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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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CMMDE/examples/larutan/UreaAir/SistemLarutan/system_init.pdb

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2 years ago
HEADER
TITLE Built with Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
ATOM 1 O SLV A 1 -1.384 -8.199 -6.097 1.00 0.00
ATOM 2 H SLV A 1 -0.658 -7.572 -6.124 1.00 0.00
ATOM 3 H1 SLV A 1 -2.194 -7.692 -6.016 1.00 0.00
ATOM 4 O SLV A 2 -4.543 -6.168 -1.653 1.00 0.00
ATOM 5 H SLV A 2 -4.810 -5.759 -2.478 1.00 0.00
ATOM 6 H1 SLV A 2 -3.947 -5.557 -1.213 1.00 0.00
ATOM 7 O SLV A 3 -8.034 -0.553 2.331 1.00 0.00
ATOM 8 H SLV A 3 -7.658 -1.315 1.885 1.00 0.00
ATOM 9 H1 SLV A 3 -8.156 -0.794 3.251 1.00 0.00
ATOM 10 O SLV A 4 -5.198 2.441 1.422 1.00 0.00
ATOM 11 H SLV A 4 -5.911 2.781 0.877 1.00 0.00
ATOM 12 H1 SLV A 4 -5.548 1.695 1.913 1.00 0.00
ATOM 13 O SLV A 5 -7.595 1.743 -8.115 1.00 0.00
ATOM 14 H SLV A 5 -8.054 0.906 -8.030 1.00 0.00
ATOM 15 H1 SLV A 5 -8.116 2.401 -7.649 1.00 0.00
ATOM 16 O SLV A 6 -7.872 1.403 8.133 1.00 0.00
ATOM 17 H SLV A 6 -8.001 2.353 8.095 1.00 0.00
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ATOM 19 O SLV A 7 -7.425 0.190 -0.404 1.00 0.00
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ATOM 25 O SLV A 9 -3.129 7.630 6.641 1.00 0.00
ATOM 26 H SLV A 9 -2.240 7.920 6.425 1.00 0.00
ATOM 27 H1 SLV A 9 -3.047 6.848 7.191 1.00 0.00
ATOM 28 O SLV A 10 5.020 4.934 1.449 1.00 0.00
ATOM 29 H SLV A 10 5.901 5.300 1.546 1.00 0.00
ATOM 30 H1 SLV A 10 5.077 4.225 0.805 1.00 0.00
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ATOM 34 O SLV A 12 -7.108 4.614 -1.356 1.00 0.00
ATOM 35 H SLV A 12 -7.813 5.182 -1.038 1.00 0.00
ATOM 36 H1 SLV A 12 -7.451 3.718 -1.374 1.00 0.00
ATOM 37 O SLV A 13 -1.490 5.489 -7.777 1.00 0.00
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ATOM 39 H1 SLV A 13 -1.916 4.632 -7.704 1.00 0.00
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ATOM 43 O SLV A 15 6.695 -3.056 -7.795 1.00 0.00
ATOM 44 H SLV A 15 5.804 -2.996 -7.443 1.00 0.00
ATOM 45 H1 SLV A 15 7.251 -3.414 -7.100 1.00 0.00
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ATOM 47 H SLV A 16 3.634 -7.578 -0.590 1.00 0.00
ATOM 48 H1 SLV A 16 2.443 -7.349 -1.546 1.00 0.00
ATOM 49 O SLV A 17 -3.232 0.100 7.727 1.00 0.00
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ATOM 58 O SLV A 20 -5.055 -7.830 -5.914 1.00 0.00
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ATOM 64 O SLV A 22 1.805 5.397 8.117 1.00 0.00
ATOM 65 H SLV A 22 2.082 4.479 8.117 1.00 0.00
ATOM 66 H1 SLV A 22 0.847 5.404 8.060 1.00 0.00
