[gmx-users] Make_ndx for gmx hbond
jalemkul at vt.edu
Mon Sep 3 20:19:34 CEST 2018
On 9/3/18 12:33 PM, rose rahmani wrote:
> 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.
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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