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transfer atomic pdb file to CG pdb.
- msaeedi
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10 years 10 months ago #1730
by msaeedi
transfer atomic pdb file to CG pdb. was created by msaeedi
When I transferred dppc.pdb and doxil.pdb files to cg_dppc.pdb and cg_doxil.pdb with ./martinize.py script, these files are empty. Why? My pdb files are wrong?
Also, I found molmaker.py script for this work, but I couldn’t use it, is it possible to put an example for this script?
I attached these pdbs, if it is possible, take look at them please.
dppc pdb:
ATOM 1 N DPP 1 34.069 1.931 16.023 1.00 0.00
ATOM 2 C13 DPP 1 33.379 0.721 16.603 1.00 0.00
ATOM 3 H13A DPP 1 34.029 -0.139 16.553 1.00 0.00
ATOM 4 H13B DPP 1 32.629 0.311 15.943 1.00 0.00
ATOM 5 H13C DPP 1 33.119 0.931 17.633 1.00 0.00
ATOM 6 C14 DPP 1 34.939 1.431 14.893 1.00 0.00
ATOM 7 H14A DPP 1 35.549 0.651 15.333 1.00 0.00
ATOM 8 H14B DPP 1 35.549 2.241 14.533 1.00 0.00
ATOM 9 H14C DPP 1 34.309 0.951 14.153 1.00 0.00
ATOM 10 C15 DPP 1 33.059 2.951 15.583 1.00 0.00
ATOM 11 H15A DPP 1 33.569 3.851 15.273 1.00 0.00
ATOM 12 H15B DPP 1 32.459 3.331 16.403 1.00 0.00
ATOM 13 H15C DPP 1 32.329 2.661 14.833 1.00 0.00
ATOM 14 C12 DPP 1 35.049 2.601 16.953 1.00 0.00
ATOM 15 H12A DPP 1 35.469 3.461 16.433 1.00 0.00
ATOM 16 H12B DPP 1 35.819 1.901 17.213 1.00 0.00
ATOM 17 C11 DPP 1 34.539 3.001 18.333 1.00 0.00
ATOM 18 H11A DPP 1 33.609 3.611 18.303 1.00 0.00
ATOM 19 H11B DPP 1 35.259 3.711 18.793 1.00 0.00
ATOM 20 P DPP 1 35.339 1.651 20.313 1.00 0.00
ATOM 21 O13 DPP 1 36.689 1.841 19.723 1.00 0.00
ATOM 22 O14 DPP 1 35.059 0.291 20.833 1.00 0.00
ATOM 23 O11 DPP 1 34.999 2.721 21.443 1.00 0.00
ATOM 24 O12 DPP 1 34.209 1.921 19.213 1.00 0.00
ATOM 25 C1 DPP 1 36.059 3.511 22.003 1.00 0.00
ATOM 26 HA DPP 1 35.679 4.491 22.343 1.00 0.00
ATOM 27 HB DPP 1 36.889 3.701 21.293 1.00 0.00
ATOM 28 C2 DPP 1 36.669 2.811 23.233 1.00 0.00
ATOM 29 HS DPP 1 37.439 2.061 22.943 1.00 0.00
ATOM 30 O21 DPP 1 35.599 2.251 24.003 1.00 0.00
ATOM 31 C21 DPP 1 35.839 0.971 24.303 1.00 0.00
ATOM 32 O22 DPP 1 36.789 0.241 24.063 1.00 0.00
ATOM 33 C22 DPP 1 34.639 0.501 25.103 1.00 0.00
ATOM 34 H2R DPP 1 34.009 -0.209 24.523 1.00 0.00
ATOM 35 H2S DPP 1 34.059 1.391 25.443 1.00 0.00
ATOM 36 C3 DPP 1 37.319 3.831 24.173 1.00 0.00
ATOM 37 HX DPP 1 36.519 4.561 24.423 1.00 0.00
ATOM 38 HY DPP 1 38.159 4.351 23.673 1.00 0.00
ATOM 39 O31 DPP 1 37.859 3.301 25.393 1.00 0.00
ATOM 40 C31 DPP 1 38.869 2.451 25.203 1.00 0.00
ATOM 41 O32 DPP 1 39.339 2.091 24.143 1.00 0.00
ATOM 42 C32 DPP 1 39.269 1.881 26.563 1.00 0.00
ATOM 43 H2X DPP 1 38.509 2.261 27.273 1.00 0.00
ATOM 44 H2Y DPP 1 40.289 2.261 26.813 1.00 0.00
ATOM 45 C23 DPP 1 35.109 -0.149 26.403 1.00 0.00
ATOM 46 H3R DPP 1 35.679 0.651 26.923 1.00 0.00
ATOM 47 H3S DPP 1 35.659 -1.079 26.133 1.00 0.00
ATOM 48 C24 DPP 1 33.879 -0.359 27.273 1.00 0.00
ATOM 49 H4R DPP 1 33.079 -0.829 26.673 1.00 0.00
ATOM 50 H4S DPP 1 33.409 0.601 27.603 1.00 0.00
ATOM 51 C25 DPP 1 34.369 -1.219 28.443 1.00 0.00
ATOM 52 H5R DPP 1 35.069 -0.639 29.093 1.00 0.00
ATOM 53 H5S DPP 1 34.919 -2.059 27.973 1.00 0.00
ATOM 54 C26 DPP 1 33.229 -1.819 29.263 1.00 0.00
ATOM 55 H6R DPP 1 32.549 -2.319 28.543 1.00 0.00
ATOM 56 H6S DPP 1 32.689 -0.949 29.693 1.00 0.00
ATOM 57 C27 DPP 1 33.769 -2.759 30.343 1.00 0.00
ATOM 58 H7R DPP 1 34.759 -2.359 30.653 1.00 0.00
ATOM 59 H7S DPP 1 33.889 -3.679 29.733 1.00 0.00
ATOM 60 C28 DPP 1 32.769 -3.029 31.463 1.00 0.00
ATOM 61 H8R DPP 1 31.909 -3.559 31.003 1.00 0.00
ATOM 62 H8S DPP 1 32.419 -2.039 31.803 1.00 0.00
ATOM 63 C29 DPP 1 33.379 -3.879 32.583 1.00 0.00
