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Fix terminal NA names

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Tjerk Straatsma 2004-12-07 23:43:00 +00:00
parent 5f88dc76b0
commit f963e2a542
1 changed files with 126 additions and 126 deletions
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examples/md/dna/dna.pdb
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@ -3,36 +3,36 @@ TITLE
TITLE 2
TITLE 3
REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996
ATOM 1 H5T DT5 1 -3.679 3.620 11.187 0.00 H
ATOM 2 O5* DT5 1 -3.662 4.205 10.426 0.00 O
ATOM 3 C5* DT5 1 -4.153 3.468 9.296 0.00 C
ATOM 4 2H5* DT5 1 -5.227 3.291 9.354 0.00 H
ATOM 5 3H5* DT5 1 -3.901 3.983 8.369 0.00 H
ATOM 6 C4* DT5 1 -3.355 2.104 9.369 0.00 C
ATOM 7 H4* DT5 1 -3.792 1.441 8.622 0.00 H
ATOM 8 O4* DT5 1 -1.969 2.319 8.996 0.00 O
ATOM 9 C1* DT5 1 -1.085 1.746 9.913 0.00 C
ATOM 10 H1* DT5 1 -0.820 0.747 9.568 0.00 H
ATOM 11 N1 DT5 1 0.118 2.569 10.119 0.00 N
ATOM 12 C6 DT5 1 0.111 3.948 10.164 0.00 C
ATOM 13 H6 DT5 1 -0.844 4.400 9.940 0.00 H
ATOM 14 C5 DT5 1 1.120 4.764 10.368 0.00 C
ATOM 15 C5M DT5 1 1.044 6.270 10.374 0.00 C
ATOM 16 2H5M DT5 1 1.304 6.652 11.361 0.00 H
ATOM 17 3H5M DT5 1 1.742 6.667 9.637 0.00 H
ATOM 18 4H5M DT5 1 0.039 6.599 10.108 0.00 H
ATOM 19 C4 DT5 1 2.443 4.142 10.594 0.00 C
ATOM 20 O4 DT5 1 3.522 4.761 10.819 0.00 O
ATOM 21 N3 DT5 1 2.477 2.739 10.520 0.00 N
ATOM 22 H3 DT5 1 3.366 2.265 10.576 0.00 H
ATOM 23 C2 DT5 1 1.324 1.948 10.335 0.00 C
ATOM 24 O2 DT5 1 1.477 0.752 10.334 0.00 O
ATOM 25 C3* DT5 1 -3.348 1.361 10.688 0.00 C
ATOM 26 H3* DT5 1 -4.148 1.658 11.367 0.00 H
ATOM 27 C2* DT5 1 -1.943 1.653 11.229 0.00 C
ATOM 28 2H2* DT5 1 -1.587 0.848 11.871 0.00 H
ATOM 29 3H2* DT5 1 -1.937 2.604 11.762 0.00 H
ATOM 30 O3* DT5 1 -3.367 -0.167 10.428 0.00 O
ATOM 1 H5T DT 1 -3.679 3.620 11.187 0.00 H
ATOM 2 O5* DT 1 -3.662 4.205 10.426 0.00 O
ATOM 3 C5* DT 1 -4.153 3.468 9.296 0.00 C
ATOM 4 2H5* DT 1 -5.227 3.291 9.354 0.00 H
ATOM 5 3H5* DT 1 -3.901 3.983 8.369 0.00 H
ATOM 6 C4* DT 1 -3.355 2.104 9.369 0.00 C
ATOM 7 H4* DT 1 -3.792 1.441 8.622 0.00 H
