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add extra integration test to make sure new defaults are applied
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| ### DETAILS: | ||
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| # Ubiquitin 1UBQ | ||
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| ### testing 'new' defaults after -scfix and -ef behaviour changed | ||
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| ### TEST: | ||
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| # -ff martini 3001 | ||
| # no -scfix | ||
| # |
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vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb
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vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,263 @@ | ||
| ATOM 1 BB MET A 1 27.168 25.742 3.357 1.00 0.00 | ||
| ATOM 2 SC1 MET A 1 24.481 24.285 5.673 1.00 0.00 | ||
| ATOM 3 BB GLN A 2 25.962 28.749 4.446 1.00 0.00 | ||
| ATOM 4 SC1 GLN A 2 26.776 32.120 2.397 1.00 0.00 | ||
| ATOM 5 BB ILE A 3 27.033 30.748 7.177 1.00 0.00 | ||
| ATOM 6 SC1 ILE A 3 26.903 28.414 9.087 1.00 0.00 | ||
| ATOM 7 BB PHE A 4 26.587 32.877 10.061 1.00 0.00 | ||
| ATOM 8 SC1 PHE A 4 25.404 34.579 7.877 1.00 0.00 | ||
| ATOM 9 SC2 PHE A 4 24.102 34.183 5.906 1.00 0.00 | ||
| ATOM 10 SC3 PHE A 4 25.636 35.236 5.594 1.00 0.00 | ||
| ATOM 11 BB VAL A 5 28.795 34.925 12.172 1.00 0.00 | ||
| ATOM 12 SC1 VAL A 5 30.044 32.850 13.157 1.00 0.00 | ||
| ATOM 13 BB LYS A 6 28.034 36.809 14.994 1.00 0.00 | ||
| ATOM 14 SC1 LYS A 6 25.484 38.706 14.521 1.00 0.00 | ||
| ATOM 15 SC2 LYS A 6 23.063 40.721 14.834 1.00 0.00 | ||
| ATOM 16 BB THR A 7 29.486 39.423 16.577 1.00 0.00 | ||
| ATOM 17 SC1 THR A 7 31.896 39.157 15.771 1.00 0.00 | ||
| ATOM 18 BB LEU A 8 29.841 41.902 19.151 1.00 0.00 | ||
| ATOM 19 SC1 LEU A 8 29.027 40.021 21.711 1.00 0.00 | ||
| ATOM 20 BB THR A 9 31.098 44.070 16.796 1.00 0.00 | ||
| ATOM 21 SC1 THR A 9 33.260 43.398 17.341 1.00 0.00 | ||
| ATOM 22 BB GLY A 10 29.381 43.791 14.001 1.00 0.00 | ||
| ATOM 23 BB LYS A 11 30.588 41.272 12.826 1.00 0.00 | ||
| ATOM 24 SC1 LYS A 11 33.571 41.201 11.734 1.00 0.00 | ||
| ATOM 25 SC2 LYS A 11 35.337 40.430 9.627 1.00 0.00 | ||
| ATOM 26 BB THR A 12 30.302 39.143 9.931 1.00 0.00 | ||
| ATOM 27 SC1 THR A 12 27.622 38.894 10.317 1.00 0.00 | ||
| ATOM 28 BB ILE A 13 30.808 35.743 9.215 1.00 0.00 | ||
| ATOM 29 SC1 ILE A 13 33.486 35.168 10.482 1.00 0.00 | ||
| ATOM 30 BB THR A 14 31.524 33.585 6.560 1.00 0.00 | ||
| ATOM 31 SC1 THR A 14 30.429 34.850 4.854 1.00 0.00 | ||
| ATOM 32 BB LEU A 15 30.772 30.109 6.105 1.00 0.00 | ||
| ATOM 33 SC1 LEU A 15 32.488 29.742 9.143 1.00 0.00 | ||