ATOM 64 H9R DPP 1 34.159 -3.219 33.033 1.00 0.00
ATOM 65 H9S DPP 1 33.839 -4.829 32.223 1.00 0.00
ATOM 66 0C21 DPP 1 32.399 -4.159 33.723 1.00 0.00
ATOM 67 H10R DPP 1 31.439 -4.589 33.363 1.00 0.00
ATOM 68 H10S DPP 1 32.169 -3.189 34.203 1.00 0.00
ATOM 69 1C21 DPP 1 32.969 -5.059 34.813 1.00 0.00
ATOM 70 H11R DPP 1 33.799 -4.589 35.383 1.00 0.00
ATOM 71 H11S DPP 1 33.479 -5.889 34.273 1.00 0.00
ATOM 72 2C21 DPP 1 31.929 -5.689 35.753 1.00 0.00
ATOM 73 H12R DPP 1 31.059 -5.959 35.123 1.00 0.00
ATOM 74 H12S DPP 1 31.619 -4.939 36.523 1.00 0.00
ATOM 75 3C21 DPP 1 32.499 -6.909 36.483 1.00 0.00
ATOM 76 H13R DPP 1 33.449 -6.689 37.013 1.00 0.00
ATOM 77 H13S DPP 1 32.679 -7.779 35.823 1.00 0.00
ATOM 78 4C21 DPP 1 31.539 -7.429 37.543 1.00 0.00
ATOM 79 H14R DPP 1 31.699 -8.529 37.583 1.00 0.00
ATOM 80 H14S DPP 1 30.549 -7.079 37.193 1.00 0.00
ATOM 81 5C21 DPP 1 31.749 -6.909 38.973 1.00 0.00
ATOM 82 H15R DPP 1 31.209 -5.939 38.953 1.00 0.00
ATOM 83 H15S DPP 1 32.849 -6.819 39.083 1.00 0.00
ATOM 84 6C21 DPP 1 31.149 -7.689 40.143 1.00 0.00
ATOM 85 H16R DPP 1 30.189 -8.199 39.913 1.00 0.00
ATOM 86 H16S DPP 1 30.929 -7.109 41.073 1.00 0.00
ATOM 87 H16T DPP 1 31.929 -8.359 40.553 1.00 0.00
ATOM 88 C33 DPP 1 39.199 0.361 26.583 1.00 0.00
ATOM 89 H3X DPP 1 39.829 0.061 25.723 1.00 0.00
ATOM 90 H3Y DPP 1 38.139 0.181 26.313 1.00 0.00
ATOM 91 C34 DPP 1 39.589 -0.409 27.853 1.00 0.00
ATOM 92 H4X DPP 1 40.639 -0.209 28.133 1.00 0.00
ATOM 93 H4Y DPP 1 39.389 -1.469 27.593 1.00 0.00
ATOM 94 C35 DPP 1 38.679 -0.009 29.023 1.00 0.00
ATOM 95 H5X DPP 1 37.629 -0.269 28.773 1.00 0.00
ATOM 96 H5Y DPP 1 38.879 1.071 29.203 1.00 0.00
ATOM 97 C36 DPP 1 38.919 -0.829 30.293 1.00 0.00
ATOM 98 H6X DPP 1 38.659 -0.179 31.153 1.00 0.00
ATOM 99 H6Y DPP 1 40.019 -1.019 30.293 1.00 0.00
ATOM 100 C37 DPP 1 38.099 -2.089 30.563 1.00 0.00
ATOM 101 H7X DPP 1 38.339 -2.849 29.793 1.00 0.00
ATOM 102 H7Y DPP 1 37.029 -1.829 30.373 1.00 0.00
ATOM 103 C38 DPP 1 38.149 -2.579 32.003 1.00 0.00
ATOM 104 H8X DPP 1 37.899 -1.879 32.833 1.00 0.00
ATOM 105 H8Y DPP 1 39.199 -2.899 32.113 1.00 0.00
ATOM 106 C39 DPP 1 37.209 -3.769 32.213 1.00 0.00
ATOM 107 H9X DPP 1 37.639 -4.609 31.613 1.00 0.00
ATOM 108 H9Y DPP 1 36.139 -3.589 32.013 1.00 0.00
ATOM 109 0C31 DPP 1 37.349 -4.219 33.673 1.00 0.00
ATOM 110 H10X DPP 1 36.899 -3.439 34.323 1.00 0.00
ATOM 111 H10Y DPP 1 38.389 -4.299 34.043 1.00 0.00
ATOM 112 1C31 DPP 1 36.639 -5.559 33.913 1.00 0.00
ATOM 113 H11X DPP 1 37.129 -6.279 33.233 1.00 0.00
ATOM 114 H11Y DPP 1 35.589 -5.419 33.553 1.00 0.00
ATOM 115 2C31 DPP 1 36.829 -5.889 35.393 1.00 0.00
ATOM 116 H12X DPP 1 36.499 -5.049 36.033 1.00 0.00
ATOM 117 H12Y DPP 1 37.879 -6.239 35.543 1.00 0.00
ATOM 118 3C31 DPP 1 36.059 -7.139 35.823 1.00 0.00
ATOM 119 H13X DPP 1 36.399 -8.049 35.283 1.00 0.00
ATOM 120 H13Y DPP 1 34.979 -6.989 35.613 1.00 0.00
ATOM 121 4C31 DPP 1 36.179 -7.449 37.323 1.00 0.00
ATOM 122 H14X DPP 1 35.839 -6.479 37.733 1.00 0.00
ATOM 123 H14Y DPP 1 37.279 -7.539 37.453 1.00 0.00
ATOM 124 5C31 DPP 1 35.459 -8.669 37.893 1.00 0.00
ATOM 125 H15X DPP 1 35.619 -9.569 37.253 1.00 0.00
ATOM 126 H15Y DPP 1 34.409 -8.319 37.943 1.00 0.00
ATOM 127 6C31 DPP 1 35.929 -8.969 39.313 1.00 0.00
ATOM 128 H16X DPP 1 35.379 -9.899 39.593 1.00 0.00
ATOM 129 H16Y DPP 1 35.749 -8.029 39.873 1.00 0.00
ATOM 130 H16Z DPP 1 37.029 -9.049 39.433 1.00 0.00
END
doxil pdb:
HETATM 1 C LIG 1 15.226 18.450 4.896 1.00 0.00 C
HETATM 2 C LIG 1 16.429 19.161 4.909 1.00 0.00 C
HETATM 3 C LIG 1 17.654 18.469 4.880 1.00 0.00 C
HETATM 4 C LIG 1 17.677 17.063 4.829 1.00 0.00 C
HETATM 5 O LIG 1 18.898 16.388 4.808 1.00 0.00 O
HETATM 6 C LIG 1 16.456 16.353 4.816 1.00 0.00 C
