[gmx-users] hydrogen bonds of peptide with lipids

[maria goranovic]

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

I hope this clarifies issues. Thank you

-Maria






On Thu, Apr 17, 2008 at 5:11 PM, <chris.neale at utoronto.ca> wrote:

> Are you using united atom lipids? If so, you may want to reconsider
> attempting this. If not, you'll be more likely to get further assistance if
> you provide quite a bit more information and demonstrate that you invested
> some time trying to solve this.
>
> -- original message --
>
> Yes, I looked into that. But could not find any information about how to
> include new acceptor or donor atoms. Could you please be more specific ?
> Thank you !
>
> On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
>
> [Hide Quoted Text]
> Quoting maria goranovic <mariagoranovic at gmail.com>:
> Dear All,
>
> Where are the donor and acceptor atoms defined for the g_hbond analysis
> ? I
> was trying to calculate h-bonds between a peptide and a popc bilayer,
> but
> there are no acceptor or donors listed for POPC. How can one change this
> ?
> Have a look at g_hbond -h
>
> -Justin
>
> Sincerely,
> -Maria
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
>
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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