| ATOM 34 BB GLU A 16 31.830 26.882 5.026 1.00 0.00 | ||
| ATOM 35 SC1 GLU A 16 31.729 28.107 0.924 1.00 0.00 | ||
| ATOM 36 BB VAL A 17 29.533 24.119 5.426 1.00 0.00 | ||
| ATOM 37 SC1 VAL A 17 29.747 25.074 7.920 1.00 0.00 | ||
| ATOM 38 BB GLU A 18 28.555 21.077 7.047 1.00 0.00 | ||
| ATOM 39 SC1 GLU A 18 28.860 20.012 3.364 1.00 0.00 | ||
| ATOM 40 BB PRO A 19 26.326 19.303 8.931 1.00 0.00 | ||
| ATOM 41 SC1 PRO A 19 24.827 19.858 6.910 1.00 0.00 | ||
| ATOM 42 BB SER A 20 28.698 17.128 9.627 1.00 0.00 | ||
| ATOM 43 SC1 SER A 20 28.765 16.177 7.488 1.00 0.00 | ||
| ATOM 44 BB ASP A 21 29.994 19.105 11.258 1.00 0.00 | ||
| ATOM 45 SC1 ASP A 21 31.897 20.425 8.722 1.00 0.00 | ||
| ATOM 46 BB THR A 22 31.696 20.027 13.870 1.00 0.00 | ||
| ATOM 47 SC1 THR A 22 32.964 17.964 14.694 1.00 0.00 | ||
| ATOM 48 BB ILE A 23 32.150 22.357 16.298 1.00 0.00 | ||
| ATOM 49 SC1 ILE A 23 29.691 22.748 17.483 1.00 0.00 | ||
| ATOM 50 BB GLU A 24 35.221 22.167 16.349 1.00 0.00 | ||
| ATOM 51 SC1 GLU A 24 37.212 19.122 18.014 1.00 0.00 | ||
| ATOM 52 BB ASN A 25 35.536 22.822 13.283 1.00 0.00 | ||
| ATOM 53 SC1 ASN A 25 35.563 21.422 10.874 1.00 0.00 | ||
| ATOM 54 BB VAL A 26 34.258 25.560 13.239 1.00 0.00 | ||
| ATOM 55 SC1 VAL A 26 31.632 25.476 13.061 1.00 0.00 | ||
| ATOM 56 BB LYS A 27 36.267 26.867 15.221 1.00 0.00 | ||
| ATOM 57 SC1 LYS A 27 34.856 26.242 18.143 1.00 0.00 | ||
| ATOM 58 SC2 LYS A 27 33.340 26.095 20.889 1.00 0.00 | ||
| ATOM 59 BB ALA A 28 38.713 26.410 13.302 1.00 0.00 | ||
| ATOM 60 SC1 ALA A 28 39.285 24.336 13.566 1.00 0.00 | ||
| ATOM 61 BB LYS A 29 37.669 28.208 10.979 1.00 0.00 | ||
| ATOM 62 SC1 LYS A 29 35.701 25.986 9.407 1.00 0.00 | ||
| ATOM 63 SC2 LYS A 29 34.858 24.630 7.053 1.00 0.00 | ||
| ATOM 64 BB ILE A 30 37.604 30.767 12.684 1.00 0.00 | ||
| ATOM 65 SC1 ILE A 30 34.773 31.012 14.047 1.00 0.00 | ||
| ATOM 66 BB GLN A 31 40.554 30.857 13.305 1.00 0.00 | ||
| ATOM 67 SC1 GLN A 31 42.686 28.923 15.862 1.00 0.00 | ||
| ATOM 68 BB ASP A 32 41.622 30.874 10.453 1.00 0.00 | ||
| ATOM 69 SC1 ASP A 32 42.604 28.593 8.949 1.00 0.00 | ||
| ATOM 70 BB LYS A 33 40.000 33.645 9.631 1.00 0.00 | ||
| ATOM 71 SC1 LYS A 33 37.395 33.079 8.328 1.00 0.00 | ||
| ATOM 72 SC2 LYS A 33 36.024 33.483 5.945 1.00 0.00 | ||
| ATOM 73 BB GLU A 34 40.230 35.519 12.664 1.00 0.00 | ||
| ATOM 74 SC1 GLU A 34 37.378 37.071 11.301 1.00 0.00 | ||
| ATOM 75 BB GLY A 35 42.134 34.179 15.169 1.00 0.00 | ||
| ATOM 76 BB ILE A 36 40.297 32.743 17.186 1.00 0.00 | ||
| ATOM 77 SC1 ILE A 36 38.067 34.832 17.587 1.00 0.00 | ||
| ATOM 78 BB PRO A 37 40.452 30.909 19.795 1.00 0.00 | ||
| ATOM 79 SC1 PRO A 37 42.307 32.248 20.426 1.00 0.00 | ||
