I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.
I have tried using the -pH_mode true and -value_pH 2.5 flags as suggested in other posts (https://www.rosettacommons.org/node/3711). However, these flags do not have any effect on the protonation states of side chains in output pdb structures or on the calculated energy values.
Does anybody know how I could make these flags work? Do they still work on the most recent versions of Rosetta? Are there any other ways to take pH into account in Rosetta?
Thank you for any help!
My command looks like this:
pmut_scan_parallel.static.macosclangrelease -s 1tie_0008_0002_0004.pdb -database database -output_mutant_structures -DDG_cutoff 999 -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -pH_mode -value_pH 2.5 -mute basic core -ex1 -ex2 > .sc