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  1. Toppar stream file generated by
  2. * CHARMM General Force Field (CGenFF) program version 2.5
  3. * For use with CGenFF version 4.6
  4. *
  5.  
  6. read rtf card append
  7. * Topologies generated by
  8. * CHARMM General Force Field (CGenFF) program version 2.5
  9. *
  10. 36 1
  11.  
  12. ! "penalty" is the highest penalty score of the associated parameters.
  13. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10
  14. ! and 50 mean some basic validation is recommended; penalties higher than
  15. ! 50 indicate poor analogy and mandate extensive validation/optimization.
  16.  
  17. RESI CMP 0.000 ! param penalty= 158.000 ; charge penalty= 112.237
  18. GROUP ! CHARGE CH_PENALTY
  19. ATOM P1 PG0 1.498 ! 112.237
  20. ATOM O1P1 OG2P1 -0.607 ! 6.690
  21. ATOM O2P1 OG311 -0.540 ! 10.035
  22. ATOM O5'1 OG3R60 -0.603 ! 80.243
  23. ATOM C5'1 CG321 0.074 ! 49.496
  24. ATOM C4'1 CG3RC1 0.025 ! 72.172
  25. ATOM O4'1 OG3C51 -0.392 ! 72.277
  26. ATOM C3'1 CG3RC1 0.212 ! 73.915
  27. ATOM O3'1 OG3R60 -0.625 ! 99.389
  28. ATOM C2'1 CG3C51 0.143 ! 16.006
  29. ATOM O2'1 OG311 -0.653 ! 7.273
  30. ATOM C1'1 CG3C51 0.099 ! 14.471
  31. ATOM N9 NG2R51 -0.063 ! 6.685
  32. ATOM C8 CG2R53 0.339 ! 0.000
  33. ATOM N7 NG2R50 -0.718 ! 0.000
  34. ATOM C5 CG2RC0 0.280 ! 0.000
  35. ATOM C6 CG2R64 0.463 ! 0.000
  36. ATOM N6 NG2S3 -0.764 ! 0.000
  37. ATOM N1 NG2R62 -0.741 ! 0.000
  38. ATOM C2 CG2R64 0.495 ! 0.000
  39. ATOM N3 NG2R62 -0.751 ! 0.000
  40. ATOM C4 CG2RC0 0.426 ! 0.000
  41. ATOM P2 PG0 1.498 ! 112.237
  42. ATOM O1P2 OG311 -0.540 ! 10.035
  43. ATOM O2P2 OG2P1 -0.607 ! 6.690
  44. ATOM O5'2 OG3R60 -0.603 ! 80.243
  45. ATOM C5'2 CG321 0.074 ! 49.496
  46. ATOM C4'2 CG3RC1 0.025 ! 72.172
  47. ATOM O4'2 OG3C51 -0.392 ! 72.277
  48. ATOM C3'2 CG3RC1 0.212 ! 73.915
  49. ATOM O3'2 OG3R60 -0.625 ! 99.389
  50. ATOM C2'2 CG3C51 0.143 ! 16.006
  51. ATOM O2'2 OG311 -0.653 ! 7.273
  52. ATOM C1'2 CG3C51 0.099 ! 14.471
  53. ATOM N10 NG2R51 -0.063 ! 6.685
  54. ATOM C10 CG2R53 0.339 ! 0.000
  55. ATOM N8 NG2R50 -0.718 ! 0.000
  56. ATOM C7 CG2RC0 0.280 ! 0.000
  57. ATOM C9 CG2R64 0.463 ! 0.000
  58. ATOM N5 NG2S3 -0.764 ! 0.000
  59. ATOM N2 NG2R62 -0.741 ! 0.000
  60. ATOM C1 CG2R64 0.495 ! 0.000
  61. ATOM N4 NG2R62 -0.751 ! 0.000
  62. ATOM C3 CG2RC0 0.426 ! 0.000
  63. ATOM H1 HGP1 0.420 ! 0.566
  64. ATOM H2 HGA2 0.090 ! 3.052
  65. ATOM H3 HGA2 0.090 ! 3.052
  66. ATOM H4 HGA1 0.090 ! 1.644
  67. ATOM H5 HGA1 0.090 ! 2.721
  68. ATOM H6 HGA1 0.090 ! 1.150
  69. ATOM H7 HGP1 0.420 ! 0.000
  70. ATOM H8 HGA1 0.090 ! 0.200
  71. ATOM H9 HGR52 0.141 ! 0.000
  72. ATOM H10 HGP4 0.377 ! 0.000
  73. ATOM H11 HGP4 0.377 ! 0.000
  74. ATOM H12 HGR62 0.128 ! 0.000
  75. ATOM H13 HGP1 0.420 ! 0.566
  76. ATOM H14 HGA2 0.090 ! 3.052
  77. ATOM H15 HGA2 0.090 ! 3.052
  78. ATOM H16 HGA1 0.090 ! 1.644
  79. ATOM H17 HGA1 0.090 ! 2.721
  80. ATOM H18 HGA1 0.090 ! 1.150
  81. ATOM H19 HGP1 0.420 ! 0.000
  82. ATOM H20 HGA1 0.090 ! 0.200
  83. ATOM H21 HGR52 0.141 ! 0.000
  84. ATOM H22 HGP4 0.377 ! 0.000
  85. ATOM H23 HGP4 0.377 ! 0.000
  86. ATOM H24 HGR62 0.128 ! 0.000
  87.  
