[gmx-users] Re: Salt bridge Calculations

[Kavyashree M]

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
>