[gmx-users] Hydrogen bond problem

[Tasneem Kausar]

Thank you for reply
I am using Justin's perl script for calculating hydrogen bond existence. I
am following the same procedure like deleting all the above lines before
[hbond_protein_drug] and using pdb file with no chain ID etc. I have read
the out file of hbm and hbn  also. Then what could be the problem.

On Wed, Feb 8, 2017 at 3:20 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> 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
> ______________________________
> 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
> hbond.ndx
> 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
> simultaneously.
>
> Thanks in Advance
> Tasneem
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