[gmx-users] Setting custom atoms in FF

[Alex]

Another question about x2top: in the previous discussion, the atom
type was determined from its environment and the element type. What if
I set up my PDB with atom labels (i think that's the third field from
the left in the PDB format), say CJ1 and CJ2 (instead of just C), while the
force field contains

CJ1   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
CJ2   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149

Will then the right distinction be made? I'm asking before trying
it, because it is quite tedious for me to do the labeling. The
issue is way beyond carbons, I just discovered that a bunch of
different atoms isn't set up correctly.

Thanks,

Alex