMM36 port for GROMACS

You need to use the -ter option and interactively choose from the prompts as to which termini you want. For polypeptides, you typically want NH3+. The MET1 patch is for carbohydrates, but pdb2gmx thinks it’s the best match because it matches the MET residue name. In this case, it’s the program trying to be too smart (though there are reasons for it that are typically associated with GLY residues).