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<DIV><FONT face=Arial size=2>Hi Sarbani,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>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).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>you have to supply *.gro file to make_ndx tools and
type</FONT></DIV>
<DIV><FONT face=Arial size=2>a c1 c2 c3 c4
c5 c6 (here c1,c2,c3,c4,c5,c6 are your ring carbon atom no)</FONT></DIV>
<DIV><FONT face=Arial size=2>a ca1 (here ca1
is your CA hydrogen atom no)</FONT></DIV>
<DIV><FONT face=Arial size=2>then you will get new index file containing these
two groups.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>2) Calculate the distance between these two groups
using g_dist (as mark already suggested).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Hope it will help.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Alok</FONT></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=sarbani_c84@rediffmail.com
href="mailto:sarbani_c84@rediffmail.com">sarbani chattopadhyay</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Tuesday, October 23, 2007 3:18
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] alpha
Carbon-Aromatic ring hydrogen bond</DIV>
<DIV><BR></DIV>
<P> Hi,<BR> I want to analyze the Hydrogen bond between
alpha Hydrogen and aromatic ring over <BR>the simulation time.g_hbond can't
recognise this bond.is there any command by which i can <BR>do that?<BR>
Sarbani<BR></P><BR><BR>
<P>
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