  88. BOND P1 O1P1
  89. BOND P1 O5'1
  90. BOND P1 O3'1
  91. BOND P1 O2P1
  92. BOND O2P1 H1
  93. BOND O5'1 C5'1
  94. BOND C5'1 C4'1
  95. BOND C5'1 H2
  96. BOND C5'1 H3
  97. BOND C4'1 O4'1
  98. BOND C4'1 C3'1
  99. BOND C4'1 H4
  100. BOND O4'1 C1'1
  101. BOND C3'1 C2'1
  102. BOND C3'1 O3'1
  103. BOND C3'1 H5
  104. BOND C2'1 C1'1
  105. BOND C2'1 O2'1
  106. BOND C2'1 H6
  107. BOND O2'1 H7
  108. BOND C1'1 N9
  109. BOND C1'1 H8
  110. BOND N9 C8
  111. BOND N9 C4
  112. BOND C8 N7
  113. BOND C8 H9
  114. BOND N7 C5
  115. BOND C5 C6
  116. BOND C5 C4
  117. BOND C6 N6
  118. BOND C6 N1
  119. BOND N6 H10
  120. BOND N6 H11
  121. BOND N1 C2
  122. BOND C2 N3
  123. BOND C2 H12
  124. BOND N3 C4
  125. BOND P2 O5'2
  126. BOND P2 O2P2
  127. BOND P2 O3'2
  128. BOND P2 O1P2
  129. BOND O1P2 H13
  130. BOND O5'2 C5'2
  131. BOND C5'2 C4'2
  132. BOND C5'2 H14
  133. BOND C5'2 H15
  134. BOND C4'2 O4'2
  135. BOND C4'2 C3'2
  136. BOND C4'2 H16
  137. BOND O4'2 C1'2
  138. BOND C3'2 C2'2
  139. BOND C3'2 O3'2
  140. BOND C3'2 H17
  141. BOND C2'2 C1'2
  142. BOND C2'2 O2'2
  143. BOND C2'2 H18
  144. BOND O2'2 H19
  145. BOND C1'2 N10
  146. BOND C1'2 H20
  147. BOND N10 C10
  148. BOND N10 C3
  149. BOND C10 N8
  150. BOND C10 H21
  151. BOND N8 C7
  152. BOND C7 C9
  153. BOND C7 C3
  154. BOND C9 N5
  155. BOND C9 N2
  156. BOND N5 H22
  157. BOND N5 H23
  158. BOND N2 C1
  159. BOND C1 N4
  160. BOND C1 H24
  161. BOND N4 C3
  162. IMPR C6 C5 N1 N6
  163. IMPR N6 H11 H10 C6
  164. IMPR C9 C7 N2 N5
  165. IMPR N5 H23 H22 C9
  166.  
  167. END
  168.  
  169. read param card flex append
  170. * Parameters generated by analogy by
  171. * CHARMM General Force Field (CGenFF) program version 2.5
  172. *
  173.  
  174. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10
  175. ! and 50 mean some basic validation is recommended; penalties higher than
  176. ! 50 indicate poor analogy and mandate extensive validation/optimization.
  177.  
  178. BONDS
  179. CG3RC1 OG3R60 334.30 1.4110 ! CMP , from CG3C51 OG301, penalty= 66
  180. OG3R60 PG0 237.00 1.5800 ! CMP , from OG311 PG0, penalty= 60
  181.  
