Skeletal animation problem(s)

Two weeks ago, I started learning how to load MD5 models and animate them. I found a Java MD5 loader online (some dude ported it from the MD5 model loader on 3dgep.com) and I fixed a bunch of bugs and removed a whole lot of unnecessary stuff.

For the entire first week, the mesh was rotated at a weird angle and wasn’t moving at all. I fixed that, and now the mesh is actually moving.

The problem is that instead of individual limbs moving, the entire mesh is moving as a whole. Initially, I was under the impression that the cause of the problem was that the per-vertex bone indices were incorrect. I soon realized that I was wrong and the problem wasn’t the result of incorrect bone indices or bone weights. This is my very first time attempting 3D animation in OpenGL (make of that what you will. I know for a fact that you can’t get very far in 3D game development without animations in the game). I don’t know about you, but I personally believe that two heads are better than one. I’ve got several heads at my disposal. I mean…er…

It would be awesome if you guys could help. Meanwhile, I’ll try and figure out a solution. If you get any brainwaves, please remember to tell me all about it.

POST SCRIPTUM: the model I’m using is ol’ Bob (carrying his lamp, which he never leaves home without) from Doom 3.