[MMTK] Defining a molecule using cartesian coordinates

[Konrad Hinsen]

> How should the definition of the cartesian coordinates be revised in
> order to let the molecule be minimized?

The problem is not in the coordinates:

>     raise KeyError, 'No parameters for angle ' + `a1` +  \
> KeyError: No parameters for angle Atom methane.H1--Atom methane.C--Atom
> methane.H2

The problem is a missing force field term; there is no
angle term for H3--CT--H3 in the Amber 94 force field.

I am no expert on the Amber force field, but it seems to me that
your H atoms should have the type H1 rather than H3.

Konrad.
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