AMBER Archive (2006)

Subject: AMBER: Problem taking the PDB to the Amber coordinates for calculations

From: Brian Stupi (bstupi15_at_yahoo.com)
Date: Mon Mar 06 2006 - 17:17:22 CST

Amber Community,

I am trying to transfer my PDB file for an 8 base DNA
Duplex and make the Amber *.prmtop and *.inpcrd files.
 I am getting the messages below.

 

I have inserted a TER line to separate the strands.
If you have any suggestions please let me know.

The same errors occur when I try a single A and T with
no backbone.

If anyone has any comments or suggestions I would love
to hear them. Thank you for your time and help in
advance.

Brian

PS – Included is the PDB file I was using.

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HETATM 1 N1 THY 4 -4.723 -4.656 12.625 0.00 0.00
HETATM 2 C2 THY 4 -3.711 -4.765 13.555 0.00 0.00
HETATM 3 O2 THY 4 -3.924 -4.919 14.745 0.00 0.00
HETATM 4 N3 THY 4 -2.430 -4.689 13.044 0.00 0.00
HETATM 5 C4 THY 4 -2.081 -4.516 11.725 0.00 0.00
HETATM 6 O4 THY 4 -0.894 -4.462 11.386 0.00 0.00
HETATM 7 C5 THY 4 -3.204 -4.406 10.826 0.00 0.00
HETATM 8 C6 THY 4 -4.468 -4.482 11.287 0.00 0.00
HETATM 9 1H2* THY 4 -6.747 -3.541 11.408 0.00 0.00
HETATM 10 2H2* THY 4 -7.223 -2.854 12.955 0.00 0.00
HETATM 11 C1* THY 4 -6.121 -4.732 13.128 0.00 0.00
HETATM 12 C2* THY 4 -7.082 -3.791 12.414 0.00 0.00
HETATM 13 C3* THY 4 -8.365 -4.609 12.383 0.00 0.00
HETATM 14 C4* THY 4 -7.851 -6.036 12.205 0.00 0.00
HETATM 15 C5* THY 4 -7.606 -6.490 10.786 0.00 0.00
HETATM 16 C7 THY 4 -2.870 -4.222 9.375 0.00 0.00
HETATM 17 H THY 4 -7.489 -5.283 8.461 0.00 0.00
HETATM 18 H1* THY 4 -6.110 -4.538 14.200 0.00 0.00
HETATM 19 H3 THY 4 -1.658 -4.772 13.720 0.00 0.00
HETATM 20 H3* THY 4 -9.015 -4.319 11.557 0.00 0.00
HETATM 21 H4* THY 4 -8.600 -6.698 12.642 0.00 0.00
HETATM 22 H6 THY 4 -5.301 -4.404 10.586 0.00 0.00
HETATM 23 H71 THY 4 -1.793 -4.298 9.238 0.00 0.00
HETATM 24 H72 THY 4 -3.367 -4.995 8.789 0.00 0.00
HETATM 25 H73 THY 4 -3.211 -3.241 9.045 0.00 0.00
HETATM 26 O3* THY 4 -9.062 -4.436 13.614 0.00 0.00
HETATM 27 O4* THY 4 -6.579 -6.055 12.929 0.00 0.00
HETATM 28 O5* THY 4 -7.087 -5.387 10.001 0.00 0.00
HETATM 29 P THY 5 -9.145 -2.984 14.268 0.00 0.00
HETATM 30 O1P THY 5 -10.415 -2.843 15.007 0.00 0.00
HETATM 31 O2P THY 5 -8.884 -1.963 13.226 0.00 0.00
HETATM 32 N1 THY 5 -4.580 -1.965 16.139 0.00 0.00
HETATM 33 C2 THY 5 -3.212 -1.932 16.315 0.00 0.00
