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  1. ;
  2. ; File 'topol.top' was generated
  3. ; By user: kevin (505)
  4. ; On host: combo.ap.cityu.edu.hk
  5. ; At date: Tue Jun 2 00:20:06 2015
  6. ;
  7. ; This is a standalone topology file
  8. ;
  9. ; Created by:
  10. ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 (double precision)
  11. ; Executable: /share/apps/gmx-double-multicore/bin/gmx_d
  12. ; Library dir: /share/apps/gmx-double-multicore/share/gromacs/top
  13. ; Command line:
  14. ; gmx_d pdb2gmx -f proline.pdb -ter
  15. ; Force field was read from the standard Gromacs share directory.
  16. ;
  17.  
  18. ; Include forcefield parameters
  19. #include "oplsaa.ff/forcefield.itp"
  20.  
  21. [ moleculetype ]
  22. ; Name nrexcl
  23. Protein_chain_P 3
  24.  
  25. [ atoms ]
  26. ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
  27. ; residue 1 PRO rtp PRO q 0.0
  28. 1 opls_309 1 PRO N 1 -0.2 14.0027 ; qtot -0.2
  29. 2 opls_310 1 PRO H1 1 0.31 1.008 ; qtot 0.11
  30. 3 opls_310 1 PRO H2 1 0.31 1.008 ; qtot 0.42
  31. 4 opls_246 1 PRO CA 1 0.13 12.011 ; qtot 0.55
  32. 5 opls_140 1 PRO HA 1 0.06 1.008 ; qtot 0.61
  33. 6 opls_136 1 PRO CB 2 -0.12 12.011 ; qtot 0.49
  34. 7 opls_140 1 PRO HB1 2 0.06 1.008 ; qtot 0.55
  35. 8 opls_140 1 PRO HB2 2 0.06 1.008 ; qtot 0.61
  36. 9 opls_136 1 PRO CG 3 -0.12 12.011 ; qtot 0.49
  37. 10 opls_140 1 PRO HG1 3 0.06 1.008 ; qtot 0.55
  38. 11 opls_140 1 PRO HG2 3 0.06 1.008 ; qtot 0.61
  39. 12 opls_296 1 PRO CD 4 0.17 12.011 ; qtot 0.78
  40. 13 opls_140 1 PRO HD1 4 0.06 1.008 ; qtot 0.84
  41. 14 opls_140 1 PRO HD2 4 0.06 1.008 ; qtot 0.9
  42. 15 opls_271 1 PRO C 5 0.7 12.011 ; qtot 1.6
  43. 16 opls_272 1 PRO O1 5 -0.8 15.9994 ; qtot 0.8
  44. 17 opls_272 1 PRO O2 5 -0.8 15.9994 ; qtot 0
  45.  
  46. [ bonds ]
  47. ; ai aj funct c0 c1 c2 c3
  48. 1 2 1
  49. 1 3 1
  50. 1 4 1
  51. 1 12 1
  52. 4 5 1
  53. 4 6 1
  54. 4 15 1
  55. 6 7 1
  56. 6 8 1
  57. 6 9 1
  58. 9 10 1
  59. 9 11 1
  60. 9 12 1
  61. 12 13 1
  62. 12 14 1
  63. 15 16 1
  64. 15 17 1
  65.  
  66. [ pairs ]
  67. ; ai aj funct c0 c1 c2 c3
  68. 1 7 1
  69. 1 8 1
  70. 1 10 1
  71. 1 11 1
  72. 1 16 1
  73. 1 17 1
  74. 2 5 1
  75. 2 6 1
  76. 2 9 1
  77. 2 13 1
  78. 2 14 1
  79. 2 15 1
  80. 3 5 1
  81. 3 6 1
  82. 3 9 1
  83. 3 13 1
  84. 3 14 1
  85. 3 15 1
  86. 4 10 1
  87. 4 11 1
  88. 4 13 1
  89. 4 14 1
  90. 5 7 1
  91. 5 8 1
  92. 5 9 1
  93. 5 12 1
  94. 5 16 1
  95. 5 17 1
  96. 6 13 1
  97. 6 14 1
  98. 6 16 1
  99. 6 17 1
  100. 7 10 1
  101. 7 11 1
  102. 7 12 1
  103. 7 15 1
  104. 8 10 1
  105. 8 11 1
  106. 8 12 1
  107. 8 15 1
  108. 9 15 1
  109. 10 13 1
  110. 10 14 1
  111. 11 13 1
  112. 11 14 1
  113. 12 15 1
  114.  
