source leaprc.ff03
source leaprc.gaff
pore = loadpdb "pore_deprotonated.pdb"
stx = loadmol2 stxagain.mol2
complex = createunit complex
complex = combine { pore stx }
savepdb complex "c3.pdb"
savepdb stx "stxmin.pdb"
savepdb pore "pore.pdb"
saveamberparm stx stx.prmtop stx.inpcrd
saveamberparm pore pore.prmtop pore.inpcrd
saveamberparm complex pore_stx.prmtop pore_stx_inpcrd
quit