On Sun, Dec 6, 2015 at 5:53 PM, mohammad r <mohammad.r0325.yahoo.com> 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 --
http://ambermd.org/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).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Dec 06 2015 - 17:00:03 PST
