[gmx-users] Rotated protein
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Sep 15 07:44:02 CEST 2012
On 15/09/2012 3:33 PM, Shima Arasteh wrote:
>
> I need to say that I generated .pdb file of protein-rotate.gro .Yes, the lines sent you, are from the pdb file.
You can't get effective help if you won't describe your method
precisely. First, you claimed the generated .gro was unusual by showing
a .pdb file fragment. Now you're saying a .pdb file you generated from
the .gro output is unusual and you haven't said how you got that .pdb
file. How is anybody meant to know whether the problem is with editconf
-rotate -princ, or whatever else you used next?
> The lines of protein.pdb is :
> ATOM 55 N PHE 9 -7.786 8.725 -5.477 1.00 0.00
> ATOM 56 CA PHE 9 -8.154 7.378 -5.863 1.00 0.00
> ATOM 57 C PHE 9 -7.352 6.345 -5.084 1.00 0.00
> ATOM 58 O PHE 9 -6.125 6.323 -5.159 1.00 0.00
> 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
>
> And the corresponding protein-rotate.pdb file are as below:
>
> ATOM 55 N PHE 9 -8.330 7.830 5.550 1.00 0.00
>> ATOM 56 CA PHE 9 -8.430 6.510 6.130 1.00 0.00
>> ATOM 57 C PHE 9 -7.240 5.640 5.740 1.00 0.00
>> ATOM 58 O PHE 9 -7.010 5.400 4.550 1.00 0.00
>> 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 1 -6.490 5.170 6.730 1.00 0.00
>> ATOM 67 CA SER 1 -5.330 4.340 6.490 1.00 0.00
>> ATOM 68 C SER 1 -5.480 2.980 7.160 1.00 0.00
>> ATOM 69 O SER 1 -5.620 2.900 8.380 1.00 0.00
>> ATOM 70 CB SER 1 -4.060 4.990 7.030 1.00 0.00
>> ATOM 71 OG SER 1 -2.940 4.130 6.760 1.00 0.00
>> ATOM 72 N SER 1 -5.460 1.910 6.360 1.00 0.00
>> ATOM 73 CA SER 1 -5.590 0.560 6.870 1.00 0.00
>> ATOM 74 C SER 1 -4.360 -0.280 6.540 1.00 0.00
>> ATOM 75 O SER 1 -4.040 -0.470 5.370 1.00 0.00
>> ATOM 76 CB SER 1 -6.810 -0.130 6.280 1.00 0.00
>> ATOM 77 CG1 SER 1 -6.660 -0.210 4.760 1.00 0.00
>> ATOM 78 CG2 SER 1 -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.
> This problem goes up to the end of the rotated output.
> Would you suggest me please?
Looks like whatever you are using to produce that .pdb file is using a
routine that is only reading and/or writing the tens column of the
residue number. You should report a bug for it to whoever wrote it. If
you want .pdb output from editconf, use
editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.pdb
just like you can with all GROMACS tools.
Mark
More information about the gromacs.org_gmx-users
mailing list