[gmx-users] Rotated protein
Shima Arasteh
shima_arasteh2001 at yahoo.com
Sat Sep 15 07:56:52 CEST 2012
Sorry for unclear explanation.
1. First step:
editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro
2. Second step:
editconf -f protein-rotate.gro -o protein-rotate.pdb
Some lines of protein.pdb are :
ATOM 59 CB PHE 9 -7.899 7.143 -7.348 1.00 0.00
ATOM 60 CG PHE 9 -8.253 5.762 -7.846 1.00 0.00
ATOM 61 CD1 PHE 9 -8.061 5.433 -9.193 1.00 0.00
ATOM 62 CD2 PHE 9 -8.775 4.811 -6.960 1.00 0.00
ATOM 63 CE1 PHE 9 -8.389 4.152 -9.654 1.00 0.00
ATOM 64 CE2 PHE 9 -9.103 3.530 -7.422 1.00 0.00
ATOM 65 CZ PHE 9 -8.910 3.201 -8.768 1.00 0.00
ATOM 66 N SER 10 -8.048 5.490 -4.333 1.00 0.00
ATOM 67 CA SER 10 -7.399 4.461 -3.545 1.00 0.00
ATOM 68 C SER 10 -7.862 3.074 -3.967 1.00 0.00
ATOM 69 O SER 10 -9.048 2.763 -3.893 1.00 0.00
ATOM 70 CB SER 10 -7.715 4.626 -2.061 1.00 0.00
ATOM 71 OG SER 10 -7.060 3.595 -1.317 1.00 0.00
ATOM 72 N VAL 11 -6.919 2.240 -4.412 1.00 0.00
ATOM 73 CA VAL 11 -7.231 0.893 -4.844 1.00 0.00
ATOM 74 C VAL 11 -6.484 -0.138 -4.010 1.00 0.00
ATOM 75 O VAL 11 -5.255 -0.142 -3.978 1.00 0.00
ATOM 76 CB VAL 11 -6.842 0.680 -6.304 1.00 0.00
ATOM 77 CG1 VAL 11 -5.344 0.911 -6.470 1.00 0.00
ATOM 78 CG2 VAL 11 -7.186 -0.746 -6.719 1.00 0.00
ATOM 79 N ALA 12 -7.230 -1.013 -3.332 1.00 0.00
ATOM 80 CA ALA 12 -6.639 -2.041 -2.501 1.00 0.00
ATOM 81 C ALA 12 -7.232 -2.023 -1.100 1.00 0.00
ATOM 82 O ALA 12 -8.430 -2.235 -0.927 1.00 0.00
ATOM 83 CB ALA 12 -6.879 -3.427 -3.090 1.00 0.00
ATOM 84 N VAL 13 -6.388 -1.768 -0.096 1.00 0.00
ATOM 85 CA VAL 13 -6.830 -1.722 1.283 1.00 0.00
ATOM 86 C VAL 13 -6.564 -0.357 1.899 1.00 0.00
ATOM 87 O VAL 13 -5.417 0.082 1.970 1.00 0.00
ATOM 88 CB VAL 13 -6.104 -2.765 2.127 1.00 0.00
ATOM 89 CG1 VAL 13 -4.604 -2.497 2.085 1.00 0.00
ATOM 90 CG2 VAL 13 -6.596 -2.685 3.568 1.00 0.00
ATOM 91 N SER 14 -7.625 0.316 2.347 1.00 0.00
ATOM 92 CA SER 14 -7.502 1.625 2.954 1.00 0.00
ATOM 93 C SER 14 -8.025 1.618 4.383 1.00 0.00
ATOM 94 O SER 14 -9.195 1.322 4.618 1.00 0.00
ATOM 95 CB SER 14 -8.295 2.670 2.173 1.00 0.00
ATOM 96 OG SER 14 -8.149 3.946 2.802 1.00 0.00
ATOM 97 N ILE 15 -7.154 1.946 5.341 1.00 0.00
ATOM 98 CA ILE 15 -7.529 1.975 6.740 1.00 0.00
ATOM 99 C ILE 15 -7.333 3.366 7.330 1.00 0.00
ATOM 100 O ILE 15 -6.221 3.889 7.337 1.00 0.00
ATOM 101 CB ILE 15 -6.665 0.989 7.518 1.00 0.00
ATOM 102 CG1 ILE 15 -7.058 1.022 8.991 1.00 0.00
ATOM 103 CG2 ILE 15 -5.197 1.377 7.376 1.00 0.00
ATOM 104 CD1 ILE 15 -6.196 0.034 9.770 1.00 0.00
ATOM 105 N ALA 16 -8.418 3.962 7.826 1.00 0.00
