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plainermanplainerman
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Add prepare_molecule.py and run for chignolin
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‎files/chignolin_folded_relaxed.pdb

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MODEL 0
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ATOM 1 N GLY A 1 -7.577 -5.524 5.337 1.00 0.00 N
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ATOM 2 CA GLY A 1 -7.610 -6.016 6.724 1.00 0.00 C
4+
ATOM 3 C GLY A 1 -8.124 -7.424 6.597 1.00 0.00 C
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ATOM 4 O GLY A 1 -7.317 -8.266 6.308 1.00 0.00 O
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ATOM 5 H GLY A 1 -6.876 -6.049 4.797 1.00 0.00 H
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ATOM 6 H2 GLY A 1 -7.388 -4.541 5.397 1.00 0.00 H
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ATOM 7 H3 GLY A 1 -8.507 -5.653 4.884 1.00 0.00 H
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ATOM 8 HA2 GLY A 1 -6.622 -6.041 7.204 1.00 0.00 H
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ATOM 9 HA3 GLY A 1 -8.279 -5.315 7.270 1.00 0.00 H
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ATOM 10 N TYR A 2 -9.409 -7.692 6.868 1.00 0.00 N
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ATOM 11 CA TYR A 2 -10.492 -6.788 7.120 1.00 0.00 C
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ATOM 12 C TYR A 2 -10.247 -5.790 8.330 1.00 0.00 C
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ATOM 13 O TYR A 2 -9.588 -6.113 9.300 1.00 0.00 O
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ATOM 14 CB TYR A 2 -11.748 -7.610 7.428 1.00 0.00 C
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ATOM 15 CG TYR A 2 -12.316 -8.357 6.211 1.00 0.00 C
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ATOM 16 CD1 TYR A 2 -12.023 -9.744 6.042 1.00 0.00 C
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ATOM 17 CD2 TYR A 2 -12.959 -7.711 5.137 1.00 0.00 C
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ATOM 18 CE1 TYR A 2 -12.313 -10.445 4.851 1.00 0.00 C
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ATOM 19 CE2 TYR A 2 -13.368 -8.412 3.969 1.00 0.00 C
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ATOM 20 CZ TYR A 2 -12.928 -9.745 3.747 1.00 0.00 C
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ATOM 21 OH TYR A 2 -13.213 -10.412 2.624 1.00 0.00 O
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ATOM 22 H TYR A 2 -9.647 -8.675 6.731 1.00 0.00 H
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ATOM 23 HA TYR A 2 -10.806 -6.222 6.208 1.00 0.00 H
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ATOM 24 HB2 TYR A 2 -11.601 -8.314 8.319 1.00 0.00 H
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ATOM 25 HB3 TYR A 2 -12.540 -6.932 7.762 1.00 0.00 H
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ATOM 26 HD1 TYR A 2 -11.586 -10.292 6.899 1.00 0.00 H
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ATOM 27 HD2 TYR A 2 -13.179 -6.664 5.039 1.00 0.00 H
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ATOM 28 HE1 TYR A 2 -11.959 -11.457 4.722 1.00 0.00 H
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ATOM 29 HE2 TYR A 2 -13.860 -7.889 3.155 1.00 0.00 H
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ATOM 30 HH TYR A 2 -12.420 -10.773 2.232 1.00 0.00 H
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ATOM 31 N ASP A 3 -10.778 -4.574 8.175 1.00 0.00 N
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ATOM 32 CA ASP A 3 -10.488 -3.482 9.108 1.00 0.00 C
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ATOM 33 C ASP A 3 -11.508 -2.324 9.044 1.00 0.00 C
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ATOM 34 O ASP A 3 -11.958 -1.957 7.927 1.00 0.00 O
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ATOM 35 CB ASP A 3 -9.028 -2.988 8.959 1.00 0.00 C
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ATOM 36 CG ASP A 3 -8.721 -2.461 7.593 1.00 0.00 C
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ATOM 37 OD1 ASP A 3 -8.797 -1.270 7.382 1.00 0.00 O
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ATOM 38 OD2 ASP A 3 -8.305 -3.296 6.729 1.00 0.00 O
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ATOM 39 H ASP A 3 -11.344 -4.356 7.378 1.00 0.00 H
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ATOM 40 HA ASP A 3 -10.584 -3.900 10.096 1.00 0.00 H
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ATOM 41 HB2 ASP A 3 -8.889 -2.186 9.703 1.00 0.00 H
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ATOM 42 HB3 ASP A 3 -8.336 -3.794 9.113 1.00 0.00 H
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ATOM 43 N PRO A 4 -11.933 -1.790 10.214 1.00 0.00 N
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ATOM 44 CA PRO A 4 -12.729 -0.537 10.310 1.00 0.00 C
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ATOM 45 C PRO A 4 -11.959 0.763 9.943 1.00 0.00 C
