[AMBER] Per-residue decomposition energy MMGBSA.py

From: maryam azimzadehirani <maryamai1988.gmail.com>
Date: Mon, 16 Mar 2015 21:49:12 +0800

Dear all,
Can anyone simply explains to me how MMGBSA.py calculates per-residue
decomposition energy?
I assume it is similar to binding energy calculation where it calculates
the free energy of ligand (solvated and in vacuum), free energy of receptor
(solvated and in vacuum) and ligand-receptor free energy (solvated and in
vacuum). Then calculate Gibbs free energy of binding, as they mentioned in
advance tutorial 3:

If we don't talk about entropy at all, which makes everything confusing...
In a simple way, the same method is used for each residue in per-residue
decomposition calculation, where the whole ligand is replaced by each
residue that we chose in the mask?
Please correct me if I am wrong.
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Received on Mon Mar 16 2015 - 07:00:07 PDT
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