Hi,
> rms reference :400-500
> rms reference :1-399 nofit out rmsd_aligned.dat
First, if you want to calculate RMSF you should use the 'atomicfluct'
(or 'rmsf') command. The commands you have up there will:
1) Perform a best-fit rotation/translation for all atoms in residues
400 to 500 to match those residues in the previously defined reference
structure.
2) Calculate the RMSD (no fitting) of all atoms in residues 1 to 399
with respect to the previously defined reference structure, i.e. you
will be measuring how much residues 1-399 move in the reference frame
of residues 400-500.
If you wanted the fluctuation of the atomic positions you'd use
something like 'rmsf :1-399 out rmsf.dat', but it's not clear that is
what you want. I recommend reading the manual entries for all of these
commands to better understand what they are doing.
Hope this helps,
-Dan
On Tue, Oct 1, 2024 at 3:57 PM Maghsoud, Yazdan via AMBER
<amber.ambermd.org> wrote:
>
> Dear AMBER users,
>
> Is it possible to align the MD trajectory to a specific region of the reference (e.g., resid 400-500) and then perform RMSF on region 1-400 with CPPTRAJ? Is it even meaningful to do such an analysis since RMSF measures the average deviation of atoms over time from their average positions?
> As far as i understand it is doable to align the trajectory with a specific region of the reference and do RMSD with respect to another region with the following lines for instance:
>
> reference ./input.pdb
> trajin ../production.dcd
>
> autoimage
>
> rms reference :400-500
> rms reference :1-399 nofit out rmsd_aligned.dat
>
> if it is doable and meaningful, could someone provide me with an example? I really appreciate if someone put some light on this matter.
>
> Best
>
> Yazdan
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Received on Wed Oct 02 2024 - 09:00:03 PDT
