!RNA_DNA_amber.par !This file is the parameter file that goes with RNA_DNA_amber.top. !It was developed from the topology file of Parkinson et al. (1). In addition !to using AMBER potentials,the principle !change is that all paths for all dihedral angles are explictly identified. Thus !torsional energies are computed as the sums of all of their components. In this !respect, thse files conform to AMBER usage (Cornell et al. (2)). !Created 9/97 by Jason P. Rife and Peter B. Moore. ! !1. Parkinson et al. (1996) Acta Cryst. D52, 57-64 !2. Cornell et al. (1995) JACS 117, 5197-5197 ! ! This file must be used in conjunction with RNA_DNA_amber.par ! ! When this file is used, NBXMod should be set to +-3 ! REMARK RNA_DNA_amber.param set echo=off message=off end evaluate ($kchbond = 340) evaluate ($kchangle = 35) evaluate ($kchimpr = 1000) !the generic bonds were taken from param11.dna BOND C5R OH 320.000 1.4300 ! 5' end BOND C5D OH 320.000 1.4300 ! 5' end BOND C3R OH 320.000 1.4300 ! 3' end BOND C3D OH 320.000 1.4300 ! 3' end BOND O2R HO 553.000 0.9572 !Phos. - combined RNA/DNA statistics used ! kq x_eq sigma BOND P O1P 525.000 1.485 ! 0.015 Phos BOND P O2P 525.000 1.485 ! 0.015 P BOND P O5R 230.000 1.593 ! 0.010 P BOND P OH 230.000 1.593 ! 0.010 P ! For 5pho patch BOND P O3R 230.000 1.607 ! 0.012 P !Sugars !RNA statistics BOND O5R C5R 320.000 1.425 ! 0.014 Sugar BOND C5R C4R 310.000 1.510 ! 0.013 S BOND C4R C3R 310.000 1.524 ! 0.011 S BOND C3R C2R 310.000 1.525 ! 0.011 S BOND C2R C1R 310.000 1.528 ! 0.010 S BOND O4R C1R 320.000 1.414 ! 0.012 S BOND O4R C4R 320.000 1.453 ! 0.012 S BOND O3R C3R 320.000 1.423 ! 0.013 S BOND C2R O2R 320.000 1.413 ! 0.013 S !DNA statistics BOND O5R C5D 320.000 1.427 ! 0.014 Sugar BOND C5D C4D 310.000 1.511 ! 0.008 S BOND C4D C3D 310.000 1.528 ! 0.010 S BOND C3D C2D 310.000 1.518 ! 0.010 S BOND C2D C1D 310.000 1.521 ! 0.014 S BOND O4D C1D 320.000 1.420 ! 0.013 S BOND O4D C4D 320.000 1.446 ! 0.011 S BOND O3R C3D 320.000 1.431 ! 0.013 S !hydrogen/carbon BOND C4R H $kchbond 1.09 BOND C3R H $kchbond 1.09 BOND C2R H $kchbond 1.09 BOND C1R H $kchbond 1.09 BOND C5R H $kchbond 1.09 BOND C4D H $kchbond 1.09 BOND C3D H $kchbond 1.09 BOND C2D H $kchbond 1.09 BOND C1D H $kchbond 1.09 BOND C5D H $kchbond 1.09 !Bases !base specific bonds taken from param11.dna BOND O2U HO 553.000 0.957 ! UR BOND HN NNA 434.000 1.010 ! URA BOND HN N1T 434.000 1.010 ! Infer. BOND HN N1C 434.000 1.010 BOND HN N9G 434.000 1.010 BOND HN N9A 434.000 1.010 BOND HN N3U 434.000 1.010 BOND HN N3T 434.000 1.010 BOND H2 N2 434.000 1.010 BOND H2 N4C 434.000 1.010 BOND H2 N2G 434.000 1.010 BOND H2 N6A 434.000 1.010 BOND HO OH 553.000 0.960 ! PARAM7 (IR stretch 3400 cm-1) !Base sugar joint bonds (scale from sugar) ! kq x_eq sigma BOND C1R N1T 337.000 1.473 ! 0.014 Base BOND C1R N1U 337.000 1.469 ! 0.009 B BOND C1R N1C 337.000 1.470 ! 0.012 B BOND C1R N9G 337.000 1.459 ! 0.009 B BOND C1R N9A 337.000 1.462 ! 0.010 B BOND C1D N1T 337.000 1.473 ! 0.014 B !DNA BOND C1D N1U 337.000 1.469 ! 0.009 B BOND C1D N1C 337.000 1.470 ! 0.012 B BOND C1D N9G 337.000 1.459 ! 0.009 B BOND C1D N9A 337.000 1.462 ! 