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ATOM 46 O PRO A 4 -12.587 1.757 9.640 1.00 0.00 O
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ATOM 47 CB PRO A 4 -13.341 -0.538 11.711 1.00 0.00 C
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ATOM 48 CG PRO A 4 -12.189 -1.170 12.478 1.00 0.00 C
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ATOM 49 CD PRO A 4 -11.516 -2.179 11.575 1.00 0.00 C
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ATOM 50 HA PRO A 4 -13.582 -0.643 9.572 1.00 0.00 H
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ATOM 51 HB2 PRO A 4 -13.651 0.424 12.005 1.00 0.00 H
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ATOM 52 HB3 PRO A 4 -14.227 -1.219 11.689 1.00 0.00 H
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ATOM 53 HG2 PRO A 4 -11.511 -0.381 12.727 1.00 0.00 H
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ATOM 54 HG3 PRO A 4 -12.600 -1.646 13.419 1.00 0.00 H
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ATOM 55 HD2 PRO A 4 -10.427 -2.201 11.837 1.00 0.00 H
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ATOM 56 HD3 PRO A 4 -11.984 -3.145 11.805 1.00 0.00 H
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ATOM 57 N GLU A 5 -10.610 0.718 10.035 1.00 0.00 N
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ATOM 58 CA GLU A 5 -9.757 1.915 9.771 1.00 0.00 C
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ATOM 59 C GLU A 5 -9.715 2.287 8.273 1.00 0.00 C
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ATOM 60 O GLU A 5 -9.795 3.466 7.994 1.00 0.00 O
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ATOM 61 CB GLU A 5 -8.345 1.773 10.374 1.00 0.00 C
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ATOM 62 CG GLU A 5 -8.434 2.025 11.906 1.00 0.00 C
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ATOM 63 CD GLU A 5 -8.969 0.838 12.667 1.00 0.00 C
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ATOM 64 OE1 GLU A 5 -9.415 1.099 13.797 1.00 0.00 O
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ATOM 65 OE2 GLU A 5 -9.031 -0.258 12.154 1.00 0.00 O
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ATOM 66 H GLU A 5 -10.148 -0.100 10.345 1.00 0.00 H
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ATOM 67 HA GLU A 5 -10.275 2.718 10.286 1.00 0.00 H
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ATOM 68 HB2 GLU A 5 -7.898 0.767 10.070 1.00 0.00 H
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ATOM 69 HB3 GLU A 5 -7.740 2.553 9.988 1.00 0.00 H
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ATOM 70 HG2 GLU A 5 -7.437 2.233 12.202 1.00 0.00 H
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ATOM 71 HG3 GLU A 5 -9.007 3.007 12.073 1.00 0.00 H
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ATOM 72 N THR A 6 -9.653 1.344 7.273 1.00 0.00 N
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ATOM 73 CA THR A 6 -9.567 1.648 5.811 1.00 0.00 C
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ATOM 74 C THR A 6 -10.679 0.973 4.972 1.00 0.00 C
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ATOM 75 O THR A 6 -10.892 1.256 3.809 1.00 0.00 O
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ATOM 76 CB THR A 6 -8.217 1.411 5.150 1.00 0.00 C
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ATOM 77 OG1 THR A 6 -8.032 0.033 5.299 1.00 0.00 O
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ATOM 78 CG2 THR A 6 -7.111 2.100 5.885 1.00 0.00 C
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ATOM 79 H THR A 6 -9.494 0.393 7.593 1.00 0.00 H
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ATOM 80 HA THR A 6 -9.774 2.724 5.543 1.00 0.00 H
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ATOM 81 HB THR A 6 -8.161 1.659 4.111 1.00 0.00 H
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ATOM 82 HG1 THR A 6 -8.329 -0.192 6.197 1.00 0.00 H
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ATOM 83 HG21 THR A 6 -7.132 3.182 5.911 1.00 0.00 H
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ATOM 84 HG22 THR A 6 -6.174 1.815 5.412 1.00 0.00 H
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ATOM 85 HG23 THR A 6 -7.103 1.673 6.842 1.00 0.00 H
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ATOM 86 N GLY A 7 -11.377 -0.070 5.490 1.00 0.00 N
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ATOM 87 CA GLY A 7 -12.442 -0.798 4.797 1.00 0.00 C
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ATOM 88 C GLY A 7 -11.839 -1.756 3.750 1.00 0.00 C
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ATOM 89 O GLY A 7 -12.564 -2.337 2.956 1.00 0.00 O
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ATOM 90 H GLY A 7 -11.172 -0.344 6.453 1.00 0.00 H
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ATOM 91 HA2 GLY A 7 -13.029 -1.296 5.548 1.00 0.00 H
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ATOM 92 HA3 GLY A 7 -13.138 -0.159 4.300 1.00 0.00 H
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ATOM 93 N THR A 8 -10.547 -1.948 3.817 1.00 0.00 N
