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
--
========================================
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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