Error using pHDock

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    • August 11, 2016 at 12:56 pm #2485
      Anonymous

        Hi,

        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]).  

         

        Thanks

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