I`ve recently read an excellent publication on pKa prediction using the Rosetta scoring function (Kilambi & Gray Biophys J. 2012 10.1016/j.bpj.2012.06.044). However, it turned out that in the recent Rosetta distribution the pH_protocol.<exe> executable mentioned in the Supplementary materials of that paper is no longer available. I am aware of the ROSIE server, but the waiting list there is quite long and also I keep getting unknown errors with my files.
I have my protein model and I want to calculate pKas of ionazible residues and protonate the model accordingly.
Could you tell me how to do this using the local installation of Rosetta?
Thank you for your time.