VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 16 2013 - 15:17:17 CST

Hi,
  In addition to what Axel has mentioned and beyond the old PSF
script solutions from 12 years back, you will want to have a look
at the VMD atom selection "getbonds" and "setbonds" commands, which you
can use to modify your structure as you wish. Once modified, you would
want to use "mol reanalyze" so that VMD rebuilds it's internal data
structures based on your corrected bond structure.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 16, 2013 at 07:37:37PM +0100, Axel Kohlmeyer wrote:
> On Mon, Dec 16, 2013 at 6:41 PM, Lee, Sa <sa.lee_at_ttu.edu> 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.
>
> axel.
>
> >
> >
> >
> > Thank you,
> >
> > Sungae Lee
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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