Mercurial > repos > chemteam > gmx_setup
comparison test-data/topol_md.top @ 14:1d4dd4f908d4 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
| author | chemteam |
|---|---|
| date | Wed, 29 Sep 2021 07:42:14 +0000 |
| parents | |
| children |
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| 13:2c349b027a01 | 14:1d4dd4f908d4 |
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| 1 ; | |
| 2 ; File 'topol.top' was generated | |
| 3 ; By user: unknown (1000) | |
| 4 ; On host: simon-notebook | |
| 5 ; At date: Tue May 12 12:59:21 2020 | |
| 6 ; | |
| 7 ; This is a standalone topology file | |
| 8 ; | |
| 9 ; Created by: | |
| 10 ; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: | |
| 11 ; | |
| 12 ; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx | |
| 13 ; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 | |
| 14 ; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working | |
| 15 ; Command line: | |
| 16 ; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all | |
| 17 ; Force field was read from the standard GROMACS share directory. | |
| 18 ; | |
| 19 | |
| 20 ; Include forcefield parameters | |
| 21 #include "oplsaa.ff/forcefield.itp" | |
| 22 | |
| 23 [ moleculetype ] | |
| 24 ; Name nrexcl | |
| 25 Protein 3 | |
| 26 | |
| 27 [ atoms ] | |
| 28 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB | |
| 29 ; residue 1 LYS rtp LYSH q +2.0 | |
| 30 1 opls_287 1 LYS N 1 -0.3 14.0027 | |
| 31 2 opls_290 1 LYS H1 1 0.33 1.008 | |
| 32 3 opls_290 1 LYS H2 1 0.33 1.008 | |
| 33 4 opls_290 1 LYS H3 1 0.33 1.008 | |
| 34 5 opls_293B 1 LYS CA 1 0.25 12.011 | |
| 35 6 opls_140 1 LYS HA 1 0.06 1.008 | |
| 36 7 opls_136 1 LYS CB 2 -0.12 12.011 | |
| 37 8 opls_140 1 LYS HB1 2 0.06 1.008 | |
| 38 9 opls_140 1 LYS HB2 2 0.06 1.008 | |
| 39 10 opls_136 1 LYS CG 3 -0.12 12.011 | |
| 40 11 opls_140 1 LYS HG1 3 0.06 1.008 | |
| 41 12 opls_140 1 LYS HG2 3 0.06 1.008 | |
| 42 13 opls_136 1 LYS CD 4 -0.12 12.011 | |
| 43 14 opls_140 1 LYS HD1 4 0.06 1.008 | |
| 44 15 opls_140 1 LYS HD2 4 0.06 1.008 | |
| 45 16 opls_292 1 LYS CE 5 0.19 12.011 | |
| 46 17 opls_140 1 LYS HE1 5 0.06 1.008 | |
| 47 18 opls_140 1 LYS HE2 5 0.06 1.008 | |
| 48 19 opls_287 1 LYS NZ 6 -0.3 14.0067 | |
| 49 20 opls_290 1 LYS HZ1 6 0.33 1.008 | |
| 50 21 opls_290 1 LYS HZ2 6 0.33 1.008 | |
| 51 22 opls_290 1 LYS HZ3 6 0.33 1.008 | |
| 52 23 opls_235 1 LYS C 7 0.5 12.011 | |
| 53 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 | |
| 54 ; residue 2 VAL rtp VAL q 0.0 | |
| 55 25 opls_238 2 VAL N 8 -0.5 14.0067 | |
| 56 26 opls_241 2 VAL H 8 0.3 1.008 | |
| 57 27 opls_224B 2 VAL CA 8 0.14 12.011 | |
| 58 28 opls_140 2 VAL HA 8 0.06 1.008 | |
| 59 29 opls_137 2 VAL CB 9 -0.06 12.011 | |
| 60 30 opls_140 2 VAL HB 9 0.06 1.008 | |
| 61 31 opls_135 2 VAL CG1 10 -0.18 12.011 | |
| 62 32 opls_140 2 VAL HG11 10 0.06 1.008 | |
