Hi, by using zinc database you can download a very large number of libraries. the link is: http://zinc.docking.org/ if you search in subset catalogues you can access to a variety of vendors and 3D database for VS.
Thanks for your help. I was able to solve my problem. The docking can be done using hex stand alone server. The docking can be done from small peptides retrieved from http://www.camp.bicnirrh.res.in/.