I could not find what the following three error messages mean in the log file. I would be grateful if you could explain what the causes are and suggest several possible solutions. Thanks.
Message 1) getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 384 atom names : C +N atom indices : 3127 0
getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 384 atom names : C CA +N O atom indices : 3127 3123 0 3128
Message 2) iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.3341 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.7680 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
Message 3) << end of ENERGY. DOPE-HR score : -13843.593750 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR