Handling intermediates in RBFE analysis tutorial

[marcobICR]

Hi everyone,

I am currently trying to follow the RBFE tutorials.
Currently, there is no information in the tutorials on how to handle "additional intermediates" (e.g. the formamide intermediate in the 02_RBFE/01_setup_rbfe.ipynb).

I have tried to keep the intermediate in as a test and running the related RBFE calculations. However, I don't know how to proceed with the analysis in this case. Can the network analysis be done using cinnabar in these cases? Do you have any hands-on experience in doing this?

Thanks

[mb2055]

hi @marcobICR

Apologies if the tutorial isn't clear, its somewhat rigid since we don't normally have the time and resources to have users actually run any simulations. The results contained within the tutorial are pre-computed, so even if you run the simulations these results won't change.

In your case, assuming that your RBFE runs have been successful, you should have a series of output folders containing the simulation data. You can then analyse each leg using BSS.FreeEnergy.Relative.analyse({your directory}) (see RBFE tutorial 1).

You can then add the result of each of these runs to freenrg_repeat_{leg number}_tyk2.csv, and ensure that you have the correct network file in your output folder. From here you should be able to use the analysis described in the tutorial to analyse your network.