i have the structure of unbound protein, ligand and protein -ligand complex?
There is are differences between absolute and relative free energy calculation.
You can calculate the relative binding energy of two ligands using molecular dynamic simulations combined with an MM-GBSA or MM-PBSA approach (search for AMBER MM-PBSA.py). If you need very accurate results, FEP calculations might be the right choice. Alchemical transformations are implemented in NAMD using a dual topology system.
Calculating the absolute binding free energy is very computationally demanding and need a lot of experience. NAMD also has a tutorial for such calculations.
Docking scores are not that accurate (depending on the scoring function) but can be calculated with little effort. Knowing the correct binding pose would be helpful. Examples for free Software are Autodock4, Autodock Vina/QuickVina, UCSF Dock.
Suitable free energy of ligand binding approximation methods are e.g. Docking, FEP, MMGBSA. If you don't have much experience with MD simulations, Docking and MMGBSA might by of choice for you.
There are free software packages for both methods like: Vina and Amber, but also commercial suites such as Schroedinger, which is rather expensive.
Others may have better suggestions.
If you are new in modeling, you can consider a docking score as a free energy.
There is are differences between absolute and relative free energy calculation.
You can calculate the relative binding energy of two ligands using molecular dynamic simulations combined with an MM-GBSA or MM-PBSA approach (search for AMBER MM-PBSA.py). If you need very accurate results, FEP calculations might be the right choice. Alchemical transformations are implemented in NAMD using a dual topology system.
Calculating the absolute binding free energy is very computationally demanding and need a lot of experience. NAMD also has a tutorial for such calculations.
Docking scores are not that accurate (depending on the scoring function) but can be calculated with little effort. Knowing the correct binding pose would be helpful. Examples for free Software are Autodock4, Autodock Vina/QuickVina, UCSF Dock.
How to extract snapshots from MD trajectory for binding free energy calculation?
Check this method to really calculate enthalpy of a protein-ligand complex.
http://ambermd.org/tutorials/advanced/tutorial21/index.html
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