Ambertools installation Download AMBERTOOLS using following commands : wget http://ambermd.org/downloads/install_ambertools.sh # Or: curl http://ambermd.org/downloads/install_ambertools.sh -O bash install_ambertools.sh -v 3 --prefix $HOME --non-conda Export AMBERHOME path to .bashrc : export AMBERHOME=/PATH/TO/amber17 ## for zsh or bash; export PATH="${PATH}:${AMBERHOME}/bin" OR source the path of AMBERHOME to .bashrc : source /PATH/TO/amber17/amber.sh Examples Commands that can be used: am1bcc am1bcc -i mol.ac -f ac -o mol.ac antechamber antechamber -i g98.out -fi gout -o sustiva_resp.prep -fo prepi -c resp antechamber -i g98.out -fi gout -o sustiva_bcc.prep -fo prepi -c bcc antechamber -i g98.out -fi gout -o sustiva_gas.prep -fo prepi -c gas antechamber -i g98.out -fi gout -o sustiva_cm2.prep -fo prepi -c cm2 antechamber -i g98.out -fi gout -o sustiva.ac -fo ac antechamber -i sustiva.ac -fi ac -o sustiva.mpdb -f