From: Leonardo Trabuco (
Date: Wed Oct 22 2008 - 11:24:09 CDT

Hi Stanley,

On Wed, Oct 22, 2008 at 3:40 AM, wayj86 wayj86 <> wrote:
> Hi, Leonardo,
> I am a VMD/NAMD user and now trying to use the salt bridge plugin of VMD.Now
> I have some questions about it.
> 1.How does the plugin define salt bridge exactly?At the website of VMD it
> said "A salt bridge is considered to be formed if the distance between the
> oxygen atoms of acidic residues and the nitrogen atoms of basic residues are
> within the cut-off distance (default 3.2 Angstroms) in at least one
> frame",and after using the plugin a salt bridge
> "GLU151_chainC_segnameCHB-LYS167_chainC_segnameCHA" was found.Then I know
> the nitrogen atom NZ at the LYS167 was one of the polar,but which atom of
> GLU151 was the another?I mean,now that the OE1 and OE2 have the same atom
> type of OC in the psf file,I am not sure the salt bridge found was between
> NZ-OE1 or NZ-OE2.

The Salt Bridges plugin uses by default the following criterion to
define a salt bridge: ANY oxygen atom of an acidic residue is within
the cut-off distance of ANY nitrogen atom of a basic residue.

If you want to know exactly which atoms are involved in the salt
bridge, you could either (1) hack the Salt Bridges plugin, (2) write a
little script that monitors the distance between each of the atoms
you're interested in, (3) create labels between them with VMD and
graph their distance; in the last case, you'll likely need to process
the output file with a script since it will be hard to tell the two
oxygen atoms apart by simply looking at a couple of graphs.

> 2.I want to monitor the distance between the oxygen atom and the nitrogen
> atom during the trajactory of SMD simulation to find out when the salt
> bridge was broken(when the distance was over 3.2A I would say it was
> broken).Do you think it is rational?

You can have the Salt Bridges plugin write the distance over time for
every salt bridge ever formed in the trajectory. The reported distance
in this case is the distance between the center of mass of the
oxygen(s) and the center of mass of the nitrogen(s).


PS: Please direct your questions to the VMD mailing list in the future.

> Thank you very much for any help.
> Best wishes,
> Stanley
> --
> The future is now!

Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign