par_all36_na.prm 60 KB

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  1. * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File ////
  2. * Alexander D. MacKerell Jr. and coworkers
  3. * April 2011
  4. * All comments to the CHARMM web site: www.charmm.org parameter
  5. * set discussion forum
  6. *
  7. !2010/2011 additions
  8. ! ejd, 2010 RNA update
  9. ! adm, 2011 DNA update
  10. ! For DNA update, new atom type required for P of DNA. This required
  11. ! replication of a number of parameters and the creation of new
  12. ! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
  13. ! CHARMM scripts to generate DNA will no longer work. Note that the
  14. ! atom type change to P3 ONLY applies to the phosphodester linkage in
  15. ! DNA and NOT to terminal phosphates, DMP etc.
  16. !
  17. !
  18. !references
  19. !
  20. !NUCLEIC ACIDS
  21. !
  22. !Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and
  23. !MacKerell Jr., A.D. “Optimization of the CHARMM additive force field
  24. !for DNA: Improved treatment of the BI/BII conformational
  25. !equilibrium,” Journal of Chemical Theory and Computation, 8:348–362,
  26. !2012, http://dx.doi.org/10.1021/ct200723y
  27. !
  28. !Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
  29. !“Impact of 2’-hydroxyl sampling on the conformational properties of
  30. !RNA: Update of the CHARMM all-atom additive force field for RNA,”
  31. !JCC, In Press, 2011, NIHMSID #272247
  32. !Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
  33. !Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
  34. !Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
  35. !
  36. !MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
  37. !Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
  38. !and RNA in Solution. JCC, 2000, 21: 105-120.
  39. !
  40. ATOMS
  41. MASS -1 HN1 1.00800 ! Nucleic acid amine proton
  42. MASS -1 HN2 1.00800 ! Nucleic acid ring nitrogen proton
  43. MASS -1 HN3 1.00800 ! Nucleic acid aromatic carbon proton
  44. MASS -1 HN4 1.00800 ! Nucleic acid phosphate hydroxyl proton
  45. MASS -1 HN5 1.00800 ! Nucleic acid ribose hydroxyl proton
  46. MASS -1 HN6 1.00800 ! Nucleic acid ribose aliphatic proton
  47. MASS -1 HN7 1.00800 ! Nucleic acid proton (equivalent to protein HA)
  48. MASS -1 HN8 1.00800 ! Bound to CN8 in nucleic acids/model compounds
  49. MASS -1 HN9 1.00800 ! Bound to CN9 in nucleic acids/model compounds
  50. MASS -1 CN1 12.01100 ! Nucleic acid carbonyl carbon
  51. MASS -1 CN1T 12.01100 ! Nucleic acid carbonyl carbon (T/U C2)
  52. MASS -1 CN2 12.01100 ! Nucleic acid aromatic carbon to amide
  53. MASS -1 CN3 12.01100 ! Nucleic acid aromatic carbon
  54. MASS -1 CN3T 12.01100 ! Nucleic acid aromatic carbon, Thy C5
  55. MASS -1 CN4 12.01100 ! Nucleic acid purine C8 and ADE C2
  56. MASS -1 CN5 12.01100 ! Nucleic acid purine C4 and C5
  57. MASS -1 CN5G 12.01100 ! Nucleic acid guanine C5
  58. MASS -1 CN7 12.01100 ! Nucleic acid carbon (equivalent to protein CT1)
  59. MASS -1 CN7B 12.01100 ! Nucleic acid aliphatic carbon for C1'
  60. MASS -1 CN8 12.01100 ! Nucleic acid carbon (equivalent to protein CT2)
  61. MASS -1 CN8B 12.01100 ! Nucleic acid carbon (equivalent to protein CT2)
  62. MASS -1 CN9 12.01100 ! Nucleic acid carbon (equivalent to protein CT3)
  63. MASS -1 NN1 14.00700 ! Nucleic acid amide nitrogen
  64. MASS -1 NN2 14.00700 ! Nucleic acid protonated ring nitrogen
  65. MASS -1 NN2B 14.00700 ! From NN2, for N9 in GUA different from ADE
  66. MASS -1 NN2U 14.00700 ! Nucleic acid protonated ring nitrogen, ura N3
  67. MASS -1 NN2G 14.00700 ! Nucleic acid protonated ring nitrogen, gua N1
  68. MASS -1 NN3 14.00700 ! Nucleic acid unprotonated ring nitrogen
  69. MASS -1 NN3A 14.00700 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
  70. MASS -1 NN3G 14.00700 ! Nucleic acid unprotonated ring nitrogen, gua N3
  71. MASS -1 NN4 14.00700 ! Nucleic acid purine N7
  72. MASS -1 NN6 14.00700 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
  73. MASS -1 ON1 15.99940 ! Nucleic acid carbonyl oxygen
  74. MASS -1 ON1C 15.99940 ! Nucleic acid carbonyl oxygen, cyt O2
  75. MASS -1 ON2 15.99940 ! Nucleic acid phosphate ester oxygen
  76. MASS -1 ON3 15.99940 ! Nucleic acid =O in phosphate
  77. MASS -1 ON4 15.99940 ! Nucleic acid phosphate hydroxyl oxygen
  78. MASS -1 ON5 15.99940 ! Nucleic acid ribose hydroxyl oxygen
  79. MASS -1 ON6 15.99940 ! Nucleic acid deoxyribose ring oxygen
  80. MASS -1 ON6B 15.99940 ! Nucleic acid ribose ring oxygen
  81. MASS -1 P 30.97400 ! phosphorus
  82. MASS -1 P2 30.97400 ! phosphorus, adm, 2011 DNA update
  83. BONDS
  84. !
  85. !V(bond) = Kb(b - b0)**2
  86. !
  87. !Kb: kcal/mole/A**2
  88. !b0: A
  89. !
  90. !atom type Kb b0
  91. !
  92. !2-(aminobutyl)-1,3-propandiol terms
  93. CN8 NN6 200.000 1.480 ! methylammonium
  94. NN6 HN1 403.000 1.040 ! methylammonium
  95. !abasic deoxynucleoside
  96. ON6 CN8B 260.0 1.420 ! susil
  97. CN8 CN8B 222.50 1.528 ! Alkanes, sacred
  98. !
  99. CN1 CN3 302.0 1.409 !U, adm jr. 11/97
  100. CN1 CN3T 302.0 1.403 !T, adm jr. 11/97
  101. CN1 CN5G 302.0 1.360 !G, adm jr. 11/97
  102. CN1 NN2 380.0 1.367 !C, adm jr. 11/97
  103. CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97
  104. CN1 NN2G 340.0 1.396 !G, adm jr. 11/97
  105. CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97
  106. CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97
  107. CN1 NN3 350.0 1.335 !C, adm jr. 11/97
  108. CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
  109. CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91
  110. CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91
  111. CN2 CN3 320.0 1.406 !C, adm jr. 11/97
  112. CN2 CN5 360.0 1.358 !A, adm jr. 11/97
  113. CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91
  114. CN2 NN2G 400.0 1.392 !G
  115. CN2 NN3 450.0 1.343 !C
  116. CN2 NN3A 400.0 1.342 !A, adm jr. 11/97
  117. CN2 NN3G 320.0 1.326 !G, adm jr. 11/97
  118. CN3 CN3 500.0 1.326 !C,U adm jr. 11/97
  119. CN3 CN3T 560.0 1.320 !T, adm jr. 11/97
  120. CN3T CN9 230.0 1.478 !T, adm jr. 11/97
  121. CN3 HN3 350.0 1.09 !C,U, JWK
  122. CN3T HN3 350.0 1.09 !T, JWK
  123. CN3 NN2 302.0 1.343 !C, adm jr. 11/97
  124. CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97
  125. CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91
  126. CN4 NN2 320.0 1.374 !A, adm jr. 11/97
  127. CN4 NN2B 300.0 1.378 !G, adm jr. 11/97
  128. CN4 NN3A 420.0 1.322 !A, adm jr. 11/97
  129. CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97
  130. CN5 CN5 310.0 1.361 !A, adm jr. 11/97
  131. CN5 CN5G 320.0 1.350 !G, adm jr. 11/97
  132. CN5 NN2 300.0 1.375 !A, adm jr. 11/97
  133. CN5 NN2B 302.0 1.375 !G, adm jr. 11/97
  134. CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91
  135. CN5 NN3G 350.0 1.315 !G, adm jr. 11/97
  136. CN5 NN4 310.0 1.355 !A, adm jr. 11/97
  137. CN5G NN4 310.0 1.365 !G, adm jr. 11/97
  138. CN8 CN8 222.50 1.528 !Alkanes, sacred
  139. CN8 CN9 222.50 1.528 !Alkanes, sacred
  140. CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR.
  141. CN8 ON5 428.0 1.42 !RIBOSE, MeOH
  142. CN9 HN9 322.0 1.111 !alkanes
  143. CN9 ON2 340.0 1.43 !DMP, ADM Jr.
  144. HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91
  145. HN2 NN2 474.0 1.01 !C,U, JWK
  146. HN2 NN2B 474.0 1.01 !G, adm jr. 11/97
  147. HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91
  148. HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91
  149. HN4 ON4 545.0 0.960 !MP_1, ADM Jr.
  150. ON2 P 270.0 1.60 !DMP, ADM Jr.
  151. ON2 P2 270.0 1.60 !DMP, ADM Jr., adm, 2011 DNA update
  152. ON3 P 580.0 1.48 !DMP, ADM Jr.
  153. ON3 P2 580.0 1.48 !DMP, ADM Jr., adm, 2011 DNA update
  154. ON4 P 237.0 1.58 !MP_1, ADM Jr.
  155. ON4 P2 237.0 1.58 !MP_1, ADM Jr., adm, 2011 DNA update
  156. !NN5 HN1 460.0 1.01 !sugar model, adm jr.
