[gmx-users] salt bridge

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 4 17:44:41 CEST 2010

shiva birgani wrote:
> Hi
> I want to see specific salt bridge residues for example which Arg by Glu 
> is in salt bridges.
> But in step we got a list pairs in which Cl ions (Cl ions added to 
> neutralize peptide in solvent by genion) are paired to residues.
> I don't know what is the problem and how can I have salt bridge residues?
> could you please help me in regards to this problem?

g_saltbr is a fairly unintelligent tool.  It analyzes all ionic pairs.  If you 
want to examine specific, known interactions, then you're better off using 
g_dist (with custom index groups) and analyzing these pairs individually.


> thanks in advance
> Shiva


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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