Re: [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ

From: Daniel Roe <>
Date: Thu, 14 Oct 2021 10:17:04 -0400


On Tue, Oct 12, 2021 at 5:23 PM Maghsoud, Yazdan
<> wrote:
> As you see the above-mentioned command gives the atom numbers (13747.000) and their related fluctuation (0.4459). What I want is something like the following:
> #Frame CA HA CB HB2 HB3 ....

Atomic fluctuations are by definition an average property - hence
getting a "per-frame" fluctuation doesn't make sense. Something that
may suit your purposes better is calculating the per-residue RMSD
using the 'rms' command and the 'perres' and related keywords. See the
manual for full details.

Hope this helps,


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Received on Thu Oct 14 2021 - 07:30:03 PDT
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