source leaprc.ff99SB

loadoff hiz.lib
loadoff hia.lib
loadoff hio.lib
loadoff cym.lib
loadoff cl.lib

NDM=loadpdb ndm-Zn.pdb

bond NDM.56.ZN NDM.58.ND1
bond NDM.56.ZN NDM.125.NE2
bond NDM.56.ZN NDM.125.OZ
bond NDM.144.ZN NDM.60.OD2
bond NDM.144.ZN NDM.125.OZ
bond NDM.95.ZN NDM.95.OXI
bond NDM.95.ZN NDM.95.OIA
bond NDM.95.ZN NDM.95.OXA

solvateoct NDM TIP3PBOX 12

addions NDM Na+ 5

check NDM

saveoff NDM NDM.lib

loadamberparams ndm-Zn.frcmod
loadoff NDM.lib
saveamberparm NDM NDM.prmtop NDM.inpcrd

quit