  182. ANGLES
  183. CG3RC1 CG321 OG3R60 75.70 110.10 ! CMP , from CG3RC1 CG321 OG303, penalty= 8
  184. CG321 CG3RC1 OG3C51 55.00 106.00 ! CMP , from OG3C51 CG3RC1 HGA1, penalty= 136.5
  185. CG3C51 CG3RC1 OG3R60 58.00 106.50 8.00 2.56100 ! CMP , from CG3C51 CG3C51 OG301, penalty= 22.5
  186. CG3RC1 CG3RC1 OG3R60 53.35 111.00 8.00 2.56100 ! CMP , from CG321 CG3RC1 CG3RC1, penalty= 45
  187. OG3R60 CG3RC1 HGA1 45.90 108.50 ! CMP , from OG301 CG3C51 HGA1, penalty= 22.5
  188. CG3C51 OG3C51 CG3RC1 170.00 109.00 ! CMP , from CG3C52 OG3C51 CG3RC1, penalty= 0.4
  189. CG321 OG3R60 PG0 20.00 120.00 35.00 2.33000 ! CMP , from CG321 OG303 PG0, penalty= 100
  190. CG3RC1 OG3R60 PG0 20.00 120.00 35.00 2.33000 ! CMP , from CG3C51 OG303 PG1, penalty= 103.5
  191. OG2P1 PG0 OG3R60 98.90 111.60 ! CMP , from OG2P1 PG0 OG303, penalty= 8
  192. OG311 PG0 OG3R60 48.10 108.00 ! CMP , from OG303 PG0 OG311, penalty= 8
  193. OG3R60 PG0 OG3R60 48.10 108.00 ! CMP , from OG303 PG0 OG303, penalty= 16
  194.  
  195. DIHEDRALS
  196. OG3R60 CG321 CG3RC1 CG3RC1 0.6000 1 0.00 ! CMP , from OG303 CG321 CG3RC1 CG3RC1, penalty= 8
  197. OG3R60 CG321 CG3RC1 CG3RC1 0.4500 2 0.00 ! CMP , from OG303 CG321 CG3RC1 CG3RC1, penalty= 8
  198. OG3R60 CG321 CG3RC1 CG3RC1 0.7000 3 0.00 ! CMP , from OG303 CG321 CG3RC1 CG3RC1, penalty= 8
  199. OG3R60 CG321 CG3RC1 OG3C51 3.4000 1 180.00 ! CMP , from OG303 CG321 CG3C51 OG3C51, penalty= 44
  200. OG3R60 CG321 CG3RC1 HGA1 0.1950 3 0.00 ! CMP , from OG301 CG321 CG3C51 HGA1, penalty= 22.5
  201. HGA2 CG321 CG3RC1 OG3C51 0.1600 3 0.00 ! CMP , from HGA2 CG321 CG3C51 OG3C51, penalty= 36
  202. CG3RC1 CG321 OG3R60 PG0 0.6000 1 180.00 ! CMP , from CG3C51 CG321 OG303 PG0, penalty= 101.5
  203. CG3RC1 CG321 OG3R60 PG0 0.6500 2 0.00 ! CMP , from CG3C51 CG321 OG303 PG0, penalty= 101.5
  204. CG3RC1 CG321 OG3R60 PG0 0.0500 3 0.00 ! CMP , from CG3C51 CG321 OG303 PG0, penalty= 101.5
  205. HGA2 CG321 OG3R60 PG0 0.0000 3 0.00 ! CMP , from HGA2 CG321 OG303 PG0, penalty= 100
  206. CG3RC1 CG3C51 CG3C51 NG2R51 0.0000 3 0.00 ! CMP , from CG3C52 CG3C51 CG3C51 NG2R51, penalty= 1.1
  207. CG3RC1 CG3C51 CG3C51 OG3C51 0.0000 3 0.00 ! CMP , from CG3C52 CG3C51 CG3C51 OG3C51, penalty= 1.1
  208. CG3C51 CG3C51 CG3RC1 OG3R60 0.6000 3 0.00 ! CMP , from CG3C51 CG3C51 CG3RC1 OG3C31, penalty= 23.5
  209. CG3C51 CG3C51 CG3RC1 OG3R60 0.5000 4 0.00 ! CMP , from CG3C51 CG3C51 CG3RC1 OG3C31, penalty= 23.5
  210. OG311 CG3C51 CG3RC1 OG3R60 0.0000 3 0.00 ! CMP , from OG301 CG3C51 CG3C51 OG311, penalty= 22.5
