Unsolved

I am trying to dock the variable domains of an antibody with its protein target in docking 2. The structure of the variable antibody domains are predicted from homology. I have a few different antibody and for all except one this works fine. One however gives the error message Prepack step failed. Check your input files. I have repredicted the structure of the antibody with various programs, but it keep on failing. What can the problem be? Is there any online program (in Rosie for instance) where I can check my input before I try to dock?

I'm trying to make a homology model for a Zn-binding metalloenzyme based on some other members of the same family that have been crystallized. My general strategy has been to do comparative modeling first with limited redesign of the loops to get the main structural features in place, and then use the loopmodel appliation to refine the structure a bit more. I had trouble incorporating the Zn residue into the comparative modeling application, so I inserted the Zn into the PDB result and now I'm trying to include it in the loop modeling step.

Did anyone do ensemble docking using rosetta3.4?
I don't know how to prepare those seemed like energy score(lowres_reference_energies_ , and highres_reference_energies_ from source code) at
the end of pdblist file?

An example of the pdblist is below:

I am doing research on affinity maturation of antibody and using Rosetta-antibody package. for modelling of my antibodies, I installed Rosetta 2015.12 but when I run the command of RossetaAntibody3 :