I answered this already:
http://lists.gromacs.org/pipermail/gmx-users/2012-November/076750.html
-Justin
On 12/2/12 7:21 AM, Hovakim Grabski wrote:
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
========================================
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