ff14sb-tip3p-leap.in

source leaprc.protein.ff14SB                                
source leaprc.gaff                                              
source leaprc.water.tip3p                                     
loadamberparams frcmod.ionsjc_tip3p 
set default PBradii mbondi3                  
rec=loadpdb rec.pdb 
loadamberparams lig.am1bcc.frcmod
lig=loadmol2 lig.am1bcc.mol2                                                 
gascomplex= combine {rec lig}                                                  
savepdb gascomplex reclig.gas.complex.pdb                  
saveamberparm gascomplex gas.complex.parm7 gas.complex.rst7
saveamberparm rec gas.receptor.parm7 gas.receptor.rst7
saveamberparm lig gas.ligand.parm7 gas.ligand.rst7                                  
solvcomplex= combine {rec lig}                                                        
solvateoct solvcomplex TIP3PBOX 12.0
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0
savepdb solvcomplex wet.complex.pdb
charge solvcomplex
check solvcomplex
saveamberparm solvcomplex solvated.parm7 solvated.rst7
quit