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?
^
/
/
BindingSite -----------> Ligand/---------->
\
\
\
v
Your clarification will be much appreciated
George
On Dec 13, 2012, at 2:01 PM, Jason Swails wrote:
> 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 - 06:00:02 PST
