[gmx-users] Hbonds between Adenine and Thymine
Justin Lemkul
jalemkul at vt.edu
Sun Dec 2 13:56:35 CET 2012
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 <jalemkul at vt.edu>
> Кому: Hovakim Grabski <hovakim_grabski at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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 <jalemkul at vt.edu>
>> *Кому:* Hovakim Grabski <hovakim_grabski at yahoo.com>; Discussion list for GROMACS
>> users <gmx-users at 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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