ATOM 8 O4* DT 1 -1.969 2.319 8.996 0.00 O
ATOM 9 C1* DT 1 -1.085 1.746 9.913 0.00 C
ATOM 10 H1* DT 1 -0.820 0.747 9.568 0.00 H
ATOM 11 N1 DT 1 0.118 2.569 10.119 0.00 N
ATOM 12 C6 DT 1 0.111 3.948 10.164 0.00 C
ATOM 13 H6 DT 1 -0.844 4.400 9.940 0.00 H
ATOM 14 C5 DT 1 1.120 4.764 10.368 0.00 C
ATOM 15 C5M DT 1 1.044 6.270 10.374 0.00 C
ATOM 16 2H5M DT 1 1.304 6.652 11.361 0.00 H
ATOM 17 3H5M DT 1 1.742 6.667 9.637 0.00 H
ATOM 18 4H5M DT 1 0.039 6.599 10.108 0.00 H
ATOM 19 C4 DT 1 2.443 4.142 10.594 0.00 C
ATOM 20 O4 DT 1 3.522 4.761 10.819 0.00 O
ATOM 21 N3 DT 1 2.477 2.739 10.520 0.00 N
ATOM 22 H3 DT 1 3.366 2.265 10.576 0.00 H
ATOM 23 C2 DT 1 1.324 1.948 10.335 0.00 C
ATOM 24 O2 DT 1 1.477 0.752 10.334 0.00 O
ATOM 25 C3* DT 1 -3.348 1.361 10.688 0.00 C
ATOM 26 H3* DT 1 -4.148 1.658 11.367 0.00 H
ATOM 27 C2* DT 1 -1.943 1.653 11.229 0.00 C
ATOM 28 2H2* DT 1 -1.587 0.848 11.871 0.00 H
ATOM 29 3H2* DT 1 -1.937 2.604 11.762 0.00 H
ATOM 30 O3* DT 1 -3.367 -0.167 10.428 0.00 O
ATOM 31 P DG 2 -4.830 -0.983 10.438 0.00 P
ATOM 32 O1P DG 2 -5.663 -0.426 11.576 0.00 O
ATOM 33 O2P DG 2 -4.392 -2.427 10.448 0.00 O
@ -159,69 +159,69 @@ ATOM 153 C2* DC 5 3.451 -3.712 -3.117 0.00 C
ATOM 154 2H2* DC 5 3.872 -2.801 -2.692 0.00 H
ATOM 155 3H2* DC 5 2.691 -4.126 -2.454 0.00 H
ATOM 156 O3* DC 5 5.732 -4.133 -3.758 0.00 O
ATOM 157 P DA3 6 7.196 -4.827 -3.514 0.00 P
ATOM 158 O1P DA3 6 7.234 -5.539 -2.204 0.00 O
ATOM 159 O2P DA3 6 8.188 -3.758 -3.759 0.00 O
ATOM 160 O5* DA3 6 7.251 -5.980 -4.644 0.00 O
ATOM 161 C5* DA3 6 7.301 -5.571 -6.081 0.00 C
ATOM 162 2H5* DA3 6 6.525 -4.832 -6.281 0.00 H
ATOM 163 3H5* DA3 6 8.280 -5.131 -6.268 0.00 H
ATOM 164 C4* DA3 6 7.114 -6.837 -6.970 0.00 C
ATOM 165 H4* DA3 6 7.873 -7.597 -6.789 0.00 H
ATOM 166 O4* DA3 6 5.774 -7.344 -6.749 0.00 O
ATOM 167 C1* DA3 6 5.207 -7.725 -8.061 0.00 C
ATOM 168 H1* DA3 6 5.273 -8.810 -8.135 0.00 H
ATOM 169 N9 DA3 6 3.788 -7.355 -8.003 0.00 N
ATOM 170 C8 DA3 6 2.749 -8.218 -7.846 0.00 C
ATOM 171 H8 DA3 6 2.866 -9.283 -7.708 0.00 H
ATOM 172 N7 DA3 6 1.595 -7.631 -7.848 0.00 N
ATOM 173 C5 DA3 6 1.900 -6.284 -7.980 0.00 C
