Dear B.Nataraj,
> For my modelled protein, I want to analyis various possible > conformare it can assume,In that connection I want to know what is the > command or in build routine to create all possible conformation for > my modelled protein ? Thank you in advance.
To analyze possible conformers avalible to your model, you can run a molecular dynamics simulation with implicit or explicit solvent. On the latter case you first add a water shell to your model and minimize just the water shell, and after that you minimize the water-protein assambly. Finally you run a looooooooong dynamic, sample conformations at regular intervals of the simulation and voila!! You now have several conformers of your model!!
You can do a search on NCBI Pubmed to get more info on this (software, parameters, etc). As always, what you do is defined by your needs and the computing resources available to you.
I hope this helps,
Kind regards, Luis.