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DNA_M2.ff
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[ citations ]
Martini2
M2_DNA
polyply
[ moleculetype ]
DT3 1
[ atoms ]
1 Q0 1 DT3 BB1 25 -1.0 72.0
2 SN0 1 DT3 BB2 26 0.0 45.0
3 SC2 1 DT3 BB3 27 0.0 45.0
4 TN0 1 DT3 SC1 28 0.0 45.0
5 TT2 1 DT3 SC2 29 0.0 45.0
6 TT3 1 DT3 SC3 30 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000 {"group": "backbone"}
BB2 BB3 1 0.19800 80000 {"group": "backbone"}
BB3 SC1 1 0.27000 30000
[ constraints ]
SC1 SC2 1 0.21700
SC2 SC3 1 0.32200
SC3 SC1 1 0.26500
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB2 SC1
BB2 SC2
BB2 SC3
BB3 SC1
BB3 SC2
BB3 SC3
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 92.00000 220
BB3 SC1 SC2 2 107.00000 300
BB2 SC1 SC3 1 145.00000 400
SC1 SC2 SC3 1 55.00000 100
SC2 SC1 SC3 1 83.00000 100
SC2 SC3 SC1 1 42.00000 100
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -75.00000 40
BB2 BB3 SC1 SC2 2 -110.00000 15
BB3 BB2 SC1 SC3 2 -145.00000 65
[ moleculetype ]
DT 1
[ atoms ]
1 Q0 1 DT BB1 7 -1.0 72.0
2 SN0 1 DT BB2 8 0.0 45.0
3 SC2 1 DT BB3 9 0.0 45.0
4 TN0 1 DT SC1 10 0.0 45.0
5 TT2 1 DT SC2 11 0.0 45.0
6 TT3 1 DT SC3 12 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.27000 30000
[ constraints ]
SC1 SC2 1 0.21700
SC2 SC3 1 0.32200
SC3 SC1 1 0.26500
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB2 SC1
BB2 SC2
BB2 SC3
BB3 SC1
BB3 SC2
BB3 SC3
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 92.00000 220
BB3 SC1 SC2 2 107.00000 300
BB2 SC1 SC3 1 145.00000 400
SC1 SC2 SC3 1 55.00000 100
SC2 SC1 SC3 1 83.00000 100
SC2 SC3 SC1 1 42.00000 100
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -75.00000 40
BB2 BB3 SC1 SC2 2 -110.00000 15
BB3 BB2 SC1 SC3 2 -145.00000 65
[ moleculetype ]
DT5 1
[ atoms ]
1 SN0 1 DT5 BB2 2 0.0 45.0
2 SC2 1 DT5 BB3 3 0.0 45.0
3 TN0 1 DT5 SC1 4 0.0 45.0
4 TT2 1 DT5 SC2 5 0.0 45.0
5 TT3 1 DT5 SC3 6 0.0 45.0
[ bonds ]
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.27000 30000
[ constraints ]
SC1 SC2 1 0.21700
SC2 SC3 1 0.32200
SC3 SC1 1 0.26500
[ exclusions ]
BB2 SC1
BB2 SC2
BB2 SC3
BB3 SC1
BB3 SC2
BB3 SC3
[ angles ]
BB2 BB3 SC1 2 92.00000 220
BB3 SC1 SC2 2 107.00000 300
BB2 SC1 SC3 1 145.00000 400
SC1 SC2 SC3 1 55.00000 100
SC2 SC1 SC3 1 83.00000 100
SC2 SC3 SC1 1 42.00000 100
[ dihedrals ]
BB2 BB3 SC1 SC2 2 -110.00000 15
BB3 BB2 SC1 SC3 2 -145.00000 65
[ moleculetype ]
DC3 1
[ atoms ]
1 Q0 1 DC3 BB1 27 -1.0 72.0
2 SN0 1 DC3 BB2 28 0.0 45.0
3 SC2 1 DC3 BB3 29 0.0 45.0
4 TN0 1 DC3 SC1 30 0.0 45.0
5 TY2 1 DC3 SC2 31 0.0 45.0
6 TY3 1 DC3 SC3 32 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.27000 30000
[ constraints ]
SC1 SC2 1 0.22000
SC2 SC3 1 0.28500
SC3 SC1 1 0.26800
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB2 SC1