  115. [ angles ]
  116. ; ai aj ak funct c0 c1 c2 c3
  117. 2 1 3 1
  118. 2 1 4 1
  119. 2 1 12 1
  120. 3 1 4 1
  121. 3 1 12 1
  122. 4 1 12 1
  123. 1 4 5 1
  124. 1 4 6 1
  125. 1 4 15 1
  126. 5 4 6 1
  127. 5 4 15 1
  128. 6 4 15 1
  129. 4 6 7 1
  130. 4 6 8 1
  131. 4 6 9 1
  132. 7 6 8 1
  133. 7 6 9 1
  134. 8 6 9 1
  135. 6 9 10 1
  136. 6 9 11 1
  137. 6 9 12 1
  138. 10 9 11 1
  139. 10 9 12 1
  140. 11 9 12 1
  141. 1 12 9 1
  142. 1 12 13 1
  143. 1 12 14 1
  144. 9 12 13 1
  145. 9 12 14 1
  146. 13 12 14 1
  147. 4 15 16 1
  148. 4 15 17 1
  149. 16 15 17 1
  150.  
  151. [ dihedrals ]
  152. ; ai aj ak al funct c0 c1 c2 c3 c4 c5
  153. 2 1 4 5 3
  154. 2 1 4 6 3
  155. 2 1 4 15 3
  156. 3 1 4 5 3
  157. 3 1 4 6 3
  158. 3 1 4 15 3
  159. 12 1 4 5 3
  160. 12 1 4 6 3
  161. 12 1 4 15 3
  162. 2 1 12 9 3
  163. 2 1 12 13 3
  164. 2 1 12 14 3
  165. 3 1 12 9 3
  166. 3 1 12 13 3
  167. 3 1 12 14 3
  168. 4 1 12 9 3
  169. 4 1 12 13 3
  170. 4 1 12 14 3
  171. 1 4 6 7 3
  172. 1 4 6 8 3
  173. 1 4 6 9 3
  174. 5 4 6 7 3
  175. 5 4 6 8 3
  176. 5 4 6 9 3
  177. 15 4 6 7 3
  178. 15 4 6 8 3
  179. 15 4 6 9 3
  180. 1 4 15 16 3
  181. 1 4 15 17 3
  182. 5 4 15 16 3
  183. 5 4 15 17 3
  184. 6 4 15 16 3
  185. 6 4 15 17 3
  186. 4 6 9 10 3
  187. 4 6 9 11 3
  188. 4 6 9 12 3
  189. 7 6 9 10 3
  190. 7 6 9 11 3
  191. 7 6 9 12 3
  192. 8 6 9 10 3
  193. 8 6 9 11 3
  194. 8 6 9 12 3
  195. 6 9 12 1 3
  196. 6 9 12 13 3
  197. 6 9 12 14 3
  198. 10 9 12 1 3
  199. 10 9 12 13 3
  200. 10 9 12 14 3
  201. 11 9 12 1 3
  202. 11 9 12 13 3
  203. 11 9 12 14 3
  204.  
  205. [ dihedrals ]
  206. ; ai aj ak al funct c0 c1 c2 c3
  207. 4 16 15 17 1 improper_O_C_X_Y
  208.  
  209. ; Include Position restraint file
  210. #ifdef POSRES
  211. #include "posre.itp"
  212. #endif
  213.  
  214. ; Include water topology
  215. #include "oplsaa.ff/tip4p.itp"
  216.  
  217. #ifdef POSRES_WATER
  218. ; Position restraint for each water oxygen
  219. [ position_restraints ]
  220. ; i funct fcx fcy fcz
  221. 1 1 1000 1000 1000
  222. #endif
  223.  
  224. ; Include topology for ions
  225. #include "oplsaa.ff/ions.itp"
  226.  
  227. [ system ]
  228. ; Name
  229. Protein
  230.  
  231. [ molecules ]
  232. ; Compound #mols
  233. Protein_chain_P 1
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