If you know the sequence of your peptide you can create it using Avogadro software. Just install it and after opening go to Build/insert/peptide. Then you can save the created structure in any format (e,g PDB).

You can do Homology Modeling or multi template modeling of your protein based on your PDB-BLAST result using Modellor software. If you are not finding satisfying similar template for your protein of interest then you can do modeling using I-TASSER like server. You can get your protein structure.

thanks all

Hi Mr Razzokov

I made a pbd file with avogadro software.now for making coarse-graine model in vmd i need psf file, how can i get topology file to make a psf file?

Thanks