[MMTK] CalphaForceField

khinsen at cea.fr khinsen at cea.fr
Fri Jul 22 19:28:57 CEST 2005

On 22.07.2005, at 18:29, Vasisht R. Tadigotla wrote:

> number of atoms in the actual pdb file. In this case the number of  
> calpha
> atoms in the PDB file are 3849 and the number of calpha atoms in the
> loaded protein are 3526. Is there any reason why this is happening ?  
> Am I
> somehow loading the file incorrectly ?

Most probably the PDB file does not respect the PDB format well enough  
to let MMTK identify all the peptide chains. This is unfortunately not  
so rare. Your code is fine.

To check what's going wrong, you could look at the residues in  
universe.protein and figure out which ones are missing. Then look at  
their PDB definition and look for anything unusual.

Konrad Hinsen
Laboratoire Leon 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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