Is gromacs interaction energy function is enough or I have to do gmx_mmpbsa assay for better insight ?

15 August 2023 1 9K Report

I am going to do md simulation of 10 receptor-ligand complex. Is the gmx_energy function is enough to decide the binding strength or I have to do gmx_mmpbsa to find free binding energy ? Is interaction energy or binding free energy are different and what they convey, is they are positively correlated?

Harvinder Singh

Mohon Paul g_mmpbsa provides more insight of P-L complex binding energies. It provides all the contribution energies i.e., Polar, Non-polar, Vanderwaals, for ligand as well as protein. Even energy decomposition analysis provides information about residues contribution into negative binding free energy.

Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...

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