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Nucleic Acid Standards

Parameter files


remark  nucleic acid rna-dna parameter file

remark  ===========================

remark  Bases 18.75% Sugar  56.6% Phos  154.8% 

remark  K= scale*(kT/sigma**2), scales=Base 0.1875, Sugar 0.566, Phos 1.548

! removed references to CA, CF, CS, MG, NH3, OS (ATB 12/30/94)

! removed TIP3 water model (ATB 12/30/94)

! mapped NA->NNA, CH3E->CC3E (ATB 12/30/94)

! G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER

! H.M.BERMAN

! NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING

! STRUCTURES

! ACTA CRYST.D  (1996)   v. 52   57-64



set echo=false end



!the generic bonds were taken from param11.dna with 3*kq

bond  C5R  OH       876.000    1.4300     ! 5' end

bond  C5D  OH       876.000    1.4300     ! 5' end

bond  C3R  OH       876.000    1.4300     ! 3' end

bond  C3D  OH       876.000    1.4300     ! 3' end

bond  HHO  O2R     1350.000    0.9572     !Mod HO to HHO 05/15/96



!Phos.  - combined RNA/DNA statistics used 

!                      kq       x_eq       sigma

bond  P    O1P     1159.000    1.485      ! 0.017  Phos

bond  P    O2P     1159.000    1.485      ! 0.017  P

bond  P    O5R     3350.720    1.593      ! 0.010  P

bond  P    O3R     2326.889    1.607      ! 0.012  P 

bond  O5R  C5R     1309.000    1.440      ! 0.016  P

bond  O5R  C5D     1309.000    1.440      ! 0.016  P



!Sugars

!RNA statistics

bond  C5R  C4R     1982.674    1.510      ! 0.013  Sugar

bond  C4R  C3R     2769.190    1.524      ! 0.011  S

bond  C3R  C2R     2769.190    1.525      ! 0.011  S

bond  C2R  C1R     3350.720    1.528      ! 0.010  S

bond  O4R  C1R     2326.888    1.414      ! 0.012  S

bond  O4R  C4R     2326.888    1.453      ! 0.012  S

bond  O3R  C3R     1709.551    1.423      ! 0.014  S

bond  C2R  O2R     1982.674    1.413      ! 0.013  S



!DNA statistics

bond  C5D  C4D     5235.500    1.511      ! 0.008  Sugar

bond  C4D  C3D     3350.720    1.528      ! 0.010  S

bond  C3D  C2D     3350.720    1.518      ! 0.010  S

bond  C2D  C1D     1709.551    1.521      ! 0.014  S

bond  O4D  C1D     1982.674    1.420      ! 0.013  S

bond  O4D  C4D     2769.190    1.446      ! 0.011  S

bond  O3R  C3D     1982.674    1.431      ! 0.013  S



!Bases

!base specific bonds taken from param11.dna , 3*kq

bond  O2U  HHO     1350.000    0.957      ! UR!Mod HO to HHO 05/15/96

bond  HN   NNA     1416.000    1.010      ! URA

bond  HN   N1T     1416.000    1.010      ! Infer.

bond  HN   N1C     1416.000    1.010

bond  HN   N9G     1416.000    1.010

bond  HN   N9A     1416.000    1.010

bond  HN   N3U     1416.000    1.010

bond  H2   N2      1416.000    1.010

bond  H2   N4C     1416.000    1.010

bond  H2   N2G     1416.000    1.010

bond  H2   N6A     1416.000    1.010



bond  HHO  OH      1350.000    0.960      ! PARAM7 (IR stretch 3400 cm-1)!Mod HO to HHO 05/15/96



!Base sugar joint bonds (scale from sugar)

