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 Tue Oct 01 2024 - 13:30:02 PDT