ATOM 174 C6 DA3 6 0.962 -5.236 -7.974 0.00 C
ATOM 175 N6 DA3 6 -0.374 -5.383 -7.904 0.00 N
ATOM 176 2H6 DA3 6 -0.726 -6.317 -7.747 0.00 H
ATOM 177 3H6 DA3 6 -0.943 -4.551 -7.834 0.00 H
ATOM 178 N1 DA3 6 1.571 -3.972 -8.110 0.00 N
ATOM 179 C2 DA3 6 2.877 -3.867 -8.234 0.00 C
ATOM 180 H2 DA3 6 3.250 -2.857 -8.319 0.00 H
ATOM 181 N3 DA3 6 3.819 -4.835 -8.211 0.00 N
ATOM 182 C4 DA3 6 3.198 -6.110 -8.090 0.00 C
ATOM 183 C3* DA3 6 7.146 -6.265 -8.404 0.00 C
ATOM 184 H3* DA3 6 6.697 -5.272 -8.372 0.00 H
ATOM 185 C2* DA3 6 6.080 -7.151 -9.074 0.00 C
ATOM 186 2H2* DA3 6 6.577 -7.957 -9.613 0.00 H
ATOM 187 3H2* DA3 6 5.517 -6.552 -9.790 0.00 H
ATOM 188 O3* DA3 6 8.401 -6.149 -9.043 0.00 O
ATOM 189 H3T DA3 6 9.048 -5.929 -8.369 0.00 H
ATOM 190 H5T DT5 7 -1.042 3.770 -9.290 0.00 H
ATOM 191 O5* DT5 7 -1.542 4.493 -8.905 0.00 O
ATOM 192 C5* DT5 7 -0.700 5.149 -8.037 0.00 C
ATOM 193 2H5* DT5 7 -0.501 6.181 -8.327 0.00 H
ATOM 194 3H5* DT5 7 -1.280 5.204 -7.116 0.00 H
ATOM 195 C4* DT5 7 0.561 4.421 -7.608 0.00 C
ATOM 196 H4* DT5 7 1.086 4.989 -6.840 0.00 H
ATOM 197 O4* DT5 7 0.128 3.111 -7.059 0.00 O
ATOM 198 C1* DT5 7 0.908 2.055 -7.676 0.00 C
ATOM 199 H1* DT5 7 1.822 1.912 -7.101 0.00 H
ATOM 200 N1 DT5 7 0.119 0.812 -7.681 0.00 N
ATOM 201 C6 DT5 7 -1.280 0.751 -7.555 0.00 C
ATOM 202 H6 DT5 7 -1.790 1.684 -7.364 0.00 H
ATOM 203 C5 DT5 7 -2.035 -0.343 -7.587 0.00 C
ATOM 204 C5M DT5 7 -3.620 -0.276 -7.380 0.00 C
ATOM 205 2H5M DT5 7 -4.127 -0.450 -8.330 0.00 H
ATOM 206 3H5M DT5 7 -3.921 -1.040 -6.663 0.00 H
ATOM 207 4H5M DT5 7 -3.907 0.697 -6.980 0.00 H
ATOM 208 C4 DT5 7 -1.376 -1.674 -7.743 0.00 C
ATOM 209 O4 DT5 7 -1.936 -2.732 -7.776 0.00 O
ATOM 210 N3 DT5 7 -0.032 -1.516 -7.833 0.00 N
ATOM 211 H3 DT5 7 0.489 -2.381 -7.852 0.00 H
ATOM 212 C2 DT5 7 0.763 -0.437 -7.860 0.00 C
ATOM 213 O2 DT5 7 2.024 -0.421 -7.953 0.00 O
ATOM 214 C3* DT5 7 1.535 4.077 -8.752 0.00 C
ATOM 215 H3* DT5 7 1.363 4.698 -9.632 0.00 H
ATOM 216 C2* DT5 7 1.268 2.597 -9.052 0.00 C
ATOM 217 2H2* DT5 7 2.150 2.101 -9.457 0.00 H
ATOM 218 3H2* DT5 7 0.424 2.504 -9.735 0.00 H
ATOM 219 O3* DT5 7 2.914 4.153 -8.337 0.00 O
