You have to take into account UCSF Chimera package. There is a tool named "Build structure" that generates the 3D model of the sequence that you want.

This program is completely free and can run under Linux, Windows and Mac environment.

If you have any question do not hesitate to contact me!

http://www.cgl.ucsf.edu/chimera/

Sorry didnt find the solution

In this case I do not understood the question.

Did you mean that you have two different files, one with each chain? That program can also combine the two chains and form a single molecule.

Yes, and suggest me how...

you can open both files with Chimera, move the chains to fit to your model and then combine both models in a single model.

Thanks but... i identified how to build model >fav>model panel>combine/copy model

more over chimera a generating structure is not accurate, the residues not in order, so i used gromacs software, from that the structure is perfectly joined

Hi Babajan,

I am also trying model protein as yours. You mean you used gromacs to join two protein chains into single model. Can you explain how you did that? 

Thanks