  157. !@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
  158. CN7B ON6 260.0 1.420 ! From exp
  159. CN7B CN8 200.0 1.518 ! From exp
  160. CN7 ON6 240.0 1.446 ! Fom exp.
  161. CN7 CN7 222.5 1.529 ! From exp
  162. CN7 CN8 222.5 1.516 ! From exp.
  163. CN7 CN9 222.5 1.516 ! for 5MET, From alkanes
  164. CN7 HN7 309.0 1.111 !Alkanes, sacred
  165. CN8 HN8 309.0 1.111 !Alkanes, sacred
  166. CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF)
  167. !@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
  168. !@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
  169. CN7B ON6B 260.0 1.420 ! From CN7B ON6
  170. CN7 ON6B 240.0 1.480 ! From CN7 ON6
  171. CN7B CN7B 200.0 1.450 !
  172. CN7 CN7B 222.5 1.460 ! Specific to RNA
  173. !@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
  174. !@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
  175. CN7 CN8B 222.5 1.512 ! From exp.
  176. CN8B ON2 320.0 1.44 ! From exp
  177. !CN8B ON5 250.0 1.44 ! From CN8B ON2
  178. CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
  179. CN7 ON2 310.0 1.433 ! From exp
  180. CN7B ON2 310.0 1.433 ! From exp, for NADPH and bkbmod
  181. !CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO
  182. CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
  183. ! C1'-N9 (purines)/C1'-N1 (pyrimidines)
  184. CN9 NN2 400.0 1.456 !9-M-A/C, adm jr.
  185. CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
  186. CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
  187. CN7B NN2 220.0 1.456 !A/C
  188. CN7B NN2B 220.0 1.458 !G/T/U
  189. ! C5'-H in model compounds and DNA
  190. CN8B HN8 309.0 1.111 !Alkanes, sacred
  191. ON5 HN5 545.0 0.960 !RIBOSE, MeOH
  192. !@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
  193. !@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
  194. !CN7B ON5 250.0 1.400 ! From CN7 ON5
  195. CN7B ON5 428.0 1.400 ! check adm jr.,
  196. !FC should be 428.000 based on Meoh
  197. !@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
  198. !@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
  199. CN8 ON2 340.0 1.44 !
  200. !@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
  201. ANGLES
  202. !
  203. !V(angle) = Ktheta(Theta - Theta0)**2
  204. !
  205. !V(Urey-Bradley) = Kub(S - S0)**2
  206. !
  207. !Ktheta: kcal/mole/rad**2
  208. !Theta0: degrees
  209. !Kub: kcal/mole/A**2 (Urey-Bradley)
  210. !S0: A
  211. !
  212. !atom types Ktheta Theta0 Kub S0
  213. !
  214. ! angle parameters have been rearranged based on model
  215. ! compounds and functional groups. Additional angle
  216. ! parameters follow sorted based on the central atom
  217. !
  218. !2-(aminobutyl)-1,3-propandiol terms
  219. CN7 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
  220. CN8 CN7 CN8 58.35 113.60 11.16 2.561 !alkane
  221. CN8 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
  222. HN1 NN6 CN8 30.00 109.50 20.00 2.074 !methylammonium
  223. NN6 CN8 HN8 45.00 107.50 35.00 2.101 !methylammonium
  224. CN7 CN8 ON2 115.00 109.70 !DNA exocyclic angles
  225. NN6 CN8 CN8 67.70 110.00 !methylammonium
  226. HN1 NN6 HN1 44.00 109.50 !methylammonium
  227. !abasic propyl linkage
  228. ON2 CN8 CN8 115.0 109.7 !DNA exocyclic angles
  229. !abasic deoxynucleoside
  230. CN7 ON6 CN8B 110.0 109.0
  231. ON6 CN8B CN8 90.0 106.0
  232. CN8B CN8 CN7 80.0 106.0
  233. ON6 CN8B HN8 45.2 107.24 !
  234. HN8 CN8B CN8 34.53 110.10 22.53 2.179 ! alkane
  235. HN8 CN8 CN8B 34.53 110.10 22.53 2.179 ! alkane
  236. ! pyrmidines
  237. !@@@@@@@@ Adenine
  238. ! ade 6-mem ring
  239. CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97
  240. NN3A CN4 NN3A 60.0 133.0 !6R)
  241. CN4 NN3A CN5 90.0 110.1 !6R)
  242. CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4
  243. CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5
  244. CN5 CN2 NN3A 60.0 110.7 !6R)
  245. CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4
  246. CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5
  247. CN4 NN4 CN5 120.0 104.6 !5R)
  248. NN2 CN4 NN4 100.0 113.4 !5R)
  249. CN4 NN2 CN5 100.0 106.3 !5R)
  250. NN2 CN5 NN3A 100.0 126.9 !bridgeC4
  251. CN2 CN5 NN4 100.0 129.0 !bridgeC5
  252. HN3 CN4 NN3A 38.0 113.5 !h2
  253. NN3A CN2 NN1 50.0 130.7 !n6
  254. CN5 CN2 NN1 50.0 118.6 !
  255. CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G
  256. HN1 NN1 HN1 31.0 117.0 !C,A,G
  257. NN4 CN4 HN3 39.0 124.8 !h8, G,A
  258. NN2 CN4 HN3 39.0 121.8 !
  259. CN5 NN2 HN2 30.0 129.4 !h9
  260. CN4 NN2 HN2 30.0 125.0 !
  261. !@@@@@@@@ Guanine
  262. ! gua 6-mem ring
  263. CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97
  264. NN2G CN2 NN3G 70.0 122.2 !6R)
  265. CN2 NN3G CN5 90.0 109.4 !6R)
  266. CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4
  267. CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5
  268. CN5G CN1 NN2G 70.0 107.8 !6R)
  269. CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4
  270. CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5
  271. CN4 NN4 CN5G 120.0 103.8 !5R)
  272. NN2B CN4 NN4 100.0 113.0 !5R)
  273. CN4 NN2B CN5 100.0 107.2 !5R)
  274. NN2B CN5 NN3G 140.0 125.5 ! bridgeC4
  275. CN1 CN5G NN4 125.0 129.0 ! bridgeC5
  276. CN1 NN2G HN2 45.0 113.3 ! h1
  277. CN2 NN2G HN2 45.0 115.6 !
  278. NN1 CN2 NN2G 95.0 115.4 ! n2
  279. NN1 CN2 NN3G 95.0 122.4 !
  280. NN2G CN1 ON1 50.0 127.5 ! o6
  281. CN5G CN1 ON1 50.0 124.7 !
  282. HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8)
  283. CN4 NN2B HN2 30.0 124.6 ! h9
  284. CN5 NN2B HN2 30.0 129.3 !
  285. !@@@@@@@@ Cytosine
  286. ! cyt 6-mem ring
  287. CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97
  288. NN2 CN1 NN3 50.0 116.8 !C
  289. CN1 NN3 CN2 85.0 119.1 !C
  290. CN3 CN2 NN3 85.0 119.3 !C
  291. CN2 CN3 CN3 85.0 117.8 !C
  292. CN3 CN3 NN2 85.0 122.9 !C
  293. CN1 NN2 HN2 37.0 121.2 !C, h1
  294. CN3 NN2 HN2 37.0 114.7 !C
  295. NN2 CN1 ON1C 130.0 119.4 !C, o2
  296. NN3 CN1 ON1C 130.0 123.8 !C
  297. NN3 CN2 NN1 81.0 122.3 !C, n4
  298. CN3 CN2 NN1 81.0 118.4 !C
  299. CN2 CN3 HN3 38.0 120.1 !C h5
  300. CN3 CN3 HN3 38.0 122.1 !C,U
  301. HN3 CN3 NN2 44.0 115.0 !C, h6
  302. !@@@@@@@@ Uracil
  303. ! ura 6-mem ring
  304. CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97
  305. NN2B CN1T NN2U 50.0 114.0 !U
  306. CN1T NN2U CN1 50.0 130.2 !U
  307. NN2U CN1 CN3 70.0 112.6 !U
  308. CN1 CN3 CN3 100.0 117.6 !U
  309. CN3 CN3 NN2B 100.0 123.6 !U
  310. CN1T NN2B HN2 40.5 122.0 !U, h1
  311. CN3 NN2B HN2 32.0 116.0 !U
  312. NN2B CN1T ON1 100.0 121.6 !U, o2
  313. NN2U CN1T ON1 100.0 124.4 !U
  314. CN1T NN2U HN2 40.5 114.4 !U, h3
  315. CN1 NN2U HN2 40.5 115.4 !U
  316. NN2U CN1 ON1 100.0 121.9 !U, o4
  317. CN3 CN1 ON1 100.0 125.5 !U,
  318. CN1 CN3 HN3 30.0 120.3 !U, h5
  319. HN3 CN3 NN2B 30.0 114.3 !U, h6
  320. ! thymine 6-mem ring (unique from ura)
