[gmx-users] free binding energy calculation

kruegerj at fh-bingen.de kruegerj at fh-bingen.de
Thu Dec 8 13:50:02 CET 2005

Dear all,

I try to calculate the free binding energy of the following pdb complex:
Therefore I use the formulae:
deltaGcomplex =(G12-G1-G2)MM

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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