Hydrogen positions with MMK

Konrad Hinsen hinsen@cnrs-orleans.fr
Wed, 22 Jul 1998 12:40:28 +0200 (DFT)

> 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 Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-
Rue Charles Sadron                       | Fax:  +33-
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais