How does a positive value indicate better binding energy for MM-PBSA binding free energy calculations?
Where did you get this statement, normally, it is not good that you got positive binding energy. The individual component in MMPBSA may be positive, but the overall binding energy should be negative.
In MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) calculations, the binding free energy (ΔG_bind) is calculated as the sum of the molecular mechanics (MM) energy, the polar solvation energy (PB), and the nonpolar solvation energy (SA). The MM energy term represents the van der Waals and electrostatic interactions between the receptor and ligand molecules, while the PB and SA terms represent the solvation effects.
In MM-PBSA calculations, a more negative value of ΔG_bind indicates a stronger binding affinity between the receptor and ligand molecules, while a less negative or positive value indicates weaker binding affinity. Therefore, a more positive value of ΔG_bind indicates a weaker binding affinity between the receptor and ligand molecules.
I got something, I performed docking of a protein to a ligand and the affinity score was -9.4 kcal/mol then after simulation, where there were 5 H bonds formed between the ligand and protein and from the results it seems like the ligend stay in the binding pocket throughout the simulation time (10ns) but mmpbsa calculations showed binding free energy of 557 kcal/mol
How could it be?
Sara Alshun I have the same problem. Did you find out how to solve it?
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