Updates for Drude disulfides.

Disulfides are now handled correctly, with exclusions, anisotropy,
lone pairs, and Thole screening treated appropriately.  Changes were
made to add these terms after special bonds have been added within
pdb2gmx.

Change-Id: Ibf681723d7d3c9df3d0d9b2b8f6b63be2108e878