Thanks Daniel and Niel for your suggestions.
So here is my input script file which is am trying for only 6 frames
as a test.
trajin prod_cen_strip_sol_ion_peptide.mdcrd 1 6
trajin ../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd 1 6
rms2d rmsout output.dat .N,CA,C,O
and the output is:
#Frame Frame_1 Frame_2 Frame_3 Frame_4 Frame_5 Frame_6
1 0.000 0.544 1.295 1.119 1.127 1.109
2 0.544 0.000 1.233 0.959 0.981 1.009
3 1.295 1.233 0.000 0.556 1.231 1.278
4 1.119 0.959 0.556 0.000 1.063 1.050
5 1.127 0.981 1.231 1.063 0.000 0.420
6 1.109 1.009 1.278 1.050 0.420 0.000
So I believe the bottom left corner or the Upper right corner are the
RMSD between the frames of the trajectories and the other two boxes
represent the RMSD values within the frames of the trajectories.
Is that correct?
Well I think I am getting the required data for my analysis. But is
there anything else I can change do?
Dilraj.
Quoting dilrajl.bii.a-star.edu.sg:
> Dear Amber Users,
> I have two separate trajectories and I want to
> compute the RMSD between each frame of the first trajectory with
> every frame of the second trajectory.
>
> Is there any means by which one can do this in ptraj or cpptraj?
>
> Or if someone has tried this before, could you please direct in
> performing this analysis.
>
> Thank you.
> Dilraj.
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Received on Wed May 29 2013 - 05:30:03 PDT
