[Molecularmechanics] first steps

[Konrad Hinsen]

On Tuesday 21 October 2003 10:51, Peter Murray-Rust wrote:

> If each atom is identified as having a specific atomType (of which there
> could be many - including residue-specific ones) does that solve most of
> the problems. Of course the algorithms for identifying atomTypes may be
> complex. Do they depend solely on the chemistry, or also on the initial
> geometry?

I am not aware of any force field whose parametrization depends on initial 
geometry. However, the identification of force field terms depends not only 
on atom types.

The Amber force field, for example, requires as input an atom type and a 
partical charge per atom plus the bond structure. With that information plus 
the universal Amber parameter file, all force field terms can be identified 
by algorithmic rules (which however are not as well documented as one could 
wish). Other force fields, e.g. CHARMM and GROMOS, require in addition an 
explicit list of improper dihedral terms for each molecule or residue. I 
suppose that such a specification could be translated to one using more atom 
types and no molecule-specific term list, but that translation is not 
necessarily simple.

Konrad.
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