HETATM 7 C LIG 1 16.409 14.946 4.803 1.00 0.00 C
HETATM 8 O LIG 1 17.561 14.211 4.771 1.00 0.00 O
HETATM 9 C LIG 1 15.196 14.209 4.817 1.00 0.00 C
HETATM 10 C LIG 1 15.164 12.808 4.784 1.00 0.00 C
HETATM 11 O LIG 1 16.295 12.032 4.788 1.00 0.00 O
HETATM 12 C LIG 1 13.929 12.131 4.758 1.00 0.00 C
HETATM 13 C LIG 1 13.995 10.639 4.786 1.00 0.00 C
HETATM 14 O LIG 1 14.592 10.397 6.123 1.00 0.00 O
HETATM 15 C LIG 1 12.711 9.868 4.523 1.00 0.00 C
HETATM 16 C LIG 1 11.569 10.600 5.359 1.00 0.00 C
HETATM 17 O LIG 1 11.611 10.753 6.835 1.00 0.00 O
HETATM 18 C LIG 1 10.269 9.864 5.071 1.00 0.00 C
HETATM 19 O LIG 1 9.543 10.187 3.954 1.00 0.00 O
HETATM 20 C LIG 1 9.825 8.804 6.033 1.00 0.00 C
HETATM 21 O LIG 1 8.617 8.191 5.670 1.00 0.00 O
HETATM 22 C LIG 1 11.432 12.065 4.766 1.00 0.00 C
HETATM 23 C LIG 1 12.729 12.807 4.799 1.00 0.00 C
HETATM 24 C LIG 1 12.761 14.224 4.827 1.00 0.00 C
HETATM 25 O LIG 1 11.570 14.889 4.797 1.00 0.00 O
HETATM 26 C LIG 1 13.985 14.924 4.822 1.00 0.00 C
HETATM 27 C LIG 1 14.007 16.349 4.853 1.00 0.00 C
HETATM 28 O LIG 1 12.853 16.988 4.878 1.00 0.00 O
HETATM 29 C LIG 1 15.244 17.040 4.865 1.00 0.00 C
HETATM 30 C LIG 1 20.164 17.131 4.894 1.00 0.00 C
HETATM 31 C LIG 1 15.508 9.325 6.325 1.00 0.00 C
HETATM 32 C LIG 1 16.662 9.744 7.308 1.00 0.00 C
HETATM 33 C LIG 1 15.986 9.896 8.700 1.00 0.00 C
HETATM 34 N LIG 1 17.069 10.218 9.702 1.00 0.00 N
HETATM 35 C LIG 1 15.236 8.613 9.132 1.00 0.00 C
HETATM 36 O LIG 1 16.324 7.597 9.201 1.00 0.00 O
HETATM 37 C LIG 1 14.150 8.254 8.082 1.00 0.00 C
HETATM 38 O LIG 1 14.828 8.116 6.752 1.00 0.00 O
HETATM 39 C LIG 1 13.470 6.895 8.316 1.00 0.00 C
END.
Also, I found molmaker.py script for this work, but I couldn’t use it, is it possible to put an example for this script?
I attached these pdbs, if it is possible, take look at them please.
dppc pdb:
ATOM 1 N DPP 1 34.069 1.931 16.023 1.00 0.00
ATOM 2 C13 DPP 1 33.379 0.721 16.603 1.00 0.00
ATOM 3 H13A DPP 1 34.029 -0.139 16.553 1.00 0.00
ATOM 4 H13B DPP 1 32.629 0.311 15.943 1.00 0.00
ATOM 5 H13C DPP 1 33.119 0.931 17.633 1.00 0.00
ATOM 6 C14 DPP 1 34.939 1.431 14.893 1.00 0.00
ATOM 7 H14A DPP 1 35.549 0.651 15.333 1.00 0.00
ATOM 8 H14B DPP 1 35.549 2.241 14.533 1.00 0.00
ATOM 9 H14C DPP 1 34.309 0.951 14.153 1.00 0.00
ATOM 10 C15 DPP 1 33.059 2.951 15.583 1.00 0.00
ATOM 11 H15A DPP 1 33.569 3.851 15.273 1.00 0.00
ATOM 12 H15B DPP 1 32.459 3.331 16.403 1.00 0.00
ATOM 13 H15C DPP 1 32.329 2.661 14.833 1.00 0.00
ATOM 14 C12 DPP 1 35.049 2.601 16.953 1.00 0.00
ATOM 15 H12A DPP 1 35.469 3.461 16.433 1.00 0.00
ATOM 16 H12B DPP 1 35.819 1.901 17.213 1.00 0.00
ATOM 17 C11 DPP 1 34.539 3.001 18.333 1.00 0.00
ATOM 18 H11A DPP 1 33.609 3.611 18.303 1.00 0.00
ATOM 19 H11B DPP 1 35.259 3.711 18.793 1.00 0.00
ATOM 20 P DPP 1 35.339 1.651 20.313 1.00 0.00
ATOM 21 O13 DPP 1 36.689 1.841 19.723 1.00 0.00
ATOM 22 O14 DPP 1 35.059 0.291 20.833 1.00 0.00
ATOM 23 O11 DPP 1 34.999 2.721 21.443 1.00 0.00
ATOM 24 O12 DPP 1 34.209 1.921 19.213 1.00 0.00
ATOM 25 C1 DPP 1 36.059 3.511 22.003 1.00 0.00
ATOM 26 HA DPP 1 35.679 4.491 22.343 1.00 0.00
ATOM 27 HB DPP 1 36.889 3.701 21.293 1.00 0.00
ATOM 28 C2 DPP 1 36.669 2.811 23.233 1.00 0.00
ATOM 29 HS DPP 1 37.439 2.061 22.943 1.00 0.00
ATOM 30 O21 DPP 1 35.599 2.251 24.003 1.00 0.00
ATOM 31 C21 DPP 1 35.839 0.971 24.303 1.00 0.00
ATOM 32 O22 DPP 1 36.789 0.241 24.063 1.00 0.00
ATOM 33 C22 DPP 1 34.639 0.501 25.103 1.00 0.00
ATOM 34 H2R DPP 1 34.009 -0.209 24.523 1.00 0.00
ATOM 35 H2S DPP 1 34.059 1.391 25.443 1.00 0.00
ATOM 36 C3 DPP 1 37.319 3.831 24.173 1.00 0.00
ATOM 37 HX DPP 1 36.519 4.561 24.423 1.00 0.00
ATOM 38 HY DPP 1 38.159 4.351 23.673 1.00 0.00
