[gmx-users] Setting custom atoms in FF

[Alex]

Hi all,

I am messing with the OPLS/AA forcefield. The idea is to functionalize
graphene edge atoms beyond passivation with hydrogen. At the
functionalization region, there is a C atom with
two C-C bonds (from graphene), while the third bond is formed with the
functional group. The particular atom from the functional group
intended to bond with that C bond is also carbon. When setting up the system, in atomname2type.n2t I have:

CJ   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142  ; bulk graphene C

but also want to introduce

CJ   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149  ; edge C

Both 996 and 1001 are defined in the ffnononbonded.itp, these are
custom, but essentially copies from oplsaa entries for carbon. Note
the third bond that's longer (which is also the case in my input PDB).  The
significant difference is of course the charge there, as I want a globally neutral
system.

Here is the problem: x2top ignores the second statement from above and the
functionalized edge C is assigned #996. Aside from manually modifying
the resulting topology, can we make this distinction stick?

Thanks,

Alex