#!

/usr/bin/sh

###Load Protein force field

source leaprc.protein.ff14SB
###Load GAFF force field (for our ligand)
source leaprc.gaff
###Load TIP3P (water) force field
source leaprc.water.tip3p
####Load Ions frcmod for the tip3p model
loadamberparams frcmod.ionsjc_tip3p

###Needed so we can use igb=8 model

set default PBradii mbondi3
###Load Protein pdb file
rec=loadpdb ../zzz.master/rec.pdb

###Load Ligand frcmod/mol2

loadamberparams ../000.parameters/ix2_lig.am1bcc.frcmod
lig=loadmol2 ../000.parameters/ix2_lig.am1bcc.mol2

###Create gas-phase complex

gascomplex= combine {rec lig}
###Write gas-phase pdb
savepdb gascomplex polx_ix2.gas.complex.pdb

###Write gas-phase toplogy and coord files for MMGBSA calc

saveamberparm gascomplex polx_ix2.gas.complex.prmtop polx_ix2.gas.complex.rst7
saveamberparm rec polx_ix2.gas.receptor.prmtop polx_ix2.gas.receptor.rst7
saveamberparm lig polx_ix2.gas.ligand.prmtop polx_ix2.gas.ligand.rst7

###Create solvated complex (albeit redundant)

solvcomplex= combine {rec lig}

###Solvate the systemsolvateoct

solvateoct solvcomplex TIP3PBOX 12.0

###Neutralize system (it will add either Na or Cl depending on net charge)

addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

###Write solvated pdb file

savepdb solvcomplex polx_ix2.wet.complex_no_na_cl.pdb

###Check the system

charge solvcomplex
check solvcomplex
###Write Solvated topology and coord file
saveamberparm solvcomplex polx_ix2.wet.complex.prmtop polx_ix2.wet.complex.rst7
quit