Soft electrostatic grid

The maximum value is set so that the electrostatic energy is less than
or equal to the Lennard-Jones repulsive energy for every heavy atom at
every grid point
In HREX.py, changed merge_dictionaries function to restore ability to
load simulations in progress without passing every argument. Made sure
that soft electrostatic grids are also scaled appropriately if they are
directly from APBS. Adapted ligand preparation to accomodate mol2 (3D
strucutures) as well as ism (SMILES strings) files.