[gmx-users] free binding energy calculation

[cesar]

kruegerj at fh-bingen.de wrote:

>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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>  
>
You could read the follow paper reference:
Ajay 1995, Journal of Medicinal Chemistry Vol. 38 number 26 
"Computational methods to predict binding Free energy in ligand-Receptor 
complexes"
It should be useful for your porpuses.