BB2 SC2
BB2 SC3
BB3 SC1
BB3 SC2
BB3 SC3
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 95.00000 210
BB3 SC1 SC2 2 95.00000 300
BB2 SC1 SC3 1 150.00000 500
SC1 SC2 SC3 1 61.00000 200
SC2 SC1 SC3 1 71.00000 200
SC2 SC3 SC1 1 47.00000 200
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -78.00000 25
BB2 BB3 SC1 SC2 2 -90.00000 20
BB3 BB2 SC1 SC3 2 -142.00000 50
[ moleculetype ]
DG 1
[ atoms ]
1 Q0 1 DG BB1 13 -1.0 72.0
2 SN0 1 DG BB2 14 0.0 45.0
3 SC2 1 DG BB3 15 0.0 45.0
4 TN0 1 DG SC1 16 0.0 45.0
5 TG2 1 DG SC2 17 0.0 45.0
6 TG3 1 DG SC3 18 0.0 45.0
7 TNa 1 DG SC4 19 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.30000 30000
SC2 SC4 1 0.38900 20000
[ constraints ]
SC1 SC2 1 0.29500
SC2 SC3 1 0.29500
SC3 SC4 1 0.28500
SC4 SC1 1 0.16100
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB1 SC4
BB2 SC1
BB2 SC2
BB2 SC3
BB2 SC4
BB3 SC1
BB3 SC2
BB3 SC3
BB3 SC4
SC1 SC3
SC2 SC4
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 94.50000 250
BB3 SC1 SC2 2 137.00000 300
BB3 SC1 SC4 2 130.00000 250
SC1 SC2 SC3 1 69.50000 200
SC2 SC1 SC4 1 125.00000 200
SC2 SC3 SC4 1 84.00000 200
SC3 SC4 SC1 1 94.00000 200
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -90.00000 20
BB2 BB3 SC1 SC2 2 -117.00000 1
BB2 BB3 SC1 SC4 2 92.00000 15
[ moleculetype ]
DC 1
[ atoms ]
1 Q0 1 DC BB1 7 -1.0 72.0
2 SN0 1 DC BB2 8 0.0 45.0
3 SC2 1 DC BB3 9 0.0 45.0
4 TN0 1 DC SC1 10 0.0 45.0
5 TY2 1 DC SC2 11 0.0 45.0
6 TY3 1 DC SC3 12 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.27000 30000
[ constraints ]
SC1 SC2 1 0.22000
SC2 SC3 1 0.28500
SC3 SC1 1 0.26800
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB2 SC1
BB2 SC2
BB2 SC3
BB3 SC1
BB3 SC2
BB3 SC3
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 95.00000 210
BB3 SC1 SC2 2 95.00000 300
BB2 SC1 SC3 1 150.00000 500
SC1 SC2 SC3 1 61.00000 200
SC2 SC1 SC3 1 71.00000 200
SC2 SC3 SC1 1 47.00000 200
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -78.00000 25
BB2 BB3 SC1 SC2 2 -90.00000 20
BB3 BB2 SC1 SC3 2 -142.00000 50
[ moleculetype ]
DA 1
[ atoms ]
1 Q0 1 DA BB1 20 -1.0 72.0
2 SN0 1 DA BB2 21 0.0 45.0
3 SC2 1 DA BB3 22 0.0 45.0
4 TN0 1 DA SC1 23 0.0 45.0
5 TA2 1 DA SC2 24 0.0 45.0
6 TA3 1 DA SC3 25 0.0 45.0
7 TNa 1 DA SC4 26 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.30000 30000
SC2 SC4 1 0.32600 20000
[ constraints ]
SC1 SC2 1 0.22900
SC2 SC3 1 0.26600
SC3 SC4 1 0.28800
SC4 SC1 1 0.16200
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB1 SC4
BB2 SC1
BB2 SC2
BB2 SC3
BB2 SC4
BB3 SC1
BB3 SC2
BB3 SC3
BB3 SC4
SC1 SC3
SC2 SC4
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 94.00000 250
BB3 SC1 SC2 2 160.00000 200
BB3 SC1 SC4 2 140.00000 200
SC1 SC2 SC3 1 85.00000 200
SC2 SC1 SC4 1 125.00000 200
