[gmx-users] Re: Salt bridge Calculations

[Kavyashree M]

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?

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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> --
> -----------------------
> Thanks and Regards,
> Bipin Singh
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