[gmx-users] protein unfolding
Aina Quintilla
aina.quintilla at int.fzk.de
Mon Mar 14 10:10:36 CET 2005
hi,
i am looking at the behaviour of a protein 1l2y.
during the run the protein is unfolding.. at every temperature, from 200 K ...
i am using the gromos96 43a1 force field
could anyone give me a hint about what is happening? is gromacs force field
not adequate to work with it?
i attach the input file (.pdb) of the run
thank you very much
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Header Topology file : 1l2ynmr.top
Header (c) 1994 Jan T Pedersen, CARB
Header Lib : /home/wenzel/projects/Protein/POEM/I/Data/HalLib3
ATOM 1 N ASN 1 -9.080 4.362 -0.252 -0.60 4.25
ATOM 2 HN1 ASN 1 -8.480 4.144 0.619 0.45 4.25
ATOM 3 HN2 ASN 1 -8.847 5.354 -0.611 0.45 4.25
ATOM 4 HN3 ASN 1 -10.127 4.311 0.010 0.45 4.25
ATOM 5 CA ASN 1 -8.787 3.370 -1.315 0.25 4.25
ATOM 6 C ASN 1 -7.296 3.199 -1.594 0.38 4.25
ATOM 7 O ASN 1 -6.813 2.084 -1.455 -0.38 4.25
ATOM 8 CB ASN 1 -9.616 3.631 -2.586 0.00 4.25
ATOM 9 CG ASN 1 -11.094 3.365 -2.308 0.38 4.25
ATOM 10 OD1 ASN 1 -11.448 2.935 -1.221 -0.38 4.25
ATOM 11 ND2 ASN 1 -11.985 3.641 -3.240 -0.56 4.25
ATOM 12 HNA ASN 1 -12.956 3.472 -3.069 0.28 4.25
ATOM 13 HNB ASN 1 -11.691 4.020 -4.117 0.28 4.25
ATOM 14 N LEU 2 -6.558 4.266 -1.925 -0.28 6.77
ATOM 15 HN LEU 2 -7.065 5.214 -2.035 0.28 6.77
ATOM 16 CA LEU 2 -5.102 4.237 -2.149 0.00 6.77
ATOM 17 C LEU 2 -4.315 3.422 -1.101 0.38 6.77
ATOM 18 O LEU 2 -3.570 2.509 -1.457 -0.38 6.77
ATOM 19 CB LEU 2 -4.590 5.685 -2.316 0.00 6.77
ATOM 20 CG LEU 2 -4.974 6.685 -1.192 0.00 6.77
ATOM 21 CD1 LEU 2 -3.791 7.038 -0.296 0.00 6.77
ATOM 22 CD2 LEU 2 -5.530 7.983 -1.781 0.00 6.77
ATOM 23 N TYR 3 -4.533 3.690 0.192 -0.28 5.30
ATOM 24 HN TYR 3 -5.233 4.474 0.443 0.28 5.30
ATOM 25 CA TYR 3 -3.869 2.973 1.284 0.00 5.30
ATOM 26 C TYR 3 -4.281 1.491 1.377 0.38 5.30
ATOM 27 O TYR 3 -3.470 0.644 1.745 -0.38 5.30
ATOM 28 CB TYR 3 -4.143 3.707 2.605 0.00 5.30
ATOM 29 CG TYR 3 -3.003 3.574 3.593 0.00 5.30
ATOM 30 CD1 TYR 3 -1.999 4.561 3.635 0.00 5.30
ATOM 31 CD2 TYR 3 -2.925 2.452 4.441 0.00 5.30
ATOM 32 CE1 TYR 3 -0.904 4.420 4.508 0.00 5.30
ATOM 33 CE2 TYR 3 -1.836 2.311 5.321 0.00 5.30
ATOM 34 CZ TYR 3 -0.818 3.288 5.346 0.03 5.30
ATOM 35 OH TYR 3 0.254 3.116 6.164 -0.38 5.30
ATOM 36 HOH TYR 3 0.307 2.311 6.755 0.35 5.30
ATOM 37 N ILE 4 -5.521 1.160 0.992 -0.28 6.89
ATOM 38 HN ILE 4 -6.191 1.962 0.718 0.28 6.89