| 63 33 opls_140 2 VAL HG12 10 0.06 1.008 | |
| 64 34 opls_140 2 VAL HG13 10 0.06 1.008 | |
| 65 35 opls_135 2 VAL CG2 11 -0.18 12.011 | |
| 66 36 opls_140 2 VAL HG21 11 0.06 1.008 | |
| 67 37 opls_140 2 VAL HG22 11 0.06 1.008 | |
| 68 38 opls_140 2 VAL HG23 11 0.06 1.008 | |
| 69 39 opls_235 2 VAL C 12 0.5 12.011 | |
| 70 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 | |
| 71 ; residue 3 PHE rtp PHE q 0.0 | |
| 72 41 opls_238 3 PHE N 13 -0.5 14.0067 | |
| 73 42 opls_241 3 PHE H 13 0.3 1.008 | |
| 74 43 opls_224B 3 PHE CA 13 0.14 12.011 | |
| 75 44 opls_140 3 PHE HA 13 0.06 1.008 | |
| 76 45 opls_149 3 PHE CB 14 -0.005 12.011 | |
| 77 46 opls_140 3 PHE HB1 14 0.06 1.008 | |
| 78 47 opls_140 3 PHE HB2 14 0.06 1.008 | |
| 79 48 opls_145 3 PHE CG 14 -0.115 12.011 | |
| 80 49 opls_145 3 PHE CD1 15 -0.115 12.011 | |
| 81 50 opls_146 3 PHE HD1 15 0.115 1.008 | |
| 82 51 opls_145 3 PHE CD2 16 -0.115 12.011 | |
| 83 52 opls_146 3 PHE HD2 16 0.115 1.008 | |
| 84 53 opls_145 3 PHE CE1 17 -0.115 12.011 | |
| 85 54 opls_146 3 PHE HE1 17 0.115 1.008 | |
| 86 55 opls_145 3 PHE CE2 18 -0.115 12.011 | |
| 87 56 opls_146 3 PHE HE2 18 0.115 1.008 | |
| 88 57 opls_145 3 PHE CZ 19 -0.115 12.011 | |
| 89 58 opls_146 3 PHE HZ 19 0.115 1.008 | |
| 90 59 opls_235 3 PHE C 20 0.5 12.011 | |
| 91 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 | |
| 92 ; residue 4 GLY rtp GLY q 0.0 | |
| 93 61 opls_238 4 GLY N 21 -0.5 14.0067 | |
| 94 62 opls_241 4 GLY H 21 0.3 1.008 | |
| 95 63 opls_223B 4 GLY CA 21 0.08 12.011 | |
| 96 64 opls_140 4 GLY HA1 21 0.06 1.008 | |
| 97 65 opls_140 4 GLY HA2 21 0.06 1.008 | |
| 98 66 opls_235 4 GLY C 22 0.5 12.011 | |
| 99 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 | |
| 100 ; residue 5 ARG rtp ARG q 0.0 | |
| 101 68 opls_238 5 ARG N 23 -0.5 14.0067 | |
| 102 69 opls_241 5 ARG H 23 0.3 1.008 | |
| 103 70 opls_283 5 ARG CA 23 0.04 12.011 | |
| 104 71 opls_140 5 ARG HA 23 0.06 1.008 | |
| 105 72 opls_136 5 ARG CB 24 -0.12 12.011 | |
| 106 73 opls_140 5 ARG HB1 24 0.06 1.008 | |
| 107 74 opls_140 5 ARG HB2 24 0.06 1.008 | |
| 108 75 opls_308 5 ARG CG 25 -0.05 12.011 | |
| 109 76 opls_140 5 ARG HG1 25 0.06 1.008 | |
| 110 77 opls_140 5 ARG HG2 25 0.06 1.008 | |
| 111 78 opls_307 5 ARG CD 26 0.19 12.011 | |
| 112 79 opls_140 5 ARG HD1 26 0.06 1.008 | |
| 113 80 opls_140 5 ARG HD2 26 0.06 1.008 | |
| 114 81 opls_303 5 ARG NE 27 -0.7 14.0067 | |
| 115 82 opls_304 5 ARG HE 27 0.44 1.008 | |
| 116 83 opls_302 5 ARG CZ 27 0.64 12.011 | |
| 117 84 opls_300 5 ARG NH1 28 -0.8 14.0067 | |
| 118 85 opls_301 5 ARG HH11 28 0.46 1.008 | |
| 119 86 opls_301 5 ARG HH12 28 0.46 1.008 | |
| 120 87 opls_300 5 ARG NH2 29 -0.8 14.0067 | |
| 121 88 opls_301 5 ARG HH21 29 0.46 1.008 | |
| 122 89 opls_301 5 ARG HH22 29 0.46 1.008 | |
| 123 90 opls_271 5 ARG C 30 0.7 12.011 | |
| 124 91 opls_272 5 ARG O1 30 -0.8 15.9994 | |
