Log file: ./leap.log
 source leaprc.ff14SB
 source leaprc.gaff
 loadoff Cup.lib
 loadoff o2.lib
 loadoff cid.lib
 loadoff hit.lib
 loadamberparams mix.frcmod
 x = loadpdb PPO_24jun.pdb
 bond x.92.SG x.109.CE1
 bond x.341.CUP x.109.NE2
 bond x.27.SG x.89.SG
 bond x.28.SG x.11.SG
 bond x.343.Omu2 x.344.Omu2
 bond x.341.CUP x.343.Omu2
 bond x.341.CUP x.344.Omu2
 bond x.342.CUP x.344.Omu2
 bond x.342.CUP x.343.Omu2
 bond x.342.CUP x.240.NE2
 check x
 saveamberparm x prmtop inpcrd
 savepdb x protein_tleap_prova.pdb
 saveoff x protein_tleap_prova.lib
 quit