Is there a tool which converts 3D models to asset bundles ? or is it
possible to convert them at run time ?
The short answer is no. You can't during the run-time because every Unity API to create Assetbundle is only available on the Editor for Editor plugins only.
But My application allows end users to upload their own 3D models and
view them in application by downloading at run time .
If what you are trying to do is allow people to import and view fbx model into Unity then you don't need Assetbundle to do this.
You have two otipns:
1.Use the TriLib (Not free) plugin if you want to support 40+ other 3D file formats too.
2.If you can't afford a paid working plugin, make your own. This requires you build a plugin with Autodesk FBX SDK in C++ and use C# to communicate with this. Since you are a beginner, I will suggest you go with #1.