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  1. Command line:
  2. gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id -v
  3.  
  4.  
  5. Select the Force Field:
  6. From current directory:
  7. 1: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
  8. From '/usr/local/gromacs/share/gromacs/top':
  9. 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
  10. 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  11. 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
  12. 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
  13. 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
  14. 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
  15. 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  16. 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  17. 10: GROMOS96 43a1 force field
  18. 11: GROMOS96 43a2 force field (improved alkane dihedrals)
  19. 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
  20. 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
  21. 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
  22. 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
  23. 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
  24. 1
  25.  
  26. Using the OplsaaPBS force field in directory ./oplsaaPBS.ff
  27.  
  28. Opening force field file ./oplsaaPBS.ff/aminoacids.r2b
  29. Reading trim.pdb...
  30. WARNING: all CONECT records are ignored
  31. Read 8332 atoms
  32. Renaming atom 'CD1' in residue 56 ILE to 'CD'
  33. Renaming atom 'CD1' in residue 59 ILE to 'CD'
  34. Renaming atom 'CD1' in residue 75 ILE to 'CD'
  35. Renaming atom 'CD1' in residue 82 ILE to 'CD'
  36. Renaming atom 'CD1' in residue 123 ILE to 'CD'
  37. Renaming atom 'CD1' in residue 140 ILE to 'CD'
  38. Renaming atom 'CD1' in residue 168 ILE to 'CD'
  39. Renaming atom 'CD1' in residue 175 ILE to 'CD'
  40. Renaming atom 'CD1' in residue 180 ILE to 'CD'
  41. Renaming atom 'CD1' in residue 187 ILE to 'CD'
  42. Renaming atom 'CD1' in residue 200 ILE to 'CD'
  43. Renaming atom 'CD1' in residue 220 ILE to 'CD'
  44. Renaming atom 'CD1' in residue 229 ILE to 'CD'
  45. Renaming atom 'CD1' in residue 5 ILE to 'CD'
  46. Renaming atom 'CD1' in residue 9 ILE to 'CD'
  47. Renaming atom 'CD1' in residue 44 ILE to 'CD'
  48. Renaming atom 'CD1' in residue 51 ILE to 'CD'
  49. Renaming atom 'CD1' in residue 52 ILE to 'CD'
  50. Renaming atom 'CD1' in residue 65 ILE to 'CD'
  51. Renaming atom 'CD1' in residue 82 ILE to 'CD'
  52. Renaming atom 'CD1' in residue 103 ILE to 'CD'
  53. Renaming atom 'CD1' in residue 123 ILE to 'CD'
  54. Renaming atom 'CD1' in residue 127 ILE to 'CD'
  55. Renaming atom 'CD1' in residue 156 ILE to 'CD'
  56. Renaming atom 'CD1' in residue 3 ILE to 'CD'
  57. Renaming atom 'CD1' in residue 4 ILE to 'CD'
  58. Renaming atom 'CD1' in residue 8 ILE to 'CD'
  59. Renaming atom 'CD1' in residue 26 ILE to 'CD'
  60. Renaming atom 'CD1' in residue 39 ILE to 'CD'
