[gmx-users] Make_ndx for gmx hbond

Justin Lemkul jalemkul at vt.edu
Mon Sep 3 20:19:34 CEST 2018

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 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


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