[gmx-users] water mediated hydrogen bond

Justin Lemkul jalemkul at vt.edu
Thu Nov 29 19:56:05 CET 2012

On 11/29/12 10:18 AM, Raj wrote:
> Hi all, I would like to measure the water mediated hydrogen bond between the
> ligand and the protein. When I searched the forum I could able to get the
> link
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt)
> for the script with which we can get the above mentioned objective. But I'm
> not sure how to use it
> Can any one help me with what data I should have before running the script
> and how I can get such a data and also how shuld I use the data as a input
> for the script?. Thanks in advance

My script will tell you how long a particular hydrogen bond persists, in terms 
of the percentage of time occupied in a given trajectory.  Likely what I 
suggested was to use the same logic to parse an hbmap.xpm file to determine when 
hydrogen bonds existed simultaneously between different proteins and a common 
water molecule.  One could, in theory, expand the script I wrote to do this.

Having never had a need to make such modifications, I cannot provide much more 
insight, but I know it is possible.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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