标题: 请教DNA在gromacs中Amber99SB-Ildn力场无法识别原子的问题 [打印本页] 作者Author: 阿帅先森 时间: 2020-12-2 18:00 标题: 请教DNA在gromacs中Amber99SB-Ildn力场无法识别原子的问题 请教各位老师，我利用avogadro搭建了一个七个碱基对的DNA分子，在gromacs下利用pdb2gmx加入立场时，发生了端部原子不匹配的现象，请问该如何解决
贴上我的原子信息以及Amber99SB-Ildn中的rna.rtp文件信息，请问老师为什么氨基酸类型为DA，会自动匹配到DA5，如果是DA的类型的话应该是没问题的
原子信息：单链的原子信息
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.90
ATOM 1 HTER DA A 1 -31.378 6.046 8.619 1.00 0.00 H
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ATOM 272 C1' DG A 9 -2.835 -4.523 3.244 1.00 0.00 C
ATOM 273 N9 DG A 9 -2.585 -5.191 4.512 1.00 0.00 N
ATOM 274 C8 DG A 9 -2.708 -6.541 4.752 1.00 0.00 C
ATOM 275 N7 DG A 9 -2.350 -6.879 5.975 1.00 0.00 N
ATOM 276 C5 DG A 9 -2.059 -5.679 6.572 1.00 0.00 C
ATOM 277 C6 DG A 9 -1.618 -5.404 7.921 1.00 0.00 C
ATOM 278 O6 DG A 9 -1.489 -6.256 8.797 1.00 0.00 O
ATOM 279 N1 DG A 9 -1.303 -4.073 8.113 1.00 0.00 N
ATOM 280 C2 DG A 9 -1.400 -3.102 7.138 1.00 0.00 C
ATOM 281 N2 DG A 9 -1.009 -1.860 7.512 1.00 0.00 N
ATOM 282 N3 DG A 9 -1.831 -3.330 5.922 1.00 0.00 N
ATOM 283 C4 DG A 9 -2.151 -4.627 5.688 1.00 0.00 C
ATOM 284 H5'1 DG A 9 -6.077 -5.807 0.700 1.00 0.00 H
ATOM 285 H5'2 DG A 9 -6.285 -5.751 2.458 1.00 0.00 H
ATOM 286 H4' DG A 9 -5.153 -3.729 1.364 1.00 0.00 H
ATOM 287 H1' DG A 9 -2.390 -3.528 3.310 1.00 0.00 H
ATOM 288 H2'1 DG A 9 -2.376 -6.329 2.118 1.00 0.00 H
ATOM 289 H2'2 DG A 9 -1.301 -5.010 1.769 1.00 0.00 H
ATOM 290 H3' DG A 9 -3.435 -5.634 0.154 1.00 0.00 H
ATOM 291 H8 DG A 9 -3.052 -7.230 3.995 1.00 0.00 H
ATOM 292 H1 DG A 9 -0.990 -3.814 9.044 1.00 0.00 H
ATOM 293 H21 DG A 9 -1.341 -1.119 6.907 1.00 0.00 H
ATOM 294 H22 DG A 9 -1.020 -1.620 8.503 1.00 0.00 H
ATOM 295 P DC A 10 -1.613 -3.384 -0.472 1.00 0.00 P
ATOM 296 O1P DC A 10 -1.768 -2.338 -1.552 1.00 0.00 O1-
ATOM 297 O2P DC A 10 -0.913 -4.685 -0.775 1.00 0.00 O
ATOM 298 O5' DC A 10 -0.910 -2.700 0.815 1.00 0.00 O
ATOM 299 C5' DC A 10 -1.512 -1.518 1.327 1.00 0.00 C
ATOM 300 C4' DC A 10 -0.482 -0.710 2.102 1.00 0.00 C
ATOM 301 O4' DC A 10 -0.245 -1.358 3.371 1.00 0.00 O
ATOM 302 C3' DC A 10 0.850 -0.604 1.355 1.00 0.00 C
ATOM 303 O3' DC A 10 1.287 0.745 1.457 1.00 0.00 O
ATOM 304 C2' DC A 10 1.700 -1.654 2.045 1.00 0.00 C
