/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb is in gromacs-data 4.5.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 | HOH 1
2 7 HW OW
HO4 1
3 10 HW OW
ACE 1
3 4 HH3 CH3 C O
NME 2
1 1 H N -C CH3
3 4 HH3 CH3 N -C
NHE 1
2 3 H N -C -CA
NH2 1
2 3 H N -C -CA
ALA 3
1 1 H N -C CA
1 5 HA CA N CB C
3 4 HB CB CA N
GLY 2
1 1 H N -C CA
2 6 HA CA N C
SER 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA OG
1 2 HG OG CB CA
THR 5
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG2 OG1
3 4 HG2 CG2 CB CA
1 2 HG1 OG1 CB CA
LEU 6
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 5 HG CG CB CD1 CD2
3 4 HD1 CD1 CG CB
3 4 HD2 CD2 CG CB
ILE 6
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG2 CG1
3 4 HG2 CG2 CB CA
2 6 HG1 CG1 CB CD
3 4 HD CD CG1 CB
VAL 5
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG1 CG2
3 4 HG1 CG1 CB CA
3 4 HG2 CG2 CB CA
ASN 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 3 HD2 ND2 CG CB
GLN 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 3 HE2 NE2 CD CG
ARG 8
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG NE
1 1 HE NE CD CZ
2 3 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
HID 6
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 ND1 CG CE1
1 1 HE1 CE1 ND1 NE2
1 1 HD2 CD2 CG NE2
HIE 6
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
HIP 7
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 ND1 CG CE1
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
TRP 9
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG NE1
1 1 HE1 NE1 CD1 CE2
1 1 HZ2 CZ2 CE2 CH2
1 1 HH2 CH2 CZ2 CZ3
1 1 HZ3 CZ3 CH2 CE3
1 1 HE3 CE3 CZ3 CD2
PHE 8
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG CE1
1 1 HE1 CE1 CD1 CZ
1 1 HZ CZ CE1 CE2
1 1 HE2 CE2 CZ CD2
1 1 HD2 CD2 CG CE2
TYR 8
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG CE1
1 1 HE1 CE1 CD1 CZ
1 2 HH OH CZ CE1
1 1 HE2 CE2 CZ CD2
1 1 HD2 CD2 CG CE2
GLU 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
ASP 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
LYS 7
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG CE
2 6 HE CE CD NZ
3 4 HZ NZ CE CD
ORN 6
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG NE
3 4 HE NE CD CG
DAB 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB ND
3 4 HD ND CG CB
LYN 7
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG CE
2 6 HE CE CD NZ
2 3 HZ NZ CE CD
PRO 4
2 6 HD CD N CG
2 6 HG CG CD CB
2 6 HB CB CG CA
1 5 HA CA N CB C
HYP 5
2 6 HD2 CD2 N CG
1 5 HG CG CD2 OD1 CB
1 2 HD1 OD1 CG CD2
2 6 HB CB CG CA
1 5 HA CA N CB C
CYS 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA SG
1 2 HG SG CB CA
CYM 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA SG
CYX 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA SG
CYS2 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA SG
MET 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB SD
3 4 HE CE SD CG
ASH 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 2 HD2 OD2 CG CB
GLH 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
1 2 HE2 OE2 CD CG
CALA 4
1 1 H N -C CA
1 5 HA CA N CB C
3 4 HB CB CA N
1 1 OC1 C CA OC2
CGLY 3
1 1 H N -C CA
2 6 HA CA N C
1 1 OC1 C CA OC2
CSER 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA OG
1 2 HG OG CB CA
1 1 OC1 C CA OC2
CTHR 6
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG2 OG1
3 4 HG2 CG2 CB CA
1 2 HG1 OG1 CB CA
1 1 OC1 C CA OC2
CLEU 7
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 5 HG CG CB CD1 CD2
3 4 HD1 CD1 CG CB
3 4 HD2 CD2 CG CB
1 1 OC1 C CA OC2
CILE 7
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG2 CG1
3 4 HG2 CG2 CB CA
2 6 HG1 CG1 CB CD
3 4 HD CD CG1 CB
1 1 OC1 C CA OC2
CVAL 6
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG1 CG2
3 4 HG1 CG1 CB CA
3 4 HG2 CG2 CB CA
1 1 OC1 C CA OC2
CASN 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 3 HD2 ND2 CG CB
1 1 OC1 C CA OC2
CGLN 6
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 3 HE2 NE2 CD CG
