VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Sun Nov 22 2015 - 22:40:44 CST

Dear all,

I have a question regarding the output of salt bridge plugin.

I understand a salt bridge is considered to be formed if the distance
between any of 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.

Now when I look at one of my output files, saltbr-ASP19-ARG11.dat,
following are the values I see:

0 3.455739012492901
1 3.4557396472199486
2 3.3294544636949475
3 3.2578318095619494
4 3.430435352779075
5 3.3305625511089834
6 4.193335272678875
7 3.3836602580806794
8 3.7031230566236633
9 3.5859244733112283
10 3.3892557891669743

These values are the average distance between the center of mass of the
oxygens in the acidic side chain and center of mass of the nitrogens in the
basic side chain?

In other words, the values in column 2 are not the criteria used to
identify salt bridges.

Just want to make sure the results indicate there is a salt bridge
between ASP19-ARG11
on all 10 frames although the values are above 3.2 A?

thanks,

Shyno 

-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University