On Thu, Dec 13, 2012 at 8:54 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Jason,
>
> Thank you.
>
> You say "Their reference to a sphere is simply that the locus of points
> that are, say, 10 angstroms away from a certain point make up a sphere of
> radius 10 with that point at the center"
>
> This is UNDERSTOOD.
>
> Next: "a ligand that is moved 10 Angstroms away from the active site could
> lie anywhere on the resulting sphere, not necessarily where you 'want it
> to' or 'think it should' land."
>
> This is also UNDERSTOOD as it stands. The next sentence though is not.
> Apologies for my lack of "vision".
>
> "while the applied force has a well-defined direction (as any vector in
> this case must have), the 'escape path' of the ligand does not".
>
> Do you mean that although the force is applied in one direction the ligand
> may escape according to the diagram below?
>
The force always has a direction. It must, otherwise, how would you know
in what direction to move the particle that time step? However, the
direction of the steering force could be any direction away from the
binding site. Consider a 2-particle system with that biasing force. The
direction of the force would simply push the particles apart along the
initial displacement vector. As a result, the direction of travel (apart
from being "away" from the binding pocket) depends strongly on the initial
conditions and environment.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Dec 13 2012 - 07:00:02 PST