SC2 SC3 SC4 1 74.00000 200
SC3 SC4 SC1 1 98.00000 200
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -90.00000 20
BB2 BB3 SC1 SC2 2 -116.00000 0.50000
BB2 BB3 SC1 SC4 2 98.00000 15
[ moleculetype ]
DC5 1
[ atoms ]
1 SN0 1 DC5 BB2 2 0.0 45.0
2 SC2 1 DC5 BB3 3 0.0 45.0
3 TN0 1 DC5 SC1 4 0.0 45.0
4 TY2 1 DC5 SC2 5 0.0 45.0
5 TY3 1 DC5 SC3 6 0.0 45.0
[ bonds ]
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.27000 30000
[ constraints ]
SC1 SC2 1 0.22000
SC2 SC3 1 0.28500
SC3 SC1 1 0.26800
[ exclusions ]
BB2 SC1
BB2 SC2
BB2 SC3
BB3 SC1
BB3 SC2
BB3 SC3
[ angles ]
BB2 BB3 SC1 2 95.00000 210
BB3 SC1 SC2 2 95.00000 300
BB2 SC1 SC3 1 150.00000 500
SC1 SC2 SC3 1 61.00000 200
SC2 SC1 SC3 1 71.00000 200
SC2 SC3 SC1 1 47.00000 200
[ dihedrals ]
BB2 BB3 SC1 SC2 2 -90.00000 20
BB3 BB2 SC1 SC3 2 -142.00000 50
[ moleculetype ]
DA5 1
[ atoms ]
1 SN0 1 DA5 BB2 21 0.0 45.0
2 SC2 1 DA5 BB3 22 0.0 45.0
3 TN0 1 DA5 SC1 23 0.0 45.0
4 TA2 1 DA5 SC2 24 0.0 45.0
5 TA3 1 DA5 SC3 25 0.0 45.0
6 TNa 1 DA5 SC4 26 0.0 45.0
[ bonds ]
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.30000 30000
SC2 SC4 1 0.32600 20000
[ constraints ]
SC1 SC2 1 0.22900
SC2 SC3 1 0.26600
SC3 SC4 1 0.28800
SC4 SC1 1 0.16200
[ exclusions ]
BB2 SC1
BB2 SC2
BB2 SC3
BB2 SC4
BB3 SC1
BB3 SC2
BB3 SC3
BB3 SC4
SC1 SC3
SC2 SC4
[ angles ]
BB2 BB3 SC1 2 94.00000 250
BB3 SC1 SC2 2 160.00000 200
BB3 SC1 SC4 2 140.00000 200
SC1 SC2 SC3 1 85.00000 200
SC2 SC1 SC4 1 125.00000 200
SC2 SC3 SC4 1 74.00000 200
SC3 SC4 SC1 1 98.00000 200
[ dihedrals ]
BB2 BB3 SC1 SC2 2 -116.00000 0.50000
BB2 BB3 SC1 SC4 2 98.00000 15
[ moleculetype ]
DA3 1
[ atoms ]
1 Q0 1 DA3 BB1 20 -1.0 72.0
2 SN0 1 DA3 BB2 21 0.0 45.0
3 SC2 1 DA3 BB3 22 0.0 45.0
4 TN0 1 DA3 SC1 23 0.0 45.0
5 TA2 1 DA3 SC2 24 0.0 45.0
5 TA3 1 DA3 SC3 25 0.0 45.0
6 TNa 1 DA3 SC4 26 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.30000 30000
SC2 SC4 1 0.32600 20000
[ constraints ]
SC1 SC2 1 0.22900
SC2 SC3 1 0.26600
SC3 SC4 1 0.28800
SC4 SC1 1 0.16200
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB1 SC4
BB2 SC1
BB2 SC2
BB2 SC3
BB2 SC4
BB3 SC1
BB3 SC2
BB3 SC3
BB3 SC4
SC1 SC3
SC2 SC4
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 94.00000 250
BB3 SC1 SC2 2 160.00000 200
BB3 SC1 SC4 2 140.00000 200
SC1 SC2 SC3 1 85.00000 200
SC2 SC1 SC4 1 125.00000 200
SC2 SC3 SC4 1 74.00000 200
SC3 SC4 SC1 1 98.00000 200
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -90.00000 20
BB2 BB3 SC1 SC2 2 -116.00000 0.50000
BB2 BB3 SC1 SC4 2 98.00000 15
[ moleculetype ]
DG5 1
[ atoms ]
2 SN0 1 DG5 BB2 14 0.0 45.0
3 SC2 1 DG5 BB3 15 0.0 45.0
4 TN0 1 DG5 SC1 16 0.0 45.0
5 TG2 1 DG5 SC2 17 0.0 45.0
6 TG3 1 DG5 SC3 18 0.0 45.0
7 TNa 1 DG5 SC4 19 0.0 45.0
[ bonds ]
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.30000 30000