| 125 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 | |
| 126 | |
| 127 [ bonds ] | |
| 128 ; ai aj funct c0 c1 c2 c3 | |
| 129 1 2 1 | |
| 130 1 3 1 | |
| 131 1 4 1 | |
| 132 1 5 1 | |
| 133 5 6 1 | |
| 134 5 7 1 | |
| 135 5 23 1 | |
| 136 7 8 1 | |
| 137 7 9 1 | |
| 138 7 10 1 | |
| 139 10 11 1 | |
| 140 10 12 1 | |
| 141 10 13 1 | |
| 142 13 14 1 | |
| 143 13 15 1 | |
| 144 13 16 1 | |
| 145 16 17 1 | |
| 146 16 18 1 | |
| 147 16 19 1 | |
| 148 19 20 1 | |
| 149 19 21 1 | |
| 150 19 22 1 | |
| 151 23 24 1 | |
| 152 23 25 1 | |
| 153 25 26 1 | |
| 154 25 27 1 | |
| 155 27 28 1 | |
| 156 27 29 1 | |
| 157 27 39 1 | |
| 158 29 30 1 | |
| 159 29 31 1 | |
| 160 29 35 1 | |
| 161 31 32 1 | |
| 162 31 33 1 | |
| 163 31 34 1 | |
| 164 35 36 1 | |
| 165 35 37 1 | |
| 166 35 38 1 | |
| 167 39 40 1 | |
| 168 39 41 1 | |
| 169 41 42 1 | |
| 170 41 43 1 | |
| 171 43 44 1 | |
| 172 43 45 1 | |
| 173 43 59 1 | |
| 174 45 46 1 | |
| 175 45 47 1 | |
| 176 45 48 1 | |
| 177 48 49 1 | |
| 178 48 51 1 | |
| 179 49 50 1 | |
| 180 49 53 1 | |
| 181 51 52 1 | |
| 182 51 55 1 | |
| 183 53 54 1 | |
| 184 53 57 1 | |
| 185 55 56 1 | |
| 186 55 57 1 | |
| 187 57 58 1 | |
| 188 59 60 1 | |
| 189 59 61 1 | |
| 190 61 62 1 | |
| 191 61 63 1 | |
| 192 63 64 1 | |
| 193 63 65 1 | |
| 194 63 66 1 | |
| 195 66 67 1 | |
| 196 66 68 1 | |
| 197 68 69 1 | |
| 198 68 70 1 | |
| 199 70 71 1 | |
| 200 70 72 1 | |
| 201 70 90 1 | |
| 202 72 73 1 | |
| 203 72 74 1 | |
| 204 72 75 1 | |
| 205 75 76 1 | |
| 206 75 77 1 | |
| 207 75 78 1 | |
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| 209 78 80 1 | |
| 210 78 81 1 | |
| 211 81 82 1 | |
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| 213 83 84 1 | |
| 214 83 87 1 | |
| 215 84 85 1 | |
| 216 84 86 1 | |
| 217 87 88 1 | |
| 218 87 89 1 | |
| 219 90 91 1 | |
| 220 90 92 1 | |
| 221 | |
| 222 [ pairs ] | |
| 223 ; ai aj funct c0 c1 c2 c3 | |
| 224 1 8 1 | |
| 225 1 9 1 | |
| 226 1 10 1 | |
| 227 1 24 1 | |
| 228 1 25 1 | |
| 229 2 6 1 | |
| 230 2 7 1 | |
| 231 2 23 1 | |
| 232 3 6 1 | |
| 233 3 7 1 | |
| 234 3 23 1 | |
| 235 4 6 1 | |
| 236 4 7 1 | |
| 237 4 23 1 | |
| 238 5 11 1 | |
| 239 5 12 1 | |
| 240 5 13 1 | |
| 241 5 26 1 | |
| 242 5 27 1 | |
| 243 6 8 1 | |
| 244 6 9 1 | |
| 245 6 10 1 | |
| 246 6 24 1 | |
| 247 6 25 1 | |
| 248 7 14 1 | |
| 249 7 15 1 | |
| 250 7 16 1 | |
| 251 7 24 1 | |
| 252 7 25 1 | |
| 253 8 11 1 | |
| 254 8 12 1 | |
| 255 8 13 1 | |
| 256 8 23 1 | |
| 257 9 11 1 | |
| 258 9 12 1 | |
| 259 9 13 1 | |
| 260 9 23 1 | |
| 261 10 17 1 | |
| 262 10 18 1 | |
| 263 10 19 1 | |
| 264 10 23 1 | |
| 265 11 14 1 | |
| 266 11 15 1 | |
| 267 11 16 1 | |
| 268 12 14 1 | |
| 269 12 15 1 | |
| 270 12 16 1 | |
| 271 13 20 1 | |
| 272 13 21 1 | |
| 273 13 22 1 | |
| 274 14 17 1 | |
| 275 14 18 1 | |
| 276 14 19 1 | |
| 277 15 17 1 | |
| 278 15 18 1 | |
