source leaprc.protein.ff14SB
source leaprc.RNA.OL3
source leaprc.water.tip3p


RNA = loadpdb pdb2mvy_noH.pdb

saveamberparm RNA pdb2mvy.prmtop pdb2mvy.inpcrd
savepdb RNA pdb2mvy_tleap.pdb

solvateOct RNA TIP3PBOX 12
addIons RNA Cl- 0
addIons RNA Na+ 0
saveamberparm RNA pdb2mvy.sol.prmtop pdb2mvy.sol.inpcrd
savepdb RNA pdb2mvy_tleap.sol.pdb
quit
