[gmx-users] Problem reading pdb files

Nawel Mele nawel.mele at gmail.com
Fri Jul 7 18:52:32 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

-- 

Nawel Mele, PhD Research Student

Jonathan W Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ


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