AMBER Archive (2009)

Subject: Re: [AMBER] Centering and reimaging with ptraj- stop rotating.

From: Thomas Cheatham (
Date: Mon Oct 19 2009 - 22:47:07 CDT

> I am trying to center my protein so that it remains as fixed as possible
> throughout the trajectory, especially the rotational movement, while
> still keeping the waters. I've tried many combinations of the center and
> image commands, buy have yet to find a strategy for this. I can center
> single or multiple residues,then the whole protein, then reimage, but it
> will still rotate around that point. Any help would be appreciated. is quite natural for the molecules to rotate and translate; for many
biomolecules, the rotational correlation times are on the ns+ scale.
"center" only puts the molecule at the center. "image" only puts
molecules back into the periodic box. If you want to put things into a
common reference frame, you likely want to RMS fit, this puts everything
in the frame of a particular instance (in this case, the first frame).

  rms first out rms.dat @CA

Note that while this will put the molecule into a common reference frame,
this could hide funny motions (like the molecule flying through the
periodic box).


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