[gmx-users] Hydrogen bonding analysis

[David]

On Sat, 2002-09-14 at 14:19, Dr. Y. U. Sasidhar wrote:
> 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 ?
This allows you to rerun g_hbond and get information on specific
hydrogens bonds (i.e. distances).
> 
> -- 
>  Sasidhar
> 
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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