Fixed topologies that were using top level .itp-s.

Removing some .itp-s such as $gmxdir/share/top/spc.itp
was causing the tests to fail. This patch fixes that.
Note that some cases in complex are fixed separately in
https://gerrit.gromacs.org/#/c/3173 and thus skipped here.

Change-Id: I0a91a1d1422bc980a06ce3fdf93ef594b467fb78