Unsolved

Hi all,

I was running the Match application and :
1. I noticed that some outputted PDBs are annotated in the log file as follows (I am using cloudPDB as output format):

Hello!
I'm new at Rosetta and was doing the tutorials for protein-protein docking. I execute the command below with no problems:

I'm doing protein-protein docking, in which the C-terminus of one of my protein chains (PDB: 2ew4) was amidated, and when I submitted it to Rosetta and ran docking_protocol.static.linuxgccrelease, I found that the amide was automatically disassembled, how can I make it so that it doesn't happen?

2ew4_ 1.pdb is the structure before docking, 2ew4_ 2.pdb is the structure after docking

<Job nstruct="5">
     <Input>
          <PDB filename="pdb_basename.pdb" />
     </Input>
     <Output>
          <SilentFile path="pdb_basename" filename="pdb_basename_relaxed.silent"  />
     </Output>
     <SecondaryOutput>
          <ScoreFile path="pdb_basename" filename="score_pdb_basename.sc" />
     </SecondaryOutput>
     <Options>
          <parser__protocol value="path/to/RELAX_MONOMER_RS" />
     </Options>
</Job>