[gmx-users] Hydrogen Bond analysis

[Justin Lemkul]

On 10/4/19 12:11 PM, Pandya, Akash wrote:
> 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?

The distinction between 0.35 and 0.24 nm is probably whether the H-bond 
is defined using the donor atom or the hydrogen itself, respectively.

-Justin

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Justin A. Lemkul, Ph.D.
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