!                      kq       x_eq       sigma

bond  C1R  N1T     1709.551    1.473      ! 0.014  Base

bond  C1R  N1U     4136.691    1.469      ! 0.009  B

bond  C1R  N1C     2326.889    1.470      ! 0.012  B

bond  C1R  N9G     4136.691    1.459      ! 0.009  B

bond  C1R  N9A     3350.720    1.462      ! 0.010  B



bond  C1D  N1T     1709.551    1.473      ! 0.014  B   !DNA

bond  C1D  N1U     4136.691    1.469      ! 0.009  B

bond  C1D  N1C     2326.889    1.470      ! 0.012  B

bond  C1D  N9G     4136.691    1.459      ! 0.009  B

bond  C1D  N9A     3350.720    1.462      ! 0.010  B



!cytosine                      kq          x_eq  sigma

bond       C2C    ON          1370.370    1.240 !0.009  B

bond       C4C    N4C         1370.370    1.335 !0.009  B

bond       N1C    C2C         1110.000    1.397 !0.010  B

bond       N1C    C6C         3083.333    1.367 !0.006  B

bond       C2C    NC          1734.375    1.353 !0.008  B

bond       NC     C4C         2265.306    1.335 !0.007  B

bond       C4C    C5C         1734.375    1.425 !0.008  B

bond       C5C    C6C         1734.375    1.339 !0.008  B



!thymine

bond       N1T    C2T         1734.375    1.376 !0.008  B

bond       C2T    NNA         1734.375    1.373 !0.008  B

bond       NNA    C4T         1734.375    1.382 !0.008  B

bond       C4T    C5T         1370.370    1.445 !0.009  B

bond       C5T    C6T         2265.306    1.339 !0.007  B

bond       C6T    N1T         2265.306    1.378 !0.007  B

bond       C2T    ON          1734.375    1.220 !0.008  B

bond       C4T    ON          1370.370    1.228 !0.009  B

bond       C5T    CC3E        3083.333    1.496 !0.006  B



!adenine

bond       NC     C2A         1370.370    1.339 !0.009  B

bond       C2A    N3A         1370.370    1.331 !0.009  B

bond       N3A    C4A         3083.333    1.344 !0.006  B

bond       C4A    C5A         2265.306    1.383 !0.007  B

bond       C5A    C6A         1370.370    1.406 !0.009  B

bond       C6A    NC          2265.306    1.351 !0.007  B

bond       C5A    N7A         3083.333    1.388 !0.006  B

bond       N7A    C8A         2265.306    1.311 !0.007  B

bond       C8A    N9A         1734.375    1.373 !0.008  B

bond       N9A    C4A         3083.333    1.374 !0.006  B

bond       C6A    N6A         1734.375    1.335 !0.008  B



!guanine

bond       NNA    C2G         1734.375    1.373 !0.008  B

bond       C2G    N3G         1734.375    1.323 !0.008  B

bond       N3G    C4G         2265.306    1.350 !0.007  B 

bond       C4G    C5G         2265.306    1.379 !0.007  B

bond       C5G    C6G         1110.000    1.419 !0.010  B 

bond       C6G    NNA         2265.306    1.391 !0.007  B 

bond       C5G    N7G         3083.333    1.388 !0.006  B 

bond       N7G    C8G         3083.333    1.305 !0.006  B 

bond       C8G    N9G         2265.306    1.374 !0.007  B 

bond       N9G    C4G         1734.375    1.375 !0.008  B

bond       C2G    N2G         1110.000    1.341 !0.010  B

bond       C6G    O6G         1370.370    1.237 !0.009  B



!uracil

bond       C2U    ON          1370.370    1.219 !0.009  B

bond       C4U    ON          1734.375    1.232 !0.008  B

bond       N1U    C2U         1370.370    1.381 !0.009  B

bond       N1U    C6U         1370.370    1.375 !0.009  B

bond       C2U    N3U         2265.306    1.373 !0.007  B

bond       N3U    C4U         1370.370    1.380 !0.009  B

bond       C4U    C5U         1370.370    1.431 !0.009  B

bond       C5U    C6U         1370.370    1.337 !0.009  B



!Phos.

!the angles were taken from param11.dna with 3*kq

angle      HHO    OH     C5R        139.500  107.300 !Mod HO to HHO 05/15/96

angle      HHO    O5R    C5R        139.500  107.300 !Mod HO to HHO 05/15/96

angle      HHO    OH     C5D        139.500  107.300 !Mod HO to HHO 05/15/96

angle      HHO    O5R    C5D        139.500  107.300 !Mod HO to HHO 05/15/96

angle      HHO    O3R    P          139.500  107.300 !Mod HO to HHO 05/15/96

angle      HHO    O2R    C2R        139.500  107.300 !Mod HO to HHO 05/15/96

angle      OH     P      O3R        144.300  102.600 !

angle      OH     P      O5R        144.300  102.600 !

angle      OH     P      O1P        296.700  108.230 !

angle      OH     P      O2P        296.700  108.230 !

angle      OH     C5R    C4R        210.000  112.000 ! 

angle      OH     C5D    C4D        210.000  112.000 ! 

angle      C4D    C3D    OH         139.500  111.000 ! 

angle      C4R    C3R    OH         139.500  111.000 ! 

angle      C2D    C3D    OH         139.500  111.000 ! 

angle      C2R    C3R    OH         139.500  111.000 ! 

angle      C3R    OH     HHO        139.500  107.300 !!Mod HO to HHO 05/15/96

angle      C3D    OH     HHO        139.500  107.300 !!Mod HO to HHO 05/15/96



!Phos.  - combined RNA/DNA statistics used 

!                                      kq      x_eq  sigma

angle      O1P    P      O2P       1337.074  119.600 !1.5 P 

angle      O5R    P      O1P        357.719  108.100 !2.9 P

angle      O5R    P      O2P        412.677  108.300 !2.7 P 

angle      O3R    P      O5R        833.356  104.000 !1.9 P 

angle      O2P    P      O3R        293.791  108.300 !3.2 P

angle      O1P    P      O3R        293.791  107.400 !3.2 P 



angle      O5R    C5R    C4R       1534.906  110.200 !1.4 P

angle      P      O5R    C5R       1175.163  120.900 !1.6 P

angle      P      O3R    C3R       2089.178  119.700 !1.2 P



angle      O5R    C5D    C4D       1534.906  110.200 !1.4 P !DNA

angle      P      O5R    C5D       1175.163  120.900 !1.6 P

angle      P      O3R    C3D       2089.178  119.700 !1.2 P



!Sugars

!RNA statistics

!                                      kq      x_eq  sigma

angle      O4R    C4R    C3R        561.212  105.500 !1.4 S

angle      C5R    C4R    C3R        488.878  115.500 !1.5 S

angle      C5R    C4R    O4R        561.212  109.200 !1.4 S

angle      C1R    O4R    C4R       1357.996  109.600 !0.9 S

angle      C4R    C3R    C2R       1099.976  102.700 !1.0 S

angle      C3R    C2R    C1R       1357.996  101.500 !0.9 S

angle      O4R    C1R    C2R        561.212  106.400 !1.4 S

angle      N1T    C1R    C2R        429.678  113.400 !1.6 S

angle      N1C    C1R    C2R        429.678  113.400 !1.6 S

angle      N1U    C1R    C2R        429.678  113.400 !1.6 S

angle      N9G    C1R    C2R        429.678  113.400 !1.6 S

angle      N9A    C1R    C2R        429.678  113.400 !1.6 S

angle      O4R    C1R    N1T       1099.976  108.200 !1.0 S

angle      O4R    C1R    N1C       1099.976  108.200 !1.0 S

angle      O4R    C1R    N1U       1099.976  108.200 !1.0 S

angle      O4R    C1R    N9A       1099.976  108.200 !1.0 S

angle      O4R    C1R    N9G       1099.976  108.200 !1.0 S

angle      C1R    C2R    O2R        334.000  110.600 !3.0 S scale from phos.

angle      C3R    C2R    O2R        357.719  113.300 !2.9 S scale from phos.

angle      C4R    C3R    O3R        445.032  110.600 !2.6 S scale from phos.

angle      C2R    C3R    O3R        383.726  111.000 !2.8 S scale from phos.



!DNA statistics

angle      O4D    C4D    C3D       1099.976  105.600 !1.0 S

angle      C5D    C4D    C3D        488.878  114.700 !1.5 S

angle      C5D    C4D    O4D        429.678  109.400 !1.6 S

angle      C1D    O4D    C4D        560.874  109.700 !1.4 S

angle      C4D    C3D    C2D       1099.976  103.200 !1.0 S

angle      C3D    C2D    C1D        560.874  102.700 !1.4 S

angle      O4D    C1D    C2D        909.071  106.100 !1.1 S

angle      N1T    C1D    C2D        429.878  114.200 !1.6 S

angle      N1C    C1D    C2D        429.878  114.200 !1.6 S

angle      N1U    C1D    C2D        429.878  114.200 !1.6 S

angle      N9G    C1D    C2D        429.878  114.200 !1.6 S

angle      N9A    C1D    C2D        429.878  114.200 !1.6 S

angle      O4D    C1D    N1T       1718.713  107.800 !0.8 S

angle      O4D    C1D    N1C       1718.713  107.800 !0.8 S

angle      O4D    C1D    N1U       1718.713  107.800 !0.8 S

angle      O4D    C1D    N9A       1718.713  107.800 !0.8 S

angle      O4D    C1D    N9G       1718.713  107.800 !0.8 S

angle      C4D    C3D    O3R        621.574  110.300 !2.2 S scale from phos.

angle      C2D    C3D    O3R        412.677  110.600 !2.7 S scale from phos.



