I have done an MD run of a protein with ATP using CHARMM force field. I want to calculate binding free energy, which commands can I use for the above.
Any suggestions. Thank you.
Binding free energy is not simply computed from post-processing a simulation. You can get an estimate from an approach like LIE, which requires an additional simulation of the ligand in water (see gmx lie help text), but entropic effects are neglected. For ATP or any other flexible molecule, that may be a poor approximation.
It is difficult to obtain reliable binding free energies, but there is a wealth of literature on this topic, including various alchemical approaches, PMF/umbrella sampling, etc.
Binding free energy is not simply computed from post-processing a simulation. You can get an estimate from an approach like LIE, which requires an additional simulation of the ligand in water (see gmx lie help text), but entropic effects are neglected. For ATP or any other flexible molecule, that may be a poor approximation.
It is difficult to obtain reliable binding free energies, but there is a wealth of literature on this topic, including various alchemical approaches, PMF/umbrella sampling, etc.
Dear Shakeel
in order to calculate binding free energy you have to run MMPBSA simulation that's highlighted in detail one of the attached paper. I have sent several papers. Find attached.
Alternatively, you can sample significant snapshots from your trajectory (e.g. adopting a cluster analysis approach) and submit them to individual MM-GBSA calculations. In such a way you can save a very lot of time, without relevant loss of information.
I think one of the best choices is the ones that Justin Lemkul, and you should try calcuting the PMF using Umbrella Sampling
Do not completely agree with Andrés. How much time (and computational resources) do you have to spent about? At what degree of details? (in the context of the aim of your project, of course)
- Badges
- Science topic