source leaprc.ff99SB source leaprc.gaff source /home/scao/docking_PLpro/MMPBSA/3E9S_methyl_F2124-0890_2/leaprc.zinc m = loadpdb revised_zinc.pdb addions m counterion 0 solvatebox m TIP3PBOX 10.0 saveamberparm m prmtop prmcrd loadamberparams TTT.frcmod loadoff TTT.lib loadamberparams F21.frcmod loadoff F21.lib LIG = loadmol2 F21_new.mol2 list complex = loadpdb 3e9s_methyl_F2124_0890_2_new.pdb receptor = loadpdb 3e9s_methyl_F2124_0890_apo.pdb set default PBRadii mbondi2 saveamberparm complex complex.prmtop complex.inpcrd addions complex Na+ 0 solvatebox complex TIP3PBOX 10.0 saveamberparm complex solv_com.prmtop solv_com.inpcrd saveamberparm LIG LIG.prmtop LIG.inpcrd saveamberparm receptor receptor.prmtop receptor.inpcrd quit