[gmx-users] metal_ligand complex

[Justin Lemkul]

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

-- 
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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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