!Bases

!cytosine                            kq       x_eq   sigma

angle      C6C    N1C    C2C       2277.447  120.300 !0.40 B

angle      N1C    C2C    NC         743.656  119.200 !0.70 B

angle      C2C    NC     C4C       1457.566  119.900 !0.50 B

angle      NC     C4C    C5C       2277.447  121.900 !0.40 B

angle      C4C    C5C    C6C       1457.566  117.400 !0.50 B

angle      C5C    C6C    N1C       1457.566  121.000 !0.50 B

angle      N1C    C2C    ON        1012.199  118.900 !0.60 B

angle      NC     C2C    ON         743.656  121.900 !0.70 B

angle      NC     C4C    N4C        743.656  118.000 !0.70 B

angle      C5C    C4C    N4C        743.656  120.200 !0.70 B

angle      C6C    N1C    C1R        763.873  120.800 !1.20 B scale from sugar

angle      C2C    N1C    C1R        909.071  118.800 !1.10 B scale from sugar

angle      C6C    N1C    C1D        763.873  120.800 !1.20 B !DNA

angle      C2C    N1C    C1D        909.071  118.800 !1.10 B



angle      C4C    N4C    H2         105.000  120.000 !from param11.dna, 3*keq 

angle      H2     N4C    H2         105.000  120.000 



!thymine                            kq        x_eq    sigma

angle      C6T    N1T    C2T       1457.566  121.300 !0.50 B

angle      N1T    C2T    NNA       1012.199  114.600 !0.60 B

angle      C2T    NNA    C4T       1012.199  127.200 !0.60 B

angle      NNA    C4T    C5T       1012.199  115.200 !0.60 B

angle      C4T    C5T    C6T       1012.199  118.000 !0.60 B

angle      C5T    C6T    N1T       1012.199  123.700 !0.60 B

angle      N1T    C2T    ON         569.362  123.100 !0.80 B

angle      NNA    C2T    ON        1012.199  122.300 !0.60 B

angle      NNA    C4T    ON        1012.199  119.900 !0.60 B

angle      C5T    C4T    ON         743.656  124.900 !0.70 B

angle      C4T    C5T    CC3E      1012.199  119.000 !0.60 B

angle      C6T    C5T    CC3E      1012.199  122.900 !0.60 B

angle      C6T    N1T    C1R        488.878  120.400 !1.50 B scale from sugar

angle      C2T    N1T    C1R        429.678  118.200 !1.60 B scale from sugar

angle      C6T    N1T    C1D        488.878  120.400 !1.50 B !DNA

angle      C2T    N1T    C1D        429.678  118.200 !1.60 B



angle      C2T    NNA    HN         105.000  116.500  !from param11.dna, 3*keq 

angle      C4T    NNA    HN         105.000  116.500  



!adenine                            kq        x_eq    sigma

angle      C6A    NC     C2A       1012.199  118.600 !0.60 B

angle      NC     C2A    N3A       1457.566  129.300 !0.50 B

angle      C2A    N3A    C4A       1457.566  110.600 !0.50 B

angle      N3A    C4A    C5A        743.656  126.800 !0.70 B

angle      C4A    C5A    C6A       1457.566  117.000 !0.50 B

angle      C5A    C6A    NC        1457.566  117.700 !0.50 B

angle      C4A    C5A    N7A       1457.566  110.700 !0.50 B

angle      C5A    N7A    C8A       1457.566  103.900 !0.50 B

angle      N7A    C8A    N9A       1457.566  113.800 !0.50 B

angle      C8A    N9A    C4A       2277.447  105.800 !0.40 B

angle      N9A    C4A    C5A       2277.447  105.800 !0.40 B

angle      N3A    C4A    N9A        569.362  127.400 !0.80 B

angle      C6A    C5A    N7A        743.656  132.300 !0.70 B

angle      NC     C6A    N6A       1012.199  118.600 !0.60 B

angle      C5A    C6A    N6A        569.362  123.700 !0.80 B

angle      C8A    N9A    C1R        339.499  127.700 !1.80 B scale from sugar

angle      C4A    N9A    C1R        339.499  126.300 !1.80 B scale from sugar

angle      C8A    N9A    C1D        339.499  127.700 !1.80 B !DNA

angle      C4A    N9A    C1D        339.499  126.300 !1.80 B



angle      C6A    N6A    H2         105.000  120.000  !from param11.dna, 3*keq 

angle      H2     N6A    H2         105.000  120.000



!guanine                             kq        x_eq    sigma

angle      C6G    NNA    C2G       1012.199  125.100 !0.60 B

angle      NNA    C2G    N3G       1012.199  123.900 !0.60 B

angle      C2G    N3G    C4G       1457.566  111.900 !0.50 B

angle      N3G    C4G    C5G       1457.566  128.600 !0.50 B

angle      C4G    C5G    C6G       1012.199  118.800 !0.60 B

angle      C5G    C6G    NNA       1457.566  111.500 !0.50 B

angle      C4G    C5G    N7G       2277.447  110.800 !0.40 B

angle      C5G    N7G    C8G       1457.566  104.300 !0.50 B

angle      N7G    C8G    N9G       1457.566  113.100 !0.50 B

angle      C8G    N9G    C4G       2277.447  106.400 !0.40 B

angle      N9G    C4G    C5G       2277.447  105.400 !0.40 B

angle      N3G    C4G    N9G       1012.199  126.000 !0.60 B

angle      C6G    C5G    N7G       1012.199  130.400 !0.60 B

angle      NNA    C2G    N2G        449.866  116.20  !0.90 B

angle      N3G    C2G    N2G        743.656  119.900 !0.70 B

angle      NNA    C6G    O6G       1012.199  119.900 !0.60 B

angle      C5G    C6G    O6G       1012.199  128.600 !0.60 B

angle      C8G    N9G    C1R        650.874  127.000 !1.30 B scale from sugar

angle      C4G    N9G    C1R        650.874  126.500 !1.30 B scale from sugar

angle      C8G    N9G    C1D        650.874  127.000 !1.30 B !DNA

angle      C4G    N9G    C1D        650.874  126.500 !1.30 B



angle      C2G    N2G    H2         105.000  120.000  !from param11.dna, 3*keq 

angle      H2     N2G    H2         105.000  120.000

