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Error using pHDock

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Error using pHDock


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 (

~/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/ 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

All input files are included (note: input_gzipped.pdb is a gzipped file [to get around size and file extension limitations]).  



packing_wts.txt1.54 KB
input_gzipped.pdb169.09 KB
Post Situation: 
Thu, 2016-08-11 05:56