The first entry in summary_HBmap.dat is index zero (i.e., the "bottom" of the
plot area). So the results look fine to me.
-Justin
On 5/14/12 1:02 PM, Yun Shi wrote:
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 <jalem...@vt.edu
<mailto:jalem...@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 <http://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
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Department of Biochemistry
Virginia Tech
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Department of Biochemistry
Virginia Tech
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