Non-integral charge problem:AutoDockTools

Fellow dockers:
 Nice day to all!
 Would someone please help me in preparing
 macromolecules for docking. Under AutoDockTools, I
 encountered hanging of the program after reading the
 pdb macromolecule file. The warning displays
 "non-integral charge".
 Any ideas will be appreciated.
 Amor San Juan
 University of the Philippines
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