0.010 B !cytosine kq x_eq sigma BOND C2C ON 570.000 1.240 !0.009 B BOND C4C N4C 481.000 1.335 !0.009 B BOND N1C C2C 436.000 1.397 !0.010 B BOND N1C C6C 448.000 1.367 !0.006 B BOND C2C NC 457.000 1.353 !0.008 B BOND NC C4C 483.000 1.335 !0.007 B BOND C4C C5C 427.000 1.425 !0.008 B BOND C5C C6C 549.000 1.339 !0.008 B BOND C5C H $kchbond 1.09 BOND C6C H $kchbond 1.09 !thymine BOND N1T C2T 424.000 1.376 !0.008 B BOND C2T N3T 418.000 1.373 !0.008 B BOND N3T C4T 418.000 1.382 !0.008 B BOND C4T C5T 410.000 1.445 !0.009 B BOND C5T C6T 549.000 1.339 !0.007 B BOND C6T N1T 448.000 1.378 !0.007 B BOND C2T ON 570.000 1.220 !0.008 B BOND C4T ON 570.000 1.228 !0.009 B BOND C5T CC3E 317.000 1.496 !0.006 B BOND C6T H $kchbond 1.09 BOND CC3E H $kchbond 1.09 !adenine BOND NC C2A 502.000 1.339 !0.009 B BOND C2A N3A 502.000 1.331 !0.009 B BOND N3A C4A 483.000 1.344 !0.006 B BOND C4A C5A 520.000 1.383 !0.007 B BOND C5A C6A 469.000 1.406 !0.009 B BOND C6A NC 481.000 1.351 !0.007 B BOND C5A N7A 414.000 1.388 !0.006 B BOND N7A C8A 529.000 1.311 !0.007 B BOND C8A N9A 440.000 1.373 !0.008 B BOND N9A C4A 436.000 1.374 !0.006 B BOND C6A N6A 481.000 1.335 !0.008 B BOND C8A H $kchbond 1.08 BOND C2A H $kchbond 1.09 !guanine BOND NNA C2G 427.000 1.373 !0.008 B BOND C2G N3G 483.000 1.323 !0.008 B BOND N3G C4G 461.000 1.350 !0.007 B BOND C4G C5G 520.000 1.379 !0.007 B BOND C5G C6G 447.000 1.419 !0.010 B BOND C6G NNA 418.000 1.391 !0.007 B BOND C5G N7G 414.000 1.388 !0.006 B BOND N7G C8G 529.000 1.305 !0.006 B BOND C8G N9G 440.000 1.374 !0.007 B BOND N9G C4G 436.000 1.375 !0.008 B BOND C2G N2G 481.000 1.341 !0.010 B BOND C6G O6G 570.000 1.237 !0.009 B BOND C8G H $kchbond 1.08 !uracil BOND C2U ON 570.000 1.219 !0.009 B BOND C4U ON 570.000 1.232 !0.008 B BOND N1U C2U 418.000 1.381 !0.009 B BOND N1U C6U 448.000 1.375 !0.009 B BOND C2U N3U 418.000 1.373 !0.007 B BOND N3U C4U 418.000 1.380 !0.009 B BOND C4U C5U 410.000 1.431 !0.009 B BOND C5U C6U 549.000 1.337 !0.009 B BOND C5U H $kchbond 1.09 BOND C6U H $kchbond 1.09 !Phos. !the ANGLe s were taken from param11.dna ANGLe HO OH C5R 55.000 107.300 ANGLe HO O5R C5R 55.000 107.300 ANGLe HO OH C5D 55.000 107.300 ANGLe HO O5R C5D 55.000 107.300 ANGLe HO O3R P 55.000 107.300 ANGLe HO OH P 55.000 107.300 ! For 5pho patch ANGLe HO O2R C2R 55.000 107.300 ANGLe OH P O3R 45.000 102.600 ! ANGLe OH P O5R 45.000 102.600 ! ANGLe OH P O1P 45.000 108.230 ! ANGLe OH P O2P 45.000 108.230 ! ANGLe OH C5R C4R 50.000 112.000 ! ANGLe OH C5D C4D 50.000 112.000 ! ANGLe C4D C3D OH 50.000 111.000 ! ANGLe C4R C3R OH 50.000 111.000 ! ANGLe C2D C3D OH 50.000 111.000 ! ANGLe C2R C3R OH 50.000 111.000 ! ANGLe C3R OH HO 55.000 107.300 ! ANGLe C3D OH HO 55.000 107.300 ! !Phos. - combined RNA/DNA statistics used ! kq x_eq sigma ANGLe O1P P O2P 140.000 119.600 !1.5 P ANGLe O5R P O1P 100.000 108.100 !2.9 P ANGLe O5R P O2P 100.000 108.300 !2.7 P ANGLe O3R P O5R 45.000 104.000 !1.9 P ANGLe O2P P O3R 45.000 108.300 !3.2 P ANGLe O1P P O3R 45.000 107.400 !3.2 P ANGLe O5R C5R C4R 50.000 110.200 !1.4 P ANGLe P O5R C5R 100.000 120.900 !1.6 P ANGLe P O3R C3R 100.000 119.700 !1.2 P ANGLe O5R C5D C4D 50.000 110.200 !1.4 P !DNA ANGLe P O5R C5D 100.000 120.900 !1.6 P ANGLe P O3R C3D 100.000 119.700 !1.2 P !Sugars !RNA statistics ! kq x_eq sigma ANGLe O4R C4R C3R 50.000 105.500 !1.4 S ANGLe C5R C4R C3R 40.000 115.500 !1.5 S ANGLe C5R C4R O4R 