Which is best for ligand-protein complex, binding affinity calculation?
I think that it is a single-trajectory simulation can be called normal, as opposed to a variety of parallel techniques.
'single-trajectory' method is mostly used for the MM-PBSA method. 'single-trajectory' simulations are normal simulation, where simulations are performed for the protein-ligand complex. One could perform multiple parallel simulations of protein-ligand complex to improve statistics.
In 'multiple-trajectory' approach for MM-PBSA method, separate simulations for unbound protein, unbound ligand and protein-ligand complex are performed and these trajectories are used for the binding energy calculation. These approach is not widely used because two additional type of simulations are required.
Dear Rajeev,
I agree with Rajendra.Multiple trajectory method is more accurate and also more time consuming.You can set receptor and ligand trajectory for MM-PBSA.py using -yr and -yl flags.
Best
Thank you Mr Rajendra and Mr Hamed for your reply and guidance.
But, Mr Rajendra I was wondering as MM-PB(GB)SA method is used for binding free energy calculation, and it uses the formula, dG(bind)= G(PL)-G(P)-G(L), I mean its including the free energy term of the unbound state of both protein and ligand, then how this 'single-trajectory' analysis approach is helpful for MM-PB(GB)SA calculation.
From the complex, protein and ligand are extracted and their energies are calculated separately. You may read the following link:
http://onlinelibrary.wiley.com/doi/10.1002/minf.201100135/abstract
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