Re: [AMBER] Translate the center of mass of the protein to the origin (0, 0, 0)

From: Daniel Roe <>
Date: Wed, 24 May 2017 09:23:32 -0400


You can use cpptraj to do this. The 'center' command with the keyword
'origin' and an atom mask will translate all atoms in the system so
that the center of the atoms specified by the mask is at the
coordinate origin. You can also use 'autoimage origin' if you want the
coordinates to be "wrapped" according to periodic boundary conditions.
Consult the Amber 17 manual for full details.


On Wed, May 24, 2017 at 5:47 AM, Meng Wu <> wrote:
> Dear All,
> I have a simulation system that has been built which includes a protein, lipids, water... to simulate a membrane protein. Now I want to translate the whole system to let the center of mass of the protein at the origin (0,0,0) , in other words, to change the coordinates of the whole system, is there any way to achieve this in Amber?
> Any suggestions would be greatly appreciated. Thank you in advance!
> All the best,
> Wu Meng
> _______________________________________________
> AMBER mailing list

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 Wed May 24 2017 - 06:30:04 PDT
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