A vital part of preparing a protein structure for MD simulation is the assignment of protonation states to acidic and basic residues. 'Black box' tools that come with certain MD packages can have limitations, so using a more sophisticated 3rd-party software tool to check this is always a good idea.
This short workshop illustrates the application of Propka to the analysis of the pKas of acidic and basic residues in the structure of the cysteine protease cruzein (PDB code 2oz2) - the results may not be what you would have expected!
A basic knowledge of Python and MD simulation methods
A Jupyter notebook and associated data files
Please direct all comments and queries to Charlie Laughton