VMD-L Mailing List

From: LW (wli148_at_aucklanduni.ac.nz)
Date: Wed Sep 02 2015 - 17:27:07 CDT

Dear John,

Thank you for your kind help. To me it has proven a very informative answer.

Cheers,

Levi

2015-09-03 6:55 GMT+12:00 John Stone <johns_at_ks.uiuc.edu>:

> Hi,
> While I'm no expert on this topic, my reading of online
> refs indicates that 4.0A is really more of an upper bound.
> That leads me to conclude that 3.2A was likely chosen as
> a conservative distance that won't return false-positives,
> given that (as I understand it) the code searches over many
> frames in a trajectory and records a salt bridge if the distance
> criterium is met for any pair in any frame. The best answer
> would be obtained by contacting Elizabeth Villa or Leonardo Trabuco,
> who co-developed this plugin. Elizabeth is now at UCSD:
> http://www-chem.ucsd.edu/faculty/profiles/villa_elizabeth.html
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Aug 28, 2015 at 09:30:00PM +1200, LW wrote:
> > Dear VMDers,
> > I have a question on sal bridge.A
> > In 'Ion-pairs in protein' by Barlow and Thornton, the salt bridges(ion
> > pairs) were analysed with a 4.0 Angstrom distance criterium.
> > On the webpage of VMD, the salt bridge cutoff distance was chosen to
> be
> > 3.2 Angstroms by the plugin. Is there any reference to this? Why 3.2?
> > Many thanks in advance.
> > Levi
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>