ATOM 157 P DA 6 7.196 -4.827 -3.514 0.00 P
ATOM 158 O1P DA 6 7.234 -5.539 -2.204 0.00 O
ATOM 159 O2P DA 6 8.188 -3.758 -3.759 0.00 O
ATOM 160 O5* DA 6 7.251 -5.980 -4.644 0.00 O
ATOM 161 C5* DA 6 7.301 -5.571 -6.081 0.00 C
ATOM 162 2H5* DA 6 6.525 -4.832 -6.281 0.00 H
ATOM 163 3H5* DA 6 8.280 -5.131 -6.268 0.00 H
ATOM 164 C4* DA 6 7.114 -6.837 -6.970 0.00 C
ATOM 165 H4* DA 6 7.873 -7.597 -6.789 0.00 H
ATOM 166 O4* DA 6 5.774 -7.344 -6.749 0.00 O
ATOM 167 C1* DA 6 5.207 -7.725 -8.061 0.00 C
ATOM 168 H1* DA 6 5.273 -8.810 -8.135 0.00 H
ATOM 169 N9 DA 6 3.788 -7.355 -8.003 0.00 N
ATOM 170 C8 DA 6 2.749 -8.218 -7.846 0.00 C
ATOM 171 H8 DA 6 2.866 -9.283 -7.708 0.00 H
ATOM 172 N7 DA 6 1.595 -7.631 -7.848 0.00 N
ATOM 173 C5 DA 6 1.900 -6.284 -7.980 0.00 C
ATOM 174 C6 DA 6 0.962 -5.236 -7.974 0.00 C
ATOM 175 N6 DA 6 -0.374 -5.383 -7.904 0.00 N
ATOM 176 2H6 DA 6 -0.726 -6.317 -7.747 0.00 H
ATOM 177 3H6 DA 6 -0.943 -4.551 -7.834 0.00 H
ATOM 178 N1 DA 6 1.571 -3.972 -8.110 0.00 N
ATOM 179 C2 DA 6 2.877 -3.867 -8.234 0.00 C
ATOM 180 H2 DA 6 3.250 -2.857 -8.319 0.00 H
ATOM 181 N3 DA 6 3.819 -4.835 -8.211 0.00 N
ATOM 182 C4 DA 6 3.198 -6.110 -8.090 0.00 C
ATOM 183 C3* DA 6 7.146 -6.265 -8.404 0.00 C
ATOM 184 H3* DA 6 6.697 -5.272 -8.372 0.00 H
ATOM 185 C2* DA 6 6.080 -7.151 -9.074 0.00 C
ATOM 186 2H2* DA 6 6.577 -7.957 -9.613 0.00 H
ATOM 187 3H2* DA 6 5.517 -6.552 -9.790 0.00 H
ATOM 188 O3* DA 6 8.401 -6.149 -9.043 0.00 O
ATOM 189 H3T DA 6 9.048 -5.929 -8.369 0.00 H
ATOM 190 H5T DT 7 -1.042 3.770 -9.290 0.00 H
ATOM 191 O5* DT 7 -1.542 4.493 -8.905 0.00 O
ATOM 192 C5* DT 7 -0.700 5.149 -8.037 0.00 C
ATOM 193 2H5* DT 7 -0.501 6.181 -8.327 0.00 H
ATOM 194 3H5* DT 7 -1.280 5.204 -7.116 0.00 H
ATOM 195 C4* DT 7 0.561 4.421 -7.608 0.00 C
ATOM 196 H4* DT 7 1.086 4.989 -6.840 0.00 H
ATOM 197 O4* DT 7 0.128 3.111 -7.059 0.00 O
ATOM 198 C1* DT 7 0.908 2.055 -7.676 0.00 C
ATOM 199 H1* DT 7 1.822 1.912 -7.101 0.00 H
ATOM 200 N1 DT 7 0.119 0.812 -7.681 0.00 N
ATOM 201 C6 DT 7 -1.280 0.751 -7.555 0.00 C
ATOM 202 H6 DT 7 -1.790 1.684 -7.364 0.00 H
ATOM 203 C5 DT 7 -2.035 -0.343 -7.587 0.00 C
