I'm trying to perform docking simulations for two identical coiled-coil homodimers modelled by the fold and dock protocol to establish the potential ways of interaction of these in higher order complexes (there's an experimental evidence for the formation of such assemblies).
The command looks as follows:
docking_protocol.linuxgccrelease -in:file:s S_029104.pdb -unboundrot S_029104.pdb -nstruct 1 -randomize1 -randomize2 -ex1 -ex2aro -partners AB_AB
The job crashes with the following error:
protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 268 -1 EDGE 1 269 1 EDGE 269 536 -1
ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 1362
What was tried so far (without success, the same error still popping out):
- renaming chains in S_029104.pdb to C and D and saving as a separate copy, running with -partners AB_CD,
- renumbering residues in S_029104.pdb so each residue has a unique number,
- merging chain A and B into single chain A with renumbering of chain B residues (unique, consecutive numbering for residues), running with -partners A_A
Job runs smoothly if no '-partners' option is selected but then it only docks chains 'A' to each other (which was already done wih F&D protocol).
Looking for some advice on this problem.