logFile leap.log source leaprc.phenix source leaprc.protein.ff14SB source leaprc.DNA.OL15 source leaprc.RNA.OL3 source leaprc.GLYCAM_06j-1 source leaprc.water.tip3p source leaprc.gaff2 set default nocenter on set default reorder_residues off set default PBRadii mbondi3 x = loadpdb 6DKZ_complete_4tleap_uc.pdb set x box { 14.061 19.862 18.632 } saveAmberParm x 6DKZ_complete_uc.prmtop 6DKZ_complete_uc.rst7 quit