Molecular dynamics software predicts interaction between molecules. And, there are some molecular dynamics softwares that I have noticed such as Accelrys Discovery Studio and Tripos Sybyl (commercial), AutoDock, NAMD and etc.
 Firstly, what is the best all-in-one software?
I've seen many functions available in Discovery Studio and Sybyl. But, what does other free softwares has to offer - are they comparable?  Rather than aiding in workflow and all-in-one-ness what should be the main driving philosophy on picking what to learn in the field of in silico drug development. I understand that most softwares mostly overlap in providing established algorithms that do the analysis for us.
I am a novice bioinformatician and I have a biology/biotech background.  I want to learn one of them so which one would I choose to have among the tools at my disposal. Let's assume I have all the time at my disposal.
PS: So far I am planning to learn R, Linux, and maybe Perl as somewhere stated in another thread which seems to be the de facto for a person in bioinformatics. I already have some decent amount of Python and web framework.