50.000 109.200 !1.4 S ANGLe C1R O4R C4R 60.000 109.600 !0.9 S ANGLe C4R C3R C2R 40.000 102.700 !1.0 S ANGLe C3R C2R C1R 40.000 101.500 !0.9 S ANGLe O4R C1R C2R 50.000 106.400 !1.4 S ANGLe N1T C1R C2R 50.000 113.400 !1.6 S ANGLe N1C C1R C2R 50.000 113.400 !1.6 S ANGLe N1U C1R C2R 50.000 113.400 !1.6 S ANGLe N9G C1R C2R 50.000 113.400 !1.6 S ANGLe N9A C1R C2R 50.000 113.400 !1.6 S ANGLe O4R C1R N1T 50.000 108.200 !1.0 S ANGLe O4R C1R N1C 50.000 108.200 !1.0 S ANGLe O4R C1R N1U 50.000 108.200 !1.0 S ANGLe O4R C1R N9A 50.000 108.200 !1.0 S ANGLe O4R C1R N9G 50.000 108.200 !1.0 S ANGLe C1R C2R O2R 50.000 110.600 !2.9 S scale from phos. ANGLe C3R C2R O2R 50.000 113.300 !2.9 S scale from phos. ANGLe C4R C3R O3R 50.000 110.500 !2.6 S scale from phos. ANGLe C2R C3R O3R 50.000 111.000 !2.8 S scale from phos. !DNA statistics ANGLe O4D C4D C3D 50.000 105.600 !1.0 S ANGLe C5D C4D C3D 40.000 114.700 !1.5 S ANGLe C5D C4D O4D 50.000 109.400 !1.6 S ANGLe C1D O4D C4D 60.000 109.700 !1.3 S ANGLe C4D C3D C2D 40.000 103.200 !1.0 S ANGLe C3D C2D C1D 40.000 102.700 !1.3 S ANGLe O4D C1D C2D 50.000 106.100 !1.1 S ANGLe N1T C1D C2D 50.000 114.200 !1.5 S ANGLe N1C C1D C2D 50.000 114.200 !1.5 S ANGLe N1U C1D C2D 50.000 114.200 !1.5 S ANGLe N9G C1D C2D 50.000 114.200 !1.5 S ANGLe N9A C1D C2D 50.000 114.200 !1.5 S ANGLe O4D C1D N1T 50.000 107.800 !0.9 S ANGLe O4D C1D N1C 50.000 107.800 !0.9 S ANGLe O4D C1D N1U 50.000 107.800 !0.9 S ANGLe O4D C1D N9A 50.000 107.800 !0.9 S ANGLe O4D C1D N9G 50.000 107.800 !0.9 S ANGLe C4D C3D O3R 50.000 110.300 !2.2 S scale from phos. ANGLe C2D C3D O3R 50.000 110.600 !2.7 S scale from phos. !Ribose terms involving non-exchageables ANGLe OH C5R H $kchangle 109.83 ANGLe O5R C5R H $kchangle 109.83 ANGLe H C5R H $kchangle 109.11 ANGLe C4R C5R H $kchangle 109.11 ANGLe C5R C4R H $kchangle 107.93 ANGLe H C4R C3R $kchangle 107.13 ANGLe H C4R O4R $kchangle 113.74 ANGLe H C3R C4R $kchangle 111.35 ANGLe H C3R O3R $kchangle 105.87 ANGLe H C3R OH $kchangle 105.87 ANGLe H C3R C2R $kchangle 112.27 ANGLe H C2R C3R $kchangle 111.41 ANGLe H C2R O2R $kchangle 113.07 ANGLe H C2R C1R $kchangle 112.38 ANGLe H C1R C2R $kchangle 111.95 ANGLe H C1R N1C $kchangle 107.70 ANGLe H C1R N1U $kchangle 107.70 ANGLe H C1R N9A $kchangle 107.70 ANGLe H C1R N9G $kchangle 107.70 ANGLe H C1R O4R $kchangle 106.86 !Deoxyribose terms involving non-exchageables ! ANGLe OH C5D H $kchangle 109.70 ANGLe O5R C5D H $kchangle 109.70 ANGLe H C5D H $kchangle 109.17 ANGLe C4D C5D H $kchangle 109.17 ANGLe C5D C4D H $kchangle 107.78 ANGLe H C4D C3D $kchangle 106.91 ANGLe H C4D O4D $kchangle 112.98 ANGLe H C3D C4D $kchangle 111.16 ANGLe H C3D O3R $kchangle 109.34 ANGLe H C3D OH $kchangle 109.34 ANGLe H C3D C2D $kchangle 111.98 ANGLe H C2D C3D $kchangle 111.36 ANGLe H C2D H $kchangle 107.52 ANGLe H C2D C1D $kchangle 112.29 ANGLe H C1D C2D $kchangle 110.94 ANGLe H C1D N1C $kchangle 108.25 ANGLe H C1D N1U $kchangle 108.25 ANGLe H C1D N1T $kchangle 108.25 ANGLe H C1D N9A $kchangle 108.25 ANGLe H C1D N9G $kchangle 108.25 ANGLe H C1D O4D $kchangle 107.95 !Bases !cytosine kq x_eq sigma ANGLe C6C N1C C2C 70.000 120.300 !0.40 B ANGLe N1C C2C NC 70.000 119.200 !0.70 B ANGLe C2C NC C4C 70.000 119.900 !0.50 B ANGLe NC C4C C5C 70.000 121.900 !0.40 