Table. 1 System setup for MD simulations
Simulation | Box dimensions | Total atoms | Type of molecule |
|---|---|---|---|
AflR-DBD run1 | a = 65.849, b = 65.849, c = 65.849, α = 60.00, β = 60.00, γ = 90.00 | 20162 | Water (6350), salt (36), protein (1) |
AflR-DBD run2 | a = 58.080, b = 58.080, c = 58.080, α = 60.00, β = 60.00, γ = 90.00 | 13887 | Water (4261), salt (28), protein (1) |
AflR-DBD run3 | a = 73.602, b = 73.602, c = 73.602, α = 60.00, β = 60.00, γ = 90.00 | 28170 | Water (9016), salt (46), protein (1) |
ver1 complexrun1 | a = 113.784, b = 113.784, c = 113.784, α = 60.00, β = 60.00, γ = 90.00 | 103711 | Water (33187), salt (220), protein (2), DNA (1) |
ver1 complex run2 | a = 114.126, b = 114.126, c = 114.126, α = 60.00, β = 60.00, γ = 90.00 | 104535 | Water (33461), salt (222), protein (2), DNA (1) |
ver1 complex run3 | a = 114.209, b = 114.209, c = 114.209, α = 60.00, β = 60.00, γ = 90.00 | 105035 | Water (33627), salt (224), protein (2), DNA (1) |
vbs complex run1 | a = 114.912, b = 114.912, c = 114.912, α = 60.00, β = 60.00, γ = 90.00 | 106898 | Water (34249), salt (228), protein (2), DNA (1) |
vbs complex run2 | a = 120.307, b = 120.307, c = 120.307, α = 60.00, β = 60.00, γ = 90.00 | 122378 | Water (39399), salt (258), protein (2), DNA (1) |
vbs complex run3 | a = 114.181, b = 114.181, c = 114.181, α = 60.00, β = 60.00, γ = 90.00 | 104612 | Water (33489), salt (222), protein (2), DNA (1) |
norA complex run1 | a = 116.406, b = 116.406, c = 116.406, α = 60.00, β = 60.00, γ = 90.00 | 111187 | Water (35653), salt (238), protein (2), DNA (1) |
norA complex run2 | a = 115.825, b = 115.825, c = 115.825, α = 60.00, β = 60.00, γ = 90.00 | 109419 | Water (35065), salt (234), protein (2), DNA (1) |
norA complex run3 | a = 115.825, b = 115.825, c = 115.825, α = 60.00, β = 60.00, γ = 90.00 | 109419 | Water (35065), salt (234), protein (2), DNA (1) |
