On Oct 12, 2009, at 4:15 AM, Jan Jensen wrote:
I didn’t write that very clearly, did I? What I mean is that the
force field calculations clearly are using charges different from
those shown by the labels when ions are used.
If you draw Cl and Na (not bonded) and compute the energy, the
energy calculations clearly uses -1 and +1 charges for the atoms (it
says so explicitly under “messages”) but the labels show the partial
charges as 0 and 0.
If you use MMFF94, then yes, there are partial charges. Other force
Your request suggests that we need some mechanism in the Molecule
class to set partial charges in code.