| 279 15 19 1 | |
| 280 17 20 1 | |
| 281 17 21 1 | |
| 282 17 22 1 | |
| 283 18 20 1 | |
| 284 18 21 1 | |
| 285 18 22 1 | |
| 286 23 28 1 | |
| 287 23 29 1 | |
| 288 23 39 1 | |
| 289 24 26 1 | |
| 290 24 27 1 | |
| 291 25 30 1 | |
| 292 25 31 1 | |
| 293 25 35 1 | |
| 294 25 40 1 | |
| 295 25 41 1 | |
| 296 26 28 1 | |
| 297 26 29 1 | |
| 298 26 39 1 | |
| 299 27 32 1 | |
| 300 27 33 1 | |
| 301 27 34 1 | |
| 302 27 36 1 | |
| 303 27 37 1 | |
| 304 27 38 1 | |
| 305 27 42 1 | |
| 306 27 43 1 | |
| 307 28 30 1 | |
| 308 28 31 1 | |
| 309 28 35 1 | |
| 310 28 40 1 | |
| 311 28 41 1 | |
| 312 29 40 1 | |
| 313 29 41 1 | |
| 314 30 32 1 | |
| 315 30 33 1 | |
| 316 30 34 1 | |
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| 318 30 37 1 | |
| 319 30 38 1 | |
| 320 30 39 1 | |
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| 322 31 37 1 | |
| 323 31 38 1 | |
| 324 31 39 1 | |
| 325 32 35 1 | |
| 326 33 35 1 | |
| 327 34 35 1 | |
| 328 35 39 1 | |
| 329 39 44 1 | |
| 330 39 45 1 | |
| 331 39 59 1 | |
| 332 40 42 1 | |
| 333 40 43 1 | |
| 334 41 46 1 | |
| 335 41 47 1 | |
| 336 41 48 1 | |
| 337 41 60 1 | |
| 338 41 61 1 | |
| 339 42 44 1 | |
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| 341 42 59 1 | |
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| 343 43 51 1 | |
| 344 43 62 1 | |
| 345 43 63 1 | |
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| 348 44 48 1 | |
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| 351 45 50 1 | |
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| 354 45 55 1 | |
| 355 45 60 1 | |
| 356 45 61 1 | |
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| 360 47 49 1 | |
| 361 47 51 1 | |
| 362 47 59 1 | |
| 363 48 54 1 | |
| 364 48 56 1 | |
| 365 48 57 1 | |
| 366 48 59 1 | |
| 367 49 52 1 | |
| 368 49 55 1 | |
| 369 49 58 1 | |
| 370 50 51 1 | |
| 371 50 54 1 | |
| 372 50 57 1 | |
| 373 51 53 1 | |
| 374 51 58 1 | |
| 375 52 56 1 | |
| 376 52 57 1 | |
| 377 53 56 1 | |
| 378 54 55 1 | |
| 379 54 58 1 | |
| 380 56 58 1 | |
| 381 59 64 1 | |
| 382 59 65 1 | |
| 383 59 66 1 | |
| 384 60 62 1 | |
| 385 60 63 1 | |
| 386 61 67 1 | |
| 387 61 68 1 | |
| 388 62 64 1 | |
| 389 62 65 1 | |
| 390 62 66 1 | |
| 391 63 69 1 | |
| 392 63 70 1 | |
| 393 64 67 1 | |
| 394 64 68 1 | |
| 395 65 67 1 | |
| 396 65 68 1 | |
| 397 66 71 1 | |
| 398 66 72 1 | |
| 399 66 90 1 | |
| 400 67 69 1 | |
| 401 67 70 1 | |
| 402 68 73 1 | |
| 403 68 74 1 | |
| 404 68 75 1 | |
| 405 68 91 1 | |
| 406 68 92 1 | |
| 407 69 71 1 | |
| 408 69 72 1 | |
| 409 69 90 1 | |
| 410 70 76 1 | |
| 411 70 77 1 | |
| 412 70 78 1 | |
| 413 71 73 1 | |
| 414 71 74 1 | |
| 415 71 75 1 | |
| 416 71 91 1 | |
| 417 71 92 1 | |
| 418 72 79 1 | |
| 419 72 80 1 | |
| 420 72 81 1 | |
| 421 72 91 1 | |
| 422 72 92 1 | |
| 423 73 76 1 | |
| 424 73 77 1 | |
| 425 73 78 1 | |
| 426 73 90 1 | |
| 427 74 76 1 | |
