AMBER Archive (2005)

Subject: Re: AMBER: ptraj Hbond analysis

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Sun Nov 20 2005 - 17:13:44 CST

> I have used the imaged trajectory file to save a
> trajectory of closest 200 waters with noimage option.
> When I viewed the trajectory in VMD the rna molecule
> is rotating with some spead in random directions. I

The RNA will rotate around (as it is expected to on a ns time scale),
ideally hopefully not in total random directions...

The reason why you see random rotation is due to the RMS command.

(1) to see if your RNA is rotating and how fast, look at the raw
trajectory in a movie (likely stripped of water and box information) with
NO rms fitting. This will show you how the RNA moves in the box (i.e. is
it slowly rotating,etc.) If you have not set NSCM to remove overall
center of mass motion of the whole box, the whole box can move over
time...

(2) Do the RMS on a particular set of residues. In your script, you have:

  trajin ade1l_9-30sets.traj
  trajout ade1l_close200.traj
  rms first
  closest 200 :1-17 oxygen noimage

If you look at the ptraj output, you will see that you are RMS fitting to
the first frame using all atoms (INCLUDING the water). As the water
exchanges very rapidly, this will lead to apparent random rotation of the
RNA.

If you want to RMS fit only to the RNA atoms,

rms first mass out rms.dat :1-17

 or

rms first :1-17

Since you are doing noimage on the closest, you might want to image the
waters prior to make sure periodically wrapped waters are included into
the closest command...

  center :1-17 mass origin
  image origin center
  rms first :1-17
  closest 200 :1-17 oxygen noimage

--tom

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