The accuracy of the calculation of the equilibrium geometry of small molecules using the pseudopotential solid state code CASTEP is analyzed. The results of the density functional calculations are presented for alkaline earth dihalides and for the metal-organic molecule Ba(C5H5)(2). The density functional theory predicts qualitatively correct geometry in all cases where the accuracy of 0.01 eV in total energy is sufficient to distinguish between different local extrema. CASTEP implementation of the gradient-corrected exchange-correlation functional is shown to be in all cases superior to the local density approximation approach.