start h2o

prepare
ffield amber
directory_1 ./amber_s/
directory_3 ./amber_x/
source h2o.pdb
periodic
new_top new_seq
new_rst 
center
orient
#solvate box 2.0
modify segment 1 quantum
update lists
ignore
write h2o_ref.rst
write h2o_ref.pdb
end

task prepare
