I was greatly helped by the books "Bioinformatics - From Genomes to Drugs" and "Bioinformatics - From Genomes to Therapies" both edited by Dr. Thomas Lengauer. There are lots of programs and tools freely available, but that will depend on what kind of docking you're interested in.

Dear Ahmed,

There is plethora of literature available on the docking studies but, I would like to suggest you a book written by D.C Young. Regarding second part of your query, Autodock is the most  widely used freeware for the docking studies.

All the best

Autodock is one of the free software which is widely used for molecular docking studies. Many other online servers are also available.

Many resources are available for learning docking. Few of them are below as links.

http://autodock.scripps.edu/

http://www.swissdock.ch/

http://www.bonvinlab.org/software/haddock2.2/

http://link.springer.com/protocol/10.1007%2F978-1-59745-177-2_19

http://ncbr.muni.cz/~martinp/C3210/StructBioinf9.pdf

I recommend the ArgusLab program, which is available free.

http://www.arguslab.com/arguslab.com/arguslab.html

Gem dock and hex are good softwares

This PDF guide will help you to understand basics of Docking.

https://training.h3abionet.org/IBT_2016/wp-content/uploads/2016/09/H3ABioNet_Docking.pdf

First you read basics of molecular docking then read research article's on it. There are good softwares for molecular docking which are free. It includes autodock, gemdock , hex etc.Also needs visulising softwares to visualise molecules and to study the molecular interactions such as acceryl discovery visulizer, Argus lab, pymol etc.