0.
Torsion profile of amide bond of N-methylacetamide using v1.2.0 fails to fit the expected minimum (parabola shape), giving a small hump at the minimum. Re-fitting to the selected torsion targets which rotate an amide bond couldn’t remove the hump.
From a closer look at the targets used to train the amide bond parameters(t69s, t70s), I found that some targets behave not as expected at around its planar geometry (having a small peak, instead of parabolic shape near the minimum), which leads the parameter set to be trained to fail to reproduce the torsion profiles with parabolic shape near the minimum (like N-methyacetamide).
So one of the easy fixes of the problem will be using simple targets which behaves exactly as we expect near the minimum (planar at 180 and small steric hindrance) and here’s what I did:
1. filtering non-planar structure at minimum geometry
explanation of scheme2 and scheme3
scheme 2 (fb-fit2):
scheme 3 (fb-fit3)
fb-fit2 vs fb-fit2-2
fb-fit2 | SMIRKS | initial guess | final |
|---|---|---|---|
t69a | [*:1]-[#7X3:2]-[#6X3$(*=[#8,#16,#7]):3]~[*:4] | 2.5 (1+cos(2x-180)) | 2.5 (1+cos(2x-180)) |
t69b | [*:1]-[#7X3:2]-!@[#6X3$(*=[#8,#16,#7]):3]~[*:4] | 2.5 (1+cos(2x-180)) | 1.652160092455e+00 (1+cos(2x-180)) |
t70 | [#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] | 3.459249459574e+00 (1+cos(2x-180)) + 1.356955617521e+00 (1+cosx) | 3.459249459574e+00 (1+cos(2x-180)) + 1.356955617521e+00 (1+cosx) |
t70a | [#1:1]-[#7X3:2]-!@[#6X3:3]=[#8,#16,#7:4] | 2.5 (1+cos(2x-180)) + 2.0 (1+cosx) | -2.081991778915e-01 (1+cos(2x-180)) + 1.400460484703e+00 (1+cosx) |
t70b | [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | 2.5 (1+cos(2x-180)) | 4.091207931356e+00 (1+cos(2x-180)) |
t70c | [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | 2.5 (1+cos(2x-180)) + 2.0 (1+cosx) | 1.301446828323e+00 (1+cos(2x-180)) + 9.476830965983e-01 (1+cosx) |
t70d | [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] | 2.5 (1+cos(2x-180)) | 1.271374777009e+00 (1+cos(2x-180)) |
fb-fit2-2 | SMIRKS | initial guess | final |
|---|---|---|---|
t69a | [*:1]-[#7X3:2]-[#6X3$(*=[#8,#16,#7]):3]~[*:4] | 2.5 (1+cos(2x-180)) | 1.679285484776e+00 (1+cos(2x-180)) |
t70 | [#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] | 3.459249459574e+00 (1+cos(2x-180)) + 1.356955617521e+00 (1+cosx) | 3.566161051804e-01 (1+cos(2x-180)) + 1.354248559088e+00 (1+cosx) |
t70b | [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | 2.5 (1+cos(2x-180)) | 4.169159533591e+00 (1+cos(2x-180)) |
t70c | [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | 2.5 (1+cos(2x-180)) + 2.0 (1+cosx) | 1.240609067243e+00 (1+cos(2x-180)) + 9.065552775144e-01 (1+cosx) |
t70d | [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] | 2.5 (1+cos(2x-180)) | 1.303139175986e+00 (1+cos(2x-180)) |