From: David A. Case (
Date: Mon Jul 30 2007 - 11:30:15 CDT

On Wed, Jul 25, 2007, Rachel wrote:
> I am using VMD to view the trajectory files from AMBER with truncated
> octahedral water box, as i need to image the trajectories into the primary
> box which I used pbctools in VMD.
> The angles between the XY and YZ planes are 109.47, and box lengthes are
> 93.30 in XYZ directions, so I used:
> pbc set {93.3 93.3 93.3 109.47 109.47 109.47} -all
> However, this gave me a pallelepiped periodic box instead of octahedral box.

The simple(?) work-around is to use Amber's ptraj program to wrap the
trajectory. Then you can view it directly in VMD.

....good luck....dave case