GROMACS version:2021
GROMACS modification: Yes/No
Here post your question Hello everyone, I’m trying to get the topology for a crystal “(PEA)2PbBr4”(please find the pdb below). I’ve tried different automated tools but I’ve always got an error.
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 Pb1 X 0 11.040 4.418 7.947 0.00 0.00 PB
ATOM 2 Pb1A X 0 11.036 4.420 8.355 0.00 0.00 PB
ATOM 3 Pb2 X 0 5.280 4.233 7.946 0.00 0.00 PB
ATOM 4 Pb2A X 0 5.261 4.184 8.358 0.00 0.00 PB
ATOM 5 C1 X 0 7.715 1.412 5.076 0.00 0.00 C
ATOM 6 N1 X 0 9.057 1.531 5.671 0.00 0.00 N
ATOM 7 C2 X 0 7.752 0.954 3.664 0.00 0.00 C
ATOM 8 C3 X 0 8.465 1.926 2.712 0.00 0.00 C
ATOM 9 C4 X 0 7.837 3.064 2.264 0.00 0.00 C
ATOM 10 C5 X 0 8.502 3.964 1.457 0.00 0.00 C
ATOM 11 C6 X 0 9.825 3.764 1.137 0.00 0.00 C
ATOM 12 C7 X 0 10.476 2.645 1.593 0.00 0.00 C
ATOM 13 C8 X 0 9.794 1.724 2.384 0.00 0.00 C
ATOM 14 H4 X 0 6.935 3.231 2.513 0.00 0.00 H
ATOM 15 H5 X 0 8.045 4.727 1.124 0.00 0.00 H
ATOM 16 H6 X 0 10.286 4.397 0.600 0.00 0.00 H
ATOM 17 H7 X 0 11.387 2.499 1.369 0.00 0.00 H
ATOM 18 H8 X 0 10.244 0.950 2.700 0.00 0.00 H
ATOM 19 H1A X 0 9.485 2.250 5.311 0.00 0.00 H
ATOM 20 H1B X 0 9.534 0.776 5.496 0.00 0.00 H
ATOM 21 H1C X 0 8.982 1.641 6.571 0.00 0.00 H
ATOM 22 H1D X 0 7.263 2.292 5.118 0.00 0.00 H
ATOM 23 H1E X 0 7.181 0.771 5.608 0.00 0.00 H
ATOM 24 H2A X 0 6.824 0.823 3.349 0.00 0.00 H
ATOM 25 H2B X 0 8.210 0.078 3.627 0.00 0.00 H
ATOM 26 C1A X 0 1.973 7.221 5.095 0.00 0.00 C
ATOM 27 N1A X 0 3.305 7.103 5.687 0.00 0.00 N
ATOM 28 C2A X 0 1.976 7.684 3.668 0.00 0.00 C
ATOM 29 C3A X 0 2.715 6.718 2.732 0.00 0.00 C
ATOM 30 C4A X 0 4.037 6.944 2.374 0.00 0.00 C
ATOM 31 C5A X 0 4.715 6.047 1.578 0.00 0.00 C
ATOM 32 C6A X 0 4.082 4.902 1.135 0.00 0.00 C
ATOM 33 C7A X 0 2.770 4.680 1.475 0.00 0.00 C
ATOM 34 C8A X 0 2.081 5.575 2.261 0.00 0.00 C
ATOM 35 H4A X 0 4.480 7.726 2.681 0.00 0.00 H
ATOM 36 H6A X 0 4.550 4.272 0.598 0.00 0.00 H
ATOM 37 H7A X 0 2.333 3.897 1.165 0.00 0.00 H
ATOM 38 H8A X 0 1.171 5.413 2.482 0.00 0.00 H
ATOM 39 H1AA X 0 3.782 6.470 5.238 0.00 0.00 H
ATOM 40 H1AB X 0 3.230 6.861 6.561 0.00 0.00 H
ATOM 41 H1AC X 0 3.736 7.903 5.630 0.00 0.00 H
ATOM 42 H1AD X 0 1.441 7.858 5.635 0.00 0.00 H
ATOM 43 H1AE X 0 1.525 6.340 5.143 0.00 0.00 H
ATOM 44 H2AA X 0 2.407 8.574 3.619 0.00 0.00 H
ATOM 45 H2AB X 0 1.041 7.781 3.359 0.00 0.00 H
ATOM 46 H5AA X 0 5.618 6.215 1.336 0.00 0.00 H
ATOM 47 C1B X 0 13.810 1.162 11.206 0.00 0.00 C
ATOM 48 N1B X 0 13.873 2.527 10.666 0.00 0.00 N
