Re: [AMBER] distance to center of geometry

From: Daniel Roe <>
Date: Tue, 16 Jan 2018 09:46:05 -0500


On Mon, Jan 15, 2018 at 10:27 PM, Meng Wu <> wrote:
> I want to calculate the distance between a atom and the center of geometry of a protein in MD trajectories. I have imaged the center of geometry to origin and tried ‘distance’ command in cpptraj, but I don’t know how to write mask of the center or the origin, could anybody give me some advices about this or other ways to get what I want? Thank you in advance!

Use 'distance <protein mask> <atom mask> geom' in cpptraj, where
<protein mask> is the mask of your entire protein, <atom mask> is the
mask selecting the atom of interest, and 'geom' is the keyword that
means "use the center of geometry of the atoms in the mask".


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 Tue Jan 16 2018 - 07:00:04 PST
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