Rafał Ślusarz
Przykład 1
Kompleks wankomycyny modyfikowanej cukrem cyklicznym oraz dekanem podstawionym na wankozaminieOryginalny wykres długości wiązań wodorowych:
Wykres zmian długości wiązań wodorowych oznaczonych przeze mnie (z tej samej trajektorii):
Powyższy wykres został wygładzony funkcją przybliżenia Bezier'a oraz nie została uwzględniona odległość WanPP - tej różnicy proszę nie brać pod uwagę - nie ma znaczenia.
To, co ma znaczenie, to WARTOŚCI oznaczonych odległości (długości kontrolnych wiązań wodorowych). Na oryginalnym wykresie są to wartości w zakresie 9-14 Å, zaś na "tym drugim" są to wartości 2-4 Å. TO jest właśnie PROBLEM: zmierzone (przeze mnie) wartości są inne, niż te umieszczone na oryginalnym wykresie. Gdzie (w czym) tkwi błąd i jak powinien być naprawiony?
Oryginalny plik wejściowy cpptraj.in, wg którego powstał wykres umieszczonmy w pracy (pierwszy wykres w tym przykładzie):
trajin ../00.crd trajin ../01.trj trajin ../02.trj trajin ../03.trj trajin ../04.trj strip :WAT rms first :1-7 out rms.out [wanko] rms first :8-9 out rms.out [cukier] rms first :10-15 out rms.out [pentapep] distance wod1 :15@O,OXT :2@H out odleglosci.out distance wod2 :15@O,OXT :3@H out odleglosci.out distance wod3 :15@O,OXT :4@H out odleglosci.out distance wod4 :15@H :4@O out odleglosci.out distance wod5 :13@O :7@H out odleglosci.out distance WanPP :1-7 :10-15 out odleglosci.out runPlik PDB, zawierający kompleks omawiany w tym przykładzie (woda została wycięta):
CRYST1 59.714 59.376 59.845 90.00 90.00 90.00 P 1 1 ATOM 1 N ILT 1 31.910 30.835 18.906 -0.7230 1.5500 N ATOM 2 H1 ILT 1 32.586 30.839 19.681 0.4500 1.3000 H ATOM 3 H2 ILT 1 32.337 31.406 18.167 0.4500 1.3000 H ATOM 4 CH3 ILT 1 30.679 31.554 19.305 0.2009 1.7000 C ATOM 5 HM1 ILT 1 30.926 32.583 19.572 0.0500 1.3000 H ATOM 6 HM2 ILT 1 29.970 31.570 18.475 0.0500 1.3000 H ATOM 7 HM3 ILT 1 30.213 31.074 20.166 0.0500 1.3000 H ATOM 8 CA ILT 1 31.665 29.465 18.352 0.2416 1.7000 C ATOM 9 HA ILT 1 30.927 29.590 17.559 0.0184 1.3000 H ATOM 10 CB ILT 1 31.040 28.512 19.399 -0.1221 1.7000 C ATOM 11 HB2 ILT 1 31.819 28.006 19.968 0.0335 1.3000 H ATOM 12 HB3 ILT 1 30.448 29.087 20.107 0.0335 1.3000 H ATOM 13 CG ILT 1 30.090 27.466 18.786 0.4490 1.7000 C ATOM 14 HG ILT 1 29.339 27.979 18.187 -0.0664 1.3000 H ATOM 15 CD1 ILT 1 30.791 26.430 17.909 -0.4281 1.7000 C ATOM 16 HD11 ILT 1 31.621 25.973 18.449 0.1065 1.3000 H ATOM 17 HD12 ILT 1 30.083 25.649 17.629 0.1065 1.3000 H ATOM 18 HD13 ILT 1 31.151 26.887 16.990 0.1065 1.3000 H ATOM 19 CD2 ILT 1 29.376 26.716 19.910 -0.4281 1.7000 C ATOM 20 HD21 ILT 1 28.825 27.419 20.536 0.1065 1.3000 H ATOM 21 HD22 ILT 1 28.663 26.007 19.489 0.1065 1.3000 H ATOM 22 HD23 ILT 1 30.096 26.175 20.525 0.1065 1.3000 H ATOM 23 C ILT 1 32.929 28.847 17.681 0.6837 1.7000 C ATOM 24 O ILT 1 32.949 28.674 16.462 -0.5819 1.5000 O ATOM 25 N TYV 2 33.989 28.561 18.447 -0.4937 1.5500 N ATOM 26 H TYV 2 33.914 28.698 19.455 0.3018 1.3000 H ATOM 27 CA TYV 2 35.282 28.079 17.923 0.1416 1.7000 C ATOM 28 HA TYV 2 35.353 28.386 16.880 0.0184 1.3000 H ATOM 29 CB TYV 2 35.394 26.536 17.935 0.2300 1.7000 C ATOM 30 OB2 TYV 2 34.264 25.891 17.382 -0.5593 1.5000 O ATOM 31 HB2 TYV 2 34.224 26.149 16.446 0.3687 0.8000 H ATOM 32 HB3 TYV 2 36.203 26.315 17.236 0.0242 1.3000 H ATOM 33 CG TYV 2 35.801 25.895 19.257 0.0293 1.7000 C ATOM 34 CD1 TYV 2 35.013 26.049 20.415 -0.0972 1.7000 C ATOM 35 HD1 TYV 2 34.046 26.527 20.358 0.1123 1.3000 H ATOM 36 CE1 TYV 2 35.508 25.643 21.667 -0.1050 1.7000 C ATOM 37 HE1 TYV 2 34.927 25.832 22.559 0.1161 1.3000 H ATOM 38 CZ TYV 2 36.787 25.057 21.775 0.1720 1.7000 C ATOM 39 OZ TYV 2 37.400 24.916 23.002 -0.4700 1.5000 O ATOM 40 CE2 TYV 2 37.498 24.759 20.597 0.2080 1.7000 C ATOM 41 Cl TYV 2 39.048 23.994 20.689 -0.1000 1.7000 CL ATOM 42 CD2 TYV 2 37.025 25.198 19.349 -0.0972 1.7000 C ATOM 43 HD2 TYV 2 37.625 25.034 18.465 0.1123 1.3000 H ATOM 44 C TYV 2 36.522 28.703 18.595 0.6731 1.7000 C ATOM 45 O TYV 2 37.646 28.416 18.179 -0.5854 1.5000 O ATOM 46 N ALT 3 36.361 29.529 19.635 -0.3450 1.5500 N ATOM 47 H ALT 3 35.436 29.639 20.031 0.1630 1.3000 H ATOM 48 CA ALT 3 37.366 30.517 20.030 0.0950 1.7000 C ATOM 49 HA ALT 3 38.259 30.413 19.411 0.0880 1.3000 H ATOM 50 CB ALT 3 36.809 31.922 19.769 0.0360 1.7000 C ATOM 51 HB1 ALT 3 35.994 32.115 20.464 0.0510 1.3000 H ATOM 52 HB2 ALT 3 37.608 32.644 19.940 0.0510 1.3000 H ATOM 53 CG ALT 3 36.292 32.073 18.339 0.2170 1.7000 C ATOM 54 OG ALT 3 35.085 32.057 18.110 -0.2740 1.5000 O ATOM 55 ND ALT 3 37.197 32.205 17.369 -0.3700 1.5500 N ATOM 56 HND1 ALT 3 38.185 32.202 17.582 0.1590 1.3000 H ATOM 57 HND2 ALT 3 36.888 32.332 16.414 0.1590 1.3000 H ATOM 58 C ALT 3 37.822 30.387 21.488 0.2410 1.7000 C ATOM 59 O ALT 3 38.926 30.827 21.797 -0.2710 