##########################################################################
### ION-PROTEIN BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
##########################################################################

read 
    mol pqr small491.pqr
    mol pqr 491.pqr 
    mol pqr complex.pqr
end

# ENERGY OF PROTEIN CHUNK
elec name protein
    mg-manual
    dime  129 129 129
    glen  67  67  75
    gcent mol 3
    mol 1
    npbe
    bcfl mdh
    ion charge 1 conc 0.050 radius 2.0
    ion charge -1 conc 0.050 radius 2.0
    pdie 2.0
    sdie 78.4
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end

# ENERGY OF ION
elec name ion
    mg-manual
    dime  129 129 129
    glen  67  67  75
    gcent mol 3
    mol 2
    npbe
    bcfl mdh
    ion charge 1 conc 0.050 radius 2.0
    ion charge -1 conc 0.050 radius 2.0
    pdie 2
    sdie 78.4
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end

# ENERGY OF COMPLEX
elec name complex
    mg-manual
    dime  129 129 129
    glen  67  67  75
    gcent mol 3
    mol 3
    npbe
    bcfl mdh
    ion charge 1 conc 0.050 radius 2.0
    ion charge -1 conc 0.050 radius 2.0
    pdie 2
    sdie 78.4
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end

# COMBINE INTO BINDING ENERGY
print elecEnergy complex - protein - ion end

quit
