From: Axel Kohlmeyer (
Date: Thu May 10 2012 - 09:05:04 CDT

On Thu, May 10, 2012 at 3:53 AM, Albert <> wrote:
> Dear:
>  I am trying to load amber MD files by command:
> vmd apo.prmtop -rst7 m6.rst
> and I get the following information for above command:
> Box Dimensions are 86.454002  79.653999  100.666603  90.000000  90.000000
>  90.000000
> when I try to type pbc box in terminal, it said:
> -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000). Have
> you forgotten to set the pbc parameters?
> I also try to open periodic molecule from representation menu, but nothing
> more displayed....
> I am wondering what happen?

very simple. this plugin was apparently written before
the VMD molfile API supported importing box dimension
information and never revised for that later on.

this needs to be fixed in the plugin source, but since
there is code to detect this already in place, it should
not be too difficult to add this.

what platform are you running VMD on?
can you send me a few small test files?


> thank you very much

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.