Re: [modeller_usage] How to get various conformar for a modelled protein?

["Luis Rosales" <>]

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.