[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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list