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