BioSimSpace.IO.savePerturbableSystem(filebase, system, property_map={})

Save a system containing a perturbable molecule. This will be written in AMBER format, with a topology file for each end state of the perturbation, i.e. ‘filebase0.prm7’ and ‘filebase1.prm7’. Coordinates for the end states are written to ‘filebase0.rst7’ and ‘filebase1.rst7’.

  • filebase (str) – The base name of the output files.

  • system (System) – The molecular system.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }