[gmx-users] Salt bridge observation

Kavyashree M hmkvsri at gmail.com
Wed Apr 3 18:50:48 CEST 2013

Dear users,

This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.

I used g_saltbr and g_hbond (with contact option) with
a cut of of 4Ang, for calculating sb in the whole protein
at a single frame.

I made sure that I considered sb between same set of
residues (ASP, GLU with LYS ARG) in both calculations.
and filtered accordingly.

While checking the individual sb it was found that most
of the results from g_saltbr matches with g_hbond but
g_saltbr gives some extra sbs. On checking these extra
sb it was found that the distance between the atoms
forming sb are more than the cut of I had mentioned (4 Ang).

Not sure why it is like this. But just wanted to convey this

Thank you

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