Отв: [gmx-users] Hbonds between Adenine and Thymine
Justin Lemkul
jalemkul at vt.edu
Thu Nov 29 20:08:56 CET 2012
On 11/29/12 2:04 PM, Hovakim Grabski wrote:
> Dear Justin,
> I only used pdb2gmx when I prepared the DNA which I created with nab.
> and the command that I used was:
>
> make_ndx -f md_0_1.gro -o index.ndx
> after that then I press r10 and r17 I get :
>
> 14 r_10 : 64 atoms
>
> 15 r_17 : 64 atoms
> This are the coordinates for the residues:
> First strand:
>
> 10DA P 281 16.129 2.602 11.551 -0.0064 -0.0090 -0.0438
> 10DA O1P 282 16.266 2.580 11.500 -0.1992 -0.7975 -0.2387
> 10DA O2P 283 16.071 2.493 11.632 -0.2097 0.0667 -0.0880
> 10DA O5' 284 16.120 2.736 11.641 -0.2017 -0.2302 0.2683
> 10DA C5' 285 16.192 2.847 11.592 -0.0631 -0.2091 0.5162
> 10DA H5'1 286 16.168 2.856 11.486 0.2017 0.7446 0.5318
> 10DA H5'2 287 16.299 2.837 11.607 0.0847 2.3049 1.7097
> 10DA C4' 288 16.169 2.980 11.662 0.0289 -0.3183 0.7520
> 10DA H4' 289 16.224 3.053 11.601 -2.8707 0.5718 -0.9869
> 10DA O4' 290 16.034 3.020 11.656 0.3066 0.6132 0.4536
> 10DA C1' 291 15.987 3.045 11.787 -0.2499 0.3562 0.3063
> 10DA H1' 292 15.998 3.152 11.802 -0.0905 0.4135 -0.2041
> 10DA N9 293 15.847 3.001 11.796 -0.1361 0.0295 0.4799
> 10DA C8 294 15.791 2.875 11.795 -0.1763 0.0476 -0.2015
> 10DA H8 295 15.862 2.793 11.796 -0.2033 0.0265 0.2737
> 10DA N7 296 15.664 2.871 11.823 -0.1286 0.2671 0.0604
> 10DA C5 297 15.619 3.001 11.805 -0.4228 0.2070 0.3483
> 10DA C6 298 15.497 3.069 11.794 -0.3949 0.2036 -0.0034
> 10DA N6 299 15.374 3.018 11.804 -0.2308 -0.1144 0.4274
> 10DA H61 300 15.305 3.085 11.771 1.7600 0.9756 -1.8289
> 10DA H62 301 15.354 2.923 11.833 -0.2605 -0.3058 -0.1869
> 10DA N1 302 15.497 3.202 11.778 0.3602 0.1422 -0.5486
> 10DA C2 303 15.612 3.265 11.760 0.0189 0.7232 -0.7343
> 10DA H2 304 15.626 3.372 11.756 3.6933 0.5922 2.5222
> 10DA N3 305 15.732 3.208 11.755 -0.4260 -0.2664 -0.3708
> 10DA C4 306 15.732 3.076 11.784 -0.2117 -0.1027 0.3843
> 10DA C3' 307 16.212 2.987 11.809 0.1076 0.4852 0.7002
> 10DA H3' 308 16.269 2.895 11.822 -0.9751 -0.4630 -0.7702
> 10DA C2' 309 16.078 2.963 11.878 -0.1301 0.3788 0.2079
> 10DA H2'1 310 16.053 2.856 11.876 -0.9477 0.5118 1.5833
> 10DA H2'2 311 16.071 3.003 11.979 0.2289 0.9076 0.0218
> 10DA O3' 312 16.289 3.101 11.839 0.7852 0.0886 0.4921
>
> 17DT P 505 14.540 2.457 13.806 -0.1135 -0.3293 0.2579
> 17DT O1P 506 14.515 2.332 13.730 -0.3178 -0.1552 0.0391
> 17DT O2P 507 14.426 2.509 13.885 -0.5793 -0.3100 -0.4187
> 17DT O5' 508 14.667 2.425 13.901 -0.0420 -0.1432 0.2251
> 17DT C5' 509 14.775 2.352 13.848 -0.0056 0.1138 -0.0585
> 17DT H5'1 510 14.807 2.394 13.753 -0.0386 0.1388 -0.0585
> 17DT H5'2 511 14.747 2.249 13.827 2.0093 -0.8479 1.6171
> 17DT C4' 512 14.889 2.350 13.950 0.3616 0.2283 -0.4642
> 17DT H4' 513 14.975 2.306 13.899 1.2315 0.1760 0.9966
