[gmx-users] metal_ligand complex

Justin Lemkul jalemkul at vt.edu
Tue Dec 4 12:59:52 CET 2012

On 12/3/12 11:55 PM, tarak karmakar wrote:
> Thanks Justin
> Yah! We can run steered MD or Umbrella Pulling ( sampling) for this
> purpose. But one thing I am wondering that how to move the entire
> complex. In my model there are no covalent bond ( bonding info)
> between the metal and ligands. So how to select a particular point in
> the complex to tie a spring with an atom in the ligand  binding site ?

No idea, but the metal itself is the logical starting place.  Just make sure you 
have some kind of restraints or pseudo-bonds between the metal and the ligands, 
otherwise the ligands will just float away (and they might do so even if the 
pulling force isn't applied).



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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