RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj

From: Thomas Cheatham <>
Date: Thu, 31 Aug 2006 15:50:33 -0600 (Mountain Daylight Time)

...assuming it is a protein, do:

  box alpha 90.0 beta 90.0 gamma 74.8 fixalpha fixbeta fixgamma
  center .CA mass origin
  image origin center triclinic

My guess is that your molecule has simply shifted such that it is no
longer in the center (i.e. spans across the periodic boundary).

> different from the structure obtained from the .rst file. The structure
> from the .rst file looks reasonable; but the one at the end of ptraj is
> wired. (it messes up - waters come in side the crystal where as the
> structure obtained from .rst file with IWRAP = 1 option water
> stays either on top or bottom of the crystal - which is reasonable - I
> think).

I think it is a matter of perspective; both are probably correct, just
each has the solute in a different place (and hence the waters in
different places)... Try the above and see if that resolves your issues.


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Received on Sun Sep 03 2006 - 06:07:16 PDT
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