AMBER Archive (2004)

Subject: Re: AMBER: Moil-view & Amber trajectory

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Fri Sep 17 2004 - 16:23:14 CDT

> When viewing the trajectory as it progresses through time in moil-view
> (version 10.1) the molecules are all over the place, in the sense that
> the bonds are way too long.

It sounds as though there is a mismatch in the trajectory and prmtop. Was
the "nobox" option specified on the trajout line (if water is there, you
need the box information otherwise moil-view or any vis program will read
the first few coords of the next frame as the box size)? A mismatch will
be obvious in a movie if the first frame looks fine and then the next show
the long bonds...

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