B ANGLe C4C C5C C6C 63.000 117.400 !0.50 B ANGLe C5C C6C N1C 70.000 121.000 !0.50 B ANGLe N1C C2C ON 80.000 118.900 !0.60 B ANGLe NC C2C ON 80.000 121.900 !0.70 B ANGLe NC C4C N4C 70.000 118.000 !0.70 B ANGLe C5C C4C N4C 70.000 120.200 !0.70 B ANGLe C6C N1C C1R 70.000 120.800 !1.20 B scale from sugar ANGLe C2C N1C C1R 70.000 118.800 !1.10 B scale from sugar ANGLe C6C N1C C1D 70.000 120.800 !1.20 B !DNA ANGLe C2C N1C C1D 70.000 118.800 !1.10 B ANGLe C4C N4C H2 35.000 120.000 !from param11.dna, 3*keq ANGLe H2 N4C H2 35.000 120.000 ANGLe N1C C6C H $kchangle 119.63 ANGLe C5C C6C H $kchangle 119.36 ANGLe C4C C5C H $kchangle 121.54 ANGLe C6C C5C H $kchangle 121.54 !thymine kq x_eq sigma ANGLe C6T N1T C2T 70.000 121.300 !0.50 B ANGLe N1T C2T N3T 70.000 114.600 !0.60 B ANGLe C2T N3T C4T 70.000 127.200 !0.60 B ANGLe N3T C4T C5T 70.000 115.200 !0.60 B ANGLe C4T C5T C6T 63.000 118.000 !0.60 B ANGLe C5T C6T N1T 70.000 123.700 !0.60 B ANGLe N1T C2T ON 80.000 123.100 !0.80 B ANGLe N3T C2T ON 80.000 122.300 !0.60 B ANGLe N3T C4T ON 80.000 119.900 !0.60 B ANGLe C5T C4T ON 80.000 124.900 !0.70 B ANGLe C4T C5T CC3E 70.000 119.000 !0.60 B ANGLe C6T C5T CC3E 70.000 122.900 !0.60 B ANGLe C6T N1T C1R 70.000 120.400 !1.50 B scale from sugar ANGLe C2T N1T C1R 70.000 118.200 !1.60 B scale from sugar ANGLe C6T N1T C1D 70.000 120.400 !1.50 B !DNA ANGLe C2T N1T C1D 70.000 118.200 !1.60 B ANGLe C2T N3T HN 30.000 116.500 !from param11.dna, 3*keq ANGLe C4T N3T HN 30.000 116.500 ANGLe C5T CC3E H $kchangle 109.50 ANGLe H CC3E H $kchangle 109.44 ANGLe N1T C6T H $kchangle 119.52 ANGLe C5T C6T H $kchangle 119.52 !adenine kq x_eq sigma ANGLe C6A NC C2A 70.000 118.600 !0.60 B ANGLe NC C2A N3A 70.000 129.300 !0.50 B ANGLe C2A N3A C4A 70.000 110.600 !0.50 B ANGLe N3A C4A C5A 70.000 126.800 !0.70 B ANGLe C4A C5A C6A 63.000 117.000 !0.50 B ANGLe C5A C6A NC 70.000 117.700 !0.50 B ANGLe C4A C5A N7A 70.000 110.700 !0.50 B ANGLe C5A N7A C8A 70.000 103.900 !0.50 B ANGLe N7A C8A N9A 70.000 113.800 !0.50 B ANGLe C8A N9A C4A 70.000 105.800 !0.40 B ANGLe N9A C4A C5A 70.000 105.800 !0.40 B ANGLe N3A C4A N9A 70.000 127.400 !0.80 B ANGLe C6A C5A N7A 70.000 132.300 !0.70 B ANGLe NC C6A N6A 70.000 118.600 !0.60 B ANGLe C5A C6A N6A 70.000 123.700 !0.80 B ANGLe C8A N9A C1R 70.000 127.700 !1.80 B scale from sugar ANGLe C4A N9A C1R 70.000 126.300 !1.80 B scale from sugar ANGLe C8A N9A C1D 70.000 127.700 !1.80 B !DNA ANGLe C4A N9A C1D 70.000 126.300 !1.80 B ANGLe C6A N6A H2 35.000 120.000 !from param11.dna, 3*keq ANGLe H2 N6A H2 35.000 120.000 ANGLe N7A C8A H $kchangle 123.16 ANGLe N9A C8A H $kchangle 123.16 ANGLe NC C2A H $kchangle 115.54 ANGLe N3A C2A H $kchangle 115.54 !guanine kq x_eq sigma ANGLe C6G NNA C2G 70.000 125.100 !0.60 B ANGLe NNA C2G N3G 70.000 123.900 !0.60 B ANGLe C2G N3G C4G 70.000 111.900 !0.50 B ANGLe N3G C4G C5G 70.000 128.600 !0.50 B ANGLe C4G C5G C6G 63.000 118.800 !0.60 B ANGLe C5G C6G NNA 70.000 111.500 !0.50 B ANGLe C4G C5G N7G 70.000 110.800 !0.40 B ANGLe C5G N7G C8G 70.000 104.300 !0.50 B ANGLe N7G C8G N9G 70.000 113.100 !0.50 B ANGLe C8G N9G C4G 70.000 106.400 !0.40 B ANGLe N9G C4G C5G 70.000 105.400 !0.40 B ANGLe N3G C4G N9G 70.000 126.000 !0.60 B ANGLe C6G C5G N7G 70.000 130.400 !0.60 B ANGLe NNA C2G N2G 70.000 