(4) 2020-09-15 Summary amide study

1. Tracing the origin of the amide issue

Torsion profile of N-methylacetamide amide bond generated using v1.2.0 failed to reproduce the QM torsion profile(left plots), forming a small hump at the energy minimum dihedral angle which doesn’t appear in the QM profile. Energy decoupling(bottom left plot) showed that torsion term contributes the most to the formation of the hump, which indicated the need to re-fit the related torsion parameters. Along with the issue, for fixing the dialkyl amide issue(for more detail, please refer to here), we’ve decided to add amide-specific torsion parameters. Re-fitting with the newly added parameters to the selected torsion targets(targets scanning amide bond dihedral) was carried out and the test calculation(right plots) showed that while the re-fitting improved the torsion energy term(bottom right plot), it forced the formation the hump at 180 degree by deforming other terms.

From a closer look at the targets used in training the amide-specific torsion parameters(t69s, t70s), I found that some targets behave not as expected at around their planar geometries (having a small peak, instead of parabolic shape near the minimum), which leads the parameter set fitted to the targets to form a small hump when scanning the simple molecules whose torsion profiles have parabolic shape near the minimum (like N-methyacetamide).

So one easy fix of the problem is using simple targets, whose torsion profiles have parabolic shape near the minimum (planar geometry at the minimum). + Expecting that this experiment to be one proof of the need for using simple-as-possible torsiondrive targets in general torsion parameter fitting.

2. Filtering non-planar structure at minimum geometry

(since the 2nd generation torsion training set is too small to filter, i pulled Roche torsion set (1st gen) and filtered with various scheme. )

• scheme 2. check improper dihedral angles at the minimum energy point of the torsion profile, take targets whose C-center and N-center improper dihedral angles are both between -5.0, 5.0 degree;

• scheme 3. check QM data to see if the profile has its local minima at 0 or 180;

• scheme 4. targets passed either scheme 2 or scheme 3

maybe 2d image of molecules?

3. fb-fit2 vs. fb-fit4

• For the test set (amide-rotating Roche torsion targets which are not selected either from scheme 2 or from scheme 3), can’t see the effect of splitting endo-cyclic rotation and exo-cyclic rotation

• Parameter sets fitted to scheme 2 and scheme 4 performs similarly, while the parameter set fitted to the scheme 4 slightly more prefer to form hump at the near-planar structure. (could be good or bad)

* Negative k1 value

Although the k1 value for t70a seems unphysical, the result below shows the plots got improved after the optimization. checked improvement for all of the four fitting targets.

4. Conclusions and what-to-do-next

* Fitting torsion parameters to simpler torsion targets (with less strong electrostatic interaction) might be needed for the next round fitting.

* so irrelevent! (move to the new page with “the new priors selection”)