source leaprc.protein.ff19SB source leaprc.gaff2 source leaprc.water.opc loadamberparams PNS.frcmod2 loadamberparams PNS.frcmod1 loadoff PNS.lib mol = loadpdb ../5kp7_clean_fix_modify.pdb solvateoct mol OPCBOX 8.0 addionsrand mol Na+ 0 saveamberparm mol 5kp7-bcc.prmtop 5kp7-bcc.inpcrd savepdb mol 5kp7-bcc.pdb quit