Re: [AMBER] bond connections

From: mohammad r <>
Date: Mon, 7 Dec 2015 08:08:15 +0000 (UTC)

Thank you so much.

    On Monday, December 7, 2015 4:24 AM, Jason Swails <> wrote:

 On Sun, Dec 6, 2015 at 5:53 PM, mohammad r <> wrote:

> 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?

​I don't know.  It was clearly the most obvious problem, but there too many
problems that I know about (and probably more that I don't) to say that
your files are problem-free.  The only time I feel confident saying that
files do not have problems are when I've prepared them.

Also, I recommend you visit the tutorials --
In particular, the one about using VMD with Amber addresses precisely this
issue (and does more to help you use VMD successfully with Amber).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
AMBER mailing list
Received on Mon Dec 07 2015 - 00:30:03 PST
Custom Search