116.20 !0.90 B ANGLe N3G C2G N2G 70.000 119.900 !0.70 B ANGLe NNA C6G O6G 80.000 119.900 !0.60 B ANGLe C5G C6G O6G 80.000 128.600 !0.60 B ANGLe C8G N9G C1R 70.000 127.000 !1.30 B scale from sugar ANGLe C4G N9G C1R 70.000 126.500 !1.30 B scale from sugar ANGLe C8G N9G C1D 70.000 127.000 !1.30 B !DNA ANGLe C4G N9G C1D 70.000 126.500 !1.30 B ANGLe C2G N2G H2 35.000 120.000 !from param11.dna, 3*keq ANGLe H2 N2G H2 35.000 120.000 ANGLe C2G NNA HN 30.000 119.300 ANGLe C6G NNA HN 30.000 119.300 ANGLe N7G C8G H $kchangle 122.91 ANGLe N9G C8G H $kchangle 122.91 !uracile kq x_eq sigma ANGLe C6U N1U C2U 70.000 121.000 !0.60 B ANGLe N1U C2U N3U 70.000 114.900 !0.60 B ANGLe C2U N3U C4U 70.000 127.000 !0.60 B ANGLe N3U C4U C5U 70.000 114.600 !0.60 B ANGLe C4U C5U C6U 63.000 119.700 !0.60 B ANGLe C5U C6U N1U 70.000 122.700 !0.50 B ANGLe N1U C2U ON 80.000 122.800 !0.70 B ANGLe N3U C2U ON 80.000 122.200 !0.70 B ANGLe N3U C4U ON 80.000 119.400 !0.70 B ANGLe C5U C4U ON 80.000 125.900 !0.60 B ANGLe C6U N1U C1R 70.000 121.200 !1.40 B ANGLe C2U N1U C1R 70.000 117.700 !1.20 B ANGLe C6U N1U C1D 70.000 121.200 !1.40 B !DNA ANGLe C2U N1U C1D 70.000 117.700 !1.20 B ANGLe C4U ON HO 35.000 120.000 !from param11.dna, 3*keq ANGLe C2U N3U HN 30.000 116.500 ANGLe C4U N3U HN 30.000 116.500 ANGLe N1U C6U H $kchangle 119.38 ANGLe C5U C6U H $kchangle 119.38 ANGLe C4U C5U H $kchangle 119.56 ANGLe C6U C5U H $kchangle 119.56 !base specific dihedrals !ADE DIHE X N9A C8A X 1.7 2 180.00 DIHE X C8A N7A X 10 2 180.00 DIHE X N7A C5A X 2.55 2 180.00 DIHE X C5A C4A X 5.45 2 180.00 DIHE X C4A N3A X 4.15 2 180.00 DIHE X N3A C2A X 6.8 2 180.00 DIHE X C2A NC X 6.8 2 180.00 DIHE X NC C6A X 4.8 2 180.00 DIHE X C6A N6A X 2.4 2 180.00 DIHE X C6A C5A X 3.5 2 180.00 DIHE X C4A N9A X 1.65 2 180.00 !base specific dihedrals !GUA DIHE X N9G C8G X 1.7 2 180.00 DIHE X C8G N7G X 10 2 180.00 DIHE X N7G C5G X 2.55 2 180.00 DIHE X C5G C4G X 5.45 2 180.00 DIHE X C4G N3G X 4.15 2 180.00 DIHE X N3G C2G X 6.8 2 180.00 DIHE X C2G NNA X 1.5 2 180.00 DIHE X NNA C6G X 1.35 2 180.00 DIHE X C2G N2G X 2.4 2 180.00 DIHE X C6G C5G X 3.5 2 180.00 DIHE X C4G N9G X 1.65 2 180.00 !CYT DIHE X N1C C6C X 1.85 2 180.00 DIHE X C6C C5C X 6.65 2 180.00 DIHE X C5C C4C X 2.55 2 180.00 DIHE X C4C NC X 2.4 2 180.00 DIHE X C4C N4C X 2.4 2 180.00 DIHE X NC C2C X 4.0 2 180.00 DIHE X C2C N1C X 1.45 2 180.00 !URI !CYT DIHE X N1U C6U X 1.85 2 180.00 DIHE X C6U C5U X 6.65 2 180.00 DIHE X C5U C4U X 2.55 2 180.00 DIHE X C4U N3U X 1.35 2 180.00 DIHE X N3U C2U X 1.35 2 180.00 DIHE X C2U N1U X 1.45 2 180.00 !Dihedrals from param11.dna (included for terminal residues) DIHEdral X C2R C3R X 1.40 3 0.000 DIHEdral X C4R C3R X 1.40 3 0.000 ! delta? DIHEdral X C2R C1R X 1.40 3 0.000 DIHEdral X C5R O5R X 1.15 3 0.000 ! beta ? DIHEdral X C3R O3R X 1.15 3 0.000 ! epsilon? DIHEdral X C3R OH X 0.50 3 0.000 DIHEdral X C5R OH X 0.50 3 0.000 DIHEdral X C2R O2R X 0.50 3 0.000 DIHEdral X O5R P X 0.75 3 0.000 !alpha? DIHEdral X OH P X 0.75 3 0.000 DIHEdral OH C5R C4R O4R 0.11 3 0.000 ! another gamma for terminals? DIHEdral OH C5R C4R C3R 1.40 3 0.000 ! gamma for terminal residues only DIHEdral C3R O3R P OH 0.75 3 0.000 ! added by infer !DIHEdral C3R O3R P OH 1.20 2 0.000 ! ATB, 7-SEP-84 ? 