Re: [AMBER] bond connections

From: Jason Swails <>
Date: Thu, 3 Dec 2015 13:05:15 -0500

On Thu, Dec 3, 2015 at 12:55 PM, mohammad r <>

> When I open the amber topology file in vmd, it can read the number of
> atoms but the number of frames is zero so it shows nothing, in opening the
> .crd file the number of frames and atoms are zero. But when I open the .gro
> file it shows the system correctly.

​You need to load both the prmtop *and* the coordinate file. The prmtop
defines the molecule, and the crd file provides the frame.

Make sure you load the coordinate file as the correct type. If it is the
inpcrd file, you need to select "Amber 7 restart", not "Amber coordinates".

As for the GRO file showing the system correctly -- I believe this is
because VMD draws the bonds based on distance, NOT necessarily what is
inside the Gromacs or Amber topology files. You really need to check the
appearance of the Amber topology file with Amber coordinates to see if some
mistake was made there.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Dec 03 2015 - 10:30:03 PST
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