ambpdb and cpptraj: option to add alternate atom label

[hainm]

When saving pdb file from LES parm7 and rst7:

ATOM     74  CG2 VAL     5       2.113  13.231  12.603  1.00  0.00           C
ATOM     75  CG2 VAL     5       2.672  12.986  10.766  1.00  0.00           C

We are using an external Perl script to add A/B label for alternative conformation but it's great if there is an option in cpptraj.

cc @dacase