9/97 DIHEdral C5R O5R P OH 0.75 3 0.000 ! added by infer !DIHEdral C5R O5R P OH 1.20 2 0.000 ! ATB, 7-SEP-84 !newstuff !BACKBONE (MISSING X-C3R-C2R-X; DEFINED UNDER NU) !X-P-O5R-X DIHE O3R P O5R C5R MULT 2 1.20 2 0 0.25 3 0!ALPHA DIHE O5T P O5R C5R MULT 2 1.20 2 0 0.25 3 0!TERMINAL PHOSPHATE DIHE O1P P O5R C5R 0.25 3 0 DIHE O2P P O5R C5R 0.25 3 0 !X-05R-C5R-X DIHE P O5R C5R H 0.383 3 0 DIHE P O5R C5R C4R 0.383 3 0 !BETA !X-C5'-C4'-X DIHE O5R C5R C4R H 0.155 3 0 DIHE OH C5R C4R H 0.155 3 0 DIHE H C5R C4R H 0.155 3 0 DIHE O5R C5R C4R O4R MULT 2 1.00 2 0 0.144 3 0!GAMMA DIHE OH C5R C4R O4R MULT 2 1.00 2 0 0.144 3 0!GAMMA DIHE H C5R C4R O4R 0.155 3 0 DIHE O5R C5R C4R C3R 0.155 3 0 DIHE OH C5R C4R C3R 0.155 3 0 DIHE H C5R C4R C3R 0.155 3 0 !X-C3R-O3R-X note: shift angle on these were 0, but beleive 210 fits !better with A-form RNA DIHE C4R C3R O3R P 0.3833 3 210 !EPSILON DIHE H C3R O3R P 0.3833 3 210 DIHE C2R C3R O3R P 0.3833 3 210 !X-O3R-P-X DIHE C3R O3R P O1P 0.25 3 0 DIHE C3R O3R P O2P 0.25 3 0 DIHE C3R O3R P O5R MULT 2 1.20 2 0 0.25 3 0 DIHE C3R O3R P O5T MULT 2 1.20 2 0 0.25 3 0 !GLYCOSIDIC X-N9/N1-C1R-X !ADE DIHE C4A N9A C1R H 0.00 2 0 DIHE C4A N9A C1R C2R 0.00 2 0 DIHE C4A N9A C1R O4R 0.00 2 0 DIHE C8A N9A C1R H 0.00 2 0 DIHE C8A N9A C1R C2R 0.00 2 0 DIHE C8A N9A C1R O4R MULT 2 2.50 1 0 0.50 2 180!CHI !GUA DIHE C4G N9G C1R H 0.00 2 0 DIHE C4G N9G C1R C2R 0.00 2 0 DIHE C4G N9G C1R O4R 0.00 2 0 DIHE C8G N9G C1R H 0.00 2 0 DIHE C8G N9G C1R C2R 0.00 2 0 DIHE C8G N9G C1R O4R MULT 2 2.50 1 0 0.50 2 180 !CHI !CYT DIHE C6C N1C C1R H 0.00 2 0 DIHE C6C N1C C1R C2R 0.00 2 0 DIHE C6C N1C C1R O4R 0.50 2 180 DIHE C2C N1C C1R H 0.00 2 0 DIHE C2C N1C C1R C2R 0.00 2 0 DIHE C2C N1C C1R O4R 0.00 2 0 !CHI !URI DIHE C6U N1U C1R H 0.00 2 0 DIHE C6U N1U C1R C2R 0.00 2 0 DIHE C6U N1U C1R O4R 0.50 2 180 DIHE C2U N1U C1R H 0.00 2 0 DIHE C2U N1U C1R C2R 0.00 2 0 DIHE C2U N1U C1R O4R 0.00 2 0 !CHI !Nu's !X-O4R-C1R-X DIHE C4R O4R C1R H 0.383 3 0 DIHE C4R O4R C1R N9A 0.383 3 0 !ADE DIHE C4R O4R C1R N9G 0.383 3 0 !GUA DIHE C4R O4R C1R N1C 0.383 3 0 !CYT DIHE C4R O4R C1R N1U 0.383 3 0 !URI DIHE C4R O4R C1R C2R MULT 2 0.1 2 180 0.383 3 0!NU0 !X-C1R-C2R-X DIHE O4R C1R C2R H 0.155 3 0 DIHE H C1R C2R H 0.155 3 0 DIHE N9A C1R C2R H 0.155 3 0 DIHE N9G C1R C2R H 0.155 3 0 DIHE N1C C1R C2R H 0.155 3 0 DIHE N1U C1R C2R H 0.155 3 0 DIHE O4R C1R C2R O2R 0.144 3 0 DIHE H C1R C2R O2R 0.155 3 0 DIHE N9A C1R C2R O2R 0.155 3 0 DIHE N9G C1R C2R O2R 0.155 3 0 DIHE N1C C1R C2R O2R 0.155 3 0 DIHE N1U C1R C2R O2R 0.155 3 0 DIHE O4R C1R C2R C3R 0.155 3 0 !NU1 DIHE H C1R C2R C3R 0.155 3 0 DIHE N9A C1R C2R C3R 0.155 3 0 DIHE N9G C1R C2R C3R 0.155 3 0 DIHE N1C C1R C2R C3R 0.155 3 0 DIHE N1U C1R C2R C3R 0.155 3 0 !X-C2R-C3R-X DIHE C1R C2R C3R H 0.155 3 0 DIHE H C2R C3R H 0.155 3 0 DIHE O2R C2R C3R H 0.155 3 0 DIHE C1R C2R C3R O3R 0.155 3 0 DIHE H C2R C3R O3R 0.155 3 0 DIHE O2R C2R C3R O3R 0.144 3 0 DIHE C1R C2R C3R OH 0.155 3 0 !TERMINAL DIHE H C2R C3R OH 0.155 3 0 !TERMINAL DIHE O2R C2R C3R OH 0.144 3 0 !TERMINAL DIHE C1R C2R C3R C4R 0.155 3 0 !NU2 DIHE H C2R C3R C4R 0.155 3 0 DIHE O2R C2R C3R C4R 0.155 3 0 !X-C3R-C4R-X DIHE C2R C3R C4R H 0.155 3 0 DIHE O3R C3R C4R H 0.155 3 0 DIHE H C3R C4R H 0.155 3 0 DIHE C2R C3R C4R 04R 0.155 3 0 !NU3 DIHE O3R C3R