In order to have MM-PBSA working with ligands having halogen atoms, it is necessary to include halogen radii in mm_pbsa_calceneent.pm
(assuming one is using MOLSURF and not LCPO). you must insert F, Cl and Br radii in this file:
"N" => 1.550 + 1.400,
"H" => 1.200 + 1.400,
"C" => 1.700 + 1.400,
"O" => 1.500 + 1.400,
"P" => 1.800 + 1.400,
"S" => 1.800 + 1.400,
"FE" => 1.300 + 1.400,
"Na+" => 1.200 + 1.400,
"Cl-" => 1.700 + 1.400,
"MG" => 1.180 + 1.400,
"F" => 1.470 + 1.400,
"Cl" => 1.750 + 1.400,
"Br" => 1.850 + 1.400,
"I" => 1.980 + 1.400,