[gmx-users] hydrogen bonds of peptide with lipids

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 18 03:20:08 CEST 2008

maria goranovic wrote:
> Yes, I am using united atoms. I am looking for H-bonds between phosphate 
> groups of lipids and the H-bonding atoms of the protein. i have used 
> g_hbond to find the relevant intra-protein H-bonds, but need to find 
> protein-lipid H-bonds.
> I tried using g_hbond, using the protein and POPC as the two groups, but 
> g_hbond does not detect any acceptor or donor atoms in POPC, because I 
> get something like:
> =====================
> Calculating hydrogen bonds between SideChain_ARG_12 (12 atoms) and POPC 
> (17524 atoms)
> Found 3 donors and 3 acceptors
> =====================
> So, the question is: where are the listings for acceptor and donor atoms 
> for using g_hbond

It seems from the first paragraph in g_hbond -h that these are 
hard-coded in the source code to the likely protein-only H-bonding groups.

However you should read further, because an alternative solution is 
described for you.


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