read 
    mol pqr ion.pqr                      # Read molecule 1
end
elec name solvated
    mg-manual                          # Use the multigrid method
    dime 65 65 65                      # Grid dimensions (c 2^(l+1) +1)
                                       #   (in x, y, z)
    nlev 4                             # Number of levels in multilevel
                                       #   hierarchy (usually 'l' from above
                                       #   definition)
    grid 0.33 0.33 0.33                # Grid spacings (A)
    # glen 100 100 100                 # You can EITHER specify the grid
                                       # lengths OR the grid spacing
    gcent mol 1                        # This can either be 'mol n' to center
                                       #   on a specific molecule or (x, y, z)
                                       #   coordinates
    chgm spl2                             # Charge disc method
    mol 1                              # Which molecule (1, 2, ...)
    lpbe                               # lpbe/npbe = linear/nonlinear PBE
    bcfl mdh                             # Boundary condition flag
                                       #  0 => Zero
                                       #  1 => Single DH sphere
                                       #  2 => Multiple DH spheres
                                       #  4 => Focusing
    ion 1 0.000 2.0                    # Counterion declaration:
    ion -1 0.000 2.0                   #  ion <charge> <conc (M)> <radius>
    pdie 1.0                           # Solute dielectric
    sdie 78.54                         # Solvent dielectric
    chgm spl2                             # Charge disc method
    srfm smol                             # Surface calculation method
                                       #  0 => Mol surface for epsilon;
                                       #       inflated VdW for kappa; no
                                       #       smoothing
                                       #  1 => As 0 with harmoic average
                                       #       smoothing
                                       #  2 => Cubic spline 
    sdens 10.0
    srad 1.4                           # Solvent radius
    swin 0.3                           # Surface cubic spline window
    temp 298.15                        # Temperature
    gamma 0.105                        # Surface tension (in kJ/mol/A^2)
    calcenergy total                      # Energy I/O (to stdout)
                                       #  0 => don't write out energy
                                       #  1 => write out total energy
                                       #  2 => write out total energy and all
                                       #       components
    calcforce no                       # Atomic forces I/O (to stdout)
                                       #  0 => don't write out forces
                                       #  1 => write out net forces on molecule
                                       #  2 => write out atom-level forces
end
elec name reference
    mg-manual                          # Use the multigrid method
    dime 65 65 65                      # Grid dimensions (c 2^(l+1) +1)
                                       #   (in x, y, z)
    nlev 4                             # Number of levels in multilevel
                                       #   hierarchy (usually 'l' from above
                                       #   definition)
    grid 0.33 0.33 0.33                # Grid spacings (A)
    # glen 100 100 100                 # You can EITHER specify the grid
                                       # lengths OR the grid spacing
    gcent mol 1                        # This can either be 'mol n' to center
                                       #   on a specific molecule or (x, y, z)
                                       #   coordinates
    mol 1                              # Which molecule (1, 2, ...)
    lpbe                               # lpbe/npbe = linear/nonlinear PBE
    bcfl mdh                             # Boundary condition flag
                                       #  0 => Zero
                                       #  1 => Single DH sphere
                                       #  2 => Multiple DH spheres
                                       #  4 => Focusing
    ion 1 0.000 2.0                    # Counterion declaration:
    ion -1 0.000 2.0                   #  ion <charge> <conc (M)> <radius>
    pdie 1.0                           # Solute dielectric
    sdie 1.0                           # Solvent dielectric
    chgm spl2                             # Charge disc method
    sdens 10.0
    srfm smol                             # Surface calculation method
                                       #  0 => Mol surface for epsilon;
                                       #       inflated VdW for kappa; no
                                       #       smoothing
                                       #  1 => As 0 with harmoic average
                                       #       smoothing
                                       #  2 => Cubic spline 
    srad 1.4                           # Solvent radius
    swin 0.3                           # Surface cubic spline window
    temp 298.15                        # Temperature
    gamma 0.105                        # Surface tension (in kJ/mol/A^2)
    calcenergy total                      # Energy I/O (to stdout)
                                       #  0 => don't write out energy
                                       #  1 => write out total energy
                                       #  2 => write out total energy and all
                                       #       components
    calcforce no                       # Atomic forces I/O (to stdout)
                                       #  0 => don't write out forces
                                       #  1 => write out net forces on molecule
                                       #  2 => write out atom-level forces
end

print energy 1 - 2 end

quit
