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!
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