ATOM 49 C2B X 0 14.337 1.085 12.635 0.00 0.00 C
ATOM 50 C3B X 0 13.633 2.004 13.602 0.00 0.00 C
ATOM 51 C4B X 0 14.245 3.150 14.094 0.00 0.00 C
ATOM 52 C5B X 0 13.567 4.001 14.921 0.00 0.00 C
ATOM 53 C6B X 0 12.255 3.775 15.246 0.00 0.00 C
ATOM 54 C7B X 0 11.640 2.646 14.782 0.00 0.00 C
ATOM 55 C8B X 0 12.293 1.773 13.953 0.00 0.00 C
ATOM 56 H3A X 0 13.794 2.499 9.760 0.00 0.00 H
ATOM 57 H4B X 0 15.143 3.345 13.854 0.00 0.00 H
ATOM 58 H5B X 0 14.012 4.763 15.277 0.00 0.00 H
ATOM 59 H6B X 0 11.780 4.394 15.788 0.00 0.00 H
ATOM 60 H7B X 0 10.744 2.465 15.038 0.00 0.00 H
ATOM 61 H8B X 0 11.841 1.008 13.617 0.00 0.00 H
ATOM 62 H1BA X 0 14.671 2.905 10.889 0.00 0.00 H
ATOM 63 H1BB X 0 13.195 3.023 11.016 0.00 0.00 H
ATOM 64 H1BC X 0 14.342 0.559 10.629 0.00 0.00 H
ATOM 65 H1BD X 0 12.871 0.849 11.188 0.00 0.00 H
ATOM 66 H2BA X 0 14.244 0.153 12.957 0.00 0.00 H
ATOM 67 H2BB X 0 15.301 1.306 12.630 0.00 0.00 H
ATOM 68 C1C X 0 8.039 7.478 11.217 0.00 0.00 C
ATOM 69 N1C X 0 8.100 6.121 10.653 0.00 0.00 N
ATOM 70 C2C X 0 8.600 7.564 12.642 0.00 0.00 C
ATOM 71 C3C X 0 7.867 6.644 13.594 0.00 0.00 C
ATOM 72 C4C X 0 6.544 6.925 13.960 0.00 0.00 C
ATOM 73 C5C X 0 5.859 6.048 14.791 0.00 0.00 C
ATOM 74 C6C X 0 6.453 4.903 15.272 0.00 0.00 C
ATOM 75 C7C X 0 7.785 4.662 14.909 0.00 0.00 C
ATOM 76 C8C X 0 8.462 5.502 14.086 0.00 0.00 C
ATOM 77 H4C X 0 6.117 7.712 13.641 0.00 0.00 H
ATOM 78 H5A X 0 7.992 6.164 9.752 0.00 0.00 H
ATOM 79 H5C X 0 4.962 6.243 15.035 0.00 0.00 H
ATOM 80 H6C X 0 5.977 4.299 15.829 0.00 0.00 H
ATOM 81 H7C X 0 8.224 3.891 15.249 0.00 0.00 H
ATOM 82 H8C X 0 9.358 5.299 13.846 0.00 0.00 H
ATOM 83 H1CA X 0 7.436 5.613 11.014 0.00 0.00 H
ATOM 84 H1CB X 0 8.907 5.748 10.846 0.00 0.00 H
ATOM 85 H1CC X 0 7.097 7.782 11.223 0.00 0.00 H
ATOM 86 H1CD X 0 8.550 8.091 10.632 0.00 0.00 H
ATOM 87 H2CA X 0 9.560 7.324 12.630 0.00 0.00 H
ATOM 88 H2CB X 0 8.524 8.496 12.967 0.00 0.00 H
ATOM 89 Br1 X 0 10.969 4.291 5.114 0.00 0.00 BR
ATOM 90 Br2 X 0 11.128 4.500 11.165 0.00 0.00 BR
ATOM 91 Br3 X 0 13.933 5.065 8.202 0.00 0.00 BR
ATOM 92 Br3A X 0 13.892 3.575 8.149 0.00 0.00 BR
ATOM 93 Br4 X 0 11.788 1.541 8.138 0.00 0.00 BR
ATOM 94 Br4A X 0 10.286 1.538 8.211 0.00 0.00 BR
ATOM 95 Br5 X 0 8.172 3.581 8.202 0.00 0.00 BR
ATOM 96 Br5A X 0 8.138 5.068 8.134 0.00 0.00 BR
ATOM 97 Br6 X 0 5.206 4.354 5.111 0.00 0.00 BR
ATOM 98 Br7 X 0 5.366 4.146 11.168 0.00 0.00 BR
ATOM 99 Br8 X 0 6.025 7.103 8.138 0.00 0.00 BR
ATOM 100 Br8A X 0 4.523 7.105 8.203 0.00 0.00 BR
END