You can animate it in milkshape using it's bone-based/keyframe animation system, then export it to md2.
To help you, get q2modeller from this thread: http://forum.cubers.net/thread-578.html
It will also show you how to make your custom world guns later. ( you will have to use q2modeller to make your custom world guns follow your model's animation)
In q2modeller, you can open the exsisting player model and move the slider to find out which frames have wich animations in it - these have to be the same in your model. You don't have to do them all (many animations are unused, like the kicking) just leave blank frames there. Animate your model in milkshape the same way as the original model is animated (same number and location of frames for the diffrent animations).
To help you, get q2modeller from this thread: http://forum.cubers.net/thread-578.html
It will also show you how to make your custom world guns later. ( you will have to use q2modeller to make your custom world guns follow your model's animation)
In q2modeller, you can open the exsisting player model and move the slider to find out which frames have wich animations in it - these have to be the same in your model. You don't have to do them all (many animations are unused, like the kicking) just leave blank frames there. Animate your model in milkshape the same way as the original model is animated (same number and location of frames for the diffrent animations).