[gmx-users] Make_ndx for gmx hbond

[Justin Lemkul]

On 9/3/18 12:33 PM, rose rahmani wrote:
> Hi,
>
> I want yo do gmx hbond analysis. I have an capped tyrosine amino acid in a
> box of water. I want to calculate number of hydrogen bonds that amino acid
> make with the waters around it. But i couldn't understand the manual
> description about how make an index file for this purpose. If i choose
> group protein and sol in make_ndx command does it give me what i want? Or i
> should specify the O and N atoms in amino acid and make index for it
> seperately? If yes, i couldn't understand how to choose an atom from the
> help which comes with make_ndx command( should i write
> atom type O
> atom type N )?
>
> Would you please help me? I couldn't understand the manual.

You don't need custom groups to analyze amino acid-water hydrogen 
bonding. They're default groups.

FYI, donor groups must include the heavy atom *and* the bonded H atom. 
Acceptor groups need only include the acceptor atom.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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