angle      C2G    NNA    HN         105.000  119.300

angle      C6G    NNA    HN         105.000  119.300



!uracile                            kq        x_eq    sigma

angle      C6U    N1U    C2U       1012.199  121.000 !0.60 B

angle      N1U    C2U    N3U       1012.199  114.900 !0.60 B

angle      C2U    N3U    C4U       1012.199  127.000 !0.60 B

angle      N3U    C4U    C5U       1012.199  114.600 !0.60 B

angle      C4U    C5U    C6U       1012.199  119.700 !0.60 B

angle      C5U    C6U    N1U       1457.566  122.700 !0.50 B

angle      N1U    C2U    ON         743.656  122.800 !0.70 B

angle      N3U    C2U    ON         743.656  122.200 !0.70 B

angle      N3U    C4U    ON         743.656  119.400 !0.70 B

angle      C5U    C4U    ON        1012.199  125.900 !0.60 B

angle      C6U    N1U    C1R        561.212  121.200 !1.40 B

angle      C2U    N1U    C1R        763.872  117.700 !1.20 B

angle      C6U    N1U    C1D        561.212  121.200 !1.40 B !DNA

angle      C2U    N1U    C1D        763.872  117.700 !1.20 B



angle      C4U    ON     HHO        105.000  120.000 !from param11.dna, 3*keq !Mod HO to HHO 05/15/96

angle      C2U    N3U    HN         105.000  116.500 

angle      C4U    N3U    HN         105.000  116.500  



!Dihedrals from param11.dna (included for terminal residues)



dihedral    X    C2R  C3R  X      4.50 3    0.000

dihedral    X    C4R  C3R  X      4.50 3    0.000

dihedral    X    C2R  C1R  X      4.50 3    0.000

dihedral    X    C5R  O5R  X      1.50 3    0.000

dihedral    X    C3R  O3R  X      1.50 3    0.000

dihedral    X    C3R  OH   X      1.50 3    0.000

dihedral    X    C5R  OH   X      1.50 3    0.000

dihedral    X    C2R  O2R  X      1.50 3    0.000

dihedral    X    O5R  P    X      2.25 3    0.000

dihedral    X    OH   P    X      2.25 3    0.000

dihedral    OH   C5R  C4R  O4R    4.50 3    0.000

dihedral    OH   C5R  C4R  C3R    4.50 3    0.000 ! gamma

dihedral    C3R  O3R  P    OH     2.25 3    0.000 ! added by infer

dihedral    C3R  O3R  P    OH     2.25 2    0.000 ! ATB, 7-SEP-84

dihedral    C5R  O5R  P    OH     2.25 3    0.000 ! added by infer

dihedral    C5R  O5R  P    OH     2.25 2    0.000 ! ATB, 7-SEP-84



dihedral    X    C2D  C3D  X      4.50 3    0.000

dihedral    X    C4D  C3D  X      4.50 3    0.000  !DNA

dihedral    X    C2D  C1D  X      4.50 3    0.000

dihedral    X    C5D  O5R  X      1.50 3    0.000

dihedral    X    C3D  O3R  X      1.50 3    0.000

dihedral    X    C3D  OH   X      1.50 3    0.000

dihedral    X    C5D  OH   X      1.50 3    0.000

dihedral    OH   C5D  C4D  O4D    4.50 3    0.000

dihedral    OH   C5D  C4D  C3D    4.50 3    0.000

dihedral    C3D  O3R  P    OH     2.25 3    0.000

dihedral    C3D  O3R  P    OH     2.25 2    0.000

dihedral    C5D  O5R  P    OH     2.25 3    0.000

dihedral    C5D  O5R  P    OH     2.25 2    0.000



!Base hydrogen dihedrals taken from param11.dna

DIHEdral    X    C2G  N2G  X     18.0  2  180.000

DIHEdral    X    C6A  N6A  X     18.0  2  180.000

DIHEdral    X    C6A  N4C  X     18.00 2  180.000

DIHEdral    X    C4C  N4C  X     18.00 2  180.000



!Dihedrals to keep the two purine rings parallel:

!guanine

DIHEdral    C8G  C4G  C5G  NNA  200.0  2  180.000

DIHEdral    C8G  C5G  C4G  C2G  200.0  2  180.000

DIHEdral    N3G  C4G  C5G  N7G  100.0  2  180.000

DIHEdral    C6G  C5G  C4G  N9G  100.0  2  180.000

!adenine

DIHEdral    C8A  C4A  C5A  N9A  200.0  2  180.000 ! WYE AND PATCHED RESIDUES

DIHEdral    C8A  C5A  C4A  C2A  200.0  2  180.000

DIHEdral    C8A  C4A  C5A  NC   200.0  2  180.000 

DIHEdral    N3A  C4A  C5A  N7A  100.0  2  180.000

DIHEdral    C6A  C5A  C4A  N9A  100.0  2  180.000



!Phos.  - periodical potentials from combined RNA/DNA statistics

!                                 kq       x_eq       (sigma in parenthesis)

dihedral    O3R  P    O5R  C5R    1.41 3    6.0   ! alpha !P (20.3)

dihedral    P    O5R  C5R  C4R    3.45 0  183.5   ! beta  !P (13.0)

dihedral    O5R  C5R  C4R  C3R   12.24 3   18.3   ! gamma !S (6.9)

dihedral    O5R  C5R  C4R  O4R   24.28 3   14.1   !       !S (4.9)

dihedral    C4R  C3R  O3R  P      7.88 0  214.0   ! eps   !P (8.6)

dihedral    C3R  O3R  P    O5R    1.75 3    0.3   ! zeta  !P (18.3)



dihedral    O3R  P    O5R  C5D    1.41 3    6.0 !DNA

dihedral    P    O5R  C5D  C4D    3.45 0  183.5

dihedral    O5R  C5D  C4D  C3D   12.24 3   18.3

dihedral    O5R  C5D  C4D  O4D   24.28 3   14.1

dihedral    C4D  C3D  O3R  P      7.88 0  214.0

dihedral    C3D  O3R  P    O5R    1.75 3    0.3



!Phos.  - discrete values from combined RNA/DNA statistics

!                                 kq       x_eq       (sigma in parenthesis)

!dihedral    O3R  P    O5R  C5R    6.07 0  285.3   ! (9.8)  alpha1 !P

!dihedral    O3R  P    O5R  C5R    3.98 0   81.0   ! (12.1) alpha2;alpha3=180.

!dihedral    P    O5R  C5R  C4R    3.44 0  183.5   ! (13.0) beta   !P

!dihedral    O5R  C5R  C4R  C3R   17.94 0   52.5   ! (5.7)  gamma1 !S

!dihedral    O5R  C5R  C4R  C3R   14.23 0  179.4   ! (6.4)  gamma2 !S

!dihedral    O5R  C5R  C4R  C3R    3.85 0  292.9   ! (12.3) gamma3 !S

!dihedral    C4R  C3R  O3R  P      7.88 0  214.0   ! (8.6)  eps    !P

!dihedral    C3R  O3R  P    O5R   25.30 0  289.2   ! (4.8)  zeta1  !P 

!dihedral    C3R  O3R  P    O5R    2.85 0   80.7   ! (14.3) zeta2;zeta3=180.