HETATM 34 O2 THY 5 -2.680 -2.107 17.397 0.00 0.00
HETATM 35 N3 THY 5 -2.478 -1.686 15.171 0.00 0.00
HETATM 36 C4 THY 5 -2.975 -1.472 13.906 0.00 0.00
HETATM 37 O4 THY 5 -2.214 -1.259 12.954 0.00 0.00
HETATM 38 C5 THY 5 -4.414 -1.520 13.820 0.00 0.00
HETATM 39 C6 THY 5 -5.164 -1.765 14.913 0.00 0.00
HETATM 40 1H2* THY 5 -7.045 -1.142 16.383 0.00 0.00
HETATM 41 1H5* THY 5 -7.085 -4.896 15.678 0.00 0.00
HETATM 42 2H2* THY 5 -6.619 -0.518 17.970 0.00 0.00
HETATM 43 2H5* THY 5 -8.730 -4.660 16.302 0.00 0.00
HETATM 44 C1* THY 5 -5.412 -2.228 17.342 0.00 0.00
HETATM 45 C2* THY 5 -6.710 -1.429 17.378 0.00 0.00
HETATM 46 C3* THY 5 -7.673 -2.415 18.024 0.00 0.00
HETATM 47 C4* THY 5 -7.197 -3.761 17.480 0.00 0.00
HETATM 48 C5* THY 5 -7.763 -4.184 16.145 0.00 0.00
HETATM 49 C7 THY 5 -5.000 -1.301 12.458 0.00 0.00
HETATM 50 H1* THY 5 -4.810 -2.029 18.228 0.00 0.00
HETATM 51 H3 THY 5 -1.454 -1.658 15.275 0.00 0.00
HETATM 52 H3* THY 5 -8.707 -2.220 17.740 0.00 0.00
HETATM 53 H4* THY 5 -7.475 -4.516 18.215 0.00 0.00
HETATM 54 H6 THY 5 -6.249 -1.805 14.823 0.00 0.00
HETATM 55 H71 THY 5 -4.197 -1.230 11.723 0.00 0.00
HETATM 56 H72 THY 5 -5.652 -2.137 12.202 0.00 0.00
HETATM 57 H73 THY 5 -5.577 -0.376 12.454 0.00 0.00
HETATM 58 O3* THY 5 -7.547 -2.332 19.441 0.00 0.00
HETATM 59 O4* THY 5 -5.748 -3.603 17.344 0.00 0.00
HETATM 60 O5* THY 5 -7.920 -3.024 15.289 0.00 0.00
HETATM 61 P ADE 6 -7.404 -0.901 20.132 0.00 0.00
HETATM 62 O1P ADE 6 -8.024 -0.930 21.472 0.00 0.00
HETATM 63 O2P ADE 6 -7.910 0.140 19.206 0.00 0.00
HETATM 64 N9 ADE 6 -2.747 0.738 19.131 0.00 0.00
HETATM 65 C8 ADE 6 -3.847 0.896 18.332 0.00 0.00
HETATM 66 N7 ADE 6 -3.560 1.218 17.107 0.00 0.00
HETATM 67 C5 ADE 6 -2.177 1.290 17.100 0.00 0.00
HETATM 68 C6 ADE 6 -1.246 1.589 16.084 0.00 0.00
HETATM 69 N6 ADE 6 -1.605 1.895 14.827 0.00 0.00
HETATM 70 N1 ADE 6 0.055 1.562 16.411 0.00 0.00
HETATM 71 C2 ADE 6 0.398 1.260 17.658 0.00 0.00
HETATM 72 N3 ADE 6 -0.366 0.959 18.687 0.00 0.00
HETATM 73 C4 ADE 6 -1.663 0.992 18.327 0.00 0.00
HETATM 74 1H2* ADE 6 -4.698 1.219 20.798 0.00 0.00
HETATM 75 1H5* ADE 6 -4.706 -2.509 19.966 0.00 0.00
HETATM 76 2H2* ADE 6 -3.510 1.904 21.899 0.00 0.00
HETATM 77 2H5* ADE 6 -5.706 -2.495 21.434 0.00 0.00
HETATM 78 C1* ADE 6 -2.699 0.371 20.571 0.00 0.00
HETATM 79 C2* ADE 6 -3.820 0.985 21.399 0.00 0.00
HETATM 80 C3* ADE 6 -4.114 -0.118 22.403 0.00 0.00
HETATM 81 C4* ADE 6 -3.889 -1.389 21.587 0.00 0.00
