Added ability to write Thole pairs.

The code has been extended such that the user can supply a
[ thole_polarization ] directive in the .rtp file that specifies
intramolecular pairs that are screened by the Thole function.

An additional check has been added in grompp for Thole use,
though it is related to nonbonded Thole screening of mobile ions.
Changes in pdb2top.* and pdb2gmx.c are directly related to the
intramolecular Thole terms.

Change-Id: Ic819a972c6ca2676e445971cdd6304d2f7878676