[gmx-users] Salt bridge observation
jalemkul at vt.edu
Wed Apr 3 18:55:46 CEST 2013
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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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