[Molecularmechanics] Molecular structure- Atoms and Sites

[Konrad Hinsen]

On Friday 24 October 2003 20:49, Peterson,Brian K. wrote:

> representation and structure representation.  Looking forward to new kinds
> of force-fields etc., might it be useful to describe structures as
> collections of sites and bonds rather than atoms and bonds?  Of course one

Useful, yes, but tricky as well, because we get into the structure/force field 
distinction again. Atoms and bonds are pretty much the same for everyone (at 
least within what I consider to be "molecular mechanics", but interaction 
sites are force field specific. 

> can think of dummy-atom = site, but it seems conceptually more clear to me
> and potentially more flexible to have an atom being composed of at least
> one site and a molecule as a collection of atoms, sites, and bonds.  The

I agree, but this does imply a force field specific desription of a system.

Perhaps we should consider to define two different levels of description:

1) Just the basics: atoms with basic information such as chemical element,
    optionally bonds. That is what one would feed to visualization and
    analysis programs. It is also what one should be able to use as a starting
    point for building a more complete and specific model.

2) A full description of the model, including interaction sites, dynamical
   constraints, explicit force field terms (possibly referring to a predefined
   collection of data to make the file more compact) etc.

The second level would be more specific but less exchangeable. Every program 
should be able to write out the first level as a least common denominator.

Konrad.
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