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RNA_CG.prm
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RNA_CG.prm
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##############################
## ##
## Force Field Definition ##
## ##
##############################
forcefield CG-RNA
radiusrule ARITHMETIC
radiustype R-MIN
radiussize DIAMETER
epsilonrule GEOMETRIC
a-expterm 184000.0
b-expterm 12.0
c-expterm 2.25
vdw-14-scale 0.0
chg-14-scale 1.0
CHG-CUTOFF 20
#############################
## ##
## Atom Type Definitions ##
## ##
#############################
atom 1 1 P1 "CG for Phosphate" 1 94.970 2
atom 2 2 S1 "CG for Sugar" 2 97.054 3
atom 3 3 CG "Base Sugar Connet A&G" 3 53.022 3
atom 4 4 N6 "Base CG for A&C" 4 42.030 2
atom 5 5 N2 "Base CG For G" 5 54.030 2
atom 6 6 O6 "Base CG For G&U" 6 43.014 2
atom 7 7 O2 "Base CG For C&U" 7 42.006 2
atom 8 8 CU "Base Sugar Connet C&U" 3 26.016 3
atom 9 9 CA "Base A" 3 39.015 2
atom 10 10 P2 "CG for Phosphate" 1 94.970 2
atom 11 11 S2 "CG for Sugar" 2 97.054 3
atom 12 12 G1 "Ghost atom S1" 8 97.054 2
atom 13 13 G2 "Ghost atom S2" 8 97.054 2
atom 20 20 MG "MG" 9 24.310 0
atom 21 21 NA "NA" 10 22.990 0
atom 22 22 K "K" 11 39.098 0
################################
## ##
## Van der Waals Parameters ##
## ##
################################
#Lee-Ping form diameter, epsilon, reduction, gamma
vdw 1 10 0.01 0 10
vdw 2 10 0.01 0 10
vdw 3 5 0.1 0 10
vdw 4 3.7 0.56 0 12
vdw 5 4.9 0.84 0 10
vdw 6 3.7 0.56 0 10
vdw 7 4.5 0.42 0 10
vdw 8 5 0.1 0 10
vdw 9 4.1 0.56 0 12
vdw 10 10 0.01 0 10
vdw 11 10 0.01 0 10
vdw 12 10 0.01 0 10
vdw 13 10 0.01 0 10
vdw 21 2.0 0.2 0 10
vdw 22 4.0 0.01 0 10
#####################################
## ##
## Van der Waals Pair Parameters ##
## ##
#####################################
#Lee-Ping form diameter, epsilon, gamma
### Phosphate and Sugar
vdwpr 1 2 5 0.01 13
vdwpr 1 3 6 0.01 12
vdwpr 1 4 4.5 0.01 19
vdwpr 1 5 4.5 0.01 16
vdwpr 1 6 5 0.01 14
vdwpr 1 7 5.4 0.01 14
vdwpr 1 8 6 0.01 12
vdwpr 1 9 6 0.01 15
vdwpr 2 3 6 0.01 12
vdwpr 2 4 5 0.01 15
vdwpr 2 5 5 0.01 15
vdwpr 2 6 5 0.01 15
vdwpr 2 7 5 0.01 15
vdwpr 2 8 6 0.01 12
vdwpr 2 9 5 0.01 15
### Phosphate and Sugar doubles ##########
vdwpr 10 2 5 0.01 13
vdwpr 10 3 6 0.01 12
vdwpr 10 4 4.5 0.01 19
vdwpr 10 5 4.5 0.01 16
vdwpr 10 6 5 0.01 14
vdwpr 10 7 5.4 0.01 14
vdwpr 10 8 6 0.01 12
vdwpr 10 9 6 0.01 15
vdwpr 11 3 6 0.01 12
vdwpr 11 4 5 0.01 15
vdwpr 11 5 5 0.01 15
vdwpr 11 6 5 0.01 15
vdwpr 11 7 5 0.01 15
vdwpr 11 8 6 0.01 12
vdwpr 11 9 5 0.01 15
## Sugar connects CG and CU
vdwpr 3 4 4.5 0.05 12