  61. Renaming atom 'CD1' in residue 42 ILE to 'CD'
  62. Renaming atom 'CD1' in residue 50 ILE to 'CD'
  63. Renaming atom 'CD1' in residue 96 ILE to 'CD'
  64. Renaming atom 'CD1' in residue 104 ILE to 'CD'
  65. Renaming atom 'CD1' in residue 107 ILE to 'CD'
  66. Renaming atom 'CD1' in residue 123 ILE to 'CD'
  67. Renaming atom 'CD1' in residue 5 ILE to 'CD'
  68. Renaming atom 'CD1' in residue 9 ILE to 'CD'
  69. Renaming atom 'CD1' in residue 44 ILE to 'CD'
  70. Renaming atom 'CD1' in residue 51 ILE to 'CD'
  71. Renaming atom 'CD1' in residue 52 ILE to 'CD'
  72. Renaming atom 'CD1' in residue 65 ILE to 'CD'
  73. Renaming atom 'CD1' in residue 82 ILE to 'CD'
  74. Renaming atom 'CD1' in residue 103 ILE to 'CD'
  75. Renaming atom 'CD1' in residue 123 ILE to 'CD'
  76. Renaming atom 'CD1' in residue 127 ILE to 'CD'
  77. Renaming atom 'CD1' in residue 156 ILE to 'CD'
  78. Renaming atom 'CD1' in residue 3 ILE to 'CD'
  79. Renaming atom 'CD1' in residue 4 ILE to 'CD'
  80. Renaming atom 'CD1' in residue 8 ILE to 'CD'
  81. Renaming atom 'CD1' in residue 26 ILE to 'CD'
  82. Renaming atom 'CD1' in residue 39 ILE to 'CD'
  83. Renaming atom 'CD1' in residue 42 ILE to 'CD'
  84. Renaming atom 'CD1' in residue 50 ILE to 'CD'
  85. Renaming atom 'CD1' in residue 96 ILE to 'CD'
  86. Renaming atom 'CD1' in residue 104 ILE to 'CD'
  87. Renaming atom 'CD1' in residue 107 ILE to 'CD'
  88. Renaming atom 'CD1' in residue 123 ILE to 'CD'
  89. Renaming atom 'CD1' in residue 5 ILE to 'CD'
  90. Renaming atom 'CD1' in residue 8 ILE to 'CD'
  91. Renaming atom 'CD1' in residue 22 ILE to 'CD'
  92. Renaming atom 'CD1' in residue 24 ILE to 'CD'
  93. Renaming atom 'CD1' in residue 32 ILE to 'CD'
  94. Renaming atom 'CD1' in residue 38 ILE to 'CD'
  95. Renaming atom 'CD1' in residue 41 ILE to 'CD'
  96. Renaming atom 'CD1' in residue 44 ILE to 'CD'
  97. Renaming atom 'CD1' in residue 51 ILE to 'CD'
  98. Renaming atom 'CD1' in residue 52 ILE to 'CD'
  99. Renaming atom 'CD1' in residue 86 ILE to 'CD'
  100. Renaming atom 'CD1' in residue 97 ILE to 'CD'
  101. Renaming atom 'CD1' in residue 104 ILE to 'CD'
  102. Renaming atom 'CD1' in residue 124 ILE to 'CD'
  103. Renaming atom 'CD1' in residue 128 ILE to 'CD'
  104. Renaming atom 'CD1' in residue 131 ILE to 'CD'
  105. Renaming atom 'CD1' in residue 138 ILE to 'CD'
  106. Renaming atom 'CD1' in residue 147 ILE to 'CD'
  107. Renaming atom 'CD1' in residue 150 ILE to 'CD'
  108. Renaming atom 'CD1' in residue 160 ILE to 'CD'
  109. Renaming atom 'CD1' in residue 161 ILE to 'CD'
  110. Renaming atom 'CD1' in residue 169 ILE to 'CD'
  111. Analyzing pdb file
  112. Splitting chemical chains based on changing chain id only (ignoring TER records).
  113. There are 6 chains and 0 blocks of water and 1016 residues with 8332 atoms
  114.  
  115. chain #res #atoms
  116. 1 'G' 203 1655
  117. 2 'H' 161 1319
  118. 3 'I' 161 1313
  119. 4 'J' 161 1319
  120. 5 'K' 161 1313
  121. 6 'L' 169 1413
  122.  
