pdb2reaction all -i 1.R.pdb 3.P.pdb -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' --refine-path --tsopt --thermo --out-dir result_mep

pdb2reaction all -i 1.R.pdb -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' --scan-lists '[("CS1 SAM 320","GPP 321 C7",1.60)]' '[("GPP 321 H11","GLU 186 OE2",0.90)]' --tsopt --thermo --out-dir result_scan