ATOM 106 CA ALA 16 -8.363 5.285 8.415 1.00 0.00
ATOM 107 C ALA 16 -9.408 6.205 7.798 1.00 0.00
ATOM 108 O ALA 16 -10.605 5.946 7.901 1.00 0.00
ATOM 109 CB ALA 16 -8.620 5.230 9.917 1.00 0.00
ATOM 110 N TRP 17 -8.952 7.281 7.154 1.00 0.00
ATOM 111 CA TRP 17 -9.845 8.231 6.524 1.00 0.00
ATOM 112 C TRP 17 -9.577 8.328 5.028 1.00 0.00
ATOM 113 O TRP 17 -8.475 8.680 4.613 1.00 0.00
ATOM 114 CB TRP 17 -9.671 9.625 7.118 1.00 0.00
ATOM 115 CG TRP 17 -10.563 10.689 6.524 1.00 0.00
ATOM 116 CD1 TRP 17 -10.610 11.984 6.862 1.00 0.00
ATOM 117 CD2 TRP 17 -11.513 10.535 5.505 1.00 0.00
ATOM 118 NE1 TRP 17 -11.601 12.598 6.034 1.00 0.00
ATOM 119 CE2 TRP 17 -12.112 11.692 5.238 1.00 0.00
ATOM 120 CE3 TRP 17 -11.874 9.386 4.792 1.00 0.00
ATOM 121 CZ2 TRP 17 -13.108 11.859 4.269 1.00 0.00
ATOM 122 CZ3 TRP 17 -12.876 9.531 3.810 1.00 0.00
ATOM 123 CH2 TRP 17 -13.466 10.718 3.561 1.00 0.00
ATOM 124 N SER 18 -10.590 8.013 4.218 1.00 0.00
ATOM 125 CA SER 18 -10.463 8.064 2.776 1.00 0.00
ATOM 126 C SER 18 -11.459 9.043 2.172 1.00 0.00
ATOM 127 O SER 18 -12.666 8.881 2.330 1.00 0.00
ATOM 128 CB SER 18 -10.717 6.695 2.153 1.00 0.00
ATOM 129 OG SER 18 -10.581 6.787 0.732 1.00 0.00
ATOM 130 N PHE 19 -10.949 10.062 1.476 1.00 0.00
ATOM 131 CA PHE 19 -11.793 11.061 0.853 1.00 0.00
ATOM 132 C PHE 19 -11.577 11.097 -0.654 1.00 0.00
ATOM 133 O PHE 19 -10.468 11.353 -1.121 1.00 0.00
ATOM 134 CB PHE 19 -11.491 12.453 1.399 1.00 0.00
ATOM 135 CG PHE 19 -12.324 13.565 0.806 1.00 0.00
ATOM 136 CD1 PHE 19 -12.135 14.885 1.233 1.00 0.00
ATOM 137 CD2 PHE 19 -13.285 13.276 -0.169 1.00 0.00
ATOM 138 CE1 PHE 19 -12.906 15.915 0.684 1.00 0.00
ATOM 139 CE2 PHE 19 -14.057 14.306 -0.719 1.00 0.00
ATOM 140 CZ PHE 19 -13.868 15.627 -0.292 1.00 0.00
ATOM 141 N ALA 20 -12.643 10.840 -1.417 1.00 0.00
ATOM 142 CA ALA 20 -12.567 10.842 -2.864 1.00 0.00
ATOM 143 C ALA 20 -13.134 9.555 -3.444 1.00 0.00
ATOM 144 O ALA 20 -14.313 9.256 -3.267 1.00 0.00
ATOM 145 CB ALA 20 -13.358 12.007 -3.452 1.00 0.00
ATOM 146 N ARG 21 -12.289 8.791 -4.140 1.00 0.00
ATOM 147 CA ARG 21 -12.706 7.541 -4.745 1.00 0.00
ATOM 148 C ARG 21 -11.901 6.372 -4.195 1.00 0.00
ATOM 149 O ARG 21 -10.680 6.340 -4.326 1.00 0.00
ATOM 150 CB ARG 21 -12.514 7.571 -6.256 1.00 0.00
ATOM 151 CG ARG 21 -12.964 6.242 -6.852 1.00 0.00
ATOM 152 CD ARG 21 -12.772 6.270 -8.364 1.00 0.00
ATOM 153 NE ARG 21 -13.198 4.992 -8.978 1.00 0.00
ATOM 154 CZ ARG 21 -13.133 4.760 -10.286 1.00 0.00
ATOM 155 NH1 ARG 21 -12.674 5.669 -11.142 1.00 0.00
ATOM 156 NH2 ARG 21 -13.544 3.575 -10.731 1.00 0.00
