* CHARMM27 All-Hydrogen Nucleic Acid Parameter File * Foloppe, N. and MacKerell, A.D., Jr.
* All-atom emiprical force field for nucleic acids: * 1) Parameter optimization based on small molecule and * condensed phase macromolecular target data.
* J. Computational Chemistry, Submitted * and
* MacKerell, A.D., Jr. and Banavali, N.
* All-atom emiprical force field for nucleic acids:
* 2) Application to molecular dynamics simulations of DNA * and RNA in solution
* J. Computational Chemistry, Submitted *
BONDS !
!V(bond) = Kb(b - b0)**2 !
!Kb: kcal/mole/A**2 !b0: A
!
!atom type Kb b0 !
CN7 CN7C 222.5 1.516 CN7C HN7 309.0 1.111 CN7 CN8B 222.5 1.512 CN8B ON2 320.0 1.44 CN8B ON5 428.0 1.42 CN7 ON2 310.0 1.433 CN7B ON2 310.0 1.433 CN7 ON5 428.0 1.42 CN9 NN2 400.0 1.456 CN8 NN2B 400.0 1.458 CN9 NN2B 400.0 1.458 CN7B NN2 220.0 1.456 CN7B NN2B 220.0 1.458 CN8B HN8 309.0 1.111 ON5 HN5 545.0 0.960 CN7B ON5 428.0 1.400 CN7C ON5 428.0 1.400 CN8 ON2 340.0 1.44 CN7B NR1 220.000 1.4620 NR1 CPH1 400.000 1.3800 NR1 CPH2 400.000 1.3600 NR2 CPH1 400.000 1.3800 NR2 CPH2 400.000 1.3200 CPH1 CPH1 410.000 1.3600 HR1 CPH2 340.000 1.0900 HR3 CPH1 365.000 1.0830 ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2 !
!V(Urey-Bradley) = Kub(S - S0)**2 !
!Ktheta: kcal/mole/rad**2 !Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A
!
!atom types Ktheta Theta0 Kub S0 !
HN3 CN3 NN2B 30.0 114.3 CN3T CN1 NN2U 70.0 113.5 CN1 CN3T CN3 120.0 116.7 CN3T CN3 NN2B 120.0 123.6 CN3T CN1 ON1 100.0 124.6 CN1 CN3T CN9 38.0 118.7 CN3 CN3T CN9 38.0 124.6 CN3T CN3 HN3 30.0 122.1 HN3 CN4 NN3I 35.0 116.75 HN3 CN4 NN2G 35.0 115.75 NN3I CN4 NN2G 80.0 127.5 CN5G CN5 NN3I 100.0 127.0 NN2B CN5 NN3I 140.0 128.4 CN1 NN2G CN4 125.0 129.7 CN4 NN2G HN2 40.5 117.0 CN4 NN3I CN5 90.0 108.4 CN1T NN2B CN9 70.0 116.0 CN3 NN2B CN9 70.0 122.0 CN1 NN2 CN9 70.0 115.4 CN3 NN2 CN9 70.0 120.5 CN5 NN2 CN9 70.0 125.9 CN4 NN2 CN9 70.0 127.8 CN5 NN2B CN9 70.0 125.9 CN4 NN2B CN9 70.0 126.9 CN5 NN2B CN8 70.0 125.9 CN4 NN2B CN8 70.0 126.9 NN2B CN8 CN9 70.0 113.7 CN1T NN2B CN7B 45.0 118.4 CN3 NN2B CN7B 45.0 119.6 CN1 NN2 CN7B 45.0 120.0 CN3 NN2 CN7B 45.0 115.9 CN5 NN2 CN7B 45.0 126.1 CN4 NN2 CN7B 45.0 127.6 CN5 NN2B CN7B 