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ATOM 74 H SLV A 25 -3.551 2.505 3.629 1.00 0.00
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ATOM 94 O SLV A 32 -2.118 5.600 4.867 1.00 0.00
ATOM 95 H SLV A 32 -1.385 5.488 5.475 1.00 0.00
ATOM 96 H1 SLV A 32 -2.792 4.964 5.114 1.00 0.00
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ATOM 102 H1 SLV A 34 6.329 -6.689 0.789 1.00 0.00
ATOM 103 O SLV A 35 7.991 -8.018 -5.145 1.00 0.00
ATOM 104 H SLV A 35 7.160 -8.046 -4.668 1.00 0.00
ATOM 105 H1 SLV A 35 8.116 -7.114 -5.445 1.00 0.00
ATOM 106 O SLV A 36 -7.544 7.205 7.129 1.00 0.00
ATOM 107 H SLV A 36 -7.926 7.771 6.455 1.00 0.00
ATOM 108 H1 SLV A 36 -8.015 7.379 7.947 1.00 0.00
ATOM 109 O SLV A 37 4.893 -4.144 8.049 1.00 0.00
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ATOM 111 H1 SLV A 37 5.499 -3.404 8.120 1.00 0.00
ATOM 112 O SLV A 38 4.724 3.602 8.066 1.00 0.00
ATOM 113 H SLV A 38 5.582 3.174 8.039 1.00 0.00
ATOM 114 H1 SLV A 38 4.730 4.292 7.399 1.00 0.00
ATOM 115 O SLV A 39 2.002 3.117 0.423 1.00 0.00
ATOM 116 H SLV A 39 1.122 2.834 0.680 1.00 0.00
ATOM 117 H1 SLV A 39 2.534 2.326 0.313 1.00 0.00
ATOM 118 O SLV A 40 -4.684 5.844 -7.176 1.00 0.00
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ATOM 122 H SLV A 41 -1.394 -7.141 -0.735 1.00 0.00
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ATOM 125 H SLV A 42 -7.738 0.796 5.455 1.00 0.00
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ATOM 134 H SLV A 45 -7.603 4.696 1.908 1.00 0.00
ATOM 135 H1 SLV A 45 -8.119 3.783 3.041 1.00 0.00
ATOM 136 O SLV A 46 2.905 6.838 0.372 1.00 0.00
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ATOM 193 O SLV A 65 5.223 2.573 5.310 1.00 0.00
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ATOM 262 O SLV A 88 6.608 7.382 3.782 1.00 0.00
ATOM 263 H SLV A 88 5.739 7.727 3.569 1.00 0.00
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ATOM 281 H SLV A 94 6.483 -0.503 7.773 1.00 0.00
ATOM 282 H1 SLV A 94 5.632 0.250 6.727 1.00 0.00
ATOM 283 O SLV A 95 2.682 -5.710 7.576 1.00 0.00
ATOM 284 H SLV A 95 2.466 -5.334 6.721 1.00 0.00
ATOM 285 H1 SLV A 95 1.901 -5.631 8.127 1.00 0.00
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ATOM 288 H1 SLV A 96 5.634 5.023 -8.114 1.00 0.00
ATOM 289 O SLV A 97 -5.998 -6.710 0.971 1.00 0.00
ATOM 290 H SLV A 97 -6.916 -6.479 0.816 1.00 0.00
ATOM 291 H1 SLV A 97 -5.801 -6.494 1.885 1.00 0.00
ATOM 292 O SLV A 98 8.083 1.417 4.228 1.00 0.00
ATOM 293 H SLV A 98 8.115 1.068 5.121 1.00 0.00
ATOM 294 H1 SLV A 98 7.620 0.773 3.688 1.00 0.00
ATOM 295 O SLV A 99 -4.396 -4.329 -8.095 1.00 0.00
ATOM 296 H SLV A 99 -4.777 -5.208 -8.122 1.00 0.00
ATOM 297 H1 SLV A 99 -5.123 -3.703 -8.131 1.00 0.00
ATOM 298 O SLV A 100 -0.129 -3.009 6.260 1.00 0.00
