How to change this parameter? I need to calculate Solvent Accessible Surface Area (ASA - all four) for 1,2-dichlorobenzene or 1,2-dibromobenzene. MarvinSketch claims that Polar Surface Areas are 0.000 for these compounds and it is obvious that they will be polar a little bit. I think that there is a problem with assumption that an absolute value of partial charge of atoms has to be bigger than 0.125, |qi|>0.125. How to change that parameter? Chlorine charge in 1,2-dichlorobenzene is -0.07 and bromine = -0.05 so neither of them fulfills this requirement.
Please give me the direction how I can change |qi|>0.125.
This parameter can not be changed.
Halogen atoms are not added to polar surface area. Usually oxygen and nitrogen atoms have increment in the polar surface area.