[AMBER] Doing alignment on a specific region and run RMSF on ther reagion with CPPTRAJ

From: Maghsoud, Yazdan via AMBER <amber.ambermd.org>
Date: Tue, 1 Oct 2024 19:56:56 +0000

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 01 2024 - 13:30:02 PDT
Custom Search