[gmx-users] protein-ligand interaction energy for oligomers

Shankar Prasad Kanaujia spkanaujia at gmail.com
Sun Jul 26 07:19:13 CEST 2009

Dear gmx-users,
I am working on a hexameric protein. I have done simulation of
protein-ligand complex (hexameric i.e. 6 protein monomers and 6 ligands). I
want to compare the interaction energy of protein-ligand (energygroups=
protein ligand sol) with the biochemical data (delta H). The protein-ligand
interaction energy which I am getting through MD simulations is
approximately 36 times more (for example, if delta_H= X kJ/mol,
Eprotein-ligand= 36X kJ/mol).

In the case of monomeric simulation, Eprotein-ligand = 1/6 (hexameric
Eprotein-ligand) which is approx. 6 times more than biochemical energy
(delta H).
In the case of dimeric simulation, Eprotein-ligand = 1/3 (hexameric
Eprotein-ligand) which is approx. 12 times more than delta H.

Could someone suggest me how to compare these values.

Thanking you.

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