[MMTK] PDB files with modified residues like MSE (selenomethionine)

khinsen@cea.fr khinsen at cea.fr
Mon Jan 23 15:20:29 CET 2006

On Jan 20, 2006, at 18:39, Peter wrote:

> I'm trying to load PDB file 1PYM, but have run into a problem with
> modified amino acid residues, held as HETATM entries.
> MMTK seems to break the peptide chain at these points (e.g. Mse14),
> giving a chain covering "Chain A" from residue Val5 to Gln13, and a  
> new
> chain starting Leu15 to Ile23, etc

Right. Note that you can fix such things at the PDBConfiguration  
level, rather than by editing the file. However, manual fixing is  
required, and I don't see how that could be avoided. The PDB file  
format with all its common variants is too big a mess to allow  
automatic handling of exceptional situations.

> I understand that the AMBER forcefields don't cover these cases,  
> but in
> order to get MMTK to load the file "properly" without breaking the
> peptides do I just need to define a new selenomethionine group in the
> database?

You need to add a definition to the database and call  
MMTK.Biopolymers.defineAminoAcidResidue() to tell MMTK which three- 
letter-code to associate with your new definition.

> Or, due to the use of HETATM rather than ATOM, is this more  
> complicated?

Yes, you have to convert HETATM to ATOM, either by modifying the file  
or by manipulating the PDBConfiguration 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: khinsen at cea.fr

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