[gmx-users] Advice needed

[Priya Das]

Dear all,

I am working with a transmembrane ion channel and have docked a ligand
which binds to its pore.
The ligand forms only one hydrogen bond with the ion channel.
I want to prove the stability of the binding of this ligand using
protein-ligand dynamics.

1) Do i need to convey to the system about the hydrogen bonds , i.e.,
between which atoms are the hydrogen bonds formed ?

2) Is gmx hbonds the command for it?

3) In the tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html)
, there is no mention about forming any hydrogen bonds between ligand and
protein , then how do we judge that the protein- ligand affinity is stable
in that site or in that conformation?

-- 
*Let us all join hands to save our " Mother Earth"*
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Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala