I am just trying to find out the limitations of the amber2lammps.py.
I observed that the number of angles and dihedrals does not change for an isolated molecule, same molecule plus 2A TIP3 waters, same molecule plus 15A TIP3 waters. However, the number of atoms and the bonds increase as expected.
I assume there is an issue with the python script, that is, that you need for every single water molecule for example the angle listed.
The rhodo example seems to do this.
I just wanted to confirm with you.