[gmx-users] Problem reading pdb files
Nawel Mele
nawel.mele at gmail.com
Mon Jul 3 15:22:54 CEST 2017
Hi all,
I have two pdb files extracted from two trajectories of same compound but
starting from two different configurations. I wanted to combined the two
trajectories but I faced a broken structures behaviour while combining the
two ensembles. I just attached two first frames of each trajectories to
show you that they seem to look fine but once you combined them and
visualised them the second file is broken or vice versa . From that if I
want to perform a PCA analysis I got problem to extract the PC extreme
frames.
Do you have any ideas?
You ca try combined these two pdb files and you will understand my problem
:(
REMARK GENERATED BY TRJCONV
TITLE t= -1.00000
MODEL 1
ATOM 1 S1 MOL 1 27.620 28.290 12.400 1.00
0.00
ATOM 2 N1 MOL 1 28.150 27.440 11.100 1.00
0.00
ATOM 3 C1 MOL 1 26.140 29.080 11.850 1.00
0.00
ATOM 4 O1 MOL 1 27.210 27.410 13.450 1.00
0.00
ATOM 5 O2 MOL 1 28.600 29.300 12.640 1.00
0.00
ATOM 6 C2 MOL 1 28.260 23.230 11.350 1.00
0.00
ATOM 7 C3 MOL 1 28.320 21.730 11.340 1.00
0.00
ATOM 8 C4 MOL 1 27.040 23.890 11.180 1.00
0.00
ATOM 9 C5 MOL 1 25.790 23.130 11.010 1.00
0.00
ATOM 10 N2 MOL 1 24.870 23.160 12.000 1.00
0.00
ATOM 11 C6 MOL 1 25.110 23.640 13.330 1.00
0.00
ATOM 12 C7 MOL 1 24.070 24.700 13.670 1.00
0.00
ATOM 13 C8 MOL 1 22.620 24.190 13.510 1.00
0.00
ATOM 14 C9 MOL 1 23.610 22.490 11.780 1.00
0.00
ATOM 15 C10 MOL 1 22.580 22.790 12.880 1.00
0.00
ATOM 16 C11 MOL 1 27.000 25.290 11.090 1.00
0.00
ATOM 17 C12 MOL 1 28.180 26.030 11.180 1.00
0.00
ATOM 18 C13 MOL 1 29.420 25.370 11.350 1.00
0.00
ATOM 19 C14 MOL 1 30.710 26.130 11.440 1.00
0.00
ATOM 20 C15 MOL 1 29.450 23.970 11.440 1.00
0.00
ATOM 21 O3 MOL 1 25.600 22.520 9.960 1.00
0.00
ATOM 22 C16 MOL 1 20.040 26.830 11.260 1.00
0.00
ATOM 23 C17 MOL 1 19.650 26.350 12.520 1.00
0.00
ATOM 24 C18 MOL 1 20.490 25.480 13.210 1.00
0.00
ATOM 25 C19 MOL 1 21.750 25.130 12.710 1.00
0.00
ATOM 26 C20 MOL 1 22.140 25.630 11.460 1.00
0.00
ATOM 27 C21 MOL 1 21.280 26.460 10.730 1.00
0.00
ATOM 28 C22 MOL 1 19.140 27.610 10.450 1.00
0.00
ATOM 29 N3 MOL 1 18.480 28.240 9.700 1.00
0.00
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE t= -1.00000
MODEL 1
ATOM 1 S1 MOL 1 21.570 24.680 12.150 1.00
0.00
ATOM 2 N1 MOL 1 21.500 26.260 12.560 1.00
0.00
ATOM 3 C1 MOL 1 21.600 23.930 13.730 1.00
0.00
ATOM 4 O1 MOL 1 20.320 24.320 11.550 1.00
0.00
ATOM 5 O2 MOL 1 22.830 24.370 11.530 1.00
0.00
ATOM 6 C2 MOL 1 24.840 28.750 11.890 1.00
0.00
ATOM 7 C3 MOL 1 26.060 29.580 11.620 1.00
0.00
ATOM 8 C4 MOL 1 23.790 28.730 10.960 1.00
0.00
ATOM 9 C5 MOL 1 22.650 27.920 11.170 1.00
0.00
ATOM 10 N2 MOL 1 26.820 27.060 14.010 1.00
0.00
ATOM 11 C6 MOL 1 21.560 27.870 10.130 1.00
0.00
ATOM 12 C7 MOL 1 22.590 27.100 12.310 1.00
0.00
ATOM 13 C8 MOL 1 23.640 27.120 13.230 1.00
0.00
ATOM 14 C9 MOL 1 24.740 27.970 13.060 1.00
0.00
ATOM 15 C10 MOL 1 25.800 27.960 14.110 1.00
0.00
ATOM 16 C11 MOL 1 29.350 25.830 13.370 1.00
0.00
ATOM 17 C12 MOL 1 28.220 25.970 12.330 1.00
0.00
ATOM 18 C13 MOL 1 26.860 26.000 13.030 1.00
0.00
ATOM 19 C14 MOL 1 27.820 26.940 15.040 1.00
0.00
ATOM 20 C15 MOL 1 29.230 26.940 14.430 1.00
0.00
ATOM 21 O3 MOL 1 25.710 28.740 15.050 1.00
0.00
ATOM 22 C16 MOL 1 33.240 25.960 11.490 1.00
0.00
ATOM 23 C17 MOL 1 34.620 26.190 11.130 1.00
0.00
ATOM 24 C18 MOL 1 32.850 24.840 12.240 1.00
0.00
ATOM 25 C19 MOL 1 31.580 24.790 12.830 1.00
0.00
ATOM 26 C20 MOL 1 30.690 25.870 12.680 1.00
0.00
ATOM 27 C21 MOL 1 31.060 26.970 11.890 1.00
0.00
ATOM 28 C22 MOL 1 32.320 27.010 11.290 1.00
0.00
ATOM 29 N3 MOL 1 0.260 26.420 10.890 1.00
0.00
TER
ENDMDL
--
Nawel Mele, PhD Research Student
Jonathan W Essex Group, School of Chemistry
University of Southampton, Highfield
Southampton, SO17 1BJ
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