# -i min input file (input)
# -o min output file (output)
# -p parm topology file formatted (input)
# -c coordinates from water md (input)
# -r coordinates (output)

rm *out md* min_*.coord
PEXE=/prog/amber9/exe

# Minimize Water Box

$PEXE/sander -O -i ../min_wat.in -o min_wat.out \
        -p ./prm_2.top  \
        -c ./prm_2.crd -r MNK.wat.rst \
#        -ref  prm_2.crd

# Minimize Protein

$PEXE/sander -O -i ../min_prot.in -o min_prot.out \
        -p ./prm_2.top  \
        -c ./MNK.wat.rst \
        -r MNK.wat.prot.rst

# Minimize all
$PEXE/sander -O -i ../min_system.in -o min_system.out \
        -p ./prm_2.top  \
        -c ./MNK.wat.prot.rst \
        -r MNK.system.rst