hydrogenbond analysis notebook

[orbeckst]

Is your feature request related to a problem? Please describe.

HydrogenBondAnalysis is one of the most used features. We recently deprecated the old approach and in 2.0.0 there will only be https://docs.mdanalysis.org/2.0.0-dev0/documentation_pages/analysis/hydrogenbonds.html. The analysis is often not straightforward and the docs are concise but not enough for someone new to MDAnalysis.

Describe the solution you'd like
I'd like to see a notebook that shows

• basic H-bond analysis (running, parsing output) (e.g. solvent)
• intermediate (between protein and drug, non-standard donors/acceptors)

Describe alternatives you've considered
Asking questions on the mailing list... but it would safe everybody time if we could direct people to a notebook in the UG.

[orbeckst]

@bieniekmateusz @p-j-smith would you be able to have a go at writing a H-bond analysis tutorial?

[p-j-smith]

Yeah sure, I should have some time this week to write a tutorial. For the intermediate-level analysis, so that I don't add another system to the datafiles unnecessarily, do you know if any of the current tpr or psf files in testsuite/Mdanalysis/data are of a protein and drug?

[orbeckst]

Not sure, maybe @IAlibay @RMeli might know?

We could also add something to MDAnalysisData if someone has a suitable system. Would be very useful.

[RMeli]

Unfortunately I don't know on top of my mind, but would be interested to find out as well. If a new trajectory needs to be added, a system with a highly symmetric ligand would be ideal for future work. =)

[IAlibay]

Off the top of my head, I don't think we do, but I'll have a thorough look through once I get back to work tomorrow.

If needed, I probably have some protein-ligand simulations that could be added to MDAnalysisData. I'm thinking some of the more classic T4 lysozyme (e.g. 2RBN) or BRD4 case studies (e.g. Bromosporine) could be appropriate?

[orbeckst]

That sounds perfect. Oliver

…

Am 20.09.2020 um 01:22 schrieb Irfan Alibay ***@***.***>:  Off the top of my head, I don't think we do, but I'll have a thorough look through once I get back to work tomorrow. If needed probably have some protein-ligand simulations that could be added to MDAnalysisData. I'm thinking some of the more classic T4 lysozyme (e.g. 2RBN) or BRD4 case studies (e.g. Bromosporine) could be appropriate? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[IAlibay]

I couldn't find anything in either the MDA test set or MDAnalysisData, so I've created an issue in MDAnalysisData to discuss this.

[orbeckst]

See also recent thread https://groups.google.com/g/mdnalysis-discussion/c/p1Q6GZuqlEg

[lilyminium]

Closed by #133