ATOM 39 CA ILE 4 -6.036 -0.214 0.916 0.00 6.89
ATOM 40 C ILE 4 -5.268 -0.986 -0.167 0.38 6.89
ATOM 41 O ILE 4 -4.800 -2.099 0.077 -0.38 6.89
ATOM 42 CB ILE 4 -7.565 -0.231 0.646 0.00 6.89
ATOM 43 CG1 ILE 4 -8.376 0.775 1.500 0.00 6.89
ATOM 44 CG2 ILE 4 -8.138 -1.649 0.804 0.00 6.89
ATOM 45 CD1 ILE 4 -8.198 0.647 3.018 0.00 6.89
ATOM 46 N GLN 5 -5.086 -0.366 -1.342 -0.28 3.71
ATOM 47 HN GLN 5 -5.543 0.602 -1.485 0.28 3.71
ATOM 48 CA GLN 5 -4.301 -0.932 -2.440 0.00 3.71
ATOM 49 C GLN 5 -2.808 -1.086 -2.087 0.38 3.71
ATOM 50 O GLN 5 -2.165 -2.005 -2.581 -0.38 3.71
ATOM 51 CB GLN 5 -4.471 -0.078 -3.710 0.00 3.71
ATOM 52 CG GLN 5 -4.423 -0.936 -4.987 0.00 3.71
ATOM 53 CD GLN 5 -5.755 -1.625 -5.282 0.38 3.71
ATOM 54 OE1 GLN 5 -5.948 -2.809 -5.032 -0.38 3.71
ATOM 55 NE2 GLN 5 -6.711 -0.911 -5.849 -0.56 3.71
ATOM 56 HNA GLN 5 -7.595 -1.332 -6.055 0.28 3.71
ATOM 57 HNB GLN 5 -6.552 0.051 -6.072 0.28 3.71
ATOM 58 N TRP 6 -2.253 -0.224 -1.225 -0.28 5.74
ATOM 59 HN TRP 6 -2.828 0.634 -0.909 0.28 5.74
ATOM 60 CA TRP 6 -0.895 -0.396 -0.690 0.00 5.74
ATOM 61 C TRP 6 -0.810 -1.531 0.347 0.38 5.74
ATOM 62 O TRP 6 0.116 -2.344 0.299 -0.38 5.74
ATOM 63 CB TRP 6 -0.400 0.938 -0.114 0.00 5.74
ATOM 64 CG TRP 6 0.969 0.887 0.497 0.00 5.74
ATOM 65 CD1 TRP 6 2.140 0.899 -0.179 0.00 5.74
ATOM 66 CD2 TRP 6 1.329 0.799 1.909 0.00 5.74
ATOM 67 NE1 TRP 6 3.192 0.795 0.714 -0.28 5.74
ATOM 68 HNE TRP 6 4.231 0.755 0.426 0.28 5.74
ATOM 69 CE2 TRP 6 2.749 0.750 2.013 0.00 5.74
ATOM 70 CE3 TRP 6 0.600 0.759 3.115 0.00 5.74
ATOM 71 CZ2 TRP 6 3.420 0.680 3.241 0.00 5.74
ATOM 72 CZ3 TRP 6 1.260 0.668 4.356 0.00 5.74
ATOM 73 CH2 TRP 6 2.663 0.642 4.423 0.00 5.74
ATOM 74 N LEU 7 -1.779 -1.625 1.270 -0.28 6.77
ATOM 75 HN LEU 7 -2.561 -0.879 1.279 0.28 6.77
ATOM 76 CA LEU 7 -1.820 -2.697 2.266 0.00 6.77
ATOM 77 C LEU 7 -2.026 -4.084 1.645 0.38 6.77
ATOM 78 O LEU 7 -1.323 -5.013 2.045 -0.38 6.77
ATOM 79 CB LEU 7 -2.889 -2.410 3.336 0.00 6.77
ATOM 80 CG LEU 7 -2.480 -1.344 4.372 0.00 6.77
ATOM 81 CD1 LEU 7 -3.654 -1.088 5.321 0.00 6.77
ATOM 82 CD2 LEU 7 -1.272 -1.772 5.217 0.00 6.77
ATOM 83 N LYS 8 -2.932 -4.246 0.663 -0.28 3.59
ATOM 84 HN LYS 8 -3.484 -3.383 0.321 0.28 3.59
ATOM 85 CA LYS 8 -3.203 -5.556 0.034 0.00 3.59
ATOM 86 C LYS 8 -1.975 -6.192 -0.634 0.38 3.59
ATOM 87 O LYS 8 -1.898 -7.413 -0.727 -0.38 3.59
ATOM 88 CB LYS 8 -4.403 -5.462 -0.929 0.00 3.59
ATOM 89 CG LYS 8 -4.109 -4.774 -2.274 0.00 3.59
ATOM 90 CD LYS 8 -3.861 -5.751 -3.433 0.12 3.59
