Thank you all. Now it's clear.
Regards
George
On Dec 13, 2012, at 3:45 PM, Adrian Roitberg wrote:
> Dear all
>
> I am not sure if I understand Gerrge's diagram correctly, but what seems
> to be missing from it is the biomolecule.
>
> Imagine that you push 'radially', meaning away from the center you
> defined. If you now hit a hard wall because a protein residue stands in
> the way, you can then move at an angle with ZERO cost for the restraint
> (because you are still at the same distance) and find yourself a better
> escape route.
>
> All this fails if you move the restraint too fast or if you use a force
> constant that is to high. In that case, you will try to push outwards
> regardless of the biomolecule and you can imagine how that would be very
> bad...
>
> adrian
>
> On 12/13/12 9:41 AM, Jason Swails wrote:
>> 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
>>
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
>
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Received on Thu Dec 13 2012 - 07:30:02 PST
