only_lig_tleapscript

source leaprc.ff99SB
source leaprc.gaff
loadoff 4a_docked_fix.acpype/4a_docked_fix_AC.lib
loadamberparams 4a_docked_fix.acpype/4a_docked_fix_AC.frcmod
complex = loadpdb 4a_docked_fix.pdb
addions complex Cl- 0
saveamberparm complex 4a_docked_fix.prmtop 4a_docked_fix.inpcrd
solvatebox complex TIP3PBOX 15.0
saveamberparm complex 4a_docked_fix_solvated_bonded.prmtop 4a_docked_fix_solvated_bonded.inpcrd
savepdb complex 4a_docked_fix_solvated.pdb
quit