We applied normal mode calculation in internal coordinates to a complex of glutamine transfer RNA (tRNA(Gln)) and glutaminyl-tRNA synthetase (GlnRS). Calculated deviations of atoms agreed well with those obtained from X-ray data. The differences of motions corresponding to low mode frequencies between the free state and the complex state were analyzed. For GlnRS, many motions in the free state were conserved in the complex state, while the dynamics of tRNA(Gln), was largely affected by the complex formation. Superimposed images of the conserved and non-conserved motions of tRNA(Gln) clearly indicated the restricted direction of motions in the complex. (C) 2003 Elsevier Science B.V. All rights reserved.