45.0 126.5 CN4 NN2B CN7B 45.0 126.3 ON6 CN7B NN2 110.0 108.0 ON6B CN7B NN2 110.0 112.0 CN8 CN7B NN2 110.0 113.7 CN7B CN7B NN2 110.0 111.0 CN7C CN7B NN2 110.0 111.0 ON6 CN7B NN2B 110.0 108.0 ON6B CN7B NN2B 110.0 112.0 CN8 CN7B NN2B 110.0 113.7 CN7B CN7B NN2B 110.0 111.0 CN7C CN7B NN2B 110.0 111.0 HN7 CN7B NN2 43.0 111.0 HN7 CN7B NN2B 43.0 111.0
CN3 CN1A NN1 85.0 113.0 80.0 2.46 CN3 CN1A ON1 85.0 118.5 20.0 2.43 NN1 CN1A ON1 85.0 128.5 20.0 2.17 CN3D CN2 NN1 110.0 116.4
CN3B CN3 CN1A 10.0 131.8 CN3 CN3A CN3 50.0 118.0 CN3A CN3 CN3B 40.0 118.0 CN3 CN3 CN8 53.5 108.5 CN3B CN3 CN8 53.5 108.5 CN3C CN3 CN8 43.5 128.0 CN3 CN3D CN9 40.0 124.2 CN3D CN3 HN3 30.0 122.0 CN3B CN3 HN3B 30.0 122.0 CN3A CN3 HN3B 30.0 119.0 CN3 CN3C HN3 42.0 119.0 CN3C CN3 HN3 42.0 116.0 CN3 CN3A HN3B 80.0 121.0 CN3 CN3B HN3B 80.0 120.5 CN3 CN3B NN2 120.0 122.0 CN3 CN3C NN2 60.0 122.0 CN3D CN3 NN2 100.0 124.2 CN8 CN3 HN3 30.0 116.0 HN3B CN3B NN2 80.0 117.5 HN3 CN3C NN2 42.0 119.0 CN3 CN8 CN3 125.0 108.0 CN3 CN8 HN8 55.0 110.10
CN9 CN8 HN8 34.6 110.10 22.53 2.179 HN8 CN8 NN2 33.43 110.1
HN8 CN8 ON5 45.9 108.89
CN3 CN9 HN9 33.43 110.10 22.53 2.179 CN3T CN9 HN9 33.43 110.10 22.53 2.179 CN3D CN9 HN9 33.43 110.10 22.53 2.179 CN8 CN9 HN9 34.60 110.10 22.53 2.179 HN9 CN9 NN2 33.43 110.1
HN9 CN9 NN2B 33.43 110.1 HN8 CN8 NN2B 33.43 110.1 HN9 CN9 ON2 60.0 109.5 CN1A NN1 HN1 35.0 120.0 CN3B NN2 CN3B 30.0 120.0 CN3C NN2 CN3C 20.0 114.0 CN3B NN2 CN7B 70.0 121.7 CN3C NN2 CN7B 70.0 121.7 CN3B NN2 HN2 32.0 117.4 CN3C NN2 HN2 39.0 123.0 HN1 NN5 HN1 39.0 106.0
CN9 ON2 P 20.0 120.0 35. 2.33 CN9 ON2 P2 20.0 120.0 35. 2.33 P ON2 P 15.0 140.0 -40.0 2.80 P2 ON2 P 15.0 140.0 -40.0 2.80 P2 ON2 P2 15.0 140.0 -40.0 2.80 HN4 ON4 P 30.0 115.0 40.0 2.35 HN5 ON5 CN8 57.5 106.0
HN9 CN9 HN9 35.500 108.40 5.40 1.802 CN7 ON6 CN7B 110.0 108.0
ON6 CN7B CN8 90.0 102.0 CN7B CN8 CN7 80.00 100.0
CN8 CN7 CN7 60.00 102.0 8.0 2.561 CN7 CN7 ON6 100.0 104.0
HN7 CN7 ON6 45.2 107.24 HN7 CN7B ON6 45.2 107.24 HN7 CN7 CN7 40.0 108.00
CN7B CN8 HN8 33.4 110.10 22.53 2.179 CN8 CN7B HN7 33.4 110.10 22.53 2.179 HN7 CN7 CN8 34.5 110.1 22.53 2.179 HN8 CN8 CN7 34.53 110.10 22.53 2.179 HN8 CN8 CN8 34.53 110.10 22.53 2.179 HN8 CN8 HN8 35.5 109.00 5.40 1.802 HN7 CN7 HN7 35.5 109.00 5.40 1.802 CN7 ON6B CN7B 110.0 115.0