| ATOM 80 BB PRO A 38 38.576 28.222 20.676 1.00 0.00 | ||
| ATOM 81 SC1 PRO A 38 40.069 27.147 18.801 1.00 0.00 | ||
| ATOM 82 BB ASP A 39 38.580 28.746 23.873 1.00 0.00 | ||
| ATOM 83 SC1 ASP A 39 40.554 28.602 25.687 1.00 0.00 | ||
| ATOM 84 BB GLN A 40 36.961 31.623 23.409 1.00 0.00 | ||
| ATOM 85 SC1 GLN A 40 40.364 33.805 23.361 1.00 0.00 | ||
| ATOM 86 BB GLN A 41 34.467 30.166 22.116 1.00 0.00 | ||
| ATOM 87 SC1 GLN A 41 35.843 30.189 18.265 1.00 0.00 | ||
| ATOM 88 BB ARG A 42 30.949 30.935 21.949 1.00 0.00 | ||
| ATOM 89 SC1 ARG A 42 29.843 31.014 24.911 1.00 0.00 | ||
| ATOM 90 SC2 ARG A 42 27.111 32.424 26.552 1.00 0.00 | ||
| ATOM 91 BB LEU A 43 28.193 29.117 20.658 1.00 0.00 | ||
| ATOM 92 SC1 LEU A 43 30.128 28.857 17.747 1.00 0.00 | ||
| ATOM 93 BB ILE A 44 24.942 30.412 19.404 1.00 0.00 | ||
| ATOM 94 SC1 ILE A 44 24.811 31.210 22.222 1.00 0.00 | ||
| ATOM 95 BB PHE A 45 21.716 28.605 19.082 1.00 0.00 | ||
| ATOM 96 SC1 PHE A 45 21.723 27.916 16.308 1.00 0.00 | ||
| ATOM 97 SC2 PHE A 45 20.484 28.426 14.315 1.00 0.00 | ||
| ATOM 98 SC3 PHE A 45 19.953 26.813 15.122 1.00 0.00 | ||
| ATOM 99 BB ALA A 46 18.627 28.819 19.893 1.00 0.00 | ||
| ATOM 100 SC1 ALA A 46 17.864 27.977 18.346 1.00 0.00 | ||
| ATOM 101 BB GLY A 47 19.668 29.225 23.002 1.00 0.00 | ||
| ATOM 102 BB LYS A 48 22.231 27.401 22.566 1.00 0.00 | ||
| ATOM 103 SC1 LYS A 48 20.213 24.827 22.126 1.00 0.00 | ||
| ATOM 104 SC2 LYS A 48 18.064 24.455 20.590 1.00 0.00 | ||
| ATOM 105 BB GLN A 49 25.049 25.843 23.458 1.00 0.00 | ||
| ATOM 106 SC1 GLN A 49 27.856 27.471 25.815 1.00 0.00 | ||
| ATOM 107 BB LEU A 50 27.608 24.637 21.687 1.00 0.00 | ||
| ATOM 108 SC1 LEU A 50 25.939 25.527 18.770 1.00 0.00 | ||
| ATOM 109 BB GLU A 51 29.078 21.449 21.268 1.00 0.00 | ||
| ATOM 110 SC1 GLU A 51 28.624 19.354 24.704 1.00 0.00 | ||
| ATOM 111 BB ASP A 52 32.050 20.088 20.010 1.00 0.00 | ||
| ATOM 112 SC1 ASP A 52 34.187 22.155 21.368 1.00 0.00 | ||
| ATOM 113 BB GLY A 53 30.918 16.866 19.371 1.00 0.00 | ||
| ATOM 114 BB ARG A 54 28.848 18.003 17.705 1.00 0.00 | ||
| ATOM 115 SC1 ARG A 54 26.519 17.453 19.841 1.00 0.00 | ||
| ATOM 116 SC2 ARG A 54 27.646 14.411 20.672 1.00 0.00 | ||
| ATOM 117 BB THR A 55 26.733 18.658 15.109 1.00 0.00 | ||
| ATOM 118 SC1 THR A 55 27.031 16.520 13.692 1.00 0.00 | ||
| ATOM 119 BB LEU A 56 24.860 20.641 13.180 1.00 0.00 | ||
| ATOM 120 SC1 LEU A 56 27.152 22.891 11.817 1.00 0.00 | ||
| ATOM 121 BB SER A 57 22.530 18.578 12.777 1.00 0.00 | ||
| ATOM 122 SC1 SER A 57 23.548 16.794 11.497 1.00 0.00 | ||
| ATOM 123 BB ASP A 58 21.786 18.228 15.811 1.00 0.00 | ||
| ATOM 124 SC1 ASP A 58 24.174 16.003 16.613 1.00 0.00 | ||
| ATOM 125 BB TYR A 59 20.601 21.380 15.641 1.00 0.00 | ||