HETATM 82 C5* ADE 6 -5.067 -1.893 20.788 0.00 0.00
HETATM 83 H1* ADE 6 -1.723 0.655 20.963 0.00 0.00
HETATM 84 H2 ADE 6 1.469 1.261 17.860 0.00 0.00
HETATM 85 H3* ADE 6 -5.138 -0.067 22.776 0.00 0.00
HETATM 86 H4* ADE 6 -3.605 -2.171 22.292 0.00 0.00
HETATM 87 H61 ADE 6 -0.884 2.106 14.122 0.00 0.00
HETATM 88 H62 ADE 6 -2.602 1.920 14.568 0.00 0.00
HETATM 89 H8 ADE 6 -4.869 0.765 18.690 0.00 0.00
HETATM 90 O3* ADE 6 -3.207 -0.011 23.497 0.00 0.00
HETATM 91 O4* ADE 6 -2.812 -1.037 20.661 0.00 0.00
HETATM 92 O5* ADE 6 -5.820 -0.769 20.264 0.00 0.00
HETATM 93 P ADE 7 -2.857 1.428 24.087 0.00 0.00
HETATM 94 O1P ADE 7 -2.583 1.322 25.534 0.00 0.00
HETATM 95 O2P ADE 7 -3.918 2.388 23.695 0.00 0.00
HETATM 96 N9 ADE 7 0.151 3.681 20.729 0.00 0.00
HETATM 97 C8 ADE 7 -1.218 3.684 20.716 0.00 0.00
HETATM 98 N7 ADE 7 -1.726 4.035 19.574 0.00 0.00
HETATM 99 C5 ADE 7 -0.621 4.296 18.785 0.00 0.00
HETATM 100 C6 ADE 7 -0.485 4.712 17.445 0.00 0.00
HETATM 101 N6 ADE 7 -1.535 4.960 16.645 0.00 0.00
HETATM 102 N1 ADE 7 0.760 4.864 16.967 0.00 0.00
HETATM 103 C2 ADE 7 1.791 4.617 17.770 0.00 0.00
HETATM 104 N3 ADE 7 1.798 4.220 19.024 0.00 0.00
HETATM 105 C4 ADE 7 0.537 4.075 19.473 0.00 0.00
HETATM 106 1H2* ADE 7 -0.524 3.900 23.244 0.00 0.00
HETATM 107 1H5* ADE 7 -0.585 0.202 22.291 0.00 0.00
HETATM 108 2H2* ADE 7 0.994 4.746 23.515 0.00 0.00
HETATM 109 2H5* ADE 7 -0.550 0.087 24.063 0.00 0.00
HETATM 110 C1* ADE 7 1.061 3.329 21.854 0.00 0.00
HETATM 111 C2* ADE 7 0.560 3.791 23.216 0.00 0.00
HETATM 112 C3* ADE 7 1.025 2.663 24.123 0.00 0.00
HETATM 113 C4* ADE 7 0.883 1.430 23.233 0.00 0.00
HETATM 114 C5* ADE 7 -0.475 0.767 23.216 0.00 0.00
HETATM 115 H1* ADE 7 2.045 3.746 21.638 0.00 0.00
HETATM 116 H2 ADE 7 2.773 4.766 17.323 0.00 0.00
HETATM 117 H3* ADE 7 0.406 2.577 25.017 0.00 0.00
HETATM 118 H4* ADE 7 1.606 0.697 23.589 0.00 0.00
HETATM 119 H61 ADE 7 -1.381 5.263 15.672 0.00 0.00
HETATM 120 H62 ADE 7 -2.493 4.848 17.003 0.00 0.00
HETATM 121 H8 ADE 7 -1.824 3.417 21.583 0.00 0.00
HETATM 122 O3* ADE 7 2.377 2.898 24.507 0.00 0.00
HETATM 123 O4* ADE 7 1.182 1.922 21.887 0.00 0.00
HETATM 124 O5* ADE 7 -1.512 1.774 23.301 0.00 0.00
HETATM 125 N1 THY 14 2.451 6.229 12.359 0.00 0.00
HETATM 126 C2 THY 14 2.344 5.796 13.665 0.00 0.00
HETATM 127 O2 THY 14 3.312 5.498 14.343 0.00 0.00
HETATM 128 N3 THY 14 1.056 5.726 14.158 0.00 0.00
HETATM 129 C4 THY 14 -0.102 6.035 13.480 0.00 0.00