  321. CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97
  322. CN1 CN3T CN3 120.0 116.7 !T
  323. CN3T CN3 NN2B 120.0 123.6 !125.3 !T
  324. CN3T CN1 ON1 100.0 124.6 !T, o4
  325. CN1 CN3T CN9 38.0 118.7 !T, c5 methyl
  326. CN3 CN3T CN9 38.0 124.6 !T
  327. CN3T CN3 HN3 30.0 122.1 !T, h6
  328. ! base to methyl connection
  329. CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr.
  330. CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91
  331. CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr.
  332. CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91
  333. CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr.
  334. CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr.
  335. CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr.
  336. CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr.
  337. CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr.
  338. CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr.
  339. NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr.
  340. !===== For glycosydic linkage, base to c1'
  341. CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A
  342. CN3 NN2B CN7B 45.0 119.6 !U/T
  343. CN1 NN2 CN7B 45.0 120.0 !C, FC from A
  344. CN3 NN2 CN7B 45.0 115.9 !C
  345. CN5 NN2 CN7B 45.0 126.1 !A
  346. CN4 NN2 CN7B 45.0 127.6 !A
  347. CN5 NN2B CN7B 45.0 126.5 !G
  348. CN4 NN2B CN7B 45.0 126.3 !G
  349. ON6 CN7B NN2 110.0 108.0 !C/A DNA
  350. ON6B CN7B NN2 110.0 112.0 !C/A RNA
  351. CN8 CN7B NN2 110.0 113.7 !C/A
  352. CN7B CN7B NN2 110.0 111.0 !C/A, RNA
  353. ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A
  354. ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A
  355. CN8 CN7B NN2B 110.0 113.7 !T/U/G
  356. CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA
  357. HN7 CN7B NN2 43.0 111.0 !
  358. HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2
  359. !===== End of glycosydic linkage
  360. ! remaining terms ordered based on central atom
  361. CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred
  362. CN9 CN7 HN7 34.6 110.10 22.53 2.179 ! Alkanes, sacred
  363. HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM
  364. HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH
  365. CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
  366. CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
  367. CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred
  368. HN9 CN9 CN7 33.43 110.1 22.53 2.179 ! Alkanes, sacred
  369. HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr.
  370. HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr.
  371. HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr.
  372. HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr.
  373. !HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr.
  374. CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr.
  375. HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr.
  376. HN4 ON4 P2 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. , adm, 2011 DNA update
  377. HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH
  378. HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH
  379. ON2 P ON2 80.0 104.3 !DMP, ADM Jr.
  380. ON2 P2 ON2 80.0 104.3 !DMP, ADM Jr., adm, 2011 DNA update
  381. ON2 P ON4 48.1 108.0 !MP_1, ADM Jr.
  382. ON2 P2 ON4 48.1 108.0 !MP_1, ADM Jr., adm, 2011 DNA update
  383. ON3 P ON4 98.9 108.23 !MP_1, ADM Jr.
  384. ON3 P2 ON4 98.9 108.23 !MP_1, ADM Jr., adm, 2011 DNA update
  385. ON4 P ON4 98.9 104.0 !MP_0, ADM Jr.
  386. ON4 P2 ON4 98.9 104.0 !MP_0, ADM Jr., adm, 2011 DNA update
  387. CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH
  388. HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92
  389. !@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@
  390. CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1'
  391. ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1'
  392. CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3'
  393. CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4'
  394. CN9 CN7 CN7 60.00 102.0 8.0 2.561 !for 5MET, adm jr.
  395. CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4'
  396. HN7 CN7 ON6 45.2 107.24 !
  397. HN7 CN7B ON6 45.2 107.24 !
  398. HN7 CN7 CN7 40.0 108.00 !
  399. CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly
  400. CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes
  401. HN7 CN7 CN8 34.5 110.1 22.53 2.179 !
  402. HN8 CN8 CN7 34.53 110.10 22.53 2.179 !
  403. HN8 CN8 CN8 34.53 110.10 22.53 2.179 !
  404. HN8 CN8 HN8 35.5 109.00 5.40 1.802 !
  405. HN7 CN7 HN7 35.5 109.00 5.40 1.802 !
  406. !@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@
  407. !@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@
  408. CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B
  409. CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6
  410. ON6B CN7B CN7B 90.0 106.0 ! 030998
  411. CN7B CN7B CN7 110.0 96.0 !
  412. CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4'
  413. HN7 CN7 ON6B 45.2 107.24 !
  414. HN7 CN7B ON6B 45.2 107.24 !
  415. CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly
  416. HN7 CN7B HN7 35.5 109.00 5.40 1.802 !
  417. !@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@
  418. !@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@
  419. ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5'
  420. ON6 CN7 CN9 90.0 108.2 !for 5MET, adm jr.
  421. CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5'
  422. CN8 CN7 CN8B 58.35 113.60 11.16 2.561 ! from alkane, 25P1
  423. CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5'
  424. CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3'
  425. CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH and bkbmod
  426. CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3'
  427. CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P
  428. CN8B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P, adm, 2011 DNA update
  429. CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P
  430. CN7 ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, adm, 2011 DNA update
  431. CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod
  432. CN7B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod, adm, 2011 DNA update
  433. ! sugar
  434. HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8
  435. HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2
  436. HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8
  437. HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred
  438. HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred
  439. HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2
  440. HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH and bkbmod
  441. !===== For 5ter patch:
  442. CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5
  443. CN8B CN7 ON5 90.0 108.2 ! phosphoramidate, carbocyclic
  444. HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5
  445. !===== For 3ter patch:
  446. ON5 CN7 CN8 75.7 110.0 ! from CHARMM22
  447. ON5 CN7 CN7 75.7 110.1 !
  448. HN7 CN7 ON5 60.0 109.5 !
  449. HN5 ON5 CN7 57.5 109.0 !
  450. !@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@
  451. !@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@
  452. !O4'-C4'-C5'
  453. ON6B CN7 CN8B 90.0 108.2 !
  454. ON6B CN7 CN9 90.0 108.2 ! for 5MET patch, adm jr.
  455. !O3'-C3'-C2'
  456. ON2 CN7 CN7B 90.0 110.0 !
  457. ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8
  458. !O2'-C2'-C1'
  459. ON5 CN7B CN7B 80.0 108.4 !
  460. !O2'-C2'-C3'
  461. ON5 CN7B CN7 90.0 108.0 !
  462. HN7 CN7B ON5 60.0 109.5 !
  463. HN5 ON5 CN7B 57.5 109.0 !
  464. HN7 CN7B CN7 34.53 110.10 22.53 2.179
  465. HN7 CN7 CN7B 34.53 110.10 22.53 2.179
  466. !@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@
  467. !@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@
  468. CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr.
  469. CN8 ON2 P2 20.0 120.0 35. 2.33 !DMP, adm jr., adm 2011 DNA update
  470. !@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@
  471. ON2 P ON3 98.9 111.6 !DMP, adm jr.
  472. ON2 P2 ON3 98.9 111.6 !DMP, adm jr., adm, 2011 DNA update
  473. ON3 P ON3 120.0 120.0 !DMP, adm jr.
  474. ON3 P2 ON3 120.0 120.0 !DMP, adm jr., adm, 2011 DNA update
  475. HN8 CN8 ON2 60.0 109.5 !DMP, adm jr.
  476. ON5 P ON3 98.9 111.6 ! From ON2 P ON3
  477. !------------------------ added for araim ----------------------
  478. ON6 CN7B CN7 120.0 106.25 !
  479. CN7B CN7 CN8 58.35 113.6 11.16 2.561 !
  480. DIHEDRALS
  481. !
  482. !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
  483. !
  484. !Kchi: kcal/mole
  485. !n: multiplicity
  486. !delta: degrees
  487. !
