Step 1 take ligand pdb with H
antechamber -i ligand.pdb -fi pdb -o ligand.prepin -fo prepi -c bcc -s 2

### This should generate prepin file

parmchk -i ligand.prepin -fi prepi -o anp.frcmod -fo frcmod

### This should generate frcmod file

tleap -s -f leaprc.ff99SB

### this will open tleap 

> source leaprc.gaff

### this will load leaprc.gaff force field

> loadamberparams ligand.frcmod ### this loads frcmod generated above

> loadamberprep ligand.prepin  #### this loads prepin generated above

> complex = loadpdb  complex.pdb  ### this loads protein-ligand complex as "complex" unit

> charge complex ### this will show charge on system (if -ve add Na+ else add Cl-)

> addions complex Na+ 0 ### this will neutralize the system by adding no. of Na+ ions

> solvateoct complex TIP3PBOX 8.0

> saveamberparm complex final.prmtop final.inpcrd