I don't know how small your ligand is. But AutoDock would be a solution. It's easy to learn. You may define the degree of freedom for better docking.

There is no doubt that AutoDock would be a solution.

But may be these programs also can help you:

https://www.phenix-online.org/documentation/reference/ligandfit.html

http://www.biosolveit.de/FlexX/

http://www.eyesopen.com/oedocking

Tayyba,

There are lot of softwares available for protein-ligand (small molecule) docking. As mentioned, AutoDock is reliable software for the task. You can try AutoDock Vina. 

Don't confuse yourself with protein-protein docking softwares for the task of your interest.

I would suggest you to provide the error and which software you have tried.

Thanks all of u . I will try these software.