  488. !atom types Kchi n delta
  489. !2-(aminobutyl)-1,3-propandiol terms
  490. X CN8 ON2 X -0.10 3 0.0 ! phosphate ester
  491. X CN7 CN8 X 0.20 3 0.0 ! alkane
  492. X CN8 NN6 X 0.10 3 0.0 ! methylammonium
  493. !abasic nucleoside terms - susil
  494. CN7 ON6 CN8B HN8 0.195 1 0.0
  495. ON6 CN8B CN8 HN8 0.195 1 0.0
  496. HN7 CN7 ON6 CN8B 0.195 3 0.0
  497. CN8B CN8 CN7 HN7 0.195 3 0.0
  498. HN8 CN8B CN8 HN8 0.195 3 0.0
  499. HN8 CN8B CN8 CN7 0.195 3 0.0
  500. ! c5'-c4'-o4'-c1', exo
  501. CN8B CN7 ON6 CN8B 0.5 5 0.0 ! min at 150 310 max at 25 200
  502. CN8B CN7 ON6 CN8B 0.1 3 180.0
  503. CN8B CN7 ON6 CN8B 0.5 1 0.0
  504. ! c1'-c2'-c3'-o3', exo
  505. CN8B CN8 CN7 ON5 0.4 5 0.0
  506. CN8B CN8 CN7 ON5 0.4 3 0.0
  507. CN8B CN8 CN7 ON5 0.7 2 0.0 !elevates energy at 0 (c3'endo), adm
  508. CN8B CN8 CN7 ON5 0.5 1 180.0 !elevates energy at 0 (c3'endo), adm
  509. CN8B CN8 CN7 ON2 0.4 5 0.0 !terms for oligonuclotide
  510. CN8B CN8 CN7 ON2 0.4 3 0.0
  511. CN8B CN8 CN7 ON2 0.7 2 0.0
  512. CN8B CN8 CN7 ON2 0.5 1 180.0
  513. ! c4'-o4'-c1'-c2', tau0
  514. CN7 ON6 CN8B CN8 0.6 6 180.0
  515. CN7 ON6 CN8B CN8 0.6 3 0.0
  516. ! o4'-c1'-c2'-c3', tau1
  517. ON6 CN8B CN8 CN7 0.7 5 180.0 !lowers 90, shifts c2endo minimum towards 200
  518. ON6 CN8B CN8 CN7 0.4 4 0.0 !lowers 90, shifts c2endo minimum towards 200
  519. ON6 CN8B CN8 CN7 0.4 3 180.0 !lowers 90, shifts c2endo minimum towards 200
  520. ! c4'-c3'-c2'-c1', tau2
  521. CN7 CN7 CN8 CN8B 0.5 4 0.0
  522. CN7 CN7 CN8 CN8B 0.1 3 0.0 !lowers energy in 150 to 250 range
  523. ! c1'-o4'-c4'-c3', tau4
  524. CN8B ON6 CN7 CN7 0.5 3 0.0 !effects surface in 200-360 region
  525. ! PHOSPHATE
  526. ON2 P2 ON2 CN7 0.90 1 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
  527. ON2 P2 ON2 CN7 0.40 2 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
  528. ON2 P2 ON2 CN7 0.20 3 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
  529. ON2 P ON2 CN7 1.20 1 180.0 !10/97, DMP, adm jr., RNA
  530. ON2 P ON2 CN7 0.10 2 180.0 !10/97, DMP, adm jr., RNA
  531. ON2 P ON2 CN7 0.10 3 180.0 !10/97, DMP, adm jr., RNA
  532. ON2 P ON2 CN7 0.00 6 0.0 !10/97, DMP, adm jr., RNA
  533. ON2 P ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr.
  534. ON2 P ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr.
  535. ON2 P ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr.
  536. ON2 P ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr.
  537. ON2 P2 ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
  538. ON2 P2 ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
  539. ON2 P2 ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
  540. ON2 P2 ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr., adm 2011 DNA update
  541. ! Added when C5' defined as CN8B (NF 041497):
  542. ON2 P2 ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
  543. ON2 P2 ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
  544. ON2 P2 ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
  545. ON2 P2 ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., adm, 2011 DNA update
  546. ON2 P ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., RNA
  547. ON2 P ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., RNA
  548. ON2 P ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., RNA
  549. ON2 P ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., RNA
  550. ON2 P ON2 CN9 1.20 1 180.0 !dmp
  551. ON2 P ON2 CN9 0.10 2 180.0 !dmp
  552. ON2 P ON2 CN9 0.10 3 180.0 !dmp
  553. ON2 P ON2 CN9 0.00 6 0.0 !dmp
  554. ON2 P2 ON2 CN9 1.20 1 180.0 !dmp, adm, 2011 DNA update
  555. ON2 P2 ON2 CN9 0.10 2 180.0 !dmp, adm, 2011 DNA update
  556. ON2 P2 ON2 CN9 0.10 3 180.0 !dmp, adm, 2011 DNA update
  557. ON2 P2 ON2 CN9 0.00 6 0.0 !dmp, adm, 2011 DNA update
  558. !
  559. ON3 P ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3'
  560. ON3 P2 ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3', adm, 2011 DNA update
  561. ON3 P ON2 CN7B 0.10 3 0.0 !for NADPH and bkbmod
  562. ON3 P ON2 CN8 0.10 3 0.0 !dmp
  563. ON3 P2 ON2 CN8 0.10 3 0.0 !dmp, adm 2011 DNA update
  564. ON3 P ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5'
  565. ON3 P2 ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5', adm, 2011 DNA update
  566. ON3 P ON2 CN9 0.10 3 0.0 !dmp
  567. ON3 P2 ON2 CN9 0.10 3 0.0 !dmp, adm, 2011 DNA update
  568. ! terminal phosphate terms, adm jr.
  569. ON4 P ON2 CN7 0.95 2 0.0 !MP_1, adm jr.
  570. ON4 P ON2 CN7 0.50 3 0.0 !MP_1, adm jr.
  571. ON4 P2 ON2 CN7 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
  572. ON4 P2 ON2 CN7 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
  573. ON4 P ON2 CN8 0.95 2 0.0 !MP_1, adm jr.
  574. ON4 P ON2 CN8 0.50 3 0.0 !MP_1, adm jr.
  575. ON4 P ON2 CN8B 0.95 2 0.0 !MP_1, adm jr.
  576. ON4 P ON2 CN8B 0.50 3 0.0 !MP_1, adm jr.
  577. ON4 P2 ON2 CN8B 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
  578. ON4 P2 ON2 CN8B 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
  579. ON4 P ON2 CN9 0.95 2 0.0 !MP_1, adm jr.
  580. ON4 P ON2 CN9 0.50 3 0.0 !MP_1, adm jr.
  581. ON4 P2 ON2 CN9 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
  582. ON4 P2 ON2 CN9 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
  583. X ON4 P X 0.30 3 0.0 !MP_1, adm jr.
  584. X ON4 P2 X 0.30 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
  585. ! When O5' is ON2 (phosphodiester linkage):
