The last email have some errors please see this one.
   In my system ,the loop is  part of the active pocket  of the protein. when the ligand is absent, the loop is disordered.  if the ligand is present , the loop can transform into helix.
   In order to simulate the disordered loop transform into helix , i should build a model that the ligand and cofactor are in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix.
   In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a structure of the protein without the liand, NAD+ and the state of the loop is disordered. The  sequences similarity of the two structure is 100% and  the  RMSD between the two structures of the protein is 0.275 .
i don't know how to build a model that  the protein, NAD+ and ligand coexsit and the loop of protein is disordered. could give me some advice and tell me how to do it detailed?
   thank you very much.