3SPN2BaseStackingInteraction #

3SPN2BaseStackingInteraction is specific to 3SPN2 Coarse-Grained DNA model.

The following potentials are available.

• "3SPN2" (Hinckley et al., (2013) JCP)
• "3SPN2C" (Freeman et al., (2014) JCP)

Example #

[[forcefields.local]]
interaction = "3SPN2BaseStacking"
potential   = "3SPN2"
topology    = "nucleotide"
parameters  = [
# `nucleotide` index starts from 5' and ends at 3'.
{strand = 0, nucleotide =  0,          S =   0, B =   1, offset = 100, Base = "A"},
{strand = 0, nucleotide =  1, P =   2, S =   3, B =   4, offset = 100, Base = "T"},
{strand = 0, nucleotide =  2, P =   5, S =   6, B =   7, offset = 100, Base = "C"},
{strand = 0, nucleotide =  3, P =   8, S =   9, B =  10, offset = 100, Base = "G"},
{strand = 1, nucleotide =  4,          S =  11, B =  12, offset = 100, Base = "C"},
{strand = 1, nucleotide =  5, P =  13, S =  14, B =  15, offset = 100, Base = "G"},
{strand = 1, nucleotide =  6, P =  16, S =  17, B =  18, offset = 100, Base = "A"},
{strand = 1, nucleotide =  7, P =  19, S =  20, B =  21, offset = 100, Base = "T"},
]

Input Reference #

• interaction: String
  • Name of the interaction. Here, it is "3SPN2BaseStacking".
• potential: String
  • Name of the potential. One of the following.
  • 3SPN2
  • 3SPN2C
• topology: String
  • Name of the topology. Debye-Huckel and 3SPN2BaseBaseInteraction should handle this correctly.
  • This interaction adds edges between all the pair of nucleotide particles that are next to each other.
• parameters: Array of Tables
  • strand: Integer
    • Index of the strand.
  • nucleotide: Integer
    • Index of the nucleotide.
  • P, S, B: Integer
    • Indices of particles that correspond to phosphate (P), sugar (S), and base (B).
    • The index is 0-based.
  • offset: Integer (Optional. By default, 0.)
    • The offset value for the index.
  • Base: String
    • One of "A", "T", "C" or "G".
  • Normally nucleotide at the edge of the DNA does not have phosphate.