Modified pdb2gmx to automatically pick the force field from the current directory

Modified pdb2gmx to automatically pick the force field from the current directory
if a choice is specified with the -ff option, even if others exist. We still
print a notice about it. The full include paths were also removed from the topology,
but we now print information about where the FF was picked up from, and a notice
that this location must be included when processing it if it is a non-standard one.