We are interested in creating a protein that will bind to a hormone at physiological pH, but unbind to the hormone at acidic pH, encountered when the complex is cycled through the cell. To do this, we would like to use the pH_mode functionality developed by Kilambi and Gray (Biophys Journal 103:587-595, 2012).
My preliminary attempts to make use of the mode, in Rosetta 3.5, have however proven unsuccessful -- the Score energy appears to be constant regardless of what pH value I enter.
Usage of the program is as follows:
score.linuxgccrelease -database database -s complex.pdb -pH_mode true -value_pH 2
score.linuxgccrelease -database database -s complex.pdb -pH_mode true -value_pH 7
Do you know of any changes I should make to properly enable the functionality? I am also curious whether or not PyRosetta has support for pH functions.