# Add the protein, ligand and water
inter_cljff.add(protein)
inter_cljff.add(ligand)
inter_cljff.add(water)
# Add the forcefields to the system
system.add(intra_cljff)
system.add(intraff)
system.add(inter_cljff)
# Set the expression used to calculate the total energy
# of the system
system.setComponent( system.totalComponent(),
intra_cljff.components().total() +
intraff.components().total() +
inter_cljff.components().total() )
# Tell the system about the periodic box
system.setProperty("space", space)
# now wrap everything so that the ligand is in the center of the box
system.add( SpaceWrapper(ligand_mol.evaluate().center(), all) )
system.applyConstraints()
system.removeAllConstraints()
# Save a binary representation of the system
# to the file "system.s3"
import Sire.Stream
Sire.Stream.save( system, "system.s3" )
# Add the protein, ligand and water
inter_cljff.add(protein)
inter_cljff.add(ligand)
inter_cljff.add(water)
# Add the forcefields to the system
system.add(intra_cljff)
system.add(intraff)
system.add(inter_cljff)
# Set the expression used to calculate the total energy
# of the system
system.setComponent(
system.totalComponent(),
intra_cljff.components().total() + intraff.components().total() +
inter_cljff.components().total())
# Tell the system about the periodic box
system.setProperty("space", space)
# now wrap everything so that the ligand is in the center of the box
system.add(SpaceWrapper(ligand_mol.evaluate().center(), all))
system.applyConstraints()
system.removeAllConstraints()
# Save a binary representation of the system
# to the file "system.s3"
import Sire.Stream
Sire.Stream.save(system, "system.s3")
