I could not find what the following three error messages mean in the log
file.
Those are not error messages - an error would terminate the Modeller
run. They are warnings ('W').
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
When constructing topology from the CHARMM topology files, Modeller
tries to build all of the bonds and angles listed in those files. If you
look at the CHARMM topology file, you will see that each amino acid
topology includes a bond between atoms C and +N, i.e. between the C atom
and the N atom in the next residue. Obviously no such bond can be formed
between the final residue in the chain since there is no "next" residue.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how
to handle the H atom.
Some of these swaps are not done if you are building heavy-atom models,
since there are no hydrogen atoms.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: THR:OXT THR
DOPE is a statistical potential, and so can only calculate energies for
pairs of atoms that were included in its training set. We did not
include OXT (C-terminal oxygens).