vdwpr 3 5 4.3 0.1 11
vdwpr 3 6 4.4 0.1 11
vdwpr 3 7 4.4 0.1 11
vdwpr 3 9 4.4 0.1 11
vdwpr 8 3 5.2 0.01 14
vdwpr 8 4 5.2 0.1 10
vdwpr 8 5 5 0.1 10
vdwpr 8 6 4.8 0.01 16
vdwpr 8 7 4.4 0.01 16
vdwpr 8 9 5.1 0.1 11
### Base atoms N6,N2,O6,O2 ###
vdwpr 4 9 4.3477 0.4091 11.0187
vdwpr 5 4 5.1507 0.8456 7.8770
vdwpr 5 9 4.3657 0.2925 12.0243
vdwpr 6 4 3.7017 1.0996 9.9072
vdwpr 6 5 5.2137 0.2096 10.6628
vdwpr 6 7 4.2823 0.4109 11.5542
vdwpr 6 9 4.4771 0.6338 10.3210
vdwpr 7 4 5.0039 0.4372 10.3768
vdwpr 7 5 3.5435 1.2489 10.0204
vdwpr 7 9 3.9567 0.7239 10.0904
#### Sugar ends ############
vdwpr 12 3 6 0.01 12
vdwpr 12 4 5 0.01 15
vdwpr 12 5 5 0.01 15
vdwpr 12 6 5 0.01 15
vdwpr 12 7 5 0.01 15
vdwpr 12 8 6 0.01 12
vdwpr 12 9 5 0.01 15
vdwpr 13 3 6 0.01 12
vdwpr 13 4 5 0.01 15
vdwpr 13 5 5 0.01 15
vdwpr 13 6 5 0.01 15
vdwpr 13 7 5 0.01 15
vdwpr 13 8 6 0.01 12
vdwpr 13 9 5 0.01 15
##################################
## ##
## Bond Stretching Parameters ##
## ##
##################################
bond 1 2 11.12440191 3.8900
bond 2 3 9.784688995 3.7400
bond 3 4 71.77033493 4.2864
bond 4 9 71.98564593 3.5261
bond 3 9 71.79425837 4.3282
bond 2 8 10.88516746 3.6146
bond 4 8 71.81818182 3.5859
bond 4 7 71.96172249 4.5499
bond 7 8 71.81818182 3.5189
bond 3 6 71.84210526 4.2829
bond 5 6 71.81818182 4.5712
bond 3 5 71.96172249 5.6590
bond 6 8 71.84210526 3.5544
bond 6 7 71.88995215 4.5255
bond 11 1 11.12440191 3.8900
bond 10 11 11.12440191 3.8900
bond 10 2 11.12440191 3.8900
bond 11 3 9.784688995 3.7400
bond 11 8 10.88516746 3.6146
bond 1 12 11.12440191 3.8900
bond 12 3 9.784688995 3.7400
bond 12 8 10.88516746 3.6146
bond 10 12 11.12440191 3.8900
bond 13 1 11.12440191 3.8900
bond 10 13 11.12440191 3.8900
bond 13 3 9.784688995 3.7400
bond 13 8 10.88516746 3.6146
################################
## ##
## Angle Bending Parameters ##
## ##
################################
angle 8 6 7 50 50
angle 8 7 6 50 52
angle 8 7 4 50 54
angle 8 4 7 50 50
angle 3 6 5 50 82
angle 3 4 9 50 67
angle 3 5 6 50 50
angle 3 9 4 50 65
angle 6 8 7 50 82
angle 7 8 4 50 82
angle 4 3 9 50 49
angle 5 3 6 50 54
angle 1 2 3 22 73
angle 10 11 3 22 73
angle 1 2 8 22 73
angle 10 11 8 22 73
angle 1 2 10 20 100
angle 10 11 1 20 100
angle 1 11 3 22 103
angle 10 2 3 22 103
angle 1 11 8 25 103
angle 10 2 8 25 103
angle 2 10 11 30 106
angle 11 1 2 30 106
angle 2 8 6 40 167
angle 11 8 6 40 167
angle 2 8 7 50 89
angle 11 8 7 50 89
angle 2 8 4 45 168
angle 11 8 4 45 168
angle 2 3 6 45 157
angle 11 3 6 45 157
angle 2 3 4 45 158
