[gmx-users] how to build the loop of protein model

[aixintiankong]

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 thant 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. can i use the Homology modeling ,docking or just use pymol extract the NAD+ and ligand from the complex and the put them into the protein with the disoreded loop ? And then to make a MD.
   In order to make the disordered into the helix using gromacs, how long should i run the MD and what is  the value of dt , 0.001 or 0.002?
   thank you very much!