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#34272 - 08/12/14 04:26 AM binding free energy of P-L
Yong Mao Offline
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Registered: 08/04/13
Posts: 41
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?
Thanks!

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#34273 - 08/12/14 07:14 AM Re: binding free energy of P-L [Re: Yong Mao]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
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 qvist 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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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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