> 17DT O4' 514 14.921 2.483 13.982 0.5698 0.0309 0.1646
> 17DT C1' 515 14.968 2.485 14.115 0.1427 0.4216 0.3154
> 17DT H1' 516 15.075 2.506 14.109 0.2135 -0.2028 -1.2027
> 17DT N1 517 14.902 2.590 14.194 -0.3299 0.5140 -0.2027
> 17DT C6 518 14.766 2.600 14.188 -0.4375 -0.3782 0.5725
> 17DT H6 519 14.711 2.537 14.119 0.9370 -0.6147 -0.3448
> 17DT C5 520 14.704 2.694 14.264 -0.2228 0.0885 0.1776
> 17DT C7 521 14.556 2.708 14.239 -0.0922 0.0466 -0.6345
> 17DT H71 522 14.520 2.617 14.190 1.5759 -0.4976 -0.9099
> 17DT H72 523 14.508 2.720 14.336 1.6175 -1.7512 0.5049
> 17DT H73 524 14.543 2.797 14.177 0.6660 0.4976 -0.1693
> 17DT C4 525 14.782 2.793 14.333 0.0191 -0.5878 0.8877
> 17DT O4 526 14.727 2.896 14.373 -0.1581 -0.1795 -0.3746
> 17DT N3 527 14.918 2.765 14.347 0.1422 -0.1924 0.4985
> 17DT H3 528 14.971 2.834 14.397 0.3132 0.9994 -1.2291
> 17DT C2 529 14.983 2.664 14.278 -0.0217 0.1747 -0.2008
> 17DT O2 530 15.106 2.660 14.287 -0.0771 -0.0313 0.4614
> 17DT C3' 531 14.859 2.268 14.075 0.3169 0.4173 -0.3515
> 17DT H3' 532 14.756 2.283 14.109 0.3908 -0.8417 0.4979
> 17DT C2' 533 14.947 2.345 14.173 0.2886 0.2008 -0.1552
> 17DT H2'1 534 14.907 2.335 14.274 -0.4318 -1.3965 -0.5681
> 17DT H2'2 535 15.047 2.302 14.178 0.9026 1.0206 -3.1872
> 17DT O3' 536 14.903 2.134 14.068 0.1630 0.3529 -0.0944
>
> Second strand:
>
> 10DA P 1106 9.991 9.662 5.857 0.2711 -0.2003 -0.2055
> 10DA O1P 1107 10.117 9.699 5.925 0.0171 -0.1521 0.2395
> 10DA O2P 1108 9.922 9.751 5.761 -0.0201 -0.3771 -0.1639
> 10DA O5' 1109 10.020 9.522 5.781 0.3327 -0.1377 -0.2950
> 10DA C5' 1110 10.103 9.418 5.826 0.0099 -0.0733 0.4779
> 10DA H5'1 1111 10.089 9.389 5.930 1.2175 -1.1397 0.3743
> 10DA H5'2 1112 10.208 9.448 5.818 -0.2723 0.9072 0.3516
> 10DA C4' 1113 10.087 9.283 5.756 0.6952 -0.0706 0.3006
> 10DA H4' 1114 10.167 9.218 5.790 0.3964 -1.0164 -0.7552
> 10DA O4' 1115 9.968 9.211 5.781 0.4042 0.2532 -0.1356
> 10DA C1' 1116 9.899 9.183 5.661 0.3657 -0.5820 0.0759
> 10DA H1' 1117 9.931 9.085 5.628 1.2101 -0.8078 1.4655
> 10DA N9 1118 9.752 9.192 5.674 0.4595 0.0856 0.8135
> 10DA C8 1119 9.677 9.305 5.687 -0.2406 -0.2729 -0.0039
> 10DA H8 1120 9.717 9.405 5.682 -0.1556 -0.2327 1.1312
> 10DA N7 1121 9.549 9.282 5.697 -0.2674 -0.0051 0.3168
> 10DA C5 1122 9.539 9.143 5.700 -0.1379 -0.0290 -0.2494
> 10DA C6 1123 9.434 9.050 5.704 0.2553 -0.4416 0.6994
> 10DA N6 1124 9.312 9.080 5.750 -0.0413 -0.4443 -0.0784
> 10DA H61 1125 9.249 9.005 5.775 0.2851 -0.4153 0.8639
> 10DA H62 1126 9.296 9.173 5.785 2.2173 -0.9878 2.7722
> 10DA N1 1127 9.459 8.918 5.703 -0.0820 -0.5081 -0.3882
> 10DA C2 1128 9.586 8.881 5.699 -0.0279 -0.4200 0.3464
> 10DA H2 1129 9.588 8.774 5.694 -0.3381 -0.4502 0.7996
> 10DA N3 1130 9.695 8.956 5.695 -0.3819 0.0971 0.2161
> 10DA C4 1131 9.665 9.088 5.697 -0.0442 0.1936 -0.5432
