> It is usually suggested that while preparing a nucleic acid system for
> simulation, 5' terminal phosphate group must be removed; or any terminal
> charged phosphate group should be removed...
>
> Can you please explain why it should be like that??
> If i am extracting a small RNA helix from a large molecule e.g. ribosomal
> RNA, do i have to still remove those flanking phosphate groups?
