Re: [AMBER] two elongated bonds while visualuizing prmtop and inprcd in vmd

From: Jason Swails <>
Date: Wed, 27 Jan 2016 09:03:59 -0500

inpcrd files are treated as "restart" files by VMD (they are the same file
format). "Amber coordinates" refers strictly to ASCII trajectory files
(mdcrd files). For visualizing mdcrd files, you have to specify whether or
not those trajectories store box information. If you get this wrong, the
first frame will look OK, but all frames after that will be wrong.


On Wed, Jan 27, 2016 at 6:05 AM, Nida Baig <> wrote:

> Dear all,
> I am facing very bizarre problem while loading my protein in prmtop and
> inpcrd files in VMD. Two of the bonds are extraordinarily elongated when we
> open the files in Amber trajectory with periodic box whereas the same files
> open in amber restart format (file type) is ok. Secondly, the problem is
> occuring only in prmtop and inpcrd visulaization while the pdb generated
> and saved from xleap module after the generation of prmtop and inpcrd was
> also normal. Attach are the snapshots of the above mentioned file for your
> visulaization. Please kindly give suggestions accordingly.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jan 27 2016 - 06:30:05 PST
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