[gmx-users] Rotated protein
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Sep 15 07:21:19 CEST 2012
On 15/09/2012 3:16 PM, Shima Arasteh wrote:
> Dear users,
>
> I rotated my protein to set in a proper direction:
> # editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro
> The generated protein-rotate.gro is something unusual, because the residue numbers and residue names are ordered incorrectly. Something 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.
>
> What's the problem? How can I solve it?
> Would you please help me
You're not showing us your output .gro file - that's a .pdb formatted
file above. In any case, you should show us corresponding sections of
your input and output if you think there's a problem.
Mark
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