1.5000 O ATOM 60 N TYS 4 36.983 29.853 22.387 -0.4937 1.5500 N ATOM 61 H TYS 4 36.053 29.561 22.086 0.3018 1.3000 H ATOM 62 CA TYS 4 37.266 29.783 23.833 0.0416 1.7000 C ATOM 63 HA TYS 4 38.263 30.156 24.054 0.0184 1.3000 H ATOM 64 CG TYS 4 37.168 28.344 24.337 0.0293 1.7000 C ATOM 65 CD1 TYS 4 37.447 27.260 23.488 -0.0504 1.7000 C ATOM 66 HD1 TYS 4 37.762 27.440 22.473 0.1123 1.3000 H ATOM 67 CE1 TYS 4 37.295 25.932 23.932 0.1207 1.7000 C ATOM 68 CZ TYS 4 36.986 25.673 25.289 0.1207 1.7000 C ATOM 69 OZ TYS 4 37.026 24.392 25.798 -0.4710 1.5000 O ATOM 70 CE2 TYS 4 36.642 26.756 26.131 0.1207 1.7000 C ATOM 71 CD2 TYS 4 36.807 28.075 25.672 -0.0504 1.7000 C ATOM 72 HD2 TYS 4 36.642 28.886 26.364 0.1123 1.3000 H ATOM 73 C TYS 4 36.213 30.640 24.548 0.6731 1.7000 C ATOM 74 O TYS 4 35.015 30.392 24.415 -0.5854 1.5000 O ATOM 75 N TYD 5 36.615 31.635 25.342 -0.4937 1.5500 N ATOM 76 H TYD 5 37.603 31.861 25.379 0.3018 1.3000 H ATOM 77 CA TYD 5 35.637 32.570 25.895 -0.0010 1.7000 C ATOM 78 HA TYD 5 34.994 32.773 25.038 0.0556 1.3000 H ATOM 79 CG TYD 5 36.149 33.922 26.310 -0.0017 1.7000 C ATOM 80 CD1 TYD 5 35.257 34.974 26.059 -0.1459 1.7000 C ATOM 81 HD1 TYD 5 34.515 34.883 25.276 0.1195 1.3000 H ATOM 82 CE1 TYD 5 35.190 36.060 26.936 -0.0020 1.7000 C ATOM 83 CZ TYD 5 36.210 36.242 27.896 0.2516 1.7000 C ATOM 84 OH TYD 5 36.226 37.335 28.709 -0.4757 1.5000 O ATOM 85 HH TYD 5 36.604 37.136 29.583 0.3583 0.8000 H ATOM 86 CE2 TYD 5 37.192 35.248 28.064 -0.1648 1.7000 C ATOM 87 HE2 TYD 5 37.937 35.354 28.839 0.1367 1.3000 H ATOM 88 CD2 TYD 5 37.143 34.068 27.296 -0.1459 1.7000 C ATOM 89 HD2 TYD 5 37.797 33.241 27.537 0.1195 1.3000 H ATOM 90 C TYD 5 34.720 32.039 27.001 0.6731 1.7000 C ATOM 91 O TYD 5 34.880 32.315 28.188 -0.5854 1.5000 O ATOM 92 N TYF 6 33.590 31.485 26.583 -0.4937 1.5500 N ATOM 93 H TYF 6 33.588 31.131 25.630 0.3018 1.3000 H ATOM 94 CA TYF 6 32.320 31.557 27.323 0.1416 1.7000 C ATOM 95 HA TYF 6 31.574 31.090 26.680 0.0184 1.3000 H ATOM 96 CB TYF 6 32.363 30.679 28.610 0.2300 1.7000 C ATOM 97 OB2 TYF 6 32.818 31.462 29.711 -0.5593 1.5000 O ATOM 98 HB2 TYF 6 33.709 31.783 29.475 0.3687 0.8000 H ATOM 99 HB3 TYF 6 31.352 30.371 28.880 0.0242 1.3000 H ATOM 100 CG TYF 6 33.233 29.416 28.486 0.0293 1.7000 C ATOM 101 CD1 TYF 6 34.456 29.281 29.187 -0.0972 1.7000 C ATOM 102 HD1 TYF 6 34.754 29.993 29.943 0.1123 1.3000 H ATOM 103 CE1 TYF 6 35.361 28.257 28.859 -0.1050 1.7000 C ATOM 104 HE1 TYF 6 36.321 28.208 29.351 0.1161 1.3000 H ATOM 105 CZ TYF 6 35.073 27.357 27.825 0.1720 1.7000 C ATOM 106 OZ TYF 6 36.089 26.540 27.375 -0.4700 1.5000 O ATOM 107 CE2 TYF 6 33.812 27.420 27.190 0.2080 1.7000 C ATOM 108 Cl TYF 6 33.392 26.310 25.927 -0.1000 1.7000 CL ATOM 109 CD2 TYF 6 32.895 28.435 27.528 -0.0972 1.7000 C ATOM 110 HD2 TYF 6 31.957 28.497 26.994 0.1123 1.3000 H ATOM 111 C TYF 6 31.796 32.999 27.604 0.6731 1.7000 C ATOM 112 O TYF 6 30.714 33.130 28.172 -0.5854 1.5000 O ATOM 113 N TOL 7 32.541 34.086 27.299 -0.4937 1.5500 N ATOM 114 H TOL 7 33.426 33.940 26.844 0.3018 1.3000 H ATOM 115 CA TOL 7 32.345 35.415 27.924 -0.0116 1.7000 C ATOM 116 HA TOL 7 31.259 35.503 27.968 0.0184 1.3000 H ATOM 117 CG TOL 7 32.789 36.653 27.107 0.0293 1.7000 C ATOM 118 CD1 TOL 7 34.135 36.970 26.751 -0.0020 1.7000 C ATOM 119 CE1 TOL 7 34.410 38.150 26.017 0.1216 1.7000 C ATOM 120 OE1 TOL 7 35.668 38.434 25.557 -0.4757 1.5000 O ATOM 121 HE1 TOL 7 36.175 37.648 25.284 0.3580 0.8000 H ATOM 122 CZ TOL 7 33.381 39.046 25.696 -0.0548 1.7000 C ATOM 123 HZ TOL 7 33.602 39.934 25.122 0.1194 1.3000 H ATOM 124 CE2 TOL 7 32.067 38.773 26.093 0.1216 1.7000 C ATOM 125 OE2 TOL 7 31.057 39.632 25.772 -0.4757 1.5000 O ATOM 126 HE2 TOL 7 31.307 40.308 25.133 0.3580 0.8000 H ATOM 127 CD2 TOL 7 31.782 37.597 26.801 -0.1248 1.7000 C ATOM 128 HD2 TOL 7 30.758 37.414 27.095 0.1195 1.3000 H ATOM 129 C TOL 7 32.777 35.442 29.405 0.6107 1.7000 C ATOM 130 O TOL 7 33.625 36.220 29.834 -0.5200 1.5000 O TER 131 TOL 7 ATOM 131 C1 2GB 8 38.314 23.905 26.304 0.3840 1.7000 C ATOM 132 H1 2GB 8 38.762 24.682 26.925 0.0000 1.3000 H ATOM 133 O5 2GB 8 39.216 23.702 25.139 -0.4710 1.5000 O ATOM 134 C5 2GB 8 40.422 22.850 25.253 0.2250 1.7000 C ATOM 135 H5 2GB 8 41.138 23.352 25.906 0.0000 1.3000 H ATOM 136 C6 2GB 8 41.028 22.715 23.841 0.2820 1.7000 C ATOM 137 H62 2GB 8 41.236 23.701 23.424 0.0000 1.3000 H ATOM 138 H61 2GB 8 40.328 22.206 23.179 0.0000 1.3000 H ATOM 139 O6 2GB 8 42.258 21.962 23.896 -0.6880 1.5000 O ATOM 140 H6O 2GB 8 42.126 21.260 24.569 0.4240 0.8000 H ATOM 141 C4 2GB 8 40.009 21.503 25.871 0.2760 1.7000 C ATOM 142 H4 2GB 8 39.304 20.991 25.213 0.0000 1.3000 H ATOM 143 O4 2GB 8 41.190 20.670 26.028 -0.7140 1.5000 O ATOM 144 H4O 2GB 8 40.949 19.982 26.670 0.4400 0.8000 H ATOM 145 C3 2GB 8 39.358 21.740 