angle 11 3 4 45 158
angle 2 3 5 50 106
angle 11 3 5 50 106
angle 2 3 9 50 110
angle 11 3 9 50 110
#12
angle 1 12 3 2 76
angle 1 12 8 2 74
angle 1 12 10 1 103
angle 10 12 3 5 102
angle 10 12 8 9 101
angle 12 10 11 2 106
angle 11 1 12 2 106
angle 12 8 6 7 164
angle 12 8 7 16 89
angle 12 8 4 7 164
angle 12 3 6 8 154
angle 12 3 4 7 155
angle 12 3 5 13 104
angle 12 3 9 11 109
#13
angle 1 13 3 5 102
angle 1 13 8 9 101
angle 2 10 13 2 106
angle 10 13 3 2 76
angle 10 13 8 2 75
angle 10 13 1 1 103
angle 13 1 2 2 106
angle 13 8 6 7 164
angle 13 8 7 16 89
angle 13 8 4 7 164
angle 13 3 6 8 154
angle 13 3 4 7 155
angle 13 3 5 13 104
angle 13 3 9 11 109
###############################
## ##
## Urey-Bradley Parameters ##
## ##
###############################
#####################################
## ##
## Improper Torsional Parameters ##
## ##
#####################################
############################
## ##
## Torsional Parameters ##
## ##
############################
torsion 1 2 10 11 0.5 40 1 0.2 240 2 0.1 110 3
torsion 10 11 1 2 0.5 40 1 0.2 240 2 0.1 110 3
torsion 2 10 11 1 0.5 345 1 0.35 160 2 0.1 340 3
torsion 11 1 2 10 0.5 345 1 0.35 160 2 0.1 340 3
torsion 3 2 10 11 0.5 100 1 0.2 30 2 0.1 320 3
torsion 3 11 1 2 0.5 100 1 0.2 30 2 0.1 320 3
torsion 11 1 2 3 0.6 250 1 0.25 320 2 0.125 10 3
torsion 2 10 11 3 0.6 250 1 0.25 320 2 0.125 10 3
torsion 10 2 3 4 0.5 245 1 0.2 290 2 0 0 3
torsion 1 11 3 4 0.5 245 1 0.2 290 2 0 0 3
torsion 10 2 3 9 0.65 260 1 0.2 330 2 0.1 20 3
torsion 1 11 3 9 0.65 260 1 0.2 330 2 0.1 20 3
torsion 10 11 3 4 0.625 340 1 0.05 120 2 0 280 3
torsion 1 2 3 4 0.625 340 1 0.05 120 2 0 280 3
torsion 10 11 3 9 0.65 0 1 0.25 170 2 0.05 0 3
torsion 1 2 3 9 0.65 0 1 0.25 170 2 0.05 0 3
torsion 11 3 4 9 1.05 200 1 0.4 220 2 0 0 3
torsion 2 3 4 9 1.05 200 1 0.4 220 2 0 0 3
torsion 11 3 9 4 1.15 0 1 0.5 180 2 0.175 10 3
torsion 2 3 9 4 1.15 0 1 0.5 180 2 0.175 10 3
torsion 8 2 10 11 0.5 100 1 0.25 40 2 0.1 315 3
torsion 8 11 1 2 0.5 100 1 0.25 40 2 0.1 315 3
torsion 11 1 2 8 0.5 250 1 0.4 320 2 0.2 40 3
torsion 2 10 11 8 0.5 250 1 0.4 320 2 0.2 40 3
torsion 10 2 8 4 0.65 230 1 0 240 2 0.15 300 3
torsion 1 11 8 4 0.65 230 1 0 240 2 0.15 300 3
torsion 10 2 8 7 0.75 260 1 0.35 330 2 0.075 80 3
torsion 1 11 8 7 0.75 260 1 0.35 330 2 0.075 80 3
torsion 10 11 8 4 0.75 330 1 0.05 70 2 0 0 3
torsion 1 2 8 4 0.75 330 1 0.05 70 2 0 0 3
torsion 10 11 8 7 0.8 0 1 0.1375 180 2 0.15 0 3
torsion 1 2 8 7 0.8 0 1 0.1375 180 2 0.15 0 3
torsion 11 8 4 7 1.1 210 1 0.3 240 2 0 0 3
torsion 2 8 4 7 1.1 210 1 0.3 240 2 0 0 3