ATOM 91 CE LYS 8 -3.673 -4.964 -4.736 0.30 3.59
ATOM 92 NZ LYS 8 -4.742 -5.248 -5.720 -0.50 3.59
ATOM 93 HZA LYS 8 -4.581 -4.715 -6.551 0.36 3.59
ATOM 94 HZB LYS 8 -4.740 -6.223 -5.943 0.36 3.59
ATOM 95 HZC LYS 8 -5.629 -4.997 -5.331 0.36 3.59
ATOM 96 N ASP 9 -1.007 -5.372 -1.052 -0.28 3.70
ATOM 97 HN ASP 9 -1.196 -4.311 -0.977 0.28 3.70
ATOM 98 CA ASP 9 0.287 -5.781 -1.602 0.00 3.70
ATOM 99 C ASP 9 1.302 -6.229 -0.529 0.38 3.70
ATOM 100 O ASP 9 2.366 -6.736 -0.891 -0.38 3.70
ATOM 101 CB ASP 9 0.854 -4.604 -2.421 -0.20 3.70
ATOM 102 CG ASP 9 0.493 -4.671 -3.907 0.34 3.70
ATOM 103 OD1 ASP 9 -0.711 -4.816 -4.219 -0.57 3.70
ATOM 104 OD2 ASP 9 1.448 -4.580 -4.714 -0.57 3.70
ATOM 105 N GLY 10 1.006 -6.043 0.767 -0.28 4.82
ATOM 106 HN GLY 10 0.045 -5.607 0.999 0.28 4.82
ATOM 107 CA GLY 10 1.881 -6.383 1.896 0.00 4.82
ATOM 108 C GLY 10 2.449 -5.177 2.656 0.38 4.82
ATOM 109 O GLY 10 3.317 -5.359 3.511 -0.38 4.82
ATOM 110 N GLY 11 1.993 -3.952 2.358 -0.28 4.82
ATOM 111 HN GLY 11 1.248 -3.860 1.581 0.28 4.82
ATOM 112 CA GLY 11 2.447 -2.732 3.026 0.00 4.82
ATOM 113 C GLY 11 3.978 -2.567 2.957 0.38 4.82
ATOM 114 O GLY 11 4.531 -2.594 1.854 -0.38 4.82
ATOM 115 N PRO 12 4.692 -2.416 4.097 -0.42 6.32
ATOM 116 CA PRO 12 6.154 -2.298 4.109 0.21 6.32
ATOM 117 C PRO 12 6.879 -3.494 3.468 0.38 6.32
ATOM 118 O PRO 12 7.960 -3.327 2.904 -0.38 6.32
ATOM 119 CB PRO 12 6.561 -2.152 5.582 0.00 6.32
ATOM 120 CG PRO 12 5.281 -1.717 6.290 0.00 6.32
ATOM 121 CD PRO 12 4.183 -2.380 5.463 0.21 6.32
ATOM 122 N SER 13 6.284 -4.694 3.508 -0.28 4.51
ATOM 123 HN SER 13 5.296 -4.746 3.943 0.28 4.51
ATOM 124 CA SER 13 6.870 -5.944 3.007 0.00 4.51
ATOM 125 C SER 13 6.718 -6.134 1.488 0.38 4.51
ATOM 126 O SER 13 6.846 -7.253 1.000 -0.38 4.51
ATOM 127 CB SER 13 6.279 -7.136 3.775 0.03 4.51
ATOM 128 OG SER 13 6.584 -7.029 5.153 -0.38 4.51
ATOM 129 HOG SER 13 6.293 -7.675 5.740 0.35 4.51
ATOM 130 N SER 14 6.458 -5.055 0.737 -0.28 4.51
ATOM 131 HN SER 14 6.428 -4.096 1.233 0.28 4.51
ATOM 132 CA SER 14 6.210 -5.080 -0.712 0.00 4.51
ATOM 133 C SER 14 7.153 -4.170 -1.520 0.38 4.51
ATOM 134 O SER 14 6.903 -3.888 -2.690 -0.38 4.51
ATOM 135 CB SER 14 4.735 -4.758 -0.962 0.03 4.51
ATOM 136 OG SER 14 4.252 -5.508 -2.055 -0.38 4.51
ATOM 137 HOG SER 14 3.376 -5.418 -2.323 0.35 4.51
ATOM 138 N GLY 15 8.240 -3.685 -0.899 -0.28 4.82
ATOM 139 HN GLY 15 8.362 -3.898 0.153 0.28 4.82
ATOM 140 CA GLY 15 9.272 -2.881 -1.567 0.00 4.82
