[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
leila karami
karami.leila1 at gmail.com
Mon Jan 3 15:17:03 CET 2011
for example ordering in final.pdb is as follows:
ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00
0.00
ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00
0.00
ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00
0.00
ATOM 1859 N3 DG3 X 86 14.160 46.250 20.930 1.00
0.00
ATOM 1860 C4 DG3 X 86 13.780 45.460 19.890 1.00
0.00
ATOM 1861 C3' DG3 X 86 10.130 43.520 22.330 1.00
0.00
ATOM 1862 H3' DG3 X 86 9.350 42.780 22.490 1.00
0.00
ATOM 1863 C2' DG3 X 86 10.400 43.920 20.880 1.00
0.00
ATOM 1864 H2'1 DG3 X 86 10.450 43.060 20.220 1.00
0.00
ATOM 1865 H2'2 DG3 X 86 9.720 44.720 20.580 1.00
0.00
ATOM 1866 O3' DG3 X 86 9.680 44.620 23.090 1.00
0.00
ATOM 1867 H3T DG3 X 86 8.790 44.770 22.760 1.00
0.00
ATOM 1868 OW SOL X 87 6.340 24.560 33.150 1.00
0.00
ATOM 1869 HW1 SOL X 87 6.550 24.130 33.980 1.00
0.00
ATOM 1870 HW2 SOL X 87 6.590 25.470 33.290 1.00
0.00
ATOM 1871 OW SOL X 88 9.070 15.110 50.520 1.00
0.00
ATOM 1872 HW1 SOL X 88 8.250 15.450 50.870 1.00
0.00
ATOM 1873 HW2 SOL X 88 9.210 15.590 49.700 1.00
0.00
ATOM 1874 OW SOL X 89 56.650 30.810 11.740 1.00
0.00
ATOM 1875 HW1 SOL X 89 56.550 30.850 12.690 1.00
0.00
ATOM 1876 HW2 SOL X 89 55.930 31.350 11.390 1.00 0.00
while I want that ordering be as follows:
ATOM 1856 N2 DG3 86 18.350 45.720 25.030 1.00 0.00
ATOM 1857 H21 DG3 86 19.090 46.250 24.600 1.00 0.00
ATOM 1858 H22 DG3 86 18.200 45.590 26.020 1.00 0.00
ATOM 1859 N3 DG3 86 16.690 44.090 24.990 1.00 0.00
ATOM 1860 C4 DG3 86 15.990 43.270 24.170 1.00 0.00
ATOM 1861 C3' DG3 86 12.600 41.300 27.150 1.00 0.00
ATOM 1862 H3' DG3 86 11.700 40.720 26.920 1.00 0.00
ATOM 1863 C2' DG3 86 12.940 42.170 25.940 1.00 0.00
ATOM 1864 1H2' DG3 86 12.480 41.850 25.010 1.00 0.00
ATOM 1865 2H2' DG3 86 12.630 43.200 26.160 1.00 0.00
ATOM 1866 O3' DG3 86 12.400 42.100 28.290 1.00 0.00
ATOM 1867 H3T DG3 86 12.270 41.510 29.030 1.00 0.00
ATOM 1868 Na Na 87 9.520 12.960 25.870 1.00 0.00
ATOM 1869 Na Na 88 10.890 27.910 9.650 1.00 0.00
ATOM 1870 Na Na 89 22.150 55.600 31.600 1.00 0.00
ATOM 1871 Na Na 90 36.340 1.500 6.140 1.00 0.00
ATOM 1872 Na Na 91 38.910 14.970 5.700 1.00 0.00
ATOM 1873 Na Na 92 37.660 9.000 16.270 1.00 0.00
ATOM 1874 Na Na 93 25.770 23.110 23.230 1.00 0.00
ATOM 1875 Na Na 94 53.000 2.470 52.760 1.00 0.00
ATOM 1876 Na Na 95 43.750 28.050 1.000 1.00 0.00
ATOM 1877 Na Na 96 44.200 48.440 0.470 1.00 0.00
ATOM 1878 Na Na 97 37.770 56.870 33.540 1.00 0.00
ATOM 1879 Na Na 98 54.240 26.650 18.640 1.00 0.00
ATOM 1880 Na Na 99 61.510 35.570 8.100 1.00 0.00
ATOM 1881 Na Na 100 61.950 46.140 43.640 1.00 0.00
ATOM 1882 OW SOL 101 28.260 19.060 16.930 1.00 0.00
ATOM 1883 HW1 SOL 101 28.610 19.950 16.980 1.00 0.00
ATOM 1884 HW SOL 101 27.370 19.140 17.290 1.00 0.00
ATOM 1885 OW SOL 102 34.220 11.510 13.510 1.00 0.00
ATOM 1886 HW1 SOL 102 34.420 11.880 12.660 1.00 0.00
ATOM 1887 HW2 SOL 102 34.660 12.090 14.140 1.00 0.00
ATOM 1888 OW SOL 103 18.620 9.650 16.990 1.00 0.00
ATOM 1889 HW1 SOL 103 18.280 8.870 17.430 1.00 0.00
ATOM 1890 HW2 SOL 103 19.560 9.620 17.160 1.00 0.00
ATOM 1891 OW SOL 104 22.090 26.530 6.110 1.00 0.00
ATOM 1892 HW1 SOL 104 21.560 25.810 6.460 1.00 0.00
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