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 3NJW_complete_4tleap_uc.pdb
set x box { 19.465  21.432  29.523 }
bond x.6.SG x.19.SG
bond x.50.SG x.63.SG
bond x.94.SG x.107.SG
bond x.138.SG x.151.SG
saveAmberParm x 3NJW_complete_uc.prmtop 3NJW_complete_uc.rst7
quit