[MMTK] Problems loading certain PDB files

khinsen@cea.fr khinsen at cea.fr
Fri Jan 20 11:36:31 CET 2006

On Jan 18, 2006, at 11:54, Peter wrote:

> Aliases '1H', '2H', '3H' are missing in the database for peptide_nt  
> and
> variants like peptide_nt_noh (missing in both MMTK 2.4.4 and MMTK  
> 2.5.13)

They are in 2.5.13, and I think it's even you who sent me the  
patches! I will also backport all the database patches to the 2.4 line.

> Fixing this exposes a further class of problems, histidine residues  
> with
> two hydrogens on the epsilon carbon (assuming I have the terminology
> right):

Identifying protonation states is something that the Protein  
constructor could learn to do automatically - I have put that on the  
feature request tracker at sourcesup.fr.

For me this is the only modification I had to make to treat that PDB  

> IOError: Atom 2HA of PDB residue GLY not found in residue Gly of  
> object
> ..Gly83

Strange.. that's defined. Are you sure you are using a recent  
database? You could have MMTKDATABASE set to some old version.

> However, this still seems to try and validate all the PDB atoms (even
> the hydrogens) during loading.

Right, because the hydrogens are in the PDB file. MMTK will never  
silently throw away atoms from the PDB structure, though it will add  
hydrogens if necessary to take care of the most frequent case of PDB  
files without hydrogens.

If you want to create a model without hydrogens from a PDB file with  
hydrogens, you have to create a PDBConfiguration object first, delete  
the hydrogens from it (using the method deleteHydrogens()), and then  
create the peptide chain and protein objects.

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: khinsen at cea.fr

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