[ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection!

Hello

I'm new to Rosetta. I followed the tutorial of RosettaAntibodyDesign and ran the program well, but there was always some ' warnings ' in the log files.

 I extracted some warnings from the log file as below:

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core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ILE 1.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 1  H   that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue TRP 1.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 1  H   that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ILE 1.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 1  H   that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 1  H   that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue TYR 1.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 1  H   that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.

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The command I used:

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antibody_designer.static.linuxgccrelease -s my_ab_relaxed.pdb -graft_design_cdrs L1 L2 L3 H1 H2 -seq_design_cdrs L1 L2 L3 H1 H2 H3 -light_chain kappa -mc_optimize_dG -do_dock -nstruct 5 -random_start -out:prefix tutC1_

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Should I ignore the warnings as long as I can get the results from the program ? What do these warnings mean ?

The warning file and common options file are in the  attachment.

Thank you

Jane