CN7 CN7 ON6B 100.0 110.0 ON6B CN7B CN7B 90.0 106.0 CN7B CN7B CN7 110.0 96.0
CN7B CN7 CN7 60.0 100.0 8.00 2.561 HN7 CN7 ON6B 45.2 107.24
HN7 CN7B ON6B 45.2 107.24
CN7B CN7B HN7 33.4 110.10 22.53 2.179 HN7 CN7B HN7 35.5 109.00 5.40 1.802 ON6 CN7B CN7C 90.0 102.0
CN7B CN7C CN7 80.00 100.0
CN7C CN7 CN7 60.00 102.0 8.00 2.561 CN7B CN7C HN7 33.4 110.10 22.53 2.179 CN7C CN7B HN7 33.4 110.10 22.53 2.179 HN7 CN7 CN7C 34.5 110.1 22.53 2.179 HN7 CN7C CN7 34.53 110.10 22.53 2.179 HN7 CN7C HN7 35.5 109.00 5.40 1.802 ON6 CN7 CN8B 90.0 108.2
CN7 CN7 CN8B 45.0 110.0 CN7 CN8B ON2 70.0 108.4 CN7 CN7 ON2 115.0 109.7 CN7B CN7B ON2 115.0 109.7 CN7 CN7B ON2 115.0 109.7 CN8 CN7 ON2 115.0 109.7
CN8B ON2 P 20.0 120.0 35.00 2.33 CN7 ON2 P 20.0 120.0 35.00 2.33 CN7B ON2 P 20.0 120.0 35.00 2.33 HN7 CN7 CN8B 34.5 110.1 22.53 2.179 HN8 CN8B ON2 60.0 109.5
HN5 ON5 CN8B 57.5 106.0
HN8 CN8B HN8 35.5 109.0 5.40 1.802 HN8 CN8B CN7 34.53 110.1 22.53 2.179 HN7 CN7 ON2 60.0 109.5
ON2 CN7 CN7B 90.0 110.0 ON5 CN7 CN7B 90.0 110.0 ON5 CN7B CN7B 80.0 108.4 ON5 CN7B CN7 90.0 108.0 HN7 CN7B ON5 60.0 109.5 HN5 ON5 CN7B 57.5 109.0
HN7 CN7B CN7 34.53 110.10 22.53 2.179 HN7 CN7 CN7B 34.53 110.10 22.53 2.179 CN7C CN7 ON2 115.0 109.7
ON5 CN7 CN7C 75.7 110.0 ON5 CN7C CN7B 80.0 108.4 ON5 CN7C CN7 90.0 108.0 HN7 CN7C ON5 60.0 109.5 HN5 ON5 CN7C 57.5 109.0
CN8 ON2 P 20.0 120.0 35.00 2.33 ON2 P ON3 98.9 111.6
ON3 P ON3 120.0 120.0 HN8 CN8 ON2 60.0 109.5 ON5 P ON3 98.9 111.6 ON6 CN7B NR1 140.0 108.00 ON6B CN7B NR1 140.0 108.00 CN8 CN7B NR1 140.0 113.70 CN7B CN7B NR1 140.0 113.70 CN7B NR1 CPH2 130.0 127.00 CN7B NR1 CPH1 130.0 126.00 HN7 CN7B NR1 30.0 106.3 CPH2 NR1 CPH1 130.0 107.00 CPH2 NR2 CPH1 130.0 104.00 NR1 CPH1 CPH1 130.0 106.00 NR1 CPH2 NR2 130.0 112.50 NR2 CPH1 CPH1 130.0 110.00
NR1 CPH2 HR1 25.0 122.50 20.00 2.140 NR2 CPH2 HR1 25.0 125.00 20.00 2.120 HR3 CPH1 CPH1 25.0 130.00 20.00 2.200 NR1 CPH1 HR3 25.0 124.00 20.00 2.140 NR2 CPH1 HR3 25.0 120.00 20.00 2.140 HT OT HT 55.0 104.52 ! TIPS3P GEOMETRY ON6 CN7B CN7 120.0 106.25
CN7B CN7 CN8 58.35 113.6 11.16 2.561 DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) !