27.248 0.2840 1.7000 C ATOM 146 H3 2GB 8 40.086 22.230 27.898 0.0000 1.3000 H ATOM 147 O3 2GB 8 39.046 20.439 27.819 -0.7090 1.5000 O ATOM 148 H3O 2GB 8 39.133 20.492 28.794 0.4320 0.8000 H ATOM 149 C2 2GB 8 38.089 22.624 27.156 0.3100 1.7000 C ATOM 150 H2 2GB 8 37.269 22.053 26.717 0.0000 1.3000 H ATOM 151 O2 2GB 8 37.733 23.071 28.531 -0.4750 1.5000 O ATOM 152 C1 VML 9 36.799 22.240 29.300 0.3420 1.7000 C ATOM 153 H1 VML 9 37.141 21.206 29.289 0.0000 1.3000 H ATOM 154 O5 VML 9 35.445 22.292 28.731 -0.5700 1.5000 O ATOM 155 C5 VML 9 34.774 23.615 28.778 0.2200 1.7000 C ATOM 156 H5 VML 9 35.380 24.321 28.215 0.0000 1.3000 H ATOM 157 C6 VML 9 33.437 23.486 28.044 0.0500 1.7000 C ATOM 158 H61 VML 9 33.588 23.266 26.987 0.0000 1.3000 H ATOM 159 H62 VML 9 32.859 24.409 28.108 0.0000 1.3000 H ATOM 160 H63 VML 9 32.819 22.687 28.457 0.0000 1.3000 H ATOM 161 C4 VML 9 34.683 24.110 30.248 0.2700 1.7000 C ATOM 162 H4 VML 9 34.290 25.129 30.250 0.0000 1.3000 H ATOM 163 O4 VML 9 33.723 23.274 30.959 -0.6160 1.5000 O ATOM 164 H4O VML 9 33.890 22.357 30.721 0.3000 0.8000 H ATOM 165 C3 VML 9 36.072 24.098 30.976 0.2000 1.7000 C ATOM 166 C7 VML 9 36.936 25.288 30.498 0.0540 1.7000 C ATOM 167 H71 VML 9 37.945 25.261 30.910 0.0000 1.3000 H ATOM 168 H72 VML 9 36.499 26.246 30.787 0.0000 1.3000 H ATOM 169 H73 VML 9 37.051 25.316 29.418 0.0000 1.3000 H ATOM 170 N3 VML 9 35.879 24.286 32.436 -0.6000 1.5500 N ATOM 171 H3 VML 9 34.939 24.153 32.792 0.2500 1.3000 H ATOM 172 C2 VML 9 36.774 22.731 30.757 0.1000 1.7000 C ATOM 173 H21 VML 9 36.271 21.965 31.351 0.0000 1.3000 H ATOM 174 H22 VML 9 37.794 22.760 31.139 0.0000 1.3000 H ATOM 175 C1 DEK 10 36.995 24.300 33.373 0.1001 1.7000 C ATOM 176 H11 DEK 10 37.925 24.390 32.814 0.0400 1.3000 H ATOM 177 H12 DEK 10 37.021 23.367 33.934 0.0400 1.3000 H ATOM 178 C2 DEK 10 36.898 25.477 34.348 -0.0600 1.7000 C ATOM 179 H21 DEK 10 36.704 26.399 33.797 0.0300 1.3000 H ATOM 180 H22 DEK 10 37.861 25.570 34.850 0.0300 1.3000 H ATOM 181 C3 DEK 10 35.807 25.252 35.406 -0.0700 1.7000 C ATOM 182 H31 DEK 10 35.954 24.271 35.861 0.0300 1.3000 H ATOM 183 H32 DEK 10 34.826 25.274 34.928 0.0300 1.3000 H ATOM 184 C4 DEK 10 35.870 26.326 36.501 -0.0800 1.7000 C ATOM 185 H41 DEK 10 35.686 27.307 36.059 0.0300 1.3000 H ATOM 186 H42 DEK 10 36.865 26.324 36.945 0.0300 1.3000 H ATOM 187 C5 DEK 10 34.831 26.059 37.600 -0.0900 1.7000 C ATOM 188 H51 DEK 10 34.952 25.039 37.968 0.0300 1.3000 H ATOM 189 H52 DEK 10 33.830 26.164 37.179 0.0300 1.3000 H ATOM 190 C6 DEK 10 34.999 27.034 38.774 -0.0900 1.7000 C ATOM 191 H61 DEK 10 34.900 28.059 38.413 0.0300 1.3000 H ATOM 192 H62 DEK 10 35.994 26.907 39.205 0.0300 1.3000 H ATOM 193 C7 DEK 10 33.941 26.774 39.856 -0.0900 1.7000 C ATOM 194 H71 DEK 10 33.991 25.728 40.166 0.0300 1.3000 H ATOM 195 H72 DEK 10 32.951 26.969 39.440 0.0300 1.3000 H ATOM 196 C8 DEK 10 34.163 27.669 41.083 -0.0900 1.7000 C ATOM 197 H81 DEK 10 34.154 28.716 40.774 0.0300 1.3000 H ATOM 198 H82 DEK 10 35.135 27.441 41.522 0.0300 1.3000 H ATOM 199 C9 DEK 10 33.065 27.437 42.130 -0.0900 1.7000 C ATOM 200 H91 DEK 10 33.034 26.379 42.397 0.0300 1.3000 H ATOM 201 H92 DEK 10 32.098 27.719 41.711 0.0300 1.3000 H ATOM 202 C10 DEK 10 33.320 28.255 43.400 -0.1000 1.7000 C ATOM 203 H101 DEK 10 34.253 27.935 43.863 0.0333 1.3000 H ATOM 204 H102 DEK 10 32.502 28.095 44.104 0.0333 1.3000 H ATOM 205 H103 DEK 10 33.382 29.317 43.160 0.0333 1.3000 H TER 206 DEK 10 ATOM 206 N1 NM2 11 32.161 34.578 30.205 -0.4600 1.5500 N ATOM 207 HN1 NM2 11 31.469 33.966 29.789 0.2750 1.3000 H ATOM 208 CA NM2 11 32.298 34.536 31.645 0.2600 1.7000 C ATOM 209 HA1 NM2 11 33.269 34.842 32.032 -0.0375 1.3000 H ATOM 210 HA2 NM2 11 32.120 33.548 32.065 -0.0375 1.3000 H ATOM 211 CB NM2 11 31.247 35.483 32.232 0.2600 1.7000 C ATOM 212 HB1 NM2 11 30.321 35.292 31.689 -0.0375 1.3000 H ATOM 213 HB2 NM2 11 31.542 36.493 31.951 -0.0375 1.3000 H ATOM 214 N2 NM2 11 31.131 35.271 33.657 -0.4600 1.5500 N ATOM 215 HN2 NM2 11 31.510 34.418 34.055 0.2750 1.3000 H ATOM 216 C1 0LB 12 29.921 35.817 34.242 0.3740 1.7000 C ATOM 217 H1 0LB 12 29.455 36.470 33.502 0.0000 1.3000 H ATOM 218 O5 0LB 12 30.350 36.655 35.372 -0.4020 1.5000 O ATOM 219 C5 0LB 12 29.223 37.343 36.054 0.1400 1.7000 C ATOM 220 H5 0LB 12 28.692 37.933 35.303 0.0000 1.3000 H ATOM 221 C6 0LB 12 29.787 38.328 37.086 0.3190 1.7000 C ATOM 222 H62 0LB 12 30.534 38.972 36.624 0.0000 1.3000 H ATOM 223 H61 0LB 12 30.249 37.799 37.920 0.0000 1.3000 H ATOM 224 O6 0LB 12 28.704 39.143 37.570 -0.6930 1.5000 O ATOM 225 H6O 0LB 12 28.612 39.913 36.972 0.4190 0.8000 H ATOM 226 C4 0LB 12 28.245 36.283 36.617 0.2030 1.7000 C ATOM 227 H4 0LB 12 27.403 36.779 37.101 0.0000 1.3000 H ATOM 228 O4 0LB 12 28.943 35.473 37.604 -0.6640 1.5000 O ATOM 229 H4O 0LB 12 