Dear all,

I would like to perform docking with respect to different pH. Here

Article Protein-Protein Docking with Dynamic Residue Protonation States

I've read that pHDock is part of Rosetta biomolecular modeling suite but I couldn't find anything about it in Rosetta documentations and tutorials. In this article there are " Command lines for pHDock, RosettaDock and ensemble pHDock. " but I've just started with Rosetta. I did basic tutorial for molecular docking:

https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

but I don't know where I can use that command lines... for now it's a bit complex for me. Could someone help me a bit with this? Are there any others possibilities of pH docking? Thank you.

Martin