3SPN2BaseBaseInteraction #

3SPN2BaseBaseInteraction is speicfic to the 3SPN2 Coarse-Grained DNA model.

The following potentials are available.

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

Example #

[[forcefields.global]]
interaction = "3SPN2BaseBase"
potential   = "3SPN2"
ignore.particles_within.nucleotide = 3
spatial_partition = {type = "CellList", margin = 0.2}
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"},
# ...
]

Input Reference #

• interaction: String
  • Name of the interaction. Here, it is "3SPN2BaseBase".
• potential: String
  • The following potentials are available.
  • 3SPN2
  • 3SPN2C
• ignore: Table
  • It describes the condition when the pair of particles does not interact to each other.
  • Since 3SPN2 only allows base pairs between nucleotides that are at least 3 nucleotides distant. Set nucleotide = 3 and name 3SPN2BaseStacking.topology as nucleotide.
  • For detail, see the ignore section of GlobalForceField
• spatial_partition: Table
  • It specifies the algorithm to construct a neighbor list.
  • For detail, see the ignore section of GlobalForceField
• 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.