logFile leap.log

source leaprc.ff99SB

#  --------------------------- END OF STANDARD HEADER   ----------------------




system = loadpdb originalt.pdb


bond system.3.SG system.18.SG
bond system.12.SG system.24.SG
bond system.17.SG system.31.SG
bond system.37.SG system.41.SG


saveamberparm system start.prmtop start.crd
savepdb system start.pdb


solvatebox system TIP3PBOX 10 

Addions system Na+ 0

Addions system Cl- 0

saveamberparm system startPBC.prmtop startPBC.crd
savepdb system startPBC.pdb

quit