set default nocenter on # Do not recenter the molecule

### Sourcing amber forcefields ###############################################

source leaprc.RNA.OL3 # Sourcing RNA force field OL3 to describe RNA.
source leaprc.water.tip4pew # Sourcing water model TIP4P-Ew
source leaprc.gaff2
loadamberparams frcmod.ions234lm_1264_tip4pew # divalent metal ion parameters


### Loading structure from file ##############################################
mol= loadpdb "SYSTEM.pdb"


### Adding counter ions ######################################################
addions mol NA 0 # Add sodium until charge is zero

### Defining box shape & size with chosen water model ########################
solvateoct mol TIP4PEWBOX 9 # solvate with truncated octahedron box 9A out

## Adding bulk ions to ensure 0.14 M concentration ##########################
addionsrand mol NA 29 CL 29 6.0 # add bulk ions, replacing random waters, ensuring 6 A distance between ions, you have to calculate how many NACL you want to reach the desired concentration

### Saving output files  #####################################################
# save parameter and restart files
saveamberparm mol SYSTEM.parm7 SYSTEM.rst7
quit