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