!Sugars

! c3'-endo conformation as the default for for RNA, c2'-endo for DNA,

!RNA statistics, C3'-endo

dihedral    C5R  C4R  C3R  O3R  30.12 0   81.0   ! delta ! c3'-endo S (4.4)

dihedral    O4R  C4R  C3R  O3R  33.10 0  201.8   !  4.2  ! c3'-endo S  

dihedral    O4R  C1R  C2R  C3R  24.28 0  335.4   !  4.9  ! c3'-endo S

dihedral    C1R  C2R  C3R  C4R  74.36 0   35.9   !  2.8  ! c3'-endo S

dihedral    C2R  C3R  C4R  O4R  60.67 0  324.7   !  3.1  ! c3'-endo S

dihedral    C3R  C4R  O4R  C1R  22.42 0   20.5   !  5.1  ! c3'-endo S

dihedral    C4R  O4R  C1R  C2R  15.67 0    2.8   !  6.1  ! c3'-endo S

dihedral    C5R  C4R  C3R  C2R  60.67 0  204.0   !  3.1  ! c3'-endo S

dihedral    O3R  C3R  C2R  O2R  28.79 0   44.3   !  4.5  ! c3'-endo S   

dihedral    C4R  O4R  C1R  N1T  13.80 0  241.4   !  6.5  ! c3'-endo S

dihedral    C4R  O4R  C1R  N1C  13.80 0  241.4   !  6.5  ! c3'-endo S

dihedral    C4R  O4R  C1R  N1U  13.80 0  241.4   !  6.5  ! c3'-endo S

dihedral    C4R  O4R  C1R  N9G  13.80 0  241.4   !  6.5  ! c3'-endo S

dihedral    C4R  O4R  C1R  N9A  13.80 0  241.4   !  6.5  ! c3'-endo S



!RNA c3'-endo sugar base joint torsions  (combined RNA/DNA statistics used)

dihedral    O4R  C1R  N1T  C2T  13.38 0  195.7   !  6.6  ! c3'-endo S

dihedral    O4R  C1R  N1C  C2C  13.38 0  195.7   !  6.6  ! c3'-endo S

dihedral    O4R  C1R  N1U  C2U  13.38 0  195.7   !  6.6  ! c3'-endo S

dihedral    O4R  C1R  N9A  C4A   2.97 0  193.3   ! 14.0  ! c3'-endo S

dihedral    O4R  C1R  N9G  C4G   2.97 0  193.3   ! 14.0  ! c3'-endo S



!DNA statistics (c2'-endo)

dihedral    C5D  C4D  C3D  O3R   36.44 0  145.2   ! delta ! c2'-endo S (4.0)

dihedral    O4D  C1D  C2D  C3D   24.28 0   32.8   !  4.9  ! c2'-endo S 

dihedral    O4D  C4D  C3D  O3R   31.53 0  265.8   !  4.3  ! c2'-endo S 

dihedral    C1D  C2D  C3D  C4D   44.99 0  326.9   !  3.6  ! c2'-endo S

dihedral    C2D  C3D  C4D  O4D   28.79 0   22.6   !  4.5  ! c2'-endo S

dihedral    C3D  C4D  O4D  C1D   15.67 0  357.7   !  6.1  ! c2'-endo S

dihedral    C4D  O4D  C1D  C2D   14.69 0  340.7   !  6.3  ! c2'-endo S

dihedral    C5D  C4D  C3D  C2D   34.68 0  262.0   !  4.1  ! c2'-endo S

dihedral    C4D  O4D  C1D  N1T   12.99 0  217.7   !  6.7  ! c2'-endo S

dihedral    C4D  O4D  C1D  N1C   12.99 0  217.7   !  6.7  ! c2'-endo S

dihedral    C4D  O4D  C1D  N1U   12.99 0  217.7   !  6.7  ! c2'-endo S

dihedral    C4D  O4D  C1D  N9G   12.99 0  217.7   !  6.7  ! c2'-endo S

dihedral    C4D  O4D  C1D  N9A   12.99 0  217.7   !  6.7  ! c2'-endo S



!DNA c2'-endo sugar base joint torsions  (combined RNA/DNA statistics used)

dihedral    O4D  C1D  N1T  C2T    1.72 0  229.8   ! 18.4  ! c2'-endo S   

dihedral    O4D  C1D  N1C  C2C    1.72 0  229.8   ! 18.4  ! c2'-endo S   

dihedral    O4D  C1D  N1U  C2U    1.72 0  229.8   ! 18.4  ! c2'-endo S   

dihedral    O4D  C1D  N9A  C4A    1.00 0  237.0   ! 24.3  ! c2'-endo S   

dihedral    O4D  C1D  N9G  C4G    1.00 0  237.0   ! 24.3  ! c2'-endo S   



!---------------------------------------------------------------------------

!In the case of c3'-endo conformation, the following dihedrals are provided

!to overwrite the c2'-endo dihedrals



!RNA statistics (c2'-endo)

!dihedral    C5R  C4R  C3R  O3R   24.28 0  147.3   ! delta ! c2'-endo S (4.9)

!dihedral    O4R  C1R  C2R  C3R   50.43 0   35.2   !  3.4  ! c2'-endo S 

!dihedral    O4R  C4R  C3R  O3R   20.75 0  268.1   !  5.3  ! c2'-endo S 

!dihedral    C1R  C2R  C3R  C4R   74.36 0  324.6   !  2.8  ! c2'-endo S

!dihedral    C2R  C3R  C4R  O4R   29.72 0   24.2   !  4.4  ! c2'-endo S

!dihedral    C3R  C4R  O4R  C1R   17.94 0  357.7   !  5.7  ! c2'-endo S

!dihedral    C4R  O4R  C1R  C2R   21.56 0  339.2   !  5.2  ! c2'-endo S

!dihedral    C5R  C4R  C3R  C2R   34.68 0  263.4   !  4.1  ! c2'-endo S

!dihedral    O3R  C3R  C2R  O2R   33.05 0  319.7   !  4.2  ! c2'-endo S   

!dihedral    C4R  O4R  C1R  N1T   19.27 0  216.6   !  5.5  ! c2'-endo S

!dihedral    C4R  O4R  C1R  N1C   19.27 0  216.6   !  5.5  ! c2'-endo S

!dihedral    C4R  O4R  C1R  N1U   19.27 0  216.6   !  5.5  ! c2'-endo S

!dihedral    C4R  O4R  C1R  N9G   19.27 0  216.6   !  5.5  ! c2'-endo S

!dihedral    C4R  O4R  C1R  N9A   19.27 0  216.6   !  5.5  ! c2'-endo S



!RNA c2'-endo sugar base joint torsions  (combined RNA/DNA statistics used) 