  586. P ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P
  587. P2 ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P, adm, 2011 DNA update
  588. P ON2 CN7B HN7 0.000 3 0.0 !for NADPH and bkbmod
  589. P ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P
  590. P2 ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P, adm, 2011 DNA update
  591. P ON2 CN8 HN8 0.000 3 0.0 !dmp
  592. P ON2 CN9 HN9 0.000 3 0.0 !dmp
  593. P2 ON2 CN9 HN9 0.000 3 0.0 !dmp, adm, 2011 DNA update
  594. ! butane gauche terms
  595. cn9 cn8 cn8 cn9 0.15 1 0.0
  596. cn9 cn8 cn8 cn8 0.15 1 0.0
  597. ! BASES
  598. ! Uracil
  599. NN2B CN1T NN2U CN1 1.5 2 180.0 ! adm jr. 11/97
  600. CN1T NN2U CN1 CN3 1.5 2 180.0 ! adm jr. 11/97
  601. NN2U CN1 CN3 CN3 1.5 2 180.0 ! adm jr. 11/97
  602. CN1 CN3 CN3 NN2B 6.0 2 180.0 ! adm jr. 11/97
  603. CN3 CN3 NN2B CN1T 1.5 2 180.0 ! adm jr. 11/97
  604. CN3 NN2B CN1T NN2U 1.5 2 180.0 ! adm jr. 11/97
  605. HN3 CN3 CN3 HN3 3.0 2 180.0 ! adm jr. 11/97
  606. HN3 CN3 CN1 ON1 6.0 2 180.0 ! adm jr. 11/97
  607. ON1 CN1T NN2B HN2 0.0 2 180.0 ! adm jr. 11/97
  608. ON1 CN1 NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
  609. ON1 CN1T NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
  610. HN2 NN2B CN3 HN3 1.5 2 180.0 ! adm jr. 11/97
  611. NN2B CN1T NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
  612. CN3 CN1 NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
  613. CN3 CN3 NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
  614. NN2U CN1T NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
  615. !Thymine
  616. CN1T NN2B CN3 CN3T 1.8 2 180.0 ! adm jr. 11/97
  617. NN2U CN1 CN3T CN3 1.8 2 180.0 ! adm jr. 11/97
  618. CN1 CN3T CN3 NN2B 3.0 2 180.0 ! adm jr. 11/97
  619. NN2B CN1 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
  620. NN2B CN3 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
  621. CN1 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
  622. CN3 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
  623. CN3T CN1 NN2U HN2 4.8 2 180.0 ! adm jr. 11/97
  624. ! Cytosine
  625. CN3 NN2 CN1 NN3 0.6 2 180.0 ! adm jr. 11/97
  626. NN2 CN1 NN3 CN2 0.6 2 180.0 ! adm jr. 11/97
  627. CN1 NN3 CN2 CN3 6.0 2 180.0 ! adm jr. 11/97
  628. NN3 CN2 CN3 CN3 0.6 2 180.0 ! adm jr. 11/97
  629. CN2 CN3 CN3 NN2 6.0 2 180.0 ! adm jr. 11/97
  630. CN3 CN3 NN2 CN1 0.6 2 180.0 ! adm jr. 11/97
  631. NN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
  632. CN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
  633. NN1 CN2 NN3 CN1 2.0 2 180.0 ! adm jr. 11/97
  634. NN1 CN2 CN3 CN3 2.0 2 180.0 ! adm jr. 11/97
  635. NN1 CN2 CN3 HN3 2.0 2 180.0 ! adm jr. 11/97
  636. ON1C CN1 NN2 HN2 3.0 2 180.0 ! adm jr. 11/97
  637. ON1C CN1 NN3 CN2 1.6 2 180.0 ! adm jr. 11/97
  638. ON1C CN1 NN2 CN3 1.6 2 180.0 ! adm jr. 11/97
  639. NN3 CN2 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
  640. NN2 CN3 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
  641. CN2 CN3 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
  642. CN1 NN2 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
  643. X CN2 NN3 X 2.0 2 180.0 ! adm jr. 11/97
  644. ! Adenine
  645. CN2 NN3A CN4 NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem
  646. NN3A CN4 NN3A CN5 2.0 2 180.0 !
  647. CN4 NN3A CN5 CN5 1.8 2 180.0 !
  648. NN3A CN5 CN5 CN2 2.0 2 180.0 ! treated 2x
  649. CN5 CN5 CN2 NN3A 1.8 2 180.0 !
  650. CN5 CN2 NN3A CN4 10.0 2 180.0 !
  651. CN5 CN5 NN4 CN4 6.0 2 180.0 ! 5-mem
  652. CN5 NN4 CN4 NN2 14.0 2 180.0 !
  653. NN4 CN4 NN2 CN5 6.0 2 180.0 !
  654. CN4 NN2 CN5 CN5 6.0 2 180.0 !
  655. NN2 CN5 CN5 NN4 14.0 2 180.0 ! treated 2x
  656. CN2 NN3A CN4 HN3 8.5 2 180.0 ! H2
  657. CN5 NN3A CN4 HN3 8.5 2 180.0 ! H2
  658. CN5 NN4 CN4 HN3 5.2 2 180.0 ! H8
  659. CN5 NN2 CN4 HN3 5.2 2 180.0 ! H8
  660. CN5 CN5 NN2 HN2 1.2 2 180.0 ! H9
  661. NN4 CN4 NN2 HN2 1.2 2 180.0 ! H9
  662. HN2 NN2 CN4 HN3 0.0 2 180.0 ! H8-C-N-H9
  663. CN4 NN3A CN2 NN1 4.0 2 180.0 ! N6
  664. CN5 CN5 CN2 NN1 4.0 2 180.0 ! N6
  665. NN4 CN5 CN2 NN1 0.0 2 180.0 ! N6
  666. CN5 CN2 NN1 HN1 0.5 2 180.0 ! 6-NH2
  667. NN3A CN2 NN1 HN1 0.5 2 180.0 !
  668. ! Butterfly motion
  669. NN3A CN5 CN5 NN4 7.0 2 180.0 !A, adm jr. 11/97
  670. CN2 CN5 CN5 NN2 7.0 2 180.0 !A
  671. NN3A CN2 CN5 NN4 2.0 2 180.0 !A
  672. CN2 CN5 NN4 CN4 2.0 2 180.0 !A
  673. CN4 NN3A CN5 NN2 2.0 2 180.0 !A
  674. NN3A CN5 NN2 CN4 2.0 2 180.0 !A
  675. ! Guanine
  676. CN1 NN2G CN2 NN3G 0.2 2 180.0 !adm jr. 11/97, 6-mem
  677. NN2G CN2 NN3G CN5 2.0 2 180.0 !
  678. CN2 NN3G CN5 CN5G 0.2 2 180.0 !
  679. NN3G CN5 CN5G CN1 2.0 2 180.0 !
  680. CN5 CN5G CN1 NN2G 0.2 2 180.0 !
  681. CN5G CN1 NN2G CN2 0.2 2 180.0 !
  682. CN5 CN5G NN4 CN4 6.0 2 180.0 !5-mem
  683. CN5G NN4 CN4 NN2B 16.0 2 180.0 !
  684. NN4 CN4 NN2B CN5 6.0 2 180.0 !
  685. CN4 NN2B CN5 CN5G 6.0 2 180.0 !
  686. NN2B CN5 CN5G NN4 10.0 2 180.0 !
  687. ! substitutents
  688. ON1 CN1 CN5G CN5 14.0 2 180.0 !G, O6
  689. ON1 CN1 CN5G NN4 0.0 2 180.0 !
  690. ON1 CN1 NN2G CN2 14.0 2 180.0 !
  691. ON1 CN1 NN2G HN2 0.0 2 180.0 !
  692. NN1 CN2 NN2G CN1 4.0 2 180.0 !G, N2
  693. NN1 CN2 NN3G CN5 4.0 2 180.0 !
  694. NN1 CN2 NN2G HN2 0.0 2 180.0 !
  695. NN2G CN2 NN1 HN1 1.2 2 180.0 !
  696. NN3G CN2 NN1 HN1 1.2 2 180.0 !
  697. HN2 NN2G CN1 CN5G 3.6 2 180.0 !G, H1
  698. HN2 NN2G CN2 NN3G 3.6 2 180.0 !
  699. HN3 CN4 NN4 CN5G 5.6 2 180.0 !G, H8
  700. HN3 CN4 NN2B CN5 5.6 2 180.0 !
  701. HN3 CN4 NN2B HN2 0.0 2 180.0 !
  702. HN2 NN2B CN5 CN5G 1.2 2 180.0 !G, H9
  703. HN2 NN2B CN5 NN3G 1.2 2 180.0 !
  704. HN2 NN2B CN4 NN4 1.2 2 180.0 !
  705. ! Butterfly motion
  706. NN3G CN5 CN5G NN4 10.0 2 180.0 !adm jr. 11/97
  707. CN1 CN5G CN5 NN2 10.0 2 180.0 !
  708. NN2G CN1 CN5G NN4 2.0 2 180.0 !
  709. CN1 CN5G NN4 CN4 2.0 2 180.0 !
  710. CN2 NN3G CN5 NN2B 2.0 2 180.0 !
  711. NN3G CN5 NN2B CN4 2.0 2 180.0 !
  712. ! Wild cards for uracil, thymine and cytosine
  713. X CN1 NN3 X 1.0 2 180.0 ! c22
  714. X CN1 NN2 X 0.9 2 180.0 ! c22
  715. X CN1T NN2B X 0.9 2 180.0 ! From X CN1 NN2 X, for thymines
  716. X CN1 NN2G X 0.9 2 180.0 ! c22
  717. X CN1 NN2U X 0.9 2 180.0 ! c22
  718. X CN1T NN2U X 0.9 2 180.0 ! c22
  719. X CN3 NN2 X 1.0 2 180.0 ! c22
  720. X CN3 NN2B X 1.0 2 180.0 ! From X CN3 NN2 X, for thymines
  721. X CN3 CN3 X 1.0 2 180.0 ! c22
  722. X CN3 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
  723. X CN1 CN3 X 1.0 2 180.0 ! c22
  724. X CN1 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
  725. X CN2 CN3 X 0.8 2 180.0 ! c22
  726. ! Wild cards for adenine and guanine
  727. X CN1 CN5G X 1.0 2 180.0 ! adm jr. 11/97
  728. X CN2 NN2G X 1.0 2 180.0 !
  729. X CN2 CN5 X 1.0 2 180.0 !
  730. X CN4 NN2 X 1.5 2 180.0 !
  731. X CN4 NN2B X 1.5 2 180.0 ! From X CN4 NN2 X
  732. X CN4 NN3A X 3.5 2 180.0 !
  733. X CN4 NN4 X 2.0 2 180.0 ! A,G
  734. X CN5 CN5 X 0.0 2 180.0 !
  735. X CN5G CN5 X 0.0 2 180.0 ! adm jr. 11/97
  736. X CN5 NN2 X 1.5 2 180.0 !
  737. X CN5 NN2B X 1.5 2 180.0 ! From X CN5 NN2 X
  738. X CN5 NN3A X 1.0 2 180.0 !
  739. X CN5 NN3G X 1.0 2 180.0 ! adm jr. 11/97
  740. X CN5 NN4 X 1.0 2 180.0 !
  741. X CN5G NN4 X 1.0 2 180.0 ! adm jr. 11/97
  742. X CN2 NN3A X 1.0 2 180.0 !
  743. X CN2 NN3G X 1.0 2 180.0 ! adm jr. 11/97
  744. ! MISC.
  745. CN1 NN2 CN9 HN9 0.19 3 0.0 ! 1-M-C
  746. CN3 NN2 CN9 HN9 0.00 3 0.0 ! 1-M-C
  747. CN4 NN2 CN9 HN9 0.00 3 0.0 ! 9-M-A
  748. CN5 NN2 CN9 HN9 0.19 3 0.0 ! 9-M-A
  749. CN1 NN2B CN9 HN9 0.19 3 0.0 ! 1-M-U
  750. CN1T NN2B CN9 HN9 0.19 3 0.0 ! 1-M-T
  751. CN3 NN2B CN9 HN9 0.00 3 0.0 ! 1-M-T/U
  752. CN4 NN2B CN9 HN9 0.00 3 0.0 ! 9-M-G
  753. CN5 NN2B CN9 HN9 0.19 3 0.0 ! 9-M-G
  754. CN4 NN2B CN8 HN8 0.00 3 0.0 ! 9-E-G
  755. CN5 NN2B CN8 HN8 0.19 3 0.0 ! 9-E-G
  756. CN4 NN2B CN8 CN9 0.00 3 0.0 ! 9-E-G
  757. CN5 NN2B CN8 CN9 0.19 3 0.0 ! 9-E-G
  758. X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
  759. X CN8 CN9 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
  760. !for nadp/nadph, adm jr.
  761. HN7 CN7B CN7B ON2 0.195 3 0.0 !for NADPH and bkbmod
  762. ON2 CN7B CN7B NN2 0.0 3 0.0 !for NADPH and bkbmod
  763. ! sugar, replace with ribose terms 021998
  764. CN7 CN7B ON6 CN7 0.6 6 180.0
  765. CN7B CN7 CN7 CN7 0.4 6 0.0 ! good for amplitudes
  766. CN7B CN7 CN7 CN9 0.4 6 0.0 ! good for amplitudes, 5MET
  767. CN7 CN7 CN7 ON6 0.6 6 0.0
  768. CN7 CN7 CN7B ON6 0.6 6 0.0
  769. ON2 CN7 CN7 CN7 0.8 6 0.0 !
  770. ON2 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
  771. ON2 CN7 CN7 CN7 2.0 3 180.0 !
  772. ! for ndph
  773. ON2 CN7B CN7 CN7 0.8 6 0.0 !
  774. ON2 CN7B CN7 CN7 0.4 5 0.0 ! Moves the barrier right
  775. ON2 CN7B CN7 CN7 2.0 3 180.0 !
  776. !
