brother, after that iI have to do simulation followed by validation through experiments

Hello,

You just develop the linker loop in some modeling application like MOE, Chimera etc, and put peptide bonds of both the termini and their corresponding terminal of the subunit protein. Subsequently, subject your complex to short md simulation to make it refined and to remove any bad contact. The validation of your complex and the appearance of the inserted loop will let you decide whether your complex is correct or not.

Good luck  

Dear @Amir zeb,

Both the terminal are apart from each other, so how can I join both terminal with short linker? how to do in chimera?

By using protein-protein docking software, you can bring two subunits close enough for linker generation.  Next, you rename the chain ID of subunits as A. Then you can perform a regular homology modeling to "fuse" two subunits and generate the linker structure. Of course, you need to do MD in order to optimize the whole conformation.

You can try loop modelling and loop optimisation with Modeller.

thanks @Jyung-Hurng Liu and @Aditi Gangopadhyay for your valuable suggestions

I have solved this problem in the following way as suggested in the comment.

1. First model the linker in MOE software

2. then merged linker with both subunit in a right way

3. then jioned the peptide bond of the linker with subunit follwed by MD simulation

Aditis Gangopadhyay is right. MODELLER is a good option for loop optimization task. Additionally, MODELLER is free and MOE is not. 

yes you are right @Miguel Quiliano

Protein-protein docking + MD simulation to remove the clashes.

We did this a few years back, but you can look in the methods section of this paper http://www.sciencedirect.com/science/article/pii/S0168165612003495