ATOM 157 N SER 22 -12.590 5.410 -3.579 1.00 0.00
ATOM 158 CA SER 22 -11.939 4.245 -3.012 1.00 0.00
ATOM 159 C SER 22 -12.455 2.964 -3.654 1.00 0.00
ATOM 160 O SER 22 -13.646 2.667 -3.586 1.00 0.00
And the corresponding rotated output.pdb is:
ATOM 59 CB PHE 9 -9.700 5.800 5.670 1.00 0.00
ATOM 60 CG PHE 9 -9.900 4.410 6.220 1.00 0.00
ATOM 61 CD1 PHE 9 -11.030 3.670 5.860 1.00 0.00
ATOM 62 CD2 PHE 9 -8.950 3.860 7.090 1.00 0.00
ATOM 63 CE1 PHE 9 -11.210 2.380 6.370 1.00 0.00
ATOM 64 CE2 PHE 9 -9.130 2.570 7.610 1.00 0.00
ATOM 65 CZ PHE 9 -10.260 1.830 7.250 1.00 0.00
ATOM 66 N SER 10 -6.490 5.170 6.730 1.00 0.00
ATOM 67 CA SER 10 -5.330 4.340 6.490 1.00 0.00
ATOM 68 C SER 10 -5.480 2.980 7.160 1.00 0.00
ATOM 69 O SER 10 -5.620 2.900 8.380 1.00 0.00
ATOM 70 CB SER 10 -4.060 4.990 7.030 1.00 0.00
ATOM 71 OG SER 10 -2.940 4.130 6.760 1.00 0.00
ATOM 72 N VAL 11 -5.460 1.910 6.360 1.00 0.00
ATOM 73 CA VAL 11 -5.590 0.560 6.870 1.00 0.00
ATOM 74 C VAL 11 -4.360 -0.280 6.540 1.00 0.00
ATOM 75 O VAL 11 -4.040 -0.470 5.370 1.00 0.00
ATOM 76 CB VAL 11 -6.810 -0.130 6.280 1.00 0.00
ATOM 77 CG1 VAL 11 -6.660 -0.210 4.760 1.00 0.00
ATOM 78 CG2 VAL 11 -6.910 -1.550 6.850 1.00 0.00
ATOM 79 N SER 1 -3.680 -0.780 7.570 1.00 0.00
ATOM 80 CA SER 1 -2.500 -1.590 7.390 1.00 0.00
ATOM 81 C SER 1 -1.340 -1.060 8.210 1.00 0.00
ATOM 82 O SER 1 -1.410 -1.020 9.440 1.00 0.00
ATOM 83 CB SER 1 -2.750 -3.030 7.820 1.00 0.00
ATOM 84 N SER 1 -0.260 -0.650 7.530 1.00 0.00
ATOM 85 CA SER 1 0.910 -0.130 8.200 1.00 0.00
ATOM 86 C SER 1 1.200 1.300 7.760 1.00 0.00
ATOM 87 O SER 1 1.430 1.550 6.580 1.00 0.00
ATOM 88 CB SER 1 2.150 -0.970 7.890 1.00 0.00
ATOM 89 CG1 SER 1 2.400 -0.970 6.390 1.00 0.00
ATOM 90 CG2 SER 1 3.360 -0.390 8.610 1.00 0.00
ATOM 91 N SER 1 1.200 2.230 8.710 1.00 0.00
ATOM 92 CA SER 1 1.460 3.630 8.410 1.00 0.00
ATOM 93 C SER 1 2.670 4.130 9.180 1.00 0.00
ATOM 94 O SER 1 2.690 4.110 10.410 1.00 0.00
ATOM 95 CB SER 1 0.270 4.500 8.800 1.00 0.00
ATOM 96 OG SER 1 0.570 5.870 8.490 1.00 0.00
ATOM 97 N SER 1 3.690 4.590 8.450 1.00 0.00
ATOM 98 CA SER 1 4.910 5.090 9.060 1.00 0.00
ATOM 99 C SER 1 5.150 6.550 8.670 1.00 0.00
ATOM 100 O SER 1 5.290 6.860 7.490 1.00 0.00
ATOM 101 CB SER 1 6.100 4.260 8.590 1.00 0.00
ATOM 102 CG1 SER 1 7.370 4.790 9.240 1.00 0.00
ATOM 103 CG2 SER 1 6.220 4.350 7.080 1.00 0.00
ATOM 104 CD1 SER 1 8.560 3.960 8.770 1.00 0.00
ATOM 105 N SER 1 5.200 7.430 9.670 1.00 0.00
ATOM 106 CA SER 1 5.430 8.840 9.430 1.00 0.00
ATOM 107 C SER 1 4.360 9.690 10.120 1.00 0.00
ATOM 108 O SER 1 2.700 8.210 11.190 1.00 0.00