C4R 04R MULT 2 1.000 2 0 0.144 3 0 DIHE H C3R C4R 04R 0.144 3 0 DIHE C2R C3R C4R C5R 0.155 3 0 DIHE O3R C3R C4R C5R 0.155 3 0 !DELTA DIHE H C3R C4R C5R 0.155 3 0 !X-C4R-O4R-C1R DIHE H C4R O4R C1R 0.380 3 0 DIHE C5R C4R O4R C1R MULT 2 0.100 2 180 0.383 3 0 DIHE C3R C4R O4R C1R MULT 2 0.100 2 180 0.383 3 0 !NU4 !end newstuff !IMPRoper for non-bridging oxegens, O1P and O2P IMPRoper O1P O3R O2P O5R $kchimpr 0 -72 ! maintain chirality ! AMBER Guanine impropers IMPRoper C2G NNA N3G N2G 1.1 0 0.0 IMPRoper C6G NNA C5G O6G 10.5 0 0.0 IMPRoper C8G N9G N7G H 1.1 0 0.0 IMPRoper NNA C2G C6G HN 1.0 0 0.0 IMPRoper N2G C2G H2 H2 1.0 0 0.0 IMPRoper N9G C4G C8G C1R 1.0 0 0.0 ! AMBER Adenine impropers IMPRoper C2A N3A NC H 1.1 0 0.0 IMPRoper C6A C5A NC N6A 1.1 0 0.0 IMPRoper C8A N9A N7A H 1.1 0 0.0 IMPRoper N6A C6A H2 H2 1.0 0 0.0 IMPRoper N9A C4A C8A C1R 1.0 0 0.0 ! AMBER Cytosine impropers IMPRoper C2C N1C NC ON 10.5 0 0.0 IMPRoper C4C N4C C5C NC 1.1 0 0.0 IMPRoper C5C C4C C6C H 1.1 0 0.0 IMPRoper C6C N1C C5C H 1.1 0 0.0 IMPRoper N1C C2C C6C C1R 1.0 0 0.0 IMPRoper N4C C4C H2 H2 1.0 0 0.0 ! AMBER Uridine impropers IMPRoper C2U N1U N3U ON 10.5 0 0.0 IMPRoper C4U N3U C5U ON 10.5 0 0.0 IMPRoper C5U C6U C4U H 1.1 0 0.0 IMPRoper C6U N1U C5U H 1.1 0 0.0 IMPRoper N1U C2U C6U C1R 1.0 0 0.0 IMPRoper N3U C2U C4U HN 1.0 0 0.0 ! AMBER Thymine impropers IMPRoper C2T N1T N3T ON 10.5 0 0.0 IMPRoper C4T N3T C5T ON 10.5 0 0.0 IMPRoper C5T C6T C4T C5T 1.1 0 0.0 IMPRoper C6T N1T C5T H 1.1 0 0.0 IMPRoper N1T C2T C6T C1R 1.0 0 0.0 IMPRoper N3T C2T C4T HN 1.0 0 0.0 !Impropers for ribose chirality IMPRoper H C2R O4R N9A $kchimpr 0 -65.000!C1R IMPRoper H C2R O4R N9G $kchimpr 0 -65.000!C1R IMPRoper H C2R O4R N1C $kchimpr 0 -65.000!C1R IMPRoper H C2R O4R N1U $kchimpr 0 -65.000!C1R IMPRoper H C2R O4R N1T $kchimpr 0 -65.000!C1R IMPRoper H C3R C1R O2R $kchimpr 0 65.000!C2R IMPRoper H C4R C2R O3R $kchimpr 0 60.300!C3R IMPRoper H C4R C2R OH $kchimpr 0 60.300!C3R; TERMINAL RES IMPRoper H C5R C3R O4R $kchimpr 0 70.300!C4R IMPRoper H O5R H C4R $kchimpr 0 72.000!C5R; IMPRoper H OH H C4R $kchimpr 0 72.000!C5R; TERMINAL RES !Impropers for deoxyribose chirality IMPRoper H C2D O4D N9A $kchimpr 0 -65.280!C1D IMPRoper H C2D O4D N9G $kchimpr 0 -65.280!C1D IMPRoper H C2D O4D N1C $kchimpr 0 -65.280!C1D IMPRoper H C2D O4D N1T $kchimpr 0 -65.280!C1D IMPRoper H C3D H C1D $kchimpr 0 -73.500!C2D IMPRoper H C4D C2D O3R $kchimpr 0 62.660!C3D IMPRoper H C4D C2D OH $kchimpr 0 62.660!C3D; TERMINAL RES IMPRoper H C5D C3D O4D $kchimpr 0 70.220!C4D IMPRoper H O5R H C4D $kchimpr 0 71.430!C5D; IMPRoper H OH H C4D $kchimpr 0 71.430!C5D; TERMINAL RES ! 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 IMPRoperOVE ON NUCL.ACID STACKING/LN ! ! Changed to Kollman values 9/6 ! ! eps sigma eps(1:4) sigma(1:4) NONBonded C5R 0.1094 3.3960 0.0547 3.3960 NONBonded C1R 0.1094 3.3960 0.0547 3.3960 NONBonded C2R 0.1094 3.3960 0.0547 3.3960 NONBonded C3R 0.1094 3.3960 0.0547 3.3960 NONBonded C4R 0.1094 3.3960 0.0547 3.3960 NONBonded C5D 0.1094 3.3960 0.0547 3.3960 !DNA NONBonded C1D 0.1094 3.3960 0.0547 3.3960 NONBonded C2D 0.1094 3.3960 0.0547 3.3960 NONBonded C3D 0.1094 3.3960 0.0547 3.3960 NONBonded C4D 0.1094 3.3960 0.0547 3.3960 NONBonded HN 0.0157 1.0680 0.0078 