!dihedral    O4R  C1R  N1T  C2T    1.72 0  229.8   ! 18.4  ! c2'-endo S   

!dihedral    O4R  C1R  N1C  C2C    1.72 0  229.8   ! 18.4  ! c2'-endo S   

!dihedral    O4R  C1R  N1U  C2U    1.72 0  229.8   ! 18.4  ! c2'-endo S   

!dihedral    O4R  C1R  N9A  C4A    1.00 0  237.0   ! 24.3  ! c2'-endo S   

!dihedral    O4R  C1R  N9G  C4G    1.00 0  237.0   ! 24.3  ! c2'-endo S   



!DNA statistics, c3'-endo (insuficient data, RNA values used)

!dihedral    C5D  C4D  C3D  O3R  30.12 0   81.1   ! delta ! c3'-endo S (4.4)

!dihedral    O4D  C4D  C3D  O3R  33.10 0  201.8   !  4.2  ! c3'-endo S  

!dihedral    O4D  C1D  C2D  C3D  24.28 0  335.4   !  4.9  ! c3'-endo S

!dihedral    C1D  C2D  C3D  C4D  74.36 0   35.9   !  2.8  ! c3'-endo S

!dihedral    C2D  C3D  C4D  O4D  60.67 0  324.7   !  3.1  ! c3'-endo S

!dihedral    C3D  C4D  O4D  C1D  22.42 0   20.5   !  5.1  ! c3'-endo S

!dihedral    C4D  O4D  C1D  C2D  15.67 0    2.8   !  6.1  ! c3'-endo S

!dihedral    C5D  C4D  C3D  C2D  60.67 0  204.0   !  3.1  ! c3'-endo S

!dihedral    C4D  O4D  C1D  N1T  13.80 0  241.4   !  6.5  ! c3'-endo S

!dihedral    C4D  O4D  C1D  N1C  13.80 0  241.4   !  6.5  ! c3'-endo S

!dihedral    C4D  O4D  C1D  N1U  13.80 0  241.4   !  6.5  ! c3'-endo S

!dihedral    C4D  O4D  C1D  N9G  13.80 0  241.4   !  6.5  ! c3'-endo S

!dihedral    C4D  O4D  C1D  N9A  13.80 0  241.4   !  6.5  ! c3'-endo S



!DNA c3'-endo sugar base joint torsions  (combined RNA/DNA statistics used)

