FlexibleLocalDihedral #

It represents dihedral angle distribution of flexible regions of proteins in a Coarse-Grained protein model.

\[U(\phi) = C + \sum_{n=1}^{3}\left( k_n^{\sin} \sin(n\phi) + k_n^{\cos} \cos(n\phi)\right)\]

It is a component of AICG2+ Coarse-Grained protein model.

It is developed in the following paper.

T. Terakawa and S. Takada, (2011) Biophys J

Example #

[[forcefields.local]]
parameters = [
    {indices = [0,1,2,3], k = 1.0, coef = [2.2356,  0.4119, -0.1283,  0.0229, -0.2708, -0.0085, -0.0641]},
    # ...
]

Input Reference #

k: Floating
- It determines the strength of the potential.
coef: Array of Floatings (length = 7)
- \( C, k_1^{\sin}, k_1^{\cos}, k_2^{\sin}, k_2^{\cos}, k_3^{\sin}, k_3^{\cos} \) , respectively.
indices: Array of Integers (length = 4)
- Indices of particles that interact with each other. The index is 0-based.
offset: Integer(Optional. By default, 0.)
- Offset of index.