[gmx-users] Salt bridge observation

[Justin Lemkul]

On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> 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
> observation.
>
>
Please provide a concrete example.  Note that running g_saltbr and g_hbond
(with the index files mentioned before) should not be expected to produce
equivalent result.  g_saltbr is relatively stupid; it considers any group
with a charge ± 0.2 to be capable of participating in a salt bridge.  In
some cases, this will include methylene groups or others than are near the
actual charged groups.  Such behavior could easily account for whatever
observation you're making.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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