!dihedral    O4D  C1D  N1T  C2T  13.38 0  195.7   !  6.6  ! c3'-endo S

!dihedral    O4D  C1D  N1C  C2C  13.38 0  195.7   !  6.6  ! c3'-endo S

!dihedral    O4D  C1D  N1U  C2U  13.38 0  195.7   !  6.6  ! c3'-endo S

!dihedral    O4D  C1D  N9A  C4A   2.97 0  193.3   ! 14.0  ! c3'-endo S

!dihedral    O4D  C1D  N9G  C4G   2.97 0  193.3   ! 14.0  ! c3'-endo S

!---------------------------------------------------------------------------

!---------------------------------------------------------------------------



!Impropers taken from param11.dna , 3*kq

improper    C5R  X    X    C2R   94.5  0   35.260

improper    C5R  X    X    C1R   94.5  0   35.260

improper    OH   X    X    C3R   94.5  0   35.260

improper    OH   X    X    C4R   94.5  0   35.260

improper    OH   X    X    C1R   94.5  0   35.260

improper    O3R  X    X    C3R   94.5  0   35.260

improper    O5R  X    X    C1R   94.5  0   35.260

improper    O2R  X    X    C2R   94.5  0   35.260

improper    C4R  O5R  C1R  N1T   94.5  0   35.260

improper    C4R  O5R  C1R  N1C   94.5  0   35.260

improper    C4R  O5R  C1R  N9G   94.5  0   35.260

improper    C4R  O5R  C1R  N9A   94.5  0   35.260

improper    C5R  O4R  C3R  C4R   94.5  0   35.260  

improper    N1T  C2R  O4R  C1R   94.5  0   35.260  

improper    N1C  C2R  O4R  C1R   94.5  0   35.260

improper    N9A  C2R  O4R  C1R   94.5  0   35.260  

improper    N9G  C2R  O4R  C1R   94.5  0   35.260  

improper    C4R  O5R  C1R  N1U   94.5  0   35.260

improper    N1U  C2R  O4R  C1R   94.5  0   35.260  



improper    C5D  X    X    C2D   94.5  0   35.260  !DNA

improper    C5D  X    X    C1D   94.5  0   35.260

improper    OH   X    X    C3D   94.5  0   35.260

improper    OH   X    X    C4D   94.5  0   35.260

improper    OH   X    X    C1D   94.5  0   35.260

improper    O3R  X    X    C3D   94.5  0   35.260

improper    O5R  X    X    C1D   94.5  0   35.260

improper    C4D  O5R  C1D  N1T   94.5  0   35.260

improper    C4D  O5R  C1D  N1C   94.5  0   35.260

improper    C4D  O5R  C1D  N9G   94.5  0   35.260

improper    C4D  O5R  C1D  N9A   94.5  0   35.260

improper    C5D  O4D  C3D  C4D   94.5  0   35.260  

improper    N1T  C2D  O4D  C1D   94.5  0   35.260  

improper    N1C  C2D  O4D  C1D   94.5  0   35.260

improper    N9A  C2D  O4D  C1D   94.5  0   35.260  

improper    N9G  C2D  O4D  C1D   94.5  0   35.260  

improper    C4D  O5R  C1D  N1U   94.5  0   35.260

improper    N1U  C2D  O4D  C1D   94.5  0   35.260  



!the following impropers were taken from param11x.dna

!the higher kq was used to enforce the ring planarity 

!cytosine

IMPRoper    C4C  X    X    ON  2400.0  0    0.000

IMPRoper    C4C  X    X    N1C  250.0  0    0.000

IMPRoper    C6C  X    X    NC   250.0  0    0.000

IMPRoper    C4C  X    X    N2  2400.0  0    0.000

IMPRoper    C2C  X    X    ON  2400.0  0    0.000

!infer

IMPRoper    C1R  C2C  C6C  N1C 2400.0  0    0.000

IMPRoper    C1D  C2C  C6C  N1C 2400.0  0    0.000

IMPRoper    N4C  NC   C5C  C4C 2400.0  0    0.000

IMPRoper    C2C  NC   C4C  C5C  250.0  0    0.000

IMPRoper    C5C  C6C  N1C  C2C  250.0  0    0.000

IMPRoper    H2   C4C  H2   N4C  250.0  0    0.000



!thymine

IMPRoper    HN   X    X    NNA  250.0  0    0.000

IMPRoper    C4T  X    X    ON  2400.0  0    0.000

IMPRoper    C4T  X    X    N1T  250.0  0    0.000

IMPRoper    C6T  X    X    NNA  250.0  0    0.000

IMPRoper    CC3E X    X    C5T 2400.0  0    0.000

IMPRoper    C2T  X    X    ON  2400.0  0    0.000

!unknown

IMPRoper    C2T  NNA  C4T  C5T  250.0  0    0.000

IMPRoper    C5T  C6T  N1T  C2T  250.0  0    0.000

IMPRoper    C1R  C2T  C6T  N1T 2400.0  0    0.000

IMPRoper    C1D  C2T  C6T  N1T 2400.0  0    0.000



!uracil

IMPRoper    C4U  X    X    ON  2400.0  0    0.000

IMPRoper    C4U  X    X    N1U  250.0  0    0.000

IMPRoper    C6U  X    X    N3U  250.0  0    0.000

IMPRoper    C4U  X    X    N2  2400.0  0    0.000

IMPRoper    C2U  X    X    ON  2400.0  0    0.000

IMPRoper    C1R  C2U  C6U  N1U 2400.0  0    0.000

IMPRoper    C1D  C2U  C6U  N1U 2400.0  0    0.000

IMPRoper    ON   N3U  C5U  C4U  250.0  0    0.000

IMPRoper    C2U  N3U  C4U  C5U  250.0  0    0.000

IMPRoper    C5U  C6U  N1U  C2U  250.0  0    0.000

IMPRoper    H2   C4U  H2   ON   250.0  0    0.000



!infer

IMPRoper    HN   C2U  C4U  N3U  250.0  0    0.000



! The ring-spanning impropers have been left out.

!adenine

IMPRoper    N2A  N3A  NC   C2A  250.0  0    0.000

IMPRoper    H2   C2A  H2   N2A  250.0  0    0.000

IMPRoper    C4A  C5A  N7A  C8A  250.0  0    0.000

IMPRoper    C5A  C4A  N9A  C8A  250.0  0    0.000

IMPRoper    C4A  X    X    NC   250.0  0    0.000

IMPRoper    C2A  X    X    N9A  250.0  0    0.000

IMPRoper    C2A  X    X    C5A  250.0  0    0.000

IMPRoper    C6A  C5A  C4A  N9A  250.0  0    0.000

IMPRoper    C6A  C5A  C4A  N3A  250.0  0    0.000

IMPRoper    C5A  X    X    N9A  250.0  0    0.000

IMPRoper    C6A  X    X    N6A 2400.0  0    0.000

IMPRoper    H2   X    X    N6A  250.0  0    0.000



!infer

IMPRoper    C1R  C4A  C8A  N9A 2400.0  0    0.000

IMPRoper    C1D  C4A  C8A  N9A 2400.0  0    0.000

IMPRoper    N9A  C4A  C5A  N7A  250.0  0    0.000

IMPRoper    N7A  C8A  N9A  C4A  250.0  0    0.000

IMPRoper    N3A  C2A  NC   C6A  250.0  0    0.000



! The ring-spanning impropers have been left out.

!guanine

IMPRoper    C4G  C5G  N7G  C8G  250.0  0    0.000

IMPRoper    C5G  C4G  N9G  C8G  250.0  0    0.000

IMPRoper    C4G  X    X    NNA  250.0  0    0.000

IMPRoper    C2G  X    X    N9G  250.0  0    0.000

IMPRoper    C2G  X    X    C5G  250.0  0    0.000

IMPRoper    C6G  C5G  C4G  N9G  250.0  0    0.000

IMPRoper    C6G  C5G  C4G  N3G  250.0  0    0.000

IMPRoper    C5G  X    X    N9G  250.0  0    0.000

IMPRoper    C6G  X    X    O6G 2400.0  0    0.000

IMPRoper    C2G  X    X    N2G 2400.0  0    0.000



!infer

IMPRoper    C1R  C4G  C8G  N9G 2400.0  0    0.000

IMPRoper    C1D  C4G  C8G  N9G 2400.0  0    0.000

IMPRoper    N9G  C4G  C5G  N7G  250.0  0    0.000

IMPRoper    N7G  C8G  N9G  C4G  250.0  0    0.000

IMPRoper    N3G  C2G  NNA  C6G  250.0  0    0.000

IMPRoper    H2   H2   C2G  N2G  250.0  0    0.000



!                   Lennard-Jones parameters

!                                       ------1-4-------

!                  epsilon   sigma       epsilon   sigma

!                 (Kcal/mol)   (A)      (Kcal/mol) (A)

! Taken from Rossky Karplus and Rahman BIOPOLY (1979)

! 0.05 ADDED TO RADII TO IMPROVE ON NUCL.ACID STACKING/LN

!

!                  eps     sigma       eps(1:4) sigma(1:4)

NONBonded  C5R     0.0900   3.2970      0.0900   3.2970

NONBonded  C1R     0.0900   3.2970      0.0900   3.2970

NONBonded  C2R     0.0900   3.2970      0.0900   3.2970

NONBonded  C3R     0.0900   3.2970      0.0900   3.2970

NONBonded  C4R     0.0900   3.2970      0.0900   3.2970



NONBonded  C5D     0.0900   3.2970      0.0900   3.2970  !DNA

NONBonded  C1D     0.0900   3.2970      0.0900   3.2970

NONBonded  C2D     0.0900   3.2970      0.0900   3.2970

NONBonded  C3D     0.0900   3.2970      0.0900   3.2970

NONBonded  C4D     0.0900   3.2970      0.0900   3.2970

NONBonded  HN      0.0045   2.6160      0.0045   2.6160

NONBonded  H2      0.0045   1.6040      0.0045   1.6040

!

! give it the same as th Hn from RKR

NONBonded  HHO     0.0045   1.6040      0.0045   1.6040  !Mod HO to HHO 05/15/96



!

