amber.load_traj should support a default ref_pdb creation if none is provided

[shaoqx]

And warn user that in this case ["ATOM_NUMBER", "RESIDUE_CHAINID", "RESIDUE_NUMBER"] are automatically determined.

[shaoqx]

A non-add-pdb prmtop file keep the chain termination information under ATOMS_PER_MOLECULE

A good plan could be using cpptraj to make a reference PDB.

In this case, the chain ids (but not segmentation), residues ids, and atom numbers will be re-assigned as 1-indexed (and A-indexed)