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Purpose: Accuracy in dose prediction of dose calculation algorithms is very important aspect in external beam radiation therapy. This study investigates the effect of deformity on dose calculations computed by treatment planning system. Methods: A phantom (30x30x30 cm3 ) containing rectangular solid water blocks with gafchromic film and two 5cm air gaps was used for central axis dose calculations computed by collapsed cone convolution superposition algorithm (CCCS) and Pencil Beam Convolution algorithm (PBC) in Oncentra Dynamic Environment treatment planning system. Phantom is scanned by computed tomography scanner and the image data set is transferred to the planning workstation. Depth dose measurements were taken using a gafchromic for identical beam parameters and monitor units as in the depth dose computations. The calculated and the measured percent depth dose (PDDs) were then compared. The data presented in this study included 6MV photon beam and field sizes of 3x3 cm2 , 5x5 cm2 , 10x10 cm2 and 15x15 cm2 . Results: The x ray beams traversed through the different media and interact as per the densities of the inhomogeneous material and deposits dose. The collapsed cone convolution superposition were within ±1.2% in the first water medium. However, upon traversing the first air gap and re entering the water medium, in comparision to the measurement s, the CCCS under predicted the dose , with difference ranged from -1.3% to -3.2% for 3x3 cm2 , from -2.3% to -4.3% for 5x5 cm2 , from -2.2% to -6.9% for 10x10 cm2 and -1.4% to -6.5% for 15x15 cm2 .After the second air gap, the CCS continued to under predict the dose , and the difference ranged from -3.1% to -3.8% for 3x3 cm2 , from -2.3% to -5.7% for 5x5 cm2 , from -2.3% to -6.3% for 10x10 cm2 , and from -1.5% to -5.7% for 15x15 cm2 . Conclusion: The CCCS under predicted the dose in water medium after the photon beam traversed the air gap region.