  777. ON5 CN7 CN7 CN7 0.8 6 0.0 !
  778. ON5 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
  779. ON5 CN7 CN7 CN7 2.0 3 180.0 !
  780. ON5 CN7 CN7 ON5 0.0 3 0.0 !
  781. ON5 CN7 CN7 ON2 0.0 3 0.0 !
  782. ON2 CN7 CN7B ON6 0.5 6 0.0 !good for amplitudes
  783. ON2 CN7 CN7B ON6 0.3 5 0.0 !impact on amplitudes
  784. ON2 CN7 CN7B ON6 0.6 4 180.0 !increases c2'endo
  785. ON2 CN7 CN7B ON6 0.2 3 0.0 !
  786. CN7 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
  787. !%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%%
  788. ! The following is for: THF3P (model for espilon), THFM3P (model for puckering),
  789. ! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue
  790. !@@@@@@ Begining of chi
  791. !============= added for torsion about chi in adenine ============
  792. !For link from sugar to base:
  793. CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF
  794. CN7B NN2 CN5 CN5 11.0 2 180.0 ! adm jr.
  795. CN7B NN2 CN4 NN4 11.0 2 180.0 ! adm jr.
  796. CN7B NN2 CN4 NN3A 11.0 2 180.0 ! adm jr.
  797. !For chi itself:
  798. !DNA:
  799. ON6 CN7B NN2 CN5 1.1 1 180.0 !
  800. ON6 CN7B NN2 CN4 1.1 1 0.0 ! NF
  801. !RNA:
  802. ON6B CN7B NN2 CN5 1.1 1 180.0 !
  803. ON6B CN7B NN2 CN4 1.1 1 0.0 !
  804. !DNA:
  805. CN8 CN7B NN2 CN5 0.3 3 0.0 ! NF
  806. CN8 CN7B NN2 CN4 0.0 3 180.0 ! NF
  807. !RNA:
  808. CN7B CN7B NN2 CN5 0.3 3 0.0 ! NF
  809. CN7B CN7B NN2 CN4 0.0 3 180.0 ! NF
  810. HN7 CN7B NN2 CN5 0.0 3 0.0 ! NF
  811. HN7 CN7B NN2 CN4 0.195 3 0.0 ! NF
  812. !@@@@@@ End of chi in adenines
  813. !============== terms for torsion about chi in cytosines ===========
  814. CN7B NN2 CN3 HN3 0.3 2 180.0 ! NF
  815. CN7B NN2 CN1 ON1C 11.0 2 180.0 ! adm jr. from A
  816. CN7B NN2 CN1 NN3 11.0 2 180.0 ! adm jr.
  817. CN7B NN2 CN3 CN3 11.0 2 180.0 ! adm jr.
  818. !DNA:
  819. ON6 CN7B NN2 CN1 0.0 3 0.0 !
  820. ON6 CN7B NN2 CN3 1.0 1 0.0 ! NF
  821. !RNA:
  822. ON6B CN7B NN2 CN1 0.0 3 0.0 !
  823. ON6B CN7B NN2 CN3 1.0 1 0.0 !
  824. !DNA:
  825. CN8 CN7B NN2 CN1 1.0 3 0.0 !
  826. CN8 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697
  827. !RNA:
  828. CN7B CN7B NN2 CN1 1.0 3 0.0 !
  829. CN7B CN7B NN2 CN3 0.0 3 180.0 !
  830. HN7 CN7B NN2 CN1 0.0 3 0.0 ! NF
  831. HN7 CN7B NN2 CN3 0.195 3 0.0 ! NF
  832. !@@@@@@ End of chi in cytosines
  833. !=========== terms for torsion about chi in uracils/thymines ===========
  834. CN7B NN2B CN3 HN3 0.3 2 180.0 ! NF
  835. CN7B NN2B CN1T ON1 11.0 2 180.0 ! adm jr. from A
  836. CN7B NN2B CN1T NN2U 11.0 2 180.0 ! adm jr.
  837. CN7B NN2B CN3 CN3T 11.0 2 180.0 ! adm jr.
  838. !DNA:
  839. ON6 CN7B NN2B CN1 0.0 3 0.0 !
  840. ON6 CN7B NN2B CN1T 0.7 3 0.0 !
  841. ON6 CN7B NN2B CN1T 0.8 1 180.0 !
  842. ON6 CN7B NN2B CN3 0.9 1 0.0 ! NF
  843. !RNA:
  844. ON6B CN7B NN2B CN1 0.0 3 0.0 !
  845. ON6B CN7B NN2B CN1T 0.7 3 0.0 !
  846. ON6B CN7B NN2B CN1T 0.8 1 180.0 !
  847. ON6B CN7B NN2B CN3 0.9 1 0.0 !
  848. !DNA:
  849. CN8 CN7B NN2B CN1T 0.2 3 180.0 !
  850. CN8 CN7B NN2B CN3 0.0 3 180.0 ! NF
  851. !RNA:
  852. CN7B CN7B NN2B CN1T 0.2 3 180.0 !
  853. CN7B CN7B NN2B CN3 0.0 3 180.0 !
  854. HN7 CN7B NN2B CN1T 0.0 3 0.0 ! NF
  855. HN7 CN7B NN2B CN3 0.195 3 0.0 ! NF
  856. !@@@@@@ End of chi in thymines
  857. !============= added for torsion about chi in guanine ============
  858. CN7B NN2B CN4 HN3 0.3 2 180.0 ! NF
  859. CN7B NN2B CN4 NN4 11.0 2 180.0 ! adm jr.
  860. CN7B NN2B CN5 CN5G 11.0 2 180.0 ! adm jr. from U
  861. CN7B NN2B CN5 NN3G 11.0 2 180.0 ! adm jr.
  862. !DNA:
  863. ON6 CN7B NN2B CN5 0.2 3 0.0 !
  864. ON6 CN7B NN2B CN5 1.1 1 180.0 !
  865. ON6 CN7B NN2B CN4 1.4 1 0.0 ! NF
  866. !RNA:
  867. ON6B CN7B NN2B CN5 0.2 3 0.0 !
  868. ON6B CN7B NN2B CN5 1.1 1 180.0 !
  869. ON6B CN7B NN2B CN4 1.4 1 0.0 !
  870. !DNA:
  871. CN8 CN7B NN2B CN5 0.0 3 0.0 ! NF
  872. CN8 CN7B NN2B CN4 0.0 3 180.0 ! NF 030697
  873. !RNA:
  874. CN7B CN7B NN2B CN5 0.0 3 0.0 ! NF
  875. CN7B CN7B NN2B CN4 0.0 3 180.0 !
  876. HN7 CN7B NN2B CN5 0.0 3 0.0 ! NF
  877. HN7 CN7B NN2B CN4 0.195 3 0.0 ! NF
  878. !@@@@@@ End of chi in guanines
  879. !@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines:
  880. !DNA:
  881. CN7 ON6 CN7B NN2 0.0 3 0.0
  882. CN7 ON6 CN7B NN2B 0.0 3 0.0
  883. !RNA:
  884. CN7 ON6B CN7B NN2 0.0 3 0.0
  885. CN7 ON6B CN7B NN2B 0.0 3 0.0
  886. !DNA:
  887. CN7 CN8 CN7B NN2 0.0 3 0.0
  888. CN7 CN8 CN7B NN2B 0.0 3 0.0
  889. HN8 CN8 CN7B NN2 0.0 3 0.0
  890. HN8 CN8 CN7B NN2B 0.0 3 0.0
  891. !RNA:
  892. CN7 CN7B CN7B NN2 0.0 3 0.0
  893. CN7 CN7B CN7B NN2B 0.0 3 0.0
  894. !RNA
  895. HN7 CN7B CN7B NN2 0.0 3 0.0
  896. HN7 CN7B CN7B NN2B 0.0 3 0.0
  897. !@@@@@@ Begining of torsions involving exocyclic sugar atoms:
  898. !======= CN7 CN8B ON2 P = C4'-C5'-O5'-P
  899. CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr.
  900. CN7 CN8B ON2 P2 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr., adm, 2011 DNA update
  901. ! the following differ significantly from the alcohols
  902. ! in the protein (based on ethanol), they also differ from other
  903. ! NA C-C-OH-H parameters (see below)
  904. ! The two following terms have been replaced by their ethanol
  905. ! counterpart (NF, 083098)
  906. CN7 CN8B ON5 HN5 1.3300 1 0.00
  907. CN7 CN8B ON5 HN5 0.1800 2 0.00
  908. CN7 CN8B ON5 HN5 0.3200 3 0.00
  909. !======= HN8 CN8B ON2 P = H-C5'-O5'-P )beta
  910. HN8 CN8B ON5 HN5 0.0 3 0.0 !bet
  911. !======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5'
  912. ! When O5' is ON2 (phosphodiester linkage):
  913. CN7 CN7 CN8B ON2 0.20 4 180.0 !gam adm jr.
  914. CN7 CN7 CN8B ON2 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
  915. CN7 CN7 CN8B ON2 0.40 2 0.0 !gam
  916. CN7 CN7 CN8B ON2 2.50 1 180.0 !gam
  917. !
