[gmx-users] Hydrogen bonds

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed May 28 12:46:53 CEST 2014


You need to inspect the -hbm and -hbn output. It's the complete existence matrix for all h-bonds encountered in the analysis and a list of corresponding acceptor-H-donor triads. Consequently those files are usually rather big, but that's where the information is. Inspect the bonds you find in pymol or whatever viewer you prefer though, for a common mistake is to read the matrix 'upside down'.

Kind regards,

On 28 May 2014, at 05:59, bharat gupta <bharat.85.monu at gmail.com> wrote:

> Hi,
> I want to find the interacting hydrogen bonding residues with the residue
> of my choice. I made an index for the residue for which I want to find the
> hydrogen bonds and I get the number of hydrogen bond it makes during the
> simulation. But how can I find the residue with which its making the
> hydrogen bonds.
> Regards
> -- 
> Bharat
> -- 
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