! THIS STILL IS AN EXTENDED ATOM

NONBonded  O3R      0.2304   2.7290      0.2304   2.7290

NONBonded  O4R      0.2304   2.7290      0.2304   2.7290

NONBonded  O4D      0.2304   2.7290      0.2304   2.7290

NONBonded  O5R      0.2304   2.7290      0.2304   2.7290

NONBonded  O1P      0.2304   2.7290      0.2304   2.7290

NONBonded  O2P      0.2304   2.7290      0.2304   2.7290

NONBonded  P        0.5849   3.3854      0.5849   3.3854



!bases

NONBonded  CN      0.0900   3.2970      0.0900   3.2970

NONBonded  C2      0.0900   3.2970      0.0900   3.2970

NONBonded  C3      0.0900   3.2970      0.0900   3.2970

NONBonded  CB      0.0900   3.2970      0.0900   3.2970

NONBonded  CE      0.0900   3.2970      0.0900   3.2970

NONBonded  CH      0.0900   3.2970      0.0900   3.2970



NONBonded  N2      0.1600   2.8591      0.1600   2.8591

NONBonded  N3U     0.1600   2.8591      0.1600   2.8591

NONBonded  NNA     0.1600   2.8591      0.1600   2.8591

NONBonded  NB      0.1600   2.8591      0.1600   2.8591

NONBonded  NC      0.1600   2.8591      0.1600   2.8591



NONBonded  NH2E    0.1600   3.0291      0.1600   3.0291

NONBonded  NS      0.1600   2.8591      0.1600   2.8591

NONBonded  N1T     0.1600   2.8591      0.1600   2.8591

NONBonded  N1C     0.1600   2.8591      0.1600   2.8591

NONBonded  N9A     0.1600   2.8591      0.1600   2.8591

NONBonded  N9G     0.1600   2.8591      0.1600   2.8591

NONBonded  N1U     0.1600   2.8591      0.1600   2.8591

NONBonded  ON      0.2304   2.7290      0.2304   2.7290

NONBonded  O2R     0.2304   2.7290      0.2304   2.7290

NONBonded  OH      0.2304   2.5508      0.2304   2.5508

NONBonded  SD      0.3515   2.6727      0.3515   2.6727   ! G U E S S



! NEW

NONBonded  C6C      0.0900   3.2970      0.0900   3.2970

NONBonded  C5C      0.0900   3.2970      0.0900   3.2970

NONBonded  C4C      0.0900   3.2970      0.0900   3.2970

NONBonded  C2C      0.0900   3.2970      0.0900   3.2970

NONBonded  C6U      0.0900   3.2970      0.0900   3.2970

NONBonded  C5U      0.0900   3.2970      0.0900   3.2970

NONBonded  C4U      0.0900   3.2970      0.0900   3.2970

NONBonded  C2U      0.0900   3.2970      0.0900   3.2970

NONBonded  C8A      0.0900   3.2970      0.0900   3.2970

NONBonded  C6A      0.0900   3.2970      0.0900   3.2970

NONBonded  C5A      0.0900   3.2970      0.0900   3.2970

NONBonded  C4A      0.0900   3.2970      0.0900   3.2970

NONBonded  C2A      0.0900   3.2970      0.0900   3.2970

NONBonded  C8G      0.0900   3.2970      0.0900   3.2970

NONBonded  C6G      0.0900   3.2970      0.0900   3.2970

NONBonded  C5G      0.0900   3.2970      0.0900   3.2970

NONBonded  C4G      0.0900   3.2970      0.0900   3.2970

NONBonded  C2G      0.0900   3.2970      0.0900   3.2970

NONBonded  C6T      0.0900   3.2970      0.0900   3.2970

NONBonded  C5T      0.0900   3.2970      0.0900   3.2970

NONBonded  C4T      0.0900   3.2970      0.0900   3.2970

NONBonded  C2T      0.0900   3.2970      0.0900   3.2970

NONBonded  N4C      0.1600   2.8591      0.1600   2.8591

NONBonded  O4U      0.2304   2.7290      0.2304   2.7290

NONBonded  N7G      0.1600   2.8591      0.1600   2.8591

NONBonded  N3G      0.1600   2.8591      0.1600   2.8591

NONBonded  N2G      0.1600   2.8591      0.1600   2.8591

NONBonded  N3A      0.1600   2.8591      0.1600   2.8591

NONBonded  N7A      0.1600   2.8591      0.1600   2.8591

NONBonded  N6A      0.1600   2.8591      0.1600   2.8591

NONBonded  O6G      0.2304   2.7290      0.2304   2.7290

NONBonded  CC3E     0.0900   3.2970      0.0900   3.2970

NONBonded  N2A      0.1600   2.8591      0.1600   2.8591



! special solute-solute hydrogen bonding potential parameters

AEXP 4

REXP 6 



HAEX 4 



AAEX 2

! "all" possible combinations of HB-pairs in nucleic acids:

!  WELL DEPTHS DEEPENED BY 0.5 KCAL TO IMPROVE BASEPAIR ENERGIES /LN

!  AND DISTANCES INCREASED BY 0.05

!                   Emin      Rmin

!                (Kcal/mol)   (A)

hbond  N*   O*      -14.0       2.95

hbond  N*   N*      -14.5       3.05

hbond  O*   O*      -15.75      2.80

hbond  O*   N*      -15.50      2.90



! the following NBFIXes are for DNA-DNA hydrogen bonding 



! terms

!                                         ------1-4------

!                   A           B           A          B

!           [Kcal/(mol A^12)] [Kcal/(mol A^6)]

!

nbfix  HHO  ON      0.05       0.1      0.05       0.1   !Mod HO to HHO 05/15/96

nbfix  HHO  O3R     0.05       0.1      0.05       0.1   !Mod HO to HHO 05/15/96

nbfix  HHO  O5R     0.05       0.1      0.05       0.1   !Mod HO to HHO 05/15/96

nbfix  HHO  OH      0.05       0.1      0.05       0.1   !Mod HO to HHO 05/15/96

nbfix  HHO  O2R     0.05       0.1      0.05       0.1   !Mod HO to HHO 05/15/96

nbfix  HHO  NC      0.05       0.1      0.05       0.1   !Mod HO to HHO 05/15/96



  



nbfix  HN   ON      0.05       0.1      0.05       0.1

nbfix  HN   O2R     0.05       0.1      0.05       0.1

nbfix  HN   OH      0.05       0.1      0.05       0.1

nbfix  HN   NC      0.05       0.1      0.05       0.1



nbfix  H2   ON      0.05       0.1      0.05       0.1

nbfix  H2   O2R     0.05       0.1      0.05       0.1

nbfix  H2   OH      0.05       0.1      0.05       0.1



nbfix  H2   NC      0.05       0.1      0.05       0.1



!----------------------------------------------------------------------------



set echo=true end

					

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