  918. CN8 CN7 CN8B ON2 0.2 3 180.0 ! from gam, carbocyclic and 25P1
  919. ! When O5' is ON5 (5TER patch):
  920. CN7 CN7 CN8B ON5 0.20 4 180.0 !gam adm jr.
  921. CN7 CN7 CN8B ON5 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
  922. CN7 CN7 CN8B ON5 0.40 2 0.0 !gam
  923. CN7 CN7 CN8B ON5 2.50 1 180.0 !gam
  924. !======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5'
  925. ! When O5' is ON2 (3'-5' phosphodiester linkage)
  926. ON6 CN7 CN8B ON2 3.4 1 180.0 !gam O4'-C4'-C5'-O5',influences +60
  927. ON6B CN7 CN8B ON2 3.4 1 180.0 !gam, RNA
  928. ! When O5' is ON5 (5TER patch):
  929. ON6 CN7 CN8B ON5 3.4 1 180.0 !gam
  930. ON6B CN7 CN8B ON5 3.4 1 180.0 !gam, RNA
  931. !======== HN8 CN8B CN7 CN7 = H-C5'-C4'-H
  932. HN8 CN8B CN7 CN7 0.195 3 0.0 !gam,H-C5'-C4'-H
  933. HN8 CN8B CN7 CN8 0.195 1 0.0 !gam, carbocylic, 25P1
  934. !======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4'
  935. HN8 CN8B CN7 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
  936. HN8 CN8B CN7 ON6B 0.195 1 0.0 !gam, RNA
  937. !======== HN7 CN7 CN8B ON2 = H-C4'-C5'-O5'
  938. ! When O5' is ON2 (phosphodiester linkage):
  939. HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5'
  940. ! When O5' is ON5 (5TER patch):
  941. HN7 CN7 CN8B ON5 0.195 3 0.0 !gam
  942. HN8 CN8 CN8 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
  943. ! terms for 5MET patch
  944. CN9 CN7 CN7 CN8B 0.5 4 180.0 !cn8 -> cn9
  945. HN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
  946. CN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
  947. ON6 CN7 CN9 HN9 0.195 3 0.0 !cn7 -> cn9
  948. HN7 CN7 CN7 CN9 0.195 3 0.0 !cn8 -> cn9
  949. ON2 CN7 CN7 CN9 0.2 4 0.0 !cn8b -> cn9
  950. ON2 CN7 CN7 CN9 0.8 3 180.0 !cn8b -> cn9
  951. CN8 CN7 CN7 CN9 0.5 4 180.0 !cn8b -> cn9
  952. !======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5'
  953. ! This term is well suited to modify the puckering surfaces, in
  954. ! particular because it is present in THF5P
  955. CN8 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
  956. CN7B CN7 CN7 CN8B 0.2 4 180.0 !del, RNA
  957. !======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3'
  958. ! These terms affect the c2endo/c3endo energy difference
  959. ! When O3' is ON2 (3'-5' phosphodiester linkage)
  960. ON2 CN7 CN7 CN8B 0.2 4 0.0 !del
  961. ! the following term controls the location of the barrier at ~75 deg.
  962. ON2 CN7 CN7 CN8B 0.8 3 180.0 !del,decreases P [100,250]
  963. ! When O3' is ON5 (patch 3TER)
  964. ON5 CN7 CN7 CN8B 0.2 4 0.0 !
  965. ON5 CN7 CN7 CN8B 0.8 3 180.0 !
  966. !======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3'
  967. ! These terms contribute to delta
  968. ! These terms are present in THF3P and THFM3P but not in THF5P
  969. ! When O3' is ON2 (3'-5' phosphodiester linkage)
  970. ON2 CN7 CN7 ON6 0.5 6 0.0 !del, good for amplitudes
  971. ON2 CN7 CN7 ON6 0.3 5 0.0 !del, impact on amplitudes
  972. ON2 CN7 CN7 ON6 0.6 4 180.0 !del, increases c2'endo
  973. ON2 CN7 CN7 ON6 0.2 3 0.0 !
  974. ON2 CN7 CN7 ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
  975. ON2 CN7 CN7 ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
  976. ON2 CN7 CN7 ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
  977. ON2 CN7 CN7 ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
  978. ! for ndph: make identical to ON2 CN7 CN7 ON6B
  979. ON2 CN7B CN7B ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
  980. ON2 CN7B CN7B ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
  981. ON2 CN7B CN7B ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
  982. ON2 CN7B CN7B ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
  983. ! When O3' is ON5 (patch 3TER)
  984. ON5 CN7 CN7 ON6 0.5 6 0.0 !
  985. ON5 CN7 CN7 ON6 0.3 5 0.0 !
  986. ON5 CN7 CN7 ON6 0.6 4 180.0 !
  987. ON5 CN7 CN7 ON6 0.2 3 0.0 !
  988. ON5 CN7 CN7 ON6B 0.4 6 0.0 !RNA
  989. ON5 CN7 CN7 ON6B 0.0 5 0.0 !RNA
  990. ON5 CN7 CN7 ON6B 0.0 4 180.0 !RNA
  991. ON5 CN7 CN7 ON6B 1.6 3 0.0 !RNA. increases c2'endo
  992. !======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1'
  993. ! This term can be used to adjust the c2'endo/c3'endo
  994. ! energy difference in THF5P
  995. CN7B ON6 CN7 CN8B 0.8 3 0.0 ! P [30,80]
  996. CN7B ON6B CN7 CN8B 2.0 3 0.0 ! To lower barrier in RNA
  997. CN7B ON6B CN7 CN9 2.0 3 0.0 ! To lower barrier in RNA, 5MET
  998. !======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1'
  999. ! This term can be used to adjust the c2'endo/c3'endo
  1000. ! When O3' is ON2
  1001. ON2 CN7 CN8 CN7B 0.8 6 0.0 !
  1002. ON2 CN7 CN8 CN7B 0.4 5 0.0 ! Moves the barrier right
  1003. ON2 CN7 CN8 CN7B 2.0 3 180.0 !
  1004. ON2 CN7 CN7B CN7B 0.6 6 0.0 ! RNA
  1005. ON2 CN7 CN7B CN7B 0.0 5 0.0 ! RNA c2/c3 endo in RNA
  1006. ON2 CN7 CN7B CN7B 1.6 3 180.0 !
  1007. !When O3' is ON5 (patch 3TER)