ATOM 109 CB SER 1 6.780 9.280 9.970 1.00 0.00
ATOM 110 N SER 1 3.590 10.440 9.320 1.00 0.00
ATOM 111 CA SER 1 2.540 11.280 9.850 1.00 0.00
ATOM 112 C SER 1 1.180 10.890 9.300 1.00 0.00
ATOM 113 O SER 1 0.970 10.920 8.090 1.00 0.00
ATOM 114 CB SER 1 2.780 12.750 9.490 1.00 0.00
ATOM 115 CG SER 1 1.740 13.710 9.990 1.00 0.00
ATOM 116 CD1 SER 1 1.710 15.040 9.820 1.00 0.00
ATOM 117 CD2 SER 1 0.600 13.410 10.750 1.00 0.00
ATOM 118 NE1 SER 1 0.540 15.530 10.480 1.00 0.00
ATOM 119 CE2 SER 1 -0.090 14.520 11.020 1.00 0.00
ATOM 120 CE3 SER 1 0.140 12.180 11.220 1.00 0.00
ATOM 121 CZ2 SER 1 -1.280 14.540 11.760 1.00 0.00
ATOM 122 CZ3 SER 1 -1.060 12.180 11.960 1.00 0.00
ATOM 123 CH2 SER 1 -1.740 13.320 12.220 1.00 0.00
ATOM 124 N SER 1 0.260 10.510 10.190 1.00 0.00
ATOM 125 CA SER 1 -1.070 10.110 9.790 1.00 0.00
ATOM 126 C SER 1 -2.130 11.010 10.410 1.00 0.00
ATOM 127 O SER 1 -2.230 11.090 11.630 1.00 0.00
ATOM 128 CB SER 1 -1.360 8.670 10.220 1.00 0.00
ATOM 129 OG SER 1 -2.690 8.310 9.810 1.00 0.00
ATOM 130 N SER 1 -2.920 11.670 9.570 1.00 0.00
ATOM 131 CA SER 1 -3.960 12.560 10.040 1.00 0.00
ATOM 132 C SER 1 -5.330 12.110 9.550 1.00 0.00
ATOM 133 O SER 1 -5.570 12.040 8.350 1.00 0.00
ATOM 134 CB SER 1 -3.730 13.990 9.550 1.00 0.00
ATOM 135 CG SER 1 -4.770 14.990 9.990 1.00 0.00
ATOM 136 CD1 SER 1 -4.670 16.330 9.590 1.00 0.00
ATOM 137 CD2 SER 1 -5.840 14.580 10.790 1.00 0.00
ATOM 138 CE1 SER 1 -5.630 17.260 10.000 1.00 0.00
ATOM 139 CE2 SER 1 -6.810 15.510 11.200 1.00 0.00
ATOM 140 CZ SER 1 -6.700 16.850 10.810 1.00 0.00
ATOM 141 N ALA 2 -6.230 11.810 10.490 1.00 0.00
ATOM 142 CA ALA 2 -7.570 11.370 10.150 1.00 0.00
ATOM 143 C ALA 2 -7.920 10.080 10.870 1.00 0.00
ATOM 144 O ALA 2 -7.960 10.040 12.090 1.00 0.00
ATOM 145 CB ALA 2 -8.610 12.420 10.540 1.00 0.00
ATOM 146 N ALA 2 -8.170 9.010 10.100 1.00 0.00
ATOM 147 CA ALA 2 -8.520 7.720 10.660 1.00 0.00
ATOM 148 C ALA 2 -7.510 6.660 10.250 1.00 0.00
ATOM 149 O ALA 2 -7.330 6.400 9.070 1.00 0.00
ATOM 150 CB ALA 2 -9.890 7.270 10.190 1.00 0.00
ATOM 151 CG ALA 2 -10.220 5.910 10.810 1.00 0.00
ATOM 152 CD ALA 2 -11.590 5.460 10.340 1.00 0.00
ATOM 153 NE ALA 2 -11.940 4.140 10.920 1.00 0.00
ATOM 154 CZ ALA 2 -13.090 3.520 10.660 1.00 0.00
ATOM 155 NH1 ALA 2 -14.020 4.050 9.870 1.00 0.00
ATOM 156 NH2 ALA 2 -13.300 2.340 11.240 1.00 0.00
ATOM 157 N ALA 2 -6.850 6.050 11.240 1.00 0.00
ATOM 158 CA ALA 2 -5.860 5.020 10.980 1.00 0.00
ATOM 159 C ALA 2 -6.260 3.700 11.640 1.00 0.00
Sincerely,
Shima
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