Dear,

   In my system ,the loop is  part of the active pocket  of the protein. when the ligand is absent, the loop is disordered and 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 is 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 protein structure without the liand, NAD+ and the state of the loop is disordered. The  sequences similarity of the two structure is 100% and sturctue the the  RMSD bettwen the two protein is 0.275 .

i don't know how to build a model that  the protein, NAD+ and ligand coexsit,but the loop of protein is disordered. could give me some advice and tell me how to do it detailed?
   thank you very much.