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.
The pH_protocol executable is not available as a public app immediately. I will work on transferring it to the public apps, but it might take a couple of weeks for it to get tested and appear in the public release. If you require this urgently, please contact me at email@example.com. I'll email you the code and help you set it up.