ATOM 39 O31 DPP 1 37.859 3.301 25.393 1.00 0.00
ATOM 40 C31 DPP 1 38.869 2.451 25.203 1.00 0.00
ATOM 41 O32 DPP 1 39.339 2.091 24.143 1.00 0.00
ATOM 42 C32 DPP 1 39.269 1.881 26.563 1.00 0.00
ATOM 43 H2X DPP 1 38.509 2.261 27.273 1.00 0.00
ATOM 44 H2Y DPP 1 40.289 2.261 26.813 1.00 0.00
ATOM 45 C23 DPP 1 35.109 -0.149 26.403 1.00 0.00
ATOM 46 H3R DPP 1 35.679 0.651 26.923 1.00 0.00
ATOM 47 H3S DPP 1 35.659 -1.079 26.133 1.00 0.00
ATOM 48 C24 DPP 1 33.879 -0.359 27.273 1.00 0.00
ATOM 49 H4R DPP 1 33.079 -0.829 26.673 1.00 0.00
ATOM 50 H4S DPP 1 33.409 0.601 27.603 1.00 0.00
ATOM 51 C25 DPP 1 34.369 -1.219 28.443 1.00 0.00
ATOM 52 H5R DPP 1 35.069 -0.639 29.093 1.00 0.00
ATOM 53 H5S DPP 1 34.919 -2.059 27.973 1.00 0.00
ATOM 54 C26 DPP 1 33.229 -1.819 29.263 1.00 0.00
ATOM 55 H6R DPP 1 32.549 -2.319 28.543 1.00 0.00
ATOM 56 H6S DPP 1 32.689 -0.949 29.693 1.00 0.00
ATOM 57 C27 DPP 1 33.769 -2.759 30.343 1.00 0.00
ATOM 58 H7R DPP 1 34.759 -2.359 30.653 1.00 0.00
ATOM 59 H7S DPP 1 33.889 -3.679 29.733 1.00 0.00
ATOM 60 C28 DPP 1 32.769 -3.029 31.463 1.00 0.00
ATOM 61 H8R DPP 1 31.909 -3.559 31.003 1.00 0.00
ATOM 62 H8S DPP 1 32.419 -2.039 31.803 1.00 0.00
ATOM 63 C29 DPP 1 33.379 -3.879 32.583 1.00 0.00
ATOM 64 H9R DPP 1 34.159 -3.219 33.033 1.00 0.00
ATOM 65 H9S DPP 1 33.839 -4.829 32.223 1.00 0.00
ATOM 66 0C21 DPP 1 32.399 -4.159 33.723 1.00 0.00
ATOM 67 H10R DPP 1 31.439 -4.589 33.363 1.00 0.00
ATOM 68 H10S DPP 1 32.169 -3.189 34.203 1.00 0.00
ATOM 69 1C21 DPP 1 32.969 -5.059 34.813 1.00 0.00
ATOM 70 H11R DPP 1 33.799 -4.589 35.383 1.00 0.00
ATOM 71 H11S DPP 1 33.479 -5.889 34.273 1.00 0.00
ATOM 72 2C21 DPP 1 31.929 -5.689 35.753 1.00 0.00
ATOM 73 H12R DPP 1 31.059 -5.959 35.123 1.00 0.00
ATOM 74 H12S DPP 1 31.619 -4.939 36.523 1.00 0.00
ATOM 75 3C21 DPP 1 32.499 -6.909 36.483 1.00 0.00
ATOM 76 H13R DPP 1 33.449 -6.689 37.013 1.00 0.00
ATOM 77 H13S DPP 1 32.679 -7.779 35.823 1.00 0.00
ATOM 78 4C21 DPP 1 31.539 -7.429 37.543 1.00 0.00
ATOM 79 H14R DPP 1 31.699 -8.529 37.583 1.00 0.00
ATOM 80 H14S DPP 1 30.549 -7.079 37.193 1.00 0.00
ATOM 81 5C21 DPP 1 31.749 -6.909 38.973 1.00 0.00
ATOM 82 H15R DPP 1 31.209 -5.939 38.953 1.00 0.00
ATOM 83 H15S DPP 1 32.849 -6.819 39.083 1.00 0.00
ATOM 84 6C21 DPP 1 31.149 -7.689 40.143 1.00 0.00
ATOM 85 H16R DPP 1 30.189 -8.199 39.913 1.00 0.00
ATOM 86 H16S DPP 1 30.929 -7.109 41.073 1.00 0.00
ATOM 87 H16T DPP 1 31.929 -8.359 40.553 1.00 0.00
ATOM 88 C33 DPP 1 39.199 0.361 26.583 1.00 0.00
ATOM 89 H3X DPP 1 39.829 0.061 25.723 1.00 0.00
ATOM 90 H3Y DPP 1 38.139 0.181 26.313 1.00 0.00
ATOM 91 C34 DPP 1 39.589 -0.409 27.853 1.00 0.00
ATOM 92 H4X DPP 1 40.639 -0.209 28.133 1.00 0.00
ATOM 93 H4Y DPP 1 39.389 -1.469 27.593 1.00 0.00
ATOM 94 C35 DPP 1 38.679 -0.009 29.023 1.00 0.00
ATOM 95 H5X DPP 1 37.629 -0.269 28.773 1.00 0.00
ATOM 96 H5Y DPP 1 38.879 1.071 29.203 1.00 0.00
ATOM 97 C36 DPP 1 38.919 -0.829 30.293 1.00 0.00
ATOM 98 H6X DPP 1 38.659 -0.179 31.153 1.00 0.00
ATOM 99 H6Y DPP 1 40.019 -1.019 30.293 1.00 0.00
ATOM 100 C37 DPP 1 38.099 -2.089 30.563 1.00 0.00
ATOM 101 H7X DPP 1 38.339 -2.849 29.793 1.00 0.00
ATOM 102 H7Y DPP 1 37.029 -1.829 30.373 1.00 0.00
ATOM 103 C38 DPP 1 38.149 -2.579 32.003 1.00 0.00
ATOM 104 H8X DPP 1 37.899 -1.879 32.833 1.00 0.00
ATOM 105 H8Y DPP 1 39.199 -2.899 32.113 1.00 0.00
ATOM 106 C39 DPP 1 37.209 -3.769 32.213 1.00 0.00
ATOM 107 H9X DPP 1 37.639 -4.609 31.613 1.00 0.00
ATOM 108 H9Y DPP 1 36.139 -3.589 32.013 1.00 0.00
ATOM 109 0C31 DPP 1 37.349 -4.219 33.673 1.00 0.00
ATOM 110 H10X DPP 1 36.899 -3.439 34.323 1.00 0.00
ATOM 111 H10Y DPP 1 38.389 -4.299 34.043 1.00 0.00
ATOM 112 1C31 DPP 1 36.639 -5.559 33.913 1.00 0.00