  123. All occupancies are one
  124. Opening force field file ./oplsaaPBS.ff/atomtypes.atp
  125. Atomtype 817
  126. Reading residue database... (oplsaaPBS)
  127. Opening force field file ./oplsaaPBS.ff/aminoacids.rtp
  128. Residue 57
  129. Sorting it all out...
  130. Opening force field file ./oplsaaPBS.ff/aminoacids.hdb
  131. Opening force field file ./oplsaaPBS.ff/aminoacids.n.tdb
  132. Opening force field file ./oplsaaPBS.ff/aminoacids.c.tdb
  133. Processing chain 1 'G' (1655 atoms, 203 residues)
  134. Identified residue MET27 as a starting terminus.
  135. Identified residue ILE229 as a ending terminus.
  136. 8 out of 8 lines of specbond.dat converted successfully
  137. Special Atom Distance matrix:
  138. MET27 MET150 CYS191
  139. SD7 SD946 SG1366
  140. MET150 SD946 4.453
  141. CYS191 SG1366 4.136 1.706
  142. MET203 SD1446 3.141 1.847 2.591
  143. Changing rtp entry of residue 62 LYS to 'LYSH'
  144. Changing rtp entry of residue 70 LYS to 'LYSH'
  145. Changing rtp entry of residue 74 LYS to 'LYSH'
  146. Changing rtp entry of residue 119 LYS to 'LYSH'
  147. Changing rtp entry of residue 128 LYS to 'LYSH'
  148. Changing rtp entry of residue 138 LYS to 'LYSH'
  149. Changing rtp entry of residue 151 LYS to 'LYSH'
  150. Changing rtp entry of residue 152 LYS to 'LYSH'
  151. Changing rtp entry of residue 191 CYS to 'CYSH'
  152. Changing rtp entry of residue 205 LYS to 'LYSH'
  153. Start terminus MET-27: NH3+
  154. End terminus ILE-229: COO-
  155. Renaming atom 'O' in residue 'ILE' 229 to 'O1'
  156. Checking for duplicate atoms....
  157. Generating any missing hydrogen atoms and/or adding termini.
  158. Now there are 203 residues with 3235 atoms
  159. Chain time...
  160. Making bonds...
  161. Number of bonds was 3259, now 3259
  162. Generating angles, dihedrals and pairs...
  163. Before cleaning: 8527 pairs
  164. Before cleaning: 8582 dihedrals
  165. Keeping all generated dihedrals
  166. Making cmap torsions...
  167. There are 8582 dihedrals, 651 impropers, 5885 angles
  168. 8485 pairs, 3259 bonds and 0 virtual sites
  169. Total mass 22924.102 a.m.u.
  170. Total charge -0.000 e
  171. Writing topology
  172. Processing chain 2 'H' (1319 atoms, 161 residues)
  173. Identified residue MET1 as a starting terminus.
  174. Identified residue SER161 as a ending terminus.
  175. 8 out of 8 lines of specbond.dat converted successfully
  176. Special Atom Distance matrix:
  177. MET1 MET72 MET96 MET133 MET149
  178. SD7 SD548 SD844 SD1113 SD1226
  179. MET72 SD548 2.933
  180. MET96 SD844 1.432 2.819
  181. MET133 SD1113 1.899 1.437 1.390
  182. MET149 SD1226 1.835 2.537 0.544 1.120
  183. CYS157 SG1295 2.013 1.722 1.551 0.811 1.421
  184. Changing rtp entry of residue 26 LYS to 'LYSH'
  185. Changing rtp entry of residue 53 LYS to 'LYSH'
  186. Changing rtp entry of residue 58 LYS to 'LYSH'
  187. Changing rtp entry of residue 113 LYS to 'LYSH'
  188. Changing rtp entry of residue 134 LYS to 'LYSH'
  189. Changing rtp entry of residue 147 LYS to 'LYSH'
  190. Changing rtp entry of residue 157 CYS to 'CYSH'
  191. Start terminus MET-1: NH3+
  192. End terminus SER-161: COO-
  193. Renaming atom 'O' in residue 'SER' 161 to 'O1'
  194. Checking for duplicate atoms....
  195. Generating any missing hydrogen atoms and/or adding termini.
  196. Now there are 161 residues with 2531 atoms
  197. Chain time...
  198. Making bonds...
  199. Warning: Long Bond (1061-1062 = 0.324178 nm)
  200. Warning: Long Bond (1066-1067 = 0.322446 nm)
  201. Warning: Long Bond (1066-1068 = 0.250909 nm)
  202. Warning: Short Bond (1068-1069 = 0.000640735 nm)
  203. Warning: Short Bond (1068-1071 = 0.000640735 nm)
  204. Number of bonds was 2552, now 2552
  205. Generating angles, dihedrals and pairs...
  206. Before cleaning: 6634 pairs
  207. Before cleaning: 6674 dihedrals
  208. Keeping all generated dihedrals
