AMBER Archive (2007)

Subject: AMBER: ptraj: RMS per residues and per time

From: Sascha Rehm (SaschaRehm_at_gmx.de)
Date: Tue Jul 03 2007 - 09:03:04 CDT

Hi all,

is there a ptraj-action (in Amber9) for calculating the RMS for each
residue and for each timestep? So that I get as result a file with say a
line for each timestep and a column for each residue which I then can
plot as a 3D-picture (x=time, y=residue, z=RMS).
I only know how to plot the RMS for the whole protein vs. the time but
that's not helpful since I want to see flexible residues through the time.

Thanks for the help,
regards,

Sacha
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