[gmx-users] Hbonds between Adenine and Thymine

Hovakim Grabski hovakim_grabski at yahoo.com
Sun Dec 2 13:21:28 CET 2012



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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