| 428 74 77 1 | |
| 429 74 78 1 | |
| 430 74 90 1 | |
| 431 75 82 1 | |
| 432 75 83 1 | |
| 433 75 90 1 | |
| 434 76 79 1 | |
| 435 76 80 1 | |
| 436 76 81 1 | |
| 437 77 79 1 | |
| 438 77 80 1 | |
| 439 77 81 1 | |
| 440 78 84 1 | |
| 441 78 87 1 | |
| 442 79 82 1 | |
| 443 79 83 1 | |
| 444 80 82 1 | |
| 445 80 83 1 | |
| 446 81 85 1 | |
| 447 81 86 1 | |
| 448 81 88 1 | |
| 449 81 89 1 | |
| 450 82 84 1 | |
| 451 82 87 1 | |
| 452 84 88 1 | |
| 453 84 89 1 | |
| 454 85 87 1 | |
| 455 86 87 1 | |
| 456 | |
| 457 [ angles ] | |
| 458 ; ai aj ak funct c0 c1 c2 c3 | |
| 459 2 1 3 1 | |
| 460 2 1 4 1 | |
| 461 2 1 5 1 | |
| 462 3 1 4 1 | |
| 463 3 1 5 1 | |
| 464 4 1 5 1 | |
| 465 1 5 6 1 | |
| 466 1 5 7 1 | |
| 467 1 5 23 1 | |
| 468 6 5 7 1 | |
| 469 6 5 23 1 | |
| 470 7 5 23 1 | |
| 471 5 7 8 1 | |
| 472 5 7 9 1 | |
| 473 5 7 10 1 | |
| 474 8 7 9 1 | |
| 475 8 7 10 1 | |
| 476 9 7 10 1 | |
| 477 7 10 11 1 | |
| 478 7 10 12 1 | |
| 479 7 10 13 1 | |
| 480 11 10 12 1 | |
| 481 11 10 13 1 | |
| 482 12 10 13 1 | |
| 483 10 13 14 1 | |
| 484 10 13 15 1 | |
| 485 10 13 16 1 | |
| 486 14 13 15 1 | |
| 487 14 13 16 1 | |
| 488 15 13 16 1 | |
| 489 13 16 17 1 | |
| 490 13 16 18 1 | |
| 491 13 16 19 1 | |
| 492 17 16 18 1 | |
| 493 17 16 19 1 | |
| 494 18 16 19 1 | |
| 495 16 19 20 1 | |
| 496 16 19 21 1 | |
| 497 16 19 22 1 | |
| 498 20 19 21 1 | |
| 499 20 19 22 1 | |
| 500 21 19 22 1 | |
| 501 5 23 24 1 | |
| 502 5 23 25 1 | |
| 503 24 23 25 1 | |
| 504 23 25 26 1 | |
| 505 23 25 27 1 | |
| 506 26 25 27 1 | |
| 507 25 27 28 1 | |
| 508 25 27 29 1 | |
| 509 25 27 39 1 | |
| 510 28 27 29 1 | |
| 511 28 27 39 1 | |
| 512 29 27 39 1 | |
| 513 27 29 30 1 | |
| 514 27 29 31 1 | |
| 515 27 29 35 1 | |
| 516 30 29 31 1 | |
| 517 30 29 35 1 | |
| 518 31 29 35 1 | |
| 519 29 31 32 1 | |
| 520 29 31 33 1 | |
| 521 29 31 34 1 | |
| 522 32 31 33 1 | |
| 523 32 31 34 1 | |
| 524 33 31 34 1 | |
| 525 29 35 36 1 | |
| 526 29 35 37 1 | |
| 527 29 35 38 1 | |
| 528 36 35 37 1 | |
| 529 36 35 38 1 | |
| 530 37 35 38 1 | |
| 531 27 39 40 1 | |
| 532 27 39 41 1 | |
| 533 40 39 41 1 | |
| 534 39 41 42 1 | |
| 535 39 41 43 1 | |
| 536 42 41 43 1 | |
| 537 41 43 44 1 | |
| 538 41 43 45 1 | |
| 539 41 43 59 1 | |
| 540 44 43 45 1 | |
| 541 44 43 59 1 | |
| 542 45 43 59 1 | |
| 543 43 45 46 1 | |
| 544 43 45 47 1 | |
| 545 43 45 48 1 | |
| 546 46 45 47 1 | |
| 547 46 45 48 1 | |
| 548 47 45 48 1 | |
| 549 45 48 49 1 | |
| 550 45 48 51 1 | |
| 551 49 48 51 1 | |
| 552 48 49 50 1 | |
| 553 48 49 53 1 | |
| 554 50 49 53 1 | |
| 555 48 51 52 1 | |
| 556 48 51 55 1 | |
| 557 52 51 55 1 | |
| 558 49 53 54 1 | |
| 559 49 53 57 1 | |
| 560 54 53 57 1 | |
| 561 51 55 56 1 | |
| 562 51 55 57 1 | |
| 563 56 55 57 1 | |
| 564 53 57 55 1 | |
| 565 53 57 58 1 | |
| 566 55 57 58 1 | |
| 567 43 59 60 1 | |
| 568 43 59 61 1 | |
| 569 60 59 61 1 | |
| 570 59 61 62 1 | |
