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 4R5R_complete_4tleap_uc.pdb
set x box { 18.083  79.986  39.497 }
bond x.4.SG x.19.SG
bond x.6.SG x.14.SG
bond x.13.SG x.36.SG
bond x.27.SG x.33.SG
bond x.32.SG x.57.SG
bond x.45.SG x.64.SG
bond x.72.SG x.87.SG
bond x.74.SG x.82.SG
bond x.81.SG x.104.SG
bond x.95.SG x.101.SG
bond x.100.SG x.125.SG
bond x.113.SG x.132.SG
bond x.404.SG x.419.SG
bond x.406.SG x.414.SG
bond x.413.SG x.436.SG
bond x.427.SG x.433.SG
bond x.432.SG x.457.SG
bond x.445.SG x.464.SG
bond x.472.SG x.487.SG
bond x.474.SG x.482.SG
bond x.481.SG x.504.SG
bond x.495.SG x.501.SG
bond x.500.SG x.525.SG
bond x.513.SG x.532.SG
saveAmberParm x 4R5R_complete_uc.prmtop 4R5R_complete_uc.rst7
quit