VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 08 2015 - 16:57:40 CST
On Thu, Jan 8, 2015 at 4:49 PM, Eric Smoll <ericsmoll_at_gmail.com> wrote:
> Hello VMD users,
> As discussed in the VMD FAQ section, when I provide a coordinate file
> without a PSF file, bonding is computed with a distance search. Is there a
> way to write this connectivity to file? If not, is anyone aware of a tool to
> do so?
you should be able to write it to a psf file straight away. at least
with VMD 1.9.2.
> How is the distance search done? Is there a hardcoded distance cutoff for
the bond search is programmed in src/BondSearch.C in the VMD source.
> bonding that applies to all nuclei? Does the distance search take the VDW
> radius of each atom into account?
in short: yes, it uses the "radius" property, if present. this is
initialized by many plugins to VDW radii (or 2.0).
a bond is set between two atoms, if the distance is shorter than the
1.2 * the averaged VDW radius (or 0.6*(radius1+radius2)).
when both atoms are flagged/guessed as hydrogen, no bond is defined.
thus, the bond detection can be tuned through setting the radius
property of atoms. as an example for how to use this to tweak the
automatic bond generation (you can redo the bond detection any time),
you can check out the VMD script code in this tutorial.
-- 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.