[gmx-users] water bridge

[Justin A. Lemkul]

On 7/12/12 8:02 AM, Raj wrote:
> Hi all,
>
> I have an protein and drg complex. I've done the MD in SPC water
> environment. Now I would like to check number of hydrogen bond formed
> between the drug and protein, water as well. What will the right command for
> me to analyse. Thanks in advance
>

g_hbond with suitable index groups.  If you're looking for water-mediated 
hydrogen bonds, there are numerous discussions about ways to accomplish that if 
you search the mailing list archive.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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