Hi Geo, index files are read internally by a Colvars internal function. We have discussed that for the case of GROMACS it would be simpler all around to just read directly the index groups that GROMACS itself has defined in memory, but this is not available yet:
Was the index file that you are providing produced with “gmx make_ndx”? Or if it isn’t, can you check that at least GROMACS can read it when you pass it as input to the same command?
If GROMACS can read it but Colvars cannot, can you put it online somewhere and paste a public link? (It is likely too big to paste in the message itself and the format will also change)