HETATM 130 O4 THY 14 -1.205 5.930 14.030 0.00 0.00
HETATM 131 C5 THY 14 0.108 6.472 12.122 0.00 0.00
HETATM 132 C6 THY 14 1.351 6.561 11.608 0.00 0.00
HETATM 133 1H2* THY 14 2.949 6.028 9.804 0.00 0.00
HETATM 134 2H2* THY 14 4.212 4.871 10.201 0.00 0.00
HETATM 135 C1* THY 14 3.820 6.322 11.785 0.00 0.00
HETATM 136 C2* THY 14 3.901 5.909 10.321 0.00 0.00
HETATM 137 C3* THY 14 4.950 6.866 9.778 0.00 0.00
HETATM 138 C4* THY 14 4.685 8.145 10.569 0.00 0.00
HETATM 139 C5* THY 14 3.638 9.079 10.009 0.00 0.00
HETATM 140 C7 THY 14 -1.126 6.828 11.347 0.00 0.00
HETATM 141 H THY 14 1.823 8.890 8.128 0.00 0.00
HETATM 142 H1* THY 14 4.491 5.720 12.397 0.00 0.00
HETATM 143 H3 THY 14 0.949 5.409 15.132 0.00 0.00
HETATM 144 H3* THY 14 4.833 7.036 8.707 0.00 0.00
HETATM 145 H4* THY 14 5.628 8.690 10.616 0.00 0.00
HETATM 146 H6 THY 14 1.485 6.901 10.582 0.00 0.00
HETATM 147 H71 THY 14 -0.856 7.051 10.315 0.00 0.00
HETATM 148 H72 THY 14 -1.822 5.990 11.367 0.00 0.00
HETATM 149 H73 THY 14 -1.597 7.702 11.796 0.00 0.00
HETATM 150 O3* THY 14 6.247 6.333 10.031 0.00 0.00
HETATM 151 O4* THY 14 4.237 7.672 11.879 0.00 0.00
HETATM 152 O5* THY 14 2.562 8.309 9.416 0.00 0.00
HETATM 153 P THY 15 6.509 4.775 9.816 0.00 0.00
HETATM 154 O1P THY 15 7.905 4.559 9.389 0.00 0.00
HETATM 155 O2P THY 15 5.464 4.223 8.920 0.00 0.00
HETATM 156 N1 THY 15 4.241 2.380 13.623 0.00 0.00
HETATM 157 C2 THY 15 3.350 2.061 14.628 0.00 0.00
HETATM 158 O2 THY 15 3.706 1.705 15.737 0.00 0.00
HETATM 159 N3 THY 15 2.016 2.174 14.288 0.00 0.00
HETATM 160 C4 THY 15 1.507 2.562 13.070 0.00 0.00
HETATM 161 O4 THY 15 0.287 2.625 12.884 0.00 0.00
HETATM 162 C5 THY 15 2.512 2.871 12.081 0.00 0.00
HETATM 163 C6 THY 15 3.825 2.779 12.378 0.00 0.00
HETATM 164 1H2* THY 15 6.075 1.936 11.821 0.00 0.00
HETATM 165 1H5* THY 15 6.239 5.614 12.835 0.00 0.00
HETATM 166 2H2* THY 15 6.714 0.673 12.865 0.00 0.00
HETATM 167 2H5* THY 15 7.819 5.417 12.049 0.00 0.00
HETATM 168 C1* THY 15 5.691 2.274 13.941 0.00 0.00
HETATM 169 C2* THY 15 6.535 1.747 12.790 0.00 0.00
HETATM 170 C3* THY 15 7.824 2.536 12.954 0.00 0.00
HETATM 171 C4* THY 15 7.331 3.891 13.457 0.00 0.00
HETATM 172 C5* THY 15 6.931 4.894 12.400 0.00 0.00
HETATM 173 C7 THY 15 2.005 3.307 10.740 0.00 0.00
HETATM 174 H1* THY 15 5.801 1.646 14.826 0.00 0.00
HETATM 175 H3 THY 15 1.330 1.944 15.022 0.00 0.00
HETATM 176 H3* THY 15 8.364 2.637 12.012 0.00 0.00
HETATM 177 H4* THY 15 8.144 4.328 14.039 0.00 0.00
