simtk.org

Hi
I would like to estimate the binding affinity of protein-ligand interaction. Can you please tell me how to run metadynamics of the complex. after i do the metadynamics , is there any function to calculate the free energy or i should do manual calculations.
Thanks

If you want to do free energy calculations, you might want to look at Yank (http://getyank.org/latest/). It's specifically designed for doing that.

Thanks