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Performs energy minimisation on a small ligand PDB file using AmberTools

Dependencies & Usage

  • AmberTools must be installed for the script to work (intended to be used with AmberTools 18-19). Please consider conda to install AmberTools
  • Python 3.6+
  • $AMBERHOME path must be set for the amber directory e.g. 'export AMBERHOME=/home/myname/amber18'. This may be optional if AmberTools was installed using conda
  • Replaces input file with the minimised version if no suffix is provided. Make a copy if you want to keep the original ligand PDB file
  • For more information about the arguments python emm.py -h