Hello,
I will try my best here.
On Tue, Jun 22, 2010 at 1:55 AM, Homa Azizian <homa.azizian.anu.edu.au>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
believe.
> 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
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All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jun 22 2010 - 07:00:03 PDT
