read mol pqr bx6_7_lig_apbs.pqr # Balanol mol pqr bx6_7_apo_apbs.pqr # Protein kinase A mol pqr bx6_7_bin_apbs.pqr # Complex end elec name bal # BALANOL ENERGY CALCULATION mg-auto dime 65 65 65 # Grid dimensions cglen 70 70 70 # Coarse grid lengths cgcent mol 3 # Coarse grid centered on the complex fglen 16 16 16 # Fine grid lengths fgcent mol 1 # Fine grid centered on the complex mol 1 lpbe # Linearized PB bcfl sdh # Monopole boundary condition ion 1 0.000 2.0 # Zero ionic strength ion -1 0.000 2.0 pdie 2.0 # Solute dielectric sdie 78.00 # Solvent dielectric chgm spl0 # Linear charge discretization srfm smol # Smoothed molecular surface srad 0.0 # Solvent probe radius swin 0.3 # Surface spline window (not used) sdens 10.0 # Sphere density temp 298.15 # Temperature gamma 0.105 # Surface tension (not used) calcenergy total calcforce no end elec name pka # PROTEIN KINASE A CALCULATION mg-auto dime 65 65 65 cglen 70 70 70 cgcent mol 3 fglen 16 16 16 fgcent mol 1 mol 2 lpbe bcfl sdh ion 1 0.000 2.0 ion -1 0.000 2.0 pdie 2.0 sdie 78.00 chgm spl0 srfm smol srad 0.0 swin 0.3 sdens 10.0 temp 298.15 gamma 0.105 calcenergy total calcforce no end elec name complex # COMPLEX CALCULATION mg-auto dime 65 65 65 cglen 70 70 70 cgcent mol 3 fglen 16 16 16 fgcent mol 1 mol 3 lpbe bcfl sdh ion 1 0.000 2.0 ion -1 0.000 2.0 pdie 2.0 sdie 78.00 chgm spl0 srfm smol srad 0.0 swin 0.3 sdens 10.0 temp 298.15 gamma 0.105 calcenergy total calcforce no end print energy complex - pka - bal end quit