1.0680 NONBonded H2 0.0157 1.0680 0.0078 1.0680 NONBonded H 0.0157 2.6460 0.0078 2.4690 ! ! give it the same as th Hn from RKR NONBonded HO 0.0000 0.0000 0.0022 1.6040 ! ! THIS STILL IS AN EXTENDED ATOM NONBonded O3R 0.1700 2.9569 0.0850 2.9569 NONBonded O4R 0.1700 2.9569 0.0850 2.9569 NONBonded O4D 0.1700 2.9569 0.0850 2.9569 NONBonded O5R 0.1700 2.9569 0.0850 2.9569 NONBonded O1P 0.1700 2.9569 0.0850 2.9569 NONBonded O2P 0.1700 2.9569 0.0850 2.9569 NONBonded P 0.2000 3.7380 0.0850 3.7380 !bases NONBonded CN 0.1094 3.3960 0.0547 3.3960 ! I don't know what these are. PBM NONBonded C2 0.1094 3.3960 0.0547 3.3960 NONBonded C3 0.1094 3.3960 0.0547 3.3960 NONBonded CB 0.1094 3.3960 0.0547 3.3960 NONBonded CE 0.1094 3.3960 0.0547 3.3960 NONBonded CH 0.1094 3.3960 0.0547 3.3960 NONBonded N2 0.1700 3.2467 0.0850 3.2467 NONBonded N3U 0.1700 3.2467 0.0850 3.2467 NONBonded N3T 0.1700 3.2467 0.0850 3.2467 NONBonded NNA 0.1700 3.2467 0.0850 3.2467 NONBonded NB 0.1700 3.2467 0.0850 3.2467 NONBonded NC 0.1700 3.2467 0.0850 3.2467 NONBonded NH2E 0.1700 3.2467 0.0850 3.2467 NONBonded NS 0.1700 3.2467 0.0850 3.2467 NONBonded N1T 0.1700 3.2467 0.0850 3.2467 NONBonded N1C 0.1700 3.2467 0.0850 3.2467 NONBonded N9A 0.1700 3.2467 0.0850 3.2467 NONBonded N9G 0.1700 3.2467 0.0850 3.2467 NONBonded N1U 0.1700 3.2467 0.0850 3.2467 NONBonded ON 0.2100 2.9569 0.1050 2.9569 NONBonded O2R 0.2104 3.0633 0.1052 3.0633 NONBonded OH 0.2104 3.0633 0.1052 3.0633 NONBonded SD 0.3515 2.6727 0.1757 2.6727 ! G U E S S. No change 9/97 NONBonded O2 0.2104 3.0633 0.1052 3.0633 ! NEW NONBonded C6C 0.0860 3.3962 0.0430 3.3962 NONBonded C5C 0.0860 3.3962 0.0430 3.3962 NONBonded C4C 0.0860 3.3962 0.0430 3.3962 NONBonded C2C 0.0860 3.3962 0.0430 3.3962 NONBonded C6U 0.0860 3.3962 0.0430 3.3962 NONBonded C5U 0.0860 3.3962 0.0430 3.3962 NONBonded C4U 0.0860 3.3962 0.0430 3.3962 NONBonded C2U 0.0860 3.3962 0.0430 3.3962 NONBonded C8A 0.0860 3.3962 0.0430 3.3962 NONBonded C6A 0.0860 3.3962 0.0430 3.3962 NONBonded C5A 0.0860 3.3962 0.0430 3.3962 NONBonded C4A 0.0860 3.3962 0.0430 3.3962 NONBonded C2A 0.0860 3.3962 0.0430 3.3962 NONBonded C8G 0.0860 3.3962 0.0430 3.3962 NONBonded C6G 0.0860 3.3962 0.0430 3.3962 NONBonded C5G 0.0860 3.3962 0.0430 3.3962 NONBonded C4G 0.0860 3.3962 0.0430 3.3962 NONBonded C2G 0.0860 3.3962 0.0430 3.3962 NONBonded C6T 0.0860 3.3962 0.0430 3.3962 NONBonded C5T 0.0860 3.3962 0.0430 3.3962 NONBonded C4T 0.0860 3.3962 0.0430 3.3962 NONBonded C2T 0.0860 3.3962 0.0430 3.3962 NONBonded N4C 0.1700 3.2467 0.0850 3.2467 NONBonded O4U 0.2100 2.9569 0.1050 3.0633 NONBonded N7G 0.1700 3.2467 0.0850 3.2467 NONBonded N3G 0.1700 3.2467 0.0850 3.2467 NONBonded N2G 0.1700 3.2467 0.0850 3.2467 NONBonded N3A 0.1700 3.2467 0.0850 3.2467 NONBonded N7A 0.1700 3.2467 0.0850 3.2467 NONBonded N6A 0.1700 3.2467 0.0850 3.2467 NONBonded O6G 0.2100 2.9569 0.1050 2.9569 NONBonded CC3E 0.0900 3.2970 0.0450 3.2970 ! no change. Amber equiv.? NONBonded N2A 0.1700 3.2467 0.0850 3.2467 ! special solute-solute hydrogen bonding potential parameters AEXP 4 REXP 6 HAEX 4 AAEX 2 !what are these above terms? !see PARAm HBONDS statement. Syntax may have been changed in CNS???, but these !are the default values, so hopefully won't make a difference...