Lester Hedges

Assuming that you have a correctly formatted PDB file, the code should now autodetect disulphide bonds and add them to the `LEaP` script for you. This has been tested on...

There's also a unit test [here](https://github.com/michellab/BioSimSpace/blob/63b14996a0583b44822204f3b8e2a246b8dcd986/test/Parameters/test_parameters.py#L16-L37) that checks that the parameterisation works and that the resulting AMBER topology does contain the required disulphide bonds.

The current `devel` is version `2023.0.0+137.g63b14996` so you seem to be using an older version. (114 commits behind.)

It's possible that it's pulling in an older version because it doesn't want to change the version of Sire in your environment. To force it to use the latest you...

This is because your original input PDB file does not have continuous residue numbers. With BioSimSpace we make the assumption that the user input file is the source of truth...

Thanks for this, I'll look into it next week.

> Assuming that the user has not preprocessed the PDB file to have continuous residues numbers, could it be a solution to write the tleap bond lines extracting from the...

Ah, apologies, I was under the impression that you had merged across some of Anna's alchemlyb edits early on, I hadn't realised that you'd done your own edits. This might...

Alternatively, I could try reviewing @fjclark's PR first, so that this PR would be consistent once that's merged.

No problem, whatever is preferable. Ultimately this is your sandpit, so what goes in there is up to you. Any comments / suggestions made in review here are mostly for...