[gmx-users] free binding energy calculation

David Mobley dmobley at gmail.com
Thu Dec 8 18:21:44 CET 2005

Accurate calculation of entropies from MD simulations is, I think, an
unsolved problem. The quasiharmonic approximation is fairly popular, but
Michael Gilson had a recent paper showing that this has serious problems. It
sounds like you are trying to do something more along the lines of MM-PBSA
though, so you may want to look at the literature on MM-PBSA. See especially
the papers by Kollman, and there is a recent one from the McCammon group.
GROMACS, however, does not have implicit solvent at present, so....

How many compounds are you trying to calculate the binding free energy for?
You may be able to use FEP/TI in explicit solvent if you are trying to do
only a small number, but it takes a lot of effort (computational and
otherwise) to get good results with this at present.


On 12/8/05, kruegerj at fh-bingen.de <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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