28.356 35.341 38.379 0.4370 0.8000 H ATOM 230 C3 0LB 12 27.730 35.399 35.452 0.2590 1.7000 C ATOM 231 H3 0LB 12 27.192 36.045 34.756 0.0000 1.3000 H ATOM 232 O3 0LB 12 26.768 34.432 35.967 -0.6940 1.5000 O ATOM 233 H3O 0LB 12 26.772 33.635 35.397 0.4330 0.8000 H ATOM 234 C2 0LB 12 28.898 34.727 34.676 0.3570 1.7000 C ATOM 235 H2 0LB 12 29.389 33.983 35.305 0.0000 1.3000 H ATOM 236 O2 0LB 12 28.385 34.074 33.475 -0.7260 1.5000 O ATOM 237 H2O 0LB 12 27.860 33.289 33.733 0.4320 0.8000 H TER 238 0LB 12 ATOM 238 HH31 ACE 13 22.078 38.356 20.559 0.0128 1.3000 H ATOM 239 CH3 ACE 13 21.419 38.280 21.425 -0.0010 1.7000 C ATOM 240 HH32 ACE 13 21.918 37.749 22.233 0.0128 1.3000 H ATOM 241 HH33 ACE 13 20.542 37.714 21.110 0.0128 1.3000 H ATOM 242 C ACE 13 20.976 39.681 21.851 0.5513 1.7000 C ATOM 243 O ACE 13 20.721 40.521 20.989 -0.5886 1.5000 O ATOM 244 N ALA 14 20.839 40.015 23.139 -0.5098 1.5500 N ATOM 245 H ALA 14 20.770 41.012 23.301 0.3229 1.3000 H ATOM 246 CA ALA 14 20.592 39.150 24.316 -0.0680 1.7000 C ATOM 247 HA ALA 14 20.258 39.801 25.123 0.1146 1.3000 H ATOM 248 CB ALA 14 19.432 38.169 24.039 -0.0148 1.7000 C ATOM 249 HB1 ALA 14 19.718 37.397 23.325 0.0283 1.3000 H ATOM 250 HB2 ALA 14 19.129 37.687 24.969 0.0283 1.3000 H ATOM 251 HB3 ALA 14 18.574 38.715 23.647 0.0283 1.3000 H ATOM 252 C ALA 14 21.876 38.484 24.870 0.6546 1.7000 C ATOM 253 O ALA 14 22.850 39.190 25.133 -0.5844 1.5000 O ATOM 254 N GLI 15 21.881 37.150 25.013 -0.4937 1.5500 N ATOM 255 H GLI 15 21.025 36.675 24.766 0.3018 1.3000 H ATOM 256 CA GLI 15 22.930 36.299 25.620 -0.2384 1.7000 C ATOM 257 CD GLI 15 22.274 35.085 26.282 0.6613 1.7000 C ATOM 258 OE1 GLI 15 21.856 35.224 27.450 -0.7362 1.5000 O ATOM 259 OE2 GLI 15 22.201 33.989 25.686 -0.7362 1.5000 O ATOM 260 HA GLI 15 23.402 36.868 26.422 0.0937 1.3000 H ATOM 261 CB GLI 15 23.983 35.880 24.572 0.3053 1.7000 C ATOM 262 HB2 GLI 15 24.337 34.866 24.761 -0.0704 1.3000 H ATOM 263 HB3 GLI 15 23.526 35.884 23.581 -0.0704 1.3000 H ATOM 264 CG GLI 15 25.216 36.790 24.548 -0.1671 1.7000 C ATOM 265 HG2 GLI 15 25.695 36.676 23.575 0.0313 1.3000 H ATOM 266 HG3 GLI 15 24.918 37.825 24.678 0.0313 1.3000 H ATOM 267 C GLI 15 26.215 36.398 25.627 0.6731 1.7000 C ATOM 268 O GLI 15 26.373 37.099 26.627 -0.5854 1.5000 O ATOM 269 N LYS 16 26.927 35.284 25.390 -0.3752 1.5500 N ATOM 270 H LYS 16 26.728 34.827 24.512 0.3004 1.3000 H ATOM 271 CA LYS 16 28.014 34.730 26.231 -0.3992 1.7000 C ATOM 272 HA LYS 16 28.288 35.455 27.003 0.1972 1.5000 H ATOM 273 CB LYS 16 27.541 33.452 26.965 -0.0135 1.7000 C ATOM 274 HB2 LYS 16 26.984 32.797 26.295 0.0565 1.3000 H ATOM 275 HB3 LYS 16 28.425 32.900 27.280 0.0565 1.3000 H ATOM 276 CG LYS 16 26.771 33.740 28.269 -0.0146 1.7000 C ATOM 277 HG2 LYS 16 26.981 32.926 28.966 0.0356 1.3000 H ATOM 278 HG3 LYS 16 27.148 34.654 28.731 0.0356 1.3000 H ATOM 279 CD LYS 16 25.244 33.823 28.128 -0.0224 1.7000 C ATOM 280 HD2 LYS 16 24.834 34.167 29.078 0.0378 1.3000 H ATOM 281 HD3 LYS 16 24.979 34.545 27.357 0.0378 1.3000 H ATOM 282 CE LYS 16 24.641 32.454 27.795 0.1242 1.7000 C ATOM 283 HE2 LYS 16 25.006 32.116 26.822 0.0848 1.3000 H ATOM 284 HE3 LYS 16 24.977 31.741 28.553 0.0848 1.3000 H ATOM 285 NZ LYS 16 23.168 32.498 27.789 -0.7709 1.5500 N ATOM 286 HZ1 LYS 16 22.815 33.073 27.017 0.4522 1.3000 H ATOM 287 HZ2 LYS 16 22.779 31.568 27.628 0.4522 1.3000 H ATOM 288 HZ3 LYS 16 22.789 32.915 28.634 0.4522 1.3000 H ATOM 289 C LYS 16 29.319 34.559 25.449 0.7825 1.7000 C ATOM 290 O LYS 16 30.058 35.527 25.312 -0.5946 1.5000 O ATOM 291 N AL2 17 29.546 33.395 24.842 -0.4937 1.5500 N ATOM 292 H AL2 17 28.872 32.657 24.978 0.3018 1.3000 H ATOM 293 CA AL2 17 30.750 33.059 24.069 0.0448 1.7000 C ATOM 294 HA AL2 17 31.636 33.443 24.577 0.0228 1.3000 H ATOM 295 CB AL2 17 30.664 33.727 22.687 -0.0909 1.7000 C ATOM 296 HB1 AL2 17 29.787 33.361 22.149 0.0425 1.3000 H ATOM 297 HB2 AL2 17 30.590 34.809 22.796 0.0425 1.3000 H ATOM 298 HB3 AL2 17 31.559 33.502 22.107 0.0425 1.3000 H ATOM 299 C AL2 17 30.911 31.533 23.894 0.6731 1.7000 C ATOM 300 O AL2 17 29.976 30.776 24.168 -0.5854 1.5000 O ATOM 301 N AL3 18 32.088 31.087 23.447 -0.4420 1.5500 N ATOM 302 H AL3 18 32.829 31.762 23.301 0.2952 1.3000 H ATOM 303 CA AL3 18 32.246 29.853 22.669 -0.0679 1.7000 C ATOM 304 HA AL3 18 31.325 29.706 22.108 0.0708 1.3000 H ATOM 305 CB AL3 18 32.416 28.617 23.564 -0.1226 1.7000 C ATOM 306 HB1 AL3 18 31.602 28.560 24.286 0.0586 1.3000 H ATOM 307 HB2 AL3 18 32.395 27.718 22.946 0.0586 1.3000 H ATOM 308 HB3 AL3 18 33.365 28.647 24.090 0.0586 1.3000 H ATOM 309 C AL3 18 33.353 30.029 21.611 0.5771 1.7000 C ATOM 310 O AL3 18 33.970 29.039 21.177 -0.7432 1.5000 O ATOM 311 OXT AL3 18 33.510 31.167 21.115 -0.7432 1.5000 O TER 312 AL3 18 ENDTen sam plik PDB można pobrać tutaj.
