Hello Everyone,
I have performed an enhanced sampling molecular dynamics simulation for the dissociation of ligand from a protein-ligand complex and generated the "Potential of mean forces" results.
Can anyone please tell me how can I calculate the free energy of binding for this case? Because I have found out that it can be calculated straight from the difference between the maximum and minimum values of the PMF curve, but in this case, as both the max (-0.15) and min (-3.5) values are negative, the free energy of binding is coming out as (+)3.35 kCal/mol. Is this correct? If yes, what can be the conclusion drawn from here considering the binding strength of the ligand with the protein?
Otherwise, how can I go ahead in calculating the free energy of binding here? I have also attached the PMF plot from where I am calculating the same.
Quyen V. Vu Initially I started with a complex of protein & ligand. So the start point of the PMF profile should be the bound state and the unbound position is at a reaction coordinate of 3.6 and a PMF value of -3.48 kCal/mol.
Quyen V. Vu thanks for the clarification. How to know what is a good sampling (like which parameters to check)? Also how to check in which parts of the complete sampling length, more sample windows need to be taken?
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