I've been playing around with Tinker 7 to do MD simulations of protonated amino acids. I am very new to this, so naturally I am not quite sure which force fields would be best suited, or how to set them up.

I am currently trying to use the "protein" tool in Tinker to set up asparagine with a protonated C-terminus. But it appears that the supplied force fields are unable to parametrize the COOH group by default; the resulting .xyz files just contain "XXX" placeholder atoms, or the program can't find any parameters for angles and torsion. I've tried the different Amber, Charmm and Amoeba versions that come with Tinker. What could I do here?

Thanks in advance!