  209. Making cmap torsions...
  210. There are 6674 dihedrals, 523 impropers, 4595 angles
  211. 6592 pairs, 2552 bonds and 0 virtual sites
  212. Total mass 18070.594 a.m.u.
  213. Total charge -2.000 e
  214. Writing topology
  215. Processing chain 3 'I' (1313 atoms, 161 residues)
  216. Identified residue MET1 as a starting terminus.
  217. Identified residue GLN161 as a ending terminus.
  218. 8 out of 8 lines of specbond.dat converted successfully
  219. Special Atom Distance matrix:
  220. MET1 MET77 MET115 MET133 CYS138
  221. SD7 SD600 SD978 SD1105 SG1141
  222. MET77 SD600 3.562
  223. MET115 SD978 2.088 1.759
  224. MET133 SD1105 2.208 2.010 1.682
  225. CYS138 SG1141 2.558 2.912 2.570 1.029
  226. MET160 SD1303 2.302 1.860 1.170 0.947 1.584
  227. Changing rtp entry of residue 6 LYS to 'LYSH'
  228. Changing rtp entry of residue 27 LYS to 'LYSH'
  229. Changing rtp entry of residue 52 LYS to 'LYSH'
  230. Changing rtp entry of residue 61 LYS to 'LYSH'
  231. Changing rtp entry of residue 113 LYS to 'LYSH'
  232. Changing rtp entry of residue 134 LYS to 'LYSH'
  233. Changing rtp entry of residue 138 CYS to 'CYSH'
  234. Start terminus MET-1: NH3+
  235. End terminus GLN-161: COO-
  236. Renaming atom 'O' in residue 'GLN' 161 to 'O1'
  237. Checking for duplicate atoms....
  238. Generating any missing hydrogen atoms and/or adding termini.
  239. Now there are 161 residues with 2546 atoms
  240. Chain time...
  241. Making bonds...
  242. Number of bonds was 2566, now 2566
  243. Generating angles, dihedrals and pairs...
  244. Before cleaning: 6691 pairs
  245. Before cleaning: 6736 dihedrals
  246. Keeping all generated dihedrals
  247. Making cmap torsions...
  248. There are 6736 dihedrals, 515 impropers, 4636 angles
  249. 6655 pairs, 2566 bonds and 0 virtual sites
  250. Total mass 18101.739 a.m.u.
  251. Total charge -4.000 e
  252. Writing topology
  253. Processing chain 4 'J' (1319 atoms, 161 residues)
  254. Identified residue MET1 as a starting terminus.
  255. Identified residue SER161 as a ending terminus.
  256. 8 out of 8 lines of specbond.dat converted successfully
  257. Special Atom Distance matrix:
  258. MET1 MET72 MET96 MET133 MET149
  259. SD7 SD548 SD844 SD1113 SD1226
  260. MET72 SD548 2.946
  261. MET96 SD844 1.635 2.672
  262. MET133 SD1113 2.075 1.220 1.455
  263. MET149 SD1226 1.754 2.188 0.525 0.984
  264. CYS157 SG1295 2.104 1.583 1.768 0.977 1.523
  265. Changing rtp entry of residue 26 LYS to 'LYSH'
  266. Changing rtp entry of residue 53 LYS to 'LYSH'
  267. Changing rtp entry of residue 58 LYS to 'LYSH'
  268. Changing rtp entry of residue 113 LYS to 'LYSH'
  269. Changing rtp entry of residue 134 LYS to 'LYSH'
  270. Changing rtp entry of residue 147 LYS to 'LYSH'
  271. Changing rtp entry of residue 157 CYS to 'CYSH'
  272. Start terminus MET-1: NH3+
  273. End terminus SER-161: COO-
  274. Renaming atom 'O' in residue 'SER' 161 to 'O1'
  275. Checking for duplicate atoms....
  276. Generating any missing hydrogen atoms and/or adding termini.
  277. Now there are 161 residues with 2531 atoms
  278. Chain time...
  279. Making bonds...
  280. Number of bonds was 2552, now 2552
  281. Generating angles, dihedrals and pairs...
  282. Before cleaning: 6634 pairs
  283. Before cleaning: 6674 dihedrals
  284. Keeping all generated dihedrals
  285. Making cmap torsions...
  286. There are 6674 dihedrals, 523 impropers, 4595 angles
  287. 6592 pairs, 2552 bonds and 0 virtual sites
  288. Total mass 18070.594 a.m.u.
  289. Total charge -2.000 e
  290. Writing topology
  291. Processing chain 5 'K' (1313 atoms, 161 residues)
  292. Identified residue MET1 as a starting terminus.
  293. Identified residue GLN161 as a ending terminus.
  294. 8 out of 8 lines of specbond.dat converted successfully
  295. Special Atom Distance matrix:
