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A computer program MSALIGN incorporating solenoidal magnet positioning errors, survey alignment errors, and structure support sag has been written and used to simulate the Advanced Test Accelerator (ATA) inorder to investigate the effects of errors on the transported beam. Runs using up to 10K particles to represent the beam were made over ensembles of up to 100 misaligned machines. They show that for the ATA design tolerances the resultant beam steering is acceptable and easily corrected using steering magnets. Also, that for changes within a factor of 2 to 3 over design values the variation is linear. The program MSALIGN is general in design. Given the appropriate misalignment procedure it can simulate other machines or study other types of errors.