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

Justin Lemkul jalemkul at vt.edu
Fri Apr 17 20:18:26 CEST 2015

On 4/17/15 2:02 PM, Ebert Maximilian wrote:
> 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.

Yes, the .ndx and .xpm are "backwards" with respect to one another from the 
top-down perspective.  I wrote a script that does all the mapping if you want 
(parse_hbmap.pl) at 

It requires some modification of the .ndx file (you have to kill off all the 
lines that don't correspond to the actual hydrogen bonds) but it may save you 
some time to look through it.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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