ATOM 305 C1' DC A 10 1.134 -1.735 3.462 1.00 0.00 C
ATOM 306 N1 DC A 10 1.236 -3.039 4.127 1.00 0.00 N
ATOM 307 C2 DC A 10 1.611 -3.097 5.476 1.00 0.00 C
ATOM 308 O2 DC A 10 1.913 -2.093 6.121 1.00 0.00 O
ATOM 309 N3 DC A 10 1.695 -4.333 6.101 1.00 0.00 N
ATOM 310 C4 DC A 10 1.315 -5.396 5.461 1.00 0.00 C
ATOM 311 N4 DC A 10 1.366 -6.609 6.096 1.00 0.00 N
ATOM 312 C5 DC A 10 0.840 -5.369 4.069 1.00 0.00 C
ATOM 313 C6 DC A 10 0.832 -4.181 3.476 1.00 0.00 C
ATOM 314 H5'1 DC A 10 -1.908 -0.911 0.508 1.00 0.00 H
ATOM 315 H5'2 DC A 10 -2.344 -1.795 1.981 1.00 0.00 H
ATOM 316 H4' DC A 10 -0.907 0.274 2.332 1.00 0.00 H
ATOM 317 H1' DC A 10 1.624 -0.979 4.080 1.00 0.00 H
ATOM 318 H2'1 DC A 10 1.578 -2.596 1.504 1.00 0.00 H
ATOM 319 H2'2 DC A 10 2.767 -1.456 2.045 1.00 0.00 H
ATOM 320 H3' DC A 10 0.746 -0.806 0.284 1.00 0.00 H
ATOM 321 H6 DC A 10 0.482 -4.080 2.457 1.00 0.00 H
ATOM 322 H5 DC A 10 0.511 -6.279 3.589 1.00 0.00 H
ATOM 323 H41 DC A 10 1.579 -6.543 7.098 1.00 0.00 H
ATOM 324 H42 DC A 10 0.519 -7.166 5.992 1.00 0.00 H
ATOM 325 P DA A 11 2.818 1.165 1.169 1.00 0.00 P
ATOM 326 O1P DA A 11 2.876 2.643 0.861 1.00 0.00 O1-
ATOM 327 O2P DA A 11 3.492 0.179 0.250 1.00 0.00 O
ATOM 328 O5' DA A 11 3.376 0.938 2.674 1.00 0.00 O
ATOM 329 C5' DA A 11 2.790 1.736 3.696 1.00 0.00 C
ATOM 330 C4' DA A 11 3.788 1.936 4.830 1.00 0.00 C
ATOM 331 O4' DA A 11 3.831 0.718 5.608 1.00 0.00 O
ATOM 332 C3' DA A 11 5.208 2.228 4.327 1.00 0.00 C
ATOM 333 O3' DA A 11 5.807 3.195 5.187 1.00 0.00 O
ATOM 334 C2' DA A 11 5.845 0.855 4.360 1.00 0.00 C
ATOM 335 C1' DA A 11 5.127 0.125 5.487 1.00 0.00 C
ATOM 336 N9 DA A 11 5.001 -1.313 5.329 1.00 0.00 N
ATOM 337 C8 DA A 11 4.705 -1.983 4.170 1.00 0.00 C
ATOM 338 N7 DA A 11 4.765 -3.290 4.309 1.00 0.00 N
ATOM 339 C5 DA A 11 5.063 -3.480 5.642 1.00 0.00 C
ATOM 340 C6 DA A 11 5.251 -4.648 6.404 1.00 0.00 C
ATOM 341 N6 DA A 11 5.130 -5.924 5.848 1.00 0.00 N
ATOM 342 N1 DA A 11 5.579 -4.525 7.713 1.00 0.00 N
ATOM 343 C2 DA A 11 5.695 -3.270 8.218 1.00 0.00 C
ATOM 344 N3 DA A 11 5.610 -2.089 7.568 1.00 0.00 N
ATOM 345 C4 DA A 11 5.246 -2.266 6.288 1.00 0.00 C
ATOM 346 H5'1 DA A 11 2.497 2.711 3.298 1.00 0.00 H
ATOM 347 H5'2 DA A 11 1.890 1.232 4.064 1.00 0.00 H
