[gmx-users] Re: Salt bridge Calculations

Kavyashree M hmkvsri at gmail.com
Tue Apr 2 19:29:46 CEST 2013 

Sir,

Thank you for the detailed insight. As you mentioned
It does not give much information. But the matrix that
it would generate would only show whether a specific
salt bridge (SB) exited at a given time within the cut-off (0.4).

I got your explanation. Yes water mediated SBs are also
interesting.

If I had a given set of known SB then I would have definitely
gone for g_dist.

Thank you very much.

Kavya


On Tue, Apr 2, 2013 at 10:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
>
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