[gmx-users] DETECTING HYDROGEN BONDS

[Subashini .K]

Thank you very much for the reply


Wanted to know what the third column represents?


The header was


# gmx hbond is part of G R O M A C S:
# # Glycine aRginine prOline Methionine Alanine Cystine Serine #
@    title "Hydrogen Bonds"
@    xaxis  label "Time (ps)"
@    yaxis  label "Number"
@TYPE xy @ view 0.15, 0.15, 0.75, 0.85
@ legend on @ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"

Through molecular docking had obtained hydrogen bonding with GLU 387 AND GLU 389

Wish to ascertain them through simulations too. How to do it?

Thanks,
Subashini.K





________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alex <nedomacho at gmail.com>
Sent: Saturday, February 11, 2017 1:45 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] DETECTING HYDROGEN BONDS

Not sure what you mean by "interpret these numbers," except that now we
know that your simulation was 2 ns long.  The xvg file contains a
header, which describes what each column is. If I recall correctly, the
second column is the number of hbonds according to the default search
cutoff. The first column is your simulated time in ps.

Alex


On 2/11/2017 1:00 AM, Subashini .K wrote:
> Hi gromacs users,
>
>
> After protein ligand simulations, gave the following command to detect hydrogen bond
>
>
> gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg
>
> After selecting protein and ligand
>
>
> Obtained the following result
>
>
> I am a beginner. Could someone help me  to interpret these numbers? The simulation was done for 2 ns
>
>
>
>                  0           2           1
>
>                100           2           1
>
>                 200           1           0
>
>                 300           1           0
>
>                 400           1           0
>
>                 500           1           0
>
>                 600           1           0
>
>                700           1           0
>
>                800           0           0
>
>                900           1           0
>
>             1000           1           0
>
>              1100           1           0
>
>           1200           1           0
>
>           1300           0           2
>
>          1400           1           0
>
>           1500           1           0
>
>           1600           1           0
>
>            1700           1           0
>
>           1800           0           1
>
>            1900           1           0
>
>           2000           1           0
>
>
> Thanks,
>
> Subashini.K