HETATM 178 H6 THY 15 4.566 3.025 11.617 0.00 0.00
HETATM 179 H71 THY 15 2.844 3.420 10.052 0.00 0.00
HETATM 180 H72 THY 15 1.316 2.558 10.352 0.00 0.00
HETATM 181 H73 THY 15 1.486 4.260 10.840 0.00 0.00
HETATM 182 O3* THY 15 8.657 1.879 13.905 0.00 0.00
HETATM 183 O4* THY 15 6.156 3.570 14.267 0.00 0.00
HETATM 184 O5* THY 15 6.295 4.210 11.291 0.00 0.00
HETATM 185 P ADE 16 8.781 0.289 13.873 0.00 0.00
HETATM 186 O1P ADE 16 10.125 -0.117 14.326 0.00 0.00
HETATM 187 O2P ADE 16 8.371 -0.205 12.536 0.00 0.00
HETATM 188 N9 ADE 16 4.445 -1.543 15.668 0.00 0.00
HETATM 189 C8 ADE 16 4.697 -1.194 14.369 0.00 0.00
HETATM 190 N7 ADE 16 3.623 -1.045 13.653 0.00 0.00
HETATM 191 C5 ADE 16 2.595 -1.329 14.534 0.00 0.00
HETATM 192 C6 ADE 16 1.193 -1.345 14.386 0.00 0.00
HETATM 193 N6 ADE 16 0.574 -1.066 13.227 0.00 0.00
HETATM 194 N1 ADE 16 0.461 -1.660 15.465 0.00 0.00
HETATM 195 C2 ADE 16 1.084 -1.936 16.607 0.00 0.00
HETATM 196 N3 ADE 16 2.372 -1.948 16.875 0.00 0.00
HETATM 197 C4 ADE 16 3.079 -1.628 15.774 0.00 0.00
HETATM 198 1H2* ADE 16 6.901 -2.326 15.246 0.00 0.00
HETATM 199 1H5* ADE 16 6.953 1.376 16.190 0.00 0.00
HETATM 200 2H2* ADE 16 6.649 -3.571 16.462 0.00 0.00
HETATM 201 2H5* ADE 16 8.655 0.941 16.456 0.00 0.00
HETATM 202 C1* ADE 16 5.422 -1.789 16.762 0.00 0.00
HETATM 203 C2* ADE 16 6.693 -2.494 16.303 0.00 0.00
HETATM 204 C3* ADE 16 7.750 -1.847 17.185 0.00 0.00
HETATM 205 C4* ADE 16 7.249 -0.410 17.319 0.00 0.00
HETATM 206 C5* ADE 16 7.664 0.551 16.229 0.00 0.00
HETATM 207 H1* ADE 16 4.922 -2.359 17.546 0.00 0.00
HETATM 208 H2 ADE 16 0.433 -2.189 17.444 0.00 0.00
HETATM 209 H3* ADE 16 8.738 -1.877 16.725 0.00 0.00
HETATM 210 H4* ADE 16 7.632 -0.028 18.265 0.00 0.00
HETATM 211 H61 ADE 16 -0.455 -1.092 13.172 0.00 0.00
HETATM 212 H62 ADE 16 1.128 -0.824 12.393 0.00 0.00
HETATM 213 H8 ADE 16 5.702 -1.052 13.973 0.00 0.00
HETATM 214 O3* ADE 16 7.792 -2.523 18.439 0.00 0.00
HETATM 215 O4* ADE 16 5.791 -0.535 17.303 0.00 0.00
HETATM 216 O5* ADE 16 7.688 -0.136 14.953 0.00 0.00
HETATM 217 P ADE 17 7.695 -4.114 18.475 0.00 0.00
HETATM 218 O1P ADE 17 8.470 -4.635 19.617 0.00 0.00
HETATM 219 O2P ADE 17 8.059 -4.655 17.143 0.00 0.00
HETATM 220 N9 ADE 17 2.910 -5.302 17.437 0.00 0.00
HETATM 221 C8 ADE 17 3.903 -5.081 16.521 0.00 0.00
HETATM 222 N7 ADE 17 3.462 -4.863 15.318 0.00 0.00
HETATM 223 C5 ADE 17 2.089 -4.963 15.446 0.00 0.00
HETATM 224 C6 ADE 17 1.036 -4.830 14.518 0.00 0.00