SC2 SC4 1 0.38900 20000
[ constraints ]
SC1 SC2 1 0.29500
SC2 SC3 1 0.29500
SC3 SC4 1 0.28500
SC4 SC1 1 0.16100
[ exclusions ]
BB2 SC1
BB2 SC2
BB2 SC3
BB2 SC4
BB3 SC1
BB3 SC2
BB3 SC3
BB3 SC4
SC1 SC3
SC2 SC4
[ angles ]
BB2 BB3 SC1 2 94.50000 250
BB3 SC1 SC2 2 137.00000 300
BB3 SC1 SC4 2 130.00000 250
SC1 SC2 SC3 1 69.50000 200
SC2 SC1 SC4 1 125.00000 200
SC2 SC3 SC4 1 84.00000 200
SC3 SC4 SC1 1 94.00000 200
[ dihedrals ]
BB2 BB3 SC1 SC2 2 -117.00000 1
BB2 BB3 SC1 SC4 2 92.00000 15
[ moleculetype ]
DG3 1
[ atoms ]
1 Q0 1 DG3 BB1 13 -1.0 72.0
2 SN0 1 DG3 BB2 14 0.0 45.0
3 SC2 1 DG3 BB3 15 0.0 45.0
4 TN0 1 DG3 SC1 16 0.0 45.0
5 TG2 1 DG3 SC2 17 0.0 45.0
6 TG3 1 DG3 SC3 18 0.0 45.0
7 TNa 1 DG3 SC4 19 0.0 45.0
[ bonds ]
BB1 BB2 1 0.36000 20000
BB2 BB3 1 0.19800 80000
BB3 SC1 1 0.30000 30000
SC2 SC4 1 0.38900 20000
[ constraints ]
SC1 SC2 1 0.29500
SC2 SC3 1 0.29500
SC3 SC4 1 0.28500
SC4 SC1 1 0.16100
[ exclusions ]
BB1 BB3
BB1 SC1
BB1 SC2
BB1 SC3
BB1 SC4
BB2 SC1
BB2 SC2
BB2 SC3
BB2 SC4
BB3 SC1
BB3 SC2
BB3 SC3
BB3 SC4
SC1 SC3
SC2 SC4
[ angles ]
BB1 BB2 BB3 2 110.00000 200 {"group": "backbone"}
BB2 BB3 SC1 2 94.50000 250
BB3 SC1 SC2 2 137.00000 300
BB3 SC1 SC4 2 130.00000 250
SC1 SC2 SC3 1 69.50000 200
SC2 SC1 SC4 1 125.00000 200
SC2 SC3 SC4 1 84.00000 200
SC3 SC4 SC1 1 94.00000 200
[ dihedrals ]
BB1 BB2 BB3 SC1 2 -90.00000 20
BB2 BB3 SC1 SC2 2 -117.00000 1
BB2 BB3 SC1 SC4 2 92.00000 15
[ link ]
resname "DT|DT3|DG|DG3|DA|DA3|DC|DC3"
[ atoms ]
BB1 { }
BB2 { }
BB3 { }
+BB1 { }
[ dihedrals ]
BB1 BB2 BB3 +BB1 2 95.00000 25 {"group": "link2"}
[ edges ]
BB3 +BB1
[ link ]
[ atoms ]
BB3 { "resname": "DT|DT5|DT3|DC|DC5|DC3" }
SC1 {"resname": "DT|DT5|DT3|DC|DC5|DC3" }
+BB1 {"resname": "DT|DT5|DT3|DG|DG3|DG5|DA|DA3|DA5|DC|DC3|DC5" }
[ angles ]
SC1 BB3 +BB1 1 180.00000 30 {"group": "DC/DT extra"}
[ edges ]
BB3 +BB1
[ link ]
[ atoms ]
BB3 { "resname": "DG|DG5|DG3" }
SC1 {"resname": "DG|DG5|DG3" }
+BB1 {"resname": "DT|DT5|DT3|DG|DG3|DG5|DA|DA3|DA5|DC|DC3|DC5" }
[ angles ]
SC1 BB3 +BB1 2 157.00000 150 {"group": "DG extra"}
[ edges ]
BB3 +BB1
[ link ]
[ atoms ]
BB3 { "resname": "DA|DA5|DA3" }
SC1 {"resname": "DA|DA5|DA3" }
+BB1 {"resname": "DT|DT5|DT3|DG|DG3|DG5|DA|DA3|DA5|DC|DC3|DC5" }
[ angles ]
SC1 BB3 +BB1 2 158.00000 200 {"group": "DA extra"}
[ edges ]
BB3 +BB1
[ link ]
resname "DT|DT5|DT3|DG|DG3|DG5|DA|DA3|DA5|DC|DC3|DC5"
[ bonds ]
BB3 +BB1 1 0.35300 10000 {"group": "link"}
[ angles ]
BB2 BB3 +BB1 2 102.00000 150 {"group": "backbone"}
BB3 +BB1 +BB2 2 106.00000 75 {"group": "backbone"}
[ exclusions ]
BB2 +BB1
BB3 +BB2
[ dihedrals ]
BB2 BB3 +BB1 +BB2 1 180.00000 2 3 {"group": "link"}
BB3 +BB1 +BB2 +BB3 9 85.00000 2 2 {"group": "link", "version": "1"}
BB3 +BB1 +BB2 +BB3 9 160.00000 2 3 {"group": "link", "version": "2"}