AMBER Archive (2008)

Subject: Re: AMBER: How to obtain the oriented trajectories?

From: Carlos Simmerling (
Date: Thu Jul 03 2008 - 09:22:03 CDT

use ptraj to overlap the frames onto a reference structure, such as
the initial structure or first frame. the tutorials on the web site show
this- for example, the DNA tutorial. use the ptraj trajin command to
read the traj file, rmsd command to overlap, and trajout to save the
reorientated traj file.

2008/7/3 Panwang Zhou <>:
> Dear all
> Can anyone tell me how to remove the effects of the overall translations and rotations and obtain the oriented trajectories in Amber?
> Many thanks in advance.
> Panwang Zhou
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: 0411-84379195 Fax: 0411-84675584
> 2008-07-03
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