HETATM 225 N6 ADE 17 1.234 -4.568 13.215 0.00 0.00
HETATM 226 N1 ADE 17 -0.216 -4.978 14.977 0.00 0.00
HETATM 227 C2 ADE 17 -0.400 -5.237 16.268 0.00 0.00
HETATM 228 N3 ADE 17 0.489 -5.377 17.228 0.00 0.00
HETATM 229 C4 ADE 17 1.732 -5.222 16.738 0.00 0.00
HETATM 230 1H2* ADE 17 5.032 -6.388 18.502 0.00 0.00
HETATM 231 1H5* ADE 17 5.040 -2.658 19.322 0.00 0.00
HETATM 232 2H2* ADE 17 3.965 -7.504 19.345 0.00 0.00
HETATM 233 2H5* ADE 17 6.206 -3.261 20.518 0.00 0.00
HETATM 234 C1* ADE 17 3.044 -5.576 18.893 0.00 0.00
HETATM 235 C2* ADE 17 4.238 -6.453 19.246 0.00 0.00
HETATM 236 C3* ADE 17 4.679 -5.867 20.577 0.00 0.00
HETATM 237 C4* ADE 17 4.391 -4.377 20.407 0.00 0.00
HETATM 238 C5* ADE 17 5.480 -3.554 19.760 0.00 0.00
HETATM 239 H1* ADE 17 2.114 -6.024 19.244 0.00 0.00
HETATM 240 H2 ADE 17 -1.439 -5.352 16.576 0.00 0.00
HETATM 241 H3* ADE 17 5.737 -6.044 20.771 0.00 0.00
HETATM 242 H4* ADE 17 4.214 -3.972 21.402 0.00 0.00
HETATM 243 H61 ADE 17 0.430 -4.482 12.579 0.00 0.00
HETATM 244 H62 ADE 17 2.193 -4.454 12.854 0.00 0.00
HETATM 245 H8 ADE 17 4.963 -5.085 16.778 0.00 0.00
HETATM 246 O3* ADE 17 3.905 -6.449 21.624 0.00 0.00
HETATM 247 O4* ADE 17 3.203 -4.336 19.553 0.00 0.00
HETATM 248 O5* ADE 17 6.136 -4.331 18.727 0.00 0.00
CONECT 9 12
CONECT 10 12
CONECT 11 1 27 18 12
CONECT 2 1 4 3
CONECT 12 10 11 13 9
CONECT 13 26 20 14 12
CONECT 5 7 6 4
CONECT 14 27 21 15 13
CONECT 7 16 8 5
CONECT 15 28 14
CONECT 8 1 22 7
CONECT 16 25 24 23 7
CONECT 18 11
CONECT 19 4
CONECT 20 13
CONECT 21 14
CONECT 22 8
CONECT 23 16
CONECT 24 16
CONECT 25 16
CONECT 1 11 8 2
CONECT 4 19 5 2
CONECT 3 2
CONECT 26 29 13
CONECT 6 5
CONECT 27 14 11
CONECT 28 15
CONECT 40 45
CONECT 41 48
CONECT 42 45
CONECT 43 48
CONECT 44 45 32 50 59
CONECT 33 35 34 32
CONECT 45 42 40 44 46
CONECT 46 45 52 47 58
CONECT 36 37 38 35
CONECT 47 53 48 46 59
CONECT 38 39 36 49
CONECT 48 43 41 47 60
CONECT 39 38 32 54
CONECT 49 38 56 57 55
CONECT 50 44
CONECT 51 35
CONECT 52 46
CONECT 53 47
CONECT 54 39
CONECT 55 49
CONECT 56 49
CONECT 57 49
CONECT 32 44 39 33
CONECT 35 36 33 51
CONECT 30 29
CONECT 34 33
CONECT 31 29
CONECT 58 61 46
CONECT 37 36
CONECT 59 44 47
CONECT 60 29 48
CONECT 29 30 31 26 60
CONECT 74 79
CONECT 75 82
CONECT 76 79
CONECT 77 82
CONECT 78 83 79 91 64
CONECT 71 84 72 70
CONECT 79 80 78 76 74
CONECT 80 90 85 81 79
CONECT 73 72 67 64
CONECT 81 86 82 80 91
CONECT 67 73 68 66
CONECT 82 81 77 75 92
CONECT 68 70 69 67