torsion 11 8 7 4 1 0 1 0.8 190 2 0.2 10 3
torsion 2 8 7 4 1 0 1 0.8 190 2 0.2 10 3
torsion 10 2 3 6 0.5 240 1 0.25 280 2 0 0 3
torsion 1 11 3 6 0.5 240 1 0.25 280 2 0 0 3
torsion 10 2 3 5 0.65 260 1 0.3 330 2 0.075 20 3
torsion 1 11 3 5 0.65 260 1 0.3 330 2 0.075 20 3
torsion 10 11 3 6 0.5 340 1 0.15 120 2 0.075 280 3
torsion 1 2 3 6 0.5 340 1 0.15 120 2 0.075 280 3
torsion 10 11 3 5 0.625 0 1 0.25 180 2 0.1 340 3
torsion 1 2 3 5 0.625 0 1 0.25 180 2 0.1 340 3
torsion 11 3 6 5 1.1 200 1 0.5 220 2 0 0 3
torsion 2 3 6 5 1.1 200 1 0.5 220 2 0 0 3
torsion 11 3 5 6 1.15 0 1 0.5 190 2 0 0 3
torsion 2 3 5 6 1.15 0 1 0.5 190 2 0 0 3
torsion 10 2 8 6 0.5 235 1 0.15 270 2 0.05 300 3
torsion 1 11 8 6 0.5 235 1 0.15 270 2 0.05 300 3
torsion 10 11 8 6 0.6 330 1 0.1 90 2 0 0 3
torsion 1 2 8 6 0.6 330 1 0.1 90 2 0 0 3
torsion 11 8 6 7 1.1 210 1 0.3 240 2 0 0 3
torsion 2 8 6 7 1.1 210 1 0.3 240 2 0 0 3
torsion 11 8 7 6 1 5 1 0.65 185 2 0.15 15 3
torsion 2 8 7 6 1 5 1 0.65 185 2 0.15 15 3
torsion 1 12 10 11 0.5 40 1 0.2 240 2 0.1 110 3
torsion 10 11 1 12 0.5 40 1 0.2 240 2 0.1 110 3
torsion 12 10 11 1 0.5 345 1 0.35 160 2 0.1 340 3
torsion 11 1 12 10 0.5 345 1 0.35 160 2 0.1 340 3
torsion 3 12 10 11 0.5 100 1 0.2 30 2 0.1 320 3
torsion 3 11 1 12 0.5 100 1 0.2 30 2 0.1 320 3
torsion 11 1 12 3 0.6 250 1 0.25 320 2 0.125 10 3
torsion 12 10 11 3 0.6 250 1 0.25 320 2 0.125 10 3
torsion 10 12 3 4 0.5 245 1 0.2 290 2 0 0 3
torsion 10 12 3 9 0.65 260 1 0.2 330 2 0.1 20 3
torsion 1 12 3 4 0.625 340 1 0.05 120 2 0 0 3
torsion 1 12 3 9 0.65 0 1 0.25 170 2 0.05 0 3
torsion 12 3 4 9 1.05 200 1 0.4 220 2 0 0 3
torsion 12 3 9 4 1.15 0 1 0.5 180 2 0.175 10 3
torsion 8 12 10 11 0.5 100 1 0.25 40 2 0.1 315 3
torsion 8 11 1 12 0.5 100 1 0.25 40 2 0.1 315 3
torsion 11 1 12 8 1 250 1 0.8 320 2 0.4 40 3
torsion 12 10 11 8 1 250 1 0.8 320 2 0.4 40 3
torsion 10 12 8 4 0.65 230 1 0 240 2 0.15 300 3
torsion 10 12 8 7 0.75 260 1 0.35 330 2 0.075 80 3
torsion 1 12 8 4 0.75 330 1 0.05 70 2 0 0 3
torsion 1 12 8 7 0.8 0 1 0.1375 180 2 0.15 0 3
torsion 12 8 4 7 1.1 210 1 0.3 240 2 0 0 3
torsion 12 8 7 4 1 0 1 0.8 190 2 0.2 10 3
torsion 10 12 3 6 0.5 240 1 0.25 280 2 0 0 3
torsion 10 12 3 5 0.65 260 1 0.3 330 2 0.075 20 3
torsion 1 12 3 6 0.5 340 1 0.15 120 2 0.075 280 3
torsion 1 12 3 5 0.625 0 1 0.25 180 2 0.1 340 3
torsion 12 3 6 5 1.1 200 1 0.5 220 2 0 0 3
torsion 12 3 5 6 1.15 0 1 0.5 190 2 0 0 3
torsion 10 12 8 6 0.5 235 1 0.15 270 2 0.05 300 3
torsion 1 12 8 6 0.6 330 1 0.1 90 2 0 0 3
torsion 12 8 6 7 1.1 210 1 0.3 240 2 0 0 3