| ATOM 126 SC1 TYR A 59 22.515 22.102 17.183 1.00 0.00 | ||
| ATOM 127 SC2 TYR A 59 24.662 21.414 18.210 1.00 0.00 | ||
| ATOM 128 SC3 TYR A 59 22.820 22.032 19.629 1.00 0.00 | ||
| ATOM 129 SC4 TYR A 59 24.935 21.374 20.693 1.00 0.00 | ||
| ATOM 130 BB ASN A 60 19.243 22.209 12.952 1.00 0.00 | ||
| ATOM 131 SC1 ASN A 60 16.554 21.255 12.303 1.00 0.00 | ||
| ATOM 132 BB ILE A 61 21.241 23.577 10.907 1.00 0.00 | ||
| ATOM 133 SC1 ILE A 61 23.203 24.990 12.869 1.00 0.00 | ||
| ATOM 134 BB GLN A 62 20.668 25.662 8.252 1.00 0.00 | ||
| ATOM 135 SC1 GLN A 62 16.876 23.760 7.212 1.00 0.00 | ||
| ATOM 136 BB LYS A 63 20.846 27.381 5.691 1.00 0.00 | ||
| ATOM 137 SC1 LYS A 63 20.703 26.551 2.854 1.00 0.00 | ||
| ATOM 138 SC2 LYS A 63 18.492 26.227 0.990 1.00 0.00 | ||
| ATOM 139 BB GLU A 64 21.610 30.746 6.606 1.00 0.00 | ||
| ATOM 140 SC1 GLU A 64 21.159 30.803 2.737 1.00 0.00 | ||
| ATOM 141 BB SER A 65 22.366 30.729 9.345 1.00 0.00 | ||
| ATOM 142 SC1 SER A 65 21.012 28.422 10.185 1.00 0.00 | ||
| ATOM 143 BB THR A 66 22.828 32.169 12.668 1.00 0.00 | ||
| ATOM 144 SC1 THR A 66 22.926 34.695 11.648 1.00 0.00 | ||
| ATOM 145 BB LEU A 67 25.477 32.626 14.755 1.00 0.00 | ||
| ATOM 146 SC1 LEU A 67 26.234 29.331 14.277 1.00 0.00 | ||
| ATOM 147 BB HIS A 68 26.716 33.258 18.001 1.00 0.00 | ||
| ATOM 148 SC1 HIS A 68 24.596 34.843 18.453 1.00 0.00 | ||
| ATOM 149 SC2 HIS A 68 22.405 35.021 17.454 1.00 0.00 | ||
| ATOM 150 SC3 HIS A 68 23.309 36.522 17.513 1.00 0.00 | ||
| ATOM 151 BB LEU A 69 29.616 35.063 19.208 1.00 0.00 | ||
| ATOM 152 SC1 LEU A 69 32.296 33.940 18.057 1.00 0.00 | ||
| ATOM 153 BB VAL A 70 31.210 34.555 22.223 1.00 0.00 | ||
| ATOM 154 SC1 VAL A 70 29.114 35.531 23.778 1.00 0.00 | ||
| ATOM 155 BB LEU A 71 33.678 35.753 24.378 1.00 0.00 | ||
| ATOM 156 SC1 LEU A 71 35.644 36.178 21.620 1.00 0.00 | ||
| ATOM 157 BB ARG A 72 36.072 33.977 26.534 1.00 0.00 | ||
| ATOM 158 SC1 ARG A 72 35.360 31.797 27.830 1.00 0.00 | ||
| ATOM 159 SC2 ARG A 72 34.377 29.113 26.651 1.00 0.00 | ||
| ATOM 160 BB LEU A 73 38.267 35.183 28.623 1.00 0.00 | ||
| ATOM 161 SC1 LEU A 73 39.151 37.446 26.048 1.00 0.00 | ||
| ATOM 162 BB ARG A 74 41.535 34.542 30.191 1.00 0.00 | ||
| ATOM 163 SC1 ARG A 74 41.718 31.351 30.456 1.00 0.00 | ||
| ATOM 164 SC2 ARG A 74 44.179 29.920 29.559 1.00 0.00 | ||
| ATOM 165 BB GLY A 75 41.317 37.180 32.109 1.00 0.00 | ||
| ATOM 166 BB GLY A 76 40.212 39.684 35.087 1.00 0.00 | ||
| TER 167 GLY A 76 | ||
| CONECT 1 2 3 | ||
| CONECT 3 4 5 | ||
| CONECT 5 6 7 | ||
| CONECT 7 8 11 | ||
| CONECT 8 9 10 | ||
| CONECT 9 10 | ||
| CONECT 11 12 13 | ||
| CONECT 13 14 16 | ||
| CONECT 14 15 | ||
