[gmx-users] metal_ligand complex

Justin Lemkul jalemkul at vt.edu
Mon Dec 3 19:29:40 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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