I have done Gromacs for FEP ( Free energy perturbation) between Protein and Ligand in Water solvent, with Positive Ions. I got DG 26.02 +/- 3.14 Kj/Mol. I got positive Delta G. How i can analyze this result? is this correct? Instead of negative Delta G, I got positive? Is this means, it requires ATP ?
Are you calculating the absolute binding affinity? If that is the case then your calculation is just a failure and meaningless. If the ligand has a positive binding affinity then it would escape from the initial bound structure very fast.
I guess that you must be calculating the relative binding affinity between two ligands to the same protein. In that case, your calculation result means that one ligand is about 26 kJ/mol favorable than the other, which actually is not very possible according to my practical experience. Here, I recommend you to think why this is not very possible yourself, as doing a lot of calculations without taking some time to understand the results is meaningless and not healthy for scientific study. You should calm down and spend some time digging it deeper before doing more calculations.
It means that the predicted binding equilibrium lies far on the side of the free components (https://en.wikipedia.org/wiki/Binding_constant)
delta G values can be used to predict how reactions will go..
Basically, minus sign in the definition of delta G was given so that a negative values of delta G favored a product process and a positive value favored to reactant process.
Thus, a product favored reaction will go on its own, without outside intervention, and can be made to do useful work in the process.
Are you calculating the absolute binding affinity? If that is the case then your calculation is just a failure and meaningless. If the ligand has a positive binding affinity then it would escape from the initial bound structure very fast.
I guess that you must be calculating the relative binding affinity between two ligands to the same protein. In that case, your calculation result means that one ligand is about 26 kJ/mol favorable than the other, which actually is not very possible according to my practical experience. Here, I recommend you to think why this is not very possible yourself, as doing a lot of calculations without taking some time to understand the results is meaningless and not healthy for scientific study. You should calm down and spend some time digging it deeper before doing more calculations.
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