This is the force field including the bonded multi-eGO parameters.
These are the guiding lines to parametrize the backbone dihedral angles: 0. steric interactions are indentified following
- Ideal geometries for secondary structure are use to guide the centers of the minima:
- alpha helix : -60, -45
- 3_10 helix: -49, -26
- strand: –135, 135
- left-alpha: 45,60
- Three classes of alpha/beta population: Jiang, et al. Biopolymers 1998 Hayward, et al. J Struct Biol 2021
Different Peptide construction for sinlge residue helicity: Robert J. Moreau, Christian R. Schubert, Khaled A. Nasr, Marianna Török, Justin S. Miller, Robert J. Kennedy, and Daniel S. Kemp Journal of the American Chemical Society 2009 131 (36), 13107-13116 DOI: 10.1021/ja904271k
- 3J coupling are matched using Karplus relation with parameters from: #https://imserc.northwestern.edu/guide/eNMR/proteins/J/HNHA.html
J coupling experimental table from https://doi.org/10.1073/pnas.0510420103:
ALA 6.06
ARG 6.85
ASN 7.45
ASP 6.93
CYS 7.31
GLN 7.14
GLU 6.63
GLY 5.85
HIS 7.89
ILE 7.33
LEU 6.88
LYS 6.83
MET 7.02
PHE 7.18
SER 7.02
THR 7.35
TRP 6.91
TYR 7.13
VAL 7.3
-
helical populations are fine tuned with Ac-(AAQAA)3-NH2
-
beta propensity is tested with: KKYTVSINGKKITVSI expected 40% folded at 303K
Helix preference (Pa ~ 65%) ALA ARG* ASP** GLU* LEU GLN* MET
Intermediate (50%-50%) HIS* ASN** LYS* SER*
Beta preference (Pb ~ 65%) CYS* PHE ILE THR VAL TRP TYR
** most left alpha after GLY (~10%)
- these should have more left alpha than the others (~5%) all others should be 1%-3%