I'm having trouble running pHDock (in an attempt to model protonated histidines). I'm using the command-line arguments described in the pHDock paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263365/):
~/rosetta/bin/docking_prepack_protocol.linuxgccrelease -s input_prep_sc.pdb -partners AB_C -dock_ppk -pH:pH_mode -pH:value_pH 5.6 -score:weights packing.wts -ex1 -ex2aro -unboundrot input_prep_sc.pdb
Fails with the error:
ERROR: ! found_aa_difference
ERROR:: Exit from: src/core/pack/task/ResidueLevelTask_.cc line: 1145
In this case, input_prep_sc.pdb is 1A2K.pdb that I've prepared using rosetta.
I've tried adding the keyword "keep_input_protonation_state" and still have the same error. The paper does mention that the input structure was pre-packed at pH 5.6, but I have not had luck modeling protonated histidines (see thread https://www.rosettacommons.org/node/9726).
All input files are included (note: input_gzipped.pdb is a gzipped file [to get around size and file extension limitations]).