Re: [AMBER] bond connections

From: mohammad r <>
Date: Sun, 6 Dec 2015 22:53:43 +0000 (UTC)

Thank you Jason,

Finally, I could open it. I used amber7 parm for top fileand amber7 restart for crd file (vmd 1.9.2 version). I could solve this problemby using pdb4amber command (using --nohyd –dry flags) and preparing the pdbfile for tleap and after getting new top and crd files those absurd bonds do not exist anymore. Was thatthe only problem with my files?


    On Sunday, December 6, 2015 5:38 PM, Jason Swails <> wrote:

 On Sun, Dec 6, 2015 at 3:59 AM, mohammad r <> wrote:

> Thank you Jonathan,
> In vmd when I load both the top and crd files with Amber 7 restart, it
> shows nothing. Indeed when loading the topology file the number of atoms
> and frames are zero but when I load the crd file the number of atoms and
> frames changed.

​It's unclear from your email whether you loaded both the topology *and*
the coordinate file as Amber 7 restart, or just the coordinate file.  But
to be precise, you need to load the top file as Amber 7 topology and the
crd file as Amber 7 coordinate.

Also, try to upgrade to the latest version of VMD.  I think I recall an
issue with some coordinate files on some systems where this could happen.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Dec 06 2015 - 15:00:03 PST
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