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ATOM 94 CA THR A 8 -9.764 -2.845 2.994 1.00 0.00 C
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ATOM 95 C THR A 8 -10.143 -4.247 3.348 1.00 0.00 C
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ATOM 96 O THR A 8 -10.099 -4.739 4.479 1.00 0.00 O
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ATOM 97 CB THR A 8 -8.309 -2.534 3.249 1.00 0.00 C
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ATOM 98 OG1 THR A 8 -8.055 -1.201 2.869 1.00 0.00 O
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ATOM 99 CG2 THR A 8 -7.313 -3.388 2.483 1.00 0.00 C
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ATOM 100 H THR A 8 -9.963 -1.295 4.428 1.00 0.00 H
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ATOM 101 HA THR A 8 -10.007 -2.601 1.981 1.00 0.00 H
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ATOM 102 HB THR A 8 -8.052 -2.645 4.309 1.00 0.00 H
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ATOM 103 HG1 THR A 8 -8.031 -0.694 3.724 1.00 0.00 H
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ATOM 104 HG21 THR A 8 -6.317 -3.147 2.929 1.00 0.00 H
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ATOM 105 HG22 THR A 8 -7.429 -3.189 1.417 1.00 0.00 H
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ATOM 106 HG23 THR A 8 -7.392 -4.464 2.697 1.00 0.00 H
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ATOM 107 N TRP A 9 -10.367 -5.016 2.305 1.00 0.00 N
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ATOM 108 CA TRP A 9 -10.777 -6.436 2.465 1.00 0.00 C
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ATOM 109 C TRP A 9 -9.700 -7.333 3.022 1.00 0.00 C
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ATOM 110 O TRP A 9 -8.540 -6.933 3.339 1.00 0.00 O
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ATOM 111 CB TRP A 9 -11.265 -6.875 1.044 1.00 0.00 C
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ATOM 112 CG TRP A 9 -12.194 -5.979 0.304 1.00 0.00 C
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ATOM 113 CD1 TRP A 9 -13.065 -5.139 0.865 1.00 0.00 C
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ATOM 114 CD2 TRP A 9 -12.410 -5.837 -1.140 1.00 0.00 C
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ATOM 115 NE1 TRP A 9 -13.620 -4.311 -0.044 1.00 0.00 N
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ATOM 116 CE2 TRP A 9 -13.313 -4.706 -1.337 1.00 0.00 C
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ATOM 117 CE3 TRP A 9 -11.994 -6.518 -2.331 1.00 0.00 C
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ATOM 118 CZ2 TRP A 9 -13.646 -4.207 -2.547 1.00 0.00 C
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ATOM 119 CZ3 TRP A 9 -12.400 -5.976 -3.560 1.00 0.00 C
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ATOM 120 CH2 TRP A 9 -13.214 -4.873 -3.690 1.00 0.00 C
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ATOM 121 H TRP A 9 -10.394 -4.673 1.310 1.00 0.00 H
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ATOM 122 HA TRP A 9 -11.622 -6.543 3.151 1.00 0.00 H
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ATOM 123 HB2 TRP A 9 -10.327 -6.985 0.495 1.00 0.00 H
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ATOM 124 HB3 TRP A 9 -11.749 -7.892 1.101 1.00 0.00 H
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ATOM 125 HD1 TRP A 9 -13.297 -5.058 1.937 1.00 0.00 H
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ATOM 126 HE1 TRP A 9 -14.183 -3.501 0.106 1.00 0.00 H
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ATOM 127 HE3 TRP A 9 -11.524 -7.443 -2.283 1.00 0.00 H
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ATOM 128 HZ2 TRP A 9 -14.184 -3.286 -2.628 1.00 0.00 H
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ATOM 129 HZ3 TRP A 9 -12.132 -6.441 -4.442 1.00 0.00 H
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ATOM 130 HH2 TRP A 9 -13.527 -4.537 -4.673 1.00 0.00 H
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ATOM 131 N GLY A 10 -10.053 -8.607 3.056 1.00 0.00 N
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ATOM 132 CA GLY A 10 -9.042 -9.691 3.243 1.00 0.00 C
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ATOM 133 C GLY A 10 -9.602 -11.062 2.781 1.00 0.00 C
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ATOM 134 O GLY A 10 -9.023 -12.091 3.146 1.00 0.00 O
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ATOM 135 OXT GLY A 10 -10.652 -11.071 2.125 1.00 0.00 O
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ATOM 136 H GLY A 10 -11.039 -8.839 2.830 1.00 0.00 H
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ATOM 137 HA2 GLY A 10 -8.178 -9.520 2.505 1.00 0.00 H
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ATOM 138 HA3 GLY A 10 -8.730 -9.771 4.304 1.00 0.00 H
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TER 139 GLY A 10
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ENDMDL
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END

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