!Kchi: kcal/mole !n: multiplicity !delta: degrees !
!atom types Kchi n delta !
HN7 CN7 ON6B CN7B 0.195 3 0.0 HN7 CN7 CN7B CN7B 0.195 3 0.0 HN7 CN7B CN7B CN7 0.195 3 0.0 HN7 CN7B CN7B ON6B 0.195 3 0.0 HN7 CN7 CN7C CN7B 0.195 3 0.0 HN7 CN7B CN7C CN7 0.195 3 0.0 HN7 CN7C CN7B ON6 0.195 3 0.0 HN7 CN7B CN7C HN7 0.195 3 0.0 HN7 CN7 CN7C HN7 0.195 3 0.0 HN7 CN7C CN7 CN7 0.195 3 0.0 NN2 CN7B CN7B ON5 0.000 3 0.0 NN2B CN7B CN7B ON5 0.000 3 0.0 ON5 CN7B CN7B HN7 0.000 3 0.0 HN7 CN7B CN7B HN7 0.000 3 0.0 CN7 CN7 CN7B ON5 0.000 3 0.0 ON6B CN7B CN7B ON5 0.000 3 0.0 ON5 CN7B CN7 ON2 0.000 3 0.0 ON5 CN7 CN7B ON2 0.000 3 0.0 ON5 CN7B CN7 ON5 0.000 3 0.0 HN7 CN7B ON5 HN5 0.000 3 0.0 HN5 ON5 CN7B CN7B 0.000 6 180.0 HN5 ON5 CN7B CN7B 0.800 3 0.0 HN5 ON5 CN7B CN7B 0.000 2 180.0 HN5 ON5 CN7B CN7B 0.000 1 180.0 HN5 ON5 CN7B CN7 0.300 3 0.0 HN5 ON5 CN7B CN7 0.000 1 0.0 ON6 CN7B CN7C ON5 0.000 3 0.0 CN7B CN7C ON5 HN5 0.000 3 0.0 CN7 CN7C ON5 HN5 0.000 3 0.0 HN7 CN7B CN7C ON5 0.000 3 0.0 CN7 CN7 CN7C ON5 0.000 3 0.0 HN7 CN7C ON5 HN5 0.000 3 0.0 ON5 CN7C CN7 HN7 0.000 3 0.0 ON5 CN7C CN7 ON2 0.000 3 0.0 IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2 !
!Kpsi: kcal/mole/rad**2 !psi0: degrees
!note that the second column of numbers (0) is ignored !
!atom types Kpsi psi0 !
!
