Protein interaction & molecular dynamics

[Martin Jones]

Antonio Rosato (antonio at risc1.lrm.fi.cnr.it) wrote:
: Dear all,
: I would like to know whether there are programs available (free or 
: commercial) that can simulate protein interaction through molecular
: dynamics. Should such a program be based on brownian dynamics?
: Suitable protocols for 'ordinary' molecular dynamics programs
: (AMBER,CHARMM..) are welcome as well.
: Thanks a lot!
: Antonio

: e-mail: antonio at risc1.lrm.fi.cnr.it

Unfortunately usable step-sizes in molecular dynamics simulations are measured 
in picoseconds. & each step takes at least a few seconds to simulate. 

So unless you are willing to wait several times the lifetime 
of the universe I'm afraid you'll find that current molecular dynamics 
techniques aren't up to this. If you already know the structure of a
protein complex at the moment of interaction you _might_ be able to 
gain some useful information on the low-level detail of that interaction
using MD, but if you're thinking about just setting a couple of copies of 
protein & substrate up in a box of waters & seeing what happens then I 
suggest that you not wait up for the results :)

Martin.