| 571 59 61 63 1 | |
| 572 62 61 63 1 | |
| 573 61 63 64 1 | |
| 574 61 63 65 1 | |
| 575 61 63 66 1 | |
| 576 64 63 65 1 | |
| 577 64 63 66 1 | |
| 578 65 63 66 1 | |
| 579 63 66 67 1 | |
| 580 63 66 68 1 | |
| 581 67 66 68 1 | |
| 582 66 68 69 1 | |
| 583 66 68 70 1 | |
| 584 69 68 70 1 | |
| 585 68 70 71 1 | |
| 586 68 70 72 1 | |
| 587 68 70 90 1 | |
| 588 71 70 72 1 | |
| 589 71 70 90 1 | |
| 590 72 70 90 1 | |
| 591 70 72 73 1 | |
| 592 70 72 74 1 | |
| 593 70 72 75 1 | |
| 594 73 72 74 1 | |
| 595 73 72 75 1 | |
| 596 74 72 75 1 | |
| 597 72 75 76 1 | |
| 598 72 75 77 1 | |
| 599 72 75 78 1 | |
| 600 76 75 77 1 | |
| 601 76 75 78 1 | |
| 602 77 75 78 1 | |
| 603 75 78 79 1 | |
| 604 75 78 80 1 | |
| 605 75 78 81 1 | |
| 606 79 78 80 1 | |
| 607 79 78 81 1 | |
| 608 80 78 81 1 | |
| 609 78 81 82 1 | |
| 610 78 81 83 1 | |
| 611 82 81 83 1 | |
| 612 81 83 84 1 | |
| 613 81 83 87 1 | |
| 614 84 83 87 1 | |
| 615 83 84 85 1 | |
| 616 83 84 86 1 | |
| 617 85 84 86 1 | |
| 618 83 87 88 1 | |
| 619 83 87 89 1 | |
| 620 88 87 89 1 | |
| 621 70 90 91 1 | |
| 622 70 90 92 1 | |
| 623 91 90 92 1 | |
| 624 | |
| 625 [ dihedrals ] | |
| 626 ; ai aj ak al funct c0 c1 c2 c3 c4 c5 | |
| 627 2 1 5 6 3 | |
| 628 2 1 5 7 3 | |
| 629 2 1 5 23 3 | |
| 630 3 1 5 6 3 | |
| 631 3 1 5 7 3 | |
| 632 3 1 5 23 3 | |
| 633 4 1 5 6 3 | |
| 634 4 1 5 7 3 | |
| 635 4 1 5 23 3 | |
| 636 1 5 7 10 3 dih_LYS_chi1_N_C_C_C | |
| 637 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO | |
| 638 1 5 7 8 3 | |
| 639 1 5 7 9 3 | |
| 640 6 5 7 8 3 | |
| 641 6 5 7 9 3 | |
| 642 6 5 7 10 3 | |
| 643 23 5 7 8 3 | |
| 644 23 5 7 9 3 | |
| 645 1 5 23 24 3 | |
| 646 1 5 23 25 3 | |
| 647 6 5 23 24 3 | |
| 648 6 5 23 25 3 | |
| 649 7 5 23 24 3 | |
| 650 7 5 23 25 3 | |
| 651 5 7 10 11 3 | |
| 652 5 7 10 12 3 | |
| 653 5 7 10 13 3 | |
| 654 8 7 10 11 3 | |
| 655 8 7 10 12 3 | |
| 656 8 7 10 13 3 | |
| 657 9 7 10 11 3 | |
| 658 9 7 10 12 3 | |
| 659 9 7 10 13 3 | |
| 660 7 10 13 14 3 | |
| 661 7 10 13 15 3 | |
| 662 7 10 13 16 3 | |
| 663 11 10 13 14 3 | |
| 664 11 10 13 15 3 | |
| 665 11 10 13 16 3 | |
| 666 12 10 13 14 3 | |
| 667 12 10 13 15 3 | |
| 668 12 10 13 16 3 | |
| 669 10 13 16 17 3 | |
| 670 10 13 16 18 3 | |
| 671 10 13 16 19 3 | |
| 672 14 13 16 17 3 | |
| 673 14 13 16 18 3 | |
| 674 14 13 16 19 3 | |
| 675 15 13 16 17 3 | |
| 676 15 13 16 18 3 | |
| 677 15 13 16 19 3 | |
| 678 13 16 19 20 3 dih_LYS_chi5_C_C_N_H | |
| 679 13 16 19 21 3 dih_LYS_chi5_C_C_N_H | |
| 680 13 16 19 22 3 dih_LYS_chi5_C_C_N_H | |
| 681 17 16 19 20 3 | |
| 682 17 16 19 21 3 | |
| 683 17 16 19 22 3 | |
| 684 18 16 19 20 3 | |
| 685 18 16 19 21 3 | |
| 686 18 16 19 22 3 | |
| 687 5 23 25 26 3 | |
| 688 5 23 25 27 3 | |
| 689 24 23 25 26 3 | |
| 690 24 23 25 27 3 | |
| 691 23 25 27 28 3 | |
| 692 23 25 27 29 3 | |
| 693 23 25 27 39 3 | |
| 694 26 25 27 28 3 | |
