[gmx-users] Can't find the reference in hbond calculation between the map and the index file

[Ebert Maximilian]

Hey List,

I already got a nice idea from Erik how to find residues bridged by a water molecule by using the hbond tool and the map and index file. I still have a question regarding the index. If I am not mistaken the first entry of bond registry entry:

[ hbonds_Water-r_216_r_244 ]
  4216   4217   3342
  7225   7226   2962

should correspond to the last entry in the xpm file matrix:

/* y-axis:  0 1 2 3 4 5 6 7 8 9 10 11 12 */
" oo ooooooooo  ooo oo  oo  ooo ooo oooooo    o o oo  o   o ooo ooo oo   o    o     o                 “,
"ooooo                                    o                                                           “


and hence the last bond entry (7225   7226   2962) corresponds to the line beneath the y-axis entry? Just to be sure. Is this correct? Couldn’t find any hint what is described by Hydrogen Bond Index in the map file.

Thank you very much,

Max