[gmx-users] how to use the triplets index file generated by g_hbond

[Yun Shi]

Hi Justin,

Thank you for the perl script. But I wonder now why there is a difference
between what shows in the hbmap.xpm file and the summary_HBmap.dat
generated.

For example, I found many occurrences of the second to last H-bond in the
20hbmap.xpm file attached (visualized by GIMP), but in the
summary_HBmap.dat file there showed only 0.1 % Exist. of this specific
H-bond.

Anything wrong with my interpretation?

Please see attached the files I used/ generated.

Thanks,
Yun



On Sat, May 5, 2012 at 10:43 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/5/12 1:22 PM, Yun Shi wrote:
>
>> Hello all,
>>
>> I have used g_hbond with -hbn option to generate a .ndx file that has
>> Acceptor -
>> Donor - Hydrogen in each line of the last index group.
>>
>> But I wonder I could I use this index file to monitor each hydrogen bond
>> specified by these triplets along the trajectory?
>>
>>
> Depending on what you're trying to do, you can map the triplets in
> hbond.ndx with the hbmap.xpm file to obtain, for instance, the % of total
> frames that a particular hydrogen bond exists.  I've done something along
> those lines with a script I call plot_hbmap.pl, available from:
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**scripts.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html>
>
> Please note the usage information in the header of the file.
>
>
>  Also, I understand that the -ins in no longer available. But how can we
>> analyze
>> those water-mediated hydrogen bonds?
>>
>>
> Doing something like this will require careful use of index groups and
> external scripting.  Presumably, if you have two groups (let's call them A
> and B), if group A forms hydrogen bonds to a certain group of SOL residues,
> and if group B does the same, with some of those SOL molecules overlapping
> in some given frames, you can make an argument for a water-mediated
> hydrogen bond. Determining the existence of the hydrogen bonds is easy with
> g_hbond and index groups.  Determining simultaneous occurrence requires an
> external script, and can make use of hbmap.xpm (to determine which frames
> contain the hydrogen bonds) and hbond.ndx (to determine which groups are
> participating in those hydrogen bonds).
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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