source leaprc.gaff
source leaprc.water.tip3p

loadamberparams frcmod.ionsjc_tip3p

loadamberparams COMPLEX.frcmod

source leaprc.DNA.bsc1

loadoff COMPLEX.lib

PRO = loadpdb "easyPARM_MetalloNucleic.pdb"

# All bond information for tLeap input file
# Metal-nucleotide coordination bonds:
bond PRO.25.Pt1 PRO.16.N7

# Phosphodiester backbone bonds:
bond PRO.15.O3' PRO.16.P
bond PRO.16.O3' PRO.17.P

solvateoct  PRO TIP3PBOX 10.0

addions PRO Cl- 0.
addions PRO Na+ 0

saveamberparm PRO 5BNA_Solvated.prmtop 5BNA_Solvated.inpcrd

savepdb PRO 5BNA_Solvated.pdb

quit