ATOM 299 H SLV A 100 0.798 -3.164 6.452 1.00 0.00
ATOM 300 H1 SLV A 100 -0.486 -2.492 6.986 1.00 0.00
ATOM 301 C URA B 101 1.391 3.285 3.377 1.00 0.00
ATOM 302 O URA B 101 0.413 2.667 3.730 1.00 0.00
ATOM 303 N URA B 101 1.382 4.636 3.188 1.00 0.00
ATOM 304 N1 URA B 101 2.596 2.690 3.137 1.00 0.00
ATOM 305 H URA B 101 0.522 5.126 3.351 1.00 0.00
ATOM 306 H1 URA B 101 2.189 5.155 2.897 1.00 0.00
ATOM 307 H2 URA B 101 2.660 1.696 3.261 1.00 0.00
ATOM 308 H3 URA B 101 3.410 3.197 2.845 1.00 0.00
ATOM 309 C URA B 102 -0.305 -6.239 -3.750 1.00 0.00
ATOM 310 O URA B 102 -0.289 -5.036 -3.879 1.00 0.00
ATOM 311 N URA B 102 0.815 -7.009 -3.867 1.00 0.00
ATOM 312 N1 URA B 102 -1.444 -6.938 -3.473 1.00 0.00
ATOM 313 H URA B 102 1.682 -6.546 -4.069 1.00 0.00
ATOM 314 H1 URA B 102 0.809 -8.005 -3.760 1.00 0.00
ATOM 315 H2 URA B 102 -2.299 -6.421 -3.376 1.00 0.00
ATOM 316 H3 URA B 102 -1.463 -7.934 -3.364 1.00 0.00
ATOM 317 C URA B 103 -0.280 1.104 6.409 1.00 0.00
ATOM 318 O URA B 103 -1.070 0.295 5.979 1.00 0.00
ATOM 319 N URA B 103 0.885 0.745 7.022 1.00 0.00
ATOM 320 N1 URA B 103 -0.481 2.451 6.322 1.00 0.00
ATOM 321 H URA B 103 1.084 -0.234 7.113 1.00 0.00
ATOM 322 H1 URA B 103 1.543 1.410 7.380 1.00 0.00
ATOM 323 H2 URA B 103 -1.322 2.772 5.880 1.00 0.00
ATOM 324 H3 URA B 103 0.170 3.126 6.676 1.00 0.00
ATOM 325 C URA B 104 7.651 1.516 -6.257 1.00 0.00
ATOM 326 O URA B 104 7.846 2.618 -5.797 1.00 0.00
ATOM 327 N URA B 104 7.236 1.314 -7.541 1.00 0.00
ATOM 328 N1 URA B 104 7.828 0.372 -5.534 1.00 0.00
ATOM 329 H URA B 104 7.090 2.121 -8.118 1.00 0.00
ATOM 330 H1 URA B 104 7.073 0.404 -7.928 1.00 0.00
ATOM 331 H2 URA B 104 8.133 0.461 -4.583 1.00 0.00
ATOM 332 H3 URA B 104 7.668 -0.544 -5.909 1.00 0.00
ATOM 333 C URA B 105 -0.700 -3.889 -7.475 1.00 0.00
ATOM 334 O URA B 105 -1.509 -3.128 -6.994 1.00 0.00
ATOM 335 N URA B 105 0.593 -3.531 -7.725 1.00 0.00
ATOM 336 N1 URA B 105 -1.004 -5.176 -7.810 1.00 0.00
ATOM 337 H URA B 105 0.871 -2.595 -7.496 1.00 0.00
ATOM 338 H1 URA B 105 1.268 -4.156 -8.122 1.00 0.00
ATOM 339 H2 URA B 105 -1.942 -5.493 -7.648 1.00 0.00
ATOM 340 H3 URA B 105 -0.338 -5.811 -8.208 1.00 0.00
ATOM 341 C URA B 106 -0.411 -0.260 1.010 1.00 0.00
ATOM 342 O URA B 106 0.295 0.423 1.716 1.00 0.00
ATOM 343 N URA B 106 -0.130 -0.502 -0.303 1.00 0.00
ATOM 344 N1 URA B 106 -1.555 -0.852 1.461 1.00 0.00
ATOM 345 H URA B 106 0.700 -0.092 -0.687 1.00 0.00
ATOM 346 H1 URA B 106 -0.711 -1.067 -0.893 1.00 0.00
ATOM 347 H2 URA B 106 -1.811 -0.706 2.420 1.00 0.00
ATOM 348 H3 URA B 106 -2.145 -1.418 0.882 1.00 0.00
ATOM 349 C URA B 107 1.280 1.287 -3.931 1.00 0.00
ATOM 350 O URA B 107 1.864 2.206 -4.457 1.00 0.00
ATOM 351 N URA B 107 -0.008 1.384 -3.492 1.00 0.00
