> Looking at it again now, it seems that the charges from Open Babel's QEq > often have the wrong sign or are simply unreasonably large. I have no idea > what causes that, as I only had a cursory look at the code. But it looks as > if there's more going on than just the additional simplifications to QEq: > even the QTPIE charges do not seem to reproduce those from the QTPIE paper by > Chen and Martinez (e.g. the charges on phenol as reported in the preprint on > arXiv, https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've used > the charge model options in the wrong way, but they seemed quite > straightforward.
Ironically, the code for both QEq and QTPIE in Open Babel were contributed by Chen. But I've heard similar things about the signs and magnitudes of the QEq charges. Naturally, considering the source of the code, I didn't question the results at the time, but it's been several years with off-and-on questions about it. > I can send the molecule geometries that we used in validating our QEq against > the Rappé and Goddard article, if that would be of help, or run our QEq > implementation on a set of molecules of your choice and send back the > results. Our coverage of elements is limited to that in the original paper, > which covers H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs. If you're willing to send some molecule geometries and charges, that would be very helpful. I probably won't have time to evaluate the code until the summer, but having a validation set would be a helpful contribution. Incidentally, I've been following the work by the Goddard group on their new polarizable QEq model (e.g., PQEq2) and I'm trying to get a test set together for an independent implantation of those. -Geoff _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
