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

aixintiankong aixintiankong at 126.com
Wed Apr 24 04:49:04 CEST 2013

   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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