ATOM 141 C GLY 15 8.805 -1.490 -2.013 0.38 4.82
ATOM 142 O GLY 15 9.360 -0.942 -2.964 -0.38 4.82
ATOM 143 N ARG 16 7.777 -0.929 -1.357 -0.28 3.32
ATOM 144 HN ARG 16 7.413 -1.432 -0.473 0.28 3.32
ATOM 145 CA ARG 16 7.110 0.319 -1.751 0.00 3.32
ATOM 146 C ARG 16 6.676 1.151 -0.526 0.38 3.32
ATOM 147 O ARG 16 6.043 0.601 0.379 -0.38 3.32
ATOM 148 CB ARG 16 5.931 -0.008 -2.691 0.00 3.32
ATOM 149 CG ARG 16 4.867 -0.936 -2.075 0.00 3.32
ATOM 150 CD ARG 16 3.744 -1.357 -3.035 0.19 3.32
ATOM 151 NE ARG 16 4.072 -2.576 -3.797 -0.50 3.32
ATOM 152 HNE ARG 16 3.778 -3.508 -3.338 0.37 3.32
ATOM 153 CZ ARG 16 4.680 -2.679 -4.971 0.46 3.32
ATOM 154 NH1 ARG 16 5.110 -1.629 -5.634 -0.50 3.32
ATOM 155 NH2 ARG 16 4.856 -3.860 -5.506 -0.50 3.32
ATOM 156 HHA ARG 16 5.564 -1.746 -6.517 0.37 3.32
ATOM 157 HHB ARG 16 4.983 -0.712 -5.255 0.37 3.32
ATOM 158 HHC ARG 16 5.313 -3.944 -6.391 0.37 3.32
ATOM 159 HHD ARG 16 4.532 -4.677 -5.030 0.37 3.32
ATOM 160 N PRO 17 6.977 2.465 -0.477 -0.42 6.32
ATOM 161 CA PRO 17 6.603 3.323 0.648 0.21 6.32
ATOM 162 C PRO 17 5.082 3.566 0.698 0.38 6.32
ATOM 163 O PRO 17 4.407 3.400 -0.321 -0.38 6.32
ATOM 164 CB PRO 17 7.375 4.629 0.422 0.00 6.32
ATOM 165 CG PRO 17 7.498 4.709 -1.098 0.00 6.32
ATOM 166 CD PRO 17 7.641 3.245 -1.513 0.21 6.32
ATOM 167 N PRO 18 4.531 3.974 1.858 -0.42 6.32
ATOM 168 CA PRO 18 3.108 4.266 1.989 0.21 6.32
ATOM 169 C PRO 18 2.722 5.540 1.216 0.38 6.32
ATOM 170 O PRO 18 3.505 6.491 1.174 -0.38 6.32
ATOM 171 CB PRO 18 2.856 4.425 3.490 0.00 6.32
ATOM 172 CG PRO 18 4.206 4.890 4.032 0.00 6.32
ATOM 173 CD PRO 18 5.214 4.184 3.126 0.21 6.32
ATOM 174 N PRO 19 1.509 5.595 0.639 -0.42 6.32
ATOM 175 CA PRO 19 1.006 6.778 -0.050 0.21 6.32
ATOM 176 C PRO 19 0.536 7.842 0.958 0.38 6.32
ATOM 177 O PRO 19 -0.303 7.559 1.816 -0.38 6.32
ATOM 178 CB PRO 19 -0.131 6.249 -0.926 0.00 6.32
ATOM 179 CG PRO 19 -0.698 5.087 -0.109 0.00 6.32
ATOM 180 CD PRO 19 0.537 4.510 0.575 0.21 6.32
ATOM 181 N SER 20 1.092 9.057 0.852 -0.28 4.51
ATOM 182 HN SER 20 1.920 9.162 0.167 0.28 4.51
ATOM 183 CA SER 20 0.673 10.262 1.588 -0.25 4.51
ATOM 184 C SER 20 -0.585 10.892 0.986 0.65 4.51
ATOM 185 O SER 20 -0.566 11.151 -0.237 -0.70 4.51
ATOM 186 OT SER 20 -1.520 11.138 1.776 -0.70 4.51
ATOM 187 CB SER 20 1.793 11.306 1.587 0.03 4.51
ATOM 188 OG SER 20 2.941 10.776 2.214 -0.38 4.51
ATOM 189 HOG SER 20 3.701 11.289 2.291 0.35 4.51
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