ATOM 113 H11X DPP 1 37.129 -6.279 33.233 1.00 0.00
ATOM 114 H11Y DPP 1 35.589 -5.419 33.553 1.00 0.00
ATOM 115 2C31 DPP 1 36.829 -5.889 35.393 1.00 0.00
ATOM 116 H12X DPP 1 36.499 -5.049 36.033 1.00 0.00
ATOM 117 H12Y DPP 1 37.879 -6.239 35.543 1.00 0.00
ATOM 118 3C31 DPP 1 36.059 -7.139 35.823 1.00 0.00
ATOM 119 H13X DPP 1 36.399 -8.049 35.283 1.00 0.00
ATOM 120 H13Y DPP 1 34.979 -6.989 35.613 1.00 0.00
ATOM 121 4C31 DPP 1 36.179 -7.449 37.323 1.00 0.00
ATOM 122 H14X DPP 1 35.839 -6.479 37.733 1.00 0.00
ATOM 123 H14Y DPP 1 37.279 -7.539 37.453 1.00 0.00
ATOM 124 5C31 DPP 1 35.459 -8.669 37.893 1.00 0.00
ATOM 125 H15X DPP 1 35.619 -9.569 37.253 1.00 0.00
ATOM 126 H15Y DPP 1 34.409 -8.319 37.943 1.00 0.00
ATOM 127 6C31 DPP 1 35.929 -8.969 39.313 1.00 0.00
ATOM 128 H16X DPP 1 35.379 -9.899 39.593 1.00 0.00
ATOM 129 H16Y DPP 1 35.749 -8.029 39.873 1.00 0.00
ATOM 130 H16Z DPP 1 37.029 -9.049 39.433 1.00 0.00
END
doxil pdb:
HETATM 1 C LIG 1 15.226 18.450 4.896 1.00 0.00 C
HETATM 2 C LIG 1 16.429 19.161 4.909 1.00 0.00 C
HETATM 3 C LIG 1 17.654 18.469 4.880 1.00 0.00 C
HETATM 4 C LIG 1 17.677 17.063 4.829 1.00 0.00 C
HETATM 5 O LIG 1 18.898 16.388 4.808 1.00 0.00 O
HETATM 6 C LIG 1 16.456 16.353 4.816 1.00 0.00 C
HETATM 7 C LIG 1 16.409 14.946 4.803 1.00 0.00 C
HETATM 8 O LIG 1 17.561 14.211 4.771 1.00 0.00 O
HETATM 9 C LIG 1 15.196 14.209 4.817 1.00 0.00 C
HETATM 10 C LIG 1 15.164 12.808 4.784 1.00 0.00 C
HETATM 11 O LIG 1 16.295 12.032 4.788 1.00 0.00 O
HETATM 12 C LIG 1 13.929 12.131 4.758 1.00 0.00 C
HETATM 13 C LIG 1 13.995 10.639 4.786 1.00 0.00 C
HETATM 14 O LIG 1 14.592 10.397 6.123 1.00 0.00 O
HETATM 15 C LIG 1 12.711 9.868 4.523 1.00 0.00 C
HETATM 16 C LIG 1 11.569 10.600 5.359 1.00 0.00 C
HETATM 17 O LIG 1 11.611 10.753 6.835 1.00 0.00 O
HETATM 18 C LIG 1 10.269 9.864 5.071 1.00 0.00 C
HETATM 19 O LIG 1 9.543 10.187 3.954 1.00 0.00 O
HETATM 20 C LIG 1 9.825 8.804 6.033 1.00 0.00 C
HETATM 21 O LIG 1 8.617 8.191 5.670 1.00 0.00 O
HETATM 22 C LIG 1 11.432 12.065 4.766 1.00 0.00 C
HETATM 23 C LIG 1 12.729 12.807 4.799 1.00 0.00 C
HETATM 24 C LIG 1 12.761 14.224 4.827 1.00 0.00 C
HETATM 25 O LIG 1 11.570 14.889 4.797 1.00 0.00 O
HETATM 26 C LIG 1 13.985 14.924 4.822 1.00 0.00 C
HETATM 27 C LIG 1 14.007 16.349 4.853 1.00 0.00 C
HETATM 28 O LIG 1 12.853 16.988 4.878 1.00 0.00 O
HETATM 29 C LIG 1 15.244 17.040 4.865 1.00 0.00 C
HETATM 30 C LIG 1 20.164 17.131 4.894 1.00 0.00 C
HETATM 31 C LIG 1 15.508 9.325 6.325 1.00 0.00 C
HETATM 32 C LIG 1 16.662 9.744 7.308 1.00 0.00 C
HETATM 33 C LIG 1 15.986 9.896 8.700 1.00 0.00 C
HETATM 34 N LIG 1 17.069 10.218 9.702 1.00 0.00 N
HETATM 35 C LIG 1 15.236 8.613 9.132 1.00 0.00 C
HETATM 36 O LIG 1 16.324 7.597 9.201 1.00 0.00 O
HETATM 37 C LIG 1 14.150 8.254 8.082 1.00 0.00 C
HETATM 38 O LIG 1 14.828 8.116 6.752 1.00 0.00 O
HETATM 39 C LIG 1 13.470 6.895 8.316 1.00 0.00 C
END.
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10 years 10 months ago #1731
by Clement
Replied by Clement on topic transfer atomic pdb file to CG pdb.
The martinize.py script takes care of proteins... Exclusively. You'll have to write something to map your compounds by yourself. And probably parameterize this doxil molecule for the Martini forcefield beforehand. We have CG DPPC bilayer available to download on this website (
http://md.chem.rug.nl/cgmartini/index.php/downloads/example-applications/66-dppc-membrane
)
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10 years 10 months ago #1739
by msaeedi
Replied by msaeedi on topic transfer atomic pdb file to CG pdb.
Thanks for your help, but I couldn’t transfer doxil.pdb with martinize.py.