Przykład 2
Kompleks wankomycyny modyfikowanej cukrem liniowymOryginalny wykres długości wiązań wodorowych:
Wykres zmian długości wiązań wodorowych oznaczonych przeze mnie (z tej samej trajektorii):
Powyższy wykres został wygładzony funkcją przybliżenia Bezier'a oraz nie została uwzględniona odległość WanPP - tej różnicy proszę nie brać pod uwagę - nie ma znaczenia.
To, co ma znaczenie, to WARTOŚCI oznaczonych odległości (długości kontrolnych wiązań wodorowych). Na oryginalnym wykresie są to wartości w zakresie 7-10 Å, zaś na "tym drugim" wykresie (po połowie symulacji) są to wartości 2-3 Å. TO jest właśnie PROBLEM: zmierzone (przeze mnie) wartości są inne, niż te umieszczone na oryginalnym wykresie. Gdzie (w czym) tkwi błąd i jak powinien być naprawiony?Oryginalny plik wejściowy cpptraj.in, wg którego powstał wykres umieszczonmy w pracy (pierwszy wykres w tym przykładzie):
trajin 00.crd trajin 01.trj trajin 02.trj trajin 03.trj trajin 04.trj strip :WAT rms first :1-7 out rms.out [wanko] rms first :8-9 out rms.out [cukier] rms first :10-15 out rms.out [pentapep] distance wod1 :15@O,OXT :2@H out odleglosci.out distance wod2 :15@O,OXT :3@H out odleglosci.out distance wod3 :15@O,OXT :4@H out odleglosci.out distance wod4 :15@H :4@O out odleglosci.out distance wod5 :13@O :7@H out odleglosci.out distance WanPP :1-7 :10-15 out odleglosci.out runPlik PDB, zawierający kompleks omawiany w tym przykładzie (woda została wycięta):
CRYST1 59.714 59.376 59.845 90.00 90.00 90.00 P 1 1 ATOM 1 N ILT 1 31.449 38.204 24.595 -0.7230 1.5500 N ATOM 2 H1 ILT 1 30.640 38.373 23.982 0.4500 1.3000 H ATOM 3 H2 ILT 1 31.341 37.285 25.055 0.4500 1.3000 H ATOM 4 CH3 ILT 1 31.405 39.263 25.627 0.2009 1.7000 C ATOM 5 HM1 ILT 1 30.443 39.228 26.143 0.0500 1.3000 H ATOM 6 HM2 ILT 1 32.206 39.117 26.356 0.0500 1.3000 H ATOM 7 HM3 ILT 1 31.513 40.242 25.153 0.0500 1.3000 H ATOM 8 CA ILT 1 32.708 38.220 23.789 0.2416 1.7000 C ATOM 9 HA ILT 1 32.666 39.084 23.127 0.0184 1.3000 H ATOM 10 CB ILT 1 32.809 36.960 22.908 -0.1221 1.7000 C ATOM 11 HB2 ILT 1 33.787 36.954 22.423 0.0335 1.3000 H ATOM 12 HB3 ILT 1 32.757 36.078 23.547 0.0335 1.3000 H ATOM 13 CG ILT 1 31.732 36.848 21.819 0.4490 1.7000 C ATOM 14 HG ILT 1 30.745 36.919 22.272 -0.0664 1.3000 H ATOM 15 CD1 ILT 1 31.886 37.933 20.753 -0.4281 1.7000 C ATOM 16 HD11 ILT 1 32.874 37.885 20.295 0.1065 1.3000 H ATOM 17 HD12 ILT 1 31.117 37.805 19.991 0.1065 1.3000 H ATOM 18 HD13 ILT 1 31.738 38.917 21.200 0.1065 1.3000 H ATOM 19 CD2 ILT 1 31.848 35.487 21.130 -0.4281 1.7000 C ATOM 20 HD21 ILT 1 31.713 34.695 21.868 0.1065 1.3000 H ATOM 21 HD22 ILT 1 31.066 35.393 20.377 0.1065 1.3000 H ATOM 22 HD23 ILT 1 32.827 35.381 20.663 0.1065 1.3000 H ATOM 23 C ILT 1 34.025 38.369 24.611 0.6837 1.7000 C ATOM 24 O ILT 1 34.788 39.312 24.387 -0.5819 1.5000 O ATOM 25 N TYV 2 34.326 37.457 25.538 -0.4937 1.5500 N ATOM 26 H TYV 2 33.681 36.669 25.683 0.3018 1.3000 H ATOM 27 CA TYV 2 35.416 37.547 26.531 0.1416 1.7000 C ATOM 28 HA TYV 2 35.492 38.606 26.779 0.0184 1.3000 H ATOM 29 CB TYV 2 36.806 37.187 25.922 0.2300 1.7000 C ATOM 30 OB2 TYV 2 37.194 38.115 24.927 -0.5593 1.5000 O ATOM 31 HB2 TYV 2 36.417 38.645 24.686 0.3687 0.8000 H ATOM 32 HB3 TYV 2 37.492 37.371 26.744 0.0242 1.3000 H ATOM 33 CG TYV 2 37.127 35.784 25.388 0.0293 1.7000 C ATOM 34 CD1 TYV 2 36.203 34.991 24.676 -0.0972 1.7000 C ATOM 35 HD1 TYV 2 35.217 35.356 24.445 0.1123 1.3000 H ATOM 36 CE1 TYV 2 36.532 33.673 24.302 -0.1050 1.7000 C ATOM 37 HE1 TYV 2 35.781 33.040 23.850 0.1161 1.3000 H ATOM 38 CZ TYV 2 37.807 33.146 24.580 0.1720 1.7000 C ATOM 39 OZ TYV 2 38.008 31.782 24.511 -0.4700 1.5000 O ATOM 40 CE2 TYV 2 38.779 33.988 25.152 0.2080 1.7000 C ATOM 41 Cl TYV 2 40.335 33.371 25.586 -0.1000 1.7000 CL ATOM 42 CD2 TYV 2 38.443 35.297 25.543 -0.0972 1.7000 C ATOM 43 HD2 TYV 2 39.201 35.916 26.003 0.1123 1.3000 H ATOM 44 C TYV 2 34.932 36.910 27.882 0.6731 1.7000 C ATOM 45 O TYV 2 33.850 37.304 28.321 -0.5854 1.5000 O ATOM 46 N ALT 3 35.537 35.972 28.636 -0.3450 1.5500 N ATOM 47 H ALT 3 34.932 35.627 29.367 0.1630 1.3000 H ATOM 48 CA ALT 3 36.908 35.464 28.754 0.0950 1.7000 C ATOM 49 HA ALT 3 37.468 35.637 27.851 0.0880 1.3000 H ATOM 50 CB ALT 3 37.638 36.216 29.888 0.0360 1.7000 C ATOM 51 HB1 ALT 3 37.049 36.138 30.803 0.0510 1.3000 H ATOM 52 HB2 ALT 3 38.612 35.753 30.059 0.0510 1.3000 H ATOM 53 CG ALT 3 37.865 37.691 29.553 0.2170 1.7000 C ATOM 