12/9 summary

Owned by Hyesu Jang
Last updated: Dec 10, 2020
2 min read

List of child parameters of t70

t70 [#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]

1. RC1

  • 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))

 

k1*(1+cos(2*theta-180)) + k2*(1+cos(1*theta))

t70c

[#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

 k1=2.49e+00, k2=1.43e+00

t70e

[#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))

 

k1*(1+cos(2*theta-180)) + k2*(1+cos(1*theta))

t70c

[#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

 k1=2.49e+00, k2=1.54e+00

t70e

[#1:1]-[#7X3:2](-[#6X3])-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

k1=2.47e+00, k2=9.12e-01

t70d

[*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3]

k1=6.08e-01

t70f

[#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

 

 

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