CN2 X X NN1 90.0 0 0.0 CN2 NN2G NN3G NN1 40.0 0 0.0 CN2 CN5 NN3A NN1 40.0 0 0.0 CN2 CN3 NN3 NN1 60.0 0 0.0 HN3 NN2G NN3I CN4 39.0 0 0.0 CN9 X X CN3T 14.0 0 0.0 HN6 CN3C CN8 CN3 15.0 0 0.0 HN3B X X CN3 15.0 0 0.0 HN3B X X CN3A 13.0 0 0.0 HN3B X X CN3B 13.0 0 0.0 HN2 CN3 CN3B NN2 50.0 0 0.0 HN1 HN1 CN1A NN1 -5.0 0 0.0 ON1 X X CN1A 40.0 0 0.0 HN3 X X CN3C 53.0 0 0.0 HN6 X X CN3C 53.0 0 0.0 HN8 CN3 CN3 CN8 18.0 0 0.0 HR1 NR1 NR2 CPH2 0.50 0 0.0 HR1 NR2 NR1 CPH2 0.50 0 0.0 HR3 CPH1 NR1 CPH1 0.50 0 0.0 HR3 CPH1 NR2 CPH1 0.50 0 0.0 HR3 NR1 CPH1 CPH1 0.50 0 0.0 HR3 NR2 CPH1 CPH1 0.50 0 0.0 NR1 CPH1 CPH2 CN7B 0.60 0 0.0 NR1 CPH2 CPH1 CN7B 0.60 0 0.0
! Wildcards used to minimize memory requirements
NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH
CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 !
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] !
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 !
HT 0.0 -0.0460 0.2245 ! TIP3P HN1 0.0 -0.0460 0.2245
HN2 0.0 -0.0460 0.2245 HN3 0.0 -0.046 1.1000 HNP 0.0 -0.03 1.3582 HN3B 0.0 -0.046 0.9000 HN3C 0.0 -0.03 1.3582 HN4 0.0 -0.0460 0.2245 HN5 0.0 -0.0460 0.2245 HN6 0.0 -0.0220 1.3200 HN7 0.0 -0.0220 1.3200 HN8 0.0 -0.0280 1.3400 HN9 0.0 -0.0240 1.3400 HR1 0.0 -0.0460 0.9000 HR3 0.0 -0.0078 1.4680 !
NN2G 0.0 -0.20 1.85 NN2U 0.0 -0.20 1.85 NN3 0.0 -0.20 1.85 NN3A 0.0 -0.20 1.85 NN3G 0.0 -0.20 1.85 NN3I 0.0 -0.20 1.85 NN4 0.0 -0.20 1.85 NN5 0.0 -0.20 1.85 NR1 0.0 -0.20 1.85 NR2 0.0 -0.20 1.85 !
ON1 0.0 -0.1200 1.70 ON1C 0.0 -0.1200 1.70 ON2 0.0 -0.1521 1.77 ON3 0.0 -0.1200 1.70 ON4 0.0 -0.1521 1.77 ON5 0.0 -0.1521 1.77 ON6 0.0 -0.1521 1.77 ON6B 0.0 -0.1521 1.77
OT 0.0 -0.1521 1.7682 ! TIP3P !
CN1 0.0 -0.10 1.9000 CN1A 0.0 -0.07 2.0000 CN1T 0.0 -0.10 1.9000 CN2 0.0 -0.10 1.9000 CN3 0.0 -0.09 1.9000 CN3A 0.0 -0.18 1.8000 CN3B 0.0 -0.18 1.8000 CN3C 0.0 -0.18 1.8000 CN3D 0.0 -0.09 1.9000 CN3T 0.0 -0.09 1.9000 CN4 0.0 -0.075 1.9000 CN5 0.0 -0.075 1.9000 CN5G 0.0 -0.075 1.9000
CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 CN7C 0.0 -0.02 2.275 0.0 -0.01 1.90 CN7D 0.0 -0.02 2.275 0.0 -0.01 1.90 CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 CPH1 0.0 -0.0500 1.8000
CPH2 0.0 -0.0500 1.8000 !
P 0.0 -0.585 2.15 P2 0.0 -0.585 2.15 !
SOD 0.0 -0.0469 1.36375 ! sodium
! D. Beglovd and B. Roux, dA=-100.8 kcal/mol MG 0.0 -0.0150 1.18500 ! Magnesium
