[gmx-users] Problem reading pdb files

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 11 15:46:23 CEST 2017


Hi,

I imagine that at least one of the trajectories did not have a good PCA
analysis because you probably want both trajectories such that molecules
are whole with respect to PBC. The frame from the second trajectory is not.
There's a useful workflow at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
Doing this means that you'll be concatenating apples to apples.

Mark

On Fri, Jul 7, 2017 at 6:52 PM Nawel Mele <nawel.mele at gmail.com> wrote:

> 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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