[gmx-users] Hydrogen bonding analysis

[K.A. Feenstra]

"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 ?

g_hbond maintains a list of all h-bonding atoms it encounters; output
files only contain information on that list of atoms. So, for example in
the .xpm file you mention, there is time on the horizontal axis and h-bond
index (i.e. the list) on the other axis. Then you can look up the 
corresponding line in the output .ndx file to see which actual atoms are
involved in that specific hydrogen bond...

For what you need to do, I'd assume you know which are the atoms '1' and
'5' you want to look at (or, it might be several atoms). Then, you can make
an index file containing these atoms as triplets of donor-hydrogen-acceptor
atom numbers. Giving this index file to g_hbond with -sel, g_hbond will 
analyze only h-bond formation and water insertion inbetween these atoms (but
for insertion, your input .ndx file must also contain a 'water' group). 
In this case the output .ndx file will be identical to the one you made
(except that maybe it will be sorted, I'm not sure). 

Most of this is also (ofcourse) explained on the manpage of g_hbond...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
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