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

[tarak karmakar]

Hi,

For the first part of your problem, I would suggest to visit this online
server where you can model your loop, http://falc-loop.seoklab.org/  . It
utilizes homology modeling kind of analogy to add the loop.

Time span within which a disordered loop gets converted to alpha-helix is
not so precise and thus can not be truly predicted. Run for a few tens of
ns and see whether any change is happening to that loop region. 2fs time
step can be used provided you have to use proper constraints.

Regards,
Tarak


On Wed, Apr 24, 2013 at 8:19 AM, aixintiankong <aixintiankong at 126.com>wrote:

> 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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-- 
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *