I want to know if there is any free open source tool available for Gasteiger-Hückel charge calculation? I know it is available on Sylbyl but is there any other(free) way to calculate these charges for small molecules?

I was actually trying this paper, if any one is interested,

How to improve docking accuracy of AutoDock4.2: a case study using different electrostatic potentials.

Hou X1, Du J, Zhang J, Du L, Fang H, Li M.X et al.
Did you have a look at [Acpype][1], there is an option (`-c` gas) that should calculate these charges on a ligand. You only need to download Antechamber (part of the Ambertools package) and acpype.

 [1]: http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype/