source leaprc.RNA.OL3

source leaprc.water.tip3p

source leaprc.RNA.LJbb

rna=loadPDB TLS1_clipped.chimera.pdb

check rna

alignAxes rna

solvateShell rna TIP3PBOX 8.00

addions rna K+ 40

solvateOct rna TIP3PBOX 11 0.8

savePdb rna TLS1_clipped_K.build.pdb

saveAmberParm rna TLS1_clipped_K.top TLS1_clipped_K.lcrd

quit