Doxil.pdb file is:
ATOM 1 C1 DM2 A 1 15.226 18.450 4.896 1.00 0.00 C
ATOM 2 C2 DM2 A 1 16.429 19.161 4.909 1.00 0.00 C
ATOM 3 C3 DM2 A 1 17.654 18.469 4.880 1.00 0.00 C
ATOM 4 C4 DM2 A 1 17.677 17.063 4.829 1.00 0.00 C
ATOM 5 O4 DM2 A 1 18.898 16.388 4.808 1.00 0.00 O
ATOM 6 C5 DM2 A 1 16.456 16.353 4.816 1.00 0.00 C
ATOM 7 C6 DM2 A 1 16.409 14.946 4.803 1.00 0.00 C
ATOM 8 O6 DM2 A 1 17.561 14.211 4.771 1.00 0.00 O
ATOM 9 C7 DM2 A 1 15.196 14.209 4.817 1.00 0.00 C
ATOM 10 C8 DM2 A 1 15.164 12.808 4.784 1.00 0.00 C
ATOM 11 O8 DM2 A 1 16.295 12.032 4.788 1.00 0.00 O
ATOM 12 C9 DM2 A 1 13.929 12.131 4.758 1.00 0.00 C
ATOM 13 C10 DM2 A 1 13.995 10.639 4.786 1.00 0.00 C
ATOM 14 O10 DM2 A 1 14.592 10.397 6.123 1.00 0.00 O
ATOM 15 C11 DM2 A 1 12.711 9.868 4.523 1.00 0.00 C
ATOM 16 C12 DM2 A 1 11.569 10.600 5.359 1.00 0.00 C
ATOM 17 O12 DM2 A 1 11.611 10.753 6.835 1.00 0.00 O
ATOM 18 C13 DM2 A 1 10.269 9.864 5.071 1.00 0.00 C
ATOM 19 O13 DM2 A 1 9.543 10.187 3.954 1.00 0.00 O
ATOM 20 C14 DM2 A 1 9.825 8.804 6.033 1.00 0.00 C
ATOM 21 O14 DM2 A 1 8.617 8.191 5.670 1.00 0.00 O
ATOM 22 C15 DM2 A 1 11.432 12.065 4.766 1.00 0.00 C
ATOM 23 C16 DM2 A 1 12.729 12.807 4.799 1.00 0.00 C
ATOM 24 C17 DM2 A 1 12.761 14.224 4.827 1.00 0.00 C
ATOM 25 O17 DM2 A 1 11.570 14.889 4.797 1.00 0.00 O
ATOM 26 C18 DM2 A 1 13.985 14.924 4.822 1.00 0.00 C
ATOM 27 C19 DM2 A 1 14.007 16.349 4.853 1.00 0.00 C
ATOM 28 O19 DM2 A 1 12.853 16.988 4.878 1.00 0.00 O
ATOM 29 C20 DM2 A 1 15.244 17.040 4.865 1.00 0.00 C
ATOM 30 C21 DM2 A 1 20.164 17.131 4.894 1.00 0.00 C
ATOM 31 C1' DM2 A 1 15.508 9.325 6.325 1.00 0.00 C
ATOM 32 C2' DM2 A 1 16.662 9.744 7.308 1.00 0.00 C
ATOM 33 C3' DM2 A 1 15.986 9.896 8.700 1.00 0.00 C
ATOM 34 N3' DM2 A 1 17.069 10.218 9.702 1.00 0.00 N
ATOM 35 C4' DM2 A 1 15.236 8.613 9.132 1.00 0.00 C
ATOM 36 O4' DM2 A 1 16.324 7.597 9.201 1.00 0.00 O
ATOM 37 C5' DM2 A 1 14.150 8.254 8.082 1.00 0.00 C
ATOM 38 O5' DM2 A 1 14.828 8.116 6.752 1.00 0.00 O
ATOM 39 C6' DM2 A 1 13.470 6.895 8.316 1.00 0.00 C
END
When I enter
./martinize.py -f doxil.pdb -o system.top -x cg_doxil.pdb
The process is complete but the cg_doxil.pdb file is:
MODEL 1
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ENDMDL
What can I do? Is it possible for you to transfer this file for me?
Doxil.pdb file is:
ATOM 1 C1 DM2 A 1 15.226 18.450 4.896 1.00 0.00 C
ATOM 2 C2 DM2 A 1 16.429 19.161 4.909 1.00 0.00 C
ATOM 3 C3 DM2 A 1 17.654 18.469 4.880 1.00 0.00 C
ATOM 4 C4 DM2 A 1 17.677 17.063 4.829 1.00 0.00 C
ATOM 5 O4 DM2 A 1 18.898 16.388 4.808 1.00 0.00 O
ATOM 6 C5 DM2 A 1 16.456 16.353 4.816 1.00 0.00 C
ATOM 7 C6 DM2 A 1 16.409 14.946 4.803 1.00 0.00 C
ATOM 8 O6 DM2 A 1 17.561 14.211 4.771 1.00 0.00 O
ATOM 9 C7 DM2 A 1 15.196 14.209 4.817 1.00 0.00 C
ATOM 10 C8 DM2 A 1 15.164 12.808 4.784 1.00 0.00 C
ATOM 11 O8 DM2 A 1 16.295 12.032 4.788 1.00 0.00 O
ATOM 12 C9 DM2 A 1 13.929 12.131 4.758 1.00 0.00 C
ATOM 13 C10 DM2 A 1 13.995 10.639 4.786 1.00 0.00 C
ATOM 14 O10 DM2 A 1 14.592 10.397 6.123 1.00 0.00 O
ATOM 15 C11 DM2 A 1 12.711 9.868 4.523 1.00 0.00 C
ATOM 16 C12 DM2 A 1 11.569 10.600 5.359 1.00 0.00 C
ATOM 17 O12 DM2 A 1 11.611 10.753 6.835 1.00 0.00 O
ATOM 18 C13 DM2 A 1 10.269 9.864 5.071 1.00 0.00 C
ATOM 19 O13 DM2 A 1 9.543 10.187 3.954 1.00 0.00 O
ATOM 20 C14 DM2 A 1 9.825 8.804 6.033 1.00 0.00 C
ATOM 21 O14 DM2 A 1 8.617 8.191 5.670 1.00 0.00 O
ATOM 22 C15 DM2 A 1 11.432 12.065 4.766 1.00 0.00 C
ATOM 23 C16 DM2 A 1 12.729 12.807 4.799 1.00 0.00 C
ATOM 24 C17 DM2 A 1 12.761 14.224 4.827 1.00 0.00 C
ATOM 25 O17 DM2 A 1 11.570 14.889 4.797 1.00 0.00 O
ATOM 26 C18 DM2 A 1 13.985 14.924 4.822 1.00 0.00 C
ATOM 27 C19 DM2 A 1 14.007 16.349 4.853 1.00 0.00 C
ATOM 28 O19 DM2 A 1 12.853 16.988 4.878 1.00 0.00 O
ATOM 29 C20 DM2 A 1 15.244 17.040 4.865 1.00 0.00 C
ATOM 30 C21 DM2 A 1 20.164 17.131 4.894 1.00 0.00 C
ATOM 31 C1' DM2 A 1 15.508 9.325 6.325 1.00 0.00 C
ATOM 32 C2' DM2 A 1 16.662 9.744 7.308 1.00 0.00 C
ATOM 33 C3' DM2 A 1 15.986 9.896 8.700 1.00 0.00 C
ATOM 34 N3' DM2 A 1 17.069 10.218 9.702 1.00 0.00 N
ATOM 35 C4' DM2 A 1 15.236 8.613 9.132 1.00 0.00 C
ATOM 36 O4' DM2 A 1 16.324 7.597 9.201 1.00 0.00 O
ATOM 37 C5' DM2 A 1 14.150 8.254 8.082 1.00 0.00 C
ATOM 38 O5' DM2 A 1 14.828 8.116 6.752 1.00 0.00 O
ATOM 39 C6' DM2 A 1 13.470 6.895 8.316 1.00 0.00 C
END
When I enter
./martinize.py -f doxil.pdb -o system.top -x cg_doxil.pdb
The process is complete but the cg_doxil.pdb file is:
MODEL 1
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ENDMDL
What can I do? Is it possible for you to transfer this file for me?
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10 years 10 months ago #1740
by djurre
as clement said, the script does proteins only. Check our flowchart to see what to do with other molecules:
http://md.chem.rug.nl/cgmartini/index.php/tutorial/flowchartfile
Replied by djurre on topic transfer atomic pdb file to CG pdb.
