[MMTK] Defining a molecule using cartesian coordinates

[Konrad Hinsen]

> :amber_charge = {C: 0.0, H1: 0.1, H2: 0.1, H3: 0.1, H4: 0.1}
> BTW, I think this is a problem: methane shouldn't have a net
> charge of +0.3.  ;)

Could become a bit explosive ;-)

> Does MMTK check for non-integer charged molecules?  I know CHARMM does, 
> but I've not tried to do such things with MMTK.

No, you can define whatever you want. Users can easily check the
charges themselves:    (caution, untested code)

  for object in universe:
     if abs(object.charge() % 1.) > 1.e-10:
        print object, "has non-integer charge"

But I don't want to rule out fractional molecule charges in principle;
perhaps some next-generation force field will need this.
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