Suitable parameter sets for the CHARMm force field were derived using the Dinur-Hagler energy second-derivative procedure, on the basis of SCF calculations at the 6-31G* level, for the uncommon structural units in poly(phenoxyphosphazenes) [P=N, P-N, P-X (X=aryloxy)]. It is shown that application of molecular dynamics (MD) simulations, in combination with experimental energy dispersive X-ray diffraction (EDXD) measurements, provide unambiguous structural and conformational information on amorphous polymers. The procedure for the analysis of the EDXD data involves comparison of computed atom-atom radial distribution function (RDF) curve from MD simulations for the various polymer backbone conformations, with the RDF obtained from experimental X-ray scattering data. The applicability of this combined experimental/computational methodology is illustrated on the amorphous poly[di(4-methylphenoxy)phosphazene] (PMPP). The results showed that (i) the backbone conformation is safely [TC](n) rather than [T3C](n) and (ii) the computed RDFs are best assessed by using a MD simulation technique that avoids assumption of static chain conformation and the needed best fit of the distance dependent parameters s(jk). In this method of analysis, the RDF that to be compared with the experimental one is directly calculated from all microstates collected during the entire simulation period. Validation of the polymer model provides a complete picture, otherwise experimentally inaccessible, of the internal fluctuations of the polymeric hains. The computational protocol delineated for analysis of EDXD data is general and its application specifically necessary when highly flexible amorphous polymers are involved.