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.

if you are looking for different conformations, you will also need templates that exhibit different conformations. Homology modelling can only build models that are structurally close. If this is the case, I would use a shell script around the call to modeller and vary the name of the template. Otherwise, you would have to look for something that comes close to ab-initio folding - but that is a domain that is not yet very mature for larger proteins..

I hope this helps,

Kind regards, Karsten.