Fixed issues with terminus generation.

Bonds were missing due to repeated atom indices in the hackblocks
(found within at2bonds in pdb2top.cpp), so I instituted special
cases for using the Drude FF with N- and C-terminal patches. These
changes should not be necessary for other FF, so the code doing
the changes is totally isolated by being contingent upon bDrude.

Change-Id: Ibd66245239150e773491c453d7718d18f2a8f9ab