PM3-D3H4 — Use PM3 Hamiltonian plus D3H4 dispersion and hydorgen-bond corrections.
One caution in using D3H4 is that the hydrogen bonding is only parameterized for hydrogen bonds involving oxygen and nitrogen. So, if this method was used with hydrogen fluoride (HF), there would be no hydrogen bonding correction!
The D3H4 correction includes special scaling for four charged groups (carboxylic acids, ammonium, guanidinium, and imidazolium) as described in the original paper. Scaling for the later two cases (guanidinium and imidazolium), however, are not included in AMPAC! The original coding of D3H4 only considered these groups in the context of PDB files where these two groups are clearly identified. Unfortunately, this could not be easily generalized to the case were these groups must be identifed dynamically. So when these two charged groups are present in a molecule, they will not recieve their special scaling factor and the final result will differ from the published method.
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