[MMTK] Defining a molecule using cartesian coordinates

Harry Zuzan hzuzan@nanodesign.com
Wed, 24 Mar 1999 16:22:13 -0500


Yes, once I changed the atom types from 'H3' to 'H1' my problem was 
solved.  Now on to more complicated molecules.

Thanks

Harry Zuzan

> > 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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