  296. MET1 MET77 MET115 MET133 CYS138
  297. SD7 SD600 SD978 SD1105 SG1141
  298. MET77 SD600 3.666
  299. MET115 SD978 2.299 1.415
  300. MET133 SD1105 2.649 2.164 1.658
  301. CYS138 SG1141 2.729 3.082 2.396 1.006
  302. MET160 SD1303 2.378 1.868 0.983 1.042 1.533
  303. Changing rtp entry of residue 6 LYS to 'LYSH'
  304. Changing rtp entry of residue 27 LYS to 'LYSH'
  305. Changing rtp entry of residue 52 LYS to 'LYSH'
  306. Changing rtp entry of residue 61 LYS to 'LYSH'
  307. Changing rtp entry of residue 113 LYS to 'LYSH'
  308. Changing rtp entry of residue 134 LYS to 'LYSH'
  309. Changing rtp entry of residue 138 CYS to 'CYSH'
  310. Start terminus MET-1: NH3+
  311. End terminus GLN-161: COO-
  312. Renaming atom 'O' in residue 'GLN' 161 to 'O1'
  313. Checking for duplicate atoms....
  314. Generating any missing hydrogen atoms and/or adding termini.
  315. Now there are 161 residues with 2546 atoms
  316. Chain time...
  317. Making bonds...
  318. Number of bonds was 2566, now 2566
  319. Generating angles, dihedrals and pairs...
  320. Before cleaning: 6691 pairs
  321. Before cleaning: 6736 dihedrals
  322. Keeping all generated dihedrals
  323. Making cmap torsions...
  324. There are 6736 dihedrals, 515 impropers, 4636 angles
  325. 6655 pairs, 2566 bonds and 0 virtual sites
  326. Total mass 18101.739 a.m.u.
  327. Total charge -4.000 e
  328. Writing topology
  329. Processing chain 6 'L' (1413 atoms, 169 residues)
  330. Identified residue MET1 as a starting terminus.
  331. Identified residue ILE169 as a ending terminus.
  332. 8 out of 8 lines of specbond.dat converted successfully
  333. Special Atom Distance matrix:
  334. MET1
  335. SD7
  336. MET142 SD1183 3.326
  337. Changing rtp entry of residue 17 LYS to 'LYSH'
  338. Changing rtp entry of residue 39 LYS to 'LYSH'
  339. Changing rtp entry of residue 50 LYS to 'LYSH'
  340. Changing rtp entry of residue 53 LYS to 'LYSH'
  341. Changing rtp entry of residue 106 LYS to 'LYSH'
  342. Changing rtp entry of residue 132 LYS to 'LYSH'
  343. Changing rtp entry of residue 143 LYS to 'LYSH'
  344. Changing rtp entry of residue 162 LYS to 'LYSH'
  345. Start terminus MET-1: NH3+
  346. End terminus ILE-169: COO-
  347. Renaming atom 'O' in residue 'ILE' 169 to 'O1'
  348. Renaming atom 'OXT' in residue 'ILE' 169 to 'O2'
  349. Checking for duplicate atoms....
  350. Generating any missing hydrogen atoms and/or adding termini.
  351. Now there are 169 residues with 2842 atoms
  352. Chain time...
  353. Making bonds...
  354. Warning: Long Bond (1157-1159 = 0.250825 nm)
  355. Number of bonds was 2866, now 2866
  356. Generating angles, dihedrals and pairs...
  357. Before cleaning: 7529 pairs
  358. Before cleaning: 7579 dihedrals
  359. Keeping all generated dihedrals
  360. Making cmap torsions...
  361. There are 7579 dihedrals, 572 impropers, 5188 angles
  362. 7484 pairs, 2866 bonds and 0 virtual sites
  363. Total mass 20019.968 a.m.u.
  364. Total charge -5.000 e
  365. Writing topology
  366. Including chain 1 in system: 3235 atoms 203 residues
  367. Including chain 2 in system: 2531 atoms 161 residues
  368. Including chain 3 in system: 2546 atoms 161 residues
  369. Including chain 4 in system: 2531 atoms 161 residues
  370. Including chain 5 in system: 2546 atoms 161 residues
  371. Including chain 6 in system: 2842 atoms 169 residues
  372. Now there are 16231 atoms and 1016 residues
  373. Total mass in system 115288.734 a.m.u.
  374. Total charge in system -17.000 e
  375.  
  376. Writing coordinate file...
  377. --------- PLEASE NOTE ------------
  378. You have successfully generated a topology from: trim.pdb.
  379. The OplsaaPBS force field and the spce water model are used.
  380. --------- ETON ESAELP ------------
  381.  
  382. gcq#304: "Gabba Gabba Hey!" (The Ramones)
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