torsion 12 8 7 6 1 5 1 0.65 185 2 0.15 15 3
torsion 1 2 10 13 0.5 40 1 0.2 240 2 0.1 110 3
torsion 10 13 1 2 0.5 40 1 0.2 240 2 0.1 110 3
torsion 2 10 13 1 0.5 345 1 0.35 160 2 0.1 340 3
torsion 13 1 2 10 0.5 345 1 0.35 160 2 0.1 340 3
torsion 3 2 10 13 0.5 100 1 0.2 30 2 0.1 320 3
torsion 3 13 1 2 0.5 100 1 0.2 30 2 0.1 320 3
torsion 13 1 2 3 0.6 250 1 0.25 320 2 0.125 10 3
torsion 2 10 13 3 0.6 250 1 0.25 320 2 0.125 10 3
torsion 1 13 3 4 0.5 245 1 0.2 290 2 0 0 3
torsion 1 13 3 9 0.65 260 1 0.2 330 2 0.1 20 3
torsion 10 13 3 4 0.625 340 1 0.05 120 2 0 0 3
torsion 10 13 3 9 0.65 0 1 0.25 170 2 0.05 0 3
torsion 13 3 4 9 1.05 200 1 0.4 220 2 0 0 3
torsion 13 3 9 4 1.15 0 1 0.5 180 2 0.175 10 3
torsion 8 2 10 13 0.5 100 1 0.25 40 2 0.1 315 3
torsion 8 13 1 2 0.5 100 1 0.25 40 2 0.1 315 3
torsion 13 1 2 8 1 250 1 0.8 320 2 0.4 40 3
torsion 2 10 13 8 1 250 1 0.8 320 2 0.4 40 3
torsion 1 13 8 4 0.65 230 1 0 240 2 0.15 300 3
torsion 1 13 8 7 0.75 260 1 0.35 330 2 0.075 80 3
torsion 10 13 8 4 0.75 330 1 0.05 70 2 0 0 3
torsion 10 13 8 7 0.8 0 1 0.1375 180 2 0.15 0 3
torsion 13 8 4 7 1.1 210 1 0.3 240 2 0 0 3
torsion 13 8 7 4 1 0 1 0.8 190 2 0.2 10 3
torsion 1 13 3 6 0.5 240 1 0.25 280 2 0 0 3
torsion 1 13 3 5 0.65 260 1 0.3 330 2 0.075 20 3
torsion 10 13 3 6 0.5 340 1 0.15 120 2 0.075 280 3
torsion 10 13 3 5 0.625 0 1 0.25 180 2 0.1 340 3
torsion 13 3 6 5 1.1 200 1 0.5 220 2 0 0 3
torsion 13 3 5 6 1.15 0 1 0.5 190 2 0 0 3
torsion 1 13 8 6 0.5 235 1 0.15 270 2 0.05 300 3
torsion 10 13 8 6 0.6 330 1 0.1 90 2 0 0 3
torsion 13 8 6 7 1.1 210 1 0.3 240 2 0 0 3
torsion 13 8 7 6 1 5 1 0.65 185 2 0.15 15 3
########################################
## ##
## Atomic Partial Charge Parameters ##
## conversion from electron**2/Ang to kcal/mole 332.063709 ##
########################################
charge 1 -1.000
charge 2 0.0000
charge 3 0.0000
charge 4 0.0000
charge 5 0.0000
charge 6 0.0000
charge 7 0.0000
charge 8 0.0000
charge 9 0.0000
charge 10 -1.000
charge 11 0.0000
charge 12 0.0000
charge 13 0.0000
charge 20 2.0000
charge 21 1.0000
charge 22 1.0000
########################################
## ##
## Biopolymer Atom Type Conversions ##
## ##
########################################
biotype 1 P1 "ACGU" 1
biotype 2 S1 "ACGU" 2
biotype 3 CG "ACGU" 3
biotype 4 N6 "ACGU" 4
biotype 5 N2 "ACGU" 5
biotype 6 O6 "ACGU" 6
biotype 7 O2 "ACGU" 7
biotype 8 CU "ACGU" 8
biotype 9 CA "ACGU" 9
biotype 10 P2 "ACGU" 10
biotype 11 S2 "ACGU" 11
biotype 12 G1 "ACGU" 12
biotype 13 G2 "ACGU" 13
biotype 20 MG "ACGU" 20
biotype 21 NA "ACGU" 21