Hi,
If you mean RMSD of every frame in trajectory traj1 to trajectory
traj2 you can use cpptraj, e.g.:
parm myparm.parm7
trajin traj1.nc
createcrd crd1
run
rms2d crdset crd1 <mask> rmsout rmsd1.dat reftraj ref.nc
-Dan
On Fri, Feb 26, 2021 at 1:31 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
>
> Dear Amber user
> Could you please guide me if it is possible to calculate pairwise RMSD of
> two different proteins?
> I have gone through the following tutorial:-
> https://ambermd.org/tutorials/analysis/tutorial_notebooks/pytraj_notebook/index.html
> However, it is about comparing an NMR structure from the trajectory.
> Please give your suggestions. Is it right to compare two different proteins
> pairwise RMSD?
>
> Regards.
> Sadaf
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Received on Fri Feb 26 2021 - 13:00:02 PST
