[gmx-users] Hydrogen bond problem

Erik Marklund erik.marklund at kemi.uu.se
Wed Feb 8 10:50:43 CET 2017

Dera Tasneem,

First thing to check is if you have read the -hbn or -hbm output upside down. This is a common mistake. Seriously.

Kind regards,
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 8 Feb 2017, at 06:06, Tasneem Kausar <tasneemkausar12 at gmail.com<mailto:tasneemkausar12 at gmail.com>> wrote:

Dear all

I am calculating hydrogen bond between protein and drug molecule using gmx
hbond tool. I am using default value for hydrogen bond radius.
Here is the command:
gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm
I am selecting group 1 and 13.
It shows many hydrogen bonds. Then I have calculated the percentage of
hydrogen bond using perl script. There are there hydrogen bonds that show a
significant existence. I wrote the snapshots of trajectories having all
three hydrogen bonds. In every snapshot, when visulaized with a
visulaization sofware such as chimera and LIGPLUS hydrogen bond of serin
does not exist though it shows hydrophobic interaction with drug molecule.
LIGPLUS gives a provision to show the missing hydrogen bond. When I have
plotted by taking consideration serin hydrogen bond, it shows a bond length
of 4.26 angstrom and like that in almost every extracted snapshot. In
existence map serin is showing 92% abundance of hydrogen bond. This problem
is occurring with serin only.

Why is this happening? Is there a cut off problem with the visualization
tools or something else?

Is there an method to write the hydrogen bond and there distance

Thanks in Advance
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