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

Eric Zollars zollars at caltech.edu
Fri Jan 20 19:05:03 CET 2006


What I have done in the past was change HETATM to ATOM in the pdb file 
and add MSE to the group database.  I don't remember if Se is in the 
atom database or not.

Eric

Peter wrote:
> Hello again,
> 
> 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
> 
> sample code:
> 
> import MMTK.Proteins
> protein = MMTK.Proteins.Protein("1PYM.pdb", model="no_hydrogens")
> assert len(protein.chains)==16
> 
> except from 1PYM file, Mse14 on chain A:-
> 
> ATOM     74  NE2 GLN A  13      20.376  71.210  49.248  ..
> HETATM   75  N   MSE A  14      20.751  70.044  55.325  ...
> HETATM   76  CA  MSE A  14      20.869  68.953  56.262  ...
> HETATM   77  C   MSE A  14      19.901  69.044  57.444  ...
> HETATM   78  O   MSE A  14      19.240  68.075  57.773  ...
> HETATM   79  CB  MSE A  14      22.285  68.827  56.761  ...
> HETATM   80  CG  MSE A  14      23.226  68.367  55.726  ...
> HETATM   81 SE   MSE A  14      25.099  68.515  56.262  ...
> HETATM   82  CE  MSE A  14      25.283  66.996  57.406  ...
> ATOM     83  N   LEU A  15      19.811  70.203  58.091  ...
> 
> The use of HETATM rather than ATOM means this is a modified residue - In 
> this case, MSE (selenomethionine) is a modified MET (methionine) where 
> there is a selenium in place of sulfur.  (See also the HET and HETNAM 
> entries in the file header).
> 
> 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?
> 
> Or, due to the use of HETATM rather than ATOM, is this more complicated?
> 
> Thank you
> 
> Peter
> 
> 
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