Clement wrote: The martinize.py script takes care of proteins... Exclusively.
as clement said, the script does proteins only. Check our flowchart to see what to do with other molecules:
http://md.chem.rug.nl/cgmartini/index.php/tutorial/flowchartfile
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10 years 10 months ago #1741
by Clement
Replied by Clement on topic transfer atomic pdb file to CG pdb.
And check this HowTo carefully:
http://md.chem.rug.nl/cgmartini/index.php/user-platform/faq#create topos
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10 years 10 months ago #1772
by msaeedi
Replied by msaeedi on topic transfer atomic pdb file to CG pdb.
Thanks for your reply..
I followed "How do I create a topology for a new molecule?" to make doxil topology.
after i mapped this molecule to cg beads, i didnt know how I can find bonded interaction parameters?
can you help me to keep step 2 and 3 for making topology?
I followed "How do I create a topology for a new molecule?" to make doxil topology.
after i mapped this molecule to cg beads, i didnt know how I can find bonded interaction parameters?
can you help me to keep step 2 and 3 for making topology?
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10 years 10 months ago #1773
by Clement
Replied by Clement on topic transfer atomic pdb file to CG pdb.
I deleted your other post since the discussion started here.
The answer of your question is yes, we can help.
But to help we need more details in what you tried and what didn't work. The best way of learning how to write topology is by trial and error... You won't understand completely what you're playing with until you'll do it by yourself.
You mapped your molecule, that's the first step. You know which beads should be bonded together; check other itp files and topologies (DPPC for instance, since you're working with it) to understand how to write from scratch this part of the topology. If you try to simulate this first test topology, you'll see where your molecule falls apart; this will define what angles/dihedrals you need to explicitly define in your topology to keep its geometry.
The answer of your question is yes, we can help.
But to help we need more details in what you tried and what didn't work. The best way of learning how to write topology is by trial and error... You won't understand completely what you're playing with until you'll do it by yourself.
You mapped your molecule, that's the first step. You know which beads should be bonded together; check other itp files and topologies (DPPC for instance, since you're working with it) to understand how to write from scratch this part of the topology. If you try to simulate this first test topology, you'll see where your molecule falls apart; this will define what angles/dihedrals you need to explicitly define in your topology to keep its geometry.
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10 years 10 months ago #1779
by msaeedi
Replied by msaeedi on topic transfer atomic pdb file to CG pdb.
Thanks for your reply.
I want to simulate a drug in course grained model. The all atom structure of this molecule is:
ATOM 1 C1 DM2 A 0 15.226 18.450 4.896 1.00 0.00
ATOM 2 C2 DM2 A 0 16.429 19.161 4.909 1.00 0.00
ATOM 3 C3 DM2 A 0 17.654 18.469 4.880 1.00 0.00
ATOM 4 C4 DM2 A 0 17.677 17.063 4.829 1.00 0.00
ATOM 5 O4 DM2 A 0 18.898 16.388 4.808 1.00 0.00
ATOM 6 C5 DM2 A 0 16.456 16.353 4.816 1.00 0.00
ATOM 7 C6 DM2 A 0 16.409 14.946 4.803 1.00 0.00
ATOM 8 O6 DM2 A 0 17.561 14.211 4.771 1.00 0.00
ATOM 9 C7 DM2 A 0 15.196 14.209 4.817 1.00 0.00
ATOM 10 C8 DM2 A 0 15.164 12.808 4.784 1.00 0.00
ATOM 11 O8 DM2 A 0 16.295 12.032 4.788 1.00 0.00
ATOM 12 C9 DM2 A 0 13.929 12.131 4.758 1.00 0.00
ATOM 13 C10 DM2 A 0 13.995 10.639 4.786 1.00 0.00
ATOM 14 O10 DM2 A 0 14.592 10.397 6.123 1.00 0.00
ATOM 15 C11 DM2 A 0 12.711 9.868 4.523 1.00 0.00
ATOM 16 C12 DM2 A 0 11.569 10.600 5.359 1.00 0.00
ATOM 17 O12 DM2 A 0 11.611 10.753 6.835 1.00 0.00
ATOM 18 C13 DM2 A 0 10.269 9.864 5.071 1.00 0.00
ATOM 19 O13 DM2 A 0 9.543 10.187 3.954 1.00 0.00
ATOM 20 C14 DM2 A 0 9.825 8.804 6.033 1.00 0.00
ATOM 21 O14 DM2 A 0 8.617 8.191 5.670 1.00 0.00
ATOM 22 C15 DM2 A 0 11.432 12.065 4.766 1.00 0.00
ATOM 23 C16 DM2 A 0 12.729 12.807 4.799 1.00 0.00
ATOM 24 C17 DM2 A 0 12.761 14.224 4.827 1.00 0.00
ATOM 25 O17 DM2 A 0 11.570 14.889 4.797 1.00 0.00
ATOM 26 C18 DM2 A 0 13.985 14.924 4.822 1.00 0.00
ATOM 27 C19 DM2 A 0 14.007 16.349 4.853 1.00 0.00
ATOM 28 O19 DM2 A 0 12.853 16.988 4.878 1.00 0.00
ATOM 29 C20 DM2 A 0 15.244 17.040 4.865 1.00 0.00
ATOM 30 C21 DM2 A 0 20.164 17.131 4.894 1.00 0.00
ATOM 31 C1' DM2 A 0 15.508 9.325 6.325 1.00 0.00
ATOM 32 C2' DM2 A 0 16.662 9.744 7.308 1.00 0.00
ATOM 33 C3' DM2 A 0 15.986 9.896 8.700 1.00 0.00
ATOM 34 N3' DM2 A 0 17.069 10.218 9.702 1.00 0.00
ATOM 35 C4' DM2 A 0 15.236 8.613 9.132 1.00 0.00
ATOM 36 O4' DM2 A 0 16.324 7.597 9.201 1.00 0.00
ATOM 37 C5' DM2 A 0 14.150 8.254 8.082 1.00 0.00
ATOM 38 O5' DM2 A 0 14.828 8.116 6.752 1.00 0.00
ATOM 39 C6' DM2 A 0 13.470 6.895 8.316 1.00 0.00
TER
I try to map this molecule to cg beads. I guess the cg structure of this molecule and bond parameters are:
;;;;;
;;;;; Doxorubicin
;;;;;
[ moleculetype ]
; molname nrexcl
DOX 1
[ atoms ]
1 P1 1 DOX OC1OH 1 0 72.0000
2 P1 1 DOX C2OH 2 0 72.0000
3 Na 1 DOX C3OO 4 0 72.0000
4 P1 1 DOX C4OH 3 0 72.0000
5 Nd 1 DOX C5NH2 5 0 72.0000
6 SP4 1 DOX R1OH 6 0 45.0000
7 SP4 1 DOX R2OH 7 0 45.0000
8 Na 1 DOX C6O 8 0 72.0000
9 Na 1 DOX C7O 9 0 72.0000
10 SC4 1 DOX R3 10 0 45.0000
11 SC4 1 DOX R4 11 0 45.0000
12 SP5 1 DOX R5O 12 0 45.0000
[ bonds ]
1 2 1 0.3 30000
2 3 1 0.42 30000
3 4 1 0.42 30000
4 5 1 0.42 30000
3 5 1 0.37 12500
2 6 1 0.3 35000
3 7 1 0.32 35000
6 8 1 0.3 30000
7 9 1 0.3 30000
8 10 1 0.3 30000
10 11 1 0.270 50000
11 12 1 0.270 50000
but I don’t know about angle,dihedral and constrain parameters.
