On Thu, Dec 13, 2012 at 7:49 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Vitaly,
>
> Thank you for the prompt reply.
>
> I also make reference to
>
> http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/
>
> where it is stated that "So SMD method will be realized by increasing or
> decreasing of initial restrained distance between ligand and some active
> site residue during simulation. Such spherical restraint doesn't specify
> certain direction"
>
> My problem is that I fail to see why this restraint is spherical.
>
I think there is a confusion of terms here. Direction IS specified by
steered MD, even in this case. That direction is given by the vector of
the distance you are restraining. However, what they mean here is that, to
simulate the ligand leaving the pocket of the enzyme, they are simply
increasing the distance between the ligand and center of the pocket
linearly. This process does not specify a particular direction that the
ligand is required to take through the protein. 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, so 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.
Therefore, 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.
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 - 05:30:02 PST
