[gmx-users] alpha Carbon-Aromatic ring hydrogen bond

Alok alokjain at iitk.ac.in
Wed Oct 24 18:54:41 CEST 2007

Hi Sarbani,

If I understand correctly your problem, you want to know hydrogen bond between center of the aromatic ring and CA hydrogen atom with time, you can do this in two steps (if you are not considering angle criteria).

1) first create the index files which should have two extra  groups first one contain only ring carbon atoms of your aromatic residue and second one with only CA hydrogen of your interest by using make_ndx tool of GROMACS.

you have to supply *.gro file to make_ndx tools and type
a       c1 c2 c3 c4 c5 c6  (here c1,c2,c3,c4,c5,c6 are your ring carbon atom no)
a       ca1 (here ca1 is your CA hydrogen atom no)
then you will get new index file containing these two groups.

2) Calculate the distance between these two groups using g_dist (as mark already suggested).

Hope it will help.

  ----- Original Message ----- 
  From: sarbani chattopadhyay 
  To: gmx-users at gromacs.org 
  Sent: Tuesday, October 23, 2007 3:18 PM
  Subject: [gmx-users] alpha Carbon-Aromatic ring hydrogen bond

      I want to analyze the Hydrogen bond between alpha Hydrogen and aromatic ring over 
  the simulation time.g_hbond can't recognise this bond.is there any command by which i can 
  do that?


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