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 Thanks in advance, Best regards, Hovakim ________________________________ От: Justin Lemkul <jalem...@vt.edu> Кому: Hovakim Grabski <hovakim_grab...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Отправлено: четверг, 29 ноября 2012 16:24 Тема: Re: [gmx-users] Hbonds between Adenine and Thymine Please keep the discussion on the gmx-users list. On 11/29/12 6:12 AM, Hovakim Grabski wrote: > Dear Justin, > > When I try to select 10DA residue from one strand and 17DT from the other > strand,I type r10 and r17 and both select 64 atoms, after r26 it selects water > molecules. You can easily check (using a text editor) which atoms make_ndx is choosing. In theory, your approach is correct and very straightforward. Can you please provide? 1. Your exact make_ndx command 2. A few lines from residue 10DA of whatever coordinate file you're using 3. The index group produced from residue 10 Did you renumber the file at any point, for instance, with pdb2gmx? That is, whatever started out as residue 10 may not still be numbered as such in the topology and any resulting coordinate files produced from the simulation. Without knowing exactly what you're using as make_ndx input, it's hard to track down what's going on. -Justin > And then I check for Hbonds with g_hbond I get 3 Hbonds, but between A and T > they form 2 Hbonds? > It seems I'm doing something wrong. > What can I do in this case? > Thanks in advance, > Best regards, > Hovakim > > -------------------------------------------------------------------------------- > *От:* Justin Lemkul <jalem...@vt.edu> > *Кому:* Hovakim Grabski <hovakim_grab...@yahoo.com>; Discussion list for > GROMACS > users <gmx-users@gromacs.org> > *Отправлено:* четверг, 29 ноября 2012 1:33 > *Тема:* Re: [gmx-users] Hbonds between Adenine and Thymine > > > > On 11/28/12 3:43 PM, Hovakim Grabski wrote: > > Dear Gromacs users, > > I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 >ns. > > After a while Thymine rotated for about 70 degrees and then returned to its > initial position. > > I wanted to find out hbonds between Adenine and Thymine but with make_ndx > things don't work so well. > > How can I select Adenine from one strand and Thymine from the other strand > and then run g_hbond ? > > You can use make_ndx to select any residues you want. You'll have to describe > exactly what you did that produced insufficient results. Saying it didn't > work > well doesn't tell us anything, because it is in fact quite easy to produce > usable index groups. > > -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 > > ======================================== > > -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
