Monday, 19 March 2018

The curious case of fluorescein and implicit waters

I recently was asked a straightforward task: get the energy scores of a given protein by itself, conjugated with fluorescein maleimide and its ring opened form. Despite that I failed miserably because of implicit waters playing odd tricks.
Given that it is of no real use, I am happy to share so to give a tutorial of how to do that in Rosetta (ligand docking), which I found taxing the first time.