After that I don’t know continue with this topology? I must covert this to .gro file and have a simulation with this?
If it is possible for you, help me to follow these steps?
I want to simulate a drug in course grained model. The all atom structure of this molecule is:
ATOM 1 C1 DM2 A 0 15.226 18.450 4.896 1.00 0.00
ATOM 2 C2 DM2 A 0 16.429 19.161 4.909 1.00 0.00
ATOM 3 C3 DM2 A 0 17.654 18.469 4.880 1.00 0.00
ATOM 4 C4 DM2 A 0 17.677 17.063 4.829 1.00 0.00
ATOM 5 O4 DM2 A 0 18.898 16.388 4.808 1.00 0.00
ATOM 6 C5 DM2 A 0 16.456 16.353 4.816 1.00 0.00
ATOM 7 C6 DM2 A 0 16.409 14.946 4.803 1.00 0.00
ATOM 8 O6 DM2 A 0 17.561 14.211 4.771 1.00 0.00
ATOM 9 C7 DM2 A 0 15.196 14.209 4.817 1.00 0.00
ATOM 10 C8 DM2 A 0 15.164 12.808 4.784 1.00 0.00
ATOM 11 O8 DM2 A 0 16.295 12.032 4.788 1.00 0.00
ATOM 12 C9 DM2 A 0 13.929 12.131 4.758 1.00 0.00
ATOM 13 C10 DM2 A 0 13.995 10.639 4.786 1.00 0.00
ATOM 14 O10 DM2 A 0 14.592 10.397 6.123 1.00 0.00
ATOM 15 C11 DM2 A 0 12.711 9.868 4.523 1.00 0.00
ATOM 16 C12 DM2 A 0 11.569 10.600 5.359 1.00 0.00
ATOM 17 O12 DM2 A 0 11.611 10.753 6.835 1.00 0.00
ATOM 18 C13 DM2 A 0 10.269 9.864 5.071 1.00 0.00
ATOM 19 O13 DM2 A 0 9.543 10.187 3.954 1.00 0.00
ATOM 20 C14 DM2 A 0 9.825 8.804 6.033 1.00 0.00
ATOM 21 O14 DM2 A 0 8.617 8.191 5.670 1.00 0.00
ATOM 22 C15 DM2 A 0 11.432 12.065 4.766 1.00 0.00
ATOM 23 C16 DM2 A 0 12.729 12.807 4.799 1.00 0.00
ATOM 24 C17 DM2 A 0 12.761 14.224 4.827 1.00 0.00
ATOM 25 O17 DM2 A 0 11.570 14.889 4.797 1.00 0.00
ATOM 26 C18 DM2 A 0 13.985 14.924 4.822 1.00 0.00
ATOM 27 C19 DM2 A 0 14.007 16.349 4.853 1.00 0.00
ATOM 28 O19 DM2 A 0 12.853 16.988 4.878 1.00 0.00
ATOM 29 C20 DM2 A 0 15.244 17.040 4.865 1.00 0.00
ATOM 30 C21 DM2 A 0 20.164 17.131 4.894 1.00 0.00
ATOM 31 C1' DM2 A 0 15.508 9.325 6.325 1.00 0.00
ATOM 32 C2' DM2 A 0 16.662 9.744 7.308 1.00 0.00
ATOM 33 C3' DM2 A 0 15.986 9.896 8.700 1.00 0.00
ATOM 34 N3' DM2 A 0 17.069 10.218 9.702 1.00 0.00
ATOM 35 C4' DM2 A 0 15.236 8.613 9.132 1.00 0.00
ATOM 36 O4' DM2 A 0 16.324 7.597 9.201 1.00 0.00
ATOM 37 C5' DM2 A 0 14.150 8.254 8.082 1.00 0.00
ATOM 38 O5' DM2 A 0 14.828 8.116 6.752 1.00 0.00
ATOM 39 C6' DM2 A 0 13.470 6.895 8.316 1.00 0.00
TER
I try to map this molecule to cg beads. I guess the cg structure of this molecule and bond parameters are:
;;;;;
;;;;; Doxorubicin
;;;;;
[ moleculetype ]
; molname nrexcl
DOX 1
[ atoms ]
1 P1 1 DOX OC1OH 1 0 72.0000
2 P1 1 DOX C2OH 2 0 72.0000
3 Na 1 DOX C3OO 4 0 72.0000
4 P1 1 DOX C4OH 3 0 72.0000
5 Nd 1 DOX C5NH2 5 0 72.0000
6 SP4 1 DOX R1OH 6 0 45.0000
7 SP4 1 DOX R2OH 7 0 45.0000
8 Na 1 DOX C6O 8 0 72.0000
9 Na 1 DOX C7O 9 0 72.0000
10 SC4 1 DOX R3 10 0 45.0000
11 SC4 1 DOX R4 11 0 45.0000
12 SP5 1 DOX R5O 12 0 45.0000
[ bonds ]
1 2 1 0.3 30000
2 3 1 0.42 30000
3 4 1 0.42 30000
4 5 1 0.42 30000
3 5 1 0.37 12500
2 6 1 0.3 35000
3 7 1 0.32 35000
6 8 1 0.3 30000
7 9 1 0.3 30000
8 10 1 0.3 30000
10 11 1 0.270 50000
11 12 1 0.270 50000
but I don’t know about angle,dihedral and constrain parameters.
After that I don’t know continue with this topology? I must covert this to .gro file and have a simulation with this?
If it is possible for you, help me to follow these steps?
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10 years 9 months ago #1780
by djurre
Replied by djurre on topic transfer atomic pdb file to CG pdb.
What you have is a very good start! What you would normally do next is a simulation with a atomistic model of the molecule (if it excists), map it to CG and measure the angles etc in this mapped simulation.
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10 years 9 months ago #1781
by msaeedi
Replied by msaeedi on topic transfer atomic pdb file to CG pdb.
Thanks for your help.
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