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

Ebert Maximilian m.ebert at umontreal.ca
Fri Apr 17 20:02:52 CEST 2015

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,


More information about the gromacs.org_gmx-users mailing list