CM5 = loadmol2 cm5.mol2
TMI = loadmol2 tmi.mol2
CPZ = loadmol2 cpz.mol2

loadoff heme.off
gaff = loadamberparams gaff.dat
heme = loadamberparams hemes3.frcmod
ions = loadamberparams frcmod_smith_dang
loadoff CYP.off


#aa = loadpdb 2BDM_cpz.pdb
aa = loadpdb min.pdb

bond aa.409.SG aa.466.FE

#saveamberparm aa 2BDM_cpz_vac.topo 2BDM_cpz_vac.coords

solvateoct aa TIP3PBOX 12.0 iso

addions aa Cl- 0

addions aa Na+ 10 Cl- 10
addions aa Na+ 10 Cl- 10
addions aa Na+ 10 Cl- 10
addions aa Na+ 10 Cl- 10
addions aa Na+ 10 Cl- 10
addions aa Na+ 10 Cl- 10
addions aa Na+ 10 Cl- 10

saveamberparm aa 2BDM_cpz.topo 2BDM_cpz.coords