> 10DA C3' 1132 10.101 9.285 5.604 -0.5201 -0.6723 0.1687
> 10DA H3' 1133 10.161 9.370 5.572 -0.3052 -0.8779 0.0340
> 10DA C2' 1134 9.954 9.286 5.563 -0.4762 -0.1783 0.0171
> 10DA H2'1 1135 9.904 9.383 5.570 0.4894 0.2435 1.3382
> 10DA H2'2 1136 9.948 9.247 5.461 1.9729 1.5168 -0.8699
> 10DA O3' 1137 10.163 9.168 5.557 -0.0628 -0.3359 -0.0703
>
> 17DT P 1327 8.385 9.782 3.374 -0.1287 0.0547 -0.2070
> 17DT O1P 1328 8.311 9.903 3.415 -0.1686 -0.1425 0.3061
> 17DT O2P 1329 8.329 9.692 3.271 0.8603 0.1387 -0.8356
> 17DT O5' 1330 8.527 9.828 3.315 0.1174 -0.3581 0.0526
> 17DT C5' 1331 8.620 9.895 3.398 -0.2303 -0.0127 0.1639
> 17DT H5'1 1332 8.630 9.834 3.487 -1.1565 -0.8620 -0.2869
> 17DT H5'2 1333 8.582 9.995 3.419 1.0346 0.9321 -1.7427
> 17DT C4' 1334 8.760 9.911 3.340 -0.2036 0.2159 0.2891
> 17DT H4' 1335 8.806 9.989 3.401 -2.5851 -1.2606 4.3717
> 17DT O4' 1336 8.836 9.793 3.352 -0.2716 0.1396 -0.0055
> 17DT C1' 1337 8.914 9.783 3.235 0.0926 -0.3554 0.2734
> 17DT H1' 1338 9.008 9.831 3.262 0.4883 -0.6564 -0.5554
> 17DT N1 1339 8.938 9.643 3.198 0.0636 -0.2414 -0.1806
> 17DT C6 1340 8.832 9.562 3.166 0.0079 -0.3091 0.1733
> 17DT H6 1341 8.732 9.601 3.175 -0.3098 -1.1052 0.0861
> 17DT C5 1342 8.845 9.432 3.133 0.2566 -0.2686 0.1071
> 17DT C7 1343 8.719 9.356 3.102 0.0587 0.1062 -0.0152
> 17DT H71 1344 8.726 9.259 3.151 2.3691 -1.1060 -2.4759
> 17DT H72 1345 8.625 9.400 3.133 -1.2182 -1.9715 -0.6885
> 17DT H73 1346 8.714 9.336 2.995 1.3622 -1.1148 0.1136
> 17DT C4 1347 8.979 9.376 3.128 0.2652 -0.2897 0.5177
> 17DT O4 1348 9.015 9.265 3.090 0.2646 -0.0365 -0.2363
> 17DT N3 1349 9.082 9.466 3.148 0.3166 0.0439 -1.0741
> 17DT H3 1350 9.178 9.438 3.134 0.6352 1.6444 -2.4527
> 17DT C2 1351 9.069 9.599 3.187 0.0655 -0.2397 -0.1591
> 17DT O2 1352 9.168 9.671 3.201 0.1858 -0.2851 -0.7312
> 17DT C3' 1353 8.760 9.970 3.199 0.4414 -0.1050 0.1494
> 17DT H3' 1354 8.659 9.970 3.158 0.9166 0.1514 -1.0617
> 17DT C2' 1355 8.845 9.865 3.127 0.0046 -0.5079 0.2147
> 17DT H2'1 1356 8.773 9.809 3.066 0.2313 -0.2753 -0.2747
> 17DT H2'2 1357 8.908 9.903 3.047 1.7584 -0.8510 1.3980
> 17DT O3' 1358 8.813 10.100 3.193 -0.3350 0.2178 0.0665
>
So you got precisely what you should have expected :)
You have redundant residue numbering, so make_ndx considers both copies of
residue 10 and residue 17 when making the index groups. Instead of getting a
single residue pair, you got two pairs, which explains why you got more hydrogen
bonds than theoretically one A:T pair could.
Either edit the index groups manually (simply deleting out the atom numbers you
don't want) or renumber the .gro file such that the residue numbers are unique
and can be chosen unambiguously.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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