[MMTK] about reading pdb files

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Jun 10 13:28:58 CEST 2004

On Jun 10, 2004, at 9:45, Hua Wong wrote:

> If I get rid of coordinate at the end 60-336 (doesn't change the order 
> of the atoms coordinate) it seems to pass
> If I get rid of coordinate at the beginning of the file (1-20) I get 
> multiple errors

Those errors have nothing to do with the PDB file itself, but with the 
fact that by default MMTK assumes peptide chains to be terminated, i.e. 
have N-terminus and C-terminus forms of the amino acids at the two 
ends. If you edit out the first residue, then your chain starts with a 
standard amino acid instead of the N-terminal form. As a consequence, 
the atom names don't match with MMTK's expectations and you get the 
error message you describe.

You can use such files by specifying the options n_terminus=0 and/or 
c_terminus=0 when creating the MMTK objects. However, as Peter pointed 
out, it is easier to read in the whole file (MMTK.PDB.PDBConfiguration) 
and then modify the resulting configuration object.

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen at llb.saclay.cea.fr

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