[gmx-users] Hydrogen bonding analysis

Dr. Y. U. Sasidhar sasidhar at chem.iitb.ac.in
Sat Sep 14 14:19:00 CEST 2002

I am looking for following types of hydrogen bonding in a pentapeptide 
in water.
1. 5--->1 hydrogen bonding broken by an inserted water molecule 
h-bonding to 5 and 1.
2. 5--->1 hydrogen bonding & simultaneous h-bonding of 5 and 1 to a 
common water molecule.
I need to know time step, identities of donor residue, acceptor residue, 
and water molecule whenever these hydrogen bonds are present. (  I need 
to generate pdb files to demonstrate such hydrogen bonds visually )
I used g_hbond. It does give an xpm file which can be converted to an 
eps picture which is summary of hydrogen bonds as a function of time. 
While I could find what I wanted in 1 and 2 above with g_dist with -dist 
option I wonder if I am missing some way of using g_hbond itself.  For 
example what is the utility of  the index file generated by -hbn option 
of g_hbond ?


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