  1008. ON5 CN7 CN8 CN7B 0.8 6 0.0 !
  1009. ON5 CN7 CN8 CN7B 0.4 5 0.0 !
  1010. ON5 CN7 CN8 CN7B 2.0 3 180.0 !
  1011. ON5 CN7 CN7B CN7B 0.6 6 0.0 ! RNA, c2/c3 endo
  1012. ON5 CN7 CN7B CN7B 0.0 5 0.0 ! RNA
  1013. ON5 CN7 CN7B CN7B 1.6 3 180.0 ! RNA
  1014. !======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H
  1015. ON2 CN7 CN8 HN8 0.195 3 0.0 !
  1016. ON5 CN7 CN8 HN8 0.195 3 180.0 !
  1017. ON2 CN7 CN7B HN7 0.195 3 0.0 ! RNA
  1018. ON5 CN7 CN7B HN7 0.195 3 180.0 ! RNA
  1019. !======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3'
  1020. HN7 CN7 CN7 ON2 0.195 3 0.0
  1021. HN7 CN7 CN7 ON5 0.195 3 0.0
  1022. !======== CN7 CN7 ON2 P = C4'-C3'-O3'-P
  1023. CN7 CN7 ON2 P2 0.6 5 0.0 !eps, adm, 2011 DNA update
  1024. CN7 CN7 ON2 P2 0.2 4 0.0 !eps, locat of 200 mimima, adm, 2011 DNA update
  1025. CN7 CN7 ON2 P2 0.0 3 180.0 !eps, barE beteen minima, adm, 2011 DNA update
  1026. CN7 CN7 ON2 P2 0.4 2 0.0 !eps, relE of 200 vs 275 min, adm, 2011 DNA update
  1027. CN7 CN7 ON2 P2 1.9 1 180.0 !eps, adm, 2011 DNA update
  1028. CN7 CN7 ON2 P 0.6 5 0.0 !eps, RNA
  1029. CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima, RNA
  1030. CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima, RNA
  1031. CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min, RNA
  1032. CN7 CN7 ON2 P 1.9 1 180.0 !eps, RNA
  1033. !======== CN8 CN7 ON2 P = C2'-C3'-O3'-P
  1034. ! This term is involved in epsilon
  1035. CN8 CN7 ON2 P 2.5 1 180.0 ! 3-terminal phosphate
  1036. CN8 CN7 ON2 P2 1.9 1 180.0 ! adm, 2011 DNA update new param, eps
  1037. CN7B CN7 ON2 P 2.5 1 180.0 !eps, RNA
  1038. CN7B CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod
  1039. CN7 CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod
  1040. ! base on thfalloh
  1041. ! the following differ significantly from the protein based
  1042. ! alcohol parameters (based on ethanol, see above)
  1043. CN7 CN7 ON5 HN5 0.5 3 0.0
  1044. CN7 CN7 ON5 HN5 0.3 2 180.0
  1045. CN7 CN7 ON5 HN5 1.5 1 0.0
  1046. CN8 CN7 ON5 HN5 0.5 3 0.0
  1047. CN8 CN7 ON5 HN5 1.0 2 180.0
  1048. CN8 CN7 ON5 HN5 0.3 1 0.0
  1049. CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA
  1050. CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA
  1051. ! Was simply transfered from HN7 CN7 ON2 P
  1052. ! adm jr. should convert to alcohol term (see ribose etc)
  1053. HN7 CN7 ON5 HN5 0.0 3 0.0
  1054. HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H
  1055. HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5'
  1056. !@@@@@@ End of torsions involving exocyclic atoms:
  1057. !@@@@@@ Begining of torsions for endocyclic atoms only:
  1058. CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4'
  1059. CN8 CN7 CN7 ON6 1.0 4 0.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; lowers c3'endo
  1060. CN8 CN7 CN7 ON6 0.3 5 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
  1061. CN8 CN7 CN7 ON6 0.3 6 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
  1062. CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier
  1063. CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA
  1064. !======== CN7 CN8 CN7B ON6 for nucleosides, transfered from =========
  1065. !======== CN7 CN8 CN8 ON6 from thfoh ==============================
  1066. CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier
  1067. CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA
  1068. !======== C1'-C2'-C3'-C4' ========
  1069. CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes
  1070. CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA
  1071. !======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ========
  1072. !======== CN7 CN7 ON6 CN8 from thfohch3 ============================
  1073. CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1'
  1074. CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA
  1075. !======== Directly adjusted with TM3P
  1076. HN7 CN7 CN7 CN8 0.0 3 0.0 !puc,H-C3'-C4'-C5'
  1077. !======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4'
  1078. HN7 CN7 CN8 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
  1079. HN7 CN7B CN8 CN7 0.195 3 0.0 !H-C1'-C2'-C3'
  1080. HN7 CN7 CN7 ON6 0.195 3 180.0 ! useful
  1081. HN8 CN8 CN7B ON6 0.195 3 0.0 !H-C2'-C1'-O4'
  1082. HN7 CN7 CN7 HN7 0.195 3 0.0 !H-C4'-C3'-H
  1083. HN7 CN7B CN8 HN8 0.195 3 0.0 !H-C1'-C2'-H
  1084. HN7 CN7 CN8 HN8 0.195 3 0.0 !H-C3'-C2'-H
  1085. HN8 CN8 CN7 CN7 0.195 3 0.0 ! useful *cccc*
  1086. HN7 CN7 ON6 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
  1087. HN7 CN7B ON6 CN7 0.000 3 0.0 !H-C1'-O4'-C4'
  1088. HN7 CN7 CN7 ON6B 0.195 3 180.0 ! RNA
  1089. HN9 CN9 CN7 ON6B 0.195 3 180.0 ! RNA, 5MET
  1090. HN8 CN8 CN7B ON6B 0.195 3 0.0 ! RNA
  1091. HN7 CN7B ON6B CN7 0.000 3 0.0 ! RNA
  1092. HN7 CN7 ON6B CN7B 0.195 3 0.0 ! RNA
  1093. HN7 CN7 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1'
  1094. HN7 CN7B CN7B CN7 0.195 3 0.0 ! RNA, H-C1'-C2'-C3'
  1095. HN7 CN7B CN7B ON6B 0.195 3 0.0 ! RNA, H-C2'-C1'-O4'
  1096. !@@@@@@ End of torsions for endocyclic atoms only
  1097. !@@@@@@ Begining of torsions specifically defined for RNA @@@@@@
  1098. ! N9-C1'-C2'-O2':
  1099. NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine
  1100. NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil
  1101. ON5 CN7B CN7B HN7 0.000 3 0.0 !
  1102. HN7 CN7B CN7B HN7 0.000 3 0.0 !
  1103. CN7 CN7 CN7B ON5 0.000 3 0.0
  1104. ON6B CN7B CN7B ON5 0.000 3 0.0
  1105. ON5 CN7B CN7 ON2 0.000 3 0.0
  1106. ! for ndph
  1107. ON5 CN7 CN7B ON2 0.000 3 0.0
  1108. ON5 CN7B CN7 ON5 0.000 3 0.0
  1109. HN7 CN7B ON5 HN5 0.000 3 0.0
  1110. !ejd, 2010 RNA update
  1111. HN5 ON5 CN7B CN7B 0.000 6 180.0 ! ejd, 2010 RNA update
  1112. HN5 ON5 CN7B CN7B 0.400 3 0.0 ! shifts min, ejd, 2010 RNA update
  1113. HN5 ON5 CN7B CN7B 0.400 2 0.0 ! ejd, 2010 RNA update
  1114. HN5 ON5 CN7B CN7B 0.800 1 0.0 ! height of right barrier and can shift min, ejd, 2010 RNA update
  1115. !to C3'
  1116. HN5 ON5 CN7B CN7 0.200 3 0.0 ! ejd, 2010 RNA update
  1117. HN5 ON5 CN7B CN7 0.000 2 180.0 ! ejd, 2010 RNA update
  1118. HN5 ON5 CN7B CN7 2.000 1 0.0 ! height of left side barrier, ejd, 2010 RNA update
  1119. !@@@@@@ End of torsions specifically defined for RNA @@@@@@
  1120. !Collection of parameters that were previously incorrectly categorized or labeled
  1121. CN7B ON6 CN7 CN9 0.0 3 0.0 ! added for sugar model compounds
  1122. HN7 CN7 CN7B ON5 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
  1123. HN7 CN7B CN7 CN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
  1124. HN7 CN7 CN7 CN7B 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
  1125. HN7 CN7 CN7B HN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
  1126. IMPROPER
  1127. !
  1128. !V(improper) = Kpsi(psi - psi0)**2
  1129. !
  1130. !Kpsi: kcal/mole/rad**2
  1131. !psi0: degrees
  1132. !note that the second column of numbers (0) is ignored
  1133. !
  1134. !atom types Kpsi psi0
  1135. !
  1136. !
  1137. HN2 X X NN2 1.0 0 0.0 !C, adm jr. 11/97
  1138. NN2B CN4 CN5 HN2 7.0 0 0.0 !G, adm jr. 11/97
  1139. HN1 X X NN1 4.0 0 0.0 !G, adm jr. 11/97
  1140. NN1 CN2 HN1 HN1 6.0 0 0.0 !A,C adm jr. 11/97
  1141. CN1 X X ON1 90.0 0 0.0 !U
  1142. CN1T X X ON1 90.0 0 0.0 !U
  1143. CN1 NN2G CN5G ON1 90.0 0 0.0 !G
  1144. CN1T NN2B NN2U ON1 110.0 0 0.0 !T/O2, adm jr. 11/97
  1145. CN1 NN2U CN3T ON1 90.0 0 0.0 !T/O4, adm jr. 11/97
  1146. CN1 X X ON1C 80.0 0 0.0 !C, par_32, adm jr. 10/2/91
  1147. CN2 X X NN1 90.0 0 0.0 !C,
  1148. CN2 NN3G NN2G NN1 40.0 0 0.0 !G
  1149. CN2 NN3A CN5 NN1 40.0 0 0.0 !A
  1150. CN2 NN3 CN3 NN1 60.0 0 0.0 !C,
  1151. CN9 X X CN3T 14.0 0 0.0 !T, adm jr. 11/97
  1152. ! Wildcards used to minimize memory requirements
  1153. NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
  1154. CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5
  1155. !
  1156. !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
  1157. !
  1158. !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
  1159. !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
  1160. !
  1161. !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
  1162. !
  1163. HN1 0.0 -0.0460 0.2245
  1164. HN2 0.0 -0.0460 0.2245
  1165. HN3 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw
  1166. HN4 0.0 -0.0460 0.2245
  1167. HN5 0.0 -0.0460 0.2245
  1168. HN6 0.0 -0.0220 1.3200
  1169. HN7 0.0 -0.0220 1.3200
  1170. HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8
  1171. HN9 0.0 -0.0240 1.3400 ! Hydrogen bound to CN9
  1172. !
  1173. NN1 0.0 -0.20 1.85
  1174. NN2 0.0 -0.20 1.85
  1175. NN2B 0.0 -0.20 1.85 ! From NN2, for N9 in guanines
  1176. NN2G 0.0 -0.20 1.85
  1177. NN2U 0.0 -0.20 1.85
  1178. NN3 0.0 -0.20 1.85
  1179. NN3A 0.0 -0.20 1.85
  1180. NN3G 0.0 -0.20 1.85
  1181. NN4 0.0 -0.20 1.85
  1182. NN6 0.0 -0.20 1.85
  1183. !
  1184. ON1 0.0 -0.1200 1.70
  1185. ON1C 0.0 -0.1200 1.70
  1186. ON2 0.0 -0.1521 1.77
  1187. ON3 0.0 -0.1200 1.70
  1188. ON4 0.0 -0.1521 1.77
  1189. ON5 0.0 -0.1521 1.77
  1190. ON6 0.0 -0.1521 1.77
  1191. ON6B 0.0 -0.1521 1.77
  1192. !
  1193. ! base ring C vdw param, 11/14/97, adm jr
  1194. CN1 0.0 -0.10 1.9000
  1195. CN1T 0.0 -0.10 1.9000
  1196. CN2 0.0 -0.10 1.9000
  1197. CN3 0.0 -0.09 1.9000
  1198. CN3T 0.0 -0.09 1.9000 ! T, adm jr.
  1199. CN4 0.0 -0.075 1.9000
  1200. CN5 0.0 -0.075 1.9000
  1201. CN5G 0.0 -0.075 1.9000
  1202. CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
  1203. CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
  1204. ! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press
  1205. CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
  1206. CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
  1207. CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 !
  1208. !
  1209. P 0.0 -0.585 2.15
  1210. P2 0.0 -0.585 2.15
  1211. NBFIX
  1212. ! Emin Rmin
  1213. ! (kcal/mol) (A)
  1214. !
  1215. HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
  1216. ! READ PARAM APPEND CARD
  1217. ! to append hbond parameters from the file: par_hbond.inp
  1218. END