Hydrogen positions with MMK

Herbert Fruchtl herbert@netcomuk.co.uk
Wed, 22 Jul 1998 11:14:21 +0100


Hi all,

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),
the routine findHydrogenPositions() aborts with error messages like

  File "hydrogen.py", line 13, in ?
    chain.findHydrogenPositions()
  File "/home/fruechtl/mmtk_and_python/mmtk/Protein.py", line 293, in
findHydrogenPositions
    raise ValueError, 'position of ' + a.fullName() + \
ValueError: position of .Phe255.peptide.O_2 is undefined

I asume there are ambiguities about the positions of some groups or
atoms. Is there a way to resolve this? Can I find out, where in the PDB
file the problem arises, and correct 'by hand'?

Or am I mising something elementary?

Thanks in advance,

  Herbert