for i in 01 do cd PDB/PDB$i rm prm_1.crd prm_1.pdb prm_1.top /prog/amber9/exe/tleap -f leaprc.ff03 -s -f leap_1_MNK.inp mv leap.log leap_1.log /prog/amber9/exe/tleap -f leaprc.ff03 -s -f leap_2_MNK.inp mv leap.log leap_2.log cd ../../ echo tleap finished for structure 1 ! done