54 OG ALT 3 36.992 38.529 29.762 -0.2740 1.5000 O ATOM 55 ND ALT 3 39.035 38.023 29.007 -0.3700 1.5500 N ATOM 56 HND1 ALT 3 39.751 37.326 28.859 0.1590 1.3000 H ATOM 57 HND2 ALT 3 39.240 38.996 28.814 0.1590 1.3000 H ATOM 58 C ALT 3 36.950 33.931 28.952 0.2410 1.7000 C ATOM 59 O ALT 3 37.942 33.411 29.457 -0.2710 1.5000 O ATOM 60 N TYS 4 35.899 33.196 28.552 -0.4937 1.5500 N ATOM 61 H TYS 4 35.100 33.667 28.132 0.3018 1.3000 H ATOM 62 CA TYS 4 35.774 31.731 28.752 0.0416 1.7000 C ATOM 63 HA TYS 4 36.592 31.350 29.363 0.0184 1.3000 H ATOM 64 CG TYS 4 35.915 31.032 27.387 0.0293 1.7000 C ATOM 65 CD1 TYS 4 37.064 31.340 26.647 -0.0504 1.7000 C ATOM 66 HD1 TYS 4 37.819 31.980 27.079 0.1123 1.3000 H ATOM 67 CE1 TYS 4 37.173 31.004 25.289 0.1207 1.7000 C ATOM 68 CZ TYS 4 36.260 30.080 24.722 0.1207 1.7000 C ATOM 69 OZ TYS 4 36.455 29.602 23.440 -0.4710 1.5000 O ATOM 70 CE2 TYS 4 35.097 29.726 25.454 0.1207 1.7000 C ATOM 71 CD2 TYS 4 34.922 30.228 26.771 -0.0504 1.7000 C ATOM 72 HD2 TYS 4 34.010 30.010 27.299 0.1123 1.3000 H ATOM 73 C TYS 4 34.499 31.386 29.564 0.6731 1.7000 C ATOM 74 O TYS 4 33.721 32.279 29.900 -0.5854 1.5000 O ATOM 75 N TYD 5 34.272 30.116 29.919 -0.4937 1.5500 N ATOM 76 H TYD 5 34.961 29.411 29.683 0.3018 1.3000 H ATOM 77 CA TYD 5 32.967 29.676 30.438 -0.0010 1.7000 C ATOM 78 HA TYD 5 32.221 30.350 30.032 0.0556 1.3000 H ATOM 79 CG TYD 5 32.862 29.774 31.951 -0.0017 1.7000 C ATOM 80 CD1 TYD 5 31.929 30.668 32.507 -0.1459 1.7000 C ATOM 81 HD1 TYD 5 31.549 31.481 31.906 0.1195 1.3000 H ATOM 82 CE1 TYD 5 31.395 30.433 33.787 -0.0020 1.7000 C ATOM 83 CZ TYD 5 31.884 29.356 34.562 0.2516 1.7000 C ATOM 84 OH TYD 5 31.297 29.002 35.743 -0.4757 1.5000 O ATOM 85 HH TYD 5 31.363 28.045 35.908 0.3583 0.8000 H ATOM 86 CE2 TYD 5 32.932 28.561 34.065 -0.1648 1.7000 C ATOM 87 HE2 TYD 5 33.303 27.738 34.658 0.1367 1.3000 H ATOM 88 CD2 TYD 5 33.429 28.775 32.768 -0.1459 1.7000 C ATOM 89 HD2 TYD 5 34.171 28.100 32.364 0.1195 1.3000 H ATOM 90 C TYD 5 32.528 28.251 30.047 0.6731 1.7000 C ATOM 91 O TYD 5 33.374 27.383 29.833 -0.5854 1.5000 O ATOM 92 N TYF 6 31.236 27.931 29.971 -0.4937 1.5500 N ATOM 93 H TYF 6 31.054 26.940 29.921 0.3018 1.3000 H ATOM 94 CA TYF 6 30.127 28.780 29.499 0.1416 1.7000 C ATOM 95 HA TYF 6 30.510 29.763 29.261 0.0184 1.3000 H ATOM 96 CB TYF 6 29.605 28.188 28.169 0.2300 1.7000 C ATOM 97 OB2 TYF 6 29.087 26.879 28.332 -0.5593 1.5000 O ATOM 98 HB2 TYF 6 28.317 26.937 28.917 0.3687 0.8000 H ATOM 99 HB3 TYF 6 28.762 28.796 27.835 0.0242 1.3000 H ATOM 100 CG TYF 6 30.651 28.187 27.049 0.0293 1.7000 C ATOM 101 CD1 TYF 6 31.735 27.280 27.074 -0.0972 1.7000 C ATOM 102 HD1 TYF 6 31.726 26.442 27.758 0.1123 1.3000 H ATOM 103 CE1 TYF 6 32.892 27.534 26.319 -0.1050 1.7000 C ATOM 104 HE1 TYF 6 33.770 26.918 26.441 0.1161 1.3000 H ATOM 105 CZ TYF 6 32.928 28.625 25.435 0.1720 1.7000 C ATOM 106 OZ TYF 6 34.116 28.960 24.830 -0.4700 1.5000 O ATOM 107 CE2 TYF 6 31.739 29.352 25.202 0.2080 1.7000 C ATOM 108 Cl TYF 6 31.631 30.470 23.887 -0.1000 1.7000 CL ATOM 109 CD2 TYF 6 30.628 29.180 26.048 -0.0972 1.7000 C ATOM 110 HD2 TYF 6 29.772 29.833 25.947 0.1123 1.3000 H ATOM 111 C TYF 6 29.037 28.959 30.582 0.6731 1.7000 C ATOM 112 O TYF 6 28.057 28.209 30.617 -0.5854 1.5000 O ATOM 113 N TOL 7 29.223 29.925 31.494 -0.4937 1.5500 N ATOM 114 H TOL 7 29.916 30.634 31.317 0.3018 1.3000 H ATOM 115 CA TOL 7 28.578 29.931 32.815 -0.0116 1.7000 C ATOM 116 HA TOL 7 27.517 30.081 32.615 0.0184 1.3000 H ATOM 117 CG TOL 7 29.008 31.104 33.706 0.0293 1.7000 C ATOM 118 CD1 TOL 7 30.321 31.234 34.243 -0.0020 1.7000 C ATOM 119 CE1 TOL 7 30.558 32.130 35.312 0.1216 1.7000 C ATOM 120 OE1 TOL 7 31.810 32.325 35.829 -0.4757 1.5000 O ATOM 121 HE1 TOL 7 32.480 31.761 35.426 0.3580 0.8000 H ATOM 122 CZ TOL 7 29.493 32.837 35.889 -0.0548 1.7000 C ATOM 123 HZ TOL 7 29.675 33.480 36.736 0.1194 1.3000 H ATOM 124 CE2 TOL 7 28.198 32.693 35.378 0.1216 1.7000 C ATOM 125 OE2 TOL 7 27.140 33.219 36.057 -0.4757 1.5000 O ATOM 126 HE2 TOL 7 27.316 33.278 37.011 0.3580 0.8000 H ATOM 127 CD2 TOL 7 27.969 31.890 34.256 -0.1248 1.7000 C ATOM 128 HD2 TOL 7 26.959 31.792 33.885 0.1195 1.3000 H ATOM 129 C TOL 7 28.688 28.630 33.642 0.6107 1.7000 C ATOM 130 O TOL 7 29.501 27.748 33.356 -0.5200 1.5000 O TER 131 TOL 7 ATOM 131 C1 2GB 8 37.541 28.639 23.185 0.3840 1.7000 C ATOM 132 H1 2GB 8 37.383 27.763 23.816 0.0000 1.3000 H ATOM 133 O5 2GB 8 38.838 