On 2/6/11 2:24 PM, Seth Tanner wrote: > 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.
See https://salilab.org/modeller/9v8/manual/node183.html 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).
Ben Webb, Modeller Caretaker