Re: [AMBER] center and image

From: Jason Swails <>
Date: Tue, 22 Jun 2010 09:39:49 -0400


I will try my best here.

On Tue, Jun 22, 2010 at 1:55 AM, Homa Azizian <>wrote:

> Hi,
> would any one please explain me the application of "center" and "image
> origin center". here is my ptraj script, my protein has 468 residues.
> because when I use center and image origin center the rmsf or other results
> is totally diffrent. I read the ptraj tutorial but cant undrestand these
> command.
> trajin L.mdcrd.gz
> center :1-468

This resets the origin to the center of mass of the selected residues, I

> image origin center

This resets all of the coordinates to the image of that particular
molecule/particle to the original box. However, if you have a truncated
octahedron, I believe you need "familiar" at the end.

> trajout L.binpos binpos
> reference minimize.rst
> rms reference out backbone.rms .C, N, CA time 1

Do not put any spaces in the mask definition. Keep this line (rms reference
out backbone.rms ".C,N,CA" time 1)

atomicfluct out rmsf.dat .CA byres bfactor
> Thank you very much for considering
> homa
> _______________________________________________
> AMBER mailing list

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jun 22 2010 - 07:00:03 PDT
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