VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Jun 19 2020 - 15:08:14 CDT

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888302/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888302/>

“The final class of interactions, involving sulfur atoms and sp hybridized carbon and nitrogen atoms (orange circle), are systematically shorter than the target data. With the sp carbon atoms, it was found that this shortening was necessary to obtain good bulk solvent properties and, in the case of nitrogen, to reproduce QM water interaction data for the linear complex. We speculate that this is due to the fact that a diffuse electron cloud surrounds sp centers in all directions except along the bond axis. Similarly, for the sulfur atoms, the discrepancy in hydrogen bond distance is due to the increased radii and diffuse character of these atoms. When this class of functional groups was initially parametrized, it was found that the HF/6–31G(d) level of theory and its standard scaling and offset rules were not appropriate, and it was necessary to apply the MP2/6–31G(d) level of calculation for the interactions with water. Subsequently, it was found that the MM minimum interaction distances had to be significantly shorter than the corresponding QM distances at this level of theory, in order to obtain the correct pure solvent properties (A.D. MacKerell, Jr., unpublished). “

And in the Figure 7 caption: “The QM level of theory is MP2/6–31G(d) for model compounds containing sulfur atoms and scaled HF/6–31G(d) for all remaining compounds."

This implies to me that no scaling was applied to the MP2 interaction energies. As for the shift, we are generally fine with reducing the distance interaction weight to, say, 0.5.

One thing to note, I’m not sure you can get the right interaction energy with FFTK when you start mixing QM levels of theory. We use the compound HF and water HF runs in order to subtract off their individual energies from the total in the combined runs. If these are run at different levels of theory, it’ll probably give nonsense. Proceed with extreme caution.

Other things to look at: are all your water interactions reasonable? Or do the waters fly away in some of them?

You could also try expanding the basis set or add diffuse functions, still with HF, as long as you do it for all QM runs.

Best,
JC

> On Jun 19, 2020, at 12:17 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz> wrote:
>
> Hi all,
>
> In the CGenFF papers, it mentions that compounds with sulfur were run at MP2/6-31G(d) level of theory. I've been having trouble getting the objective function to fit using the HF/6-31G(d) water data, so I thought I would try it with MP2.
>
> I was wondering, do the water shift (-0.2) and scale (1.16) settings need to be changed? And should I just give FFTK the location of the MP2 file where it asks for HF? And use an MP2 calculation of the water-sp?
>
> Also, I've seen it mentioned in the CHARMM forums that the distances aren't actually considered in the original CGenFF procedure, and I certainly get much better convergence if I turn the distance weight down. I wonder how this would relate to sulfur-containing compounds?
>
>
> Daniel Fellner BSc(Hons)
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326