[gmx-users] Salt bridge Calculations

Kavyashree M hmkvsri at gmail.com
Mon Apr 1 12:18:30 CEST 2013

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

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