1 1 OC1 C CA OC2
CARG 9
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG NE
1 1 HE NE CD CZ
2 3 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
1 1 OC1 C CA OC2
CHID 7
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 ND1 CG CE1
1 1 HE1 CE1 ND1 NE2
1 1 HD2 CD2 CG NE2
1 1 OC1 C CA OC2
CHIE 7
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
1 1 OC1 C CA OC2
CHIP 8
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 ND1 CG CE1
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
1 1 OC1 C CA OC2
CTRP 10
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG NE1
1 1 HE1 NE1 CD1 CE2
1 1 HZ2 CZ2 CE2 CH2
1 1 HH2 CH2 CZ2 CZ3
1 1 HZ3 CZ3 CH2 CE3
1 1 HE3 CE3 CZ3 CD2
1 1 OC1 C CA OC2
CPHE 9
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG CE1
1 1 HE1 CE1 CD1 CZ
1 1 HZ CZ CE1 CE2
1 1 HE2 CE2 CZ CD2
1 1 HD2 CD2 CG CE2
1 1 OC1 C CA OC2
CTYR 9
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG CE1
1 1 HE1 CE1 CD1 CZ
1 2 HH OH CZ CE1
1 1 HE2 CE2 CZ CD2
1 1 HD2 CD2 CG CE2
1 1 OC1 C CA OC2
CGLU 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
1 1 OC1 C CA OC2
CASP 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 OC1 C CA OC2
CLYS 8
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG CE
2 6 HE CE CD NZ
3 4 HZ NZ CE CD
1 1 OC1 C CA OC2
CPRO 5
2 6 HD CD N CG
2 6 HG CG CD CB
2 6 HB CB CG CA
1 5 HA CA N CB C
1 1 OC1 C CA OC2
CCYS 5
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA SG
1 2 HG SG CB CA
1 1 OC1 C CA OC2
CCYX 4
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA SG
1 1 OC1 C CA OC2
CMET 6
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB SD
3 4 HE CE SD CG
1 1 OC1 C CA OC2
NALA 3
3 4 H N CA CB
1 5 HA CA N CB C
3 4 HB CB CA N
NGLY 2
3 4 H N CA C
2 6 HA CA N C
NSER 4
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA OG
1 2 HG OG CB CA
NTHR 5
3 4 H N CA CB
1 5 HA CA N CB C
1 5 HB CB CA CG2 OG1
3 4 HG2 CG2 CB CA
1 2 HG1 OG1 CB CA
NLEU 6
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 5 HG CG CB CD1 CD2
3 4 HD1 CD1 CG CB
3 4 HD2 CD2 CG CB
NILE 6
3 4 H N CA CB
1 5 HA CA N CB C
1 5 HB CB CA CG2 CG1
3 4 HG2 CG2 CB CA
2 6 HG1 CG1 CB CD
3 4 HD CD CG1 CB
NVAL 5
3 4 H N CA CB
1 5 HA CA N CB C
1 5 HB CB CA CG1 CG2
3 4 HG1 CG1 CB CA
3 4 HG2 CG2 CB CA
NASN 4
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
2 3 HD2 ND2 CG CB
NGLN 5
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 3 HE2 NE2 CD CG
NARG 8
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG NE
1 1 HE NE CD CZ
2 3 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
NHID 6
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 ND1 CG CE1
1 1 HE1 CE1 ND1 NE2
1 1 HD2 CD2 CG NE2
NHIE 6
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
NHIP 7
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 ND1 CG CE1
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
NTRP 9
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG NE1
1 1 HE1 NE1 CD1 CE2
1 1 HZ2 CZ2 CE2 CH2
1 1 HH2 CH2 CZ2 CZ3
1 1 HZ3 CZ3 CH2 CE3
1 1 HE3 CE3 CZ3 CD2
NPHE 8
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG CE1
1 1 HE1 CE1 CD1 CZ
1 1 HZ CZ CE1 CE2
1 1 HE2 CE2 CZ CD2
1 1 HD2 CD2 CG CE2
NTYR 8
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
1 1 HD1 CD1 CG CE1
1 1 HE1 CE1 CD1 CZ
1 2 HH OH CZ CE1
1 1 HE2 CE2 CZ CD2
1 1 HD2 CD2 CG CE2
NGLU 4
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
NASP 3
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
NLYS 7
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CG CE
2 6 HE CE CD NZ
3 4 HZ NZ CE CD
NPRO 5
2 6 H N CA CD
2 6 HD CD N CG
2 6 HG CG CD CB
2 6 HB CB CG CA
1 5 HA CA N CB C
NCYS 4
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA SG
1 2 HG SG CB CA
NCYX 3
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA SG
NMET 5
3 4 H N CA CB
1 5 HA CA N CB C
2 6 HB CB CA CG
2 6 HG CG CB SD
3 4 HE CE SD CG
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