[gmx-users] Re: Salt bridge Calculations

Tue Apr 2 19:15:06 CEST 2013

On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Sir,
>
> This g_hbond will generate a matrix similar to
> what g_saltbr would have given in terms of variation
> of distance between two charge groups.
>
>
I suppose, in that sense, the output can be useful.

> I want to find out the variation of all the salt bridges
> in the protein over the trajectory, if I have to use g_dist
> with an index of positive atoms and another of negative
> atoms, then it will calculate the distance between the
> centre of mass of these two groups.. according to manual.
>
>
Yes, but that's not what I suggested you do.  You would need an index group
for each residue individually, not "all negative atoms" and "all positive
atoms."  That would definitely be useless.  If you consider each residue
individually, you can get a very detailed look at what's going on.  What
you're doing now is saying "a salt bridge exists if N and O atoms are
within 0.4 nm."  Is that an accurate descriptor?  Upon what precedent have
you based that assessment?  g_dist will also show you frames where those
atoms may not be within 0.4 nm, but what about the case of water-mediated
interactions; are those not interesting, as well?  What I think you should
be doing is approaching the problem from multiple perspectives to get a
real look at what's going on.

-Justin

> So How can I use g_dist for this kind of calculation.
> I am little confused.
>
> If I take a cut of of 0.4nm (as we mention in g_saltbr), will
> it be wrong if I have to calculate salt bridges between
> these two indices -
>
> group 1: ASP_GLU_&_OD1_OD2_OE1_OE2
> group 2: ARG_LYS_&_NZ_NE_NH1_NH2
>
> Thank you
> Kavya
>
>
> On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/2/13 11:58 AM, Kavyashree M wrote:
> >
> >> Sir,
> >>
> >> Thank you very much for your reply. I wanted to calculate
> >> Salt bridge in the whole protein so i am not mentioning the
> >> residues involved. The problem with g_saltbr was that if I
> >> have to calculate the accessibility of these atoms it will be
> >> a problem because it gives the charge groups but not exact
> >> atoms.
> >>
> >> This is the reason I thought of using g_hbond. But I wanted
> >> clarification from experts in using this method.
> >>
> >> So Is there any problem if I use g_hbond?
> >>
> >>
> > Does this really give you any useful information?  You'll get an output
> > file with putative contacts derived from an arbitrary cutoff for any
> > possible positive-negative pair defined in the index group.  I think the
> > g_dist approach is far more useful and gives you exact insight into
> > specific pairs.  It takes a bit more prep work, but looping the
> > calculations is trivial to do to make them efficient.
> >
> > -Justin
> >
> >
> >  Thank you
> >> kavya
> >>
> >>
> >>
> >> On Tue, Apr 2, 2013 at 9:03 PM, bipin singh <bipinelmat at gmail.com>
> wrote:
> >>
> >>  You can use g_dist with specific atoms indices to calculate distances,
> >>> if you already have the information about atoms involved in salt
> >>> bridge interactions.
> >>>
> >>> On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M <hmkvsri at gmail.com>
> wrote:
> >>>
> >>>> Dear users,
> >>>>
> >>>> Kindly clarify my doubt regarding salt bridge calculation.
> >>>>
> >>>> Thank you
> >>>> Regards
> >>>> Kavya
> >>>>
> >>>>
> >>>> On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M <hmkvsri at gmail.com>
> wrote:
> >>>>
> >>>>  Dear users,
> >>>>>
> >>>>> For calculating salt bridge in proteins I
> >>>>> am using g_hbond instead of g_saltbr.
> >>>>>
> >>>>> In g_hbond I use contact and mention two
> >>>>> indices consisting of
> >>>>> group 1: ASP_GLU_&_OD1_OD2_OE1_OE2:
> >>>>> group 2: ARG_LYS_&_NZ_NE_NH1_NH2:
> >>>>>
> >>>>> I use the command:
> >>>>> g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm
> >>>>> matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 50000
> >>>>>
> >>>>> Is this approach correct?
> >>>>>
> >>>>> Thank you
> >>>>> Kavya
> >>>>>
> >>>>>  --
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> >>> Bipin Singh
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> > --
> > ==============================**==========
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================