29.237 23.561 -0.4710 1.5000 O ATOM 134 C5 2GB 8 40.101 28.528 23.252 0.2250 1.7000 C ATOM 135 H5 2GB 8 40.116 27.599 23.826 0.0000 1.3000 H ATOM 136 C6 2GB 8 41.276 29.413 23.728 0.2820 1.7000 C ATOM 137 H62 2GB 8 42.225 29.055 23.327 0.0000 1.3000 H ATOM 138 H61 2GB 8 41.335 29.367 24.816 0.0000 1.3000 H ATOM 139 O6 2GB 8 41.079 30.797 23.346 -0.6880 1.5000 O ATOM 140 H6O 2GB 8 40.146 31.000 23.550 0.4240 0.8000 H ATOM 141 C4 2GB 8 40.144 28.183 21.752 0.2760 1.7000 C ATOM 142 H4 2GB 8 40.311 29.087 21.163 0.0000 1.3000 H ATOM 143 O4 2GB 8 41.243 27.251 21.530 -0.7140 1.5000 O ATOM 144 H4O 2GB 8 42.089 27.709 21.360 0.4400 0.8000 H ATOM 145 C3 2GB 8 38.834 27.489 21.291 0.2840 1.7000 C ATOM 146 H3 2GB 8 38.802 26.492 21.737 0.0000 1.3000 H ATOM 147 O3 2GB 8 38.897 27.334 19.845 -0.7090 1.5000 O ATOM 148 H3O 2GB 8 39.783 27.018 19.619 0.4320 0.8000 H ATOM 149 C2 2GB 8 37.531 28.228 21.694 0.3100 1.7000 C ATOM 150 H2 2GB 8 37.426 29.135 21.096 0.0000 1.3000 H ATOM 151 O2 2GB 8 36.350 27.330 21.496 -0.4750 1.5000 O ATOM 152 C1 VAM 9 35.677 27.434 20.198 0.3420 1.7000 C ATOM 153 H1 VAM 9 36.396 27.232 19.405 0.0000 1.3000 H ATOM 154 O5 VAM 9 35.126 28.787 20.006 -0.5700 1.5000 O ATOM 155 C5 VAM 9 34.047 29.189 20.937 0.2200 1.7000 C ATOM 156 H5 VAM 9 34.396 29.079 21.962 0.0000 1.3000 H ATOM 157 C6 VAM 9 33.760 30.675 20.711 0.0500 1.7000 C ATOM 158 H61 VAM 9 34.631 31.284 20.955 0.0000 1.3000 H ATOM 159 H62 VAM 9 32.938 31.022 21.335 0.0000 1.3000 H ATOM 160 H63 VAM 9 33.494 30.887 19.674 0.0000 1.3000 H ATOM 161 C4 VAM 9 32.857 28.230 20.705 0.2700 1.7000 C ATOM 162 H4 VAM 9 32.037 28.493 21.374 0.0000 1.3000 H ATOM 163 O4 VAM 9 32.394 28.385 19.326 -0.7130 1.5000 O ATOM 164 H4O VAM 9 33.123 28.788 18.829 0.4300 0.8000 H ATOM 165 C3 VAM 9 33.264 26.733 20.930 0.2800 1.7000 C ATOM 166 C7 VAM 9 33.459 26.435 22.433 0.0540 1.7000 C ATOM 167 H71 VAM 9 33.711 25.388 22.608 0.0000 1.3000 H ATOM 168 H72 VAM 9 32.553 26.644 23.007 0.0000 1.3000 H ATOM 169 H73 VAM 9 34.252 27.028 22.884 0.0000 1.3000 H ATOM 170 N3 VAM 9 32.125 25.850 20.470 -0.7230 1.5500 N ATOM 171 H31 VAM 9 32.375 24.867 20.363 0.4200 1.3000 H ATOM 172 H32 VAM 9 31.792 26.202 19.584 0.4200 1.3000 H ATOM 173 H33 VAM 9 31.337 25.910 21.116 0.4200 1.3000 H ATOM 174 C2 VAM 9 34.543 26.390 20.112 0.1000 1.7000 C ATOM 175 H21 VAM 9 34.278 26.288 19.057 0.0000 1.3000 H ATOM 176 H22 VAM 9 34.924 25.406 20.393 0.0000 1.3000 H TER 177 VAM 9 ATOM 177 N1 NM2 10 27.853 28.529 34.675 -0.4600 1.5500 N ATOM 178 HN1 NM2 10 27.150 29.248 34.789 0.2750 1.3000 H ATOM 179 CA NM2 10 27.884 27.489 35.687 0.2600 1.7000 C ATOM 180 HA1 NM2 10 27.436 27.807 36.626 -0.0375 1.3000 H ATOM 181 HA2 NM2 10 28.879 27.147 35.965 -0.0375 1.3000 H ATOM 182 CB NM2 10 27.079 26.265 35.218 0.2600 1.7000 C ATOM 183 HB1 NM2 10 26.125 26.624 34.833 -0.0375 1.3000 H ATOM 184 HB2 NM2 10 26.832 25.705 36.119 -0.0375 1.3000 H ATOM 185 N2 NM2 10 27.880 25.514 34.267 -0.4600 1.5500 N ATOM 186 HN2 NM2 10 28.690 25.975 33.863 0.2750 1.3000 H ATOM 187 O6 GKI 11 26.221 18.556 37.962 -0.7000 1.5000 O ATOM 188 H6O GKI 11 26.584 17.876 37.361 0.4200 0.8000 H ATOM 189 C6 GKI 11 26.704 19.837 37.498 0.2200 1.7000 C ATOM 190 H61 GKI 11 26.521 20.572 38.281 0.0000 1.3000 H ATOM 191 H62 GKI 11 26.123 20.130 36.623 0.0000 1.3000 H ATOM 192 C5 GKI 11 28.213 19.798 37.150 0.2200 1.7000 C ATOM 193 H5 GKI 11 28.752 19.358 37.991 0.0000 1.3000 H ATOM 194 O5 GKI 11 28.402 18.954 35.984 -0.7000 1.5000 O ATOM 195 H5O GKI 11 28.431 19.526 35.196 0.4200 0.8000 H ATOM 196 C4 GKI 11 28.767 21.229 36.883 0.2200 1.7000 C ATOM 197 H4 GKI 11 28.435 21.845 37.718 0.0000 1.3000 H ATOM 198 O4 GKI 11 30.230 21.253 36.913 -0.7000 1.5000 O ATOM 199 H4O GKI 11 30.507 21.309 37.843 0.4200 0.8000 H ATOM 200 C3 GKI 11 28.235 21.915 35.592 0.2200 1.7000 C ATOM 201 H3 GKI 11 27.149 21.818 35.610 0.0000 1.3000 H ATOM 202 O3 GKI 11 28.701 21.217 34.403 -0.7000 1.5000 O ATOM 203 H3O GKI 11 29.604 21.511 34.219 0.4200 0.8000 H ATOM 204 C2 GKI 11 28.531 23.431 35.488 0.2200 1.7000 C ATOM 205 H2 GKI 11 28.147 23.899 36.395 0.0000 1.3000 H ATOM 206 O2 GKI 11 29.968 23.670 35.440 -0.7000 1.5000 O ATOM 207 H2O GKI 11 30.380 23.055 36.074 0.4200 0.8000 H ATOM 208 C1 GKI 11 27.817 24.059 34.269 0.3000 1.7000 C ATOM 209 H11 GKI 11 28.254 23.693 33.339 0.0000 1.3000 H ATOM 210 H12 GKI 11 26.765 23.774 34.281 0.0000 1.3000 H TER 211 GKI 11 ATOM 211 