ATOM 204 C5M DT 7 -3.620 -0.276 -7.380 0.00 C
ATOM 205 2H5M DT 7 -4.127 -0.450 -8.330 0.00 H
ATOM 206 3H5M DT 7 -3.921 -1.040 -6.663 0.00 H
ATOM 207 4H5M DT 7 -3.907 0.697 -6.980 0.00 H
ATOM 208 C4 DT 7 -1.376 -1.674 -7.743 0.00 C
ATOM 209 O4 DT 7 -1.936 -2.732 -7.776 0.00 O
ATOM 210 N3 DT 7 -0.032 -1.516 -7.833 0.00 N
ATOM 211 H3 DT 7 0.489 -2.381 -7.852 0.00 H
ATOM 212 C2 DT 7 0.763 -0.437 -7.860 0.00 C
ATOM 213 O2 DT 7 2.024 -0.421 -7.953 0.00 O
ATOM 214 C3* DT 7 1.535 4.077 -8.752 0.00 C
ATOM 215 H3* DT 7 1.363 4.698 -9.632 0.00 H
ATOM 216 C2* DT 7 1.268 2.597 -9.052 0.00 C
ATOM 217 2H2* DT 7 2.150 2.101 -9.457 0.00 H
ATOM 218 3H2* DT 7 0.424 2.504 -9.735 0.00 H
ATOM 219 O3* DT 7 2.914 4.153 -8.337 0.00 O
ATOM 220 P DG 8 3.712 5.586 -8.520 0.00 P
ATOM 221 O1P DG 8 3.340 6.257 -9.808 0.00 O
ATOM 222 O2P DG 8 5.148 5.280 -8.251 0.00 O
@ -348,39 +348,39 @@ ATOM 342 C2* DC 11 5.766 0.187 5.973 0.00 C
ATOM 343 2H2* DC 11 5.062 -0.318 5.311 0.00 H
ATOM 344 3H2* DC 11 6.083 1.130 5.528 0.00 H
ATOM 345 O3* DC 11 6.654 -2.044 6.289 0.00 O
ATOM 346 P DA3 12 7.719 -3.273 5.958 0.00 P
ATOM 347 O1P DA3 12 8.660 -2.883 4.836 0.00 O
ATOM 348 O2P DA3 12 6.809 -4.461 5.810 0.00 O
ATOM 349 O5* DA3 12 8.610 -3.392 7.249 0.00 O
ATOM 350 C5* DA3 12 8.138 -3.973 8.440 0.00 C
ATOM 351 2H5* DA3 12 7.117 -3.650 8.647 0.00 H
ATOM 352 3H5* DA3 12 8.128 -5.050 8.276 0.00 H
ATOM 353 C4* DA3 12 9.043 -3.697 9.620 0.00 C
ATOM 354 H4* DA3 12 10.020 -4.110 9.372 0.00 H
ATOM 355 O4* DA3 12 9.174 -2.213 9.779 0.00 O
ATOM 356 C1* DA3 12 9.078 -1.905 11.219 0.00 C
ATOM 357 H1* DA3 12 10.065 -1.961 11.677 0.00 H
ATOM 358 N9 DA3 12 8.525 -0.536 11.267 0.00 N
ATOM 359 C8 DA3 12 9.347 0.604 11.426 0.00 C
ATOM 360 H8 DA3 12 10.422 0.532 11.491 0.00 H
ATOM 361 N7 DA3 12 8.738 1.762 11.393 0.00 N
ATOM 362 C5 DA3 12 7.364 1.356 11.249 0.00 C
ATOM 363 C6 DA3 12 6.138 2.064 11.149 0.00 C
ATOM 364 N6 DA3 12 6.124 3.386 11.232 0.00 N
ATOM 365 2H6 DA3 12 5.245 3.848 11.044 0.00 H
ATOM 366 3H6 DA3 12 7.019 3.839 11.114 0.00 H
ATOM 367 N1 DA3 12 5.004 1.415 11.004 0.00 N
ATOM 368 C2 DA3 12 5.069 0.048 10.890 0.00 C
