AMBER Archive (2006)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Thu Aug 31 2006 - 16:50:33 CDT

...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.

--tom

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