VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sun Aug 24 2014 - 01:28:22 CDT

Easiest way to find your answer is to have a look at the source for the saltbr plugin (this is well worth doing, because learning a bit of TCL is invaluable when you want to start doing your own analyses). You’ll find it at /path/to/vmd/plugins/noarch/tcl/saltbr1.1/saltbr.tcl and the bit you’re looking for starts at line 790.

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Dawid das
Sent: Sunday, 24 August 2014 4:56 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: How does saltbr calculate distance?

Dear VMD experts,
I have technical question about calculating salt bridges in VMD. When VMD plots the distance between let's say GLU7 and ARG56 as a function of time, what distance it actually is? Between what atoms of these residues? Or is it distance between centers of mass of negative and positive charge?
Thank you,
Dawid Grabarek