[modeller_usage] post translational modification

Hi,

Can Modeller be used to study the effect of post translational modification on the structure of protein. For instance if a lysine in a protein is modified to carboxymethyllysine. In such situation, can the modified template be used for modeling. The model so obtained by the alignment of modified protein as template and native protein reflect the effect of modification on the structure. Is it necessary to consider the modified amonoacid (carboxymethyllysine)as unnatural amino acid and modify the charmm topology and parameter files.

Kindly help

Suji george Dept of Life Sciences University Of Mumbai India