ATOM 352 N1 URA B 107 1.855 0.066 -3.728 1.00 0.00
ATOM 353 H URA B 107 -0.480 2.260 -3.616 1.00 0.00
ATOM 354 H1 URA B 107 -0.497 0.626 -3.056 1.00 0.00
ATOM 355 H2 URA B 107 2.803 -0.062 -4.032 1.00 0.00
ATOM 356 H3 URA B 107 1.377 -0.700 -3.293 1.00 0.00
ATOM 357 C URA B 108 -0.295 6.921 -1.192 1.00 0.00
ATOM 358 O URA B 108 -0.138 7.863 -1.935 1.00 0.00
ATOM 359 N URA B 108 -1.026 7.001 -0.043 1.00 0.00
ATOM 360 N1 URA B 108 0.244 5.691 -1.434 1.00 0.00
ATOM 361 H URA B 108 -1.447 7.883 0.184 1.00 0.00
ATOM 362 H1 URA B 108 -1.160 6.224 0.576 1.00 0.00
ATOM 363 H2 URA B 108 0.793 5.576 -2.266 1.00 0.00
ATOM 364 H3 URA B 108 0.118 4.907 -0.823 1.00 0.00
ATOM 365 C URA B 109 5.924 -0.034 -2.463 1.00 0.00
ATOM 366 O URA B 109 6.529 -0.992 -2.887 1.00 0.00
ATOM 367 N URA B 109 5.337 0.888 -3.279 1.00 0.00
ATOM 368 N1 URA B 109 5.772 0.213 -1.130 1.00 0.00
ATOM 369 H URA B 109 5.417 0.755 -4.270 1.00 0.00
ATOM 370 H1 URA B 109 4.834 1.684 -2.934 1.00 0.00
ATOM 371 H2 URA B 109 6.185 -0.434 -0.483 1.00 0.00
ATOM 372 H3 URA B 109 5.272 1.005 -0.772 1.00 0.00
ATOM 373 C URA B 110 -1.841 -7.151 2.658 1.00 0.00
ATOM 374 O URA B 110 -1.653 -8.212 2.108 1.00 0.00
ATOM 375 N URA B 110 -2.656 -6.186 2.142 1.00 0.00
ATOM 376 N1 URA B 110 -1.256 -6.820 3.846 1.00 0.00
ATOM 377 H URA B 110 -3.113 -6.377 1.270 1.00 0.00
ATOM 378 H1 URA B 110 -2.817 -5.306 2.593 1.00 0.00
ATOM 379 H2 URA B 110 -0.645 -7.493 4.271 1.00 0.00
ATOM 380 H3 URA B 110 -1.408 -5.943 4.306 1.00 0.00
ATOM 381 C URA B 111 1.886 -4.400 -0.162 1.00 0.00
ATOM 382 O URA B 111 1.068 -5.268 -0.362 1.00 0.00
ATOM 383 N URA B 111 2.915 -4.545 0.722 1.00 0.00
ATOM 384 N1 URA B 111 1.858 -3.196 -0.803 1.00 0.00
ATOM 385 H URA B 111 2.985 -5.412 1.221 1.00 0.00
ATOM 386 H1 URA B 111 3.597 -3.830 0.892 1.00 0.00
ATOM 387 H2 URA B 111 1.122 -3.035 -1.465 1.00 0.00
ATOM 388 H3 URA B 111 2.533 -2.473 -0.641 1.00 0.00
ATOM 389 C URA B 112 -6.701 -2.225 -3.163 1.00 0.00
ATOM 390 O URA B 112 -6.140 -3.070 -2.504 1.00 0.00
ATOM 391 N URA B 112 -7.671 -2.524 -4.075 1.00 0.00
ATOM 392 N1 URA B 112 -6.419 -0.895 -3.055 1.00 0.00
ATOM 393 H URA B 112 -7.919 -3.489 -4.195 1.00 0.00
ATOM 394 H1 URA B 112 -8.141 -1.830 -4.624 1.00 0.00
ATOM 395 H2 URA B 112 -5.713 -0.617 -2.398 1.00 0.00
ATOM 396 H3 URA B 112 -6.881 -0.190 -3.598 1.00 0.00
ATOM 397 C URA B 113 -3.739 2.277 -3.817 1.00 0.00
ATOM 398 O URA B 113 -3.872 1.295 -3.123 1.00 0.00
ATOM 399 N URA B 113 -4.320 3.475 -3.520 1.00 0.00
ATOM 400 N1 URA B 113 -2.995 2.278 -4.961 1.00 0.00
ATOM 401 H URA B 113 -4.878 3.531 -2.688 1.00 0.00
ATOM 402 H1 URA B 113 -4.213 4.292 -4.090 1.00 0.00
ATOM 403 H2 URA B 113 -2.544 1.423 -5.228 1.00 0.00
ATOM 404 H3 URA B 113 -2.881 3.089 -5.540 1.00 0.00
END