On 12/3/12 12:09 PM, tarak karmakar wrote:
Dear All,
In my system, I want to see the binding of a ligand, composed of a
divalent metal and 6 ligands, to a protein. I am not sure that
movement of this type of complex ( ligand) towards the protein active
site cavity can be feasible or not. If anyone has some experience or
idea for this kind of problem, please describe me in brief.
Trying to see this by free diffusion is probably an exercise in futility. The
time required to observe such phenomena may be prohibitive, depending on the
size of the system and the binding site itself. Steered MD may be your friend,
but observing the binding process is still like trying to hit a moving target.
The dissociation pathway would be easier, if you have a suitable structure for
the complex.
Should we assign charges of the metal ions as they have their own or
in presence of ligands ( mainly negative charges) , reduced charges ??
Metals are hard to deal with in MD simulations, and their treatment by MM force
fields is certainly lacking. QM literature is your friend here, as charge
delocalization is certainly in play. Deciding how to assign the charges is no
trivial matter.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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