[Chimera-users] To except box information in MD movie

David E. Konerding dekonerding at lbl.gov
Wed Oct 25 07:40:09 PDT 2006

Atsutoshi Okabe wrote:
> Hello,
> I viewed Amber format trajectory files ( topology/parameter file and 
> trajectory file ) by MD movie.
> But I got the figure( attached file) I didn’t intend. I think the 
> reason is to read box information in
> the Amber trajectory file . How can I except the box information in MD 
> movie window ?


When reading an AMBER format trajectory, not only does the existence of 
box information at each
frame in the trajectory have to correspond to the box information in the 
prmtop (which can have a box
or not), but also the number of atoms in the trajectory has to 
correspond to the number of atoms in the prmtop.

 From looking at your snapshot, I think you may have a problem with the 
prmtop not corresponding to the trajectory-
did you strip out the waters? If you did, then you need a prmtop file 
that also has the waters stripped.

There is an answer to your question (how to see the box data) but it is 
programatically, not GUI-available.


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