[gmx-users] Hydrogen Bond analysis

[Pandya, Akash]

Hi all,

This may sound like a stupid question, but is there a "selection process" within gromacs whereby I can determine the correct donor-acceptor distance and angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing various literature that study protein-water/ protein-ligand/ligand-water interactions, the authors seem to use varying cut-offs e.g. 0.35/0.24 nm. I know 0.35 nm is used for moderate hydrogen bond and 0.24 nm is a strong hydrogen bond. So basically what I am asking is how do I find the optimum cut-off values? Do I simply use trial and error? Or can I used other gromacs utilities such as gmx gangle and distance to help me make a decision?

Akash