t70t70 [#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4]
t70b [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]
t70c [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]
t70d [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3]
Goal: test separation of torsions having sp2 carbon attached to the amide nitrogen from t70c
param modification:
t70e [#1:1]-[#7X3:2](-[#6X3])-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]
resulting parameters:
k1*(1+cos(2*theta-180)) + k2*(1+cos(1*theta)) | ||
|---|---|---|
| [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | k1=2.49e+00, k2=1.43e+00 |
| [#1:1]-[#7X3:2](-[#6X3])-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | k1=2.44e+00, k2=6.04e-01 |
The final parameters show the clear separation between two groups. But still there are few torsion profiles, the final parameter set fails to reproduce cis/trans preference.
(1) Torsions with sp3 N attached to amide carbon, [#7X3]-!@[#6X3](=[#8,#16,#7])-[#7X3]
Plots in the red box are torsional profiles whose rotating bond has two t69a and two t70d ([*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3]) assigned. This plots show that they have cis/trans preference which indicates that there should be a separation of t70d into one group with any atom but hydrogen terminal atom and another group with hydrogen as a terminal atom
2. RC2
Goal: test separation of torsions having sp2 carbon attached to the amide nitrogen from t70c + consideration of cis/trans preference of amide with sp3 N attached to the amide carbon
param modification:
t70e [#1:1]-[#7X3:2](-[#6X3])-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] (between t70c and t70d)
t70f [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] (after t70d)
resulting parameters:
k1*(1+cos(2*theta-180)) + k2*(1+cos(1*theta)) | ||
|---|---|---|
| [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | k1=2.49e+00, k2=1.54e+00 |
| [#1:1]-[#7X3:2](-[#6X3])-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | k1=2.47e+00, k2=9.12e-01 |
| [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] | k1=6.08e-01 |
| [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] | k1=6.98e-01 , k2=8.60e-01 |
case where rc2 fails to reproduce cis/trans preference
(3) RC6
param modification:
t70e [#1:1]-[#7X3:2](-@[#6X3](-@[#8,#16]))-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] (between t70c and t70d)
t70f [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] (after t70d)
v1.3.0 | v1.3.1-RC1 | v1.3.1-RC2 | v1.3.1-RC6 | ||
|---|---|---|---|---|---|
1st stg fitting (td targets) | priors | 1/10 of default prior widths for bond and angle parameters | |||
X2 | 2.16e+02 → 6.29e+01 | 2.09e+02 → 5.03e+01 | 2.09e+02 → 4.23e+01 | 2.16e+02 → 3.66e+01 | |