Hydrogen positions with MMK

[Konrad Hinsen]

> I am just trying out MMTK on a few PDB files from Brookhaven. In all
> cases I tried so far (OK, it was only three, and rather similar ones),

Could it be that these PDB files do cont contain the C terminus
of some chain?

> ValueError: position of .Phe255.peptide.O_2 is undefined

The atom O_2 in a peptide group is the second oxygen found in the
C terminus, labelled as OXT in PDB files.

If you want to construct a peptide chain without C terminus in MMTK,
you have to specify c_terminus=0 as an argument to PeptideChain.

Konrad.
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