CONECT 65 89 66 64
CONECT 83 78
CONECT 84 71
CONECT 85 80
CONECT 86 81
CONECT 87 69
CONECT 88 69
CONECT 89 65
CONECT 70 71 68
CONECT 72 73 71
CONECT 69 88 87 68
CONECT 66 67 65
CONECT 64 78 73 65
CONECT 62 61
CONECT 63 61
CONECT 90 93 80
CONECT 91 81 78
CONECT 92 82 61
CONECT 61 92 63 62 58
CONECT 106 111
CONECT 107 114
CONECT 108 111
CONECT 109 114
CONECT 110 96 111 115 123
CONECT 103 102 104 116
CONECT 111 106 108 110 112
CONECT 112 111 113 117 122
CONECT 105 96 99 104
CONECT 113 112 114 118 123
CONECT 99 98 100 105
CONECT 114 107 109 113 124
CONECT 100 99 101 102
CONECT 97 96 98 121
CONECT 115 110
CONECT 116 103
CONECT 117 112
CONECT 118 113
CONECT 119 101
CONECT 120 101
CONECT 121 97
CONECT 102 100 103
CONECT 104 103 105
CONECT 101 100 119 120
CONECT 98 97 99
CONECT 96 97 105 110
CONECT 94 93
CONECT 95 93
CONECT 122 112
CONECT 123 110 113
CONECT 124 93 114
CONECT 93 94 90 95 124
CONECT 133 136
CONECT 134 136
CONECT 135 151 125 136 142
CONECT 126 125 127 128
CONECT 136 133 134 135 137
CONECT 137 150 136 138 144
CONECT 129 128 130 131
CONECT 138 151 137 139 145
CONECT 131 129 132 140
CONECT 139 138 152
CONECT 132 125 131 146
CONECT 140 147 148 149 131
CONECT 142 135
CONECT 143 128
CONECT 144 137
CONECT 145 138
CONECT 146 132
CONECT 147 140
CONECT 148 140
CONECT 149 140
CONECT 125 126 132 135
CONECT 128 126 129 143
CONECT 127 126
CONECT 150 137 153
CONECT 130 129
CONECT 151 135 138
CONECT 152 139
CONECT 164 169
CONECT 165 172
CONECT 166 169
CONECT 167 172
CONECT 168 156 169 174 183
CONECT 157 156 158 159
CONECT 169 164 166 168 170
CONECT 170 169 171 176 182
CONECT 160 159 161 162
CONECT 171 170 172 177 183
CONECT 162 160 163 173
CONECT 172 165 167 171 184
CONECT 163 156 162 178
CONECT 173 162 179 180 181
CONECT 174 168
CONECT 175 159
CONECT 176 170
CONECT 177 171
CONECT 178 163
CONECT 179 173
CONECT 180 173
CONECT 181 173
CONECT 156 157 163 168
CONECT 159 157 160 175
CONECT 154 153
CONECT 158 157
CONECT 155 153
CONECT 182 170 185
CONECT 161 160
CONECT 183 168 171
CONECT 184 153 172
CONECT 153 150 154 155 184
CONECT 198 203
CONECT 199 206
CONECT 200 203
CONECT 201 206
CONECT 202 188 203 207 215
CONECT 195 194 196 208
CONECT 203 198 200 202 204
CONECT 204 203 205 209 214
CONECT 197 188 191 196
CONECT 205 204 206 210 215
CONECT 191 190 192 197
CONECT 206 199 201 205 216
CONECT 192 191 193 194
CONECT 189 188 190 213
CONECT 207 202
CONECT 208 195
CONECT 209 204
CONECT 210 205
