## $Revision$
## $Date$
## last $Author$
##
## Build Amber topology from cleaned PDB file
## to be used with AmberParmBuilder.py

logFile %(f_out)s

source %(leaprc)s

%(fmod)s
%(fprep)s

p = loadPdb %(in_pdb)s

%(ss_bonds)s

solvateBox p TIP3PBOX %(box)f
#amber 7: solvateBox p WATBOX216 %(box)f

addIons p Na+ 0

addIons p Cl- 0

check p

center p

saveAmberParm p %(out_parm)s %(out_crd)s 

quit