[gmx-users] Salt bridge observation

Kavyashree M hmkvsri at gmail.com
Thu Apr 4 06:27:30 CEST 2013


That is true, previously you had explained regarding this.

Calculation using g_saltbr
1. For g_saltbr I included the following residues -
    ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
    which contained only these residues. sb was calculated using -

   g_saltbr -f traj.xtc  -s md.tpr  -b 4000 -e 4000 -t 0.4 -sep

2. Files that were generated were filtered and only those having
    sb between ASP, GLU and ARG LYS were retained.

3. Further, out of these sbs, those which had the following atoms
    were retained.

Calculation using g_hbond -
It was done using the index file mentioned in my previous post using

g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm
-hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000

So essentially the final results in both are composed of sbs formed
between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr
while charged atoms in case of g_hbond.

The comparison showed that all sbs from g_hbond were present
in the output from g_saltbr. But g_saltbr had some additional sbs
off-course between the same charged groups. But only the distance
was greater than 4 Ang for ex-
distance between NH2 ARG and OD2 ASP is 4.32Ang
Since it considers charged group CG of ASP instead of OD2 ASP
distance between NH2 ARG and CG ASP is 5.54 Ang

There are some 10 more such examples. I can send the calculations
if requires.

Thank you

On Wed, Apr 3, 2013 at 10:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ========================================
> 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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