From: Axel Kohlmeyer (
Date: Mon Dec 16 2013 - 12:37:37 CST

On Mon, Dec 16, 2013 at 6:41 PM, Lee, Sa <> wrote:
> Hello,
> The number of bonds of my carbon structure exceeds 4 which is not real.
> To correct bonds, I found that PSF file or Python scripts can be used in the
> mailing list, and it was 12 years ago.
> I was wondering if there is any up to date way that is facilitated.

VMD is a *visualization* tool, i.e. it shows you the information that
you give it. in some cases, when you give it too little information,
it uses simple heuristics to augment that information. if that doesn't
work the way you expect it, it is your task to provide more complete
information. this can be done through writing scripts or using file
formats that do not lose information. VMD very deliberately does not
try to be smart, since whatever is smart in one case, may be very
wrong (and dumb) in another. it is easy to query the information about
bonding for each atom and there are packages that simplify this
process. similarly, you can tweak the bond heuristics (which are based
on atomic radii) and recompute the bond topology on the basis of that.

what you do and how you do it is up to you. that is the strength of
VMD. it doesn't get in the way and insists on doing things in a
specific manner.


> Thank you,
> Sungae Lee

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.