AMBER Archive (2009)

Subject: Re: [AMBER] ptraj and namd charmm dcd

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Wed Apr 01 2009 - 11:08:51 CDT

> I would like to use ptraj (AmberTools-1.2) to analyse dcd trajectories
> produced by NAMD with CHARMm ff. I can transform dcd to restart format
> but I am not able to center a tripeptide solute within its water box.
> For the simulation I used the the psf file in X-PLOR format as required
> by NAMD, while with ptraj I use the same file in the CHARMm format, both
> obtained from the VMD-1.8.6 AutoPSF. Is this the expected behaviour of
> ptraj or there something wrong in the attached small case?

With your script,

  trajin trj.dcd
  trajout wsw pdb
  center :1-3

"center :1-3" should move the center of mass of residues 1-3 to the box
center (or origin if origin is specified). This will also shift the
waters too, so effectively it will still look the same as before, simply
translated.

If you want the waters to be re-imaged as well, therefore surrounding
residues 1-3 with water, you want to do the following:

  trajin trj.dcd
  trajout wsw pdb
  center :1-3 mass origin
  image origin center familiar

(if in a rectangular box, your can omit the familiar keyword).

--tec3

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