Reindexing of atoms causes problem in mapping

[ppxasjsm]

I am not sure if this is intended, but in order to overcome poor mapping one way of doing so is giving an explicit mapping. if I use atom indexes from the input pdb file the explicit mapping will still fail, because FESetup changed the atom indexing in the parametrisation. So only once I have generated a set of vacuum.rst7 and vacuum.parm7 files is it possible to do explicit mapping with the atom indexes in these files.

Input file before parametrisation with atom indexes:

Atom indexes after parametrisation:

[skfegan]

I don't think this is explicitly an FESetup problem. The reindexing is as far as I know happening in one of the dependencies, probably tleap or in a format conversion (from pdb to mol2 or the like).