AMBER Archive (2008)

Subject: Re: AMBER: about RMSD per residue

From: Wei Huang (
Date: Wed Jul 16 2008 - 09:20:03 CDT


        As I understood, RMSD per residue should equal to the RMSF of each
residue. In the paper you mentioned, maybe they used different reference
structures. For RMSD per residue, maybe the starting structure, so the
values are larger; for RMSF, maybe the average strucutre.

        In ptraj, you can use the 'atomicfluct' to calculate. And set different
reference structures in 'rms' step.

On Wed, 2008-07-16 at 09:48 -0400, wrote:
> Hi,
> Thanks for several response. However, I guess I didn't make it
> clear what RMSD per residue means. There are several papers using RMSD
> per residue. I am quite sure it is not RMSF and I don't know how to
> use PTRAJ to calculate. IF you have access to biophysical chemistry,
> please check this paper:
> Biophysical Chemistry 130 (2007) 65–75
> Figure 1C
> any suggestion about how to calculate it is welcome. Thanks in
> advance.

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