Re: [AMBER] Too many iterations in routine! in RMSD calculation

From: Daniel Roe <>
Date: Mon, 1 May 2017 12:23:09 -0400

On Mon, May 1, 2017 at 12:09 PM, kungking Hanpaibool
<> wrote:
> Rmsd calculation for protein backbone, The result showed all of frame got
> 0.000.
> Why didn't I got the result for backbone?

Difficult to say without seeing the original data. Have you tried
visualizing the trajectory data? I suppose it's possible that the RMSD
to your reference is smaller than the printed precision but that seems

If there is something weird with your unit cell (e.g. from a prior
coordinate rotation with 'rms') it's possible the imaging is resulting
in bad coordinates. You could take away the 'autoimage' command to
check for this.


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Mon May 01 2017 - 09:30:04 PDT
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