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Posted By: Yong Mao binding free energy of P-L - 08/12/14 08:26 AM
Hi, I have get the trajectory of the MD simulaation,I want to compute the binding free energy between protein and ligand, how to do it?
Posted By: lennart Re: binding free energy of P-L - 08/12/14 11:14 AM
This does not seem to be a question concerning any of the examples in this forum.

The most reliable methods to compute free energies require a special simulation ("free-energy perturbation","thermodynamic integration","potential of mean force") and are not used with a standard trajectory.
Your question should have been asked BEFORE you started your simulations.

MM-PB/SA (or variants) can be used, but may be of lesser quality. The LIE method of Johan Åqvist is another possibility, but you still have to have a trajectory of the free ligand, and you should check for convergence of your results in all cases.
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