| CONECT 16 17 18 | ||
| CONECT 18 19 20 | ||
| CONECT 20 21 22 | ||
| CONECT 22 23 | ||
| CONECT 23 24 26 | ||
| CONECT 24 25 | ||
| CONECT 26 27 28 | ||
| CONECT 28 29 30 | ||
| CONECT 30 31 32 | ||
| CONECT 32 33 34 | ||
| CONECT 34 35 36 | ||
| CONECT 36 37 38 | ||
| CONECT 38 39 40 | ||
| CONECT 40 41 42 | ||
| CONECT 42 43 44 | ||
| CONECT 44 45 46 | ||
| CONECT 46 47 48 | ||
| CONECT 48 49 50 | ||
| CONECT 50 51 52 | ||
| CONECT 52 53 54 | ||
| CONECT 54 55 56 | ||
| CONECT 56 57 59 | ||
| CONECT 57 58 | ||
| CONECT 59 60 61 | ||
| CONECT 61 62 64 | ||
| CONECT 62 63 | ||
| CONECT 64 65 66 | ||
| CONECT 66 67 68 | ||
| CONECT 68 69 70 | ||
| CONECT 70 71 73 | ||
| CONECT 71 72 | ||
| CONECT 73 74 75 | ||
| CONECT 75 76 | ||
| CONECT 76 77 78 | ||
| CONECT 78 79 80 | ||
| CONECT 80 81 82 | ||
| CONECT 82 83 84 | ||
| CONECT 84 85 86 | ||
| CONECT 86 87 88 | ||
| CONECT 88 89 91 | ||
| CONECT 89 90 | ||
| CONECT 91 92 93 | ||
| CONECT 93 94 95 | ||
| CONECT 95 96 99 | ||
| CONECT 96 97 98 | ||
| CONECT 97 98 | ||
| CONECT 99 100 101 | ||
| CONECT 101 102 | ||
| CONECT 102 103 105 | ||
| CONECT 103 104 | ||
| CONECT 105 106 107 | ||
| CONECT 107 108 109 | ||
| CONECT 109 110 111 | ||
| CONECT 111 112 113 | ||
| CONECT 113 114 | ||
| CONECT 114 115 117 | ||
| CONECT 115 116 | ||
| CONECT 117 118 119 | ||
| CONECT 119 120 121 | ||
| CONECT 121 122 123 | ||
| CONECT 123 124 125 | ||
| CONECT 125 126 130 | ||
| CONECT 126 127 128 | ||
| CONECT 127 128 129 | ||
| CONECT 128 129 | ||
| CONECT 130 131 132 | ||
| CONECT 132 133 134 | ||
| CONECT 134 135 136 | ||
| CONECT 136 137 139 | ||
| CONECT 137 138 | ||
| CONECT 139 140 141 | ||
| CONECT 141 142 143 | ||
| CONECT 143 144 145 | ||
| CONECT 145 146 147 | ||
| CONECT 147 148 151 | ||
| CONECT 148 149 150 | ||
| CONECT 149 150 | ||
| CONECT 151 152 153 | ||
| CONECT 153 154 155 | ||
| CONECT 155 156 157 | ||
| CONECT 157 158 160 | ||
| CONECT 158 159 | ||
| CONECT 160 161 162 | ||
| CONECT 162 163 165 | ||
| CONECT 163 164 | ||
| CONECT 165 166 | ||
| END |
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vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation
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| McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015 | ||
| Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 |
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vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command
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| martinize2 | ||
| -f ../aa.pdb | ||
| -ff martini3001 | ||
| -x cg.pdb | ||
| -o topol.top | ||
| -ignore HOH | ||
| -dssp | ||
| -elastic |
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