[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.
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Konrad Hinsen
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