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sis.ff
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title = 'SIS force field file template'
[potential]
[potential.bond]
k = 15.0
r0 = 5.84
[potential.angle]
k = 10.0
a0 = 2.643
# [potential.angle_ReB]
# k = 5.0
# a0 = 2.643
[potential.dihedral]
k = 5.0
phi0 = 2.861
# [potential.dihedral_exp]
# k = 5.0
# w = 3.0
# phi0 = 0.28
[potential.basepair]
[potential.basepair.GC]
U0 = -8.40
bond_k = 3.0
bond_r = 13.8
angl_k1 = 3.2
angl_k2 = 3.2
angl_theta1 = 1.8326
angl_theta2 = 0.9425
dihd_k1 = 1.3
dihd_k2 = 1.3
dihd_phi1 = 1.8326
dihd_phi2 = 1.1345
[potential.basepair.AU]
U0 = -4.20
bond_k = 3.0
bond_r = 13.8
angl_k1 = 3.2
angl_k2 = 3.2
angl_theta1 = 1.8326
angl_theta2 = 0.9425
dihd_k1 = 1.3
dihd_k2 = 1.3
dihd_phi1 = 1.8326
dihd_phi2 = 1.1345
[potential.basepair.GU]
U0 = -2.80
bond_k = 3.0
bond_r = 13.8
angl_k1 = 3.2
angl_k2 = 3.2
angl_theta1 = 1.8326
angl_theta2 = 0.9425
dihd_k1 = 1.3
dihd_k2 = 1.3
dihd_phi1 = 1.8326
dihd_phi2 = 1.1345
[potential.wca]
sigma = 10.0
epsilon = 2.0
[NN]
# Nearest neighbor parameters taken from
# J Zuber, S.J. Schroeder, H. Sun, D.H. Turner, and D.H. Mathews (2022) Nucl. Acids Res. 50, 5251-5262
#
# NN format XY_WZ indicates that one strand is 5'-XY-3' and the other is 3'-WZ-5'.
#
#NN dG
GC_CG = -3.46
CC_GG = -3.28
GA_CU = -2.42
CG_GC = -2.33
AC_UG = -2.25
CA_GU = -2.07
AG_UC = -2.01
UA_AU = -1.29
AU_UA = -1.09
AA_UU = -0.94
GC_UG = -2.23
CU_GG = -1.93
GG_CU = -1.80
CG_GU = -1.05
AU_UG = -0.76
GA_UU = -0.60
UG_GU = -0.38
UA_GU = -0.22
GG_UU = -0.20
GU_UG = -0.19
AG_UU = 0.02