[MMTK] Dealing with non-protein ligands

Konrad Hinsen konrad.hinsen at cea.fr
Fri Mar 17 13:03:56 CET 2006

On Mar 16, 2006, at 17:53, vanitha at cs.wisc.edu wrote:

> I am looking at protein-ligand pairs where the ligands are either  
> sugars
> or amino acids. What would I read these in as? For example, I'm  
> looking at

You have two options:

1) Read them in as AtomCluster objects. This is what a system  
construction from a PDB file does by default for unknown residues.  
Advantage: it is easy. Disadvantage: AtomClusters don't have energy  
tems, so you can't use them in energy evaluations.

2) Read them in as Molecule objects. This takes a bit more work (you  
have to define the molecule in the database, or through a  
MoleculeFactory) but there are no limitations on their use. Of  
course, if you want to do energy calculations, you need to have  
parameters for some force field.

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: konrad.hinsen at cea.fr

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