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Visualization of Electrostatic Potentials

Solvation Energy Calculation

 Binding Energy Calculation


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In this section we will calculate the electrostatic solvation energy for methanol and methoxide. Quantitative calculations require a finer grid mesh than we used in the previous example. We can easily afford a 0.25 grid resolution with these small molecules. This is specified by grid in the following input file. 

        
read 
    mol pqr methanol.pqr
    mol pqr methoxide.pqr
end

# METHANOL SOLVATION ENERGY -- SOLVATED STATE
elec name methanol-solv
    mg-manual
    dime 65 65 65
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 1
    mol 1
    lpbe
    bcfl mdh
    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
    temp 300.00
    gamma 0.105
    calcenergy total
    calcforce no            
end

# METHANOL SOLVATION ENERGY -- REFERENCE STATE
elec name methanol-ref
    mg-manual
    dime 65 65 65
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 1
    mol 1
    lpbe
    bcfl mdh
    ion 1 0.000 2.0                
    ion -1 0.000 2.0 
    pdie 2.0
    sdie 1.00
    chgm spl0
    srfm smol
    srad 0.0
    swin 0.3
    temp 300.00
    gamma 0.105
    calcenergy total
    calcforce no
end

# METHOXIDE SOLVATION ENERGY -- SOLVATED STATE
elec name methoxide-solv
    mg-manual
    dime 65 65 65
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 2
    mol 2
    lpbe
    bcfl mdh
    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
    temp 300.00
    gamma 0.105
    calcenergy total
    calcforce no
end

# METHOXIDE SOLVATION ENERGY -- REFERENCE STATE
elec name methoxide-ref
    mg-manual
    dime 65 65 65
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 2
    mol 2
    lpbe
    bcfl mdh
    ion 1 0.000 2.0                
    ion -1 0.000 2.0 
    pdie 2.0
    sdie 1.0
    chgm spl0
    srfm smol
    srad 0.0
    swin 0.3
    temp 300.00
    gamma 0.105
    calcenergy total
    calcforce no
end

# Methanol solvation energy
print energy methanol-solv - methanol-ref end

# Methoxide solvation energy
print energy methoxide-solv - methoxide-ref end

# Solvation energy difference
print energy methoxide-solv - methoxide-ref - methanol-solv + methanol-ref end

quit

This can be executed with the following:

        

apbs solvation.in > solvation.out

Fortunately quantitative results are easy to spot. Look for the PRINT STATEMENTS near the end of the logfile. 

        

----------------------------------------
PRINT STATEMENTS
print energy 1 (methanol-solv) - 2 (methanol-ref) end
  Local net energy (PE 0) = -2.525374575998E+01 kJ/mol
  Global net energy = -2.525374575998E+01 kJ/mol

print energy 3 (methoxide-solv) - 4 (methoxide-ref) end
  Local net energy (PE 0) = -2.015875408811E+02 kJ/mol
  Global net energy = -2.015875408811E+02 kJ/mol

print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end
  Local net energy (PE 0) = -1.763337951212E+02 kJ/mol
  Global net energy = -1.763337951212E+02 kJ/mol
----------------------------------------

☻ As expected methoxide has a much larger solvation energy than methanol! ☻