ATOM 369 H2 DA3 12 4.128 -0.463 10.750 0.00 H
ATOM 370 N3 DA3 12 6.140 -0.713 10.997 0.00 N
ATOM 371 C4 DA3 12 7.287 -0.027 11.134 0.00 C
ATOM 372 C3* DA3 12 8.608 -4.236 10.983 0.00 C
ATOM 373 H3* DA3 12 7.839 -5.004 10.901 0.00 H
ATOM 374 C2* DA3 12 8.139 -2.998 11.744 0.00 C
ATOM 375 2H2* DA3 12 8.201 -3.114 12.826 0.00 H
ATOM 376 3H2* DA3 12 7.099 -2.846 11.452 0.00 H
ATOM 377 O3* DA3 12 9.791 -4.689 11.784 0.00 O
ATOM 378 H3T DA3 12 10.110 -3.950 12.307 0.00 H
ATOM 346 P DA 12 7.719 -3.273 5.958 0.00 P
ATOM 347 O1P DA 12 8.660 -2.883 4.836 0.00 O
ATOM 348 O2P DA 12 6.809 -4.461 5.810 0.00 O
ATOM 349 O5* DA 12 8.610 -3.392 7.249 0.00 O
ATOM 350 C5* DA 12 8.138 -3.973 8.440 0.00 C
ATOM 351 2H5* DA 12 7.117 -3.650 8.647 0.00 H
ATOM 352 3H5* DA 12 8.128 -5.050 8.276 0.00 H
ATOM 353 C4* DA 12 9.043 -3.697 9.620 0.00 C
ATOM 354 H4* DA 12 10.020 -4.110 9.372 0.00 H
ATOM 355 O4* DA 12 9.174 -2.213 9.779 0.00 O
ATOM 356 C1* DA 12 9.078 -1.905 11.219 0.00 C
ATOM 357 H1* DA 12 10.065 -1.961 11.677 0.00 H
ATOM 358 N9 DA 12 8.525 -0.536 11.267 0.00 N
ATOM 359 C8 DA 12 9.347 0.604 11.426 0.00 C
ATOM 360 H8 DA 12 10.422 0.532 11.491 0.00 H
ATOM 361 N7 DA 12 8.738 1.762 11.393 0.00 N
ATOM 362 C5 DA 12 7.364 1.356 11.249 0.00 C
ATOM 363 C6 DA 12 6.138 2.064 11.149 0.00 C
ATOM 364 N6 DA 12 6.124 3.386 11.232 0.00 N
ATOM 365 2H6 DA 12 5.245 3.848 11.044 0.00 H
ATOM 366 3H6 DA 12 7.019 3.839 11.114 0.00 H
ATOM 367 N1 DA 12 5.004 1.415 11.004 0.00 N
ATOM 368 C2 DA 12 5.069 0.048 10.890 0.00 C
ATOM 369 H2 DA 12 4.128 -0.463 10.750 0.00 H
ATOM 370 N3 DA 12 6.140 -0.713 10.997 0.00 N
ATOM 371 C4 DA 12 7.287 -0.027 11.134 0.00 C
ATOM 372 C3* DA 12 8.608 -4.236 10.983 0.00 C
ATOM 373 H3* DA 12 7.839 -5.004 10.901 0.00 H
ATOM 374 C2* DA 12 8.139 -2.998 11.744 0.00 C
ATOM 375 2H2* DA 12 8.201 -3.114 12.826 0.00 H
ATOM 376 3H2* DA 12 7.099 -2.846 11.452 0.00 H
ATOM 377 O3* DA 12 9.791 -4.689 11.784 0.00 O
ATOM 378 H3T DA 12 10.110 -3.950 12.307 0.00 H
ATOM 379 Na Na 13 6.110 -9.510 2.862 0.00 Na
ATOM 380 Na Na 14 11.032 0.506 -4.564 0.00 Na
ATOM 381 Na Na 15 -0.452 -6.171 10.288 0.00 Na