Hi,
On Wed, Oct 2, 2024 at 2:03 PM Maghsoud, Yazdan
<
YazdanMaghsoud.my.unt.edu> wrote:
>
> I have a system consisting of 500 residues, and my goal is to align the MD trajectory (e.g., 20 ns) to residues 400-500 in the reference PDB file. After aligning, I want to calculate the RMSF for residues 1-399 to evaluate how that region fluctuates during the trajectory.
If you fit on residues 400-500 and then calculate the RMSF of atoms in
residues 1-399, you will be looking at the atomic fluctuations of
those atoms *with respect to* residues 400-500. This could potentially
be very noisy if the two regions move somewhat independently. When
calculate RMSF I tend to fit the atoms I'm interested in the
fluctuations for to an average structure, since RMSF makes the most
sense to me as "variance in position around an average center", but
you might be looking for something different. You could also do a
'nofit' RMSD of residues 1-399 after fitting to residues 400-500,
which will give you a sense for how much overall movement there is in
atoms of residues 1-399 with respect to residues 400-500.
> This way, I can focus on the fluctuations in residues 1-399 without including the variations in residues 400-500 in the analysis. I used some combinations for the <atomicfluct:1-399> line of my CPPTRAJ script but i believe I'm doing something wrong. I'm totally confused.
>
> This is my actual script for the CPPTRAJ with issues in the 5th line!
>
> reference ./input.pdb
> trajin ../production.dcd
> autoimage
> rms reference :400-500
> atomicfluct:1-399 ???
Well, other than there being no space after the 'atomicfluct' command
before your atom mask (which you need), the only other thing you may
want to do is to print the results to a file with the 'out' keyword.
Again, I recommend reading the manual entries for the commands you are
using. If you're brand new to CPPTRAJ you may also want to check out
some tutorials (just google cpptraj tutorials).
Hope this helps,
-Dan
>
> ________________________________
> From: Maghsoud, Yazdan
> Sent: Tuesday, October 1, 2024 2:56 PM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Doing alignment on a specific region and run RMSF on ther reagion with CPPTRAJ
>
> 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 Thu Oct 03 2024 - 12:00:02 PDT
