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