source oldff/leaprc.ff99SB source leaprc.gaff2 mol= loadmol2 avmocntf2_monomer-a1.mol2 check mol loadamberparams avmocntf2_monomer-a1.frcmod solvent = copy mol1 solvateBox mol solvent 20 savepdb mol avmocntf2_monomer-a1.pdb saveamberparm mol avmocntf2_monomer-a1.prmtop avmocntf2_monomer-a1.inpcrd quit