[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 20:37:44 CEST 2015

Hey Justin,

Thank you for your answer. I wanted just to be sure since other programs define H-bonds slightly different so identification of each line is a bit complicated when comparing frame by frame. I was trying to find the exact same number of H-bonds for instance in pymol but I could never get the definition about right so that gromacs and pymol find exactly the same hbonds.

thanks for the offer I also wrote a program now to determine hydrogen bond networks across one water molecule. not sure if this can be any helpful to anyone. if so just contact me.

have a good day,


On Apr 17, 2015, at 2:18 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

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 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html

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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441

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