| 695 26 25 27 29 3 | |
| 696 26 25 27 39 3 | |
| 697 25 27 29 31 3 dih_VAL_chi1_N_C_C_C | |
| 698 25 27 29 35 3 dih_VAL_chi1_N_C_C_C | |
| 699 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO | |
| 700 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO | |
| 701 25 27 29 30 3 | |
| 702 28 27 29 30 3 | |
| 703 28 27 29 31 3 | |
| 704 28 27 29 35 3 | |
| 705 39 27 29 30 3 | |
| 706 25 27 39 40 3 | |
| 707 25 27 39 41 3 | |
| 708 28 27 39 40 3 | |
| 709 28 27 39 41 3 | |
| 710 29 27 39 40 3 | |
| 711 29 27 39 41 3 | |
| 712 27 29 31 32 3 | |
| 713 27 29 31 33 3 | |
| 714 27 29 31 34 3 | |
| 715 30 29 31 32 3 | |
| 716 30 29 31 33 3 | |
| 717 30 29 31 34 3 | |
| 718 35 29 31 32 3 | |
| 719 35 29 31 33 3 | |
| 720 35 29 31 34 3 | |
| 721 27 29 35 36 3 | |
| 722 27 29 35 37 3 | |
| 723 27 29 35 38 3 | |
| 724 30 29 35 36 3 | |
| 725 30 29 35 37 3 | |
| 726 30 29 35 38 3 | |
| 727 31 29 35 36 3 | |
| 728 31 29 35 37 3 | |
| 729 31 29 35 38 3 | |
| 730 27 39 41 42 3 | |
| 731 27 39 41 43 3 | |
| 732 40 39 41 42 3 | |
| 733 40 39 41 43 3 | |
| 734 39 41 43 44 3 | |
| 735 39 41 43 45 3 | |
| 736 39 41 43 59 3 | |
| 737 42 41 43 44 3 | |
| 738 42 41 43 45 3 | |
| 739 42 41 43 59 3 | |
| 740 41 43 45 46 3 | |
| 741 41 43 45 47 3 | |
| 742 41 43 45 48 3 | |
| 743 44 43 45 46 3 | |
| 744 44 43 45 47 3 | |
| 745 44 43 45 48 3 | |
| 746 59 43 45 46 3 | |
| 747 59 43 45 47 3 | |
| 748 59 43 45 48 3 | |
| 749 41 43 59 60 3 | |
| 750 41 43 59 61 3 | |
| 751 44 43 59 60 3 | |
| 752 44 43 59 61 3 | |
| 753 45 43 59 60 3 | |
| 754 45 43 59 61 3 | |
| 755 43 45 48 49 3 | |
| 756 43 45 48 51 3 | |
| 757 46 45 48 49 3 | |
| 758 46 45 48 51 3 | |
| 759 47 45 48 49 3 | |
| 760 47 45 48 51 3 | |
| 761 45 48 49 50 3 | |
| 762 45 48 49 53 3 | |
| 763 51 48 49 50 3 | |
| 764 51 48 49 53 3 | |
| 765 45 48 51 52 3 | |
| 766 45 48 51 55 3 | |
| 767 49 48 51 52 3 | |
| 768 49 48 51 55 3 | |
| 769 48 49 53 54 3 | |
| 770 48 49 53 57 3 | |
| 771 50 49 53 54 3 | |
| 772 50 49 53 57 3 | |
| 773 48 51 55 56 3 | |
| 774 48 51 55 57 3 | |
| 775 52 51 55 56 3 | |
| 776 52 51 55 57 3 | |
| 777 49 53 57 55 3 | |
| 778 49 53 57 58 3 | |
| 779 54 53 57 55 3 | |
| 780 54 53 57 58 3 | |
| 781 51 55 57 53 3 | |
| 782 51 55 57 58 3 | |
| 783 56 55 57 53 3 | |
| 784 56 55 57 58 3 | |
| 785 43 59 61 62 3 | |
| 786 43 59 61 63 3 | |
| 787 60 59 61 62 3 | |
| 788 60 59 61 63 3 | |
| 789 59 61 63 64 3 | |
| 790 59 61 63 65 3 | |
| 791 59 61 63 66 3 | |
| 792 62 61 63 64 3 | |
| 793 62 61 63 65 3 | |
| 794 62 61 63 66 3 | |
| 795 61 63 66 67 3 | |
| 796 61 63 66 68 3 | |
| 797 64 63 66 67 3 | |
| 798 64 63 66 68 3 | |
| 799 65 63 66 67 3 | |
| 800 65 63 66 68 3 | |
| 801 63 66 68 69 3 | |
| 802 63 66 68 70 3 | |
| 803 67 66 68 69 3 | |
| 804 67 66 68 70 3 | |
| 805 66 68 70 71 3 | |
| 806 66 68 70 72 3 | |
| 807 66 68 70 90 3 | |
| 808 69 68 70 71 3 | |
