What previous post are you talking about? Before we can help you please help us by pointing out your original post.

regarding my previous post:
So to calculate a binding energy, following the recent review that i've read in meth. cell. biology, to calculate the polar contribution to the binding energy one would follow this formula:

ÄG(complex-reference) -  ÄG(complex-water) -  ÄG(mol2-water) -  ÄG(mol2-reference) - ÄG(mol1-water) - ÄG(mol1-reference) = ÄGsolvation

ÄGcouloumb= ÄGcouloumb(complex) - ( ÄGcouloumb(mol1) + ÄGcouloumb(mol2) )

polar contribution to the binding energy = ÄGsolvation+ÄGcouloumb

This is partly correct. The polar contribution to the free energy of binding is

deltaG(polar)= deltadeltaG(solvation) + deltadeltaG(coulomb)


The reference is represented by putting the dielectric value in solvent and solute equal ( like for example 2)?

The reference should be the dielectric constant of vacuum (epsilon=1).

So retrieving the input files (as starting point) from the pdb2pqr and doing the math we have the value, is this right?
The apolar part isn't contemplated in APBS? Any alternative on doing this apolar contribution to binding calculation?

The apolar solvation energy can be approximated by calculated by using the solvent-accessible surface area (As described in the original MM/PBSA method; see  Kollman et al., Acc. Chem. Res. 2000, 33, 889). Alternatively, the apolar solvation energy can be estimated using APBS (http://bakergroup.wustl.edu/baker/classes/BME-540/2008/apbs-tutorial/#id450929). The apolar contribution to the free energy of binding will be simply the sum of the van der Waals energy plus the apolar solvation energy.




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