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 ?
Atsutoshi, 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. Dave