| 809 69 68 70 72 3 | |
| 810 69 68 70 90 3 | |
| 811 68 70 72 75 3 dih_ARG_chi1_N_C_C_C | |
| 812 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO | |
| 813 68 70 72 73 3 | |
| 814 68 70 72 74 3 | |
| 815 71 70 72 73 3 | |
| 816 71 70 72 74 3 | |
| 817 71 70 72 75 3 | |
| 818 90 70 72 73 3 | |
| 819 90 70 72 74 3 | |
| 820 68 70 90 91 3 | |
| 821 68 70 90 92 3 | |
| 822 71 70 90 91 3 | |
| 823 71 70 90 92 3 | |
| 824 72 70 90 91 3 | |
| 825 72 70 90 92 3 | |
| 826 70 72 75 76 3 | |
| 827 70 72 75 77 3 | |
| 828 70 72 75 78 3 | |
| 829 73 72 75 76 3 | |
| 830 73 72 75 77 3 | |
| 831 73 72 75 78 3 | |
| 832 74 72 75 76 3 | |
| 833 74 72 75 77 3 | |
| 834 74 72 75 78 3 | |
| 835 72 75 78 79 3 | |
| 836 72 75 78 80 3 | |
| 837 72 75 78 81 3 | |
| 838 76 75 78 79 3 | |
| 839 76 75 78 80 3 | |
| 840 76 75 78 81 3 | |
| 841 77 75 78 79 3 | |
| 842 77 75 78 80 3 | |
| 843 77 75 78 81 3 | |
| 844 75 78 81 82 3 | |
| 845 75 78 81 83 3 | |
| 846 79 78 81 82 3 | |
| 847 79 78 81 83 3 | |
| 848 80 78 81 82 3 | |
| 849 80 78 81 83 3 | |
| 850 78 81 83 84 3 | |
| 851 78 81 83 87 3 | |
| 852 82 81 83 84 3 | |
| 853 82 81 83 87 3 | |
| 854 81 83 84 85 3 | |
| 855 81 83 84 86 3 | |
| 856 87 83 84 85 3 | |
| 857 87 83 84 86 3 | |
| 858 81 83 87 88 3 | |
| 859 81 83 87 89 3 | |
| 860 84 83 87 88 3 | |
| 861 84 83 87 89 3 | |
| 862 | |
| 863 [ dihedrals ] | |
| 864 ; ai aj ak al funct c0 c1 c2 c3 | |
| 865 5 25 23 24 1 improper_O_C_X_Y | |
| 866 23 27 25 26 1 improper_Z_N_X_Y | |
| 867 27 41 39 40 1 improper_O_C_X_Y | |
| 868 39 43 41 42 1 improper_Z_N_X_Y | |
| 869 43 61 59 60 1 improper_O_C_X_Y | |
| 870 45 48 51 49 1 improper_Z_CA_X_Y | |
| 871 48 53 49 50 1 improper_Z_CA_X_Y | |
| 872 48 55 51 52 1 improper_Z_CA_X_Y | |
| 873 49 57 53 54 1 improper_Z_CA_X_Y | |
| 874 51 57 55 56 1 improper_Z_CA_X_Y | |
| 875 53 55 57 58 1 improper_Z_CA_X_Y | |
| 876 59 63 61 62 1 improper_Z_N_X_Y | |
| 877 63 68 66 67 1 improper_O_C_X_Y | |
| 878 66 70 68 69 1 improper_Z_N_X_Y | |
| 879 70 91 90 92 1 improper_O_C_X_Y | |
| 880 78 83 81 82 1 improper_Z_N_X_Y | |
| 881 81 84 83 87 1 improper_O_C_X_Y | |
| 882 83 85 84 86 1 improper_Z_N_X_Y | |
| 883 83 88 87 89 1 improper_Z_N_X_Y | |
| 884 | |
| 885 ; Include Position restraint file | |
| 886 #ifdef POSRES | |
| 887 #include "posres.itp" | |
| 888 #endif | |
| 889 | |
| 890 ; Include water topology | |
| 891 #include "oplsaa.ff/spce.itp" | |
| 892 | |
| 893 #ifdef POSRES_WATER | |
| 894 ; Position restraint for each water oxygen | |
| 895 [ position_restraints ] | |
| 896 ; i funct fcx fcy fcz | |
| 897 1 1 1000 1000 1000 | |
| 898 #endif | |
| 899 | |
| 900 ; Include topology for ions | |
| 901 #include "oplsaa.ff/ions.itp" | |
| 902 | |
| 903 [ system ] | |
| 904 ; Name | |
| 905 TEST in water | |
| 906 | |
| 907 [ molecules ] | |
| 908 ; Compound #mols | |
| 909 Protein 1 | |
| 910 CL 2 |