# load components separately
load my_ligand.pdb
load my_target.pdb
 
# get hydrogens onto everything (NOTE: must have valid valences on the ligand...)
h_add
 
# make sure all atoms within an object occlude one another
flag ignore, none
 
# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3
 
# measure the components individually
ligand_area=cmd.get_area("my_ligand")
target_area=cmd.get_area("my_target")
 
# create the complex
create my_complex, my_ligand my_target
 
# measure the complex
complex_area=cmd.get_area("my_complex")
 
# now print results
print ligand_area
print target_area
print complex_area
print (ligand_area + target_area) - complex_area

Categories: Commands | Biochemical Properties