CONECT 211 193
CONECT 212 193
CONECT 213 189
CONECT 194 192 195
CONECT 196 195 197
CONECT 193 192 211 212
CONECT 190 189 191
CONECT 188 189 197 202
CONECT 186 185
CONECT 187 185
CONECT 214 217 204
CONECT 215 202 205
CONECT 216 185 206
CONECT 185 182 186 187 216
CONECT 230 235
CONECT 231 238
CONECT 232 235
CONECT 233 238
CONECT 234 220 235 239 247
CONECT 227 226 228 240
CONECT 235 230 232 234 236
CONECT 236 235 237 241 246
CONECT 229 220 223 228
CONECT 237 236 238 242 247
CONECT 223 222 224 229
CONECT 238 231 233 237 248
CONECT 224 223 225 226
CONECT 221 220 222 245
CONECT 239 234
CONECT 240 227
CONECT 241 236
CONECT 242 237
CONECT 243 225
CONECT 244 225
CONECT 245 221
CONECT 226 224 227
CONECT 228 227 229
CONECT 225 224 243 244
CONECT 222 221 223
CONECT 220 221 229 234
CONECT 218 217
CONECT 219 217
CONECT 246 236
CONECT 247 234 237
CONECT 248 217 238
CONECT 217 218 219 214 248
END

COMPND ADENandTHYM_wocarbon_PDBfile_mod_gcg_b_WCvalues_a.PDB
HETATM 1 N -3.807 -3.534 -0.375
HETATM 2 C -4.595 -2.478 -0.744
HETATM 3 N -3.950 -1.354 -0.840
HETATM 4 C -2.649 -1.687 -0.497
HETATM 5 C -1.466 -0.928 -0.408
HETATM 6 N -1.419 0.391 -0.659
HETATM 7 N -0.344 -1.572 -0.050
HETATM 8 C -0.404 -2.878 0.200
HETATM 9 N -1.435 -3.693 0.144
HETATM 10 C -2.541 -3.019 -0.219
HETATM 11 C -4.079 -4.517 -0.237
HETATM 15 H -5.663 -2.571 -0.942
HETATM 13 H -0.527 0.900 -0.578
HETATM 14 H -2.277 0.892 -0.933
HETATM 12 H 0.538 -3.337 0.490
HETATM 16 N 4.426 -0.053 0.656
HETATM 17 C 3.272 -0.798 0.519
HETATM 18 O 3.240 -2.000 0.709
HETATM 19 N 2.148 -0.083 0.158
HETATM 20 C 2.076 1.272 -0.083
HETATM 21 O 1.006 1.802 -0.404
HETATM 22 C 3.330 1.967 0.079
HETATM 23 C 4.447 1.302 0.441
HETATM 24 C 5.283 -0.555 0.928
HETATM 25 C 3.298 3.445 -0.164
HETATM 26 H 1.272 -0.618 0.053
HETATM 27 H 5.380 1.851 0.563
HETATM 28 H 4.309 3.845 -0.106
HETATM 29 H 2.884 3.644 -1.152
HETATM 30 H 2.677 3.923 0.594
CONECT 1 2 10 11
CONECT 2 1 3 15
CONECT 3 2 4
CONECT 4 3 5 10
CONECT 5 4 6 7
CONECT 6 5 13 14
CONECT 7 5 8
CONECT 8 7 9 12
CONECT 9 8 10
CONECT 10 1 4 9
CONECT 11 1
CONECT 15 2
CONECT 13 6
CONECT 14 6
CONECT 12 8
CONECT 16 17 23 24
CONECT 17 16 18 19
CONECT 18 17
CONECT 19 17 20 26
CONECT 20 19 21 22
CONECT 21 20
CONECT 22 20 23 25
CONECT 23 16 22 27
CONECT 24 16
CONECT 25 22 28 29 30
CONECT 26 19
CONECT 27 23
CONECT 28 25
CONECT 29 25
CONECT 30 25
END

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