Hi,
I've looked into this a bit more and I think the current behaviour is the
best. Of all the MMFF94 atom types the most appropriate one seems to be the
one that OpenBabel selects.
Thanks,
Toby
--
InhibOx Ltd
On 19 May 2014 21:46, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote:
> Sorry for the delayed reply.. my interpretation is certainly "aromatic OH"
> for phenolic H, which is certainly how the code is written. The
> implementation validates against the MMFF94 test set, which does not have
> an OH on a heterocyclic aromatic.
>
> I think my question would be .. do you think there would be radically
> different results?
>
> Thanks,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu
> web: http://hutchison.chem.pitt.edu/
>
> On Apr 14, 2014, at 9:00 AM, Toby Wright <toby.wri...@inhibox.com> wrote:
>
> > Hi,
> >
> > I'm attempting to use the MMFF94 forcefield to generate partial charges.
> I noticed that the molecule whose smiles is Oc1ncccn1 (aka a phenol with
> two carbons switched to nitrogens) gave the atom type 29 to the hydrogen
> attached to the oxygen.
> >
> > Looking into the code in forcefields/forcefieldmmff94.cpp I see the
> pertinent parts of the code path taken in atom typing goes:
> >
> > if (atom->GetAtomicNum() == 1) {
> > FOR_NBORS_OF_ATOM (nbr, atom) {
> > if (nbr->IsOxygen()) {
> > FOR_NBORS_OF_ATOM (nbrNbr, &*nbr) {
> > if (nbrNbr->IsCarbon()) {
> > if (nbrNbr->IsAromatic()) {
> > return 29; // phenol
> > }
> >
> > So the atom typing code states that any hydrogen neighbouring an oxygen
> which in turn neighbours an aromatic carbon is the H in the HO of a phenol.
> But I believe the existence of the nitrogen in the aromatic ring makes it
> not a phenol. Am I wrong to think that or is this a bug?
> >
> > Yours,
> >
> > Toby Wright
> >
> > --
> > InhibOx Ltd
> >
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