Improvements to GROMACS tools

gmx pdb2gmx now resolves generated hydrogen names from the residue topology

When gmx pdb2gmx adds hydrogens from the hydrogen database, it now looks up their names in the residue topology entry of the selected force field instead of relying on hard-coded numbering rules. This allows force fields that use different hydrogen naming schemes, such as original AMBER/IUPAC names for methylene hydrogens, to work without naming-specific code paths or command-line options.