HH31 ACE 12 19.082 37.862 40.718 0.0128 1.3000 H ATOM 212 CH3 ACE 12 19.282 36.946 40.160 -0.0010 1.7000 C ATOM 213 HH32 ACE 12 18.657 36.906 39.266 0.0128 1.3000 H ATOM 214 HH33 ACE 12 19.044 36.112 40.820 0.0128 1.3000 H ATOM 215 C ACE 12 20.766 36.892 39.804 0.5513 1.7000 C ATOM 216 O ACE 12 21.612 36.944 40.696 -0.5886 1.5000 O ATOM 217 N ALA 13 21.065 36.798 38.504 -0.5098 1.5500 N ATOM 218 H ALA 13 20.295 36.750 37.848 0.3229 1.3000 H ATOM 219 CA ALA 13 22.393 36.667 37.879 -0.0680 1.7000 C ATOM 220 HA ALA 13 23.033 37.486 38.205 0.1146 1.3000 H ATOM 221 CB ALA 13 23.076 35.371 38.345 -0.0148 1.7000 C ATOM 222 HB1 ALA 13 22.447 34.512 38.099 0.0283 1.3000 H ATOM 223 HB2 ALA 13 24.040 35.258 37.846 0.0283 1.3000 H ATOM 224 HB3 ALA 13 23.246 35.397 39.422 0.0283 1.3000 H ATOM 225 C ALA 13 22.282 36.703 36.343 0.6546 1.7000 C ATOM 226 O ALA 13 21.205 36.437 35.811 -0.5844 1.5000 O ATOM 227 N GLI 14 23.378 37.012 35.635 -0.4937 1.5500 N ATOM 228 H GLI 14 24.222 37.231 36.142 0.3018 1.3000 H ATOM 229 CA GLI 14 23.449 37.028 34.155 -0.2384 1.7000 C ATOM 230 CD GLI 14 24.219 38.247 33.644 0.6613 1.7000 C ATOM 231 OE1 GLI 14 23.581 39.276 33.326 -0.7362 1.5000 O ATOM 232 OE2 GLI 14 25.458 38.180 33.501 -0.7362 1.5000 O ATOM 233 HA GLI 14 22.431 37.132 33.779 0.0937 1.3000 H ATOM 234 CB GLI 14 24.033 35.694 33.648 0.3053 1.7000 C ATOM 235 HB2 GLI 14 25.068 35.597 33.971 -0.0704 1.3000 H ATOM 236 HB3 GLI 14 23.477 34.882 34.113 -0.0704 1.3000 H ATOM 237 CG GLI 14 23.912 35.524 32.126 -0.1671 1.7000 C ATOM 238 HG2 GLI 14 23.268 34.671 31.912 0.0313 1.3000 H ATOM 239 HG3 GLI 14 23.449 36.412 31.697 0.0313 1.3000 H ATOM 240 C GLI 14 25.254 35.321 31.433 0.6731 1.7000 C ATOM 241 O GLI 14 25.413 34.396 30.638 -0.5854 1.5000 O ATOM 242 N LYS 15 26.188 36.262 31.618 -0.3752 1.5500 N ATOM 243 H LYS 15 25.983 36.934 32.356 0.3004 1.3000 H ATOM 244 CA LYS 15 27.487 36.360 30.927 -0.3992 1.7000 C ATOM 245 HA LYS 15 27.335 36.166 29.865 0.1972 1.5000 H ATOM 246 CB LYS 15 28.070 37.780 31.110 -0.0135 1.7000 C ATOM 247 HB2 LYS 15 27.823 38.180 32.096 0.0565 1.3000 H ATOM 248 HB3 LYS 15 29.158 37.707 31.069 0.0565 1.3000 H ATOM 249 CG LYS 15 27.687 38.761 29.982 -0.0146 1.7000 C ATOM 250 HG2 LYS 15 28.254 39.682 30.122 0.0356 1.3000 H ATOM 251 HG3 LYS 15 28.036 38.323 29.045 0.0356 1.3000 H ATOM 252 CD LYS 15 26.198 39.124 29.796 -0.0224 1.7000 C ATOM 253 HD2 LYS 15 26.033 39.258 28.727 0.0378 1.3000 H ATOM 254 HD3 LYS 15 25.553 38.308 30.111 0.0378 1.3000 H ATOM 255 CE LYS 15 25.750 40.428 30.470 0.1242 1.7000 C ATOM 256 HE2 LYS 15 26.478 41.197 30.190 0.0848 1.3000 H ATOM 257 HE3 LYS 15 24.784 40.740 30.064 0.0848 1.3000 H ATOM 258 NZ LYS 15 25.673 40.341 31.947 -0.7709 1.5500 N ATOM 259 HZ1 LYS 15 26.058 39.480 32.343 0.4522 1.3000 H ATOM 260 HZ2 LYS 15 26.041 41.143 32.429 0.4522 1.3000 H ATOM 261 HZ3 LYS 15 24.710 40.194 32.274 0.4522 1.3000 H ATOM 262 C LYS 15 28.477 35.262 31.343 0.7825 1.7000 C ATOM 263 O LYS 15 28.406 34.703 32.429 -0.5946 1.5000 O ATOM 264 N AL2 16 29.462 35.024 30.485 -0.4937 1.5500 N ATOM 265 H AL2 16 29.456 35.522 29.614 0.3018 1.3000 H ATOM 266 CA AL2 16 30.476 33.981 30.666 0.0448 1.7000 C ATOM 267 HA AL2 16 30.070 33.212 31.323 0.0228 1.3000 H ATOM 268 CB AL2 16 31.710 34.587 31.360 -0.0909 1.7000 C ATOM 269 HB1 AL2 16 32.148 35.372 30.739 0.0425 1.3000 H ATOM 270 HB2 AL2 16 31.407 35.012 32.320 0.0425 1.3000 H ATOM 271 HB3 AL2 16 32.452 33.807 31.543 0.0425 1.3000 H ATOM 272 C AL2 16 30.792 33.279 29.326 0.6731 1.7000 C ATOM 273 O AL2 16 30.347 32.145 29.105 -0.5854 1.5000 O ATOM 274 N AL3 17 31.512 33.977 28.433 -0.4420 1.5500 N ATOM 275 H AL3 17 31.915 34.858 28.728 0.2952 1.3000 H ATOM 276 CA AL3 17 31.636 33.700 26.997 -0.0679 1.7000 C ATOM 277 HA AL3 17 30.639 33.617 26.552 0.0708 1.3000 H ATOM 278 CB AL3 17 32.450 32.418 26.779 -0.1226 1.7000 C ATOM 279 HB1 AL3 17 31.905 31.558 27.171 0.0586 1.3000 H ATOM 280 HB2 AL3 17 32.636 32.291 25.709 0.0586 1.3000 H ATOM 281 HB3 AL3 17 33.409 32.517 27.285 0.0586 1.3000 H ATOM 282 C AL3 17 32.349 34.893 26.333 0.5771 1.7000 C ATOM 283 O AL3 17 33.597 34.906 26.300 -0.7432 1.5000 O ATOM 284 OXT AL3 17 31.676 35.839 25.883 -0.7432 1.5000 O TER 285 AL3 17 ATOM 285 Cl- Cl- 18 29.096 39.822 23.017 -1.0000 1.7000 CL ENDTen sam plik PDB można pobrać tutaj.
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Data ostatniej modyfikacji strony: 09.08.2023 r.