AMBER Archive (2009)

Subject: Re: [AMBER] extract frames from a .mdcrd

From: Carlos Simmerling (
Date: Fri Feb 06 2009 - 05:12:00 CST

you can use vmd to load the entire trajectory directly, and scroll
through the frames.
just make sure to image the trajectory first, since it may be that you
did not set iwrap=1
and your water has diffused. there is plenty of information about this
in the archives (including examples) - search for ptraj and image (or
look in the ptraj manual)

On Fri, Feb 6, 2009 at 5:48 AM, <> wrote:
> Dear amber users,
> I've made a MD job. The output file seems correct, but when I check the
> final structure in the restart file with the VMD (.rst file + .top file)
> there are something wrong (appears a hole in the solvatation cubic box).
> For this reason I want extract different frames from the mdcrd file. What is
> the best option for made this? Can I visualize the frames directly with
> ptraj? or I create a crd file with ptraj, and then I visualize this file
> with VMD?
> A lot of thanks,
> Josť Luis
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