[gmx-users] free binding energy calculation

[kruegerj at fh-bingen.de]

Dear all,

I try to calculate the free binding energy of the following pdb complex:
1VFA.pdb.
Therefore I use the formulae:
deltaGcomplex =(G12-G1-G2)MM
+(deltaG12-deltaG1-deltaG2)solv+(G12-G1-G2)unpolar_solvation-T(S12-S1-S2)

To calculate the solvation term I used APBS (in the APBS script I subtracted the
homogenous dielectricum (with epsilon = 1) from the inhomogenous dielectricum
(epsilon for the solvent = 80)

For the unpolar solvation term I used g_sas.

Does anyone know how to calculate the entropies? (4 different terms:
translational and rotational entropies, vibrational entropiy an d
conformational entropie)
And how can I calculate the implicit solvation via MM-PBSA approach with gromacs
or is there another possibility to calculate this term?

Thanks a lot for help

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