Thank you for your reply. I am aware of NBXMod. Is just that the description of it is bit vague, but I subsequently found the previous post that explains it:http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23646
Another reason I ask this is because in the paper reference for CHARMM19 (E. Neria et.al. JCP, vol.5, p1902 (1996)), nonbonded energy terms are considered for all atom pairs except those bonded or separated by a single bond (page 1918). This sounds to me non-bonded atoms separated by two bonds (1-3 interactions) are included for calculations.
I wonder if I have misunderstood something here?