ATOM 348 H4' DA A 11 3.416 2.720 5.500 1.00 0.00 H
ATOM 349 H1' DA A 11 5.652 0.293 6.430 1.00 0.00 H
ATOM 350 H2'1 DA A 11 5.680 0.369 3.394 1.00 0.00 H
ATOM 351 H2'2 DA A 11 6.918 0.857 4.516 1.00 0.00 H
ATOM 352 H3' DA A 11 5.213 2.664 3.323 1.00 0.00 H
ATOM 353 H8 DA A 11 4.473 -1.469 3.249 1.00 0.00 H
ATOM 354 H61 DA A 11 4.393 -5.916 5.146 1.00 0.00 H
ATOM 355 H62 DA A 11 4.960 -6.633 6.566 1.00 0.00 H
ATOM 356 H2 DA A 11 5.893 -3.208 9.286 1.00 0.00 H
ATOM 357 P DT A 12 7.404 3.436 5.216 1.00 0.00 P
ATOM 358 O1P DT A 12 7.714 4.796 5.798 1.00 0.00 O1-
ATOM 359 O2P DT A 12 8.066 2.999 3.933 1.00 0.00 O
ATOM 360 O5' DT A 12 7.770 2.340 6.352 1.00 0.00 O
ATOM 361 C5' DT A 12 7.145 2.500 7.616 1.00 0.00 C
ATOM 362 C4' DT A 12 8.008 1.863 8.697 1.00 0.00 C
ATOM 363 O4' DT A 12 7.942 0.428 8.578 1.00 0.00 O
ATOM 364 C3' DT A 12 9.489 2.232 8.591 1.00 0.00 C
ATOM 365 O3' DT A 12 10.114 2.248 9.889 1.00 0.00 O
ATOM 366 C2' DT A 12 10.092 1.096 7.790 1.00 0.00 C
ATOM 367 C1' DT A 12 9.231 -0.086 8.225 1.00 0.00 C
ATOM 368 N1 DT A 12 9.087 -1.187 7.279 1.00 0.00 N
ATOM 369 C2 DT A 12 9.171 -2.485 7.783 1.00 0.00 C
ATOM 370 O2 DT A 12 9.591 -2.758 8.908 1.00 0.00 O
ATOM 371 N3 DT A 12 8.852 -3.484 6.901 1.00 0.00 N
ATOM 372 C4 DT A 12 8.717 -3.331 5.555 1.00 0.00 C
ATOM 373 O4 DT A 12 8.772 -4.273 4.769 1.00 0.00 O
ATOM 374 C5 DT A 12 8.586 -1.944 5.068 1.00 0.00 C
ATOM 375 C5M DT A 12 8.267 -1.766 3.619 1.00 0.00 C
ATOM 376 C6 DT A 12 8.741 -0.957 5.959 1.00 0.00 C
ATOM 377 H5'1 DT A 12 7.004 3.562 7.840 1.00 0.00 H
ATOM 378 H5'2 DT A 12 6.160 2.026 7.590 1.00 0.00 H
ATOM 379 H4' DT A 12 7.591 2.123 9.677 1.00 0.00 H
ATOM 380 H1' DT A 12 9.656 -0.469 9.161 1.00 0.00 H
ATOM 381 H2'1 DT A 12 10.010 1.308 6.721 1.00 0.00 H
ATOM 382 H2'2 DT A 12 11.150 0.917 8.006 1.00 0.00 H
ATOM 383 H3' DT A 12 9.663 3.214 8.141 1.00 0.00 H
ATOM 384 H6 DT A 12 8.619 0.076 5.655 1.00 0.00 H
ATOM 385 H51 DT A 12 9.175 -1.883 3.020 1.00 0.00 H
ATOM 386 H52 DT A 12 7.856 -0.780 3.402 1.00 0.00 H
ATOM 387 H53 DT A 12 7.535 -2.506 3.277 1.00 0.00 H
ATOM 388 H3 DT A 12 8.901 -4.439 7.244 1.00 0.00 H
ATOM 389 HCAP DT A 12 9.627 1.608 10.443 1.00 0.00 H