source leaprc.ff03 loadamberparams ../../Dati_LEAP/parm_copZ.dat loadAmberPrep ../../Dati_LEAP/CU.prep loadAmberPrep ../../Dati_LEAP/CYG.prep MNK = loadPdb prm_1.pdb bond MNK.148.CU MNK.12.SG bond MNK.148.CU MNK.87.SG bond MNK.148.CU MNK.90.SG solvateBox MNK TIP3PBOX 10.2 saveAmberParm MNK prm_2.top prm_2.crd savepdb MNK prm_2.pdb quit