  211. HGA1 CG3C51 CG3RC1 OG3R60 0.1950 3 0.00 ! CMP , from OG301 CG3C51 CG3C51 HGA1, penalty= 22.5
  212. CG3C51 CG3C51 OG3C51 CG3RC1 0.5000 3 0.00 ! CMP , from CG3C51 CG3C52 OG3C51 CG3RC1, penalty= 4
  213. NG2R51 CG3C51 OG3C51 CG3RC1 0.0000 3 0.00 ! CMP , from NG2R51 CG3C51 OG3C51 CG3C52, penalty= 21.1
  214. HGA1 CG3C51 OG3C51 CG3RC1 0.3000 3 0.00 ! CMP , from HGA2 CG3C52 OG3C51 CG3RC1, penalty= 4
  215. CG321 CG3RC1 CG3RC1 OG3R60 0.1500 3 0.00 ! CMP , from CG321 CG3RC1 CG3RC1 CG321, penalty= 45
  216. OG3C51 CG3RC1 CG3RC1 OG3R60 1.2000 3 0.00 ! CMP , from CG3C52 CG3RC1 CG3RC1 OG3C51, penalty= 68
  217. OG3R60 CG3RC1 CG3RC1 HGA1 0.3000 3 0.00 ! CMP , from OG3C31 CG3RC1 CG3RC1 HGA1, penalty= 23.5
  218. CG321 CG3RC1 OG3C51 CG3C51 0.0000 3 0.00 ! CMP , from CG3RC1 CG3RC1 OG3C51 CG3C52, penalty= 72.9
  219. CG3RC1 CG3RC1 OG3C51 CG3C51 0.0000 3 0.00 ! CMP , from CG3RC1 CG3RC1 OG3C51 CG3C52, penalty= 0.4
  220. HGA1 CG3RC1 OG3C51 CG3C51 0.3000 3 0.00 ! CMP , from HGA1 CG3RC1 OG3C51 CG3C52, penalty= 0.4
  221. CG3C51 CG3RC1 OG3R60 PG0 2.5000 1 180.00 ! CMP , from CG3C51 CG3C51 OG303 PG1, penalty= 118
  222. CG3RC1 CG3RC1 OG3R60 PG0 2.4000 1 180.00 ! CMP , from CG3RC1 CG3C51 OG303 PG1, penalty= 158
  223. CG3RC1 CG3RC1 OG3R60 PG0 0.4000 2 180.00 ! CMP , from CG3RC1 CG3C51 OG303 PG1, penalty= 158
  224. CG3RC1 CG3RC1 OG3R60 PG0 1.5000 3 180.00 ! CMP , from CG3RC1 CG3C51 OG303 PG1, penalty= 158
  225. HGA1 CG3RC1 OG3R60 PG0 0.0000 3 0.00 ! CMP , from HGA1 CG3C51 OG303 PG1, penalty= 118
  226. HGP1 OG311 PG0 OG3R60 1.6000 1 180.00 ! CMP , from HGP1 OG311 PG0 OG303, penalty= 8
  227. HGP1 OG311 PG0 OG3R60 0.9000 2 0.00 ! CMP , from HGP1 OG311 PG0 OG303, penalty= 8
  228. CG321 OG3R60 PG0 OG2P1 0.1000 3 0.00 ! CMP , from CG321 OG303 PG0 OG2P1, penalty= 100
  229. CG321 OG3R60 PG0 OG311 0.9500 2 0.00 ! CMP , from CG321 OG303 PG0 OG311, penalty= 100
  230. CG321 OG3R60 PG0 OG311 0.5000 3 0.00 ! CMP , from CG321 OG303 PG0 OG311, penalty= 100
  231. CG321 OG3R60 PG0 OG3R60 0.5000 3 0.00 ! CMP , from CG321 OG303 PG0 OG303, penalty= 108
  232. CG3RC1 OG3R60 PG0 OG2P1 0.1000 3 0.00 ! CMP , from CG321 OG303 PG0 OG2P1, penalty= 113.8
  233. CG3RC1 OG3R60 PG0 OG311 0.9500 2 0.00 ! CMP , from CG321 OG303 PG0 OG311, penalty= 113.8
  234. CG3RC1 OG3R60 PG0 OG311 0.5000 3 0.00 ! CMP , from CG321 OG303 PG0 OG311, penalty= 113.8
  235. CG3RC1 OG3R60 PG0 OG3R60 0.5000 3 0.00 ! CMP , from CG321 OG303 PG0 OG303, penalty= 121.8
  236.  
  237. IMPROPERS
  238.  
  239. END
  240. RETURN
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