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Previous development information
The original version of BAC (as described in the paper) was written in Perl and was developed over a number of years. Over time the original design became unsustainable and the code is now hard to extend, but remains usable. It supports both ESMACS and TIES protocols but requires pre-preparation of protein and ligand. Convenience interfaces are provided for running HIV protease systems (including incorporating point mutations using VMD based scripts).
Repository: github.com/UCL-CCS/BacBuilder
Documentation can be read at: ucl-ccs.github.io/esmacs-input-creation-docs/
Repository: github.com/UCL-CCS/esmacs-input-creation-docs
The current implementation of TIES is based on the NAMD approach to alchemical free energy calculations. We have traditionally used Gaussian/RESP to create individual ligand topologies in Amber prep format. Creating hybrid ligands from these for relative free energy calculations is a real pain and tools like FESetup concentrate on using AM1-BCC and mol2 formats. Consequently, we wrote our own scripts. The process is labyrinthine and there are undoubted bugs but they cover a reasonable amount of our use cases.
Repository: github.com/dww100/ties_hybrid_topology_creator
Over the years we have accreted a lot of benchmarks, helpful scripts and the like. These were stored in a grab bag repository. Note: the version of TIES hybrid topology script within helps in a couple of limited cases but breaks 99% of all tested examples.
Repository: github.com/UCL-CCS/BacScratch
For the INSPIRE project we created some OpenMM scripts for ESMACS/MMGBSA style calculations: https://github.com/inspiremd/Model-generation
There are a lot of cloud and docker related repositories in the group organisation (UCL-CCS). These are all straight forward wrappers - it is likely that for any new deployment the details will need to be updated.
The repository for the most recent Azure project is helpful for understanding the approaches taked and can be found here.